Fri May 10 07:33:27 UTC 2024 I: starting to build transdecoder/trixie/amd64 on jenkins on '2024-05-10 07:33' Fri May 10 07:33:27 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_1/5374/console.log Fri May 10 07:33:27 UTC 2024 I: Downloading source for trixie/transdecoder=5.7.1-2 --2024-05-10 07:33:27-- http://deb.debian.org/debian/pool/main/t/transdecoder/transdecoder_5.7.1-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2260 (2.2K) [text/prs.lines.tag] Saving to: ‘transdecoder_5.7.1-2.dsc’ 0K .. 100% 199M=0s 2024-05-10 07:33:27 (199 MB/s) - ‘transdecoder_5.7.1-2.dsc’ saved [2260/2260] Fri May 10 07:33:27 UTC 2024 I: transdecoder_5.7.1-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: transdecoder Binary: transdecoder, transdecoder-doc Architecture: all Version: 5.7.1-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://transdecoder.github.io/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/transdecoder Vcs-Git: https://salsa.debian.org/med-team/transdecoder.git Testsuite: autopkgtest Testsuite-Triggers: hmmer, make, ncbi-blast+ Build-Depends: debhelper-compat (= 13), liburi-perl, ncbi-blast+ , hmmer , r-base-core , r-cran-ggplot2 , r-bioc-seqlogo Package-List: transdecoder deb science optional arch=all transdecoder-doc deb doc optional arch=all Checksums-Sha1: d142301a7599069cc6c2a778f0614f0c0b6f2f87 15039636 transdecoder_5.7.1.orig.tar.xz 3f9b987a11ae15f1db182cc9cd7ad5e67511f431 5940 transdecoder_5.7.1-2.debian.tar.xz Checksums-Sha256: 308010e42203975877edf18633c8ae01ba1045be2b746eb18289d016479a9b70 15039636 transdecoder_5.7.1.orig.tar.xz 7980d0423281844e91e7d32366d798704e9079cc49b996b4ca50d1576c5b49c6 5940 transdecoder_5.7.1-2.debian.tar.xz Files: 80490e4e8965ab7c33163def9dd0cbc2 15039636 transdecoder_5.7.1.orig.tar.xz b93dcd48091ac9275ae619457771a351 5940 transdecoder_5.7.1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmUC4uMACgkQPCZ2P2xn 5uJ3YBAAuBg1lS2NrMO3xqXjZuLC4tAz6Rrpef1s6FtGvXcPiv+0qma0+jwHouGF 7wfWIiKj4+s7HoPcaiyUgtUDh29Yk4TK7kBSNHytjp1ONW7g0zGzg/6qcZV8p6/k yPri6vz77KHdjP+iGHe8ZzOWH4ElaVjw1kstfFo3LqAa6sZgulPOIcOPHIUFMAXY 0hrLqQSmlBafzwPtorE27jTFNmKmCocq1kc7J/JMa0IKsT33IoLM/mBtAMaLBrYS BHzW2o3k/x3vNc+VRATYAEkj7ic/Si4qufYwB/QNafjmZWGSbeuIlf6yaaoOZIFz quxymYmy3lIhma7wIdd61Oy5ITT+3EeBhtGbK7/YnuxMAG8eywh3OOrc6blm6tdI 4tozGSCElSxeImNJriCXcda/CopsbINHj0LUL8ucO427f6FRvj4nVwKuOwAXFN9v 78rjGGo0LE6iWuDfgv0rILW8kUQCt3ktHDX/m2wi44dyMiIbnWeEGTE4SNA1yjpn h36T/n1sOR6mi5gQ+lG4ITLMHRbZBjlIu/PX9CRcMIoQGRvl0qjnNvZ7COmpNEAT HLJk2uZX9Nrx6pjerkLLePEWqwHsrmVlaUgoR51j/CzSP1gu880r6+7qtn7nB7qj /URzBDJN3TIQ/3AHQrSSGpEjtCaQX89OCmDMmmiNeidArEp1pW4= =mqNA -----END PGP SIGNATURE----- Fri May 10 07:33:27 UTC 2024 I: Checking whether the package is not for us Fri May 10 07:33:27 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri May 10 07:33:27 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri May 10 07:56:07 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 9 19:33:29 -12 2024 I: pbuilder-time-stamp: 1715326409 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [transdecoder_5.7.1-2.dsc] I: copying [./transdecoder_5.7.1.orig.tar.xz] I: copying [./transdecoder_5.7.1-2.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Sep 14 10:39:31 2023 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./transdecoder_5.7.1-2.dsc: no acceptable signature found dpkg-source: info: extracting transdecoder in transdecoder-5.7.1 dpkg-source: info: unpacking transdecoder_5.7.1.orig.tar.xz dpkg-source: info: unpacking transdecoder_5.7.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying test_path.patch dpkg-source: info: applying no_sudo dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2647587/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='f58685b73bf04e17956b897596dc6edd' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2647587' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.XPFKHr3Q/pbuilderrc_WdkG --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XPFKHr3Q/b1 --logfile b1/build.log transdecoder_5.7.1-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 8 11:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2647587/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), liburi-perl, ncbi-blast+, hmmer, r-base-core, r-cran-ggplot2, r-bioc-seqlogo dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on liburi-perl; however: Package liburi-perl is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on r-cran-ggplot2; however: Package r-cran-ggplot2 is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-seqlogo; however: Package r-bioc-seqlogo is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-override-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} liburi-perl{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} openssl{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} r-base-core{a} r-bioc-biocgenerics{a} r-bioc-seqlogo{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} sensible-utils{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx publicsuffix r-base-dev r-cran-bit64 r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dichromat r-cran-digest r-cran-dplyr r-cran-formattable r-cran-fs r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-pkgdown r-cran-processx r-cran-profvis r-cran-ps r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-stringi r-cran-svglite r-cran-testthat r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-vdiffr r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 121 MB of archives. After unpacking 332 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 74 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-3 [441 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.80.1-1 [1485 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 108 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get: 122 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-13 [230 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.3.2-1 [26.8 MB] Get: 126 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 r-bioc-seqlogo all 1.68.0+dfsg-1 [164 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.1-2 [1405 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.4+dfsg-1 [221 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-60.0.1-1 [1118 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-5-1 [1394 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] Fetched 121 MB in 4s (32.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21007 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package ucf. Preparing to unpack .../013-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.4.7-7_all.deb ... 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Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/transdecoder-5.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../transdecoder_5.7.1-2_source.changes dpkg-buildpackage: info: source package transdecoder dpkg-buildpackage: info: source version 5.7.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' cd ./sample_data && for script in ./*/cleanme.pl; do $($script); done make[1]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_auto_test make -j20 test make[2]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' cd ./sample_data/ && make test make[3]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Running example in $... make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example' ./runMe.sh incl_pfam_n_blast export PERL_HASH_SEED=0 if [ ! -e test.genome.fasta ]; then gunzip -c test.genome.fasta.gz > test.genome.fasta fi if [ ! -e transcripts.gtf ]; then gunzip -c transcripts.gtf.gz > transcripts.gtf fi if [ ! -e mini_Pfam-A.hmm ]; then gunzip -c mini_Pfam-A.hmm.gz > mini_Pfam-A.hmm fi if [ ! -e mini_sprot.db.pep ]; then gunzip -c mini_sprot.db.pep.gz > mini_sprot.db.pep fi ## generate alignment gff3 formatted output ../../util/gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3 ## generate transcripts fasta file ../../util/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta -parsing cufflinks output: transcripts.gtf -parsing genome fasta: test.genome.fasta -done parsing genome. // processing 7000000090838467 ## Extract the long ORFs ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir * [Thu May 9 19:35:36 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. - extracting ORFs from transcripts. -total transcripts to examine: 64 CMD: touch /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. cmd="" ## Predict likely ORFs if [ "$1" == "" ]; then # always doing this now. # just coding metrics cmd="../../TransDecoder.Predict -t transcripts.fasta" else # this is how I would have run blast and pfam but I'm using precomputed results for ease of demonstration. #BLASTDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/uniprot_sprot.pep #PFAMDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/Pfam-A.hmm # ## run blast #blastp -query transcripts.fasta.transdecoder_dir/longest_orfs.pep -db $BLASTDB -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > blastp.outfmt6 makeblastdb -in mini_sprot.db.pep -dbtype prot blastp -query transcripts.fasta.transdecoder_dir/longest_orfs.pep -db mini_sprot.db.pep -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > blastp.outfmt6 # ## run pfam #hmmsearch --domtblout pfam.domtblout $PFAMDB transcripts.fasta.transdecoder_dir/longest_orfs.pep > pfam.log hmmpress -f mini_Pfam-A.hmm hmmsearch --domtblout pfam.domtblout mini_Pfam-A.hmm transcripts.fasta.transdecoder_dir/longest_orfs.pep ## use pfam and blast results: cmd="../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v" fi Building a new DB, current time: 05/09/2024 19:35:37 New DB name: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/mini_sprot.db.pep New DB title: mini_sprot.db.pep Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 240 sequences in 0.0190918 seconds. Warning: [blastp] Examining 5 or more matches is recommended Working... done. Pressed and indexed 118 HMMs (118 names and 118 accessions). Models pressed into binary file: mini_Pfam-A.hmm.h3m SSI index for binary model file: mini_Pfam-A.hmm.h3i Profiles (MSV part) pressed into: mini_Pfam-A.hmm.h3f Profiles (remainder) pressed into: mini_Pfam-A.hmm.h3p # hmmsearch :: search profile(s) against a sequence database # HMMER 3.4 (Aug 2023); http://hmmer.org/ # Copyright (C) 2023 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: mini_Pfam-A.hmm # target sequence database: transcripts.fasta.transdecoder_dir/longest_orfs.pep # per-dom hits tabular output: pfam.domtblout # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AA_permease [M=479] Accession: PF00324.20 Description: Amino acid permease Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-25 80.4 51.2 7.3e-25 80.0 51.2 1.0 1 CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411( Domain annotation for each sequence (and alignments): >> CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 80.0 51.2 7.7e-27 7.3e-25 19 463 .. 70 500 .. 53 509 .. 0.76 Alignments for each domain: == domain 1 score: 80.0 bits; conditional E-value: 7.7e-27 AA_permease 19 lgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpe....lGfviGlnylfswitvlaleltaasiliqfwelvtdlp 111 + + ++G++g++ ++++++++++ v +slge+a+ +p sgg y+++ +p+ l +v+G+ ++ ++t +a + as+++q + + + + CUFF.38.1.p2 70 SLIFSMNCGGGGMVWSWIIGCICLIPVSISLGELASSMPTSGGLYFWIFTLASPSsrafLCWVCGYVSVLGYATIYASTVYSASSMVQALAVIGSPS 166 44455689999************************************99999987222255555555555566666666666666666664444333 PP AA_permease 112 kawvt..........gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkga..gfrflgdngsifknnlppgfakeeeg 196 + a +l+v+++++ + +v +++ +i + + ++ i++ii ++ ++ + +n g ++ f++++g n+ CUFF.38.1.p2 167 ----YsptkyeqygiYAALLFVISAMTAIPSRVIAKVNIINITFQFLVSIILIIALAAGSDSTTRNSGSfiFGDFTNYSGW---SNM---------- 246 ....02345666666999**********************99999999999999996555555555553333333333333...111.......... PP AA_permease 197 afknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplin 293 +fi f + v +G+e+ a++a+E+ + +k+ P a+++ + ti+ +++++++++++ + +l +s+ + + ++ g++++ ++ CUFF.38.1.p2 247 -GWAFILSFTTPVWVVSGFESSAAVAEESTNAAKAAPFAMISSLGVATILGWCIVITVVATMGHDFNAILGSSLGQ-PVAQVLVNNVGNKGALGIFS 341 .246888888899999*******************************************************99966.7888889999********** PP AA_permease 294 aviltaalssansslysasRvlyslakdglaP..kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl 388 +++++ +l++ +s+l++asR ++++++dg +P ++l+ ++k++vPl+aill+++ sll+ ll +n+ ais + +l++ l i+ + CUFF.38.1.p2 342 LLVIALCLNC-ISLLIAASREVFAFCRDGGIPgsRYLRLLTKQKVPLNAILLVLLYSLLVGLLILVNVT---------AISSVFNLAIIALYIAYSG 428 *999999998.79************************************************99999999.........4444444444444444444 PP AA_permease 389 rfRkalkyqgrsieelgfkaallplgvi..lvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliil 463 +++ + y++ + + + + p ++ +++ ++i++ll+ + ++ + + +++a +++ +++v++++ ++ CUFF.38.1.p2 429 PLMCRFVYNKFQPGVFYVGKWSKPAALWslVWMWFMILMLLFPQYQKPNQ-----DEMNWAIVVLGFVMVFCVVYYY 500 55555555555555555555666555540045555555555555555555.....6788888899999998888777 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (479 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 12 (0.126316); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 840.11 // Query: AA_permease_2 [M=425] Accession: PF13520.5 Description: Amino acid permease Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-56 184.1 57.6 2.6e-56 183.8 57.6 1.0 1 CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411( Domain annotation for each sequence (and alignments): >> CUFF.38.1.p2 type:complete gc:universal CUFF.38.1:1759-3411(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 183.8 57.6 2.7e-58 2.6e-56 1 425 [] 48 491 .. 48 491 .. 0.85 Alignments for each domain: == domain 1 score: 183.8 bits; conditional E-value: 2.7e-58 AA_permease_2 1 lsllsafalvigsv......igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf....gkkvaflsawfnwf 86 +s++s f+ ++gs+ +gs if +++ gg +++++i+++++ ++v++ + El+s +p+sgG+y + + ++ +++++ +++ CUFF.38.1.p2 48 FSYVSIFGQSFGSMglcpamAGSLIF---SMNCGGGGMVWSWIIGCICL-IPVSISLGELASSMPTSGGLYFWIFTLAspssRAFLCWVCGYVSVL 139 799***********777755555555...57888888888888888888.9*********888***********8886333356666********* PP AA_permease_2 87 ayvpvlasilsvaasyl..lnalg.pdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfssl.ste 178 +y+ as++++a s+ l ++g p++ ++++ +y+i++a+l ++ +++++ + +ak++ i +++ +l + iili ++l++++ ++ ++ s++ CUFF.38.1.p2 140 GYATIYASTVYSASSMVqaLAVIGsPSYSPTKYEQYGIYAALLFVISAMTAIPSRVIAKVNIINITFQFL-VSIILI-IALAAGSDSTTRNSgSFI 233 ****9999888777777433345547*******************************************5.555454.566666555444334444 PP AA_permease_2 179 tdtffpn.gwp..g..vllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsn.lgs.vaalffe 265 + f++ gw+ g ++l++++ +w+++Gfes+a v+ee + k +p+a++++l+++++l++ + i++++ ++ d a l++ lg+ va+++++ CUFF.38.1.p2 234 FGDFTNYsGWSnmGwaFILSFTTPVWVVSGFESSAAVAEESTNaaKAAPFAMISSLGVATILGWCIVITVVATMGHDFNAILGSsLGQpVAQVLVN 329 4444444477743133699*********************8887789*****************************999887773444569***** PP AA_permease_2 266 avggkvvaiivvilialsllgaintavigssrvlealardgvlP..rffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgli 359 +vg+k + +i++ l++++l+++ ++++i++sr ++a++rdg++P r+++ k++ p++ai l++++sl+++ll+l+ + +a++ +++++ ++l+ CUFF.38.1.p2 330 NVGNKGALGIFS-LLVIALCLNCISLLIAASREVFAFCRDGGIPgsRYLRLLTKQKVPLNAILLVLLYSLLVGLLILV-NVTAISSVFNLAIIALY 423 ***999999999.8999****************************************************888877765.69*************** PP AA_permease_2 360 isyllliigalilrkkrphl...krpgkilvaiigalfllfllvalffppkgpatqssliytiiltval 425 i y ++ +++++ k +p +++ + a+ ++++ f++ +l fp+ + +q++++++i++++++ CUFF.38.1.p2 424 IAYSGPLMCRFVYNKFQPGVfyvGKW-SKPAALWSLVWMWFMILMLLFPQYQKPNQDEMNWAIVVLGFV 491 **********9999999977444444.468**********************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (425 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 20 (0.210526); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.02s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 576.26 // Query: Acetyltransf_1 [M=117] Accession: PF00583.24 Description: Acetyltransferase (GNAT) family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-15 48.5 0.0 5.6e-15 48.3 0.0 1.1 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 5.3e-15 48.4 0.0 6.2e-15 48.1 0.0 1.1 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) Domain annotation for each sequence (and alignments): >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 48.3 0.0 1.2e-16 5.6e-15 18 117 .] 35 129 .. 16 129 .. 0.77 Alignments for each domain: == domain 1 score: 48.3 bits; conditional E-value: 1.2e-16 HHHHHHHHHHHHSTTS.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE.SEEEEEEETTCHHHH CS Acetyltransf_1 18 daseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi.kkivlaveedndaai 109 ++ + e+ e+ + + +l + +g+l+++++l + ++ +++ i +++V+p+ r++G+G++L+ +++e ++e k vl ++++ a+ CUFF.34.1.p2 35 KCAYPEVDEI--DLKCgHLMLRNANGKLVAYARLIPEQQ---QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfSSsKTFVL---SSQEYAQ 121 4444443333..2556345558888***********999...9*********************************877344466...99***** PP HHHHH.TTE CS Acetyltransf_1 110 rlYek.lGF 117 +lY + +GF CUFF.34.1.p2 122 PLY-RsVGF 129 ***.65**9 PP >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 48.1 0.0 1.3e-16 6.2e-15 18 117 .] 35 129 .. 16 129 .. 0.77 Alignments for each domain: == domain 1 score: 48.1 bits; conditional E-value: 1.3e-16 HHHHHHHHHHHHSTTS.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE.SEEEEEEETTCHHHH CS Acetyltransf_1 18 daseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi.kkivlaveedndaai 109 ++ + e+ e+ + + +l + +g+l+++++l + ++ +++ i +++V+p+ r++G+G++L+ +++e ++e k vl ++++ a+ CUFF.35.1.p1 35 KCAYPEVDEI--DLKCgHLMLRNANGKLVAYARLIPEQQ---QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfSSsKTFVL---SSQEYAQ 121 4444443333..2556345558888***********999...9*********************************877344466...99***** PP HHHHH.TTE CS Acetyltransf_1 110 rlYek.lGF 117 +lY + +GF CUFF.35.1.p1 122 PLY-RsVGF 129 ***.65**9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (117 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1168.96 // Query: Acetyltransf_10 [M=127] Accession: PF13673.6 Description: Acetyltransferase (GNAT) domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-22 71.0 0.0 5.3e-22 70.8 0.0 1.1 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 1.7e-20 65.9 0.0 2e-20 65.7 0.0 1.1 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- Domain annotation for each sequence (and alignments): >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 70.8 0.0 1.1e-23 5.3e-22 32 127 .] 50 150 .. 28 150 .. 0.90 Alignments for each domain: == domain 1 score: 70.8 bits; conditional E-value: 1.1e-23 Acetyltransf_10 32 lllvaeeggkivGviel.rdgs...hisllfVdpeyqgqGigkaLleaveeeaekdglkl.eltvnaspyavpfYeklGFkavgeeqeenGirf 120 +l++ + +gk+v +++l +++ +i++++Vdp+ +++G+g++L+ +++e +++ ++ ++ + ++ ya+p+Y+++GFk++++ e+Gi + CUFF.35.1.p1 50 HLMLRNANGKLVAYARLiPEQQqtvRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSkTFVLSSQEYAQPLYRSVGFKKCSDAYLEDGIPH 143 67888899*******9986666799***************************98888888888889999************************* PP Acetyltransf_10 121 vpMekel 127 v+M++el CUFF.35.1.p1 144 VEMRLEL 150 ****986 PP >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 65.7 0.0 4.1e-22 2e-20 32 123 .. 50 146 .] 28 146 .] 0.90 Alignments for each domain: == domain 1 score: 65.7 bits; conditional E-value: 4.1e-22 Acetyltransf_10 32 lllvaeeggkivGviel.rdgs...hisllfVdpeyqgqGigkaLleaveeeaekdglkl.eltvnaspyavpfYeklGFkavgeeqeenGirf 120 +l++ + +gk+v +++l +++ +i++++Vdp+ +++G+g++L+ +++e +++ ++ ++ + ++ ya+p+Y+++GFk++++ e+Gi + CUFF.34.1.p2 50 HLMLRNANGKLVAYARLiPEQQqtvRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSkTFVLSSQEYAQPLYRSVGFKKCSDAYLEDGIPH 143 67888899*******9986666799***************************98888888888889999************************* PP Acetyltransf_10 121 vpM 123 v+M CUFF.34.1.p2 144 VEM 146 **9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1122.96 // Query: Acetyltransf_15 [M=210] Accession: PF17013.4 Description: Putative acetyl-transferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-06 21.0 0.1 3e-06 19.4 0.1 1.7 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) 4.7e-06 18.8 0.1 1.2e-05 17.4 0.1 1.7 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- Domain annotation for each sequence (and alignments): >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 19.4 0.1 6.3e-08 3e-06 28 154 .. 5 149 .. 1 150 [. 0.84 Alignments for each domain: == domain 1 score: 19.4 bits; conditional E-value: 6.3e-08 Acetyltransf_15 28 eaitknenkydivqykkkeeLvasvfivkkky.yslvs.......................silieknvleiYtlyvsekyrgkGlakklLees 97 e ++k+ n d+ + + L ++vf+v++k+ y v+ i ++++ + i ++v+++ r+ G+ +kl+ ++ CUFF.35.1.p1 5 EFVYKYFNSLDVKELYDIYLLRTNVFVVEQKCaYPEVDeidlkcghlmlrnangklvayarLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQA 98 5578888888888888888888999999988734444479999999999999999999987777889999************************ PP Acetyltransf_15 98 lkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl..fvksgPeelkkrle 154 l++ k++++ + ++l+ s + + lY+s+gF+k + +++ g ++++ rle CUFF.35.1.p1 99 LETSKQEFSSSKTFVLS--------SQEYAQPLYRSVGFKKCSdaYLEDGIPHVEMRLE 149 **********9888774........6789999*******99744499999998888876 PP >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.4 0.1 2.6e-07 1.2e-05 28 145 .. 5 140 .. 1 146 [] 0.81 Alignments for each domain: == domain 1 score: 17.4 bits; conditional E-value: 2.6e-07 Acetyltransf_15 28 eaitknenkydivqykkkeeLvasvfivkkky.yslvs.......................silieknvleiYtlyvsekyrgkGlakklLees 97 e ++k+ n d+ + + L ++vf+v++k+ y v+ i ++++ + i ++v+++ r+ G+ +kl+ ++ CUFF.34.1.p2 5 EFVYKYFNSLDVKELYDIYLLRTNVFVVEQKCaYPEVDeidlkcghlmlrnangklvayarLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQA 98 5678888888888888888888999999988734444479999999999999999999987777889999************************ PP Acetyltransf_15 98 lkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl..fvksg 145 l++ k++++ + ++l+ s + + lY+s+gF+k + +++ g CUFF.34.1.p2 99 LETSKQEFSSSKTFVLS--------SQEYAQPLYRSVGFKKCSdaYLEDG 140 *********99887774........5677888888888887633366655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (210 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 325.85 // Query: Acetyltransf_5 [M=101] Accession: PF13444.5 Description: Acetyltransferase (GNAT) domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-07 23.3 0.0 9.5e-07 22.2 0.0 1.7 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 4.6e-07 23.2 0.0 1.3e-06 21.7 0.0 1.7 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) Domain annotation for each sequence (and alignments): >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 22.2 0.0 2e-08 9.5e-07 1 82 [. 25 102 .. 25 123 .. 0.81 Alignments for each domain: == domain 1 score: 22.2 bits; conditional E-value: 2e-08 Acetyltransf_5 1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegfysesefdlsklaa.lrrrllElg 82 LR +vF+ e + ++ +De D c hl++++++ ++V++ Rl++++++ r+++++ + + +++ + l+ ++lE++ CUFF.34.1.p2 25 LRTNVFVVEQKCAYPE------VDEIDLKCGHLMLRNANGKLVAYARLIPEQQQTvRIGRVVVDPDERKNGYGRkLMLQALETS 102 7888888888888777......*************988889*********9999987777776666665555443555666666 PP >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 21.7 0.0 2.7e-08 1.3e-06 1 82 [. 25 102 .. 25 106 .. 0.78 Alignments for each domain: == domain 1 score: 21.7 bits; conditional E-value: 2.7e-08 Acetyltransf_5 1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegfysesefdlsklaa.lrrrllElg 82 LR +vF+ e + ++ +De D c hl++++++ ++V++ Rl++++++ r+++++ + + +++ + l+ ++lE++ CUFF.35.1.p1 25 LRTNVFVVEQKCAYPE------VDEIDLKCGHLMLRNANGKLVAYARLIPEQQQTvRIGRVVVDPDERKNGYGRkLMLQALETS 102 7888888888888777......*************988889*********9999877777776666665555443555677666 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (101 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 257.33 // Query: Acetyltransf_7 [M=76] Accession: PF13508.6 Description: Acetyltransferase (GNAT) domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-13 42.3 0.0 5.6e-13 41.8 0.0 1.2 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 4.6e-13 42.1 0.0 6.2e-13 41.7 0.0 1.2 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) Domain annotation for each sequence (and alignments): >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 41.8 0.0 1.2e-14 5.6e-13 5 76 .] 29 131 .. 25 131 .. 0.68 Alignments for each domain: == domain 1 score: 41.8 bits; conditional E-value: 1.2e-14 EEEEEET......................TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE.EEEE.THH.HHH CS Acetyltransf_7 5 vfVaedd......................gkivGfialsled...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile.qlel.nae.kai 66 vfV+e++ gk v +++l +e+ i+r++Vdp+ r++G+Gr+L+ +a + + + + ++ + +++ +a+ CUFF.34.1.p2 29 VFVVEQKcaypevdeidlkcghlmlrnanGKLVAYARLIPEQqqtVRIGRVVVDPDERKNGYGRKLMlQAletsK-QEFS-SsKTFVlSSQeYAQ 121 66666666666666666666666666666999999999999999888888****************944533321.2221.1112223333499* PP HHHHHTTEEE CS Acetyltransf_7 67 kfYeklGFee 76 ++Y++ GF++ CUFF.34.1.p2 122 PLYRSVGFKK 131 ********95 PP >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 41.7 0.0 1.3e-14 6.2e-13 5 76 .] 29 131 .. 25 131 .. 0.68 Alignments for each domain: == domain 1 score: 41.7 bits; conditional E-value: 1.3e-14 EEEEEET......................TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE.EEEE.THH.HHH CS Acetyltransf_7 5 vfVaedd......................gkivGfialsled...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile.qlel.nae.kai 66 vfV+e++ gk v +++l +e+ i+r++Vdp+ r++G+Gr+L+ +a + + + + ++ + +++ +a+ CUFF.35.1.p1 29 VFVVEQKcaypevdeidlkcghlmlrnanGKLVAYARLIPEQqqtVRIGRVVVDPDERKNGYGRKLMlQAletsK-QEFS-SsKTFVlSSQeYAQ 121 66666666666666666666666666666999999999999999888888****************944533321.2221.1112223333499* PP HHHHHTTEEE CS Acetyltransf_7 67 kfYeklGFee 76 ++Y++ GF++ CUFF.35.1.p1 122 PLYRSVGFKK 131 ********95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1151.25 // Query: Acetyltransf_9 [M=128] Accession: PF13527.6 Description: Acetyltransferase (GNAT) domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-07 23.6 0.0 8.3e-07 21.8 0.0 1.8 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 2.6e-07 23.4 0.0 9.2e-07 21.6 0.0 1.8 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) Domain annotation for each sequence (and alignments): >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 21.8 0.0 1.7e-08 8.3e-07 72 127 .. 72 131 .. 11 132 .. 0.71 Alignments for each domain: == domain 1 score: 21.8 bits; conditional E-value: 1.7e-08 EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--..SSHHHHHTTT-EE CS Acetyltransf_9 72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfP..ssipiYrrfGyei 127 ++ ++ V v+p++r++g+ +kL+ +ale ++e + +l ++ p+Yr+ G+++ CUFF.34.1.p2 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfsSSKTFVLSSqeYAQPLYRSVGFKK 131 4567999*************************9986556666667566669******975 PP >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 21.6 0.0 1.9e-08 9.2e-07 72 127 .. 72 131 .. 11 132 .. 0.71 Alignments for each domain: == domain 1 score: 21.6 bits; conditional E-value: 1.9e-08 EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--..SSHHHHHTTT-EE CS Acetyltransf_9 72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfP..ssipiYrrfGyei 127 ++ ++ V v+p++r++g+ +kL+ +ale ++e + +l ++ p+Yr+ G+++ CUFF.35.1.p1 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEfsSSKTFVLSSqeYAQPLYRSVGFKK 131 4567999*************************9986556666667566669******975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (128 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 279.36 // Query: Acetyltransf_CG [M=80] Accession: PF14542.5 Description: GCN5-related N-acetyl-transferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-05 18.0 0.0 2.3e-05 17.2 0.0 1.4 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 1.3e-05 17.9 0.0 2.5e-05 17.1 0.0 1.4 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) Domain annotation for each sequence (and alignments): >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.2 0.0 4.8e-07 2.3e-05 8 56 .. 57 105 .. 50 108 .. 0.87 Alignments for each domain: == domain 1 score: 17.2 bits; conditional E-value: 4.8e-07 Acetyltransf_CG 8 dgeevafleYekrkegvldlthTeVpealrGkGiAkkLvkaalddaree 56 +g+ va+++ ++++++ + ++V++ r G+++kL+ +al+ ++e CUFF.34.1.p2 57 NGKLVAYARLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQE 105 5677888888778999***************************998875 PP >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.1 0.0 5.2e-07 2.5e-05 8 56 .. 57 105 .. 50 108 .. 0.87 Alignments for each domain: == domain 1 score: 17.1 bits; conditional E-value: 5.2e-07 Acetyltransf_CG 8 dgeevafleYekrkegvldlthTeVpealrGkGiAkkLvkaalddaree 56 +g+ va+++ ++++++ + ++V++ r G+++kL+ +al+ ++e CUFF.35.1.p1 57 NGKLVAYARLIPEQQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQE 105 5677888888778999***************************998875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (80 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 146.11 // Query: Aldo_ket_red [M=292] Accession: PF00248.20 Description: Aldo/keto reductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-69 225.5 0.0 4.6e-69 225.3 0.0 1.0 1 CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+ Domain annotation for each sequence (and alignments): >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.3 0.0 4.8e-71 4.6e-69 1 289 [. 21 340 .. 21 342 .. 0.91 Alignments for each domain: == domain 1 score: 225.3 bits; conditional E-value: 4.8e-71 .EEEE-SSS-ST.......TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE..................... CS Aldo_ket_red 1 elglGtwqlgsk......eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv..................... 70 +l+lG +++g k ++ee+++++++a++aGi++fDtA+ Y g seel+G++++k++ +r +++i +K+ CUFF.17.1.p1 21 KLILGCMSYGKKeywedwVLEDEEEVFKIMKAAYDAGIRTFDTANCYSAGVSEELVGKFIRKYEIPRSSIVILSKCffpvrkdlikifgdlssrgvh 117 689999999999888663334678999*********************************************************************9 PP ..--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH....HHTTT--EEEEE- CS Aldo_ket_red 71 ..dkrdaeiksglskenieesleeslkrLgtdyvDllllHrpdpslpieevldaleelvkeGkiraiGvSnfsveqleka....kkkkkvkivavqv 161 d +++ gls+++i ++e+s+krLgt y+D+l++Hr dp ++ eev++al+++v++Gk+r+iG S q ++ +k++ +k+++ q+ CUFF.17.1.p1 118 flDSPELANQCGLSRKHIFDAVEDSVKRLGT-YIDVLQIHRYDPHVSAEEVMRALNDVVESGKVRYIGASTMRCYQFIELqntaEKHGWHKFISMQN 213 998888889999******************6.**************************************88866655566778************* PP B-BTTB-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC------....S-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT CS Aldo_ket_red 162 eynllkreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkr....rtsknqdaaeelselakehgvsiaqvalryalsqpa 254 +nll ++ee++++++c+k gv+li++spl++Gllt+ + +e++ + +++ ++ + +++++elak+++vs+a++a ++ l + CUFF.17.1.p1 214 YHNLL-YREEEREMIPYCQKTGVGLIPWSPLARGLLTRSIDANEETIRSKTD-LY-TraleFGAGYKAILSRVEELAKKYNVSMATLATAWSL--HK 305 *****.*******************************999988887743332.33.2479555556666799*********************..9* PP -SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS Aldo_ket_red 255 vgivipgasnieqlednldalelklseeevaelde 289 + +i+g s++e+l+d l+a+elklsee++++l+e CUFF.17.1.p1 306 GDYPIVGISKVERLKDALAAVELKLSEEDIKYLEE 340 *******************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (292 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1024.51 // Query: Amidohydro_1 [M=344] Accession: PF01979.19 Description: Amidohydrolase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-82 268.7 0.4 5.3e-82 268.4 0.4 1.1 1 CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-13 4.5e-82 268.6 0.4 5.4e-82 268.4 0.4 1.1 1 CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471( Domain annotation for each sequence (and alignments): >> CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-1388(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.4 0.4 1.1e-83 5.3e-82 1 343 [. 55 420 .. 55 421 .. 0.96 Alignments for each domain: == domain 1 score: 268.4 bits; conditional E-value: 1.1e-83 EEEE-EEEEEEEEETTECSSS....GHHHHH..........SCTHHHHHHHHHHHHHHHCTTEEEEEEECHSSTHHHHHHHHHHCTSSSEEEEEEES CS Amidohydro_1 1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 iv+PGlI +HvHl qsllr+a +l +wl ++e+ ++a++ i+++lksGttt+ ++ +++ +gie +a+ e g+r ++gk CUFF.26.1.p1 55 IVMPGLISLHVHLAQSLLRSAaddlPLISWLcdtvwkmqgnFTQEDGYVASQLTIAEMLKSGTTTFVEALFAQRYGIEGAVKAVIES--GIRGCIGK 149 79************************************************************************************9..******** PP SEGGS...............GHCCSHHHHHHHHHHCHHHHHHHTTTTCEECEEEECGSGCSHHHHHHHHHHHHHHCTTEEEEEETSSSCCHHHHHHH CS Amidohydro_1 84 vsldr...............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaa 165 v++d+ ++++s++++++ ++ + +gk++g+v+++++ + + ++s+e+ ++++k a++ ++ +++H++e k++ + CUFF.26.1.p1 150 VVMDQpryatqtgvsmheglIENSNSLNQAVESHSKF----HGKGNGRVEIWFGARTPGGVSEELYRKMVKIARANNIGITMHCAEVKADR----EF 238 ******************9988899999999999999....*******************************************9999996....67 PP HTTTEEEETTTTCTTSHCTTTGCCEEECTTCEEEHHCCCHHHHHHHHHHEEHHHHHHHHCEHHHHHHHHHHHHTCEEEEEEETTTSSBCCGHHHHHH CS Amidohydro_1 166 fgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelr 262 f+ + eh t+ ++++lgll++ k++lah+vhl+ ++e+l +++++++vahcp sns+l+sg+++l+++l+++++vg+g+Dg+ ++n+++ll+e++ CUFF.26.1.p1 239 FA-SKEH-TPMTYCKDLGLLGP-KTVLAHMVHLDTQDLEILEKHGNGTSVAHCPVSNSKLGSGIAPLKEMLEKSIIVGIGCDGCPCNNTMDLLQEMK 332 76.6677.8*************.************************************************************************** PP HHHHHHHHSTTTTCHHHHHHHHHHHHCTHHHHHHTT-TTTSSSS-TTSB--EEEESS..TT........CGGGTTTCTSEEEEEEEETTEE CS Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di........laafvglkkdgnvkkvivkGkl 343 +a +l ++l+ d+ ++++++++maTingAkalg+d ++Gs+evGk+AD++ +dl ++ +a+v+++ v++v+++Gkl CUFF.26.1.p1 333 MASLLPKALHG-DPSI-VPAEKIVEMATINGAKALGRD-DLGSLEVGKKADFISLDLsnKLyaqplrdlVSAVVYIATGADVATVVIDGKL 420 ***99998888.6677.89999***************6.******************972255668888********************97 PP >> CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.4 0.4 1.1e-83 5.4e-82 1 343 [. 57 422 .. 57 423 .. 0.96 Alignments for each domain: == domain 1 score: 268.4 bits; conditional E-value: 1.1e-83 EEEE-EEEEEEEEETTECSSS....GHHHHH..........SCTHHHHHHHHHHHHHHHCTTEEEEEEECHSSTHHHHHHHHHHCTSSSEEEEEEES CS Amidohydro_1 1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 iv+PGlI +HvHl qsllr+a +l +wl ++e+ ++a++ i+++lksGttt+ ++ +++ +gie +a+ e g+r ++gk CUFF.27.1.p1 57 IVMPGLISLHVHLAQSLLRSAaddlPLISWLcdtvwkmqgnFTQEDGYVASQLTIAEMLKSGTTTFVEALFAQRYGIEGAVKAVIES--GIRGCIGK 151 79************************************************************************************9..******** PP SEGGS...............GHCCSHHHHHHHHHHCHHHHHHHTTTTCEECEEEECGSGCSHHHHHHHHHHHHHHCTTEEEEEETSSSCCHHHHHHH CS Amidohydro_1 84 vsldr...............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaa 165 v++d+ ++++s++++++ ++ + +gk++g+v+++++ + + ++s+e+ ++++k a++ ++ +++H++e k++ + CUFF.27.1.p1 152 VVMDQpryatqtgvsmheglIENSNSLNQAVESHSKF----HGKGNGRVEIWFGARTPGGVSEELYRKMVKIARANNIGITMHCAEVKADR----EF 240 ******************9988899999999999999....*******************************************9999996....67 PP HTTTEEEETTTTCTTSHCTTTGCCEEECTTCEEEHHCCCHHHHHHHHHHEEHHHHHHHHCEHHHHHHHHHHHHTCEEEEEEETTTSSBCCGHHHHHH CS Amidohydro_1 166 fgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelr 262 f+ + eh t+ ++++lgll++ k++lah+vhl+ ++e+l +++++++vahcp sns+l+sg+++l+++l+++++vg+g+Dg+ ++n+++ll+e++ CUFF.27.1.p1 241 FA-SKEH-TPMTYCKDLGLLGP-KTVLAHMVHLDTQDLEILEKHGNGTSVAHCPVSNSKLGSGIAPLKEMLEKSIIVGIGCDGCPCNNTMDLLQEMK 334 76.6677.8*************.************************************************************************** PP HHHHHHHHSTTTTCHHHHHHHHHHHHCTHHHHHHTT-TTTSSSS-TTSB--EEEESS..TT........CGGGTTTCTSEEEEEEEETTEE CS Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di........laafvglkkdgnvkkvivkGkl 343 +a +l ++l+ d+ ++++++++maTingAkalg+d ++Gs+evGk+AD++ +dl ++ +a+v+++ v++v+++Gkl CUFF.27.1.p1 335 MASLLPKALHG-DPSI-VPAEKIVEMATINGAKALGRD-DLGSLEVGKKADFISLDLsnKLyaqplrdlVSAVVYIATGADVATVVIDGKL 422 ***99998888.6677.89999***************6.******************972255668888********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 781.97 // Query: Amidohydro_3 [M=473] Accession: PF07969.10 Description: Amidohydrolase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-17 55.5 0.1 1.6e-13 43.4 0.0 2.2 2 CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-13 3.6e-17 55.5 0.1 1.6e-13 43.4 0.0 2.2 2 CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471( Domain annotation for each sequence (and alignments): >> CUFF.26.1.p1 type:5prime_partial gc:universal CUFF.26.1:3-1388(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 10.0 0.1 4.8e-05 0.0023 5 25 .. 51 71 .. 50 82 .. 0.86 2 ! 43.4 0.0 3.4e-15 1.6e-13 265 472 .. 211 421 .. 163 422 .. 0.75 Alignments for each domain: == domain 1 score: 10.0 bits; conditional E-value: 4.8e-05 Amidohydro_3 5 akGrlvlPGFvDsHtHlaggg 25 ++G +v+PG++ H Hla CUFF.26.1.p1 51 LEGHIVMPGLISLHVHLAQSL 71 89**************99865 PP == domain 2 score: 43.4 bits; conditional E-value: 3.4e-15 Amidohydro_3 265 laelvaaadergldvaihaigdaavddvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperarg 356 +++v+ a+++ + + +h+ + +a +++++ e + +++g+ + l+h ++++++e + + + +v + ++ + + ++g CUFF.26.1.p1 211 YRKMVKIARANNIGITMHCAEVKADREFFASKEHTpmtyCKDLGLLGPKtVLAHMVHLDTQDLEILEKHGNGTSVAHCPVS---------NSKLGSG 298 567777777777777777777777776666666666666666666666455555555577777777777777777755544.........2466789 PP Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adp 449 ++p+ke+l++ + v g D +p ++++ +++ ++ ++ ++ e+++ + T ++Akalg +d G+LevG++AD++ ld + CUFF.26.1.p1 299 IAPLKEMLEKSIIVGIGCD-----GCPCNNTMDLLQEMKMASLlpkALHGDPSIVPAEKIVEMATINGAKALGRDDL-GSLEVGKKADFISLDlSNK 389 9******************.....4444444444433333333666999***************************8.***************9555 PP Amidohydro_3 450 ldvdppelaear.........vrltvvdGrvv 472 l ++p ++ v +v+dG+ + CUFF.26.1.p1 390 LYAQPLRDLVSAvvyiatgadVATVVIDGKLI 421 55555443333346666888899999999876 PP >> CUFF.27.1.p1 type:complete gc:universal CUFF.27.1:2862-1471(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 10.0 0.1 4.9e-05 0.0023 5 25 .. 53 73 .. 52 84 .. 0.86 2 ! 43.4 0.0 3.4e-15 1.6e-13 265 472 .. 213 423 .. 165 424 .. 0.75 Alignments for each domain: == domain 1 score: 10.0 bits; conditional E-value: 4.9e-05 Amidohydro_3 5 akGrlvlPGFvDsHtHlaggg 25 ++G +v+PG++ H Hla CUFF.27.1.p1 53 LEGHIVMPGLISLHVHLAQSL 73 89**************99865 PP == domain 2 score: 43.4 bits; conditional E-value: 3.4e-15 Amidohydro_3 265 laelvaaadergldvaihaigdaavddvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperarg 356 +++v+ a+++ + + +h+ + +a +++++ e + +++g+ + l+h ++++++e + + + +v + ++ + + ++g CUFF.27.1.p1 213 YRKMVKIARANNIGITMHCAEVKADREFFASKEHTpmtyCKDLGLLGPKtVLAHMVHLDTQDLEILEKHGNGTSVAHCPVS---------NSKLGSG 300 567777777777777777777777776666666666666666666666455555555577777777777777777755544.........2466789 PP Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adp 449 ++p+ke+l++ + v g D +p ++++ +++ ++ ++ ++ e+++ + T ++Akalg +d G+LevG++AD++ ld + CUFF.27.1.p1 301 IAPLKEMLEKSIIVGIGCD-----GCPCNNTMDLLQEMKMASLlpkALHGDPSIVPAEKIVEMATINGAKALGRDDL-GSLEVGKKADFISLDlSNK 391 9******************.....4444444444433333333666999***************************8.***************9555 PP Amidohydro_3 450 ldvdppelaear.........vrltvvdGrvv 472 l ++p ++ v +v+dG+ + CUFF.27.1.p1 392 LYAQPLRDLVSAvvyiatgadVATVVIDGKLI 423 55555443333346666888899999999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (473 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 873.88 // Query: Aminotran_1_2 [M=363] Accession: PF00155.20 Description: Aminotransferase class I and II Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-06 18.7 0.0 7.3e-06 17.9 0.0 1.4 1 CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+ Domain annotation for each sequence (and alignments): >> CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.9 0.0 7.6e-08 7.3e-06 48 334 .. 65 357 .. 61 375 .. 0.71 Alignments for each domain: == domain 1 score: 17.9 bits; conditional E-value: 7.6e-08 HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHH...HHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHT CS Aminotran_1_2 48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyk...nilrlsggevvryplyseedfhldlealeealk 140 e ++ lak+l+ ++++++++ +++++++++ + lk pgd++++ d +++ +l++ g+ev+ +p +e ++h ++ + ++ CUFF.40.1.p1 65 ETRSLLAKLLN------ASTKDSITFTRDTTEGLNLFQRSLKWKPGDNVVILDNEHPNQGfgwIALQNDGLEVRLVP--NEGQYHANASTFAPYVD 152 778999*****......45555***********************************987333568999********..77999999999*99999 PP THHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTTSGGG-EEEEEEE CS Aminotran_1_2 141 eapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgn 236 + +tk i + s+ +G+ +++++++++ + ++++++ D + +++ ++ +v++ +++ s+ K +G++ +G ++++ CUFF.40.1.p1 153 S------RTKAIGLSSVMFHSGQ---KNDVKDIANAFRPKGIHVLADLTQQVGLSK--------IDVQDLNVSACAFSCHKGLGCPT-GLGVLYVS 230 9......9***********9*97...5677777777*************9999998........55555544688889999999975.58999998 PP H.........................HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHS.....TEEE CS Aminotran_1_2 237 a.........................avvsqlrklsrpfls.ssllqaavaaalsdallkqs..eleemrqrlqkrrkelrdeLael.....glkv 299 + +++ ++ ++++ + + ++++ +al++ l+ +++ + lq + k l +eL++l g k CUFF.40.1.p1 231 PlaiselrstppfvgggavedfkedlKLKLNAKYHQSALRYeHTNNAYMLITALRAYLKFLLkvGISNVERYLQGLGKDLIKELESLnvsviGYKD 326 866666666666666666666666555555555555555555555666666666666555554434444444555555666666555444444444 PP ECCS.CSSEEEEEETHHCHHHHHHHHHHTCTEEEEE CS Aminotran_1_2 300 lasq.sgmflltdlsaetakelskkLleevgvyvtp 334 ++++ s+ ++l l++e ++ L+++ gv v++ CUFF.40.1.p1 327 FDKHsSHSYVLKILNPE----WFDFLRQQ-GVCVSR 357 44444555555555555....44445555.666655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 380.28 // Query: Aminotran_5 [M=371] Accession: PF00266.18 Description: Aminotransferase class-V Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-47 153.1 0.0 8.8e-47 152.3 0.0 1.3 1 CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+ Domain annotation for each sequence (and alignments): >> CUFF.40.1.p1 type:complete gc:universal CUFF.40.1:316-1620(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 152.3 0.0 9.2e-49 8.8e-47 41 369 .. 59 376 .. 25 378 .. 0.89 Alignments for each domain: == domain 1 score: 152.3 bits; conditional E-value: 9.2e-49 HHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCHHH-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-- CS Aminotran_5 41 atkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln 137 ++ ee+r+ +a+l+na++++ i ft+ tte++nl+ +sl ++kpgd++v+ ++eh + w +l+ g++v+ +p + + + + ++++ +++ CUFF.40.1.p1 59 WKERTEETRSLLAKLLNASTKDSITFTRDTTEGLNLFQRSL--KWKPGDNVVILDNEHPNQGFGWIALQ-NDGLEVRLVPNEGQYHANASTFAPYVD 152 56789************************************..59***********************8.67************************* PP TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHHS.....SS.STTS CS Aminotran_5 138 ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekl...eplllggem 230 +tk++ ++ v +G ++v++i+++++ kg+ vl+D +q+vg +idv++l+v afs hK l PtG+Gvlyv++ ++ +l +p+ +gg+ CUFF.40.1.p1 153 SRTKAIGLSSVMFHSGQKNDVKDIANAFRPKGIHVLADLTQQVGLSKIDVQDLNVSACAFSCHKgLGCPTGLGVLYVSPLAISELrstPPF-VGGGA 248 ****************************************************************8888*************9999774455.55555 PP EEEEET.....TEEEEHHTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTSSHH CS Aminotran_5 231 veevsl.....eettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhae 322 ve+ + +++++++ ++e+ + i +l+a l++l ++g++++e++ + l + l ++l+sl+ + g k+ ++s s ++k +++e CUFF.40.1.p1 249 VEDFKEdlklkLNAKYHQSALRYEHTNNAYMLITALRAYLKFLLKVGISNVERYLQGLGKDLIKELESLNVSVI-G-YKDFDKHSSHSYVLKILNPE 343 665554110044555999*******555578899***********************************98766.8.67899999999999999998 PP HHHHHHHHTTEEEEEE-TTTHHHHHHHT.S-EEEEE--TTS-HHHHH CS Aminotran_5 323 dvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevd 369 + +L+++g++v+ e+++R+S+++ynt++++ CUFF.40.1.p1 344 WF-DFLRQQGVCVSR-------------FESGIRVSFGLYNTSKDII 376 65.79******9974.............45999***********996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (371 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 403.02 // Query: Arginase [M=280] Accession: PF00491.20 Description: Arginase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-91 298.4 0.0 3.4e-91 298.2 0.0 1.0 1 CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122 Domain annotation for each sequence (and alignments): >> CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122-1(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 298.2 0.0 3.6e-93 3.4e-91 2 277 .. 75 373 .. 74 374 .] 0.93 Alignments for each domain: == domain 1 score: 298.2 bits; conditional E-value: 3.6e-93 EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE...SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHTTCEE......... CS Arginase 2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv...leelkivdlgdvavtpvdneevleqieeavaeilkagklp......... 86 d+a+lG+Pfd+++s+rpGarfGP+ ire+s+rl+ + +yn+ ++ +++kivd+gd+++t +dn+ +++qie+ e+l+++ + CUFF.38.1.p4 75 DIAFLGAPFDTGTSYRPGARFGPSGIREGSRRLNLYGGYNVPMETnpfNNWAKIVDCGDIPLTSYDNAVAIKQIENGHFELLTRKPTSysekdgyal 171 89********************************8778888887788999******************9***************4444555555555 PP ........EEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSC......TTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSH..HHHH CS Arginase 87 ........ivlGGDHsialgilralaekygkplgvihfDAHaDlrtpe......tegsgnshGtpfrraaeegllkpkklvqiGirsvdne..eyel 167 i+lGGDH+i l+ilr+++++yg p+++ihfD+H+D ++p+ ++ +++hGt+f++a++egl+++++ +++Gir++ ++ +y+ CUFF.38.1.p4 172 dgsvlprvITLGGDHTIVLPILRSVSRAYG-PVSIIHFDSHLDSWKPKvfgggkSSVGSINHGTYFYHASQEGLVSNDSNIHAGIRTTLSGlsDYDN 267 55555666********************99.6****************99988877778********************************999999 PP HHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTT CS Arginase 168 akelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteae 264 ++++g+++i++reid +g++a++++i++rvg ++ ylS+DiDvlDpa+aP+tGtpe G+t+rel+++lr+l + +lvgaD+vEv+Pa+d ae CUFF.38.1.p4 268 DADCGFEIIEAREIDTIGIDAIIKRIRDRVG--DGIAYLSIDIDVLDPAYAPATGTPESAGWTTRELRTILRGLDG-IKLVGADIVEVAPAYDF-AE 360 999***************************8..57***************************************99.*****************.67 PP HHHHHHHHHHHHH CS Arginase 265 qtarlaarlvrel 277 t+++aa++++e+ CUFF.38.1.p4 361 VTTLAAADILFEV 373 ***********95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (280 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1320.22 // Query: Asparaginase [M=191] Accession: PF00710.19 Description: Asparaginase, N-terminal Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-54 176.5 0.6 2.9e-54 176.1 0.6 1.2 1 CUFF.15.1.p1 type:5prime_partial gc:universal CUFF.15.1:3-11 Domain annotation for each sequence (and alignments): >> CUFF.15.1.p1 type:5prime_partial gc:universal CUFF.15.1:3-1103(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 176.1 0.6 3.1e-56 2.9e-54 1 182 [. 47 233 .. 47 241 .. 0.96 Alignments for each domain: == domain 1 score: 176.1 bits; conditional E-value: 3.1e-56 EEEEEEEESGGGBB-SSSS--SS-B...S-HHHHHTTSTTHHHHSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHH.HT.--EEEEE--STTHHHHH CS Asparaginase 1 kvlvlatGGTiasekdesggalapa...lsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.ee.ydgfVvlhGTDTlaytA 92 +v v a+GGTia +++s + +++ + +e+l+ea+p+++ ia+++ q++n+ S+n+tpad+lkla+ i +++ + ++g+V++hGTD+l++tA CUFF.15.1.p1 47 NVTVFAMGGTIAGCANSSLEIVNYIpgsVGIEKLIEAVPAIKAIANINGVQVTNMGSENLTPADVLKLAKLILAEVaKPnVHGIVITHGTDSLEETA 143 599***************99999878899***********************************************7669***************** PP HHHHHH---.-S-EEEE--SS-TTSTT-SHHHHHHHHHHHHHSGG.TTS-SEEEETTEEEETTT-EE-BSSSSS-EE-TTT--SEEEETTE CS Asparaginase 93 saLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasse.riagvlvvfngkllranrvtKvhtssldaFespnlgplaevegsk 182 ++L+l++ + +kp+v++G++rp++++++Dgp+Nll+A++va+s++ ++g lv +n+++ +a ++tK++ ++ld+F+s ++g+l+ v ++k CUFF.15.1.p1 144 MFLDLTIST-AKPIVVVGAMRPSTAIGADGPMNLLNAVAVASSNQsMGRGTLVLLNDRIGSAFYTTKTNGNTLDTFKSYEAGSLGIVLNQK 233 *******99.***************************************************************************986655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (191 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 9 (0.0947368); expected 1.9 (0.02) Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1325.24 // Query: Asp_Glu_race [M=224] Accession: PF01177.21 Description: Asp/Glu/Hydantoin racemase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-06 19.8 0.0 5.8e-06 18.9 0.0 1.4 1 CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722- 3.6e-06 19.6 0.0 6.9e-06 18.6 0.0 1.4 1 CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) Domain annotation for each sequence (and alignments): >> CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.9 0.0 1.2e-07 5.8e-06 49 98 .. 157 205 .. 141 211 .. 0.87 Alignments for each domain: == domain 1 score: 18.9 bits; conditional E-value: 1.2e-07 H.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEEC CS Asp_Glu_race 49 esgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgi 98 +++++++++l e+a++Lek ga+++v+ C ++a++++k i+iP +gi CUFF.52.1.p3 157 GREQSAAARLIENAQQLEKFGAQLLVLECIPE-SLAEQITKTISIPTIGI 205 34455667**********************99.****************7 PP >> CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.6 0.0 1.4e-07 6.9e-06 49 98 .. 157 205 .. 141 212 .. 0.87 Alignments for each domain: == domain 1 score: 18.6 bits; conditional E-value: 1.4e-07 H.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEEC CS Asp_Glu_race 49 esgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgi 98 +++++++++l e+a++Lek ga+++v+ C ++a++++k i+iP +gi CUFF.50.1.p3 157 GREQSAAARLIENAQQLEKFGAQLLVLECIPE-SLAEQITKTISIPTIGI 205 34455667**********************99.****************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (224 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1577.53 // Query: Beta_elim_lyase [M=293] Accession: PF01212.20 Description: Beta-eliminating lyase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-06 19.7 0.0 4.2e-06 18.8 0.0 1.4 1 CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+ Domain annotation for each sequence (and alignments): >> CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.8 0.0 4.4e-08 4.2e-06 29 201 .. 619 786 .. 611 886 .. 0.76 Alignments for each domain: == domain 1 score: 18.8 bits; conditional E-value: 4.4e-08 T--HHHHHHHHHHHHHTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT........-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHH CS Beta_elim_lyase 29 gedktvnrLedavaelfgkeaalfvp.qGtaAnsillkillqrgeevivtep........ahihfdetgaiaelagvklrdlknkeaGkmdlek 113 g + +++L+ ++ ++g++aa f p +G a++ l+++ + ++ +++ ah+ ++ a a++ag +++++k ++G++d+++ CUFF.57.1.p1 619 GYRHVIEDLQLMLTTITGFDAACFQPnSGAAGEYTGLSVIRAYQRSIGQGHRniclipvsAHG---TNPASAAMAGFTVIPVKCLNNGYLDMQD 709 555667788999999*********9956*******9977765555555555445444344443...55677889*********9999******* PP HHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH...HHHTS-CHHHHTTSSEEEEESSSTT- CS Beta_elim_lyase 114 leaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa...kslgeivkemfsyvDsvtmslkKdll 201 l+++ + h++k ++ ++t G ++e+ ++ +++g ++ +DgA +na+ ++ ++ ++D++ + l K + CUFF.57.1.p1 710 LKEKASK---HADKLAAFMVTYPSTF--GI--FEPDVKEALEVIHEHGGQVYFDGAN-MNAMvglC----KAGDI--GADVCHLNLHKTFC 786 ***9999...8889999999888887..54..44579*******************5.45552332....33333..23444444444444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (293 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1114.14 // Query: Chitin_synth_1 [M=163] Accession: PF01644.16 Description: Chitin synthase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-83 270.9 0.2 3.3e-83 270.1 0.2 1.4 1 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 1.9e-83 270.9 0.2 3.3e-83 270.1 0.2 1.4 1 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ Domain annotation for each sequence (and alignments): >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 270.1 0.2 7e-85 3.3e-83 1 163 [] 196 358 .. 196 358 .. 1.00 Alignments for each domain: == domain 1 score: 270.1 bits; conditional E-value: 7e-85 Chitin_synth_1 1 mynEdkellarTLkgvmkNieelkkrkkskvwgkdsWkkivVcivsDGrekideetldllaalgvyqegvakkkvngkevkahlfeyttqlsvde 95 mynEd++l+arT+++vmkNi++l++rk+s+vwgkd+Wkk+vVci+sDGr+ki+++tl++laa+gvyq+g+ak++vn+kevkah++eyttqls+d+ CUFF.60.1.p1 196 MYNEDEVLFARTMHSVMKNISHLCTRKNSQVWGKDAWKKVVVCIISDGRTKIHPRTLAYLAAIGVYQDGIAKNQVNDKEVKAHIYEYTTQLSIDP 290 9********************************************************************************************** PP Chitin_synth_1 96 elklkenekslvpvqllfclkeknakkinShrWffnafarllqPevcvlldvGtkpgkkslyklwkaf 163 +lk+k++++++vpvq++fclkekn+kk+nSh Wff+af+++l+Pevc+lld+Gt+pg++s+y+lwk+f CUFF.60.1.p1 291 NLKFKGSDRGIVPVQMIFCLKEKNQKKLNSHLWFFQAFCPILKPEVCILLDAGTRPGDQSIYHLWKSF 358 ******************************************************************98 PP >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 270.1 0.2 7e-85 3.3e-83 1 163 [] 196 358 .. 196 358 .. 1.00 Alignments for each domain: == domain 1 score: 270.1 bits; conditional E-value: 7e-85 Chitin_synth_1 1 mynEdkellarTLkgvmkNieelkkrkkskvwgkdsWkkivVcivsDGrekideetldllaalgvyqegvakkkvngkevkahlfeyttqlsvde 95 mynEd++l+arT+++vmkNi++l++rk+s+vwgkd+Wkk+vVci+sDGr+ki+++tl++laa+gvyq+g+ak++vn+kevkah++eyttqls+d+ CUFF.60.2.p1 196 MYNEDEVLFARTMHSVMKNISHLCTRKNSQVWGKDAWKKVVVCIISDGRTKIHPRTLAYLAAIGVYQDGIAKNQVNDKEVKAHIYEYTTQLSIDP 290 9********************************************************************************************** PP Chitin_synth_1 96 elklkenekslvpvqllfclkeknakkinShrWffnafarllqPevcvlldvGtkpgkkslyklwkaf 163 +lk+k++++++vpvq++fclkekn+kk+nSh Wff+af+++l+Pevc+lld+Gt+pg++s+y+lwk+f CUFF.60.2.p1 291 NLKFKGSDRGIVPVQMIFCLKEKNQKKLNSHLWFFQAFCPILKPEVCILLDAGTRPGDQSIYHLWKSF 358 ******************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (163 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 925.81 // Query: Chitin_synth_1N [M=73] Accession: PF08407.10 Description: Chitin synthase N-terminal Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-29 92.8 0.1 1.2e-28 91.6 0.1 1.7 1 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 5e-29 92.8 0.1 1.2e-28 91.6 0.1 1.7 1 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ Domain annotation for each sequence (and alignments): >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 91.6 0.1 2.5e-30 1.2e-28 2 73 .] 124 195 .. 123 195 .. 0.96 Alignments for each domain: == domain 1 score: 91.6 bits; conditional E-value: 2.5e-30 Chitin_synth_1N 2 kkvkLlngnlvldlpvpkkllkalpeeekeseEfthmRYtAvTcdPddftkegytLRqalyg..ReteLlIviT 73 k+vkL++gnl+ld+p+pkkll +lp++ +++Ef +mRY+A+TcdP+df+k+ +tLRq l+ R+te++I+iT CUFF.60.1.p1 124 KRVKLFHGNLILDCPIPKKLLVTLPQQ--TEREFAYMRYSAATCDPQDFSKSLFTLRQPLFFqpRKTEICIAIT 195 89***********************65..9******************************8779*********9 PP >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 91.6 0.1 2.5e-30 1.2e-28 2 73 .] 124 195 .. 123 195 .. 0.96 Alignments for each domain: == domain 1 score: 91.6 bits; conditional E-value: 2.5e-30 Chitin_synth_1N 2 kkvkLlngnlvldlpvpkkllkalpeeekeseEfthmRYtAvTcdPddftkegytLRqalyg..ReteLlIviT 73 k+vkL++gnl+ld+p+pkkll +lp++ +++Ef +mRY+A+TcdP+df+k+ +tLRq l+ R+te++I+iT CUFF.60.2.p1 124 KRVKLFHGNLILDCPIPKKLLVTLPQQ--TEREFAYMRYSAATCDPQDFSKSLFTLRQPLFFqpRKTEICIAIT 195 89***********************65..9******************************8779*********9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (73 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 745.23 // Query: Chitin_synth_2 [M=527] Accession: PF03142.14 Description: Chitin synthase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-24 77.5 9.9 2.7e-21 68.3 0.0 2.7 4 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 4.3e-24 77.5 9.9 2.7e-21 68.3 0.0 2.7 4 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ Domain annotation for each sequence (and alignments): >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.5 0.0 0.33 16 27 49 .. 190 212 .. 180 222 .. 0.78 2 ? -3.2 0.0 0.27 13 236 264 .. 242 270 .. 225 278 .. 0.78 3 ! 68.3 0.0 5.7e-23 2.7e-21 203 433 .. 335 576 .. 320 600 .. 0.76 4 ! 12.2 3.7 5.6e-06 0.00027 434 491 .. 665 722 .. 612 732 .. 0.87 Alignments for each domain: == domain 1 score: -3.5 bits; conditional E-value: 0.33 Chitin_synth_2 27 ticlvtaysedeeglrttldsla 49 + + +t y ede + +t+ s+ CUFF.60.1.p1 190 ICIAITMYNEDEVLFARTMHSVM 212 3446999*****99999999986 PP == domain 2 score: -3.2 bits; conditional E-value: 0.27 Chitin_synth_2 236 cGetkiankkeswvtaiqvfeyyishhls 264 G tki ++ ++++ai v++ i+++++ CUFF.60.1.p1 242 DGRTKIHPRTLAYLAAIGVYQDGIAKNQV 270 38899999999999999999988887776 PP == domain 3 score: 68.3 bits; conditional E-value: 5.7e-23 Chitin_synth_2 203 eivlmvdadtkvfpdsltrlvaalvkdpeilglcGetkiankk.es.w...vtaiqvfeyyishhlskafesvfGgvtclPGcfslyrikaakgs 292 e+++++da t+ s+ +l ++ +p++ g cGe + k s + a q fey +s l k esvfG ++ lPG fs yr +a ++ CUFF.60.1.p1 335 EVCILLDAGTRPGDQSIYHLWKSFDLNPQVAGACGEIVVMKGKlGSgLinpLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQND 429 8899********************************9876543244222225789************************************9886 PP Chitin_synth_2 293 dgywvPilvspeiveeysenvvdtlhkknllllGedrylt.tlllktfpkrktvfvpkakcktvvPdkfkvllsqrrrwinstvhnllelvl..v 384 ++ P+ e ++ + + n ++l edr l l+ k+ + +v++a + t vPd+ ++ qrrrw+n + + + CUFF.60.1.p1 430 SQGNGPLAS--YFKGELQNTGKSGIFEAN-MYLAEDRILCfELVSKKNEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSFFAAAYAIChyY 521 666778643..334455555566777777.579******84578888889999****************************98877655443113 PP Chitin_synth_2 385 rdlcGtfcfsmrfvvfieli...gtlvl...Paaiaftlylivvailkskpvpvi 433 r + s +f++ ie+i +t+v + f+++ i+++ l+s+ + + CUFF.60.1.p1 522 RFFRTSHTISRKFMLSIEFIyqlATIVFgwfNIGNFFIIFYILTSSLASTSANFL 576 4445556778888887776522256665111344556666666666655555555 PP == domain 4 score: 12.2 bits; conditional E-value: 5.6e-06 Chitin_synth_2 434 slvllaivlGlpailivltarklsyvawlvvyllalPifnfvlPlyafwklddfswGe 491 ++ l+ +G+ ++ ++ +++ + +v y++ +++ vl +yaf + d swG CUFF.60.1.p1 665 IVISLSSTYGMYLVVSIISFDPWHMFTSFVQYIFLSIMYTNVLNVYAFCNTHDVSWGT 722 34558999*************************************************6 PP >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.5 0.0 0.33 16 27 49 .. 190 212 .. 180 222 .. 0.78 2 ? -3.2 0.0 0.27 13 236 264 .. 242 270 .. 225 278 .. 0.78 3 ! 68.3 0.0 5.7e-23 2.7e-21 203 433 .. 335 576 .. 320 600 .. 0.76 4 ! 12.2 3.7 5.6e-06 0.00027 434 491 .. 665 722 .. 612 732 .. 0.87 Alignments for each domain: == domain 1 score: -3.5 bits; conditional E-value: 0.33 Chitin_synth_2 27 ticlvtaysedeeglrttldsla 49 + + +t y ede + +t+ s+ CUFF.60.2.p1 190 ICIAITMYNEDEVLFARTMHSVM 212 3446999*****99999999986 PP == domain 2 score: -3.2 bits; conditional E-value: 0.27 Chitin_synth_2 236 cGetkiankkeswvtaiqvfeyyishhls 264 G tki ++ ++++ai v++ i+++++ CUFF.60.2.p1 242 DGRTKIHPRTLAYLAAIGVYQDGIAKNQV 270 38899999999999999999988887776 PP == domain 3 score: 68.3 bits; conditional E-value: 5.7e-23 Chitin_synth_2 203 eivlmvdadtkvfpdsltrlvaalvkdpeilglcGetkiankk.es.w...vtaiqvfeyyishhlskafesvfGgvtclPGcfslyrikaakgs 292 e+++++da t+ s+ +l ++ +p++ g cGe + k s + a q fey +s l k esvfG ++ lPG fs yr +a ++ CUFF.60.2.p1 335 EVCILLDAGTRPGDQSIYHLWKSFDLNPQVAGACGEIVVMKGKlGSgLinpLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQND 429 8899********************************9876543244222225789************************************9886 PP Chitin_synth_2 293 dgywvPilvspeiveeysenvvdtlhkknllllGedrylt.tlllktfpkrktvfvpkakcktvvPdkfkvllsqrrrwinstvhnllelvl..v 384 ++ P+ e ++ + + n ++l edr l l+ k+ + +v++a + t vPd+ ++ qrrrw+n + + + CUFF.60.2.p1 430 SQGNGPLAS--YFKGELQNTGKSGIFEAN-MYLAEDRILCfELVSKKNEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSFFAAAYAIChyY 521 666778643..334455555566777777.579******84578888889999****************************98877655443113 PP Chitin_synth_2 385 rdlcGtfcfsmrfvvfieli...gtlvl...Paaiaftlylivvailkskpvpvi 433 r + s +f++ ie+i +t+v + f+++ i+++ l+s+ + + CUFF.60.2.p1 522 RFFRTSHTISRKFMLSIEFIyqlATIVFgwfNIGNFFIIFYILTSSLASTSANFL 576 4445556778888887776522256665111344556666666666655555555 PP == domain 4 score: 12.2 bits; conditional E-value: 5.6e-06 Chitin_synth_2 434 slvllaivlGlpailivltarklsyvawlvvyllalPifnfvlPlyafwklddfswGe 491 ++ l+ +G+ ++ ++ +++ + +v y++ +++ vl +yaf + d swG CUFF.60.2.p1 665 IVISLSSTYGMYLVVSIISFDPWHMFTSFVQYIFLSIMYTNVLNVYAFCNTHDVSWGT 722 34558999*************************************************6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (527 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 12 (0.126316); expected 1.9 (0.02) Passed bias filter: 10 (0.105263); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 536.14 // Query: CO_dh [M=168] Accession: PF02552.15 Description: CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-07 22.4 0.0 2.4e-06 20.0 0.0 2.1 2 CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092( Domain annotation for each sequence (and alignments): >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.3 0.0 0.091 8.6 18 41 .. 130 154 .. 125 156 .. 0.80 2 ! 20.0 0.0 2.5e-08 2.4e-06 14 78 .. 194 257 .. 175 297 .. 0.74 Alignments for each domain: == domain 1 score: -1.3 bits; conditional E-value: 0.091 --EEE--SHHHHHHHHHS.SSEEEE CS CO_dh 18 katleealkvvakmikka.krPlli 41 + ++ ++l+ +a +ik+a + P++i CUFF.32.1.p1 130 QMEIAKKLTCAAVAIKRAeDAPVMI 154 6788899999*******93468877 PP == domain 2 score: 20.0 bits; conditional E-value: 2.5e-08 XXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEETHHHTT-G. CS CO_dh 14 anskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvatalkeaglkd 78 s k +le+a +a++i+k ++P+l+ Gp+++ a e a++k + + + + +g + CUFF.32.1.p1 194 EISDKESLEKATDIAAELISKKEKPILLAGPKLRAAGAESAFVKLAEALNCAAFIMP-AAKGFYS 257 455677899999*******************************99887776654444.3555554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1265.90 // Query: CRCB [M=95] Accession: PF02537.14 Description: CrcB-like protein, Camphor Resistance (CrcB) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-32 104.7 23.7 4.8e-18 58.0 3.7 2.5 3 CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+ Domain annotation for each sequence (and alignments): >> CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 56.7 7.3 1.2e-19 1.2e-17 3 92 .. 8 118 .. 6 123 .. 0.83 2 ? -2.4 0.1 0.33 32 44 56 .. 166 180 .. 143 183 .. 0.58 3 ! 58.0 3.7 5e-20 4.8e-18 3 93 .. 190 296 .. 188 299 .. 0.86 Alignments for each domain: == domain 1 score: 56.7 bits; conditional E-value: 1.2e-19 HHHHHHHHHHHHHHH.HHHHB-....BHHHHHHHHHHHHHHHHHHH................HHTTTHHHHH--SHHHHHHHHHHHHHT-HHHHH.. CS CRCB 3 valggalGallRyllssllnkr....plgtlavNvlGsfllgllla................llttGflGglTTfStfvlelvslleegellkal.. 77 +++++lG+l+R++l ++ln+ + g l+v ++G++++g++ + ++ttGf+G+lTTfS+++l++++ +++ + ++ + CUFF.14.1.p1 8 FCIMSMLGTLARLGL-TALNTYpgapFSGLLWVQFVGCVIMGFCQTesvffprpkhnatfllAITTGFCGSLTTFSSWMLQMFTGMANLDPFERRgr 103 6899***********.7677777997569**************99988887777777777666*********************8877665555566 PP HHHHHHHHHHHHHHH CS CRCB 78 lyvllsvvlgllavv 92 y +lsvv +++++ CUFF.14.1.p1 104 GYSFLSVVSDFMVTM 118 999999998887665 PP == domain 2 score: -2.4 bits; conditional E-value: 0.33 H..HHTTTHHHHH-- CS CRCB 44 a..llttGflGglTT 56 +++ f ++TT CUFF.14.1.p1 166 IcfFVGAAFYTAYTT 180 122455555555555 PP == domain 3 score: 58.0 bits; conditional E-value: 5e-20 HHHHHHHHHHHHHHH.HHHHB-....BHHHHHHHHHHHHHHHHHHH................HHTTTHHHHH--SHHHHHHHHHHHHHT-HHHHHHH CS CRCB 3 valggalGallRyllssllnkr....plgtlavNvlGsfllgllla................llttGflGglTTfStfvlelvslleegellkally 79 ++++++ al+R++l++ ln+ p+gtl++Nv++++ll ++++ +++Gf+ l+T Stf++el+++ + +a +y CUFF.14.1.p1 190 SLIFSPFAALTRLYLARFLNSPqyfiPYGTLCANVFATLLLSIMYMipqithctpvsrsvmyGIQNGFCAVLSTLSTFSNELHTMP----IKRAYIY 282 689************9988888***999***************99977766666655555555*********************96....4458999 PP HHHHHHHHHHHHHH CS CRCB 80 vllsvvlgllavvl 93 +++sv++++ ++v+ CUFF.14.1.p1 283 CIISVAISFSICVI 296 9****999987765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (95 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1003.61 // Query: CTP_transf_like [M=143] Accession: PF01467.25 Description: Cytidylyltransferase-like Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00037 13.3 0.0 0.00069 12.4 0.0 1.4 1 CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+ Domain annotation for each sequence (and alignments): >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.4 0.0 7.3e-06 0.00069 9 43 .. 33 66 .. 29 73 .. 0.88 Alignments for each domain: == domain 1 score: 12.4 bits; conditional E-value: 7.3e-06 --HHHHHHHHHHHHHSSESEEEEEESSTHCCST-S CS CTP_transf_like 9 iHlGHlrlleqakklleedlivgvpsdeppkkkkk 43 +H GH l+++ak++ e+ ++v + ++ ++ + CUFF.50.1.p2 33 LHEGHFSLVREAKRHAEK-VVVSIFVNPMQFNNPQ 66 7*****************.9999999988887754 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (143 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1877.84 // Query: Dak1 [M=307] Accession: PF02733.16 Description: Dak1 domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-110 360.0 0.4 6.1e-110 359.4 0.4 1.3 1 CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+ 1.4e-52 171.0 1.0 1.7e-52 170.8 1.0 1.1 1 CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612- Domain annotation for each sequence (and alignments): >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 359.4 0.4 1.3e-111 6.1e-110 2 304 .. 75 396 .. 74 399 .. 0.92 Alignments for each domain: == domain 1 score: 359.4 bits; conditional E-value: 1.3e-111 HHHHH-TTEEEETTTTEEEETT-S....-TTS-EEEEEEEESSTTTTGGGBSBTSBSEEEEEEETS---HHHHHHHHHHH--SS-EEEEEESSHHHH CS Dak1 2 Glvaanpelklleeekvvvrkkek....kkgkValisgGGSGHePahagfVGkGmldaavaGevFaSPsadqilaaikavdsgkGvllivkNYtGDv 94 Gl+++np l++ e+++v++r+ ++ + kV+l+sgGGSGHeP+hagfVG+G lda+++G++FaSPs++qi++a+kav+s+kG+l+ivkNYtGD+ CUFF.19.1.p1 75 GLARSNPGLTVIEHDRVIYRTASApgsgDLPKVTLVSGGGSGHEPTHAGFVGDGALDAVACGDIFASPSTKQIYSALKAVASPKGTLIIVKNYTGDI 171 899*****************94444666779****************************************************************** PP HHHHHHHHHHHHTT--EEEEEE--B-SSS.SSTTCSSSB--THHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTEEEEEEEEE--B-TTTSSBSS-- CS Dak1 95 lnfglAaekakaegikvetvvvdDDvave.dseekagrRGvagtvlveKiaGaaaeegasLeevaelaekvnenlrsigvalsactvpgagkpsfel 190 ++fglAae+aka g++ve v v+DDv+v+ +++ +grRG+++tvlv+KiaG aa+ g +L++va++a++v++n ++i+++l++c vpg++ +++ l CUFF.19.1.p1 172 IHFGLAAERAKAAGMNVELVAVGDDVSVGkKRGALVGRRGLGATVLVHKIAGSAAALGLDLHQVAQVAQSVIDNAATIAASLDHCAVPGRKFETN-L 267 ****************************9799999********************************************************8886.* PP -TTEEEETE-TTS---SEEEE.---HHHHHHHHHHHHHH............TT-EEEEEEEE-BSS-HHHHHHHHHHHHHHHHHTT-EEEEEEEESS CS Dak1 191 eedemelGvGiHgEpGverek.lksadelveelleklled...........kgdevvllvnglGgtsllelyivarevaelleekgikvvrvlvGey 275 ++de+e+G+GiH+EpG+ +++ l s+ elv+e+l+ l+ + ++d+v+llvn++Gg+s+lel ++ v e+l+++gi ++r+++G++ CUFF.19.1.p1 268 GPDEYEIGMGIHNEPGTFKSSpLPSIPELVTEMLSILFGEknpdnsfvefsSKDDVILLVNNMGGMSNLELGYATEVVSEQLAKRGIIPKRTMSGTF 364 ****************977651566789**********64356666666655********************************************* PP S--TTBEEEEEEEEEE-...HHHHHHHHS-EE CS Dak1 276 vTsldmaGfsitllkld...dellelldapve 304 vT+l+++Gf itl++++ ++ +++d p++ CUFF.19.1.p1 365 VTALNGPGFGITLVNASkatPDIFKYFDLPTT 396 ***************98444566667776665 PP >> CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612-1(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 170.8 1.0 3.5e-54 1.7e-52 2 125 .. 75 202 .. 74 204 .] 0.95 Alignments for each domain: == domain 1 score: 170.8 bits; conditional E-value: 3.5e-54 HHHHH-TTEEEETTTTEEEETT-S....-TTS-EEEEEEEESSTTTTGGGBSBTSBSEEEEEEETS---HHHHHHHHHHH--SS-EEEEEESSHHHH CS Dak1 2 Glvaanpelklleeekvvvrkkek....kkgkValisgGGSGHePahagfVGkGmldaavaGevFaSPsadqilaaikavdsgkGvllivkNYtGDv 94 Gl+++np l++ e+++v++r+ ++ + kV+l+sgGGSGHeP+hagfVG+G lda+++G++FaSPs++qi++a+kav+s+kG+l+ivkNYtGD+ CUFF.20.1.p2 75 GLARSNPGLTVIEHDRVIYRTASApgsgDLPKVTLVSGGGSGHEPTHAGFVGDGALDAVACGDIFASPSTKQIYSALKAVASPKGTLIIVKNYTGDI 171 899*****************94444666779****************************************************************** PP HHHHHHHHHHHHTT--EEEEEE--B-SSSSS CS Dak1 95 lnfglAaekakaegikvetvvvdDDvaveds 125 ++fglAae+aka g++ve v v+DDv+v+++ CUFF.20.1.p2 172 IHFGLAAERAKAAGMNVELVAVGDDVSVGKK 202 ****************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 615.92 // Query: Dak2 [M=174] Accession: PF02734.16 Description: DAK2 domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-45 146.9 3.1 4.9e-45 146.1 2.0 2.0 2 CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+ Domain annotation for each sequence (and alignments): >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.4 0.0 0.22 21 70 88 .. 437 455 .. 422 460 .. 0.64 2 ! 146.1 2.0 5.2e-47 4.9e-45 2 173 .. 467 642 .. 466 643 .. 0.96 Alignments for each domain: == domain 1 score: -2.4 bits; conditional E-value: 0.22 TT---HHHHHHHHHHHHHH CS Dak2 70 ldaedlaaalkaaleaiqa 88 +d + + ++lkaa++ai++ CUFF.19.1.p1 437 ADPKMFTKILKAAVDAINE 455 5666677777777777765 PP == domain 2 score: 146.1 bits; conditional E-value: 5.2e-47 TS-S-HHHHHHHHHHHHHHHHHC-..--SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.......TT---HHHHHHHHHHHHHHHH---T CS Dak2 2 vGDGDtGtnmargaeavlkaleel..eeaslaevlkalakallsgagGtsGvlysqflralakalke..keeldaedlaaalkaaleaiqavgkarp 94 +GDGD+Gt++ +g ea++ka++++ + ++ + +++la ++++++gGtsG lys++l+alak ++e +el++ ++a a k al+a+ ++++ar+ CUFF.19.1.p1 467 AGDGDCGTTLVNGGEAITKAINDKsiRLDDGVNGIDDLAYIVEDSMGGTSGGLYSIYLSALAKGVHEsgDSELSVHTFAFASKYALDALFKYTRARK 563 8***********************9****************************************8865777************************* PP TSSSTHHHHHHHHHHHHT...........T---HHHHHHHHHHCCS---SSGGGGGGGGGTT.......S--HHHHHHHHHHHHHH CS Dak2 95 gdkTmlDvlrpavealekakdgedlkealekaakaaekgaeaTkellaklgrAsylgerslg.......vvDpGAvglalileala 173 g +T++D+++p+ve+l++ k l++aakaa++g e+T+++ a++grAsy+++++l+ +DpGA +la+il+a++ CUFF.19.1.p1 564 GFRTLIDAIQPFVETLNEGKG-------LDAAAKAATEGSEQTRKMDAVVGRASYVAKEELHkldseggLPDPGAFALAAILNAIV 642 ******************999.......*******************************9966999999**************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (174 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1322.91 // Query: DJ-1_PfpI [M=165] Accession: PF01965.23 Description: DJ-1/PfpI family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-16 50.8 0.0 3e-15 49.0 0.0 1.9 1 CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028( 3e-15 49.0 0.0 4.5e-15 48.4 0.0 1.2 1 CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 3.7e-10 32.4 0.0 6.7e-10 31.6 0.0 1.5 1 CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) Domain annotation for each sequence (and alignments): >> CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 49.0 0.0 9.5e-17 3e-15 12 125 .. 30 168 .. 26 239 .. 0.74 Alignments for each domain: == domain 1 score: 49.0 bits; conditional E-value: 9.5e-17 EHHHHHHHHHHHHHTTEEEEEEESS......TSEEEETT.S...EEEE-SEEGG............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHH CS DJ-1_PfpI 12 edvElivpvdvlkragikvdvvsvd......keevkgsr.G...lkvtvdasld............dvkaaeyDalvlpGGragperlrenekvvel 86 El +p++v+k+ag++v+ vs + + +++s+ G kv+ d+ d d+ ++y +l + GG+a +l + + ++++ CUFF.46.1.p1 30 HFSELLIPYNVFKKAGFNVQFVSENgsykfdDHSIEESKlGdfeRKVFNDKNDDfwtnlnnmkkasDIVGKDYQLLFVAGGHAAMFDLPKATNLQAV 126 5579**************************955554433134444444444444666666667777******************************* PP HHHHHHTT-EEEEETTTHHHHHHTT...TTTTSEE--SGGGH CS DJ-1_PfpI 87 vkefaekgklvaaICagpqlLaaag...vlkgrrvTsypavk 125 ++e++++g+++ a+C+gp+lLa+ + ++g++v ++ v+ CUFF.46.1.p1 127 AREVFTNGGVLSAVCHGPVLLANVKnpqSVEGKTVVYHKHVT 168 **********************87512245555554444443 PP >> CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 48.4 0.0 1.4e-16 4.5e-15 12 111 .. 51 172 .. 47 198 .. 0.78 Alignments for each domain: == domain 1 score: 48.4 bits; conditional E-value: 1.4e-16 EHHHHHHHHHHHHHTTEEEEEEESS......TSEEEETT.S...EEEE-SEEGG............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHH CS DJ-1_PfpI 12 edvElivpvdvlkragikvdvvsvd......keevkgsr.G...lkvtvdasld............dvkaaeyDalvlpGGragperlrenekvvel 86 El +p++v+k+ag++v+ vs + + +++s+ G kv+ d+ d d+ ++y +l + GG+a +l + + ++++ CUFF.47.1.p1 51 HFSELLIPYNVFKKAGFNVQFVSENgsykfdDHSIEESKlGdfeRKVFNDKNDDfwtnlnnmkkasDIVGKDYQLLFVAGGHAAMFDLPKATNLQAV 147 5579**************************955554433134444444444444666666667777******************************* PP HHHHHHTT-EEEEETTTHHHHHHTT CS DJ-1_PfpI 87 vkefaekgklvaaICagpqlLaaag 111 ++e++++g+++ a+C+gp+lLa+ + CUFF.47.1.p1 148 AREVFTNGGVLSAVCHGPVLLANVK 172 *********************9865 PP >> CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 31.6 0.0 2.1e-11 6.7e-10 52 161 .. 75 215 .. 15 219 .. 0.78 Alignments for each domain: == domain 1 score: 31.6 bits; conditional E-value: 2.1e-11 EEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHH......HHTTTTTTSEE--SGGGH.HHH............. CS DJ-1_PfpI 52 aslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlL......aaagvlkgrrvTsypavk.dkl............. 128 + +d++ ++y + GG+ ++ + + + + + ++ g+++aa+C+gp++L +++kg++vT++ + +++ CUFF.42.1.p2 75 KNASDINFSDYSIFFAAGGHGTLFDFPSATNLHKGAAKIYSMGGVIAAVCHGPVILpcikdsTGFSIVKGKTVTAFNEIAeQQMnlmptfekyhfkt 171 445699***************9999999999999999****************99955332223469***********995556999*9*9999999 PP .....HHTTSEE-SS......SEEEETTEEEESSGGGHHHHHHH CS DJ-1_PfpI 129 .....ekagakyvdk......rvvvdgnlvTsrgpgaaiefale 161 ++ag+++vd v +dg+lvT ++p +a a++ CUFF.42.1.p2 172 lnklfQEAGSNFVDPqepfddFVKTDGKLVTGANPASAASTAKA 215 9999999999999999***977889*********9998776665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (165 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 228.11 // Query: DLH [M=217] Accession: PF01738.17 Description: Dienelactone hydrolase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-11 35.4 0.0 4.8e-11 35.2 0.0 1.1 1 CUFF.18.1.p1 type:5prime_partial gc:universal CUFF.18.1:1-77 Domain annotation for each sequence (and alignments): >> CUFF.18.1.p1 type:5prime_partial gc:universal CUFF.18.1:1-771(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 35.2 0.0 5e-13 4.8e-11 3 215 .. 41 254 .. 39 256 .. 0.72 Alignments for each domain: == domain 1 score: 35.2 bits; conditional E-value: 5e-13 DLH 3 aylatpknakkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqa........ldpndeaeaaraldelvskvaeekvlddlkaavaylks 91 +y ++ ++ k v + + ++fG+ ++ik+ +++la+ + +Pd++ ++ + + e+++a ++ ++k ++ +l ++ ++ CUFF.18.1.p1 41 TYFTGKRSS-KVVLIGFMDVFGLSKQIKEGADQLANHELAIYLPDFLNGETasiemidpK----TIEQKEARSKFMEKISSPLHWPKLTKVIEDIER 132 555566666.4455559**********************************898863332....333344444555555555566677777888888 PP DLH 92 vpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHa 188 ++ k+g+ GfC+G+++ + + ++ ++ + ++ s+ ++ +a+++ +p+ +l + + + d+ +k e+ + + ++ + H+ CUFF.18.1.p1 133 IH-GQDVKIGAYGFCWGAKVLITYPNKE-RFLRIGCAHP-SLLDPV-DAKHVHCPVCFLCSKDEDPEEVDAWKKSFENS-PYFSESYFETFGKMHHG 224 88.44589****************9999.5667777899.555555.578999***99998766665555544433333.46677778888888888 PP DLH 189 Fandsre...syneeaaedawervlelfkq 215 ++++++ +n + +++ +l++fk+ CUFF.18.1.p1 225 WMAARANlsdPENRKYFDLGYQIFLKFFKE 254 888888766677777777778888888776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (217 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1743.70 // Query: DsrD [M=64] Accession: PF08679.10 Description: Dissimilatory sulfite reductase D (DsrD) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.0008 12.3 0.0 0.0023 10.9 0.0 1.8 2 CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+ Domain annotation for each sequence (and alignments): >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -4.1 0.0 1 95 21 33 .. 102 114 .. 97 116 .. 0.82 2 ! 10.9 0.0 2.4e-05 0.0023 2 58 .. 132 188 .. 131 192 .. 0.80 Alignments for each domain: == domain 1 score: -4.1 bits; conditional E-value: 1 HHHHHH-TTS-HH CS DsrD 21 kDlekalPdakpr 33 kDl k++ d ++r CUFF.17.1.p1 102 KDLIKIFGDLSSR 114 7999999888877 PP == domain 2 score: 10.9 bits; conditional E-value: 2.4e-05 HHHHHHHHSSCCCSS-EEHH..HHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEETTEEE CS DsrD 2 kkaiveflekkkkKskfYfk..DlekalPdakpreiKkvvneLVnegkLeywSsGSTtm 58 +k+i + +e + k+ Y+ +++ +P +++ e+ +++n+ V+ gk+ y G +tm CUFF.17.1.p1 132 RKHIFDAVEDSVKRLGTYIDvlQIHRYDPHVSAEEVMRALNDVVESGKVRYI--GASTM 188 578899999999877788762245567***********************95..66666 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (64 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1039.11 // Query: DUF1129 [M=206] Accession: PF06570.10 Description: Protein of unknown function (DUF1129) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.0012 10.9 1.9 0.0033 9.5 0.7 2.2 2 CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280( Domain annotation for each sequence (and alignments): >> CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 9.5 0.7 3.4e-05 0.0033 88 189 .. 128 229 .. 124 236 .. 0.73 2 ? -1.5 0.0 0.083 7.9 119 133 .. 451 465 .. 423 478 .. 0.59 Alignments for each domain: == domain 1 score: 9.5 bits; conditional E-value: 3.4e-05 DUF1129 88 llalfallfgilalfskkkqtasiGlitl.llvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvl 183 +la++++ ++ lfs ++++ Gli+ l+++l+ G+++ ++ +lt + +k++ + + +l+++++l ++ lf+ + + N ++++ CUFF.45.1.p2 128 MLAFISFAWSMTVLFSG-FMSSYGGLIATrLILGLLEGCLFPALNLYLTTHYTRKEQCQRLSYLFASAGLAGAFGGLFAYALEQVHAGNKEGWQWIY 223 67778888889999998.777787988543899****************997788877777777777777777666665544444555555555555 PP DUF1129 184 iiigvi 189 i+ g + CUFF.45.1.p2 224 IVEGLV 229 555555 PP == domain 2 score: -1.5 bits; conditional E-value: 0.083 DUF1129 119 valvgGlamvlvyrl 133 + +vgGla+v++ CUFF.45.1.p2 451 CVIVGGLAYVVMFFS 465 345555555554332 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (206 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1588.03 // Query: DUF1989 [M=167] Accession: PF09347.9 Description: Domain of unknown function (DUF1989) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-57 186.4 0.0 2e-57 186.1 0.0 1.1 1 CUFF.34.1.p1 type:complete gc:universal CUFF.34.1:2072-1164( Domain annotation for each sequence (and alignments): >> CUFF.34.1.p1 type:complete gc:universal CUFF.34.1:2072-1164(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 186.1 0.0 2.1e-59 2e-57 2 167 .] 58 231 .. 57 231 .. 0.98 Alignments for each domain: == domain 1 score: 186.1 bits; conditional E-value: 2.1e-59 DUF1989 2 tiparsgravevkaGqvlriidleGnqvvdllafnaddprerlsaadTrklqesahlttgdrlysnl..grplltiveDtv.........gvHDtlg 87 ++++r+g av++++ +++ i+ +eG+qv+dl+++n ++prer++aa+Tr+++ sah++t+drl+s+l rpl+ti+ D++ +vHDtlg CUFF.34.1.p1 58 VCQPRTGLAVKIPQKSIFSIVVPEGPQVCDLNIWNFHNPRERFWAARTRQIH-SAHVSTYDRLWSTLpyLRPLVTIIGDSLqarhdewggRVHDTLG 153 6899************************************************.************************************99****** PP DUF1989 88 gacdpevnellygegkeyhrnCrdnllralakyglterdvpdvlNlFmnvgvdedgrlfmeespskpGdyvelraemDll 167 ++cdp++ +l + gk+++ +C++nl+ra+ yglte+dv+dvlN+F+++g++e +++fme++p++ dy++++ae+Dll CUFF.34.1.p1 154 TRCDPYIDKLIS--GKDNDLHCHSNLTRAIMPYGLTEFDVHDVLNVFQVTGLNEYDQYFMETCPATSKDYFQCFAEQDLL 231 *********999..678*************99**********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (167 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1892.38 // Query: DUF2157 [M=147] Accession: PF09925.8 Description: Predicted membrane protein (DUF2157) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- ------ inclusion threshold ------ 0.023 7.1 8.8 0.0029 10.0 3.5 2.1 2 CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+ Domain annotation for each sequence (and alignments): >> CUFF.14.1.p1 type:complete gc:universal CUFF.14.1:321-1256(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.5 0.2 0.055 5.2 109 109 .. 75 75 .. 10 128 .. 0.54 2 ? 10.0 3.5 3.1e-05 0.0029 34 120 .. 156 243 .. 142 265 .. 0.89 Alignments for each domain: == domain 1 score: -0.5 bits; conditional E-value: 0.055 DUF2157 109 a 109 + CUFF.14.1.p1 75 C 75 1 PP == domain 2 score: 10.0 bits; conditional E-value: 3.1e-05 DUF2157 34 fleallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg.avlwrdrrvpprlgeallllaalllgaaialvgqifqls 120 +++ll+l ++++ +G + A+ + +r + f l+++++++ l a++++ ++ + g + + + a+ll+ + ++ qi + + CUFF.14.1.p1 156 VVRVLLLLLSICFFVGAAFYTAYTTNVTHRGIGFSLIFSPFAALTRLYlARFLNSPQYFIPYGTLCANVFATLLLSIMYMIPQITHCT 243 489999999***********************************99999***99999999999999999999********99997766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (147 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 622.92 // Query: DUF2868 [M=328] Accession: PF11067.7 Description: Protein of unknown function (DUF2868) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00065 11.7 0.3 0.001 11.1 0.3 1.2 1 CUFF.9.1.p1 type:complete gc:universal CUFF.9.1:173-640(+) Domain annotation for each sequence (and alignments): >> CUFF.9.1.p1 type:complete gc:universal CUFF.9.1:173-640(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.1 0.3 1.1e-05 0.001 47 74 .. 97 123 .. 92 126 .. 0.94 Alignments for each domain: == domain 1 score: 11.1 bits; conditional E-value: 1.1e-05 DUF2868 47 fllGalltlllllatrdlaFgWetTLnl 74 +llGa++ l + ++r+l++gW+ TL l CUFF.9.1.p1 97 LLLGAIFPLFAESLFRRLNYGWGCTL-L 123 689***********************.6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (328 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1955.50 // Query: DUF2976 [M=88] Accession: PF11190.7 Description: Protein of unknown function (DUF2976) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00011 14.6 4.9 0.00058 12.3 0.1 3.5 3 CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) Domain annotation for each sequence (and alignments): >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.3 0.1 6.1e-06 0.00058 28 76 .. 120 168 .. 107 177 .. 0.90 2 ! 2.3 0.1 0.0082 0.78 39 77 .. 307 348 .. 282 351 .. 0.68 3 ? -1.6 0.1 0.13 13 58 75 .. 404 421 .. 371 425 .. 0.73 Alignments for each domain: == domain 1 score: 12.3 bits; conditional E-value: 6.1e-06 DUF2976 28 villgLvlaavaflaVakaalkkfnevregkaewgkfgltlvvGvvllv 76 ++ L +a++ + V+k +l kf+++ + +++ + l+ v+G++++ CUFF.25.1.p1 120 SMISTLEIATAIISSVCKPILGKFSDITSRPMTYTLVLLFYVIGFIVVA 168 678889999*************************************996 PP == domain 2 score: 2.3 bits; conditional E-value: 0.0082 DUF2976 39 aflaVaka.alkkfnevregkaewg..kfgltlvvGvvllvv 77 +l V ++ +l f+ + k+ w ++++++vvG v+l++ CUFF.25.1.p1 307 ILLGVGWSiLLLPFSLTSYAKNGWKnpSMIAMMVVGGVILIA 348 445555441345677777778888733588888999988876 PP == domain 3 score: -1.6 bits; conditional E-value: 0.13 DUF2976 58 kaewgkfgltlvvGvvll 75 +w+ f t+ ++ ++ CUFF.25.1.p1 404 YRDWTYFNNTMTIALCVF 421 567888888888888775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (88 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 897.62 // Query: DUF2997 [M=47] Accession: PF11211.7 Description: Protein of unknown function (DUF2997) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00049 12.5 0.0 0.0011 11.5 0.0 1.5 1 CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+ Domain annotation for each sequence (and alignments): >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.5 0.0 1.1e-05 0.0011 10 25 .. 83 98 .. 83 103 .. 0.91 Alignments for each domain: == domain 1 score: 11.5 bits; conditional E-value: 1.1e-05 DUF2997 10 rVeeeveGikGksCle 25 +V+ +ve+i+GksCl+ CUFF.54.1.p1 83 KVKLRVEDIQGKSCLT 98 79************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (47 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 976.72 // Query: DUF3288 [M=89] Accession: PF11691.7 Description: Protein of unknown function (DUF3288) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-05 15.3 0.0 0.00013 14.6 0.0 1.2 1 CUFF.32.1.p3 type:complete gc:universal CUFF.32.1:911-549(-) Domain annotation for each sequence (and alignments): >> CUFF.32.1.p3 type:complete gc:universal CUFF.32.1:911-549(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 14.6 0.0 1.4e-06 0.00013 17 62 .. 72 117 .. 68 119 .. 0.90 Alignments for each domain: == domain 1 score: 14.6 bits; conditional E-value: 1.4e-06 DUF3288 17 LlaeepedenlaelArLliRYegFpGardiqkdldkvlkkWqltee 62 L++++++ +l e++r l+R +F G +++++ l+ l +W+++++ CUFF.32.1.p3 72 LIEGSANLLSLEEISRTLLRILDFVGNKNMRTYLEVPLCRWHISQA 117 55667777899********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (89 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.07 # Mc/sec: 37.74 // Query: DUF4208 [M=96] Accession: PF13907.5 Description: Domain of unknown function (DUF4208) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00081 12.5 0.4 0.0012 11.9 0.4 1.2 1 CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115( 0.00081 12.5 0.4 0.0012 11.9 0.4 1.2 1 CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) Domain annotation for each sequence (and alignments): >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.9 0.4 2.6e-05 0.0012 38 82 .. 22 67 .. 11 78 .. 0.86 Alignments for each domain: == domain 1 score: 11.9 bits; conditional E-value: 2.6e-05 DUF4208 38 erakilkkeLlkiGdfIdellkekkeekkeklkkhlWefvs.kfwp 82 ++ k++L+++G+ ++e++ ++ +++++++k lW v + wp CUFF.48.1.p3 22 TLHNVAKDTLIQLGHTVQETVVDEGYDENTEVEKILWANVIiYQWP 67 5567899**************99877***********999855576 PP >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.9 0.4 2.6e-05 0.0012 38 82 .. 22 67 .. 11 78 .. 0.86 Alignments for each domain: == domain 1 score: 11.9 bits; conditional E-value: 2.6e-05 DUF4208 38 erakilkkeLlkiGdfIdellkekkeekkeklkkhlWefvs.kfwp 82 ++ k++L+++G+ ++e++ ++ +++++++k lW v + wp CUFF.49.1.p2 22 TLHNVAKDTLIQLGHTVQETVVDEGYDENTEVEKILWANVIiYQWP 67 5567899**************99877***********999855576 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (96 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1068.42 // Query: DUF705 [M=304] Accession: PF05152.11 Description: Protein of unknown function (DUF705) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00044 12.4 0.0 0.00076 11.6 0.0 1.4 1 CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659( Domain annotation for each sequence (and alignments): >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.6 0.0 8e-06 0.00076 225 270 .. 70 116 .. 58 152 .. 0.73 Alignments for each domain: == domain 1 score: 11.6 bits; conditional E-value: 8e-06 DUF705 225 vlditnskrl..PksvkvvlkyLsdknleffksitLvDDladnninYD 270 + + n+++l Pks ++v+ sd n+ f+s L DD ++n i+Y CUFF.52.1.p2 70 YTATVNHEDLnePKSHEIVMLLASDGNVGSFESN-LLDDCFKNRIEYA 116 555566665333********************95.78*******9874 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 2294.67 // Query: DUF999 [M=143] Accession: PF06198.10 Description: Protein of unknown function (DUF999) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-94 305.8 5.8 2.4e-94 305.5 5.8 1.0 1 CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) 9.5e-91 293.9 4.2 1.5e-90 293.2 4.2 1.3 1 CUFF.3.1.p1 type:complete gc:universal CUFF.3.1:207-1073(+) Domain annotation for each sequence (and alignments): >> CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 305.5 5.8 5e-96 2.4e-94 1 143 [] 21 163 .. 21 163 .. 0.99 Alignments for each domain: == domain 1 score: 305.5 bits; conditional E-value: 5e-96 DUF999 1 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftniikpqkdklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiiv 98 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftn+ikpqkdk+niktnkikeflndlftefskfhnsyypdgristrs++rw+lliiwsiiiv CUFF.5.1.p1 21 MVEDVCNVDLEQGLDLCKPEKVNKQSQRSRQSRQSLFTNTIKPQKDKMNIKTNKIKEFLNDLFTEFSKFHNSYYPDGRISTRSNFRWPLLIIWSIIIV 118 9************************************************************************************************* PP DUF999 99 laidkkfevkeflsiwinenrfyseiwgpiaiyvcllvllllali 143 +a+dkkfev++flsiwinenrfyseiw+piaiyvcllvl+ll+li CUFF.5.1.p1 119 FAVDKKFEVQKFLSIWINENRFYSEIWVPIAIYVCLLVLMLLSLI 163 ******************************************996 PP >> CUFF.3.1.p1 type:complete gc:universal CUFF.3.1:207-1073(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 293.2 4.2 3.2e-92 1.5e-90 1 143 [] 21 163 .. 21 163 .. 0.99 Alignments for each domain: == domain 1 score: 293.2 bits; conditional E-value: 3.2e-92 DUF999 1 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftniikpqkdklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiiv 98 mvedvcnvdleqgldlckpekvnkqsqrsrqsrqslftn+ikpqkdk+niktnkikeflndlftefskfhnsyyp+grist++k+rwvlliiwsii++ CUFF.3.1.p1 21 MVEDVCNVDLEQGLDLCKPEKVNKQSQRSRQSRQSLFTNTIKPQKDKMNIKTNKIKEFLNDLFTEFSKFHNSYYPNGRISTQDKSRWVLLIIWSIITI 118 9************************************************************************************************* PP DUF999 99 laidkkfevkeflsiwinenrfyseiwgpiaiyvcllvllllali 143 l+idkkf++ke++++wi+en+++seiwgpi+iyv+l++lll+a++ CUFF.3.1.p1 119 LTIDKKFKIKESYLEWIGENQSHSEIWGPIVIYVGLFILLLSAFN 163 ******************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (143 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1142.73 // Query: FAD_syn [M=158] Accession: PF06574.11 Description: FAD synthetase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00019 14.0 0.0 0.00065 12.2 0.0 1.8 2 CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+ Domain annotation for each sequence (and alignments): >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.2 0.0 6.8e-06 0.00065 18 82 .. 33 92 .. 22 109 .. 0.84 2 ? -1.4 0.0 0.1 9.9 112 145 .. 141 174 .. 125 188 .. 0.77 Alignments for each domain: == domain 1 score: 12.2 bits; conditional E-value: 6.8e-06 FAD_syn 18 vHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlv 82 +H GH +l+++a+++a+ ++vv +F + P+++ ++++ t+++ ++l++lgvd v+ CUFF.50.1.p2 33 LHEGHFSLVREAKRHAE----KVVVSIFVN-PMQFNNPQDLLLYPRTMDQDCSQLQNLGVDLVYA 92 7*******999998884....577888865.99999988888888899999**********9986 PP == domain 2 score: -1.4 bits; conditional E-value: 0.1 FAD_syn 112 vvGfdfrfGkkregdvellkelgaklgfevevvp 145 v + +fG+k +v+ +k++ + l+f +e+++ CUFF.50.1.p2 141 VNPDVACFGEKDFQQVAIIKKMVRDLNFFIEIIQ 174 5555568999999999999999999997776654 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) Passed Vit filter: 5 (0.0526316); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1249.76 // Query: Fe-ADH [M=364] Accession: PF00465.18 Description: Iron-containing alcohol dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-127 415.8 1.9 7.6e-127 415.6 1.9 1.0 1 CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267( Domain annotation for each sequence (and alignments): >> CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.6 1.9 8e-129 7.6e-127 1 364 [] 52 414 .. 52 414 .. 0.96 Alignments for each domain: == domain 1 score: 415.6 bits; conditional E-value: 8e-129 -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHH CS Fe-ADH 1 PtrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGsviDtA 97 P+ +fgkg+l+e ++ +k g+k+ livtd+g++ k gl+dkv++ lee+ i+v+++dgv+pnpt+ +v+++++++++e++d +++GGGs++D+A CUFF.50.1.p1 52 PSFNLFGKGCLAEAAKQIKMSGFKNTLIVTDPGII-KVGLYDKVKALLEEQSITVHLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCA 147 56678****************************99.************************************************************* PP HHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHH CS Fe-ADH 98 Kaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahal 193 K+iall++n++ ++dy+g++k+ k++lpliai TtaGt+se+t++a+it e ++ k++i d++++P l++ Dpe +++lP+++taatg+Dal+ha+ CUFF.50.1.p1 148 KGIALLATNGGkIADYEGVDKS-SKPQLPLIAINTTAGTASEMTRFAIITEETRHIKMAIIDKHTMPILSVNDPETMYGLPPSLTAATGMDALTHAV 243 *********956*****99987.8999***********************99999****************************************** PP HHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH........ CS Fe-ADH 194 EayvskkanplsdalaleairliaknleravadgedleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaa. 289 Eayvs+ anp++da+a ++i+l+ k+l+rav++g+d ear +m++a +l+g+af+na+lg vHa+ah+lg+++giphg++na+ll++v +fn ++ CUFF.50.1.p1 244 EAYVSTAANPITDACAVKCIELVNKYLKRAVDNGKDEEARDNMAYAEFLGGMAFNNASLGYVHAMAHQLGGFYGIPHGVCNAVLLAHVQKFNSRDPr 340 ***********************************************************************99********************5554 PP ....HHHHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-TSGGGGSSS---HHHH CS Fe-ADH 290 p.erlaqlaralggesdeeaaeeliealrellkelglptsLselgvdeedldklaeaalkdrslannpreltaedv 364 + +rl ++a lg +e ae++++++ +l+ e+++ +L +lgv+e+d+d l+++a+kd + a+np ++t+++v CUFF.50.1.p1 341 AnARLGDIAFHLGC--EEHTAEAALDRISQLVLEVKIRPHLVDLGVKEKDFDVLVDHAMKDACGATNPIQPTHDEV 414 44888888888864..699*****************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (364 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1172.93 // Query: Fe-ADH_2 [M=250] Accession: PF13685.5 Description: Iron-containing alcohol dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-23 74.1 4.0 2.3e-20 65.9 2.6 2.4 2 CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267( Domain annotation for each sequence (and alignments): >> CUFF.50.1.p1 type:complete gc:universal CUFF.50.1:3999-5267(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 65.9 2.6 2.4e-22 2.3e-20 2 245 .. 57 320 .. 56 323 .. 0.89 2 ? -3.6 0.0 0.4 38 27 60 .. 355 388 .. 350 399 .. 0.70 Alignments for each domain: == domain 1 score: 65.9 bits; conditional E-value: 2.4e-22 Fe-ADH_2 2 igegaleklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvs.. 95 +g+g l + ++ +k ++k+ l+v+d ++ k+ + +kv+ l+e+ i+v++++ v++++++ +v++ +e ++++++d +v++GgG+++D ak ++ CUFF.50.1.p1 57 FGKGCLAEAAKQIKMSGFKNTLIVTDPGIIKVgLYDKVKALLEEQSITVHLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCAKGIAll 153 57899999********************9999899*********************************************************98622 PP Fe-ADH_2 96 ................aklnvpyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwkl 173 +k ++p++++ T+a + +a ++++ + k + k ++P+ + D + + P +l+a+ D+l + + + + CUFF.50.1.p1 154 atnggkiadyegvdksSKPQLPLIAINTTAGTASEMTRFAIITEEtrHIKMAIiDKHTMPILSVNDPETMYGLPPSLTAATGMDALTHAVEAYVSTA 250 222222222222222256689*********9999999999999887788888888999*************************************** PP Fe-ADH_2 174 anevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalH 245 an +++ a + ++ v + ++++v+++k++ea +++ a l+g+++ ++ G H ++H l + H CUFF.50.1.p1 251 ANPITDACAVKCIELVNKYLKRAVDNGKDEEARDNMAYAEFLGGMAFNNASLGYVHAMAHQLGGFY--GIPH 320 ************************************************************997666..5555 PP == domain 2 score: -3.6 bits; conditional E-value: 0.4 Fe-ADH_2 27 dentkkaagekveeslkeagikvevveeveeead 60 +e+t +aa +++++ + e +i++++v+ +e+d CUFF.50.1.p1 355 EEHTAEAALDRISQLVLEVKIRPHLVDLGVKEKD 388 5778888888888888888888887765555554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (250 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 405.06 // Query: Fig1 [M=188] Accession: PF12351.7 Description: Ca2+ regulator and membrane fusion protein Fig1 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00077 12.0 0.1 0.0012 11.4 0.1 1.2 1 CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659( Domain annotation for each sequence (and alignments): >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.4 0.1 1.2e-05 0.0012 73 147 .. 7 79 .. 2 95 .. 0.75 Alignments for each domain: == domain 1 score: 11.4 bits; conditional E-value: 1.2e-05 Fig1 73 sdnvvhpyllmvaiiLtlllfllllyfplgseipllPfkskavskvalvlsflllllwlvgalwqhvassaastl 147 ++++ +l+m a+++++ f + lyf +ei ++ fk a++ ++v+s ++l+ + ++l++ ++ + l CUFF.52.1.p2 7 KNTLTKRKLIMLALAIVFTFFAFGLYFIPHDEISVFDFKLPALQYETTVTSLDNFLIGGSTTLYTATVN--HEDL 79 5566677899999999999999999998899**********7777777777777888777777765543..3555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 2113.09 // Query: Flavodoxin_2 [M=198] Accession: PF02525.16 Description: Flavodoxin-like fold Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-36 117.9 0.1 3.1e-36 117.5 0.1 1.1 1 CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115( 2.4e-36 117.9 0.1 3.1e-36 117.5 0.1 1.1 1 CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) Domain annotation for each sequence (and alignments): >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 117.5 0.1 6.5e-38 3.1e-36 1 192 [. 1 181 [. 1 189 [. 0.88 Alignments for each domain: == domain 1 score: 117.5 bits; conditional E-value: 6.5e-38 -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT...TEEEEEEHHCCT.....CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--H CS Flavodoxin_2 1 mkiLiinahprpeksfssalaqafvealekagp...hevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPa 94 mkiL+in+ ++++ ++++++++++ + ++++ h+v+++ ++++ +d+ +e ek+l+a +i++q P ww+g+P+ CUFF.48.1.p3 1 MKILLINGAQEFA-HSQGKFNKTLHNVAKDTLIqlgHTVQETVVDEG--------------------YDENTEV-EKILWANVIIYQWPGWWMGTPW 75 9***********6.666999999999999988777899999999995....................8899***.********************** PP HHHHHHHHHS-TTTSC.E.......ETTCS.SCCCCTTTTSEEEEEEEESS-GGGSSTTSS..S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT. CS Flavodoxin_2 95 ilKgwiDrvltagfaf.y.......teegg.egrgggLkgkkalvivttGgpeesyqergl..egaamdellpplrgilgfiGikdvepvlvegva. 179 +lK ++D+v+tag+ + y +++++ +g+gg+L+ ++++++t+++p+++++e g +g+++d +l ++++ +f+G+k+++++ v++v CUFF.48.1.p3 76 KLKRYMDEVFTAGYGQlYandgrssKNPTQnYGKGGLLHEHRYMISCTWNAPAAAFEEVGNffDGRGVDGTLLTFHKANQFLGMKPLPTFMVNDVIk 172 **************999999****97777778878888899******************999999****************************9644 PP CCCHHHHHHHHHH CS Flavodoxin_2 180 gaedeealaeale 192 +++ ++ a+ CUFF.48.1.p3 173 NPK----VDIAVC 181 443....444444 PP >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 117.5 0.1 6.5e-38 3.1e-36 1 192 [. 1 181 [. 1 189 [. 0.88 Alignments for each domain: == domain 1 score: 117.5 bits; conditional E-value: 6.5e-38 -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT...TEEEEEEHHCCT.....CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--H CS Flavodoxin_2 1 mkiLiinahprpeksfssalaqafvealekagp...hevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPa 94 mkiL+in+ ++++ ++++++++++ + ++++ h+v+++ ++++ +d+ +e ek+l+a +i++q P ww+g+P+ CUFF.49.1.p2 1 MKILLINGAQEFA-HSQGKFNKTLHNVAKDTLIqlgHTVQETVVDEG--------------------YDENTEV-EKILWANVIIYQWPGWWMGTPW 75 9***********6.666999999999999988777899999999995....................8899***.********************** PP HHHHHHHHHS-TTTSC.E.......ETTCS.SCCCCTTTTSEEEEEEEESS-GGGSSTTSS..S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT. CS Flavodoxin_2 95 ilKgwiDrvltagfaf.y.......teegg.egrgggLkgkkalvivttGgpeesyqergl..egaamdellpplrgilgfiGikdvepvlvegva. 179 +lK ++D+v+tag+ + y +++++ +g+gg+L+ ++++++t+++p+++++e g +g+++d +l ++++ +f+G+k+++++ v++v CUFF.49.1.p2 76 KLKRYMDEVFTAGYGQlYandgrssKNPTQnYGKGGLLHEHRYMISCTWNAPAAAFEEVGNffDGRGVDGTLLTFHKANQFLGMKPLPTFMVNDVIk 172 **************999999****97777778878888899******************999999****************************9644 PP CCCHHHHHHHHHH CS Flavodoxin_2 180 gaedeealaeale 192 +++ ++ a+ CUFF.49.1.p2 173 NPK----VDIAVC 181 443....444444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1470.45 // Query: FMN_red [M=155] Accession: PF03358.14 Description: NADPH-dependent FMN reductase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00021 13.6 0.0 0.0029 10.0 0.0 2.2 1 CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115( 0.00021 13.6 0.0 0.0029 10.0 0.0 2.2 1 CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) Domain annotation for each sequence (and alignments): >> CUFF.48.1.p3 type:complete gc:universal CUFF.48.1:4705-4115(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 10.0 0.0 6.1e-05 0.0029 1 98 [. 1 84 [. 1 96 [. 0.70 Alignments for each domain: == domain 1 score: 10.0 bits; conditional E-value: 6.1e-05 -EEEEEES--S....TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHH CS FMN_red 1 mkilvisGSlr....kgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnal 95 mkil+i+G +g+++++l ++a+++l i+l+ + ++d++ d+ e +eki +a ++i P ++ + + lK+ + CUFF.48.1.p3 1 MKILLINGAQEfahsQGKFNKTLHNVAKDTL---------IQLGHTVQE-TVVDEGY-------DENTE-VEKILWANVIIYQWPGWWMGTPWKLKRYM 81 8999999998866666667777777766666.........666665333.1444333.......34444.68999999999999999999999999999 PP HCH CS FMN_red 96 Drl 98 D + CUFF.48.1.p3 82 DEV 84 976 PP >> CUFF.49.1.p2 type:complete gc:universal CUFF.49.1:214-804(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 10.0 0.0 6.1e-05 0.0029 1 98 [. 1 84 [. 1 96 [. 0.70 Alignments for each domain: == domain 1 score: 10.0 bits; conditional E-value: 6.1e-05 -EEEEEES--S....TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHH CS FMN_red 1 mkilvisGSlr....kgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnal 95 mkil+i+G +g+++++l ++a+++l i+l+ + ++d++ d+ e +eki +a ++i P ++ + + lK+ + CUFF.49.1.p2 1 MKILLINGAQEfahsQGKFNKTLHNVAKDTL---------IQLGHTVQE-TVVDEGY-------DENTE-VEKILWANVIIYQWPGWWMGTPWKLKRYM 81 8999999998866666667777777766666.........666665333.1444333.......34444.68999999999999999999999999999 PP HCH CS FMN_red 96 Drl 98 D + CUFF.49.1.p2 82 DEV 84 976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (155 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 346.02 // Query: FPP [M=866] Accession: PF05911.10 Description: Filament-like plant protein, long coiled-coil Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00068 10.5 0.1 0.00099 9.9 0.1 1.2 1 CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907( 0.00085 10.2 0.1 0.0013 9.6 0.1 1.2 1 CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658( Domain annotation for each sequence (and alignments): >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 9.9 0.1 2.1e-05 0.00099 518 597 .. 171 250 .. 146 265 .. 0.76 Alignments for each domain: == domain 1 score: 9.9 bits; conditional E-value: 2.1e-05 FPP 518 lkedslevekeeevseeeksseeeskqkiqqelekaiskiielveglskealklqdsssksselsevleeFsavvndlls 597 + +d+l v +++ + +++++ + +++++l + i ii+ ++g+sk+a+ + +s+s+++ ++l eF+++ ++ll+ CUFF.60.1.p2 171 KPKDTLSVMITDTKQPKSTKKLVQGVFELKERLPTVIDSIIDAIDGISKSAVLALTSESDKNSSAKKLGEFIVLNQKLLE 250 333333333333333334444455778999************************9*******************999985 PP >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 9.6 0.1 2.7e-05 0.0013 518 597 .. 222 301 .. 197 316 .. 0.76 Alignments for each domain: == domain 1 score: 9.6 bits; conditional E-value: 2.7e-05 FPP 518 lkedslevekeeevseeeksseeeskqkiqqelekaiskiielveglskealklqdsssksselsevleeFsavvndlls 597 + +d+l v +++ + +++++ + +++++l + i ii+ ++g+sk+a+ + +s+s+++ ++l eF+++ ++ll+ CUFF.60.2.p2 222 KPKDTLSVMITDTKQPKSTKKLVQGVFELKERLPTVIDSIIDAIDGISKSAVLALTSESDKNSSAKKLGEFIVLNQKLLE 301 333333333333333334444455778999************************9*******************999985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (866 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 1017.17 // Query: FR47 [M=86] Accession: PF08445.9 Description: FR47-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-06 18.8 0.0 9e-06 18.3 0.0 1.2 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 6.7e-06 18.7 0.0 9.8e-06 18.2 0.0 1.2 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) Domain annotation for each sequence (and alignments): >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.3 0.0 1.9e-07 9e-06 18 81 .. 70 133 .. 53 137 .. 0.85 Alignments for each domain: == domain 1 score: 18.3 bits; conditional E-value: 1.9e-07 E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS FR47 18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 +++ +g + v+p+ r+ G+g++l + + ++ + v s + ++ ly ++Gf+k CUFF.34.1.p2 70 QQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSKTFVLSSQEYAQPLYRSVGFKKCS 133 455578********************999999899999999999999*************9975 PP >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.2 0.0 2.1e-07 9.8e-06 18 81 .. 70 133 .. 53 137 .. 0.85 Alignments for each domain: == domain 1 score: 18.2 bits; conditional E-value: 2.1e-07 E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS FR47 18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 +++ +g + v+p+ r+ G+g++l + + ++ + v s + ++ ly ++Gf+k CUFF.35.1.p1 70 QQQTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSSKTFVLSSQEYAQPLYRSVGFKKCS 133 455578********************999999899999999999999*************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (86 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 140.27 // Query: Fungal_trans [M=267] Accession: PF04082.17 Description: Fungal specific transcription factor domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-42 137.9 0.2 2.2e-42 137.5 0.2 1.1 1 CUFF.40.1.p2 type:complete gc:universal CUFF.40.1:3736-2759( 1.6e-42 137.9 0.2 2.2e-42 137.5 0.2 1.1 1 CUFF.41.1.p1 type:complete gc:universal CUFF.41.1:303-1280(+ 4.1e-28 90.7 6.2 4.5e-27 87.3 5.9 2.2 2 CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772( 2.5e-12 38.9 4.7 1e-11 36.9 4.7 1.9 1 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( Domain annotation for each sequence (and alignments): >> CUFF.40.1.p2 type:complete gc:universal CUFF.40.1:3736-2759(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 137.5 0.2 9.3e-44 2.2e-42 1 200 [. 120 311 .. 120 324 .. 0.93 Alignments for each domain: == domain 1 score: 137.5 bits; conditional E-value: 9.3e-44 Fungal_trans 1 ldrffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsL 97 l++ff++ +pqf +++++ fl+++ + + ++ +y+s++ll+a++a+G+++s +++ ++ +i +++++i ++ s+++++q+L CUFF.40.1.p2 120 LKLFFKWQYPQFLFINREAFLVDY-YYRYHEGRYCSEHLLYAMCAIGSRMSVDPNIAALAKNFY----QI----AWNKII--EYGLGKSHITSIQCL 205 799*********************.*****************************9998444444....66....******..*************** PP Fungal_trans 98 lllelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlp....LPcddd 190 l+l ++++++++++l ++++g+a+r+ ++lg++ np +++ + +++++++a r R++w+ +++D++i+++lGrp++l++s++++p LP+ d CUFF.40.1.p2 206 LCLGYFNIGMGNTSLGWMLSGMAFRMGQDLGFQLNPRNWSVNDHPVVSPADAAVRSRIYWGSYVTDIFISFVLGRPTTLKKSDTSIPdsesLPDFDG 302 ****************************************999**********************************99********9999997776 PP Fungal_trans 191 dlwesddase 200 ++e +++ CUFF.40.1.p2 303 -VNEYRVNNA 311 .777766665 PP >> CUFF.41.1.p1 type:complete gc:universal CUFF.41.1:303-1280(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 137.5 0.2 9.3e-44 2.2e-42 1 200 [. 120 311 .. 120 324 .. 0.93 Alignments for each domain: == domain 1 score: 137.5 bits; conditional E-value: 9.3e-44 Fungal_trans 1 ldrffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsL 97 l++ff++ +pqf +++++ fl+++ + + ++ +y+s++ll+a++a+G+++s +++ ++ +i +++++i ++ s+++++q+L CUFF.41.1.p1 120 LKLFFKWQYPQFLFINREAFLVDY-YYRYHEGRYCSEHLLYAMCAIGSRMSVDPNIAALAKNFY----QI----AWNKII--EYGLGKSHITSIQCL 205 799*********************.*****************************9998444444....66....******..*************** PP Fungal_trans 98 lllelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlp....LPcddd 190 l+l ++++++++++l ++++g+a+r+ ++lg++ np +++ + +++++++a r R++w+ +++D++i+++lGrp++l++s++++p LP+ d CUFF.41.1.p1 206 LCLGYFNIGMGNTSLGWMLSGMAFRMGQDLGFQLNPRNWSVNDHPVVSPADAAVRSRIYWGSYVTDIFISFVLGRPTTLKKSDTSIPdsesLPDFDG 302 ****************************************999**********************************99********9999997776 PP Fungal_trans 191 dlwesddase 200 ++e +++ CUFF.41.1.p1 303 -VNEYRVNNA 311 .777766665 PP >> CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 87.3 5.9 1.9e-28 4.5e-27 3 234 .. 203 429 .. 201 459 .. 0.81 2 ? 1.2 0.0 0.035 0.82 1 23 [. 471 492 .. 471 504 .. 0.87 Alignments for each domain: == domain 1 score: 87.3 bits; conditional E-value: 1.9e-28 Fungal_trans 3 rffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsLll 99 ++f++++ ++p + +++f+++++ ++++ l+ +l+ ++ +++ + s++ ++s ++ ++ df+ +s + +q+L CUFF.38.1.p1 203 SYFQHVNWWWPTFVYNDFMYEFERLYAFGFHSNNAWLISFYSILALSSIRKRLGNSKTLAESLF------STAWVFVQKSDFFLTPS-IDKVQALIV 292 8999999999999999999999666666666677777766777777778888887766666643......34777666667777777.********* PP Fungal_trans 100 lelyektssdralherhhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlpLPcddddlwesd 196 + y +s+ +l+ ++g a+ +a++l Lhr++s +e+ aes++R++w++++lDk i+l++G p+ ++d +i+++LP++ +l + CUFF.38.1.p1 293 MTQYAAYLSSSSLCRTLCGQACLMAQQLNLHRKQSTDV------EPEK-AESWKRIFWMCYILDKNISLIFGTPSVFNDKDIDCNLPDSKYELLFGV 382 **********************************9988......7777.**************************99**********9998887777 PP Fungal_trans 197 daseetlvetk.........lsneeksrkiasfllaLkkilskiags 234 + + + n+ s+k ++++ a ki+ i+ + CUFF.38.1.p1 383 QSGGDLIFVPTvsltiiqseIRNRLYSVKSPTQMAAREKIIIPIHQK 429 77666666544667777777777777777777777766666666554 PP == domain 2 score: 1.2 bits; conditional E-value: 0.035 Fungal_trans 1 ldrffsnfhpqfpilhkpsflpk 23 ++++fs+++ ++ ilh+ps +++ CUFF.38.1.p1 471 MEVYFSYLNTLI-ILHRPSSSTE 492 679******998.****997665 PP >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 36.9 4.7 4.3e-13 1e-11 4 197 .. 151 329 .. 148 351 .. 0.75 Alignments for each domain: == domain 1 score: 36.9 bits; conditional E-value: 4.3e-13 Fungal_trans 4 ffsnfhpqfpilhkpsflpktssenssksayaspllllailalGalfsesetkesnssltsesqefiafplraeilihedfsspssslwilqsLlll 100 +f++fhp fp++h+ sf+++ + +l+++a+l++G + s + + s ++ + l + +++ w+ qs ll+ CUFF.45.1.p1 151 YFEWFHPVFPFIHQASFNSEN-----VAASFLRSLVVIACLCTGIESDFSMALLFWDSGFHVL---------QLYL--QGDPERVKKAWVFQSRLLF 231 *********************.....4444444444555555555555555555544444433.........3333..3566667779********* PP Fungal_trans 101 elyektssdralher.....hhgvavrlarslgLhrnpsyvgkkslwklweeeaesrrRlwwaaFylDktialklGrppllddsqinlpLPcddddl 192 ++ ++ + ++ ++ v+ +r+ g + +v+ ++ + ++ e+ rR ++ ++l+ ++al+++ pp l+ ++++pLP ++ l CUFF.45.1.p1 232 CTASLFEKT--ACFSgighvLLKDLVHESRTFGWTKLNWSVEGDTDISNLID-LECIRRSVFCLYILEWFLALIFNKPPSLSVLELQMPLPISSA-L 324 *99988775..55555445666666676777777666666676668888899.**************************99**************.9 PP Fungal_trans 193 wesdd 197 w+s + CUFF.45.1.p1 325 WSSKE 329 99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (267 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 324.65 // Query: GalKase_gal_bdg [M=49] Accession: PF10509.8 Description: Galactokinase galactose-binding signature Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00013 14.2 0.0 0.00024 13.3 0.0 1.4 1 CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658( Domain annotation for each sequence (and alignments): >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.3 0.0 2.6e-06 0.00024 12 44 .. 5 37 .. 2 41 .. 0.90 Alignments for each domain: == domain 1 score: 13.3 bits; conditional E-value: 2.6e-06 EEEEEEEEEEEE--S-TTTT-EEEEEEEEEEEE CS GalKase_gal_bdg 12 fvasAPGRvnLiGEHtDYngGfVlpmAieldiy 44 +++s+PG + L GEH g l++A+ l+ y CUFF.60.2.p2 5 LIVSSPGKTILFGEHAVVYGATALAAAVSLRSY 37 799************************998866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (49 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 880.20 // Query: GDC-P [M=430] Accession: PF02347.15 Description: Glycine cleavage system P-protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-215 707.3 0.0 1.6e-202 665.5 0.0 3.2 3 CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+ Domain annotation for each sequence (and alignments): >> CUFF.57.1.p1 type:complete gc:universal CUFF.57.1:189-3284(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 665.5 0.0 1.7e-204 1.6e-202 2 430 .] 66 504 .. 65 504 .. 0.99 2 ! 36.7 0.0 1.2e-13 1.2e-11 22 285 .. 529 810 .. 525 822 .. 0.77 3 ? 0.7 0.0 0.01 0.96 332 373 .. 840 881 .. 836 926 .. 0.78 Alignments for each domain: == domain 1 score: 665.5 bits; conditional E-value: 1.7e-204 HH-SS-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S-------............--HHHHHHHHHHHHTTB---EE--BTTB------HHHHHH CS GDC-P 2 rhigpsekdqkemLetlGlkslddliekavPkeiklkkelkleap............ksEeellaelekiasknkvvksfiGaGyydtilPaviqrn 86 rhigps++dq+++Le+lG+k++d+++++ +P+++++++++ ++ + +sE+e+++ +++a++nk++ksfiG+Gyy+++lPa+iqrn CUFF.57.1.p1 66 RHIGPSKTDQQYQLESLGYKDFDSFLKDVIPDSVRTPESQLMAFGsvnpneknppvnYSESEFTTLANNVANQNKLIKSFIGMGYYNVKLPAAIQRN 162 9******************************************9999************************************************** PP TTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--EEEEETTS-HHHHHHHHHHHGGGT-EEE CS GDC-P 87 ilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakkvvvdkkvhpqtlevlktrakglgieiv 183 +lenpewyt+YtPYqaEisqGrLe+++n+qt++adltGl+i+nasllDegtAa+EA++++++++kkk+k+++vdk+++p+tl+vl+tra+g+gi+i+ CUFF.57.1.p1 163 VLENPEWYTQYTPYQAEISQGRLESMMNYQTMIADLTGLSISNASLLDEGTAAGEAMVMLMANDKKKRKTFLVDKNIYPNTLSVLRTRASGFGIKIE 259 ************************************************************************************************* PP EE-GGG--S-...S-EEEEEEEES-TTSB----HHHHHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GGG CS GDC-P 184 evdlteekvtdkekevagvlvqypnteGriedlkelvekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkekl 280 ++++t e +t+++k+v+g++vqyp+++G+i d+ +l+++a++ +++vv+a+dllaLt+lk+Pge+gaD++vGs+qrfG+P+gyGGPhagffA++e++ CUFF.57.1.p1 260 LDNITPELITKSAKHVFGIFVQYPAADGSIFDYGHLAATARSFNMHVVAATDLLALTILKSPGEWGADVAVGSTQRFGLPMGYGGPHAGFFACSEEF 356 ************************************************************************************************* PP GGG--S-EEEEEEBTTS-EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SSBSS CS GDC-P 281 kRkiPGRlvGvskDaegkralrlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkkffd 377 kRkiPGRl+G+skD+ +++a+rlalqtREqHirR+kAtsniCtaqaLlAn++a+ya+yhG++gl+eia+ri+++t++l+++l+++ ++ ++k++ffd CUFF.57.1.p1 357 KRKIPGRLIGLSKDRLENPAYRLALQTREQHIRREKATSNICTAQALLANMSAFYAIYHGPNGLQEIANRIYASTSFLKSALESSGYKIVNKSHFFD 453 ************************************************************************************************* PP EEEEE--TTTHHHHHHHHHHTTEE-EEESTTEEEEE--TT--HHHHHHHHHHH CS GDC-P 378 tllieveekaaekvlkkaekeglnlrkvelktvgialdEtvtkedieallkvl 430 tl+ieve +a+kvl+ka+++g+nlrkv++++vg++ldEtv+++di+al++++ CUFF.57.1.p1 454 TLTIEVE--SADKVLAKALDHGYNLRKVDDSHVGLSLDETVCDKDIQALFSIF 504 ****999..889**************************************987 PP == domain 2 score: 36.7 bits; conditional E-value: 1.2e-13 SHHHHHHHHS-GGGB--S-------.....--HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SSGG.G-HHHHHH CS GDC-P 22 slddliekavPkeiklkkelkleap.....ksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYqaE.isqGrLea 111 ++d+l ++P++ + +++l l++p +sE+el++ ++++ sk+ ++ + G ++l av + + np + ++ PY +E ++G + CUFF.57.1.p1 529 TVDNLSICSLPENFR-RTTLYLQHPvfnryHSETELMRYIHHLQSKDLSlAHAMTPLGSCTMKLNAVTEMMPITNPLF-ANIHPYVPEeQAKGYRHV 623 677888888899985.456667777777779****************987899999************9988999976.5678999963789***** PP HHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHH.HH-SSS.....--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-......... CS GDC-P 112 llnfqtlvadltGldianasllDegtAaaEAvllaa.raskkk.....akkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd........ 194 + + q +++ +tG+d a + ++ Aa+E l++ ra ++ ++ ++ + h + a g+ ++ v++ +++ d CUFF.57.1.p1 624 IEDLQLMLTTITGFDAA--CFQPNSGAAGEYTGLSViRAYQRSigqghRNICLIPVSAHGTN----PASAAMAGFTVIPVKCLNNGYLDmqdlkeka 714 **************975..6778888888877665412222221111134444444444333....3445566666666666666666666677777 PP ....S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEE.EE-TTGGGTB--HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGGGGG-- CS GDC-P 195 ..kekevagvlvqypnteGried.lkelvekakkkkslvvv.aadllaLtllkpPgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkeklkRkiP 285 +++++a+ +v yp+t+G e+ +ke e ++++ v a++ a++ l g++gaD+ + + f +P g GGP +g + vk++l+ +P CUFF.57.1.p1 715 skHADKLAAFMVTYPSTFGIFEPdVKEALEVIHEHGGQVYFdGANMNAMVGLCKAGDIGADVChLNLHKTFCIPHGGGGPGVGPICVKKHLADFLP 810 768899**************99669*********99888763689999999***********84667889******************99988777 PP == domain 3 score: 0.7 bits; conditional E-value: 0.01 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--S CS GDC-P 332 aalyavyhGkeglkeiarrihkkteilakelkkkleeelkkk 373 + y+ + G gl++ ++ + +++++ak l ++ + + ++k CUFF.57.1.p1 840 SWAYMRMMGLAGLRDASKAALLNANYMAKRLSSHYKLVYTNK 881 567999*************************98755444443 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (430 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 344.97 // Query: GHMP_kinases_C [M=85] Accession: PF08544.12 Description: GHMP kinases C terminal Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-08 27.7 0.0 5e-08 25.9 0.0 1.9 1 CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907( 1.8e-08 27.3 0.0 6.2e-08 25.6 0.0 1.9 1 CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658( Domain annotation for each sequence (and alignments): >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 25.9 0.0 1.1e-09 5e-08 8 66 .. 233 287 .. 221 298 .. 0.90 Alignments for each domain: == domain 1 score: 25.9 bits; conditional E-value: 1.1e-09 GHMP_kinases_C 8 gdiellgellnlnqrseplavvgilppeleellealeelGalgaklsGaGgGptvfalf 66 +++ lge + lnq +l ++g+++ +++++l+a ++ G kl+GaGgG++ + l CUFF.60.1.p2 233 SSAKKLGEFIVLNQK--LLECLGVSHYSIDRVLQATKSIG--WTKLTGAGGGGCTITLL 287 6678999********..899********************..*************9997 PP >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 25.6 0.0 1.3e-09 6.2e-08 8 66 .. 284 338 .. 272 349 .. 0.90 Alignments for each domain: == domain 1 score: 25.6 bits; conditional E-value: 1.3e-09 GHMP_kinases_C 8 gdiellgellnlnqrseplavvgilppeleellealeelGalgaklsGaGgGptvfalf 66 +++ lge + lnq +l ++g+++ +++++l+a ++ G kl+GaGgG++ + l CUFF.60.2.p2 284 SSAKKLGEFIVLNQK--LLECLGVSHYSIDRVLQATKSIG--WTKLTGAGGGGCTITLL 338 6678999********..899********************..*************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (85 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 241.10 // Query: GHMP_kinases_N [M=66] Accession: PF00288.25 Description: GHMP kinases N terminal domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-18 58.0 1.6 8.7e-18 57.0 1.6 1.6 1 CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907( 1.1e-17 56.7 4.8 1.1e-17 56.7 1.6 2.3 2 CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658( Domain annotation for each sequence (and alignments): >> CUFF.60.1.p2 type:complete gc:universal CUFF.60.1:3846-4907(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 57.0 1.6 1.8e-19 8.7e-18 2 66 .] 75 152 .. 74 152 .. 0.87 Alignments for each domain: == domain 1 score: 57.0 bits; conditional E-value: 1.8e-19 EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTT.......EHHHH.......HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS GHMP_kinases_N 2 ivvkseiPigaGLGSSAAlavalvaAlaallg.......lslee.......aklaleaerlahggngsggDvaasvyGg 66 ++++s +P+gaGLGSSA+++v +++ l+ ++g +sl++ +++ +e+++h g +sg+D+a+++ Gg CUFF.60.1.p2 75 LTISSQVPLGAGLGSSATISVVVATSLLLAFGnieppssNSLQNnkalaliEAWSFLGECCIH-GTPSGIDNAVATNGG 152 799****************************877765543352257899999***********.************998 PP >> CUFF.60.2.p2 type:complete gc:universal CUFF.60.2:3444-4658(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 0.1 0.1 0.11 5.2 19 40 .. 25 47 .. 22 57 .. 0.68 2 ! 56.7 1.6 2.3e-19 1.1e-17 2 66 .] 126 203 .. 125 203 .. 0.87 Alignments for each domain: == domain 1 score: 0.1 bits; conditional E-value: 0.11 HHHHHHHHHHHHHTTEHH.HHHH CS GHMP_kinases_N 19 AlavalvaAlaallglsl.eeak 40 A a+a+++ l +++ l+ ++++ CUFF.60.2.p2 25 ATALAAAVSLRSYCKLQTtNNNE 47 77888888888999655323344 PP == domain 2 score: 56.7 bits; conditional E-value: 2.3e-19 EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTT.......EHHHH.......HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS GHMP_kinases_N 2 ivvkseiPigaGLGSSAAlavalvaAlaallg.......lslee.......aklaleaerlahggngsggDvaasvyGg 66 ++++s +P+gaGLGSSA+++v +++ l+ ++g +sl++ +++ +e+++h g +sg+D+a+++ Gg CUFF.60.2.p2 126 LTISSQVPLGAGLGSSATISVVVATSLLLAFGnieppssNSLQNnkalaliEAWSFLGECCIH-GTPSGIDNAVATNGG 203 799****************************877765543352257899999***********.************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (66 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 797.41 // Query: GLEYA [M=91] Accession: PF10528.8 Description: GLEYA domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-21 67.8 1.8 1.7e-20 65.9 1.8 2.0 1 CUFF.31.1.p1 type:complete gc:universal CUFF.31.1:244-1401(+ 2.4e-20 65.5 3.2 2.9e-20 65.2 2.1 1.8 2 CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-88 4.1e-19 61.5 0.7 1.6e-18 59.6 0.7 2.1 1 CUFF.30.1.p1 type:3prime_partial gc:universal CUFF.30.1:1007 9.4e-19 60.3 0.7 9.4e-19 60.3 0.7 1.9 3 CUFF.30.2.p1 type:3prime_partial gc:universal CUFF.30.2:749- Domain annotation for each sequence (and alignments): >> CUFF.31.1.p1 type:complete gc:universal CUFF.31.1:244-1401(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 65.9 1.8 7.1e-22 1.7e-20 2 89 .. 256 345 .. 255 347 .. 0.95 Alignments for each domain: == domain 1 score: 65.9 bits; conditional E-value: 7.1e-22 EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE-S-.EEEEEEE CS GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyangggagslnfsv 89 +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang g+++f + CUFF.31.1.p1 256 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANGAYIGGFDFAF 345 789***********************************************9666899999999************************987 PP >> CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-884(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.6 0.0 3.6 85 70 84 .. 13 27 .. 3 33 .. 0.60 2 ! 65.2 2.1 1.2e-21 2.9e-20 2 90 .. 157 253 .. 156 254 .. 0.92 Alignments for each domain: == domain 1 score: -3.6 bits; conditional E-value: 3.6 EEEEEEEEE-S-.EE CS GLEYA 70 yPiRivyangggags 84 +P+ +a++ g+ s CUFF.11.1.p1 13 LPFTTTLAQASGTVS 27 577777777766555 PP == domain 2 score: 65.2 bits; conditional E-value: 1.2e-21 EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.......TSSSSEEEEE.EEE-TT-BEEEEEEEEE-S-.EEEEEEEE CS GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.......sgssesktvt.vtltaGtyyPiRivyangggagslnfsvt 90 +++++ +++ p+t tYt+ ++n+Dd+++ w+GdkA+s+w+++n d+++ + g+ + +++t + +G+++P+R+v+ang g+++f +t CUFF.11.1.p1 157 VIVYQFFLRIPETDTYTLVVNNVDDVFFGWFGDKAISGWSNNNFDAYSYWhespnmgLGTVGMGNFTvGNYPEGYFLPVRFVVANGAYIGGFDFYFT 253 689***********************************************9999888444677777757899**********************998 PP >> CUFF.30.1.p1 type:3prime_partial gc:universal CUFF.30.1:1007-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 59.6 0.7 6.9e-20 1.6e-18 2 79 .. 256 335 .] 255 335 .] 0.95 Alignments for each domain: == domain 1 score: 59.6 bits; conditional E-value: 6.9e-20 EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE- CS GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyang 79 +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang CUFF.30.1.p1 256 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANG 335 789***********************************************9666899999999***************96 PP >> CUFF.30.2.p1 type:3prime_partial gc:universal CUFF.30.2:749-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.0 0.0 2.3 55 59 86 .. 20 45 .. 14 50 .. 0.50 2 ? -2.0 0.1 1.1 26 75 75 .. 66 66 .. 31 96 .. 0.59 3 ! 60.3 0.7 4e-20 9.4e-19 2 79 .. 170 249 .] 169 249 .] 0.95 Alignments for each domain: == domain 1 score: -3.0 bits; conditional E-value: 2.3 EEEEEE-TT-BEEEEEEEEE-S-.EEEE CS GLEYA 59 tvtvtltaGtyyPiRivyangggagsln 86 + +v+++ G+ + +y g ++++ CUFF.30.2.p1 20 SSSVSVETGSCVRYTTIYSSGS--SEFT 45 4455666666554444444433..3444 PP == domain 2 score: -2.0 bits; conditional E-value: 1.1 E CS GLEYA 75 v 75 CUFF.30.2.p1 66 H 66 1 PP == domain 3 score: 60.3 bits; conditional E-value: 4e-20 EEEEEEEE--SSSEEEEEEE.EEESEEEEEESBTTBBTTBHHS-SEEEET.TSSSSEEEEE.EEE-TT-BEEEEEEEEE- CS GLEYA 2 alelrGYfyapktgtYtfslsnaDdiallwlGdkAfscwtranadleaty.sgssesktvt.vtltaGtyyPiRivyang 79 +++++ +f+ p+t ++++ ++n+Dd+++ w+GdkA+s+w++ n+d++a++ g + +t+ +l++++++P+R+v+ang CUFF.30.2.p1 170 TIVYQFFFRVPATDNWSLFVKNVDDAFFGWFGDKAISGWSNVNYDAYAHWrIGAYGMGTFDlGYLEQDSFVPVRFVLANG 249 789***********************************************9666899999999***************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (91 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 423.18 // Query: Glyco_hydro_cc [M=239] Accession: PF11790.7 Description: Glycosyl hydrolase catalytic core Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-61 199.6 0.0 4.3e-61 199.1 0.0 1.3 1 CUFF.59.1.p1 type:complete gc:universal CUFF.59.1:158-1750(+ Domain annotation for each sequence (and alignments): >> CUFF.59.1.p1 type:complete gc:universal CUFF.59.1:158-1750(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.1 0.0 4.5e-63 4.3e-61 1 239 [] 298 528 .. 298 528 .. 0.92 Alignments for each domain: == domain 1 score: 199.1 bits; conditional E-value: 4.5e-63 Glyco_hydro_cc 1 GlaynadasddkllsaksskisWyYnwsskpsselssaalefvPmlwgaksadtdalanvksaakenskylLgFNePDlks.qsnmspeeAaklw 94 Gla++ +++ ++ + ++ i+WyYnw+s++s+ +ss e+v ++a+s + +++s+ ++ +++gFNePDl+ + +++++Aa+++ CUFF.59.1.p1 298 GLAWIPGTDLGYSDNFVNKGINWYYNWGSYSSGLSSSF--EYVLNQHDANSLS-----SASSV-FTGGATVIGFNEPDLSAaGNPIDAATAASYY 384 78999888888888999**************9988885..********99865.....44444.55579**********8889************ PP Glyco_hydro_cc 95 kqliqplre..kgvklvsPavaatnseegleWldeFleacskdckvdflavHwYkgdfeelkehieelheaynkpiWvTEfalqs..esgdasqe 185 q+++plre +l+sPa+++ g +Wl+eF++acs dck+df+a+HwY+ df++l+++i++l ++y++piW+TEfa+++ +s+ s + CUFF.59.1.p1 385 LQYLTPLREsgAIGYLGSPAISN--V--GEDWLSEFMSACS-DCKIDFIACHWYGIDFSNLQDYINSL-ANYGLPIWLTEFACTNwdDSNLPSLD 473 ********6355669******33..3..669**********.************999***********.9***************999999**** PP Glyco_hydro_cc 186 etkeflnevlawldsqeyVeryawfg.frsevsnvgannaLldenGeltelgsaY 239 e+k++++++l +ld + +Very+wf+ +++ ++vg+nnaL++++G+l+e+g++Y CUFF.59.1.p1 474 EVKTLMTSALGFLDGHGSVERYSWFApATELGAGVGNNNALISSSGGLSEVGEIY 528 *****************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (239 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1140.96 // Query: Glyco_tranf_2_3 [M=230] Accession: PF13641.5 Description: Glycosyltransferase like family 2 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00012 14.6 0.0 0.00045 12.7 0.0 1.8 2 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 0.00012 14.6 0.0 0.00045 12.7 0.0 1.8 2 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ Domain annotation for each sequence (and alignments): >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.4 0.0 0.19 9.2 90 110 .. 237 257 .. 197 265 .. 0.73 2 ! 12.7 0.0 9.5e-06 0.00045 83 229 .. 329 507 .. 309 508 .. 0.89 Alignments for each domain: == domain 1 score: -1.4 bits; conditional E-value: 0.19 Glyco_tranf_2_3 90 lvllvDdDtvvePdtlkrllq 110 + ++ D+ t ++P+tl++l++ CUFF.60.1.p1 237 VCIISDGRTKIHPRTLAYLAA 257 45688999*******999876 PP == domain 2 score: 12.7 bits; conditional E-value: 9.5e-06 Glyco_tranf_2_3 83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs......tlvsalgalefaerhlrflaarralgv.ltlnGsgslir 168 +++ k+++ +l+D+ t+ ++ ++ l f l p+v+ + + ++ ++ + + a++++e++ ++ + +g+ l G++s++r CUFF.60.1.p1 329 CPILKPEVCILLDAGTRPGDQSIYHLWKSFdLNPQVAGACGEIVVMKGKlgsgliNPLVATQNFEYKMSNILDKPVESVFGFiSVLPGAFSAYR 422 5667889999********************9999999999999888766666666668888********************8566779****** PP Glyco_tranf_2_3 169 revlkele.....................gldplflltdDyelglrlrr...agfrtayvpgaavrevfpsslkayikqrnRwvy 229 e l++ + ++ +l++D +l+++l + + + +yv+ a + p+ + +++ qr+Rw+ CUFF.60.1.p1 423 FEALQNDSqgngplasyfkgelqntgksgIFEANMYLAEDRILCFELVSkknEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLN 507 ******999****************9984466699************9988899*****************************86 PP >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.4 0.0 0.19 9.2 90 110 .. 237 257 .. 197 265 .. 0.73 2 ! 12.7 0.0 9.5e-06 0.00045 83 229 .. 329 507 .. 309 508 .. 0.89 Alignments for each domain: == domain 1 score: -1.4 bits; conditional E-value: 0.19 Glyco_tranf_2_3 90 lvllvDdDtvvePdtlkrllq 110 + ++ D+ t ++P+tl++l++ CUFF.60.2.p1 237 VCIISDGRTKIHPRTLAYLAA 257 45688999*******999876 PP == domain 2 score: 12.7 bits; conditional E-value: 9.5e-06 Glyco_tranf_2_3 83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs......tlvsalgalefaerhlrflaarralgv.ltlnGsgslir 168 +++ k+++ +l+D+ t+ ++ ++ l f l p+v+ + + ++ ++ + + a++++e++ ++ + +g+ l G++s++r CUFF.60.2.p1 329 CPILKPEVCILLDAGTRPGDQSIYHLWKSFdLNPQVAGACGEIVVMKGKlgsgliNPLVATQNFEYKMSNILDKPVESVFGFiSVLPGAFSAYR 422 5667889999********************9999999999999888766666666668888********************8566779****** PP Glyco_tranf_2_3 169 revlkele.....................gldplflltdDyelglrlrr...agfrtayvpgaavrevfpsslkayikqrnRwvy 229 e l++ + ++ +l++D +l+++l + + + +yv+ a + p+ + +++ qr+Rw+ CUFF.60.2.p1 423 FEALQNDSqgngplasyfkgelqntgksgIFEANMYLAEDRILCFELVSkknEAWILHYVKSAYADTDVPDRIPEFVLQRRRWLN 507 ******999****************9984466699************9988899*****************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (230 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 780.63 // Query: Glyco_transf_34 [M=239] Accession: PF05637.11 Description: galactosyl transferase GMA12/MNN10 family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-87 284.1 0.3 6.5e-87 283.8 0.3 1.1 1 CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+ 2.8e-86 281.7 0.0 3.4e-86 281.4 0.0 1.1 1 CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659( Domain annotation for each sequence (and alignments): >> CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.8 0.3 1.4e-88 6.5e-87 2 238 .. 98 334 .. 97 335 .. 0.97 Alignments for each domain: == domain 1 score: 283.8 bits; conditional E-value: 1.4e-88 Glyco_transf_34 2 epeivlllvsnekkcenssgdhelllkvikNrvdYaekhgyeifykkvsallaeemnsvWaklpairaamkkyPeaewiWwlDqdAlimnmdls 95 +++ivlllvs+ ++++ ++ +++++++i+NrvdY++k++y+++y++v+ l ++vW+k+pa+ ++mkkyP+aewiW+lDqdA+i+n++ls CUFF.51.1.p2 98 SQNIVLLLVSDGHTSY--NNGANTFEEAIQNRVDYSTKQNYNFEYVNVTGLPI---PAVWSKMPAVLQTMKKYPKAEWIWLLDQDAIITNTHLS 186 789***********97..455559***************************99...************************************** PP Glyco_transf_34 96 leehvlkperLeelllkntpv........vplrryketnlvedgedvlviisqdwnglnagsflirnsewsklllDlwadpllrekkkavtesd 181 l++++lkpe+L+++l++nt + +lr+++++++ +d+e+ +viisqd+nglnags+l+rns +++l+lD+w+dp+++e++ka ++ CUFF.51.1.p2 187 LQDSFLKPENLQKTLITNTILtkrpinanGDLRYTPSNYSLKDIENLMVIISQDHNGLNAGSILFRNSPATALFLDIWTDPVVAECAKA---NN 277 *******************999*****9999**********************************************************...** PP Glyco_transf_34 182 eqsaleyllekhpevlskvglveqkvinsydegekelgykegdlvvhfagCkvankc 238 eq++l+yl++kh++++s vgl++q+ in+++eg++++++++gdlv+hfagC+v+n+c CUFF.51.1.p2 278 EQDMLGYLISKHSQLASLVGLIPQRKINAFHEGPENMEWQKGDLVIHFAGCWVENRC 334 ********************************************************9 PP >> CUFF.52.1.p2 type:complete gc:universal CUFF.52.1:3670-4659(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.4 0.0 7.1e-88 3.4e-86 2 239 .] 84 318 .. 83 318 .. 0.98 Alignments for each domain: == domain 1 score: 281.4 bits; conditional E-value: 7.1e-88 Glyco_transf_34 2 epeivlllvsnekkcenssgdhelllkvikNrvdYaekhgyeifykkvsallaeemnsvWaklpairaamkkyPeaewiWwlDqdAlimnmdls 95 ++eiv+ll+s+ + s +++ll++++kNr++Ya++++y++++++vs+l + vW k+pai ++m+kyP+a+wiWwlDqdAlimn++ls CUFF.52.1.p2 84 SHEIVMLLASDGNVG---SFESNLLDDCFKNRIEYAKLQNYNFEFVNVSSLVV---PPVWGKMPAILQTMRKYPSAKWIWWLDQDALIMNKNLS 171 79**********997...58999***************************999...************************************** PP Glyco_transf_34 96 leehvlkperLeelllkntpv......vplrryketnlvedgedvlviisqdwnglnagsflirnsewsklllDlwadpllrekkkavtesdeq 183 l+e +l+p +L+++ll+++p+ ++ r ++ +++e++e+++++isqd+nglnagsfl+rns+ +ll+Dl++dp+l++++++ ++eq CUFF.52.1.p2 172 LQELFLSPAMLQKSLLREQPIinsfgeDNFRITPAAYSKEMIEQIQFLISQDHNGLNAGSFLVRNSRSIALLMDLLTDPSLADAGVV---RHEQ 262 **************************999**********************************************************...**** PP Glyco_transf_34 184 saleyllekhpevlskvglveqkvinsydegekelgykegdlvvhfagCkvankca 239 ++++y+++kh++v+s+vg+++q++in+++eg+++++++egdl++hfagC+v+nkca CUFF.52.1.p2 263 DLIGYFIQKHSQVASMVGILPQRFINAFHEGPPTMQWQEGDLALHFAGCWVENKCA 318 ******************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (239 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1096.45 // Query: Glyco_transf_8 [M=256] Accession: PF01501.19 Description: Glycosyl transferase family 8 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-12 39.3 1.6 1e-11 37.5 1.6 1.8 1 CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747( Domain annotation for each sequence (and alignments): >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 37.5 1.6 1.1e-13 1e-11 9 221 .. 84 321 .. 77 336 .. 0.81 Alignments for each domain: == domain 1 score: 37.5 bits; conditional E-value: 1.1e-13 Glyco_transf_8 9 nYllgasvviksllknakepawfalnfhiltaeievenleklnklassykevlellesdkksledfesklklrspkylsllnylRlylpelfpkl 103 Y ++ v+i+ l + +++ +++ + ++++ ++e+++k + s++ ++++ sd+ ++++++++ ++ + ++ +l+++e ++ CUFF.51.1.p1 84 YYFNATRVLIHRLKYHPTTKSKYPIHIL-ALRGVDEWKIERFRKDGASVIVIDPIASSDIVY----DTSSFSQEISARYEQMFSKLRIFEQ-IQF 172 5677778888888888886556666666.7899*******************9999998843....3578899999999999*********.9** PP Glyco_transf_8 104 dkilylDaDvvvqgdlseLwdldlk.gkvlaaved............................krfkkylnksepliaenfkp..eacyFnaGvl 167 dki +D+D+++ +++++++d++ ++++ + + + + l + + +++p + yFnaG++ CUFF.51.1.p1 173 DKICVIDSDILIMKNIDDIFDTPYMyQQINTLNYTrlpsytkpdddtvyhfnedfkeygasrsEFYPYLLAAVSDRGEHHSIPpeDTPYFNAGLM 267 **********************9997888888888*************************8863333333444444444444411567******* PP Glyco_transf_8 168 lfdldewrkenitetlikwlnlnekrtllklgdqdilnivfk....gkvkeldkkynv 221 l+ + e + + i + + ++e+ k ++q +ln++f + +ld++yn CUFF.51.1.p1 268 LIRPSELHFNRILKI-GRFPYMYEN---AKMMEQSLLNLAFSldgwFPWTRLDPYYNG 321 *******99988764.455566666...89***********86655789999999995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 465.17 // Query: Glyco_trans_2_3 [M=197] Accession: PF13632.5 Description: Glycosyl transferase family group 2 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-11 36.3 7.3 1.5e-10 33.9 7.3 2.2 1 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 2.8e-11 36.3 7.3 1.5e-10 33.9 7.3 2.2 1 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ Domain annotation for each sequence (and alignments): >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 33.9 7.3 3.2e-12 1.5e-10 3 191 .. 338 564 .. 336 713 .. 0.80 Alignments for each domain: == domain 1 score: 33.9 bits; conditional E-value: 3.2e-12 Glyco_trans_2_3 3 lllDaDtvlppdclreiaaela.spevaivqgpvlvm......nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalq.... 85 +llDa t++ ++++ + ++ +p va ++g ++vm + n l+ ++ ++++ + + d +v + +g ++G+ ++ r +alq CUFF.60.1.p1 338 ILLDAGTRPGDQSIYHLWKSFDlNPQVAGACGEIVVMkgklgsGLINPLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQndsq 431 799**************999*988************97765333347788888888**********************************8888 PP Glyco_trans_2_3 86 .................evggwdgdessvsEDfdmglrlqrkG...yrvrfapeslvkekspltlraelrQrkRwayGc....el....eklil 151 + g ++ + ++ED +++ l +k ++++++ ++ + +p+++ ++ Qr+Rw+ G + ++ CUFF.60.1.p1 432 gngplasyfkgelqntgKSGIFE-ANMYLAEDRILCFELVSKKneaWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSffaaAYaichY--YR 522 77777777777665555555777.568************9888789999999999***********************766541145432..22 PP Glyco_trans_2_3 152 lvrll.gylgsllwsalplhlallllfslla.....lalvllllll 191 +r++ +++++s ++ +++++f+++ + ++++l CUFF.60.1.p1 523 FFRTShTISRKFMLSIEFIYQLATIVFGWFNignffI----IFYIL 564 3333313445555555555555566665544333321....22222 PP >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 33.9 7.3 3.2e-12 1.5e-10 3 191 .. 338 564 .. 336 713 .. 0.80 Alignments for each domain: == domain 1 score: 33.9 bits; conditional E-value: 3.2e-12 Glyco_trans_2_3 3 lllDaDtvlppdclreiaaela.spevaivqgpvlvm......nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalq.... 85 +llDa t++ ++++ + ++ +p va ++g ++vm + n l+ ++ ++++ + + d +v + +g ++G+ ++ r +alq CUFF.60.2.p1 338 ILLDAGTRPGDQSIYHLWKSFDlNPQVAGACGEIVVMkgklgsGLINPLVATQNFEYKMSNILDKPVESVFGFISVLPGAFSAYRFEALQndsq 431 799**************999*988************97765333347788888888**********************************8888 PP Glyco_trans_2_3 86 .................evggwdgdessvsEDfdmglrlqrkG...yrvrfapeslvkekspltlraelrQrkRwayGc....el....eklil 151 + g ++ + ++ED +++ l +k ++++++ ++ + +p+++ ++ Qr+Rw+ G + ++ CUFF.60.2.p1 432 gngplasyfkgelqntgKSGIFE-ANMYLAEDRILCFELVSKKneaWILHYVKSAYADTDVPDRIPEFVLQRRRWLNGSffaaAYaichY--YR 522 77777777777665555555777.568************9888789999999999***********************766541145432..22 PP Glyco_trans_2_3 152 lvrll.gylgsllwsalplhlallllfslla.....lalvllllll 191 +r++ +++++s ++ +++++f+++ + ++++l CUFF.60.2.p1 523 FFRTShTISRKFMLSIEFIYQLATIVFGWFNignffI----IFYIL 564 3333313445555555555555566665544333321....22222 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (197 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 11 (0.115789); expected 1.9 (0.02) Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 156.63 // Query: GNAT_acetyltr_2 [M=227] Accession: PF13718.5 Description: GNAT acetyltransferase 2 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00031 12.8 0.0 0.00041 12.4 0.0 1.1 1 CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440- 0.00032 12.7 0.0 0.00043 12.3 0.0 1.1 1 CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) Domain annotation for each sequence (and alignments): >> CUFF.34.1.p2 type:3prime_partial gc:universal CUFF.34.1:440-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.4 0.0 8.6e-06 0.00041 94 131 .. 72 109 .. 67 128 .. 0.78 Alignments for each domain: == domain 1 score: 12.4 bits; conditional E-value: 8.6e-06 GNAT_acetyltr_2 94 sGaRivRiAvhpelqrmGYGsralellekyyegklssl 131 + +Ri R+ v+p+ ++ GYG + + + + ++++ss CUFF.34.1.p2 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSS 109 679******************98766666666665554 PP >> CUFF.35.1.p1 type:complete gc:universal CUFF.35.1:542-994(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.3 0.0 9e-06 0.00043 94 131 .. 72 109 .. 67 130 .. 0.79 Alignments for each domain: == domain 1 score: 12.3 bits; conditional E-value: 9e-06 GNAT_acetyltr_2 94 sGaRivRiAvhpelqrmGYGsralellekyyegklssl 131 + +Ri R+ v+p+ ++ GYG + + + + ++++ss CUFF.35.1.p1 72 QTVRIGRVVVDPDERKNGYGRKLMLQALETSKQEFSSS 109 679******************98766666666665554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (227 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 4 (0.0421053); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1710.29 // Query: His_Phos_1 [M=194] Accession: PF00300.21 Description: Histidine phosphatase superfamily (branch 1) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-24 77.6 0.0 6.6e-24 77.3 0.0 1.1 1 CUFF.48.1.p2 type:complete gc:universal CUFF.48.1:1221-1880( Domain annotation for each sequence (and alignments): >> CUFF.48.1.p2 type:complete gc:universal CUFF.48.1:1221-1880(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 77.3 0.0 7e-26 6.6e-24 1 181 [. 9 203 .. 9 215 .. 0.86 Alignments for each domain: == domain 1 score: 77.3 bits; conditional E-value: 7e-26 EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTT..S---EEEE-SSHHHHHHHHHHHHCTT.......--EEE-GGGS----GGGT. CS His_Phos_1 1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlag..epidaiysSplkRarqTaeliaealg.......lpveldegLrEidfGdwe. 86 +yL+RHG+ ++n+ d+ Lt eG+eq eala+ l++ +pid i++Sp++R+ qT+e+++++ +pv + + ++E+ + ++ CUFF.48.1.p2 9 VYLIRHGQAQHNVGPDeDHNIRDPVLTSEGIEQCEALAKELESkqIPIDGIVCSPMRRTLQTMEIALKKYLaeggpdkVPVYISPFFQEVGHLPCDi 105 69*********99877778889999****************9988999999***************99876788999************99999999 PP T-B.HHHHHH..HSHHHHHHHHH-GGG-B....S-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHH.T--GGGGG.GB---TT-EE CS His_Phos_1 87 glttaeiaeeypeeleawlrdpadvrppg....gEsledvaaRvaaaleelaarhegetvlvVsHggvirallarll.glpleelr.rleldnaslt 177 gl+ +++++ yp++ + +d p++ + a R ++ale laa +++ ++v++H ++ir ll++++ ++++l+ +l ++n++ CUFF.48.1.p2 106 GLELDKLNKLYPKYNFQSCQDGIY--PEKrdiyASDVTISAIRSKEALEYLAALPQQQ-IAVITHSAFIRFLLKKMVkAADIDFLPpQLSFKNCEFR 199 **********99987777666653..3334587888888899***********99987.*****************966777766546777999887 PP EEEE CS His_Phos_1 178 vley 181 + ++ CUFF.48.1.p2 200 IYDL 203 7765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (194 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1935.96 // Query: Hpt [M=85] Accession: PF01627.22 Description: Hpt domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00033 13.6 0.3 0.0011 11.9 0.3 1.8 1 CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+ Domain annotation for each sequence (and alignments): >> CUFF.19.1.p1 type:complete gc:universal CUFF.19.1:524-2467(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.9 0.3 1.1e-05 0.0011 32 64 .. 217 248 .. 205 267 .. 0.74 Alignments for each domain: == domain 1 score: 11.9 bits; conditional E-value: 1.1e-05 HHHHHHHHHHHTTBHHHHHHHHHHHHHHHHCTS CS Hpt 32 aaHtLKGsagmlGltelaelahelEdlldrage 64 ++H+++Gsa+ lGl+ l ++a+ ++++d a CUFF.19.1.p1 217 LVHKIAGSAAALGLD-LHQVAQVAQSVIDNAAT 248 79***********64.66666666666654444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (85 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1253.53 // Query: HTH_29 [M=63] Accession: PF13551.5 Description: Winged helix-turn helix Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00071 12.3 0.0 0.1 5.3 0.0 2.6 2 CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+ Domain annotation for each sequence (and alignments): >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 5.3 0.0 0.0011 0.1 16 35 .. 122 141 .. 111 145 .. 0.88 2 ! 4.0 0.0 0.0027 0.26 10 30 .. 278 298 .. 271 301 .. 0.83 Alignments for each domain: == domain 1 score: 5.3 bits; conditional E-value: 0.0011 HTH_29 16 sqiAkllglsrrtvyrwlkr 35 ++A ++glsr+++++++++ CUFF.17.1.p1 122 PELANQCGLSRKHIFDAVED 141 589************99986 PP == domain 2 score: 4.0 bits; conditional E-value: 0.0027 HTH_29 10 eGvstvsqiAkllglsrrtvy 30 +s+v ++Ak +++s+ t CUFF.17.1.p1 278 AILSRVEELAKKYNVSMATLA 298 456799************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (63 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 996.07 // Query: HTH_psq [M=45] Accession: PF05225.15 Description: helix-turn-helix, Psq domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00097 11.5 0.3 0.2 4.1 0.0 3.0 3 CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+ Domain annotation for each sequence (and alignments): >> CUFF.17.1.p1 type:complete gc:universal CUFF.17.1:231-1286(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 3.8 0.0 0.0026 0.25 24 33 .. 81 90 .. 80 93 .. 0.91 2 ? -1.9 0.0 0.16 16 7 16 .. 169 179 .. 165 180 .. 0.80 3 ! 4.1 0.0 0.0021 0.2 21 33 .. 285 297 .. 281 304 .. 0.87 Alignments for each domain: == domain 1 score: 3.8 bits; conditional E-value: 0.0026 HTH_psq 24 rkYgiPrsTL 33 rkY+iPrs++ CUFF.17.1.p1 81 RKYEIPRSSI 90 79******98 PP == domain 2 score: -1.9 bits; conditional E-value: 0.16 HTH_psq 7 aAleavv.nGk 16 +Al++vv +Gk CUFF.17.1.p1 169 RALNDVVeSGK 179 8******8887 PP == domain 3 score: 4.1 bits; conditional E-value: 0.0021 HTH_psq 21 kAArkYgiPrsTL 33 ++A+kY+++ TL CUFF.17.1.p1 285 ELAKKYNVSMATL 297 79********999 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 853.79 // Query: Hydantoinase_A [M=291] Accession: PF01968.17 Description: Hydantoinase/oxoprolinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-107 349.6 0.2 6.5e-107 349.6 0.2 1.7 2 CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+ 7.5e-91 296.9 0.0 1.3e-90 296.2 0.0 1.4 1 CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111 Domain annotation for each sequence (and alignments): >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.5 0.2 0.54 26 82 95 .. 5 18 .. 4 22 .. 0.87 2 ! 349.6 0.2 1.4e-108 6.5e-107 1 290 [. 239 540 .. 239 541 .. 0.98 Alignments for each domain: == domain 1 score: -3.5 bits; conditional E-value: 0.54 Hydantoinase_A 82 ItfDmGGTstDvsl 95 I +D GGT tD+++ CUFF.44.1.p1 5 IHIDRGGTFTDAIA 18 889********875 PP == domain 2 score: 349.6 bits; conditional E-value: 1.4e-108 Hydantoinase_A 1 rtetavvnAylspilreylesvekslekrgak......arlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaat.sklagekkvItfDmGG 88 r+++a+ +Aylsp++r+yl ++++ + + ++ r+ +mqsdGglv+++++++ ++ilSGPa+Gvvg+a t ++++ + +vI+fDmGG CUFF.44.1.p1 239 RATSATADAYLSPVVRRYLAGFQSGFLHGLKTkdnskgVRCEFMQSDGGLVDVNKFSGL--HAILSGPAGGVVGFALTsYDEDVKIPVIGFDMGG 331 7889*********************9997776999999********************9..*****************77888888********* PP Hydantoinase_A 89 TstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls. 182 TstDvs++ g++e+++et++agv++++p+ldi+tv+agGgs+l ++++g + vgpesaga+pgp+cyrkGg ltvTDanl+LGrl pe+f++ CUFF.44.1.p1 332 TSTDVSRYG-GSYEHVFETTTAGVTIQSPQLDINTVAAGGGSRL-FWKNGLFVVGPESAGAHPGPVCYRKGG-YLTVTDANLLLGRLLPESFPKi 423 *********.**********************************.***************************.********************** PP Hydantoinase_A 183 .gpdgdqkldvelarrafeelakelnlk........veevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkv 268 gp++d++ldve +r++fe+l++e+n + ++evA g++++a+e+ma+++r l++++g+d++ + l++fGGaG+qh+aa+a++lg+++v CUFF.44.1.p1 424 fGPNEDESLDVESTRKEFEKLTAEINSGlekerqmtADEVAFGFIKIANETMARPIRALTEAKGHDISIHRLTSFGGAGGQHCAAIAKSLGITQV 518 *********************************************************************************************** PP Hydantoinase_A 269 ivppyagvlsalGmalAdvree 290 +v++y+++lsa+GmalAdv +e CUFF.44.1.p1 519 LVHKYSSILSAYGMALADVVSE 540 ******************9876 PP >> CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111-1142(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 296.2 0.0 2.7e-92 1.3e-90 44 290 .. 1 252 [. 1 253 [. 0.97 Alignments for each domain: == domain 1 score: 296.2 bits; conditional E-value: 2.7e-92 Hydantoinase_A 44 lvsadearkkpvetilSGPaaGvvgaaat..sklagekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvde 136 lv++d+++ +i+SGPaaG vg+a+t + ++++++I+fDmGGTstDvs+++ g++e+ +e +i g+ +++p+ldi+tv+agGgs+l +++ CUFF.42.1.p1 1 LVDIDNFTAI--SAIMSGPAAGTVGFAKTssLHADDKTPAIGFDMGGTSTDVSRYD-GKFEHIYEANIFGLYIQSPQLDIQTVAAGGGSRL-FWR 91 6789999987..*****************5445567788*****************.**********************************.999 PP Hydantoinase_A 137 ggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls..gpdgdqkldvelarrafeelakelnlk......veevAegilsvave 223 ++ ++vgpesaga pgpacy +Gg +ltvTDan++LGr+ p++f++ gp+++++++++++ ++f+el + +n + +ee+A+g+++va+e CUFF.42.1.p1 92 NQLFSVGPESAGAFPGPACYLNGG-PLTVTDANVLLGRIIPDFFPKifGPKENESMNKDIVIEKFSELRDIINIDiekektIEEIAMGFIQVANE 185 ************************.********************************************************************** PP Hydantoinase_A 224 nmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290 +m++++rkl+++rgld + ++l+vfGGaG+qha+a+a l+++k+i+++y++vlsa+G+alA+v++e CUFF.42.1.p1 186 TMCRPIRKLTESRGLDLSAHHLAVFGGAGGQHACAIASLLNIEKIIIHKYSSVLSAYGLALAHVTHE 252 ****************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (291 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 700.56 // Query: Hydantoinase_B [M=516] Accession: PF02538.13 Description: Hydantoinase B/oxoprolinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-215 708.9 0.1 2.7e-215 708.2 0.1 1.3 1 CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+ 2.2e-213 701.8 0.3 2.8e-213 701.5 0.3 1.1 1 CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111 Domain annotation for each sequence (and alignments): >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 708.2 0.1 5.6e-217 2.7e-215 1 516 [] 749 1285 .. 749 1285 .. 0.98 Alignments for each domain: == domain 1 score: 708.2 bits; conditional E-value: 5.6e-217 Hydantoinase_B 1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvlltNdPyagg 93 Dpi l+vf +r+m++ae+mgr+lq+t++S+n+kerlD+scalfda+g+lva+aph+pvhlgsms++v+++++ +eg+lkpGDvl+tN+P +gg CUFF.44.1.p1 749 DPIYLSVFGSRFMAVAEQMGRALQKTSVSTNVKERLDYSCALFDAKGNLVANAPHMPVHLGSMSTCVRTQAKIHEGKLKPGDVLVTNHPSYGG 841 9**********************************************************************99999***************** PP Hydantoinase_B 94 tHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege.leedvlelllanv.........Rtpednl 176 tHlpDit+itP f +e++f+va+raHhaDiGGi pGsmp++++e+ eEG+ i++ klv +g+ +ee++++ll +++ R+++dnl CUFF.44.1.p1 842 THLPDITTITPHFEGDEIMFYVAARAHHADIGGILPGSMPSSSKELSEEGATIKSEKLVVDGVfQEERMIDLLYNEPakveggsgsRCLRDNL 934 *************9889*********************************************************999**************** PP Hydantoinase_B 177 gDlkAqiaanqvgerrlkelieeyGletveaamdeildnaeravraalaelpd....gtyeaedylddgipikvtvtidgde..atvDftgts 263 +DlkAq++anq+g+++++ li+eyG++ v ++m++i++nae avr++l +++ +++ aed++ddg++i++++tid+++ a++Dftgt CUFF.44.1.p1 935 NDLKAQVSANQKGINLITSLIKEYGKNSVLRYMKAIQENAESAVRQLLLGVRErflgEDLYAEDHMDDGSKICLRITIDEENgdAIFDFTGTT 1027 ************************************************7777777778899*******************9999********* PP Hydantoinase_B 264 pqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtm 356 ++++gniNap+avt+sa+iy+lr+l++e+iplN+Gcl pi+v++p++++l+pse+aavvggnv+tsqr++d++lka++ ++Aasqg++ CUFF.44.1.p1 1028 EEIYGNINAPEAVTYSAIIYCLRVLISENIPLNQGCLLPIKVIIPDNCFLKPSETAAVVGGNVLTSQRITDTILKAFQ------ACAASQGDT 1114 ******************************************************************************......********* PP Hydantoinase_B 357 nnltf..ggvderg...geffgyyetiagGsGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreief 444 nnltf gg+d+++ + fgyyeti+gGsGA g dG+s+vh+hmtntr+td E+lErryPv++++f +r++sgGaGky+GGdGv+r+ief CUFF.44.1.p1 1115 NNLTFgiGGKDPETgevKPGFGYYETICGGSGAIDGLDGTSGVHTHMTNTRITDLEVLERRYPVILRKFIIRENSGGAGKYKGGDGVIRDIEF 1207 ****94446677669998889************************************************************************ PP Hydantoinase_B 445 lepevtvsilserrvfapwGlaGGepGargrvvlnllvr..........greenlggkatvelkagdvlvietpGGGGyGdp 516 + p vt+silserr ++p+G++GG+++++g+ n+++r r++n+ggk+t++++agd +vi+tpGGGGyG p CUFF.44.1.p1 1208 RIP-VTLSILSERRAYHPYGMKGGKDAECGK---NIWIRkdilpsgeqrVRQINVGGKNTCHMQAGDHIVIMTPGGGGYGPP 1285 **9.***************************...88888899999998899*****************************86 PP >> CUFF.42.1.p1 type:5prime_partial gc:universal CUFF.42.1:4111-1142(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 701.5 0.3 5.9e-215 2.8e-213 1 515 [. 459 986 .. 459 987 .. 0.98 Alignments for each domain: == domain 1 score: 701.5 bits; conditional E-value: 5.9e-215 Hydantoinase_B 1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvlltNdPyaggtH 95 Dpit+ +f+nr+msi e+mg++lq+ta+S+n+kerlD+scalf++dg+lva+aph+p +lgsm++avk+++++++g+l pGDvll+N+P+agg H CUFF.42.1.p1 459 DPITMTIFANRFMSISEQMGQVLQKTAVSVNVKERLDYSCALFSPDGGLVANAPHVPAMLGSMQTAVKWQHNYWKGKLVPGDVLLSNHPIAGGVH 553 9********************************************************************************************** PP Hydantoinase_B 96 lpDitvitPvfhege.lvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege.leedvlelllanv.........RtpednlgDl 179 lpD+tv+tPvf +++ ++f++a+r+H++D+GGitpGsmp++++ i+eEG++i+++k+v++g+ +e+++++ll +++ Rt++dn++D+ CUFF.42.1.p1 554 LPDLTVVTPVFDNNKdIIFYCAARGHMVDVGGITPGSMPSNSKAIYEEGAAIKTFKVVKAGTfDEKGLTQLLFDEPakypdcsgsRTLRDNISDV 648 ***********98879******************************************************************************* PP Hydantoinase_B 180 kAqiaanqvgerrlkelieeyGletveaamdeildnaeravraalaelpd....gtyeaedylddgipikvtvtidgde..atvDftgtspqvkg 268 kA+++a+++g++ +++l+ eyGl+ v++ m i++ ae+avr++l++++ + ++a dy+ddg+p++++v+id+++ a++Df+gt+p+v+g CUFF.42.1.p1 649 KAMLSACHRGRSMVEKLVVEYGLDIVQRSMYGIQAAAEKAVRDVLKAFSVqnsqKPLKAIDYMDDGTPLQLEVKIDPETgdAVFDFEGTGPEVYG 743 *********************************************9877766777899********************99*************** PP Hydantoinase_B 269 niNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfgg 363 n+Nap a+t+s viy+lr+++++diplNeGcl+pie+++p+ ++lnpse+aavvggnv+tsqr++dv+lka++ ++Aasqg+mnnltfg CUFF.42.1.p1 744 NWNAPIAITYSSVIYCLRSIINQDIPLNEGCLKPIEIRIPPSCFLNPSETAAVVGGNVLTSQRITDVILKAFS------ICAASQGCMNNLTFGY 832 *************************************************************************......***************7 PP Hydantoinase_B 364 vderggeffgyyetiagGsGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserr 458 e+g+e f++yetiagG+GA+p+++G+s+vh+hmtntr+td+E++Err Pv+++rf lr++sgG+G+y+GGdGv+r++ef+++ +++silserr CUFF.42.1.p1 833 DGENGEEGFAMYETIAGGAGAGPTWNGTSGVHTHMTNTRITDPEVVERRAPVILRRFCLRENSGGKGEYHGGDGVIRHFEFRRS-MHCSILSERR 926 777779999**************************************************************************7.********** PP Hydantoinase_B 459 vfapwGlaGGepGargrvvlnllvr......greenlggkatvelkagdvlvietpGGGGyGd 515 + ap+G++GGe+Ga+g n+++ r +nlggk++v + +gd +vietpGGGGyG CUFF.42.1.p1 927 SRAPYGMNGGEDGAMGV---NTWIDcsnpdfPRYVNLGGKNHVLMGKGDHIVIETPGGGGYGA 986 *****************...99999999999*******************************6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (516 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 420.56 // Query: Hydant_A_N [M=178] Accession: PF05378.12 Description: Hydantoinase/oxoprolinase N-terminal region Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-66 214.0 1.6 1.1e-64 210.0 0.0 2.4 2 CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+ Domain annotation for each sequence (and alignments): >> CUFF.44.1.p1 type:complete gc:universal CUFF.44.1:232-4185(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 210.0 0.0 1.1e-66 1.1e-64 1 178 [] 4 220 .. 4 220 .. 0.98 2 ! 2.4 0.6 0.0062 0.59 2 14 .. 325 337 .. 324 355 .. 0.82 Alignments for each domain: == domain 1 score: 210.0 bits; conditional E-value: 1.1e-66 Hydant_A_N 1 rigIDvGGTfTDavaldeke.eevavlKllst.....pdavaegirealeevleesipr.....tskidvvrmGTTvatNallerkgervaLittkg 86 +i+ID+GGTfTDa+a+ ++e + +v+Klls+ +da +e++r++le v+++sipr ts+i+++r+GTTvatNallerkger+a+ittkg CUFF.44.1.p1 4 KIHIDRGGTFTDAIATFADEsRPPIVIKLLSEdpsnyKDASIEAVRRILEIVQGKSIPRtekldTSCINHLRCGTTVATNALLERKGERCAFITTKG 100 699************998777999************************************************************************* PP Hydant_A_N 87 frdlleigrqnrpdlfelrikkplvlyeevvevdervead............................gevlkpldeeevrealkalkaagvesiav 155 f+d l ig+q+rp++fel i++p+vly++v+evderv+++ ++++k++d++++r++l+al+++g++siav CUFF.44.1.p1 101 FKDGLLIGNQSRPNIFELGIRRPEVLYSKVIEVDERVTLEdyvedpmkvkttidgsdpslvvgrsgevVRIMKKVDCDALRKDLQALYDEGFTSIAV 197 ***************************************99******************************************************** PP Hydant_A_N 156 vllhSylnpehElrvaeiareig 178 +l+hS+++p+hEl v++ia+e+g CUFF.44.1.p1 198 CLAHSFTFPDHELLVGKIAEEVG 220 ********************975 PP == domain 2 score: 2.4 bits; conditional E-value: 0.0062 Hydant_A_N 2 igIDvGGTfTDav 14 ig D+GGT TD+ CUFF.44.1.p1 325 IGFDMGGTSTDVS 337 899********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (178 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 911.20 // Query: IBR [M=62] Accession: PF01485.20 Description: IBR domain, a half RING-finger domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00056 12.8 2.4 0.0012 11.8 2.4 1.4 1 CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+ Domain annotation for each sequence (and alignments): >> CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.8 2.4 1.2e-05 0.0012 10 51 .. 569 611 .. 561 613 .. 0.71 Alignments for each domain: == domain 1 score: 11.8 bits; conditional E-value: 1.2e-05 IBR 10 kslesdpnlkwCprpdCeaiiekseg...cksvtCskCgfefCfn 51 ++ ++++++ C C i ++ e ++ +Cs+C +e+C++ CUFF.12.1.p1 569 TTQNNNESFAVCL--ACAIIQRSLERkklSTPTQCSSCFQEYCWD 611 33455777999*9..9997776555544445578**********6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (62 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1041.24 // Query: Lung_7-TM_R [M=295] Accession: PF06814.12 Description: Lung seven transmembrane receptor Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-08 25.0 18.7 8e-08 24.4 18.7 1.4 1 CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953( Domain annotation for each sequence (and alignments): >> CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 24.4 18.7 8.4e-10 8e-08 59 258 .. 80 270 .. 26 288 .. 0.83 Alignments for each domain: == domain 1 score: 24.4 bits; conditional E-value: 8.4e-10 Lung_7-TM_R 59 vllgilWlfilakykkdilkiqkliaavivlkmlelaf.vyieYatinskGssievlavlasilsalkktlsrlliliislGygivkpkLgdllkkvl 155 +l+ W++ ++ + k i++ qk+i + i+l +l++ + ie ++++s+ + ++ +++i+ l+ + rl ++ +lG+gi ++ + k l CUFF.6.1.p1 80 LLFLSYWIWTCLHFSKIIFPAQKVICLYIFLFALNQTLqECIEEYVFSSECIKYRQFYSVYEIIDFLRTNFYRLFVIYCALGFGITRT-----VPKYL 172 466778*******************9999887776655167899999**************************************865.....66666 PP Lung_7-TM_R 156 llglllfvla.evlelvresseesessakllkvllfliplalldlffvvwifrsLqktlrdlklkrnlvklklYrkftvvlvisvvasviivlvekil 252 ++ ++ +v+a + + + ++ ++++ +i+ + ++ v+++ +L k + + n k++ +r+ +++ ++ + as + ++++i+ CUFF.6.1.p1 173 MIKGISIVIAlCSVYWISLYKDVYVV-----SEIFDMIQYEVS-PAIWVYSICHLLKQCTSVTTYENASKARFFRRMLNAFIFIFCASPMLHYLSNII 264 66555544441455555555444444.....689999999666.578888999********************************************9 PP Lung_7-TM_R 253 lktvds 258 + ++d+ CUFF.6.1.p1 265 FGNFDY 270 988775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (295 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 524.71 // Query: malic [M=182] Accession: PF00390.18 Description: Malic enzyme, N-terminal domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-20 66.1 0.0 2.4e-20 65.7 0.0 1.1 1 CUFF.1.1.p1 type:5prime_partial gc:universal CUFF.1.1:3-368( Domain annotation for each sequence (and alignments): >> CUFF.1.1.p1 type:5prime_partial gc:universal CUFF.1.1:3-368(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 65.7 0.0 2.5e-22 2.4e-20 3 76 .. 32 108 .. 30 110 .. 0.95 Alignments for each domain: == domain 1 score: 65.7 bits; conditional E-value: 2.5e-22 TECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGET..CHHHHHTTSS..SS..EEEEE-SS CS malic 3 knetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdke..kikeilknlp.eedvkvivvtdge 76 +n+tlfy+l++++l e++pi+YtPt g+a++++s++yr+++g+yl+i++++ ik++l+++ +++v++i++td+e CUFF.1.1.p1 32 TNQTLFYALISQHLIEMIPIIYTPTEGDAIKQFSDIYRYPEGCYLDIDHSDlsYIKQQLSEFGkSDSVEYIIITDSE 108 799*******************************************99988779********97899********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (182 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 2237.55 // Query: Mannosyl_trans3 [M=275] Accession: PF11051.7 Description: Mannosyltransferase putative Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00023 13.1 1.3 0.00039 12.4 1.2 1.5 1 CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747( Domain annotation for each sequence (and alignments): >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.4 1.2 4.1e-06 0.00039 92 143 .. 171 223 .. 85 298 .. 0.70 Alignments for each domain: == domain 1 score: 12.4 bits; conditional E-value: 4.1e-06 Mannosyl_trans3 92 sFeevllLDaDnvplknpdklFese.eYkktglllw.kdrdlwkrstspkfyei 143 F+++ ++D+D +++kn+d++F+++ Y++ ++l + + ++++k +++ y++ CUFF.51.1.p1 171 QFDKICVIDSDILIMKNIDDIFDTPyMYQQINTLNYtRLPSYTKPD-DDTVYHF 223 69*********************97358888888882224443333.4444444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 646.79 // Query: MatE [M=161] Accession: PF01554.17 Description: MatE Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-64 206.6 23.8 7.4e-38 122.3 4.7 2.3 2 CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907( 9e-64 206.6 23.8 7.4e-38 122.3 4.7 2.3 2 CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+ Domain annotation for each sequence (and alignments): >> CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 122.3 4.7 1.6e-39 7.4e-38 1 161 [] 17 177 .. 17 177 .. 0.99 2 ! 89.9 11.1 1.5e-29 6.9e-28 4 159 .. 240 396 .. 239 398 .. 0.98 Alignments for each domain: == domain 1 score: 122.3 bits; conditional E-value: 1.6e-39 MatE 1 PialenllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseq 96 P++l ++l+++l++ +++++grlg+++l+++++a ++++ +++ ++lg ta +tl ++ +Ga+++++++ l++g+i+l +l+l+i+l+ +++s++ CUFF.38.1.p3 17 PVILGYALQNSLQTSSVIVTGRLGPSELSVAAFAYMFAMSTGWlIALGGTTAFDTLGSNLWGAGKKQELGILLQTGFIVLSILYLPICLV-WWYSKP 112 99****************************************************************************************.****** PP MatE 97 ilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161 il +++q++e++e+++++lr+li+g ++++++++l+++l+++++t+++ yi+l++++ln+ ln+l CUFF.38.1.p3 113 ILIFLHQTPELAEASQKFLRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFL 177 ***************************************************************86 PP == domain 2 score: 89.9 bits; conditional E-value: 1.5e-29 MatE 4 lenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilsl 100 +++ +e++ + i+ l++g+lg++ lAa s+ +++ +ll ++++gl++ ++ +v+++lGa+ +++a+ ++ ++ i++++++ +i++ +++ +++ ++ CUFF.38.1.p3 240 VMVGTEWWAFEIVALVAGKLGAVPLAAQSVIMTTDQLLNTIPFGLGIITSNRVAYYLGAGLPDNASLTAKVAAIVGVAVGSVIMITMIAVRNIYGRI 336 667789******************************************************************************************* PP MatE 101 ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159 ft+d++v++l++ +++++ +++ ++l+ + g+lrg+g++kv++++++ ++ l+ +pl+ CUFF.38.1.p3 337 FTNDPDVIQLVALVMPLVAAFQISDSLNGTMGGALRGTGRQKVGAIVNITAYyLFALPLG 396 *******************************************************99997 PP >> CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 122.3 4.7 1.6e-39 7.4e-38 1 161 [] 17 177 .. 17 177 .. 0.99 2 ! 89.9 11.1 1.5e-29 6.9e-28 4 159 .. 240 396 .. 239 398 .. 0.98 Alignments for each domain: == domain 1 score: 122.3 bits; conditional E-value: 1.6e-39 MatE 1 PialenllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseq 96 P++l ++l+++l++ +++++grlg+++l+++++a ++++ +++ ++lg ta +tl ++ +Ga+++++++ l++g+i+l +l+l+i+l+ +++s++ CUFF.39.1.p1 17 PVILGYALQNSLQTSSVIVTGRLGPSELSVAAFAYMFAMSTGWlIALGGTTAFDTLGSNLWGAGKKQELGILLQTGFIVLSILYLPICLV-WWYSKP 112 99****************************************************************************************.****** PP MatE 97 ilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161 il +++q++e++e+++++lr+li+g ++++++++l+++l+++++t+++ yi+l++++ln+ ln+l CUFF.39.1.p1 113 ILIFLHQTPELAEASQKFLRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFL 177 ***************************************************************86 PP == domain 2 score: 89.9 bits; conditional E-value: 1.5e-29 MatE 4 lenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilsl 100 +++ +e++ + i+ l++g+lg++ lAa s+ +++ +ll ++++gl++ ++ +v+++lGa+ +++a+ ++ ++ i++++++ +i++ +++ +++ ++ CUFF.39.1.p1 240 VMVGTEWWAFEIVALVAGKLGAVPLAAQSVIMTTDQLLNTIPFGLGIITSNRVAYYLGAGLPDNASLTAKVAAIVGVAVGSVIMITMIAVRNIYGRI 336 667789******************************************************************************************* PP MatE 101 ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159 ft+d++v++l++ +++++ +++ ++l+ + g+lrg+g++kv++++++ ++ l+ +pl+ CUFF.39.1.p1 337 FTNDPDVIQLVALVMPLVAAFQISDSLNGTMGGALRGTGRQKVGAIVNITAYyLFALPLG 396 *******************************************************99997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (161 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 22 (0.231579); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 774.99 // Query: MDM31_MDM32 [M=525] Accession: PF08118.10 Description: Yeast mitochondrial distribution and morphology (MDM) proteins Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00098 10.4 0.1 0.0016 9.7 0.1 1.2 1 CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+ Domain annotation for each sequence (and alignments): >> CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 9.7 0.1 1.7e-05 0.0016 365 448 .. 134 218 .. 124 228 .. 0.68 Alignments for each domain: == domain 1 score: 9.7 bits; conditional E-value: 1.7e-05 MDM31_MDM32 365 eeevtskkaleeeekseelakeaks.aeeseeekeeeeekeeeeeekyvvvdlklklndvkAavPlftkdlsyvnnaliRpivay 448 e++++k+++ ++ +++++++a+s a++s + + + + + +++ k v ++klnd A++P ++ +s ++a Rp v++ CUFF.20.1.p1 134 VEKISQKNQEARSRANSRVNSRANSrANSSVSLAGMDGSPNWKRKMKSAVFGSRVKLNDEEAQLPRNKSSVSIAEQAASRPKVSF 218 33344443333333333444333330333444444555666678889999*********************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (525 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1657.85 // Query: MFS_1 [M=353] Accession: PF07690.15 Description: Major Facilitator Superfamily Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-41 135.1 27.5 1.4e-41 135.1 27.5 1.6 2 CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+ 1.3e-39 128.6 21.0 1.3e-39 128.6 21.0 1.5 2 CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280( 1.3e-23 76.0 37.2 3.5e-17 54.9 16.8 2.3 2 CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) 1.8e-20 65.7 28.3 1.3e-16 53.0 19.0 2.1 2 CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+ Domain annotation for each sequence (and alignments): >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 135.1 27.5 5.9e-43 1.4e-41 2 349 .. 113 492 .. 112 497 .. 0.82 2 ? -1.5 0.1 0.2 4.8 230 256 .. 500 529 .. 493 543 .. 0.53 Alignments for each domain: == domain 1 score: 135.1 bits; conditional E-value: 5.9e-43 MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltl.yalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGl 97 +++++++++a+s++++ + +a++l++s +++l ++ + +g++v+slp+++lsd +Gr +++++ll+f ++ + + a+++w+l+++r++qG+ CUFF.37.1.p1 113 SVITIVVTFASSVYSSGII-DIASELHSSIP-VSTLGSCtFLVGFGVGSLPFAPLSDIYGRFIIYFVTLLIFTIFQVGGGCAHNVWTLAIVRFFQGV 207 56889999**********9.9******5555.56666664888********************************6666645*************** PP MFS_1 98 gagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeee..... 188 ++++ +++++ i+d+f++ +r+ ++ + ++ lG+i+gp++g +++ s+l Wr++f+i+ i ++ ++v++++++pe++ + + +++ + CUFF.37.1.p1 208 FGSTPLANAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIGPIIGDFITqSYLEWRWTFWINMIWAAAVIVFVFIFFPETHEDTILDYKAKYLrkttg 304 ************************************************99999*********************************999999***** PP MFS_1 189 ..........kgtgpaplvp....awkallkdpvlwillialllfffgfsglltllplylqevlgls.glllaglllallalvgail....allagr 266 +++ + ++++ a +++++ p + +++ l++ +++++ + ++ +g++ g +++ +++++ +++++ ++ + + CUFF.37.1.p1 305 ntayytiherERDPKNAMIQaatqAVSLIFTEPIVV-CFTLYLTVVYIINYINFEGYPIVFAKYGFNkG-EQGLSFIGVGVGIVCAGlctpFIYWHY 399 ******9999777777777789999********554.44444444444444444444446888899984.555555555555544444444888888 PP MFS_1 267 ls.dr.....lgrrrrlllallllllaalglallavt...ssavllll..vlvliGf.glgfvfpsllalasdlappeeagtasglfntagslgg 349 l ++ + ++ rl+ +++++l+ ++++++a+t ++ ++++ +++++Gf l ++f+s++++++++ ++a +a+++++++++ ++ CUFF.37.1.p1 400 LKvNKkrngvICPEDRLYPLFIGCFLLPISMFWFAWTcypHHIHWIVPiiASAFFGFsLLIVFFVSYNYIIDSYQ--HMAPSALAAATLVRYSAS 492 8766666666555************************98855555544558888***888888899888888888..999999999998877443 PP == domain 2 score: -1.5 bits; conditional E-value: 0.2 MFS_1 230 lplylqevlgls....glllaglllallalv 256 p+yl+ +++ g +++++++++++++ CUFF.37.1.p1 500 RPMYLNLGDHWAtsvlG-FISVAMVPIPFIF 529 57777777777744443.3333333333333 PP >> CUFF.45.1.p2 type:complete gc:universal CUFF.45.1:4776-3280(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 128.6 21.0 5.6e-41 1.3e-39 2 352 .. 66 429 .. 65 430 .. 0.87 2 ? -2.4 0.0 0.39 9.4 282 296 .. 450 464 .. 440 476 .. 0.44 Alignments for each domain: == domain 1 score: 128.6 bits; conditional E-value: 5.6e-41 MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlg 98 +++++++l+rs++g a+ ++e+l + + ++ +++++++++++ p +l+ r+ + r+l + ++++ ++l+ f ss+ l++ r++ Gl CUFF.45.1.p2 66 GFLYLMAFLDRSNIGNAAVAGMTEALSLYGERLNVAVSIFYVLYILVETPSVVLVKRIKASRMLAFISFAWSMTVLFSGFMSSYGGLIATRLILGLL 162 6899******************************************************999988888888888834444536666************ PP MFS_1 99 agalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg....Wravfyilaivsllafvlfllllpeepperkrkspkeee.. 188 +g+lfpa + +++ ++++e+ + +++l a+++l+ ++g l++ +l ++g W++++++ ++vs++++ l l+ lp++ + + + +e+e CUFF.45.1.p2 163 EGCLFPALNLYLTTHYTRKEQCQRLSYLFASAGLAGAFGGLFAYALEqVHAGnkegWQWIYIVEGLVSFIGVPLCLFALPDKMENAWFLTREEREva 259 ********************************************999666669******************776555555555555555555555** PP MFS_1 189 ..........kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275 +g +++++++ ++ +kdp +++ ++ +++ ++++g++++lp++ + lg+ g l++ ++ ++++g+i++l++++lsdr++ CUFF.45.1.p2 260 iirrdinaryHGEQHFEWSE-VRKAFKDPKVYVSATSQFCADMVLYGFSSFLPVI-IKGLGFVG-LQTNYMTIPVYIAGVISFLFVAWLSDRTQL-- 351 ********************.888888888878*********************7.*******8.888889999999999************776.. PP MFS_1 276 rlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdla.ppeeagtasglfntagslggalg 352 r + +++ +++a+g++++ +++s+++ + + ++i +g + ++ l ++++++ + +++ta+g+ +t+ + +g+++ CUFF.45.1.p2 352 RAVYLISASTVVAVGYIIMLASDSNAAKYTATYIIAIGCYIGPGLNLGWLNNNVaGHYKRATAIGIQQTLANSSGIVA 429 88889999999999999999998999999988887775555566666666665546689*********9999999987 PP == domain 2 score: -2.4 bits; conditional E-value: 0.39 MFS_1 282 lllllaalglallav 296 ++++++ l+++++ + CUFF.45.1.p2 450 GCVIVGGLAYVVMFF 464 222222222222222 PP >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 54.9 16.8 1.5e-18 3.5e-17 2 263 .. 92 349 .. 85 361 .. 0.77 2 ! 26.7 12.4 5.4e-10 1.3e-08 212 353 .] 370 516 .. 357 516 .. 0.76 Alignments for each domain: == domain 1 score: 54.9 bits; conditional E-value: 1.5e-18 MFS_1 2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslwlllvlrvlqGl 97 l + + sa+++s++++ + + +++ s i++l + a+ ++v ++lG +sd +r ++ l ll++++g ++ + + s++ + +++ v+ ++ CUFF.25.1.p1 92 LACSWASAIQSSTTYSYQV-YATASFN-RTSMISTLEIATAIISSVCKPILGKFSDITSRPMTYTLVLLFYVIG-FIVVASsSTISAYVIGSVFISI 185 5677778888888777777.8999999.88889999999******************96666************.55552446677*********** PP MFS_1 98 gagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslgWravfyilaivsllafv.lfllllpeepperkrkspkeee.... 188 g+++l + ++ d+++ + rg++++lls+ + + + g ++ g++ +Wr+ + ++ai++ ++ +++l++ e+ ++k ++ k+ CUFF.25.1.p1 186 GSSGLDYLNTLVVGDLTSLKWRGFMTALLSTPYIATVwFTGFIVQGIID--SNWRWGYGMFAIIMPAVMTpAVIILMYLERQANKDENIKKIInyqt 280 *************************************666677777777..45*****999999999955533444444444444444333335577 PP MFS_1 189 ...kgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqevlglsglllaglllallalvgailall 263 ++ +++++ ++wka+l l+ +ll+ +g+s+ l + l++y g+++ +++ +++++ v++i+ CUFF.25.1.p1 281 eekNKNKQSKWQKLWKAVLEVD----LFGLILLG-VGWSIllLPFSLTSY--AKNGWKNPSMIA--MMVVGGVILIA--Y 349 77788999999999*****999....44444444.366665588888887..777777335555..77777776666..4 PP == domain 2 score: 26.7 bits; conditional E-value: 5.4e-10 MFS_1 212 llialllfffgfsg....lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallll.llaalglallavt.ssavl 302 +i+++++ f++++ ++++++y+ +++s + +++ + ++ ++++++ag++++ + r ++l +++l++ ++++ +l+ +++ + +v CUFF.25.1.p1 370 TFITAVIIDFFYYLagylQSMYFTTYTWILYDWS-YRDWTYFNNTMTIALCVFGVFAGAMHRVFHRYKYLQIIGLVIkIVGYGILIRPNFAaTGKVD 465 3444444444444445558889999999******.55555556666666666689999999998887766655555505555555555555999999 PP MFS_1 303 lllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353 l+++l+liG+g++f ++ +++ ++ ++p + + as+l ++ ++gga+g+ CUFF.25.1.p1 466 LAWSLILIGMGGSFSVVGSQVSCQASVPHQDLAIASSLLPLYTNIGGAIGA 516 999**********************************************96 PP >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 53.0 19.0 5.4e-18 1.3e-16 23 293 .. 47 347 .. 6 350 .. 0.71 2 ! 26.7 11.5 5.6e-10 1.3e-08 3 201 .. 267 475 .. 266 507 .. 0.74 Alignments for each domain: == domain 1 score: 53.0 bits; conditional E-value: 5.4e-18 MFS_1 23 laedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpke 117 +++++ +s+ + ll+++ +g+++++++ +++++r+G + +++ +++++ lll + a ++w +lv+ +l+G+g gal ++ + ++++p++ CUFF.24.1.p1 47 ISNSYSYSAWRQALLTGTINAGCLFGAMLSSPFTERIGKKYSICFFSGVYIIAeLLLVT-AVPSWiQVLVGKILAGVGIGALSVLSPGYQSEVAPPQ 142 24444466666888999999*********************************666666.567787******************************* PP MFS_1 118 ergraigllsagfslGailgpllgg...llasslgWravfyilaivsllafvlfllllpeepperkrkspkeee....................... 188 rg +++ +++++ +a++++ + l ++Wr +f i+ + ++l++v ++l+lpe+p+ k ee CUFF.24.1.p1 143 IRGAVVATYQIFSTGAALVAACINMgthKLRKTASWRTSFGINMLWGILLMV-GVLFLPESPRYLIYKGRDEEAlrimcnmaelspeseiiqtnfnt 238 ***********999999999888772323335555***************88.558888888888887777776*******9888887777666666 PP MFS_1 189 ........kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrl 277 g+a w +++ + + +++l++ f + + + y+ +v++ +g + l +l++++++ + a + +d lgrr++l CUFF.24.1.p1 239 iksdieieMAGGKA----RWIEIFGKDIRYRTCLGFLVMLFRELIGNNYYFYYATQVFKGTGMTDIFLPAVILGAINFGTTFGALYTIDNLGRRNPL 331 65555444344444....4444555553322333333333333334444444455555555533444446777777777676666667********* PP MFS_1 278 llallllllaalglal 293 +++ ++ +++++++a CUFF.24.1.p1 332 IFGAAFQSICFFIYAA 347 ************9986 PP == domain 2 score: 26.7 bits; conditional E-value: 5.6e-10 MFS_1 3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrl..sdrfGrrrvlllglllfalglllll.fa............s 83 +++fl++l r ++g ++ + ++ + ++ + +l + + lga+ + +G+l +d++Grr l++g+++ ++++++ + ++ + CUFF.24.1.p1 267 CLGFLVMLFRELIGNNYYFyYATQVFKGTGMTDIFLPA-VILGAINFGTTFGALytIDNLGRRNPLIFGAAFQSICFFIYAaVGdrkliykngtsdH 362 67889999999999999987888888855555555444.556666666666655569*******************555552314444455555664 PP MFS_1 84 slw.lllvlrvlqGlgagalf.pagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178 +++v+ +l + +++++ p+g +++ + fp + r++ +++++g+ lG + + +++ ++g+ + ++ ++i ++ +f+ +++++++++ CUFF.24.1.p1 363 RAGsVMIVFSCLFLFSYCCSWgPMGWVIVGETFPIRYRSKCASVATSGNWLGNFMISFFTPFINNAIGFKLGYIYACINLFSSFM---IFFLAKETK 456 45556777777777777666537777999*****************************************998888888888877...677677766 PP MFS_1 179 rkrkspkeeekgtgpaplvpawk 201 + +++ ++ ++++p w+ CUFF.24.1.p1 457 GLTLEEVNDL---YMSNIKP-WE 475 6666666663...4444444.44 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 27 (0.284211); expected 1.9 (0.02) Passed bias filter: 9 (0.0947368); expected 1.9 (0.02) Passed Vit filter: 5 (0.0526316); expected 0.1 (0.001) Passed Fwd filter: 4 (0.0421053); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.12u 0.02s 00:00:00.13 Elapsed: 00:00:00.12 # Mc/sec: 85.19 // Query: MFS_3 [M=522] Accession: PF05977.12 Description: Transmembrane secretion effector Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.0022 9.0 5.5 0.0033 8.4 5.5 1.2 1 CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+ Domain annotation for each sequence (and alignments): >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 8.4 5.5 3.5e-05 0.0033 258 364 .. 60 168 .. 49 202 .. 0.73 Alignments for each domain: == domain 1 score: 8.4 bits; conditional E-value: 3.5e-05 MFS_3 258 illgalGvGAilgalllsrLRerlsser.lvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavql.avPrWvvgRalavYltvl 352 +l g++ +G ++ga+l+s er++++ + + v + + ll ++ ++s ++++ +l+G i als l q + P ++g ++a Y+ + CUFF.24.1.p1 60 LLTGTINAGCLFGAMLSSPFTERIGKKYsICFFSGVYIIAELLLVTAVPSWIQVLVGKILAG-VGIGALSVLSPGYQSeVAPPQIRGAVVATYQIFS 155 688999******************98861555666665555555555555555555555555.56********9999735699************** PP MFS_3 353 aGg.laaGsllWG 364 +G+ l a + G CUFF.24.1.p1 156 TGAaLVAACINMG 168 9972455555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (522 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 972.65 // Query: MFS_4 [M=363] Accession: PF06779.13 Description: Uncharacterised MFS-type transporter YbfB Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-06 18.6 6.1 1.6e-05 16.9 0.5 2.7 3 CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+ Domain annotation for each sequence (and alignments): >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.2 0.2 0.053 5.1 146 206 .. 101 156 .. 98 157 .. 0.65 2 ! 16.9 0.5 1.7e-07 1.6e-05 38 175 .. 152 288 .. 132 311 .. 0.84 3 ! 4.3 0.1 0.0012 0.11 119 144 .. 374 399 .. 365 405 .. 0.85 Alignments for each domain: == domain 1 score: -1.2 bits; conditional E-value: 0.053 MFS_4 146 sasslWlalavlsavllllvalllpraalreasaaaeaakaeqkslpllalllaYglaGfG 206 s s W+++ +s++ +++ ++ + + ++++s+p+ l +l+GfG CUFF.37.1.p1 101 SHSYKWWIVIQVSVITIVVTFASSV---YSSGIIDIA--SELHSSIPVSTLGSCTFLVGFG 156 5566699999999998888877665...333333333..3677777777777777777776 PP == domain 2 score: 16.9 bits; conditional E-value: 1.7e-07 MFS_4 38 ylGYLvGallaafalsagaeRlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiavs 133 ++G+ vG+l + ls R + ll ++ + ++++++++++++Rf Gv + + l ++ ++ ++ +r v+ + + lG +++ CUFF.37.1.p1 152 LVGFGVGSLPF-APLSDIYGRFIiYFVTLLIFTIFQVGGGCAHNVWTLAIVRFFQGVFGSTPLANAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIG 247 57999999988.677888888884567778888899999*********************************************99999******** PP MFS_4 134 gllvllllqlglsasslWlalavlsavllllvalllpraalr 175 ++ ++ q l++ ++ ++ + +a++++ v++ p + ++ CUFF.37.1.p1 248 PIIGDFITQSYLEWRWTFWINMIWAAAVIVFVFIFFP-ETHE 288 ****************977777889999999999999.3333 PP == domain 3 score: 4.3 bits; conditional E-value: 0.0012 MFS_4 119 gallfaGvGlGiavsgllvllllqlg 144 ++l f GvG+Gi+ +gl+ +++ + CUFF.37.1.p1 374 QGLSFIGVGVGIVCAGLCTPFIYWHY 399 6899*************999887665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 539.46 // Query: MIP [M=227] Accession: PF00230.19 Description: Major intrinsic protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-51 167.6 6.0 2.3e-51 167.2 6.0 1.1 1 CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+ Domain annotation for each sequence (and alignments): >> CUFF.20.1.p1 type:complete gc:universal CUFF.20.1:908-2704(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 167.2 6.0 2.4e-53 2.3e-51 6 227 .] 308 548 .. 303 548 .. 0.91 Alignments for each domain: == domain 1 score: 167.2 bits; conditional E-value: 2.4e-53 HHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHH CS MIP 6 kflravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisllrailYivaQllG 102 +f r+ +AEfl+tl+lv++gvgs+l+ +v++ + +++e+ ++a+g++ + +vy+a+giSG+H+NPavT++l+++rk++ ++++Yi Q+ G CUFF.20.1.p1 308 HFFREGFAEFLGTLVLVVFGVGSNLQA--TVTN---GAGGSFESLSFAWGFGCMLGVYIAGGISGGHVNPAVTISLAIFRKFPWYKVPIYIFFQIWG 399 6899******************99844..3433...34579******************************************************** PP HHHHHHHHHHHCHHH............HHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHH CS MIP 103 aivaaallklltkgl............esraglfanslkpglsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgiplt 187 a+ + al ++ + + g + +kp+++ +a++ E+i t+vLv ++fa+ dd+++ + +++ +gll+a+i ++ +++t CUFF.20.1.p1 400 AFFGGALAYGYHWSSitefeggkdirtPATGGCLYTNPKPYVTWRNAFFDEFIGTAVLVGCLFAILDDTNSPPTQGMTAFIVGLLIAAIGMALGYQT 496 *********99988889******9976556666678899*********************************99899******************** PP ST-SSHHHHHHHHHHHTH............STTTTHHHHHHHHHHHHHHHHH CS MIP 188 GaamNpArslgpavvlnk............fedhwvylvGPliGailgalvY 227 +++NpAr+lgp+++++ + w + G + G+i+g+l+Y CUFF.20.1.p1 497 SFTLNPARDLGPRMFAWWigygphsfhlyhWWWTWGAWGGTIGGGIAGGLIY 548 *************************98855555566788999999999**99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (227 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1283.06 // Query: MVP_shoulder [M=118] Accession: PF11978.7 Description: Shoulder domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00057 12.5 0.0 0.0018 11.0 0.0 1.8 1 CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+ 0.00057 12.5 0.0 0.0018 11.0 0.0 1.8 1 CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+ Domain annotation for each sequence (and alignments): >> CUFF.60.1.p1 type:complete gc:universal CUFF.60.1:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.0 0.0 3.7e-05 0.0018 40 100 .. 65 124 .. 55 134 .. 0.84 Alignments for each domain: == domain 1 score: 11.0 bits; conditional E-value: 3.7e-05 HTSSGSHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHTTHHHHHGGGSB---EESS-EEEE CS MVP_shoulder 40 eklFsvedfvgdackalasrvRgavasvtfdeFhknsakiireavfgvdeegevrkellfe 100 +k F ++ +++d +++++s g a+ +f +F k+++++ rea f+ +++++++++ ++ CUFF.60.1.p1 65 DKEFDLDYYLKDETESIQSPFEGFTAQPNFSNFNKQGNTMNREANFQ-RTNEKIQRNKSIK 124 57799999**************************************9.5555555554444 PP >> CUFF.60.2.p1 type:complete gc:universal CUFF.60.2:311-2842(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.0 0.0 3.7e-05 0.0018 40 100 .. 65 124 .. 55 134 .. 0.84 Alignments for each domain: == domain 1 score: 11.0 bits; conditional E-value: 3.7e-05 HTSSGSHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHTTHHHHHGGGSB---EESS-EEEE CS MVP_shoulder 40 eklFsvedfvgdackalasrvRgavasvtfdeFhknsakiireavfgvdeegevrkellfe 100 +k F ++ +++d +++++s g a+ +f +F k+++++ rea f+ +++++++++ ++ CUFF.60.2.p1 65 DKEFDLDYYLKDETESIQSPFEGFTAQPNFSNFNKQGNTMNREANFQ-RTNEKIQRNKSIK 124 57799999**************************************9.5555555554444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (118 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 765.86 // Query: Na_H_Exchanger [M=381] Accession: PF00999.20 Description: Sodium/hydrogen exchanger family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-42 138.8 8.5 1.3e-42 138.5 8.5 1.1 1 CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) 3.7e-27 87.6 2.1 4.1e-27 87.5 2.1 1.0 1 CUFF.13.1.p2 type:3prime_partial gc:universal CUFF.13.1:1414 8.2e-16 50.3 1.9 1.1e-15 49.8 1.9 1.1 1 CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-58 Domain annotation for each sequence (and alignments): >> CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 138.5 8.5 4.2e-44 1.3e-42 1 198 [. 83 291 .] 83 291 .] 0.97 Alignments for each domain: == domain 1 score: 138.5 bits; conditional E-value: 4.2e-44 XHHHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS...........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHH CS Na_H_Exchanger 1 ivllillallvgl..l.arrlklpeivgliiaGlllGpsglglieps......eedlevlselglilllFlaGleldlrelrknlksilllallg 86 iv+++++++++++ + ++l ++e v+ i+Gl++Gp+ +l++p ++ + ++++++l + +F++++el+ +++++n++si++++l++ CUFF.13.2.p1 83 IVAGGFITFFCYFseVfRKKLLVGEAVLGSITGLIFGPHAAKLVDPFswgdhgDYLTVEICRIVLDVRVFASAIELPGAYFQHNFRSIIVMLLPV 177 6889999******997799999********************99999************************************************ PP HHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSX CS Na_H_Exchanger 87 vlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavvllavllalakeeaggetslll 178 ++ +++++ ++y+ l+++i++l +ll++++++ tdpv+ + i+ ++++per+++ll++es++nD++av++++++++l++ + +++++ ++ CUFF.13.2.p1 178 MAYGWLVTAGFAYA-LFPQINFLGSLLIAGCITSTDPVLSALIVGegpLAKKTPERIRSLLIAESGCNDGMAVPFFYFAIKLLTVKPSRNAGRDW 271 **********9**8.69***************************988889**********************************99********* PP HHHHHHHHHHHHHHHHHHHH CS Na_H_Exchanger 179 llliflvvavgglllglvig 198 +ll++l+++++g+++g+vig CUFF.13.2.p1 272 VLLVVLYECAFGIFFGCVIG 291 ******************97 PP >> CUFF.13.1.p2 type:3prime_partial gc:universal CUFF.13.1:1414-1770(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 87.5 2.1 1.3e-28 4.1e-27 82 198 .. 1 119 [] 1 119 [] 0.97 Alignments for each domain: == domain 1 score: 87.5 bits; conditional E-value: 1.3e-28 HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTS CS Na_H_Exchanger 82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavvllavllalakeeagge 173 ++l++++ +++++ ++y+ l+++i++l +ll++++++ tdpv+ + i+ ++++per+++ll++es++nD++av++++++++l++ + +++ CUFF.13.1.p2 1 MLLPVMAYGWLVTAGFAYA-LFPQINFLGSLLIAGCITSTDPVLSALIVGegpLAKKTPERIRSLLIAESGCNDGMAVPFFYFAIKLLTVKPSRN 94 67999*******9999998.79***************************988889**********************************99**** PP SSTSXHHHHHHHHHHHHHHHHHHHH CS Na_H_Exchanger 174 tslllllliflvvavgglllglvig 198 ++ +++ll++l+++++g+++g+vig CUFF.13.1.p2 95 AGRDWVLLVVLYECAFGIFFGCVIG 119 ***********************97 PP >> CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-584(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 49.8 1.9 3.6e-17 1.1e-15 1 93 [. 83 184 .. 83 185 .. 0.96 Alignments for each domain: == domain 1 score: 49.8 bits; conditional E-value: 3.6e-17 XHHHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS...........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHH CS Na_H_Exchanger 1 ivllillallvgl..l.arrlklpeivgliiaGlllGpsglglieps......eedlevlselglilllFlaGleldlrelrknlksilllallg 86 iv+++++++++++ + ++l ++e v+ i+Gl++Gp+ +l++p ++ + ++++++l + +F++++el+ +++++n++si++++l++ CUFF.13.3.p1 83 IVAGGFITFFCYFseVfRKKLLVGEAVLGSITGLIFGPHAAKLVDPFswgdhgDYLTVEICRIVLDVRVFASAIELPGAYFQHNFRSIIVMLLPV 177 6889999******997799999********************99999************************************************ PP HHHHHHH CS Na_H_Exchanger 87 vlitvvl 93 ++ +++ CUFF.13.3.p1 178 MAYGWIF 184 ****987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (381 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 20 (0.210526); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1198.64 // Query: NEMO [M=68] Accession: PF11577.7 Description: NF-kappa-B essential modulator NEMO Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00049 12.8 0.0 0.0014 11.3 0.0 1.7 1 CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+ Domain annotation for each sequence (and alignments): >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.3 0.0 1.5e-05 0.0014 22 55 .. 54 87 .. 50 98 .. 0.93 Alignments for each domain: == domain 1 score: 11.3 bits; conditional E-value: 1.5e-05 NEMO 22 lkqsNqalkeRlEeLsawqekqkeerefleeklr 55 lk N++lk+R+ e s ++ ee f + klr CUFF.54.1.p1 54 LKNANDSLKGRILEVSLADLQKDEEHSFRKVKLR 87 89**************************999998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (68 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1043.71 // Query: Nucleotid_trans [M=212] Accession: PF03407.15 Description: Nucleotide-diphospho-sugar transferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-05 15.8 0.0 9.9e-05 15.0 0.0 1.4 1 CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+ Domain annotation for each sequence (and alignments): >> CUFF.51.1.p2 type:complete gc:universal CUFF.51.1:317-1357(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 15.0 0.0 1e-06 9.9e-05 106 189 .. 238 318 .. 210 333 .. 0.81 Alignments for each domain: == domain 1 score: 15.0 bits; conditional E-value: 1e-06 Nucleotid_trans 106 desknliNsGfffvrateatkallkkwaeelase.sglw.DqdvfnlllregaakesglkvrvLdtalfvngkgyfvq.vrdeeevk 189 ++++n +N G + +r+++at +l+ w + + +e +++ +qd++ +l + + + v++++++++ + f + ++ e+ k CUFF.51.1.p2 238 SQDHNGLNAGSILFRNSPATALFLDIWTDPVVAEcAKANnEQDMLGYLISKHSQ--LASLVGLIPQRKI----NAFHEgPENMEWQK 318 4567888************************999855556*********99664..8888999999999....77777655555554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (212 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1659.67 // Query: Oleosin [M=113] Accession: PF01277.16 Description: Oleosin Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- ------ inclusion threshold ------ 0.037 6.4 6.6 0.007 8.8 1.0 2.3 3 CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) Domain annotation for each sequence (and alignments): >> CUFF.5.1.p1 type:complete gc:universal CUFF.5.1:207-713(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.3 0.0 0.21 20 87 107 .. 57 77 .. 47 82 .. 0.60 2 ? -0.2 0.1 0.045 4.3 35 46 .. 107 118 .. 104 127 .. 0.85 3 ? 8.8 1.0 7.4e-05 0.007 41 63 .. 141 163 .. 140 167 .. 0.86 Alignments for each domain: == domain 1 score: -2.3 bits; conditional E-value: 0.21 Oleosin 87 gadqldqakrrlaekasevke 107 +++++ k++++ k++++ke CUFF.5.1.p1 57 FTNTIKPQKDKMNIKTNKIKE 77 455555666666666666655 PP == domain 2 score: -0.2 bits; conditional E-value: 0.045 Oleosin 35 tPllvlfSPvlv 46 Pll++ S ++v CUFF.5.1.p1 107 WPLLIIWSIIIV 118 69*****99998 PP == domain 3 score: 8.8 bits; conditional E-value: 7.4e-05 Oleosin 41 fSPvlvPaaivialavagflasg 63 +S ++vP+ai + l+v ++l+ CUFF.5.1.p1 141 YSEIWVPIAIYVCLLVLMLLSLI 163 688*************9999864 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (113 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1125.09 // Query: Orthopox_A5L [M=271] Accession: PF06193.10 Description: Orthopoxvirus A5L protein-like Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.0058 8.6 4.9 0.008 8.2 4.9 1.2 1 CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-88 Domain annotation for each sequence (and alignments): >> CUFF.11.1.p1 type:5prime_partial gc:universal CUFF.11.1:3-884(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 8.2 4.9 8.4e-05 0.008 146 192 .. 3 49 .. 1 92 [. 0.77 Alignments for each domain: == domain 1 score: 8.2 bits; conditional E-value: 8.4e-05 Orthopox_A5L 146 ttpstqpsqtlPtttcvrqsdasistttdivtppqppivatvctptP 192 t t s tlP tt q+ +++s t +iv+p + p t + CUFF.11.1.p1 3 TVTETITSGTLPFTTTLAQASGTVSGTVEIVSPKNNPTTVYSGTVAT 49 56678899*************************98886543322222 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 2053.16 // Query: Oxidored_FMN [M=341] Accession: PF00724.19 Description: NADH:flavin oxidoreductase / NADH oxidase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-138 453.2 0.0 3.6e-138 453.0 0.0 1.0 1 CUFF.52.1.p1 type:complete gc:universal CUFF.52.1:1902-3080( 1e-136 448.2 0.0 1.1e-136 448.0 0.0 1.0 1 CUFF.48.1.p1 type:complete gc:universal CUFF.48.1:2695-3843( 1e-136 448.2 0.0 1.1e-136 448.0 0.0 1.0 1 CUFF.49.1.p1 type:complete gc:universal CUFF.49.1:2224-1076( Domain annotation for each sequence (and alignments): >> CUFF.52.1.p1 type:complete gc:universal CUFF.52.1:1902-3080(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.0 0.0 1.1e-139 3.6e-138 1 341 [] 12 360 .. 12 360 .. 0.99 Alignments for each domain: == domain 1 score: 453.0 bits; conditional E-value: 1.1e-139 CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 kLF+Pik+gn++L++R+v+ap+trlr+ ++g v++dl++eYy+qrs+ipgtl+ite++f+++ksggf+n p++++de++e+wk++++a+h+n++f++ CUFF.52.1.p1 12 KLFQPIKVGNMQLQHRMVHAPATRLRCLDNGLVMTDLVKEYYKQRSSIPGTLLITESLFSGAKSGGFSNIPCLYNDEHVEAWKPIVQAIHDNDCFVF 108 7************************************************************************************************ PP EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 +q+w+l++e+k++yl+d+e ++p+dp++l+a+ ++g+el k++tk++i+e+i++y+eAAkra+ +G+DgVe+h++nG+Lld+ CUFF.52.1.p1 109 IQFWNLPGELKVDYLEDQErlekvtqGECPMDPTGLPAALGsaysICGEELyvdKFMTKQDIQEHITTYTEAAKRAVFgCGADGVEVHQVNGFLLDK 205 *************************99************99999999999999******************************************** PP HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 F+ +++++++D+++ Gs+enRarF+le++++v++a+g+ervgyR+Sp+++++k++d++e+ +++++k++++r++ +la++h++epr++++g+v+ CUFF.52.1.p1 206 FVLNGYGDKCDPEYcGSLENRARFCLELLESVVNAIGQERVGYRISPFSDIWKDKDSFEA--HVFMIKKIKERFP---NLAYLHAIEPRQYWNGHVH 297 ************************************************************..*************...******************* PP CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 ++q+ kn+ ++k++w +p+it+G++d+++ a+++a++e+tlvafgR+fl++pdl+++lk+++pln CUFF.52.1.p1 298 ITQE-KNTLIYKNLWGDPFITAGGHDRDS--AIQMAEQENTLVAFGRYFLSNPDLPFRLKYNLPLN 360 **66.************************..********************************997 PP >> CUFF.48.1.p1 type:complete gc:universal CUFF.48.1:2695-3843(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.0 0.0 3.6e-138 1.1e-136 1 341 [] 6 353 .. 6 353 .. 0.99 Alignments for each domain: == domain 1 score: 448.0 bits; conditional E-value: 3.6e-138 CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 +LFkPik+gn+ L++Riv+apmtrlra+++g ++++l++eYysqrs+ipgtl+i++atfv++ksggf+n+p+++++eq+esw +l+eavhkn+sf++ CUFF.48.1.p1 6 ELFKPIKVGNMLLQHRIVHAPMTRLRATDYG-KITGLMVEYYSQRSMIPGTLLIADATFVGEKSGGFPNNPRCFTKEQAESWIPLVEAVHKNKSFLF 101 69*****************************.9999************************************************************* PP EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 +q+w l++++k+ey++d e +d+p+dp +l+a ++ ++g e+ k+++k++i+e+iq++v+AA++a++ A++DgVeih++nG+Lld+ CUFF.48.1.p1 102 IQFWPLPGDLKDEYRNDLEkmqkitySDCPQDPGGLPAGIHsfdaVQGVEVykkKYMSKRDIQEHIQDFVNAADLAVNiAKADGVEIHQVNGFLLDR 198 *************************9***************9999888888999******************************************* PP HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 F+ ++++++D+++ GsienR+rF+lev++av++++g+ervgyR+Sp++ +++++d++e+ ++yl++e++kr++ kla+ih++eprk+++g++ CUFF.48.1.p1 199 FVLGGFGDQCDPEYrGSIENRCRFPLEVLEAVTRKIGQERVGYRISPFSGWMQKIDFMEV--NIYLMSEIAKRFP---KLAYIHAIEPRKYWSGHKL 290 ************************************************************..*************...******************* PP CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 ++++ +n++f++k+wkgp+it+G++d e+ a+++a+++ lvafgR+f+a+pdlv+++k+++pln CUFF.48.1.p1 291 VSSE-QNTSFLQKYWKGPFITAGGYDPET--AVQAANERGVLVAFGRNFIANPDLVFRIKHHIPLN 353 **66.9**********************9..********************************987 PP >> CUFF.49.1.p1 type:complete gc:universal CUFF.49.1:2224-1076(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.0 0.0 3.6e-138 1.1e-136 1 341 [] 6 353 .. 6 353 .. 0.99 Alignments for each domain: == domain 1 score: 448.0 bits; conditional E-value: 3.6e-138 CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHHHHHHHHHHHTT-EEE CS Oxidored_FMN 1 kLFkPikignttLknRivmapmtrlrasedgnvledlaaeYysqrseipgtliiteatfvspksggfenapgiwddeqieswkklteavhkngsfav 97 +LFkPik+gn+ L++Riv+apmtrlra+++g ++++l++eYysqrs+ipgtl+i++atfv++ksggf+n+p+++++eq+esw +l+eavhkn+sf++ CUFF.49.1.p1 6 ELFKPIKVGNMLLQHRIVHAPMTRLRATDYG-KITGLMVEYYSQRSMIPGTLLIADATFVGEKSGGFPNNPRCFTKEQAESWIPLVEAVHKNKSFLF 101 69*****************************.9999************************************************************* PP EEEE--GGGS..SCSTCEC.........SS.ESSSSSTTT-.....S...C...EE--HHHHHHHHHHHHHHHHHHHH.TT-SEEEEEE-CTSHHHH CS Oxidored_FMN 98 vqlwhlGreakaeyladae.......vdspsdpvaleasek....eagnel...keltkeeikeiiqeyveAAkraie.AGfDgVeihganGYLldq 179 +q+w l++++k+ey++d e +d+p+dp +l+a ++ ++g e+ k+++k++i+e+iq++v+AA++a++ A++DgVeih++nG+Lld+ CUFF.49.1.p1 102 IQFWPLPGDLKDEYRNDLEkmqkitySDCPQDPGGLPAGIHsfdaVQGVEVykkKYMSKRDIQEHIQDFVNAADLAVNiAKADGVEIHQVNGFLLDR 198 *************************9***************9999888888999******************************************* PP HH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS Oxidored_FMN 180 FlspksnkrtDkyg.GsienRarFllevvdavkeavgeervgyRlSplevvekgldgaetaqkayllkelekrlkdgkklalihlveprkrgagsve 275 F+ ++++++D+++ GsienR+rF+lev++av++++g+ervgyR+Sp++ +++++d++e+ ++yl++e++kr++ kla+ih++eprk+++g++ CUFF.49.1.p1 199 FVLGGFGDQCDPEYrGSIENRCRFPLEVLEAVTRKIGQERVGYRISPFSGWMQKIDFMEV--NIYLMSEIAKRFP---KLAYIHAIEPRKYWSGHKL 290 ************************************************************..*************...******************* PP CCTTHHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCGG CS Oxidored_FMN 276 teqqgknnefvkkvwkgplitvGriddeevaalivakneatlvafgRefladpdlveklkkgrpln 341 ++++ +n++f++k+wkgp+it+G++d e+ a+++a+++ lvafgR+f+a+pdlv+++k+++pln CUFF.49.1.p1 291 VSSE-QNTSFLQKYWKGPFITAGGYDPET--AVQAANERGVLVAFGRNFIANPDLVFRIKHHIPLN 353 **66.9**********************9..********************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (341 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 379.03 // Query: Pantoate_ligase [M=266] Accession: PF02569.14 Description: Pantoate-beta-alanine ligase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-104 341.7 0.0 1.4e-104 341.6 0.0 1.0 1 CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+ Domain annotation for each sequence (and alignments): >> CUFF.50.1.p2 type:complete gc:universal CUFF.50.1:870-1721(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 341.6 0.0 1.5e-106 1.4e-104 4 265 .. 5 278 .. 2 279 .. 0.91 Alignments for each domain: == domain 1 score: 341.6 bits; conditional E-value: 1.5e-106 -SHHHHHHHHHHHHHTT-EEEEEEE-SS--HHHHHHHHHHHHHSSEEEEEE---GGGSSTTSCTTTS---HHHHHHHHHHTT-SEEE---HHHH CS Pantoate_ligase 4 ktvaelrellkelrkegkkvglVpTmGaLHeGHlsLvkaakeendvvvvSiFvNplqFgpkedlekYPrtleaDlelleeagvdlvFaPsveem 97 k+ ++++++++rk+g+++++VpTmG+LHeGH sLv++ak+++++vvvSiFvNp+qF++ +dl YPrt+++D+++l+++gvdlv+aP+vee+ CUFF.50.1.p2 5 KEKLLIHQQVDNWRKDGNRIAFVPTMGNLHEGHFSLVREAKRHAEKVVVSIFVNPMQFNNPQDLLLYPRTMDQDCSQLQNLGVDLVYAPTVEEL 98 55566788999***9999**************************************************************************** PP ST......EEEEECSGGCSTHHHHSTTHHHHHHHHHHHHHHHH--SEEEEEGGGHHHHHHHHHHHHHTT-SSEEEEE-XXBXTTSXBXXGGGGG CS Pantoate_ligase 98 yp......tevevkelsevlegasrpghFrGVatvvtkLfnivqpdrayfGqKDaqqlavirrlvkdlnlpveivavpivReedgLAlSSRNky 185 yp t v+v++ls++legasrpghFrGV+tvv+kLf+iv+pd+a+fG+KD+qq+a+i+++v+dln+ +ei++vpivR++dgLAlSSRN y CUFF.50.1.p2 99 YPegsqdiTFVDVPKLSTMLEGASRPGHFRGVTTVVSKLFHIVNPDVACFGEKDFQQVAIIKKMVRDLNFFIEIIQVPIVRADDGLALSSRNGY 192 ********99************************************************************************************ PP SXHHHHHHTTHHHHHHHHHH........BHHHHHHHHHHHHHTHTTEEEEEEEEEETTTSSX.BSSBXSEEEEEEEEEETTEEEEEEE CS Pantoate_ligase 186 LseeerkaAlvlykaLkaak........eaealkeaakeeleeeelekadyveivdaetleeleleeekkavllvaakvgkvrLiDni 265 L++eerk A++lyk+Lk+++ + e+l +++++el++ ++ d +ei+d++tle+++ + +k++v+l+aa++gk+rLiDni CUFF.50.1.p2 193 LTSEERKIAPNLYKILKKLAqelsngngDLEKLIAETNTELSRCRFI-PDQLEICDSTTLEPFT-AGTKNVVILAAAWLGKARLIDNI 278 *******************9555555444444445555555544433.5***********9964.55588*****************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (266 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 996.63 // Query: Pantoate_transf [M=259] Accession: PF02548.14 Description: Ketopantoate hydroxymethyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-104 341.9 0.0 1.3e-104 341.7 0.0 1.0 1 CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) 7.2e-98 319.6 0.0 8.1e-98 319.5 0.0 1.0 1 CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722- Domain annotation for each sequence (and alignments): >> CUFF.50.1.p3 type:complete gc:universal CUFF.50.1:35-838(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 341.7 0.0 2.8e-106 1.3e-104 2 258 .. 6 261 .. 5 262 .. 0.99 Alignments for each domain: == domain 1 score: 341.7 bits; conditional E-value: 2.8e-106 Pantoate_transf 2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqa 95 +t+++lr++k +++k+a++Tayda++++l++e+g+ v+LVGDslgm+++g+++tlpv++e+++yhtk+V+rga++ l++adlPf+sy ++ e+a CUFF.50.1.p3 6 ITISTLRQWKLANKKFACITAYDASFSRLFAEQGMPVMLVGDSLGMTAQGHSTTLPVSVEDIAYHTKSVRRGAPNRLLMADLPFMSY-STWEDA 98 79*************************************************************************************.99**** PP Pantoate_transf 96 lenAarllkeggadavKleggae.vaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaela 188 ++nAa+++++ ga++vK+egg + + e+v++l+e+ +pV gH+GltPqsvn +ggyk+qg+++++a++l+e+a++le+ Ga++lvlE++p++la CUFF.50.1.p3 99 CKNAATVMRA-GANIVKIEGGGNwIFEIVQRLTERSVPVAGHLGLTPQSVNIFGGYKIQGREQSAAARLIENAQQLEKFGAQLLVLECIPESLA 191 *********9.********99866********************************************************************** PP Pantoate_transf 189 keiteklsiptIGiGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesieeavkaYaeevkegsFPa 258 ++it+++siptIGiGAG+++dGq+lv+hD+lg+t + pkf+k++++ a +i++a+++Y+ ev++g +Pa CUFF.50.1.p3 192 EQITKTISIPTIGIGAGKHTDGQILVMHDALGITGGRPPKFAKNFLSGAGDIRTAIQRYIYEVEQGLYPA 261 *********************************************************************8 PP >> CUFF.52.1.p3 type:3prime_partial gc:universal CUFF.52.1:722-3(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 319.5 0.0 1.7e-99 8.1e-98 2 235 .. 6 238 .. 5 240 .] 0.98 Alignments for each domain: == domain 1 score: 319.5 bits; conditional E-value: 1.7e-99 Pantoate_transf 2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqa 95 +t+++lr++k +++k+a++Tayda++++l++e+g+ v+LVGDslgm+++g+++tlpv++e+++yhtk+V+rga++ l++adlPf+sy ++ e+a CUFF.52.1.p3 6 ITISTLRQWKLANKKFACITAYDASFSRLFAEQGMPVMLVGDSLGMTAQGHSTTLPVSVEDIAYHTKSVRRGAPNRLLMADLPFMSY-STWEDA 98 79*************************************************************************************.99**** PP Pantoate_transf 96 lenAarllkeggadavKleggae.vaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaela 188 ++nAa+++++ ga++vK+egg + + e+v++l+e+ +pV gH+GltPqsvn +ggyk+qg+++++a++l+e+a++le+ Ga++lvlE++p++la CUFF.52.1.p3 99 CKNAATVMRA-GANIVKIEGGGNwIFEIVQRLTERSVPVAGHLGLTPQSVNIFGGYKIQGREQSAAARLIENAQQLEKFGAQLLVLECIPESLA 191 *********9.********99866********************************************************************** PP Pantoate_transf 189 keiteklsiptIGiGAGaacdGqvlvlhDllgltekfkpkfvkkyae 235 ++it+++siptIGiGAG+++dGq+lv+hD+lg+t + pkf+k++++ CUFF.52.1.p3 192 EQITKTISIPTIGIGAGKHTDGQILVMHDALGITGGRPPKFAKNFLS 238 ********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (259 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1060.10 // Query: Phosphodiest [M=357] Accession: PF01663.21 Description: Type I phosphodiesterase / nucleotide pyrophosphatase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-16 53.9 2.6 1.5e-12 40.3 0.1 2.1 2 CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675( Domain annotation for each sequence (and alignments): >> CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.6 0.3 2e-06 0.00019 1 59 [. 48 108 .. 48 116 .. 0.87 2 ! 40.3 0.1 1.6e-14 1.5e-12 143 237 .. 166 261 .. 117 275 .. 0.77 Alignments for each domain: == domain 1 score: 13.6 bits; conditional E-value: 2e-06 EEEEEETT-BCCHHHHCGGTSHHHHHHHHHSEEESE..EE-SSS-SHHHHHHHHHHSS-HH CS Phosphodiest 1 vlvislDGlradlldrlaellpnlaaLakegvsapn..lrpvfPtlTfpnhaslvTGlyPg 59 v+++ +D lrad ++ ++ +p+ ++L+ +++++ + Pt+T+p + +l TG+ Pg CUFF.53.1.p1 48 VVFVMVDALRADFVFSKSHNMPFTQSLLYNSTHGIGfsAFARSPTVTMPRLKALTTGTIPG 108 7999***********9448*********977666643488889***************997 PP == domain 2 score: 40.3 bits; conditional E-value: 1.6e-14 THHHHHHHHHHCHHHHCHTHCHHHHHTT.TSECEEEEEEEHHHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEE....EEEEES--- CS Phosphodiest 143 pledkvdkavlqtwldaafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetn....iilvSDHGm 234 ++ ++v + ++++f +++l+ +l +d l++++ ++D++gH +Gp sp ++ +l ++D i +++++l+e +++tn i+l +DHGm CUFF.53.1.p1 166 SFFVSDYTEVD-NNVTRNF-DHALPSSLsHSWDALILHYLGVDHIGHLYGPSSPLLNIKLLEIDTIISRIYKYLQEY--DEKTNthslIVLCGDHGM 258 33332223344.4478888.568888889**********************************************98..444444466********* PP EE- CS Phosphodiest 235 adv 237 ++v CUFF.53.1.p1 259 NEV 261 998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 515.71 // Query: PLA2_B [M=491] Accession: PF01735.17 Description: Lysophospholipase catalytic domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-206 677.9 1.8 4.2e-206 677.6 1.8 1.1 1 CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+ Domain annotation for each sequence (and alignments): >> CUFF.12.1.p1 type:complete gc:universal CUFF.12.1:228-2249(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 677.6 1.8 4.4e-208 4.2e-206 1 490 [. 132 614 .. 132 615 .. 0.99 Alignments for each domain: == domain 1 score: 677.6 bits; conditional E-value: 4.4e-208 PLA2_B 1 iaiavSGGGyramltgaGvlkAldsRtdnatglgGlLqsatYlaGlsGgsWlvgslavNnftsvqellkkkeedsvwdlensivnpeglnlvknikr 97 ++ia+SGGG+ram++g+G+ +A+dsR + + l+GlLqsa+Y++GlsGgsWlvgs+a+Nnft+++ l++ +vw+le+s+++p+g n+++n+++ CUFF.12.1.p1 132 LGIAFSGGGLRAMVNGGGAFNAFDSRFESDSPLSGLLQSAMYISGLSGGSWLVGSVAINNFTNITYLRD-----NVWNLEHSVFAPHGDNVIENLNY 223 69*******************************************************************.....8********************** PP PLA2_B 98 yeeivdevekKksagfnvsltDiwGralseklveleegganltlsslkdaekfqnaemplPiivadgrkpgesvinlNatvfEfsPyelgswdakln 194 y+++ +e+++Kk+agf+ sltD+wGrals+klv++e+gg+ +t+ss++++++fqna++p+Piivad+r ++e++i +N+++fEf+ ye+g+wd++++ CUFF.12.1.p1 224 YNDLRKEIDQKKHAGFDCSLTDLWGRALSRKLVDAERGGPGITYSSMRNQSWFQNADYPYPIIVADSRLEEETAIPANTSIFEFTAYEFGTWDNGIK 320 ************************************************************************************************* PP PLA2_B 195 sFvdvkylGtklsnGtvvkkgkcvagfdnaGflmgtsstlFnevlleinstsmlesllkellkkllkdlsedsediaqyapnpfkdaeeenqnatqs 291 +F++++y+Gt+l +G+++ +++c++++dnaGf+mgts+tlFn++ll++n++ +++ +++l+ +l+dls+ ++dia y+ np++++++ n+ + ++ CUFF.12.1.p1 321 AFIPMEYVGTHLLDGVPP-DKSCIHNYDNAGFVMGTSATLFNSFLLDWNENVKKNDTYYDILHAILEDLSKHQDDIAPYP-NPYQNYTTSNTSVVNA 415 ******************.*********************************9**************************9.**************** PP PLA2_B 292 ivesktLdlvdggedgqniplvpllqkerkvdvifaldssadteeswpdgsslvktyeRvle...ssqvkgkkfpyvpdqntfvnlgLnkrptffGc 385 ++ +t+dlvdgged +nipl+pll+++r vdv+fa+ds+++ + wp gss+v+tyeRv++ +++v++++fpy+pd+nt+++lgLn+rptffGc CUFF.12.1.p1 416 FEPYDTIDLVDGGEDRENIPLWPLLHPQRFVDVVFAIDSTYNDPYGWPLGSSIVATYERVVTfnaNKSVDVRGFPYIPDENTIISLGLNTRPTFFGC 512 ************************************************************999889999**************************** PP PLA2_B 386 DarnltdlsatvdestpPlvvylpnekytylsnlstfklsykdseregliengfeaatqdnekdddefaacvacaiirRklerknittpseckkcFe 482 D++n+t++++ vd++tpPl+vy+pn+++ty+sn+stf++s++d++ +g++en+f ++tq+n +++fa+c+acaii+R+lerk ++tp +c++cF+ CUFF.12.1.p1 513 DGKNTTAGNHDVDNNTPPLLVYFPNYPWTYYSNISTFTMSMDDKMANGILENAFMSTTQNN---NESFAVCLACAIIQRSLERKKLSTPTQCSSCFQ 606 ************************************************************9...9******************************** PP PLA2_B 483 nycwngtv 490 +ycw+gt+ CUFF.12.1.p1 607 EYCWDGTL 614 ******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (491 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 738.72 // Query: Polysacc_synt_C [M=142] Accession: PF14667.5 Description: Polysaccharide biosynthesis C-terminal domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-09 30.5 3.6 1.7e-09 30.5 3.6 4.0 4 CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907( 1.7e-09 30.5 3.6 1.7e-09 30.5 3.6 4.0 4 CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+ Domain annotation for each sequence (and alignments): >> CUFF.38.1.p3 type:complete gc:universal CUFF.38.1:7274-5907(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.8 1.1 0.34 16 13 26 .. 51 64 .. 18 109 .. 0.61 2 ! 30.5 3.6 3.5e-11 1.7e-09 2 115 .. 131 252 .. 130 273 .. 0.79 3 ? -0.6 2.6 0.14 6.8 109 136 .. 295 326 .. 266 332 .. 0.55 4 ! 6.0 5.5 0.0013 0.06 4 79 .. 353 430 .. 343 444 .. 0.76 Alignments for each domain: == domain 1 score: -1.8 bits; conditional E-value: 0.34 Polysacc_synt_C 13 slstvlssiLqglg 26 +++ ++++ L++lg CUFF.38.1.p3 51 YMFAMSTGWLIALG 64 33333333333332 PP == domain 2 score: 30.5 bits; conditional E-value: 3.5e-11 Polysacc_synt_C 2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrrllgikl...llrrl 90 L++l+++ + ++ + +l Lq +++ ++l+++ ++++ln+ll++++ g+ Ga +at l++ ++++l+ +++ g + +r+ CUFF.38.1.p3 131 LRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFLLVHYYglGLKGAPLATGLSYWLSFILLTQYAKYVKGAEAwngWNKRC 224 7899999999999999*********************************8883357******************99999999999889955555 PP Polysacc_synt_C 91 l...kpllaalvmgivvylllllllgll 115 l p++ ++giv++ ++ +++ CUFF.38.1.p3 225 LenfGPFVKLSLLGIVMVGTEWWAFEIV 252 4444666666666666555555555543 PP == domain 3 score: -0.6 bits; conditional E-value: 0.14 Polysacc_synt_C 109 llllglllla....alalllavlvgalvYlll 136 +l gl+ +a +a +++v+vg ++ + + CUFF.38.1.p3 295 YLGAGLPDNAsltaKVAAIVGVAVGSVIMITM 326 33333333331111335555555555555544 PP == domain 4 score: 6.0 bits; conditional E-value: 0.0013 Polysacc_synt_C 4 ilalsiiflslstvlssiLqglgrqkialkal.vigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 ++a i sl+ ++++ L g+grqk ++++ + l+ l l ++l + g+vG i+ v+al +v +l l +++ CUFF.38.1.p3 353 LVAAFQISDSLNGTMGGALRGTGRQKVGAIVNiTAYYLFALPLGIYLAfHGKGLVGLWIGQVIALSIVGILELKIVMA 430 566666777899999999999999998555440455668888888888344488**************9999888775 PP >> CUFF.39.1.p1 type:complete gc:universal CUFF.39.1:342-1709(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.8 1.1 0.34 16 13 26 .. 51 64 .. 18 109 .. 0.61 2 ! 30.5 3.6 3.5e-11 1.7e-09 2 115 .. 131 252 .. 130 273 .. 0.79 3 ? -0.6 2.6 0.14 6.8 109 136 .. 295 326 .. 266 332 .. 0.55 4 ! 6.0 5.5 0.0013 0.06 4 79 .. 353 430 .. 343 444 .. 0.76 Alignments for each domain: == domain 1 score: -1.8 bits; conditional E-value: 0.34 Polysacc_synt_C 13 slstvlssiLqglg 26 +++ ++++ L++lg CUFF.39.1.p1 51 YMFAMSTGWLIALG 64 33333333333332 PP == domain 2 score: 30.5 bits; conditional E-value: 3.5e-11 Polysacc_synt_C 2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrrllgikl...llrrl 90 L++l+++ + ++ + +l Lq +++ ++l+++ ++++ln+ll++++ g+ Ga +at l++ ++++l+ +++ g + +r+ CUFF.39.1.p1 131 LRYLIPGGLGYVCFELLKKFLQTQEITRAGSYILLVTSPLNVALNFLLVHYYglGLKGAPLATGLSYWLSFILLTQYAKYVKGAEAwngWNKRC 224 7899999999999999*********************************8883357******************99999999999889955555 PP Polysacc_synt_C 91 l...kpllaalvmgivvylllllllgll 115 l p++ ++giv++ ++ +++ CUFF.39.1.p1 225 LenfGPFVKLSLLGIVMVGTEWWAFEIV 252 4444666666666666555555555543 PP == domain 3 score: -0.6 bits; conditional E-value: 0.14 Polysacc_synt_C 109 llllglllla....alalllavlvgalvYlll 136 +l gl+ +a +a +++v+vg ++ + + CUFF.39.1.p1 295 YLGAGLPDNAsltaKVAAIVGVAVGSVIMITM 326 33333333331111335555555555555544 PP == domain 4 score: 6.0 bits; conditional E-value: 0.0013 Polysacc_synt_C 4 ilalsiiflslstvlssiLqglgrqkialkal.vigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 ++a i sl+ ++++ L g+grqk ++++ + l+ l l ++l + g+vG i+ v+al +v +l l +++ CUFF.39.1.p1 353 LVAAFQISDSLNGTMGGALRGTGRQKVGAIVNiTAYYLFALPLGIYLAfHGKGLVGLWIGQVIALSIVGILELKIVMA 430 566666777899999999999999998555440455668888888888344488**************9999888775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 18 (0.189474); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 136.69 // Query: Pombe_5TM [M=256] Accession: PF09437.9 Description: Pombe specific 5TM protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-158 516.6 19.2 9.1e-158 516.1 19.2 1.2 1 CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953( Domain annotation for each sequence (and alignments): >> CUFF.6.1.p1 type:5prime_partial gc:universal CUFF.6.1:3-953(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 516.1 19.2 9.6e-160 9.1e-158 15 256 .] 1 242 [. 1 242 [. 1.00 Alignments for each domain: == domain 1 score: 516.1 bits; conditional E-value: 9.6e-160 Pombe_5TM 15 sfaysgnsesvlvgenitsirktllinetgsycvaarpmtmdgaefnldlmgysvsedqinndeigiwnyisvaemggvllflsywiwtclhfskiif 112 sfaysgnsesv++genitsi+kt+linetgsycvaarpmtmdgaefnldlmgysvsedqinndeigiwnyisvaemggvllflsywiwtclhfskiif CUFF.6.1.p1 1 SFAYSGNSESVWTGENITSIWKTILINETGSYCVAARPMTMDGAEFNLDLMGYSVSEDQINNDEIGIWNYISVAEMGGVLLFLSYWIWTCLHFSKIIF 98 8************************************************************************************************* PP Pombe_5TM 113 paqkviclyiflfalnqtlqekieeyvfssevikyrkfysvyeiidflrtnfyrlfviycalgigiirtvskylvikgisivialesvyrislkkdvy 210 paqkviclyiflfalnqtlqe+ieeyvfsse+ikyr+fysvyeiidflrtnfyrlfviycalg+gi+rtv+kyl+ikgisivial+svy+isl+kdvy CUFF.6.1.p1 99 PAQKVICLYIFLFALNQTLQECIEEYVFSSECIKYRQFYSVYEIIDFLRTNFYRLFVIYCALGFGITRTVPKYLMIKGISIVIALCSVYWISLYKDVY 196 ************************************************************************************************** PP Pombe_5TM 211 vvseifdliqyevfpaiwvysichllkqctsvttyenaskarfirr 256 vvseifd+iqyev paiwvysichllkqctsvttyenaskarf+rr CUFF.6.1.p1 197 VVSEIFDMIQYEVSPAIWVYSICHLLKQCTSVTTYENASKARFFRR 242 *********************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1047.53 // Query: PsbN [M=43] Accession: PF02468.14 Description: Photosystem II reaction centre N protein (psbN) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00014 14.3 0.0 0.00043 12.8 0.0 1.9 1 CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-58 0.00021 13.8 0.0 0.00075 12.0 0.0 2.0 1 CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) Domain annotation for each sequence (and alignments): >> CUFF.13.3.p1 type:5prime_partial gc:universal CUFF.13.3:3-584(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.8 0.0 9e-06 0.00043 27 43 .] 118 136 .. 106 136 .. 0.85 Alignments for each domain: == domain 1 score: 12.8 bits; conditional E-value: 9e-06 PsbN 27 FGPPskeLaDPF..edHED 43 FGP +++L DPF dH D CUFF.13.3.p1 118 FGPHAAKLVDPFswGDHGD 136 ***********84469988 PP >> CUFF.13.2.p1 type:internal gc:universal CUFF.13.2:3-875(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.0 0.0 1.6e-05 0.00075 27 43 .] 118 136 .. 107 136 .. 0.84 Alignments for each domain: == domain 1 score: 12.0 bits; conditional E-value: 1.6e-05 PsbN 27 FGPPskeLaDPF..edHED 43 FGP +++L DPF dH D CUFF.13.2.p1 118 FGPHAAKLVDPFswGDHGD 136 ***********84469988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (43 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 782.33 // Query: REPA_OB_2 [M=98] Accession: PF16900.4 Description: Replication protein A OB domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00048 12.7 0.0 0.00085 11.9 0.0 1.4 1 CUFF.40.1.p3 type:complete gc:universal CUFF.40.1:2783-1899( 0.00048 12.7 0.0 0.00085 11.9 0.0 1.4 1 CUFF.41.1.p2 type:complete gc:universal CUFF.41.1:1256-2140( Domain annotation for each sequence (and alignments): >> CUFF.40.1.p3 type:complete gc:universal CUFF.40.1:2783-1899(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.9 0.0 1.8e-05 0.00085 50 96 .. 143 196 .. 134 198 .. 0.81 Alignments for each domain: == domain 1 score: 11.9 bits; conditional E-value: 1.8e-05 REPA_OB_2 50 rsvevtlWgkeaekfe.......sseepvvalkgvkvsdFggrslstlssstlk 96 +sv + lW++e+ ++ + +v +k+ kv d +s+ +++ss l CUFF.40.1.p3 143 CSVLLMLWNDEDPILNrqvietkLNFFLIVLVKASKVWDLATKSIHLIKSSLLS 196 689999****555554444444367789**********************9875 PP >> CUFF.41.1.p2 type:complete gc:universal CUFF.41.1:1256-2140(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.9 0.0 1.8e-05 0.00085 50 96 .. 143 196 .. 134 198 .. 0.81 Alignments for each domain: == domain 1 score: 11.9 bits; conditional E-value: 1.8e-05 REPA_OB_2 50 rsvevtlWgkeaekfe.......sseepvvalkgvkvsdFggrslstlssstlk 96 +sv + lW++e+ ++ + +v +k+ kv d +s+ +++ss l CUFF.41.1.p2 143 CSVLLMLWNDEDPILNrqvietkLNFFLIVLVKASKVWDLATKSIHLIKSSLLS 196 689999****555554444444367789**********************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (98 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1239.06 // Query: Ribosomal_S3Ae [M=205] Accession: PF01015.17 Description: Ribosomal S3Ae family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-93 303.3 3.9 4.7e-93 303.1 3.9 1.0 1 CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+ Domain annotation for each sequence (and alignments): >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 303.1 3.9 5e-95 4.7e-93 2 205 .] 16 221 .. 15 221 .. 0.99 Alignments for each domain: == domain 1 score: 303.1 bits; conditional E-value: 5e-95 S----S-TTSSEEEEEEE--TTSSSSEECEEEEE--BTTC-SCCCHCC-EEEEESHCCCTTCCCSS-EEEEEEEEEETT.EEEEEEEEE--HHHH CS Ribosomal_S3Ae 2 kkkkvvDkfkkKeWydvkaPalfgkreiGktlvtrtqgtkiaseglkgrvvevslaDLtndeeqafrklklkiedvqgk.altnFhgmeltrDkl 95 kk+vvD+f++K+Wyd+kaPa+f+ +++Gktlv+rt+g k+a+++lkgr++evslaDL++dee++frk+kl++ed+qgk +lt+F+g ++t+Dkl CUFF.54.1.p1 16 IKKRVVDPFSRKDWYDIKAPAFFEVKNVGKTLVNRTAGLKNANDSLKGRILEVSLADLQKDEEHSFRKVKLRVEDIQGKsCLTSFNGFDMTSDKL 110 599***********************************************************99******************************* PP HHC--CTB-EEEEEEEEEETTTEEEEEEEEEEE--TGCGS.S-B---HHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHCTTHHHHHHHHHHTTTS CS Ribosomal_S3Ae 96 rslvrkwsslIeaivdvkttDgyllrvfvvafTkkrenqk.ktsyakssqvkaIrkkmveilteeaseldlkelvkklipesigkeiekeakkIy 189 rslvrkw+s+Iea+ ++kttDgyl r+fv++fT +r nq+ kt+ya+ssq++aI++km+++++++a+ +++kelv+klipe ig+ iek++++Iy CUFF.54.1.p1 111 RSLVRKWQSTIEANQTIKTTDGYLCRIFVIGFTSRRVNQVkKTTYAQSSQIRAIHQKMFQVIQNQANGCSMKELVQKLIPEVIGRAIEKATNNIY 205 *********************************************************************************************** PP -EEEEEEEEEEEEE-- CS Ribosomal_S3Ae 190 plrnveirKvkvlkkP 205 pl+nv++rKvk+lk+P CUFF.54.1.p1 206 PLQNVFVRKVKILKAP 221 **************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (205 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1654.61 // Query: Ribosomal_S6e [M=126] Accession: PF01092.18 Description: Ribosomal protein S6e Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-62 200.2 0.0 6.2e-62 199.8 0.0 1.2 1 CUFF.58.1.p1 type:internal gc:universal CUFF.58.1:1-603(+) Domain annotation for each sequence (and alignments): >> CUFF.58.1.p1 type:internal gc:universal CUFF.58.1:1-603(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.8 0.0 6.5e-64 6.2e-62 1 126 [] 11 136 .. 11 136 .. 1.00 Alignments for each domain: == domain 1 score: 199.8 bits; conditional E-value: 6.5e-64 -EEEEEETTTTEEEEEE---HHHHTTCTT-BSSEEEESTTT-SSS-S-EEEEEEEEESCC-BB-TT--SSSEEEEEE-TTSSS---SSSS--EEEE CS Ribosomal_S6e 1 mklnisdpatgkqklievddekklrtfiekrigeevdgdalgeelkgyvlkitggsdkqGfpmkqgvlthgrvrlLlskggsgyrprrkGerkrks 96 mklnis+pa+g+qklie+dd+++lr f+ekr+g+ev gd++g+e++gyv+kitgg+dkqGfpm qgvl ++rvrlLl+ g+++yrprr+Gerkrks CUFF.58.1.p1 11 MKLNISYPANGTQKLIEIDDDRRLRVFMEKRMGQEVPGDSVGPEFAGYVFKITGGNDKQGFPMFQGVLLPHRVRLLLRAGHPCYRPRRDGERKRKS 106 9*********************************************************************************************** PP EE-SB--SSEEEEEEEEEE--SS--TTSSS CS Ribosomal_S6e 97 vrgcivsadlsvlnlvivkkgekdiegLtd 126 vrgciv +dl+vl l i+k+ge+di+gLtd CUFF.58.1.p1 107 VRGCIVGQDLAVLALAIIKQGEQDIPGLTD 136 *****************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (126 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1403.72 // Query: RNA_POL_M_15KD [M=36] Accession: PF02150.15 Description: RNA polymerases M/15 Kd subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-05 16.1 0.0 0.0043 9.6 0.0 2.4 2 CUFF.7.1.p1 type:complete gc:universal CUFF.7.1:159-560(+) Domain annotation for each sequence (and alignments): >> CUFF.7.1.p1 type:complete gc:universal CUFF.7.1:159-560(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 9.6 0.0 4.5e-05 0.0043 19 33 .. 56 70 .. 53 72 .. 0.78 2 ! 4.0 0.0 0.0026 0.24 8 24 .. 112 128 .. 109 130 .. 0.87 Alignments for each domain: == domain 1 score: 9.6 bits; conditional E-value: 4.5e-05 STEEEETTSS-EEES CS RNA_POL_M_15KD 19 gknfeCrqCgYeepa 33 +k++ C+qC+ +epa CUFF.7.1.p1 56 NKVLRCSQCDWHEPA 70 33466*********8 PP == domain 2 score: 4.0 bits; conditional E-value: 0.0026 TSBEEEEECSSSTEEEE CS RNA_POL_M_15KD 8 gNlLlpkedkegknfeC 24 Nl l+k+++eg++f C CUFF.7.1.p1 112 QNLFLSKSKEEGVIFLC 128 59**********99988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (36 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 742.28 // Query: SAUGI [M=111] Accession: PF06106.10 Description: S. aureus uracil DNA glycosylase inhibitor Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00064 12.5 0.8 0.062 6.1 0.1 2.1 2 CUFF.26.1.p2 type:complete gc:universal CUFF.26.1:734-372(-) 0.00064 12.5 0.8 0.062 6.1 0.1 2.1 2 CUFF.27.1.p2 type:complete gc:universal CUFF.27.1:2125-2487( Domain annotation for each sequence (and alignments): >> CUFF.26.1.p2 type:complete gc:universal CUFF.26.1:734-372(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 5.5 0.1 0.0021 0.099 66 92 .. 12 38 .. 3 50 .. 0.79 2 ! 6.1 0.1 0.0013 0.062 57 90 .. 64 98 .. 46 105 .. 0.77 Alignments for each domain: == domain 1 score: 5.5 bits; conditional E-value: 0.0021 SAUGI 66 iypflmyannqlisvgylnhfdmdfly 92 y ++ n ++i g +nhf ++++ CUFF.26.1.p2 12 FYFCTVHRNSNIICSGNFNHFTIQLFR 38 4666788999***********998754 PP == domain 2 score: 6.1 bits; conditional E-value: 0.0013 SAUGI 57 ynnelhdlsiyp.flmyannqlisvgylnhfdmdf 90 +n + + i+ lm+an l s+ +l h+ + + CUFF.26.1.p2 64 FNCLVERIRIFNqTLMHANSSLSSIPWLIHYHFSY 98 555566667764269**************997654 PP >> CUFF.27.1.p2 type:complete gc:universal CUFF.27.1:2125-2487(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 5.5 0.1 0.0021 0.099 66 92 .. 12 38 .. 3 50 .. 0.79 2 ! 6.1 0.1 0.0013 0.062 57 90 .. 64 98 .. 46 105 .. 0.77 Alignments for each domain: == domain 1 score: 5.5 bits; conditional E-value: 0.0021 SAUGI 66 iypflmyannqlisvgylnhfdmdfly 92 y ++ n ++i g +nhf ++++ CUFF.27.1.p2 12 FYFCTVHRNSNIICSGNFNHFTIQLFR 38 4666788999***********998754 PP == domain 2 score: 6.1 bits; conditional E-value: 0.0013 SAUGI 57 ynnelhdlsiyp.flmyannqlisvgylnhfdmdf 90 +n + + i+ lm+an l s+ +l h+ + + CUFF.27.1.p2 64 FNCLVERIRIFNqTLMHANSSLSSIPWLIHYHFSY 98 555566667764269**************997654 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (111 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 260.46 // Query: Smim3 [M=60] Accession: PF17307.1 Description: Small integral membrane protein 3 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00099 11.3 0.5 0.068 5.4 0.1 2.5 2 CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747( Domain annotation for each sequence (and alignments): >> CUFF.51.1.p1 type:complete gc:universal CUFF.51.1:2632-3747(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 3.5 0.0 0.0027 0.26 12 33 .. 11 32 .. 2 35 .. 0.70 2 ! 5.4 0.1 0.00072 0.068 42 56 .. 88 102 .. 85 106 .. 0.89 Alignments for each domain: == domain 1 score: 3.5 bits; conditional E-value: 0.0027 Smim3 12 vLPkhiLDiWvivLiiLativi 33 LP++ ++ +vLii+ t ++ CUFF.51.1.p1 11 SLPRYKFLLFSVVLIIVMTTLV 32 5677777777788877766555 PP == domain 2 score: 5.4 bits; conditional E-value: 0.00072 Smim3 42 ataviiYRvrthPvl 56 at v+i+R++ hP+ CUFF.51.1.p1 88 ATRVLIHRLKYHPTT 102 9************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (60 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1020.04 // Query: SnoaL [M=126] Accession: PF07366.11 Description: SnoaL-like polyketide cyclase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-08 25.3 0.2 4.1e-07 22.5 0.1 2.1 2 CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+ Domain annotation for each sequence (and alignments): >> CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 5.8 0.0 0.00065 0.062 45 64 .. 7 26 .. 3 28 .. 0.89 2 ! 22.5 0.1 4.3e-09 4.1e-07 5 110 .. 14 107 .. 9 114 .. 0.90 Alignments for each domain: == domain 1 score: 5.8 bits; conditional E-value: 0.00065 HHHHHHHHHCTTCEEEEEEE CS SnoaL 45 afveelfkafPDlkvevedl 64 f+++lfkaf D++++ve+l CUFF.36.1.p1 7 SFIRQLFKAFTDFSTDVESL 26 5889*************986 PP == domain 2 score: 22.5 bits; conditional E-value: 4.3e-09 HHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEESSEBTTBE-TT-EEEEEEEE CS SnoaL 5 rfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGthtgeflGipptGkkvkfeeit 101 ++++++ s d++ l+ ++++d+ + ++++ l++f ++++l++ + l ++v+++v++g k+a+ + + i +G + +++ i CUFF.36.1.p1 14 KAFTDF--STDVESLRGFLTPDYRQL--VDGRELTLDDFISHAKALRTHLHRLDINVQQIVCQGNKAATVHIA--------HAIRSSGESSRIKVIA 98 556666..779***********9988..559**********************************99998885........56999*********** PP EEEEETTEE CS SnoaL 102 llrvedGkI 110 ++ ++dG+I CUFF.36.1.p1 99 FYSFKDGRI 107 ********9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (126 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 451.83 // Query: SnoaL_2 [M=102] Accession: PF12680.6 Description: SnoaL-like domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-12 38.7 0.0 8.1e-12 38.4 0.0 1.1 1 CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+ Domain annotation for each sequence (and alignments): >> CUFF.36.1.p1 type:complete gc:universal CUFF.36.1:895-1287(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 38.4 0.0 8.5e-14 8.1e-12 2 100 .. 10 108 .. 9 110 .. 0.92 Alignments for each domain: == domain 1 score: 38.4 bits; conditional E-value: 8.5e-14 HHHHHHHH..TTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEEET CS SnoaL_2 2 rrflaaln..agdldalaalfapdvvwedpggelrGreairaffraafaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvtvrgvdvfrved 96 r+++ a++ + d++ l+ +++pd+++ g e ++++ + +a++ ++ l++ ++++v++g+++a+ +++ i+ +g+ ++++++++ ++d CUFF.36.1.p1 10 RQLFKAFTdfSTDVESLRGFLTPDYRQLVDGRE-LTLDDFISHAKALRTHLHRLDINVQQIVCQGNKAATVHIAHA-IRSSGESSRIKVIAFYSFKD 104 789999998899***************999865.5889999999999999*******************9888877.9******************* PP TEEE CS SnoaL_2 97 GkIv 100 G+I CUFF.36.1.p1 105 GRIS 108 ***6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (102 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1599.42 // Query: Sugar_tr [M=452] Accession: PF00083.23 Description: Sugar (and other) transporter Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-113 370.7 24.1 6.7e-113 370.4 24.1 1.1 1 CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+ 6.2e-10 31.0 30.1 1.3e-09 30.0 30.1 1.5 1 CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+ Domain annotation for each sequence (and alignments): >> CUFF.24.1.p1 type:complete gc:universal CUFF.24.1:689-2356(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.4 24.1 1.4e-114 6.7e-113 2 451 .. 10 466 .. 9 467 .. 0.95 Alignments for each domain: == domain 1 score: 370.4 bits; conditional E-value: 1.4e-114 HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTST.T--SHHHHHH....HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-T CS Sugar_tr 2 alvaalggllfgYdtgvigafltllkfaknfg.lsksksskee.ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaa 96 +++++++g l+g dtg i+++l + +f+++f ++ s+ ++ s+ ++ l+++ ++G+++G+++++++++r+G+k+s+ +++ +++i+ +l ++a CUFF.24.1.p1 10 VVFISMSGWLQGADTGSISGILGMRDFQSRFAdRYNPISNSYSySAWRQALLTGTINAGCLFGAMLSSPFTERIGKKYSICFFSGVYIIAELLLVTA 106 67899**********************99987534433333334899************************************************** PP TTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS-- CS Sugar_tr 97 kgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPE 193 s+ +++vg++l+G+g+G+ svl+P y+sE+Ap+++Rga+v yq + t lvaa++++g+ k +++ wr +g+++++ +ll++++lflPE CUFF.24.1.p1 107 V--PSWIQVLVGKILAGVGIGALSVLSPGYQSEVAPPQIRGAVVATYQIFSTGAALVAACINMGTHKLRKTASWRTSFGINMLWGILLMVGVLFLPE 201 *..89******************************************************************************************** PP -HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.........HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS- CS Sugar_tr 194 SPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeee....kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlgl 286 SPryl+ kg++eea +++ ++ + +++++ ++ +++++ e e ka w e++++ ++r+r+ +g+++++f l G+n+ +yy++++f+ +g+ CUFF.24.1.p1 202 SPRYLIYKGRDEEALRIMCNMAELSPESEIIQTNFNTIKSDIEIEmaggKARWIEIFGK-DIRYRTCLGFLVMLFRELIGNNYYFYYATQVFKGTGM 297 ********************99999999988888888888888888888*********9.99*********************************** PP THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH.....HHHHTTSS.....CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH CS Sugar_tr 287 sksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg...ivalllvaks..kaasivaivfialfialfalgwgpvpwvlvsEl 378 ++ +l +i+g++nf +tf a++++d +GRR+ l++Gaa+++icf+i++ l++++++ a+ v+ivf +lf++ + ++wgp+ wv+v E+ CUFF.24.1.p1 298 TDIFLPAVILGAINFGTTFGALYTIDNLGRRNPLIFGAAFQSICFFIYAavgDRKLIYKNGTsdHRAGSVMIVFSCLFLFSYCCSWGPMGWVIVGET 394 *************************************************87655667777768899******************************* PP SHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGG CS Sugar_tr 379 fpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeieel 451 fp + Rsk++++a+ nwl nf is+++p+i +aig ++ ++++a++++++ +++ff etkg+tlee++ l CUFF.24.1.p1 395 FPIRYRSKCASVATSGNWLGNFMISFFTPFINNAIG-FKLGYIYACINLFSSFMIFFLAKETKGLTLEEVNDL 466 ************************************.********************************9976 PP >> CUFF.37.1.p1 type:complete gc:universal CUFF.37.1:195-1835(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 30.0 30.1 2.7e-11 1.3e-09 25 437 .. 121 530 .. 105 534 .. 0.75 Alignments for each domain: == domain 1 score: 30.0 bits; conditional E-value: 2.7e-11 HHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS Sugar_tr 25 llkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121 + + ++ g s+ +s s+l + flvG +Gsl + +l+d++GR ++ ++ ++f i +v ++a+ +v+ l++ R++ G++ + + CUFF.37.1.p1 121 FASSVYSSGIIDIASELHSSIPVSTLGSCTFLVGFGVGSLPFAPLSDIYGRFIIYFVTLLIFTIFQVGGGCAH---NVWTLAIVRFFQGVFGSTPLA 214 5555555555555555555677899999*********************************************...********************* PP HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHG.GGS---HHHHHHTT-HHHHHHHHHHHHH CS Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllill.lflPESPrylvekgkeeeakevlaklrg 216 + +is + ++ R ++ + ++ +G +++ i+g ++ + + + wr+++++++++a ++++++ +f+PE+ e + + + l+k g CUFF.37.1.p1 215 NAGGTISDLFTPVQRTYVLPGFCTFPYLGPIIGPIIGDFItQSYLE---WRWTFWINMIWAAAVIVFVfIFFPET----HEDTILDYKAKYLRKTTG 304 *********999999999999999999********99888455555...**************99998689****....333333333334444333 PP C....HHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHT.TTHHHHSS-THH.....HHHHHHHHHH.HHH CS Sugar_tr 217 e....edadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyys.ptifenlglsks.....llvtiivgvv.nfv 302 + + +re + + ++++a+ ++ ++ ++++ ++++ + ++ + in+i + + p +f + g++k + + ++vg+v + CUFF.37.1.p1 305 NtayyTIHERERDPKNAMIQAA----TQAVSLIFTE------PIVVCFTLYLTVVYIINYINFEGyPIVFAKYGFNKGeqglsF-IGVGVGIVcAGL 390 3123333333333333333333....3344444444......455555666666777787777654889********9988844.444444440445 PP HHHHHHHHHHHS-SHHHHHHH........HHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH..SHTTTHHHHHH CS Sugar_tr 303 atfvaiflvdrfGRRtllllG........aagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsEl..fpqsvRskala 389 t + + ++ +++ +++ ++g++++ + + ++++ i iv ++ a+f++++ v++v + + q++ ++ala CUFF.37.1.p1 391 CTPFIYWHYLKVNKKRNGVICpedrlyplFIGCFLLPISMF--WFAWTCYP--HHIHWIVP-IIASAFFGFSLLIVFFVSYNYIidSYQHMAPSALA 482 56666688999999999****9***7765555555555554..44444443..23444444.455699999******999999844469******** PP HHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS CS Sugar_tr 390 iavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffv 437 a+ v a+ is++ + ++g + v +++ v+++ + f+f+ CUFF.37.1.p1 483 AATLVRYSASGGISMVARPMYLNLGDHWATSVLGFISVAMVPIPFIFY 530 *************************99999999999999999998886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (452 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 11 (0.115789); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 2 (0.0210526); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 220.15 // Query: SUI1 [M=76] Accession: PF01253.21 Description: Translation initiation factor SUI1 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-05 18.2 0.3 4.8e-05 16.5 0.2 2.0 2 CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+ Domain annotation for each sequence (and alignments): >> CUFF.54.1.p1 type:complete gc:universal CUFF.54.1:774-1532(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.5 0.2 5e-07 4.8e-05 3 52 .. 82 132 .. 80 177 .. 0.88 2 ? -1.8 0.0 0.26 25 16 38 .. 167 188 .. 158 189 .. 0.69 Alignments for each domain: == domain 1 score: 16.5 bits; conditional E-value: 5e-07 SUI1 3 pkihirveqrggrKkvTtvsglepfgidlkklakelkkkfacsgsvvk.dg 52 +k+++rve +g+ ++T +g+++ +l +l+++++++ ++ ++ dg CUFF.54.1.p1 82 RKVKLRVEDIQGKSCLTSFNGFDMTSDKLRSLVRKWQSTIEANQTIKTtDG 132 69*******************************************944444 PP == domain 2 score: -1.8 bits; conditional E-value: 0.26 SUI1 16 KkvTtvsglepfgidlkklakel 38 K ++++ ++g +k+l+++l CUFF.54.1.p1 167 KMFQVIQNQ-ANGCSMKELVQKL 188 444455555.8888888888876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 346.14 // Query: Sulfatase [M=309] Accession: PF00884.22 Description: Sulfatase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-08 25.4 0.1 0.00069 11.6 0.1 2.3 2 CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675( Domain annotation for each sequence (and alignments): >> CUFF.53.1.p1 type:complete gc:universal CUFF.53.1:1399-3675(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.6 0.1 7.3e-06 0.00069 3 61 .. 48 106 .. 46 125 .. 0.91 2 ! 11.6 0.0 7.7e-06 0.00073 218 309 .] 223 321 .. 221 321 .. 0.71 Alignments for each domain: == domain 1 score: 11.6 bits; conditional E-value: 7.3e-06 EEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS- CS Sulfatase 3 vvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgry 61 vv++++d l+a+ + + ++ ++ t+ l + ++g+ f+ f + +++ p + al tg CUFF.53.1.p1 48 VVFVMVDALRADFVFSKSHNMPFTQSLLYNSTHGIGFSAFARSPTVTMPRLKALTTGTI 106 9***********9999999999999999999**********999************975 PP == domain 2 score: 11.6 bits; conditional E-value: 7.7e-06 HHHHHHHHHHHHHHHHHTTTGGGE..EEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC......EEECSEEE......GGGHH CS Sulfatase 218 veyvDdligrvlaaLeenglldnt..lvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap......rvseelvs......hiDlf 300 + ++D i+r++++L+e ++ nt l+v +Dhg + +gg + + + t l+ ++e+++ ++++++s ++D++ CUFF.53.1.p1 223 LLEIDTIISRIYKYLQEYDEKTNThsLIVLCGDHGMNEVG----NHGGSS---SGETTAALSLLFPSNELSHinkpilNMDDNPYSilerveQVDVV 312 6799************999999987789999****94322....222222...33444444455555555556666776888888888888899999 PP HHHHHHTTE CS Sulfatase 301 ptildlagi 309 pti l+gi CUFF.53.1.p1 313 PTICLLLGI 321 999888875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1317.05 // Query: ThiJ_like [M=196] Accession: PF17124.4 Description: ThiJ/PfpI family-like Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-10 33.8 0.3 3.3e-09 29.3 0.3 2.2 1 CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) 1.7e-10 33.5 0.2 3.9e-09 29.1 0.2 2.2 1 CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028( 0.00078 11.8 0.2 0.0014 10.9 0.2 1.7 1 CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) Domain annotation for each sequence (and alignments): >> CUFF.47.1.p1 type:internal gc:universal CUFF.47.1:597-1(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 29.3 0.3 1.1e-10 3.3e-09 3 155 .. 47 185 .. 46 198 .. 0.78 Alignments for each domain: == domain 1 score: 29.3 bits; conditional E-value: 1.1e-10 ThiJ_like 3 deGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstleeF.keplslssesFsl..eeydlvllpGGsdk 96 ++G e+ ip++v+k+agf v+Fv+e+g d+++ ++ ++ + + +++++ + ++F ++ +++++ s ++ ++y l+++ GG+ CUFF.47.1.p1 47 NTGVHFSELLIPYNVFKKAGFNVQFVSENGSYKFDDHSIEESKLGDF------ERKVFND--KNDDFwTNLNNMKKAS-DIvgKDYQLLFVAGGHAA 134 6799999************************9988888888888877......4556665..3344403333343333.332268**********99 PP ThiJ_like 97 avrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlw 155 + +l + l+++ +e + + vl+a+c+g + la+ k++ ++ t+ + CUFF.47.1.p1 135 MF-DLPKATNLQAVAREVF-------TNGGVLSAVCHGPVLLANVKNPQSVEGKTVVYH 185 99.9999999999988888.......4568*****************999998887655 PP >> CUFF.46.1.p1 type:complete gc:universal CUFF.46.1:1306-2028(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 29.1 0.2 1.2e-10 3.9e-09 3 160 .. 26 169 .. 25 185 .. 0.78 Alignments for each domain: == domain 1 score: 29.1 bits; conditional E-value: 1.2e-10 ThiJ_like 3 deGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstleeF.keplslssesFsl..eeydlvllpGGsdk 96 ++G e+ ip++v+k+agf v+Fv+e+g d+++ ++ ++ + + +++++ + ++F ++ +++++ s ++ ++y l+++ GG+ CUFF.46.1.p1 26 NTGVHFSELLIPYNVFKKAGFNVQFVSENGSYKFDDHSIEESKLGDF------ERKVFND--KNDDFwTNLNNMKKAS-DIvgKDYQLLFVAGGHAA 113 6799999************************9988888888888877......4556665..3344403333343333.332268**********99 PP ThiJ_like 97 avrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlwmerts 160 + +l + l+++ +e + + vl+a+c+g + la+ k++ ++ t+ + t+ CUFF.46.1.p1 114 MF-DLPKATNLQAVAREVF-------TNGGVLSAVCHGPVLLANVKNPQSVEGKTVVYHKHVTA 169 99.9999999999988888.......4568*****************99999998866655555 PP >> CUFF.42.1.p2 type:complete gc:universal CUFF.42.1:152-820(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 10.9 0.2 4.5e-05 0.0014 77 169 .. 77 164 .. 16 190 .. 0.77 Alignments for each domain: == domain 1 score: 10.9 bits; conditional E-value: 4.5e-05 ThiJ_like 77 sesFsleeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpe...ldlktttlPlwmertsillgstaek 169 ++ ++ +y++ + GG++ ++ lh+ ++ + v++a+c+g + l + k+ +k t+ ++ e + ++ +++ CUFF.42.1.p2 77 ASDINFSDYSIFFAAGGHGTLF-DFPSATNLHKGAAKIY-------SMGGVIAAVCHGPVILPCIKDStgfSIVKGKTVTAFNEIAEQQMNLMPTF 164 3345889************999.9999999999988877.......5568********99998887775554456666666666555555555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (196 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 8 (0.0842105); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 3 (0.0315789); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 207.79 // Query: TPP_enzyme_C [M=153] Accession: PF02775.20 Description: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-27 86.5 0.6 2.2e-25 81.8 0.0 2.6 3 CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092( Domain annotation for each sequence (and alignments): >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 2.2 0.0 0.0076 0.72 115 153 .] 132 172 .. 107 172 .. 0.80 2 ? -3.6 0.1 0.47 45 112 124 .. 234 246 .. 227 252 .. 0.76 3 ! 81.8 0.0 2.3e-27 2.2e-25 24 153 .] 415 539 .. 395 539 .. 0.85 Alignments for each domain: == domain 1 score: 2.2 bits; conditional E-value: 0.0076 HHHHHTTSE.EE..EESSH.HHHHHHHHHHHHCSSSEEEEEE CS TPP_enzyme_C 115 klaealGak.ga..rvekadveeleealkealekkgpaliev 153 ++a+ l + +a r e+a + ++ a+++a+ +++p++ie+ CUFF.32.1.p1 132 EIAKKLTCAaVAikRAEDA-PVMIDHAIRQAILQHKPVYIEI 172 6788887775667665555.78899*******999****996 PP == domain 2 score: -3.6 bits; conditional E-value: 0.47 -HHHHHHHTTSEE CS TPP_enzyme_C 112 dfaklaealGakg 124 f+klaeal + + CUFF.32.1.p1 234 AFVKLAEALNCAA 246 6999999998874 PP == domain 3 score: 81.8 bits; conditional E-value: 2.3e-27 ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHT CS TPP_enzyme_C 24 sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaeal 120 + +g++G+++p A+G ++a+p+r+ +++vGDG+f+ ++qe+++++r++lp+++++lnN+gy + ++ ++ r ++ dfa+++e+l CUFF.32.1.p1 415 EMQWGHIGWSVPSAMGYAVAAPERRTIVMVGDGSFQLTGQEISQMIRHKLPVLIFLLNNRGYTIEIQIHDGPYN-R--------IQNWDFAAFCESL 502 56789*********************************************************766666666664.2........6799********* PP TSE.EE....EESSH.HHHHHHHHHHHH.CSSSEEEEEE CS TPP_enzyme_C 121 Gak.ga....rvekadveeleealkeal.ekkgpaliev 153 + g ++ eel a+k al +k+gp+lie+ CUFF.32.1.p1 503 NGEtGKakglHAKTG--EELTSAIKVALqNKEGPTLIEC 539 666555674455555..***********99*******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (153 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1109.34 // Query: TPP_enzyme_M [M=137] Accession: PF00205.21 Description: Thiamine pyrophosphate enzyme, central domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-24 77.7 0.0 6.9e-24 76.8 0.0 1.4 1 CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092( Domain annotation for each sequence (and alignments): >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 76.8 0.0 7.2e-26 6.9e-24 3 113 .. 207 316 .. 205 325 .. 0.90 Alignments for each domain: == domain 1 score: 76.8 bits; conditional E-value: 7.2e-26 HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGSCHHHHHHH.HH-SEEEEES-SSSTCCCTTTT CS TPP_enzyme_M 3 raaellkkakrpvilvGggvsrsgaskelrelaeklgiPvvttlmgkgaipedhplylG.mlgllgspaaneal.eeaDlvlllGarlsdirttgss 97 aael++k+++p++l+G + + +ga+ ++++lae+l++ + ++++kg+++e+h++y+G ++g ++s++ +a+ e++Dlv+ G+ ++d++t g CUFF.32.1.p1 207 IAAELISKKEKPILLAGPKLRAAGAESAFVKLAEALNCAAFIMPAAKGFYSEEHKNYAGvYWGEVSSSETTKAVyESSDLVIGAGVLFNDYSTVGWR 303 599***************************************************************99999999899****************9966 PP TTTTTT-EEEEEESSC CS TPP_enzyme_M 98 pefapeakiihididp 113 + +p+ i +++d CUFF.32.1.p1 304 AAPNPN---ILLNSDY 316 666666...5555554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (137 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 5 (0.0526316); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 1282.76 // Query: TPP_enzyme_N [M=172] Accession: PF02776.17 Description: Thiamine pyrophosphate enzyme, N-terminal TPP binding domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-39 126.5 0.0 1.3e-37 121.7 0.1 2.3 2 CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092( Domain annotation for each sequence (and alignments): >> CUFF.32.1.p1 type:complete gc:universal CUFF.32.1:1308-3092(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 121.7 0.1 1.3e-39 1.3e-37 1 170 [. 9 183 .. 9 185 .. 0.94 2 ! 2.6 0.0 0.005 0.48 136 161 .. 516 541 .. 428 545 .. 0.91 Alignments for each domain: == domain 1 score: 121.7 bits; conditional E-value: 1.3e-39 EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEE CS TPP_enzyme_N 1 ltvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvls 97 +tv+++l+++L + g++ f vpG+ +l lld l+ +g++ + + +E ++afaA+gyar+ g +++++vt+ +Ga+ a+ ++ +A+ +++P++++s CUFF.32.1.p1 9 MTVGTYLAQRLVEIGIKNHFVVPGDYNLRLLDFLEYYPGLSEIGCCNELNCAFAAEGYARSNG-IACAVVTYSVGALTAFDGIGGAYAENLPVILVS 104 89**********************************************************976.********************************* PP EE--CCCHH.....S--TC.-T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-EEEH CS TPP_enzyme_N 98 gdrptslrg.....qgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvlleevde 170 g+++t + + +++l q+++++++t +a+ ++++e++p++++ Air+a ++ Pvy+e+p ++ +++++ CUFF.32.1.p1 105 GSPNTNDLSsghllHHTLGTHDfeYQMEIAKKLTCAAVAIKRAEDAPVMIDHAIRQA-ILQHKPVYIEIPTNMANQPCPV 183 *********9888755555333657********************************.99****************9986 PP == domain 2 score: 2.6 bits; conditional E-value: 0.005 HHHHHHHHHHHHHSSS--EEEEEEEH CS TPP_enzyme_N 136 lpealrrAirtalsgrpgPvylelpk 161 + e+l Ai++al+++ gP ++e + CUFF.32.1.p1 516 TGEELTSAIKVALQNKEGPTLIECAI 541 568999***************99665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (172 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 3 (0.0315789); expected 1.9 (0.02) Passed bias filter: 3 (0.0315789); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1266.54 // Query: Transferase [M=434] Accession: PF02458.14 Description: Transferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00025 12.3 0.0 0.0003 12.1 0.0 1.0 1 CUFF.2.1.p1 type:complete gc:universal CUFF.2.1:577-948(+) Domain annotation for each sequence (and alignments): >> CUFF.2.1.p1 type:complete gc:universal CUFF.2.1:577-948(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.1 0.0 3.1e-06 0.0003 348 403 .. 49 107 .. 37 111 .. 0.76 Alignments for each domain: == domain 1 score: 12.1 bits; conditional E-value: 3.1e-06 Transferase 348 nstlkaelv..skgkkdgeevtvsswlklplyevdFGwgkP..vyvvpvvsskkdnkill 403 n tl+a+++ ++g ++ + +v +wlk++l v FG g P v++ +++s+ + ++i++ CUFF.2.1.p1 49 N-TLMAHCFetYNGVEKSGTQCVADWLKVGLLAVTFGAGGPrlVNTLGGSSPTTKRVIYI 107 4.5666664226777777*********************995566777888888877554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (434 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 2737.05 // Query: TRAPP [M=146] Accession: PF04051.15 Description: Transport protein particle (TRAPP) component Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-26 83.5 0.2 8e-26 83.1 0.2 1.1 1 CUFF.55.1.p1 type:5prime_partial gc:universal CUFF.55.1:2-50 Domain annotation for each sequence (and alignments): >> CUFF.55.1.p1 type:5prime_partial gc:universal CUFF.55.1:2-505(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 83.1 0.2 8.5e-28 8e-26 1 99 [. 34 142 .. 34 163 .. 0.88 Alignments for each domain: == domain 1 score: 83.1 bits; conditional E-value: 8.5e-28 TRAPP 1 fefllgelvsylirdskdveeve..........krLekmGyrvGlrllelllarerpretdilevlkfickdlWkalfgkqidnlktnhrgeyvltd 87 ++fll+elv+++ r ++d ++ + + Le++G++vG +++e +l+ +r+r t++ +v+ f+c++lW ++f+k+ dnlktn+rg +vltd CUFF.55.1.p1 34 LDFLLIELVHTAKRLAEDRKKKSsseksiesdfQMLESIGFQVGRKITE-RLLLNRNRITETTDVMRFLCRELWPIVFRKPLDNLKTNRRGIFVLTD 129 58************9999888889999**********************.888888***************************************** PP TRAPP 88 nef.pltrfvelp 99 + f ++t+++ + CUFF.55.1.p1 130 TYFyWFTKMTAMT 142 *********6433 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (146 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 4 (0.0421053); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1737.48 // Query: TRI12 [M=599] Accession: PF06609.12 Description: Fungal trichothecene efflux pump (TRI12) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-10 30.8 27.0 1.2e-09 29.7 27.0 1.4 1 CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) Domain annotation for each sequence (and alignments): >> CUFF.25.1.p1 type:complete gc:universal CUFF.25.1:24-1916(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 29.7 27.0 1.3e-11 1.2e-09 31 494 .. 69 553 .. 49 575 .. 0.69 Alignments for each domain: == domain 1 score: 29.7 bits; conditional E-value: 1.3e-11 TRI12 31 elpegyyrsprvvasfaafslnvvatyfvlqasasa.lpnilqdvgqsensslfstlwttgqavsil...vmgrltdrfgrrpfvilthilglvgai 123 + + y+ r + af + ++a + +s+ + + +s++stl +s + ++g+++d r l ++ ++g i CUFF.25.1.p1 69 AVRDSIYQNKRGMYLAYAFGIAILACSWASAIQSSTtYSYQVYATASFNRTSMISTLEIATAIISSVckpILGKFSDITSRPMTYTLVLLFYVIGFI 165 4567777777777666778877777766543333330333334445556679999998776665544233899999987765555666677788889 PP TRI12 124 vgctatkfntllaamtllgv.aagpagasplfvgelmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiy.iitsaiav.llivvwy 217 v ++++ + + + ++ + ++g l+vg+l s k + + ++s p ++t + ++ q + i+ +wrw + ++ ii+ a+ +i++ y CUFF.25.1.p1 166 VVASSSTISAYVIGSVFISIgSSGLDYLNTLVVGDLTSLKWRGFMTALLSTPYIATVWFTGFIVQGI-IDSNWRWGYGMFaIIMPAVMTpAVIILMY 261 888888888877777776662457777899*********9987777889********9999999986.9******9987646777765514555555 PP TRI12 218 ypps......fa.....qlhgk...kvrkreelak....ldwigiilvivgvslfllgvswggkpnspwnsakviglissglgslvvfalyevygkp 296 ++ q k k +k ++l k +d g+il+ vg s++ll s ++ w+ +i ++ g l+ ++ ye++ p CUFF.25.1.p1 262 LERQankdenIKkiinyQTEEKnknKQSKWQKLWKavleVDLFGLILLGVGWSILLLPFSLTSYAKNGWKNPSMIAMMVVGGVILIAYSGYEMFIAP 358 4332111111221111122223111444555554444448*******************************************************99 PP TRI12 297 vrpivppalfkdtrgfvcillissimgamnlslviiypqq.vvnifgsslknwee..tawmsatasfgtgagvvvlgslfhlvrhirwqilvgalwl 390 p p +++ r f+ ++i + l +y ++ s ++w + a + fg +ag + +fh ++++ lv + CUFF.25.1.p1 359 Y-PSCPRRVMN--RTFITAVIIDFFYY-LAGYLQSMYFTTyTWILYDWSYRDWTYfnNTMTIALCVFGVFAGAM--HRVFHRYKYLQIIGLVIKI-- 447 6.888998875..77999888876554.44455556655504556889*****8521334457789******87..6899977776544444333.. PP TRI12 391 taflgamssvnrd.nknaaialsv.lsgfvvawaqditmllvqfittdedlgvafavvaaarpfagsiftaafislysnrypkelashlssalrgtd 485 g + n + +a s+ l g+ +++ + + q +dl +a +++ + g+i +a ++sn+ pk l +l s++ t+ CUFF.25.1.p1 448 -VGYGILIRPNFAaTGKVDLAWSLiLIGMGGSFSVVGSQVSCQASVPHQDLAIASSLLPLYTNIGGAIGAAIASPIFSNKVPKYLREYLPSSINDTQ 543 .33344433332202233344443144555555555566778999999***************999999999999*******************999 PP TRI12 486 ipq.asfssl 494 + + s ssl CUFF.25.1.p1 544 VYNfYSDSSL 553 7651455555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (599 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 363.15 // Query: UPF0489 [M=178] Accession: PF12640.6 Description: UPF0489 domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00064 12.6 0.0 0.00099 12.0 0.0 1.2 1 CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122 Domain annotation for each sequence (and alignments): >> CUFF.38.1.p4 type:3prime_partial gc:universal CUFF.38.1:1122-1(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.0 0.0 1e-05 0.00099 7 43 .. 186 229 .. 183 270 .. 0.67 Alignments for each domain: == domain 1 score: 12.0 bits; conditional E-value: 1e-05 UPF0489 7 HheaLeaiyraigskklpsdlslvHlDaHpDllipk..........k 43 H+ +L+ i r +++ + ++s++H+D+H D pk CUFF.38.1.p4 186 HTIVLP-ILRSVSRAY--GPVSIIHFDSHLDSWKPKvfgggkssvgS 229 444444.555566666..99***********8777666555554440 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (178 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 1 (0.0105263); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 1864.39 // Query: Usher [M=551] Accession: PF00577.19 Description: Outer membrane usher protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00057 11.4 0.0 0.00069 11.1 0.0 1.1 1 CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612- Domain annotation for each sequence (and alignments): >> CUFF.20.1.p2 type:3prime_partial gc:universal CUFF.20.1:612-1(-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.1 0.0 7.2e-06 0.00069 35 132 .. 17 114 .. 2 116 .. 0.77 Alignments for each domain: == domain 1 score: 11.1 bits; conditional E-value: 7.2e-06 EEEEEEEEEETTTTEEEEEEEEE--SSSS---EEEEEEEEE-GGGS-CCCCCEEEEEEEEESSSEEEEEECTTEEEEEEEE-SEEEEE-S---TTTT CS Usher 35 ssrtylqraipqlkskLtlGesytssdiFdsvsfrGvsLasddnmlPdslrgyaPevrGiArtnAkVtirqnGyviYqtlVppGpFeiqdlnptsss 131 +s + r + +l+++ G s+++++i + + + +L+ + + + ++ +P G Ar+n +t+ + +viY+t+ +pG + + s++ CUFF.20.1.p2 17 WSARRVCRIFANLRTHRARGSSNVKNEIKKQEGNVSFQLKMSVKQFVSDGHIVRPYLLGLARSNPGLTVIEHDRVIYRTASAPGSGDLPKVTLVSGG 113 5555566667777777777777777777777777777777776666667777889999**************************9888888777766 PP C CS Usher 132 g 132 g CUFF.20.1.p2 114 G 114 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (551 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 7 (0.0736842); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1286.72 // Query: zf-C2H2 [M=23] Accession: PF00096.25 Description: Zinc finger, C2H2 type Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-10 32.1 9.4 4.4e-06 19.7 1.9 2.7 2 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( Domain annotation for each sequence (and alignments): >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.2 1.0 5.9e-07 5.6e-05 1 20 [. 31 50 .. 31 51 .. 0.95 2 ! 19.7 1.9 4.7e-08 4.4e-06 2 23 .] 60 82 .. 59 82 .. 0.96 Alignments for each domain: == domain 1 score: 16.2 bits; conditional E-value: 5.9e-07 EEETTTTEEESSHHHHHHHH CS zf-C2H2 1 ykCpdCgksFkrksnLkrHi 20 ++C+ C k+F+r +nL+rH CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 89*****************5 PP == domain 2 score: 19.7 bits; conditional E-value: 4.7e-08 EETTTTEEESSHHHHHHHHHC.C CS zf-C2H2 2 kCpdCgksFkrksnLkrHirt.H 23 +Cp+C ++krk++LkrHi++ H CUFF.45.1.p1 60 PCPYCEIKCKRKDLLKRHIQRfH 82 6********************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (23 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 6 (0.0631579); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 409.96 // Query: zf-C2H2_4 [M=24] Accession: PF13894.5 Description: C2H2-type zinc finger Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-05 18.6 12.9 0.00084 12.9 1.6 2.9 2 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( Domain annotation for each sequence (and alignments): >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 10.0 4.0 7.8e-05 0.0074 1 20 [. 31 50 .. 31 53 .. 0.89 2 ! 12.9 1.6 8.8e-06 0.00084 2 24 .] 60 82 .. 59 82 .. 0.93 Alignments for each domain: == domain 1 score: 10.0 bits; conditional E-value: 7.8e-05 zf-C2H2_4 1 fkCpiCgksFsskkaLlrHl 20 f+C++C k+F+++++L rH CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 89********99999****4 PP == domain 2 score: 12.9 bits; conditional E-value: 8.8e-06 zf-C2H2_4 2 kCpiCgksFsskkaLlrHlkthH 24 +Cp+C +++k+ L+rH+++ H CUFF.45.1.p1 60 PCPYCEIKCKRKDLLKRHIQRFH 82 7********99999*****9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (24 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 9 (0.0947368); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 444.94 // Query: zf-C2H2_6 [M=27] Accession: PF13912.5 Description: C2H2-type zinc finger Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-06 20.0 3.1 2.6e-06 20.0 3.1 2.0 2 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( Domain annotation for each sequence (and alignments): >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 20.0 3.1 2.7e-08 2.6e-06 1 26 [. 30 55 .. 30 56 .. 0.96 2 ? -3.5 0.6 0.62 59 4 7 .. 61 64 .. 60 65 .. 0.86 Alignments for each domain: == domain 1 score: 20.0 bits; conditional E-value: 2.7e-08 zf-C2H2_6 1 vfeCdeCsksFpslqaLggHkksHrk 26 vf Cd+C k+F + +L+ Hk++H k CUFF.45.1.p1 30 VFPCDQCAKRFTRHENLTRHKACHSK 55 79**********************97 PP == domain 2 score: -3.5 bits; conditional E-value: 0.62 zf-C2H2_6 4 CdeC 7 C++C CUFF.45.1.p1 61 CPYC 64 **** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (27 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 5 (0.0526316); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 464.36 // Query: zf-C2H2_jaz [M=27] Accession: PF12171.7 Description: Zinc-finger double-stranded RNA-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.002 11.1 5.8 0.017 8.2 0.2 2.8 3 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( Domain annotation for each sequence (and alignments): >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 8.2 0.2 0.00018 0.017 2 21 .. 31 50 .. 30 51 .. 0.92 2 ! 5.3 0.1 0.0014 0.13 4 21 .. 61 78 .. 58 79 .. 0.93 3 ? -3.8 0.1 1 95 10 16 .. 166 172 .. 165 172 .. 0.83 Alignments for each domain: == domain 1 score: 8.2 bits; conditional E-value: 0.00018 CBBTTTTBBBSSHHHHHCCT CS zf-C2H2_jaz 2 fYCvlCdKyFksenaldnHl 21 f C C+K F +++l H+ CUFF.45.1.p1 31 FPCDQCAKRFTRHENLTRHK 50 77*****************6 PP == domain 2 score: 5.3 bits; conditional E-value: 0.0014 BTTTTBBBSSHHHHHCCT CS zf-C2H2_jaz 4 CvlCdKyFksenaldnHl 21 C++C+ +k l+ H+ CUFF.45.1.p1 61 CPYCEIKCKRKDLLKRHI 78 *****************8 PP == domain 3 score: -3.8 bits; conditional E-value: 1 BBSSHHH CS zf-C2H2_jaz 10 yFksena 16 F+sen+ CUFF.45.1.p1 166 SFNSENV 172 59***96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (27 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 2 (0.0210526); expected 1.9 (0.02) Passed bias filter: 1 (0.0105263); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 484.48 // Query: zf-Di19 [M=54] Accession: PF05605.11 Description: Drought induced 19 protein (Di19), zinc-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- ------ inclusion threshold ------ 0.027 7.5 8.1 0.0019 11.2 1.0 2.2 1 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( Domain annotation for each sequence (and alignments): >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.2 1.0 2e-05 0.0019 3 28 .. 59 85 .. 57 88 .. 0.79 Alignments for each domain: == domain 1 score: 11.2 bits; conditional E-value: 2e-05 zf-Di19 3 ftCPyCgkeltvkeLv.eHvedeHrve 28 ++CPyC+ + + k L+ +H++ H ++ CUFF.45.1.p1 59 IPCPYCEIKCKRKDLLkRHIQRFHNDK 85 68*****99877776527***999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (54 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 10 (0.105263); expected 1.9 (0.02) Passed bias filter: 10 (0.105263); expected 1.9 (0.02) Passed Vit filter: 2 (0.0210526); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 220.49 // Query: zf-H2C2_2 [M=26] Accession: PF13465.5 Description: Zinc-finger double domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00054 13.1 15.4 0.0047 10.1 4.9 3.4 3 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( Domain annotation for each sequence (and alignments): >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 7.6 0.4 0.0003 0.028 12 26 .] 28 42 .. 26 42 .. 0.83 2 ! 10.1 4.9 4.9e-05 0.0047 1 21 [. 45 65 .. 45 70 .. 0.90 3 ? 0.9 0.1 0.042 4 2 10 .. 74 83 .. 74 89 .. 0.70 Alignments for each domain: == domain 1 score: 7.6 bits; conditional E-value: 0.0003 zf-H2C2_2 12 ekpyeCplCdkaFkt 26 ++ + C+ C+k+F++ CUFF.45.1.p1 28 KRVFPCDQCAKRFTR 42 4559*********85 PP == domain 2 score: 10.1 bits; conditional E-value: 4.9e-05 zf-H2C2_2 1 nLrrHlrkHtgekpyeCplCd 21 nL+rH + H + p Cp+C CUFF.45.1.p1 45 NLTRHKACHSKAEPIPCPYCE 65 8*******************7 PP == domain 3 score: 0.9 bits; conditional E-value: 0.042 zf-H2C2_2 2 LrrHlr.kHt 10 L+rH+ +H CUFF.45.1.p1 74 LKRHIQrFHN 83 89**962586 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 4 (0.0421053); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 416.44 // Query: zf-TRAF [M=60] Accession: PF02176.17 Description: TRAF-type zinc finger Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- ------ inclusion threshold ------ 0.029 7.8 9.9 0.04 7.3 8.4 1.9 2 CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850( Domain annotation for each sequence (and alignments): >> CUFF.45.1.p1 type:complete gc:universal CUFF.45.1:1093-2850(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 7.3 8.4 0.00042 0.04 9 56 .. 30 72 .. 27 80 .. 0.77 2 ? -2.0 0.0 0.33 31 26 43 .. 276 293 .. 274 294 .. 0.77 Alignments for each domain: == domain 1 score: 7.3 bits; conditional E-value: 0.00042 EEE-TT--S-BEEETTTCCCCCCTTSTTS--XXSSXXXXSXXXXXHHH CS zf-TRAF 9 pvpCpnecckkkilRkdlkdHlekdCkkaevkCkfkevGCkekvkrea 56 pC ++c+k ++l H + k +++C++ C+ k+kr++ CUFF.45.1.p1 30 VFPC-DQCAKRFTRHENLTRHKACHSKAEPIPCPY----CEIKCKRKD 72 5689.88**9999999*****997777889*****....555555554 PP == domain 2 score: -2.0 bits; conditional E-value: 0.33 CCCCCCTTSTTS--XXSS CS zf-TRAF 26 lkdHlekdCkkaevkCkf 43 + + ++ +C + v C + CUFF.45.1.p1 276 ISNLIDLECIRRSVFCLY 293 666678889999999988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (60 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 7 (0.0736842); expected 1.9 (0.02) Passed bias filter: 6 (0.0631579); expected 1.9 (0.02) Passed Vit filter: 3 (0.0315789); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 787.68 // Query: Zn_clus [M=40] Accession: PF00172.17 Description: Fungal Zn(2)-Cys(6) binuclear cluster domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-10 31.5 13.0 1.2e-09 30.8 13.0 1.4 1 CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772( Domain annotation for each sequence (and alignments): >> CUFF.38.1.p1 type:complete gc:universal CUFF.38.1:3859-5772(+) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 30.8 13.0 1.3e-11 1.2e-09 1 39 [. 5 42 .. 5 44 .. 0.91 Alignments for each domain: == domain 1 score: 30.8 bits; conditional E-value: 1.3e-11 -S-HHHHHCT---STSSSS-HHHHHCT---ECCCTCCCE CS Zn_clus 1 haCdnCrkkKvKCdakkPaCsnCkklnleCtfysesskr 39 +aCd Cr kK+KC++++P C+ C +++C ys++ +r CUFF.38.1.p1 5 KACDLCRLKKIKCSRGQPRCQTCTLFQADCH-YSNRARR 42 59*****************************.7777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 95 (31269 residues searched) Passed MSV filter: 8 (0.0842105); expected 1.9 (0.02) Passed bias filter: 2 (0.0210526); expected 1.9 (0.02) Passed Vit filter: 1 (0.0105263); expected 0.1 (0.001) Passed Fwd filter: 1 (0.0105263); expected 0.0 (1e-05) Initial search space (Z): 95 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 697.47 // [ok] eval $cmd ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v * [Thu May 9 19:35:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * [Thu May 9 19:35:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: CUFF.60.1.p1, not unique enough -skipping training candidate: CUFF.26.1.p1, not unique enough -skipping training candidate: CUFF.38.1.p3, not unique enough -skipping training candidate: CUFF.48.1.p1, not unique enough -skipping training candidate: CUFF.60.1.p2, not unique enough -skipping training candidate: CUFF.30.1.p1, not unique enough -skipping training candidate: CUFF.41.1.p1, not unique enough -skipping training candidate: CUFF.41.1.p2, not unique enough -skipping training candidate: CUFF.30.2.p1, not unique enough -skipping training candidate: CUFF.52.1.p3, not unique enough -skipping training candidate: CUFF.20.1.p2, not unique enough -skipping training candidate: CUFF.47.1.p1, not unique enough -skipping training candidate: CUFF.48.1.p3, not unique enough -skipping training candidate: CUFF.13.3.p1, not unique enough -skipping training candidate: CUFF.28.1.p1, not unique enough -skipping training candidate: CUFF.34.1.p2, not unique enough -skipping training candidate: CUFF.13.1.p1, not unique enough -skipping training candidate: CUFF.38.1.p5, not unique enough -skipping training candidate: CUFF.27.1.p2, not unique enough -skipping training candidate: CUFF.41.1.p3, not unique enough -skipping training candidate: CUFF.13.1.p2, not unique enough -skipping training candidate: CUFF.27.1.p3, not unique enough -skipping training candidate: CUFF.41.1.p4, not unique enough -redundancy-minimized set includes 72 / 95 = 75.79% * [Thu May 9 19:35:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 37 * [Thu May 9 19:35:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores * [Thu May 9 19:35:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores * [Thu May 9 19:35:43 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfsblastp output found (blastp.outfmt6) and processing... PFAM output found (pfam.domtblout) and processing... * [Thu May 9 19:35:43 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement Training start codon pattern recognition* [Thu May 9 19:35:43 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * [Thu May 9 19:35:43 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:36:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * [Thu May 9 19:36:36 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 * [Thu May 9 19:36:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 * [Thu May 9 19:36:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:36:42 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:36:43 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 62 num_incorporate: 18 -feature swap of score: -0.0856480966312914 instead of -1.67227165897837 -feature swap of score: 1.94858034627835 instead of -0.884029553505083 -feature swap of score: 2.12188175995298 instead of -0.685343860113718 -feature swap of score: 2.31823471239686 instead of 1.3320086516586 -feature swap of score: 3.37895288616016 instead of 1.93080159572592 -feature swap of score: 3.63482432490867 instead of 3.22946119764082 -feature swap of score: 5.41689919345157 instead of 3.20580366781557 -num feature swaps: 7 * [Thu May 9 19:36:43 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:37:26 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * [Thu May 9 19:37:34 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 * [Thu May 9 19:37:36 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 * [Thu May 9 19:37:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:37:39 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 1 * [Thu May 9 19:37:40 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3* [Thu May 9 19:37:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.bed * [Thu May 9 19:37:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.pep * [Thu May 9 19:37:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example/transcripts.fasta.transdecoder.* ## convert to genome coordinates ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 transcripts.gff3 transcripts.fasta > transcripts.fasta.transdecoder.genome.gff3 -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1, 612 -Warning [2], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [3], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1471, 2862 -Warning [4], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [5], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CUFF.30.2.p1. -Warning [7], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [8], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1164, 2072 -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 3, 440 -Warning [10], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [12], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1899, 2783 -Warning [13], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 2759, 3736 -Warning [14], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1142, 4111 -Warning [16], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 3280, 4776 -Warning [17], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1, 534 -Warning [18], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 4115, 4705 -Warning [19], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [20], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 3, 722 Done. 81 / 82 transcript orfs could be propagated to the genome ## make bed files for viewing with GenomeView # covert cufflinks gtf to bed ../../util/gtf_to_bed.pl transcripts.gtf > transcripts.bed # convert the genome-based gene-gff3 file to bed ../../util/gff3_file_to_bed.pl transcripts.fasta.transdecoder.genome.gff3 > transcripts.fasta.transdecoder.genome.bed # ensure no fatal problems w/ pep file ../../util/fasta_prot_checker.pl transcripts.fasta.transdecoder.pep # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* exit 0 make[4]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/cufflinks_example' Running example in $... make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example' ./runMe.sh #!/bin/bash -ve if [ ! -e genome.fasta ]; then gunzip -c genome.fasta.gz > genome.fasta fi if [ ! -e pasa_assemblies.fasta ]; then gunzip -c pasa_assemblies.fasta.gz > pasa_assemblies.fasta fi if [ ! -e pasa_assemblies.gff3 ]; then gunzip -c pasa_assemblies.gff3.gz > pasa_assemblies.gff3 fi if [ ! -e pasa_assemblies_described.txt ]; then gunzip -c pasa_assemblies_described.txt.gz > pasa_assemblies_described.txt fi # get the gene-to-transcript relationships cut -f2,3 pasa_assemblies_described.txt > pasa.gene_trans_map.txt ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir * [Thu May 9 19:37:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. - extracting ORFs from transcripts. -total transcripts to examine: 858 [100/858] = 11.66% done [200/858] = 23.31% done [300/858] = 34.97% done [400/858] = 46.62% done [500/858] = 58.28% done [600/858] = 69.93% done [700/858] = 81.59% done [800/858] = 93.24% done CMD: touch /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. ../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir * [Thu May 9 19:37:45 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * [Thu May 9 19:37:45 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: asmbl_804.p1, not unique enough -skipping training candidate: asmbl_395.p1, not unique enough -skipping training candidate: asmbl_805.p1, not unique enough -skipping training candidate: asmbl_446.p1, not unique enough -skipping training candidate: asmbl_745.p1, not unique enough -skipping training candidate: asmbl_692.p1, not unique enough -skipping training candidate: asmbl_570.p1, not unique enough -skipping training candidate: asmbl_558.p1, not unique enough -skipping training candidate: asmbl_694.p1, not unique enough -skipping training candidate: asmbl_434.p1, not unique enough -skipping training candidate: asmbl_688.p1, not unique enough -skipping training candidate: asmbl_725.p1, not unique enough -skipping training candidate: asmbl_507.p1, not unique enough -skipping training candidate: asmbl_814.p1, not unique enough -skipping training candidate: asmbl_632.p1, not unique enough -skipping training candidate: asmbl_654.p1, not unique enough -skipping training candidate: asmbl_777.p1, not unique enough -skipping training candidate: asmbl_290.p1, not unique enough -skipping training candidate: asmbl_745.p2, not unique enough -skipping training candidate: asmbl_746.p1, not unique enough -skipping training candidate: asmbl_290.p2, not unique enough -skipping training candidate: asmbl_746.p2, not unique enough -skipping training candidate: asmbl_115.p1, not unique enough -skipping training candidate: asmbl_560.p1, not unique enough -skipping training candidate: asmbl_561.p1, not unique enough -skipping training candidate: asmbl_784.p1, not unique enough -skipping training candidate: asmbl_778.p1, not unique enough -skipping training candidate: asmbl_508.p1, not unique enough -skipping training candidate: asmbl_21.p1, not unique enough -skipping training candidate: asmbl_22.p1, not unique enough -skipping training candidate: asmbl_450.p1, not unique enough -skipping training candidate: asmbl_448.p1, not unique enough -skipping training candidate: asmbl_449.p1, not unique enough -skipping training candidate: asmbl_772.p1, not unique enough -skipping training candidate: asmbl_556.p1, not unique enough -skipping training candidate: asmbl_68.p1, not unique enough -skipping training candidate: asmbl_363.p1, not unique enough -skipping training candidate: asmbl_470.p1, not unique enough -skipping training candidate: asmbl_471.p1, not unique enough -skipping training candidate: asmbl_773.p1, not unique enough -skipping training candidate: asmbl_667.p1, not unique enough -skipping training candidate: asmbl_576.p1, not unique enough -skipping training candidate: asmbl_774.p1, not unique enough -skipping training candidate: asmbl_234.p1, not unique enough -skipping training candidate: asmbl_639.p1, not unique enough -skipping training candidate: asmbl_640.p1, not unique enough -skipping training candidate: asmbl_727.p1, not unique enough -skipping training candidate: asmbl_672.p1, not unique enough -skipping training candidate: asmbl_852.p1, not unique enough -skipping training candidate: asmbl_565.p1, not unique enough -skipping training candidate: asmbl_813.p1, not unique enough -skipping training candidate: asmbl_786.p1, not unique enough -skipping training candidate: asmbl_726.p1, not unique enough -skipping training candidate: asmbl_635.p1, not unique enough -skipping training candidate: asmbl_501.p1, not unique enough -skipping training candidate: asmbl_559.p1, not unique enough -skipping training candidate: asmbl_624.p1, not unique enough -skipping training candidate: asmbl_599.p1, not unique enough -skipping training candidate: asmbl_768.p1, not unique enough -skipping training candidate: asmbl_537.p1, not unique enough -skipping training candidate: asmbl_787.p1, not unique enough -skipping training candidate: asmbl_585.p1, not unique enough -skipping training candidate: asmbl_519.p1, not unique enough -skipping training candidate: asmbl_734.p1, not unique enough -skipping training candidate: asmbl_844.p1, not unique enough -skipping training candidate: asmbl_789.p1, not unique enough -skipping training candidate: asmbl_847.p1, not unique enough -skipping training candidate: asmbl_554.p1, not unique enough -skipping training candidate: asmbl_462.p1, not unique enough -skipping training candidate: asmbl_514.p1, not unique enough -skipping training candidate: asmbl_711.p1, not unique enough -skipping training candidate: asmbl_790.p1, not unique enough -skipping training candidate: asmbl_744.p1, not unique enough -skipping training candidate: asmbl_50.p1, not unique enough -skipping training candidate: asmbl_491.p1, not unique enough -skipping training candidate: asmbl_489.p1, not unique enough -skipping training candidate: asmbl_49.p1, not unique enough -skipping training candidate: asmbl_51.p1, not unique enough -skipping training candidate: asmbl_492.p1, not unique enough -skipping training candidate: asmbl_490.p1, not unique enough -skipping training candidate: asmbl_621.p1, not unique enough -skipping training candidate: asmbl_728.p1, not unique enough -skipping training candidate: asmbl_167.p1, not unique enough -skipping training candidate: asmbl_625.p1, not unique enough -skipping training candidate: asmbl_8.p1, not unique enough -skipping training candidate: asmbl_460.p1, not unique enough -skipping training candidate: asmbl_815.p1, not unique enough -skipping training candidate: asmbl_9.p1, not unique enough -skipping training candidate: asmbl_459.p1, not unique enough -skipping training candidate: asmbl_662.p1, not unique enough -skipping training candidate: asmbl_854.p1, not unique enough -skipping training candidate: asmbl_636.p1, not unique enough -skipping training candidate: asmbl_851.p1, not unique enough -skipping training candidate: asmbl_291.p1, not unique enough -skipping training candidate: asmbl_743.p1, not unique enough -skipping training candidate: asmbl_467.p1, not unique enough -skipping training candidate: asmbl_569.p1, not unique enough -skipping training candidate: asmbl_592.p1, not unique enough -skipping training candidate: asmbl_710.p1, not unique enough -skipping training candidate: asmbl_686.p1, not unique enough -skipping training candidate: asmbl_649.p1, not unique enough -skipping training candidate: asmbl_431.p1, not unique enough -skipping training candidate: asmbl_32.p1, not unique enough -skipping training candidate: asmbl_441.p1, not unique enough -skipping training candidate: asmbl_438.p1, not unique enough -skipping training candidate: asmbl_740.p1, not unique enough -skipping training candidate: asmbl_30.p1, not unique enough -skipping training candidate: asmbl_439.p1, not unique enough -skipping training candidate: asmbl_779.p1, not unique enough -skipping training candidate: asmbl_447.p1, not unique enough -skipping training candidate: asmbl_780.p1, not unique enough -skipping training candidate: asmbl_803.p1, not unique enough -skipping training candidate: asmbl_442.p1, not unique enough -skipping training candidate: asmbl_503.p1, not unique enough -skipping training candidate: asmbl_443.p1, not unique enough -skipping training candidate: asmbl_531.p1, not unique enough -skipping training candidate: asmbl_687.p1, not unique enough -skipping training candidate: asmbl_719.p1, not unique enough -skipping training candidate: asmbl_822.p1, not unique enough -skipping training candidate: asmbl_287.p1, not unique enough -skipping training candidate: asmbl_685.p1, not unique enough -skipping training candidate: asmbl_260.p1, not unique enough -skipping training candidate: asmbl_715.p1, not unique enough -skipping training candidate: asmbl_775.p1, not unique enough -skipping training candidate: asmbl_31.p1, not unique enough -skipping training candidate: asmbl_440.p1, not unique enough -skipping training candidate: asmbl_377.p1, not unique enough -skipping training candidate: asmbl_378.p1, not unique enough -skipping training candidate: asmbl_821.p1, not unique enough -skipping training candidate: asmbl_818.p1, not unique enough -skipping training candidate: asmbl_493.p1, not unique enough -skipping training candidate: asmbl_553.p1, not unique enough -skipping training candidate: asmbl_659.p1, not unique enough -skipping training candidate: asmbl_258.p1, not unique enough -skipping training candidate: asmbl_713.p1, not unique enough -skipping training candidate: asmbl_653.p1, not unique enough -skipping training candidate: asmbl_628.p1, not unique enough -skipping training candidate: asmbl_824.p1, not unique enough -skipping training candidate: asmbl_597.p1, not unique enough -skipping training candidate: asmbl_753.p1, not unique enough -skipping training candidate: asmbl_614.p1, not unique enough -skipping training candidate: asmbl_310.p1, not unique enough -skipping training candidate: asmbl_724.p1, not unique enough -skipping training candidate: asmbl_382.p1, not unique enough -skipping training candidate: asmbl_819.p1, not unique enough -skipping training candidate: asmbl_699.p1, not unique enough -skipping training candidate: asmbl_700.p1, not unique enough -skipping training candidate: asmbl_643.p1, not unique enough -skipping training candidate: asmbl_571.p1, not unique enough -skipping training candidate: asmbl_259.p1, not unique enough -skipping training candidate: asmbl_521.p1, not unique enough -skipping training candidate: asmbl_761.p1, not unique enough -skipping training candidate: asmbl_735.p1, not unique enough -skipping training candidate: asmbl_856.p1, not unique enough -skipping training candidate: asmbl_648.p1, not unique enough -skipping training candidate: asmbl_607.p1, not unique enough -skipping training candidate: asmbl_163.p1, not unique enough -skipping training candidate: asmbl_629.p1, not unique enough -skipping training candidate: asmbl_517.p1, not unique enough -skipping training candidate: asmbl_178.p1, not unique enough -skipping training candidate: asmbl_482.p1, not unique enough -skipping training candidate: asmbl_770.p1, not unique enough -skipping training candidate: asmbl_858.p1, not unique enough -skipping training candidate: asmbl_481.p1, not unique enough -skipping training candidate: asmbl_776.p1, not unique enough -skipping training candidate: asmbl_609.p1, not unique enough -skipping training candidate: asmbl_457.p1, not unique enough -skipping training candidate: asmbl_796.p1, not unique enough -skipping training candidate: asmbl_329.p1, not unique enough -skipping training candidate: asmbl_509.p1, not unique enough -skipping training candidate: asmbl_755.p1, not unique enough -skipping training candidate: asmbl_812.p1, not unique enough -skipping training candidate: asmbl_483.p1, not unique enough -skipping training candidate: asmbl_730.p1, not unique enough -skipping training candidate: asmbl_795.p1, not unique enough -skipping training candidate: asmbl_227.p1, not unique enough -skipping training candidate: asmbl_647.p1, not unique enough -skipping training candidate: asmbl_479.p1, not unique enough -skipping training candidate: asmbl_13.p1, not unique enough -skipping training candidate: asmbl_224.p1, not unique enough -skipping training candidate: asmbl_458.p1, not unique enough -skipping training candidate: asmbl_651.p1, not unique enough -skipping training candidate: asmbl_650.p1, not unique enough -skipping training candidate: asmbl_682.p1, not unique enough -skipping training candidate: asmbl_633.p1, not unique enough -skipping training candidate: asmbl_522.p1, not unique enough -skipping training candidate: asmbl_630.p1, not unique enough -skipping training candidate: asmbl_512.p1, not unique enough -skipping training candidate: asmbl_737.p1, not unique enough -skipping training candidate: asmbl_739.p1, not unique enough -skipping training candidate: asmbl_829.p1, not unique enough -skipping training candidate: asmbl_702.p1, not unique enough -skipping training candidate: asmbl_568.p1, not unique enough -skipping training candidate: asmbl_158.p1, not unique enough -skipping training candidate: asmbl_634.p1, not unique enough -skipping training candidate: asmbl_542.p1, not unique enough -skipping training candidate: asmbl_854.p2, not unique enough -skipping training candidate: asmbl_598.p1, not unique enough -skipping training candidate: asmbl_788.p1, not unique enough -skipping training candidate: asmbl_69.p1, not unique enough -skipping training candidate: asmbl_472.p1, not unique enough -skipping training candidate: asmbl_717.p1, not unique enough -skipping training candidate: asmbl_365.p1, not unique enough -skipping training candidate: asmbl_771.p1, not unique enough -skipping training candidate: asmbl_619.p1, not unique enough -skipping training candidate: asmbl_616.p1, not unique enough -skipping training candidate: asmbl_85.p1, not unique enough -skipping training candidate: asmbl_518.p1, not unique enough -skipping training candidate: asmbl_668.p1, not unique enough -skipping training candidate: asmbl_828.p1, not unique enough -skipping training candidate: asmbl_608.p1, not unique enough -skipping training candidate: asmbl_709.p1, not unique enough -skipping training candidate: asmbl_420.p1, not unique enough -skipping training candidate: asmbl_445.p1, not unique enough -skipping training candidate: asmbl_855.p1, not unique enough -skipping training candidate: asmbl_654.p2, not unique enough -skipping training candidate: asmbl_708.p1, not unique enough -skipping training candidate: asmbl_524.p1, not unique enough -skipping training candidate: asmbl_849.p1, not unique enough -skipping training candidate: asmbl_583.p1, not unique enough -skipping training candidate: asmbl_477.p1, not unique enough -skipping training candidate: asmbl_712.p1, not unique enough -skipping training candidate: asmbl_811.p1, not unique enough -skipping training candidate: asmbl_90.p1, not unique enough -skipping training candidate: asmbl_177.p1, not unique enough -skipping training candidate: asmbl_488.p1, not unique enough -skipping training candidate: asmbl_513.p1, not unique enough -skipping training candidate: asmbl_615.p1, not unique enough -skipping training candidate: asmbl_551.p1, not unique enough -skipping training candidate: asmbl_816.p1, not unique enough -skipping training candidate: asmbl_837.p1, not unique enough -skipping training candidate: asmbl_853.p1, not unique enough -skipping training candidate: asmbl_693.p1, not unique enough -skipping training candidate: asmbl_546.p1, not unique enough -skipping training candidate: asmbl_538.p1, not unique enough -skipping training candidate: asmbl_539.p1, not unique enough -skipping training candidate: asmbl_631.p1, not unique enough -skipping training candidate: asmbl_463.p1, not unique enough -skipping training candidate: asmbl_452.p1, not unique enough -skipping training candidate: asmbl_146.p1, not unique enough -skipping training candidate: asmbl_173.p1, not unique enough -skipping training candidate: asmbl_549.p1, not unique enough -skipping training candidate: asmbl_586.p1, not unique enough -skipping training candidate: asmbl_618.p1, not unique enough -skipping training candidate: asmbl_52.p1, not unique enough -skipping training candidate: asmbl_53.p1, not unique enough -skipping training candidate: asmbl_461.p1, not unique enough -skipping training candidate: asmbl_486.p1, not unique enough -skipping training candidate: asmbl_487.p1, not unique enough -skipping training candidate: asmbl_765.p1, not unique enough -skipping training candidate: asmbl_785.p1, not unique enough -skipping training candidate: asmbl_432.p1, not unique enough -skipping training candidate: asmbl_246.p1, not unique enough -skipping training candidate: asmbl_328.p1, not unique enough -skipping training candidate: asmbl_678.p1, not unique enough -skipping training candidate: asmbl_754.p1, not unique enough -skipping training candidate: asmbl_515.p1, not unique enough -skipping training candidate: asmbl_105.p1, not unique enough -skipping training candidate: asmbl_572.p1, not unique enough -skipping training candidate: asmbl_611.p1, not unique enough -skipping training candidate: asmbl_172.p1, not unique enough -skipping training candidate: asmbl_617.p1, not unique enough -skipping training candidate: asmbl_823.p1, not unique enough -skipping training candidate: asmbl_1.p1, not unique enough -skipping training candidate: asmbl_146.p2, not unique enough -skipping training candidate: asmbl_528.p1, not unique enough -skipping training candidate: asmbl_586.p2, not unique enough -skipping training candidate: asmbl_606.p1, not unique enough -skipping training candidate: asmbl_454.p1, not unique enough -skipping training candidate: asmbl_110.p1, not unique enough -skipping training candidate: asmbl_525.p1, not unique enough -skipping training candidate: asmbl_566.p1, not unique enough -skipping training candidate: asmbl_626.p1, not unique enough -skipping training candidate: asmbl_681.p1, not unique enough -skipping training candidate: asmbl_792.p1, not unique enough -skipping training candidate: asmbl_310.p2, not unique enough -skipping training candidate: asmbl_724.p2, not unique enough -skipping training candidate: asmbl_304.p1, not unique enough -skipping training candidate: asmbl_732.p1, not unique enough -skipping training candidate: asmbl_451.p1, not unique enough -skipping training candidate: asmbl_57.p1, not unique enough -skipping training candidate: asmbl_246.p2, not unique enough -skipping training candidate: asmbl_484.p1, not unique enough -skipping training candidate: asmbl_678.p2, not unique enough -skipping training candidate: asmbl_682.p2, not unique enough -skipping training candidate: asmbl_35.p1, not unique enough -skipping training candidate: asmbl_436.p1, not unique enough -skipping training candidate: asmbl_437.p1, not unique enough -skipping training candidate: asmbl_848.p1, not unique enough -skipping training candidate: asmbl_478.p1, not unique enough -skipping training candidate: asmbl_720.p1, not unique enough -skipping training candidate: asmbl_857.p1, not unique enough -skipping training candidate: asmbl_846.p1, not unique enough -skipping training candidate: asmbl_125.p1, not unique enough -skipping training candidate: asmbl_444.p1, not unique enough -skipping training candidate: asmbl_552.p1, not unique enough -skipping training candidate: asmbl_845.p1, not unique enough -skipping training candidate: asmbl_246.p3, not unique enough -skipping training candidate: asmbl_659.p2, not unique enough -skipping training candidate: asmbl_678.p3, not unique enough -skipping training candidate: asmbl_420.p2, not unique enough -skipping training candidate: asmbl_855.p2, not unique enough -skipping training candidate: asmbl_809.p1, not unique enough -skipping training candidate: asmbl_303.p1, not unique enough -skipping training candidate: asmbl_390.p1, not unique enough -skipping training candidate: asmbl_731.p1, not unique enough -skipping training candidate: asmbl_810.p1, not unique enough -skipping training candidate: asmbl_494.p1, not unique enough -skipping training candidate: asmbl_693.p2, not unique enough -skipping training candidate: asmbl_199.p1, not unique enough -skipping training candidate: asmbl_605.p1, not unique enough -skipping training candidate: asmbl_593.p1, not unique enough -skipping training candidate: asmbl_504.p1, not unique enough -skipping training candidate: asmbl_575.p1, not unique enough -skipping training candidate: asmbl_745.p3, not unique enough -skipping training candidate: asmbl_574.p1, not unique enough -skipping training candidate: asmbl_817.p1, not unique enough -skipping training candidate: asmbl_455.p1, not unique enough -skipping training candidate: asmbl_480.p1, not unique enough -skipping training candidate: asmbl_77.p1, not unique enough -skipping training candidate: asmbl_453.p1, not unique enough -skipping training candidate: asmbl_526.p1, not unique enough -skipping training candidate: asmbl_584.p1, not unique enough -skipping training candidate: asmbl_778.p2, not unique enough -skipping training candidate: asmbl_101.p1, not unique enough -skipping training candidate: asmbl_165.p1, not unique enough -skipping training candidate: asmbl_366.p1, not unique enough -skipping training candidate: asmbl_502.p1, not unique enough -skipping training candidate: asmbl_627.p1, not unique enough -skipping training candidate: asmbl_769.p1, not unique enough -skipping training candidate: asmbl_765.p2, not unique enough -skipping training candidate: asmbl_207.p1, not unique enough -skipping training candidate: asmbl_242.p1, not unique enough -skipping training candidate: asmbl_331.p1, not unique enough -skipping training candidate: asmbl_669.p1, not unique enough -skipping training candidate: asmbl_684.p1, not unique enough -skipping training candidate: asmbl_757.p1, not unique enough -skipping training candidate: asmbl_199.p2, not unique enough -skipping training candidate: asmbl_200.p1, not unique enough -skipping training candidate: asmbl_593.p2, not unique enough -skipping training candidate: asmbl_594.p1, not unique enough -skipping training candidate: asmbl_536.p1, not unique enough -skipping training candidate: asmbl_660.p1, not unique enough -skipping training candidate: asmbl_794.p1, not unique enough -skipping training candidate: asmbl_435.p1, not unique enough -skipping training candidate: asmbl_554.p2, not unique enough -skipping training candidate: asmbl_614.p2, not unique enough -skipping training candidate: asmbl_588.p1, not unique enough -skipping training candidate: asmbl_676.p1, not unique enough -skipping training candidate: asmbl_706.p1, not unique enough -skipping training candidate: asmbl_590.p1, not unique enough -skipping training candidate: asmbl_68.p2, not unique enough -skipping training candidate: asmbl_197.p1, not unique enough -skipping training candidate: asmbl_246.p4, not unique enough -skipping training candidate: asmbl_470.p2, not unique enough -skipping training candidate: asmbl_471.p2, not unique enough -skipping training candidate: asmbl_591.p1, not unique enough -skipping training candidate: asmbl_678.p4, not unique enough -skipping training candidate: asmbl_564.p1, not unique enough -skipping training candidate: asmbl_200.p2, not unique enough -skipping training candidate: asmbl_612.p1, not unique enough -skipping training candidate: asmbl_594.p2, not unique enough -skipping training candidate: asmbl_436.p2, not unique enough -skipping training candidate: asmbl_532.p1, not unique enough -skipping training candidate: asmbl_688.p2, not unique enough -skipping training candidate: asmbl_122.p1, not unique enough -skipping training candidate: asmbl_555.p1, not unique enough -skipping training candidate: asmbl_646.p1, not unique enough -skipping training candidate: asmbl_807.p1, not unique enough -skipping training candidate: asmbl_498.p1, not unique enough -skipping training candidate: asmbl_724.p3, not unique enough -skipping training candidate: asmbl_122.p2, not unique enough -skipping training candidate: asmbl_555.p2, not unique enough -skipping training candidate: asmbl_718.p1, not unique enough -skipping training candidate: asmbl_35.p2, not unique enough -skipping training candidate: asmbl_437.p2, not unique enough -skipping training candidate: asmbl_588.p2, not unique enough -skipping training candidate: asmbl_791.p1, not unique enough -skipping training candidate: asmbl_856.p2, not unique enough -skipping training candidate: asmbl_548.p1, not unique enough -skipping training candidate: asmbl_602.p1, not unique enough -skipping training candidate: asmbl_497.p1, not unique enough -skipping training candidate: asmbl_311.p2, not unique enough -skipping training candidate: asmbl_601.p1, not unique enough -skipping training candidate: asmbl_725.p2, not unique enough -skipping training candidate: asmbl_73.p1, not unique enough -skipping training candidate: asmbl_529.p1, not unique enough -skipping training candidate: asmbl_2.p1, not unique enough -skipping training candidate: asmbl_241.p1, not unique enough -skipping training candidate: asmbl_683.p1, not unique enough -skipping training candidate: asmbl_816.p2, not unique enough -skipping training candidate: asmbl_231.p1, not unique enough -skipping training candidate: asmbl_644.p1, not unique enough -skipping training candidate: asmbl_133.p1, not unique enough -skipping training candidate: asmbl_544.p1, not unique enough -skipping training candidate: asmbl_577.p1, not unique enough -skipping training candidate: asmbl_623.p1, not unique enough -skipping training candidate: asmbl_134.p1, not unique enough -skipping training candidate: asmbl_545.p1, not unique enough -skipping training candidate: asmbl_649.p2, not unique enough -skipping training candidate: asmbl_69.p2, not unique enough -skipping training candidate: asmbl_132.p1, not unique enough -skipping training candidate: asmbl_472.p2, not unique enough -skipping training candidate: asmbl_533.p1, not unique enough -skipping training candidate: asmbl_543.p1, not unique enough -skipping training candidate: asmbl_664.p1, not unique enough -skipping training candidate: asmbl_677.p1, not unique enough -skipping training candidate: asmbl_748.p1, not unique enough -skipping training candidate: asmbl_802.p1, not unique enough -skipping training candidate: asmbl_117.p2, not unique enough -skipping training candidate: asmbl_559.p2, not unique enough -skipping training candidate: asmbl_825.p1, not unique enough -skipping training candidate: asmbl_596.p1, not unique enough -skipping training candidate: asmbl_703.p1, not unique enough -skipping training candidate: asmbl_838.p1, not unique enough -skipping training candidate: asmbl_469.p1, not unique enough -skipping training candidate: asmbl_698.p1, not unique enough -skipping training candidate: asmbl_798.p1, not unique enough -skipping training candidate: asmbl_290.p3, not unique enough -skipping training candidate: asmbl_409.p2, not unique enough -skipping training candidate: asmbl_746.p3, not unique enough -skipping training candidate: asmbl_780.p2, not unique enough -skipping training candidate: asmbl_838.p2, not unique enough -skipping training candidate: asmbl_295.p1, not unique enough -skipping training candidate: asmbl_741.p1, not unique enough -skipping training candidate: asmbl_232.p1, not unique enough -skipping training candidate: asmbl_645.p1, not unique enough -skipping training candidate: asmbl_589.p1, not unique enough -skipping training candidate: asmbl_657.p1, not unique enough -skipping training candidate: asmbl_218.p1, not unique enough -skipping training candidate: asmbl_658.p1, not unique enough -skipping training candidate: asmbl_656.p1, not unique enough -skipping training candidate: asmbl_675.p1, not unique enough -skipping training candidate: asmbl_697.p1, not unique enough -skipping training candidate: asmbl_808.p1, not unique enough -skipping training candidate: asmbl_674.p1, not unique enough -skipping training candidate: asmbl_465.p1, not unique enough -skipping training candidate: asmbl_443.p2, not unique enough -skipping training candidate: asmbl_673.p1, not unique enough -skipping training candidate: asmbl_788.p2, not unique enough -skipping training candidate: asmbl_4.p1, not unique enough -skipping training candidate: asmbl_278.p3, not unique enough -skipping training candidate: asmbl_408.p2, not unique enough -skipping training candidate: asmbl_464.p1, not unique enough -skipping training candidate: asmbl_693.p3, not unique enough -skipping training candidate: asmbl_837.p2, not unique enough -skipping training candidate: asmbl_463.p2, not unique enough -skipping training candidate: asmbl_13.p2, not unique enough -skipping training candidate: asmbl_457.p2, not unique enough -skipping training candidate: asmbl_458.p2, not unique enough -skipping training candidate: asmbl_637.p1, not unique enough -skipping training candidate: asmbl_750.p1, not unique enough -skipping training candidate: asmbl_485.p1, not unique enough -skipping training candidate: asmbl_562.p1, not unique enough -skipping training candidate: asmbl_636.p2, not unique enough -skipping training candidate: asmbl_748.p2, not unique enough -skipping training candidate: asmbl_310.p4, not unique enough -skipping training candidate: asmbl_724.p4, not unique enough -skipping training candidate: asmbl_723.p1, not unique enough -skipping training candidate: asmbl_305.p1, not unique enough -skipping training candidate: asmbl_733.p1, not unique enough -skipping training candidate: asmbl_644.p2, not unique enough -skipping training candidate: asmbl_498.p2, not unique enough -skipping training candidate: asmbl_704.p1, not unique enough -skipping training candidate: asmbl_725.p3, not unique enough -skipping training candidate: asmbl_230.p2, not unique enough -skipping training candidate: asmbl_221.p1, not unique enough -skipping training candidate: asmbl_622.p1, not unique enough -skipping training candidate: asmbl_655.p1, not unique enough -skipping training candidate: asmbl_643.p2, not unique enough -skipping training candidate: asmbl_716.p1, not unique enough -skipping training candidate: asmbl_726.p2, not unique enough -skipping training candidate: asmbl_516.p1, not unique enough -skipping training candidate: asmbl_587.p1, not unique enough -skipping training candidate: asmbl_813.p2, not unique enough -skipping training candidate: asmbl_310.p5, not unique enough -skipping training candidate: asmbl_537.p2, not unique enough -skipping training candidate: asmbl_578.p1, not unique enough -skipping training candidate: asmbl_724.p5, not unique enough -skipping training candidate: asmbl_751.p1, not unique enough -skipping training candidate: asmbl_815.p2, not unique enough -skipping training candidate: asmbl_151.p1, not unique enough -skipping training candidate: asmbl_410.p1, not unique enough -skipping training candidate: asmbl_582.p1, not unique enough -skipping training candidate: asmbl_580.p1, not unique enough -skipping training candidate: asmbl_839.p1, not unique enough -skipping training candidate: asmbl_290.p4, not unique enough -skipping training candidate: asmbl_557.p1, not unique enough -skipping training candidate: asmbl_660.p2, not unique enough -skipping training candidate: asmbl_700.p2, not unique enough -skipping training candidate: asmbl_745.p4, not unique enough -skipping training candidate: asmbl_746.p4, not unique enough -skipping training candidate: asmbl_779.p2, not unique enough -skipping training candidate: asmbl_696.p1, not unique enough -skipping training candidate: 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asmbl_772.p2, not unique enough -skipping training candidate: asmbl_786.p2, not unique enough -skipping training candidate: asmbl_773.p2, not unique enough -skipping training candidate: asmbl_826.p1, not unique enough -skipping training candidate: asmbl_15.p1, not unique enough -skipping training candidate: asmbl_456.p1, not unique enough -skipping training candidate: asmbl_530.p2, not unique enough -skipping training candidate: asmbl_601.p2, not unique enough -skipping training candidate: asmbl_641.p1, not unique enough -skipping training candidate: asmbl_290.p5, not unique enough -skipping training candidate: asmbl_519.p2, not unique enough -skipping training candidate: asmbl_691.p1, not unique enough -skipping training candidate: asmbl_745.p5, not unique enough -skipping training candidate: asmbl_746.p5, not unique enough -skipping training candidate: asmbl_288.p2, not unique enough -skipping training candidate: asmbl_431.p2, not unique enough -skipping training candidate: asmbl_687.p2, not unique enough -skipping training candidate: asmbl_689.p1, not unique enough -skipping training candidate: asmbl_685.p2, not unique enough -skipping training candidate: asmbl_742.p1, not unique enough -skipping training candidate: asmbl_765.p3, not unique enough -skipping training candidate: asmbl_21.p2, not unique enough -skipping training candidate: asmbl_22.p2, not unique enough -skipping training candidate: asmbl_228.p2, not unique enough -skipping training candidate: asmbl_378.p2, not unique enough -skipping training candidate: asmbl_379.p2, not unique enough -skipping training candidate: asmbl_450.p2, not unique enough -skipping training candidate: asmbl_448.p2, not unique enough -skipping training candidate: asmbl_449.p2, not unique enough -skipping training candidate: asmbl_642.p1, not unique enough -skipping training candidate: asmbl_647.p2, not unique enough -skipping training candidate: asmbl_648.p2, not unique enough -skipping training candidate: 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asmbl_90.p2, not unique enough -skipping training candidate: asmbl_512.p2, not unique enough -skipping training candidate: asmbl_513.p2, not unique enough -skipping training candidate: asmbl_635.p2, not unique enough -skipping training candidate: asmbl_764.p1, not unique enough -skipping training candidate: asmbl_835.p1, not unique enough -skipping training candidate: asmbl_303.p2, not unique enough -skipping training candidate: asmbl_414.p1, not unique enough -skipping training candidate: asmbl_479.p2, not unique enough -skipping training candidate: asmbl_693.p4, not unique enough -skipping training candidate: asmbl_716.p2, not unique enough -skipping training candidate: asmbl_742.p2, not unique enough -skipping training candidate: asmbl_731.p2, not unique enough -skipping training candidate: asmbl_794.p2, not unique enough -skipping training candidate: asmbl_799.p1, not unique enough -skipping training candidate: asmbl_833.p1, not unique enough -skipping training candidate: asmbl_433.p1, not unique enough -skipping training candidate: asmbl_677.p2, not unique enough -skipping training candidate: asmbl_847.p2, not unique enough -skipping training candidate: asmbl_570.p2, not unique enough -skipping training candidate: asmbl_535.p1, not unique enough -skipping training candidate: asmbl_627.p2, not unique enough -skipping training candidate: asmbl_719.p2, not unique enough -skipping training candidate: asmbl_722.p1, not unique enough -skipping training candidate: asmbl_150.p1, not unique enough -skipping training candidate: asmbl_579.p1, not unique enough -skipping training candidate: asmbl_584.p2, not unique enough -skipping training candidate: asmbl_682.p3, not unique enough -skipping training candidate: asmbl_712.p2, not unique enough -skipping training candidate: asmbl_815.p3, not unique enough -skipping training candidate: asmbl_49.p2, not unique enough -skipping training candidate: asmbl_50.p2, not unique enough -skipping training candidate: asmbl_51.p2, not unique enough -skipping training candidate: asmbl_343.p1, not unique enough -skipping training candidate: asmbl_491.p2, not unique enough -skipping training candidate: asmbl_492.p2, not unique enough -skipping training candidate: asmbl_489.p2, not unique enough -skipping training candidate: asmbl_490.p2, not unique enough -skipping training candidate: asmbl_793.p1, not unique enough -skipping training candidate: asmbl_198.p3, not unique enough -skipping training candidate: asmbl_199.p3, not unique enough -skipping training candidate: asmbl_200.p3, not unique enough -skipping training candidate: asmbl_507.p3, not unique enough -skipping training candidate: asmbl_592.p3, not unique enough -skipping training candidate: asmbl_606.p2, not unique enough -skipping training candidate: asmbl_593.p3, not unique enough -skipping training candidate: asmbl_594.p3, not unique enough -skipping training candidate: asmbl_839.p2, not unique enough -skipping training candidate: asmbl_6.p1, not unique enough -skipping training candidate: asmbl_146.p3, not unique enough -skipping training candidate: asmbl_446.p2, not unique enough -skipping training candidate: asmbl_466.p1, not unique enough -skipping training candidate: asmbl_531.p2, not unique enough -skipping training candidate: asmbl_585.p2, not unique enough -skipping training candidate: asmbl_586.p3, not unique enough -skipping training candidate: asmbl_606.p3, not unique enough -skipping training candidate: asmbl_635.p3, not unique enough -skipping training candidate: asmbl_726.p3, not unique enough -skipping training candidate: asmbl_8.p2, not unique enough -skipping training candidate: asmbl_9.p2, not unique enough -skipping training candidate: asmbl_57.p2, not unique enough -skipping training candidate: asmbl_365.p2, not unique enough -skipping training candidate: asmbl_459.p2, not unique enough -skipping training candidate: asmbl_460.p2, not unique enough -skipping training candidate: asmbl_461.p2, not unique enough -skipping training candidate: asmbl_462.p2, not unique enough -skipping training candidate: asmbl_484.p2, not unique enough -skipping training candidate: asmbl_770.p2, not unique enough -skipping training candidate: asmbl_771.p2, not unique enough -skipping training candidate: asmbl_820.p1, not unique enough -skipping training candidate: asmbl_259.p2, not unique enough -skipping training candidate: asmbl_349.p2, not unique enough -skipping training candidate: asmbl_692.p2, not unique enough -skipping training candidate: asmbl_713.p2, not unique enough -skipping training candidate: asmbl_765.p4, not unique enough -skipping training candidate: asmbl_787.p2, not unique enough -skipping training candidate: asmbl_85.p2, not unique enough -skipping training candidate: asmbl_518.p2, not unique enough -skipping training candidate: asmbl_517.p2, not unique enough -skipping training candidate: asmbl_709.p2, not unique enough -skipping training candidate: asmbl_778.p3, not unique enough -skipping training candidate: asmbl_830.p1, not unique enough -skipping training candidate: asmbl_847.p3, not unique enough -skipping training candidate: asmbl_530.p3, not unique enough -skipping training candidate: asmbl_722.p2, not unique enough -skipping training candidate: asmbl_817.p2, not unique enough -skipping training candidate: asmbl_799.p2, not unique enough -skipping training candidate: asmbl_813.p3, not unique enough -skipping training candidate: asmbl_290.p6, not unique enough -skipping training candidate: asmbl_746.p6, not unique enough -skipping training candidate: asmbl_536.p2, not unique enough -skipping training candidate: asmbl_534.p1, not unique enough -skipping training candidate: asmbl_692.p3, not unique enough -skipping training candidate: asmbl_115.p2, not unique enough -skipping training candidate: asmbl_278.p5, not unique enough -skipping training candidate: asmbl_320.p1, not unique enough -skipping training candidate: asmbl_452.p3, not unique enough -skipping training candidate: asmbl_569.p2, not unique enough -skipping training candidate: asmbl_560.p2, not unique enough -skipping training candidate: asmbl_561.p2, not unique enough -skipping training candidate: asmbl_693.p5, not unique enough -skipping training candidate: asmbl_695.p1, not unique enough -skipping training candidate: asmbl_734.p2, not unique enough -skipping training candidate: asmbl_721.p1, not unique enough -skipping training candidate: asmbl_765.p5, not unique enough -skipping training candidate: asmbl_766.p1, not unique enough -skipping training candidate: asmbl_807.p2, not unique enough -skipping training candidate: asmbl_800.p1, not unique enough -skipping training candidate: asmbl_164.p2, not unique enough -skipping training candidate: asmbl_531.p3, not unique enough -skipping training candidate: asmbl_558.p2, not unique enough -skipping training candidate: asmbl_626.p2, not unique enough -skipping training candidate: asmbl_831.p1, not unique enough -redundancy-minimized set includes 396 / 1067 = 37.11% * [Thu May 9 19:37:46 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 42 * [Thu May 9 19:37:46 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores * [Thu May 9 19:37:49 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores * [Thu May 9 19:38:03 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs * [Thu May 9 19:38:03 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement Training start codon pattern recognition* [Thu May 9 19:38:03 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * [Thu May 9 19:38:04 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:39:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * [Thu May 9 19:39:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 * [Thu May 9 19:39:54 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 * [Thu May 9 19:39:56 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:39:58 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:39:59 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced num features: 238 num_incorporate: 71 -feature swap of score: 0.52233068358735 instead of -2.4838353992418 -feature swap of score: 3.4925122435335 instead of -2.69571560364119 -feature swap of score: -0.479799656028566 instead of -2.28706103601398 -feature swap of score: -0.0881342990948846 instead of -2.01923571762916 -feature swap of score: 3.70320425069563 instead of -2.540266312821 -feature swap of score: -1.18001089627022 instead of -2.19874275195072 -feature swap of score: 0.890711131288117 instead of -1.48110814799594 -feature swap of score: -1.05010135127967 instead of -1.29405271062499 -feature swap of score: -0.0660971314530546 instead of -1.10945144224631 -feature swap of score: 4.44453897240347 instead of -0.978468124148539 -feature swap of score: -0.464399759591707 instead of -0.841794961146521 -feature swap of score: 0.255068847557726 instead of -0.83142113951215 -feature swap of score: 1.95582633064074 instead of -0.76896518568472 -feature swap of score: -0.0332453222172366 instead of -0.682979129272786 -feature swap of score: 1.8228745697833 instead of -0.653744437026382 -feature swap of score: 1.00115669145456 instead of -0.336891026477184 -feature swap of score: 0.672803798904712 instead of -0.578246064931 -feature swap of score: 1.8162642359003 instead of -0.452564095078051 -feature swap of score: 0.280846761877589 instead of -0.647264557316993 -feature swap of score: 0.366355095526699 instead of -0.615212412314209 -feature swap of score: 2.52986097726451 instead of -0.758989032460075 -feature swap of score: -0.0952627696553691 instead of -0.817191160815284 -feature swap of score: 0.996754631653053 instead of -0.80551837636419 -feature swap of score: 0.354999699462731 instead of -0.274911636492182 -feature swap of score: 1.28605443964402 instead of 0.0980797372313064 -feature swap of score: 0.32578718956916 instead of -0.042861330285221 -feature swap of score: 2.48770150611293 instead of -0.0868957590364158 -feature swap of score: 2.64754362015744 instead of 0.2916904256282 -feature swap of score: 1.01988302433125 instead of 0.036666467034015 -feature swap of score: 0.702376236311601 instead of -0.128287580103504 -feature swap of score: 2.99676647453095 instead of 0.320673377955444 -feature swap of score: 4.3305495710187 instead of 0.295875888654129 -feature swap of score: 1.17421891679809 instead of 0.254710288367653 -feature swap of score: 0.401521517315352 instead of 0.370606147577384 -feature swap of score: 3.89634731515857 instead of 0.389772413567672 -feature swap of score: 2.74749373854816 instead of 0.451140083480975 -feature swap of score: 4.14790539102617 instead of 0.173512045799991 -feature swap of score: 2.68928352460324 instead of 0.0987413441847772 -feature swap of score: 0.570947526770153 instead of -0.152678189275884 -feature swap of score: 2.87693452246047 instead of 0.175971771120871 -feature swap of score: 0.345761582949679 instead of 0.189210540579853 -feature swap of score: 1.75381703871986 instead of -0.176138170873724 -feature swap of score: 6.3225755214291 instead of 0.182318752228176 -feature swap of score: -0.00356336589610784 instead of -0.074332288426649 -feature swap of score: 1.25652300984573 instead of 0.440440454930295 -feature swap of score: 4.35627103288236 instead of 0.601792868596411 -feature swap of score: 3.34305077634812 instead of 0.646355594435306 -feature swap of score: 0.89148415481126 instead of 0.847522010634187 -feature swap of score: 3.6953445371134 instead of 0.751030612474935 -feature swap of score: 5.78699079524925 instead of 0.699840066363169 -feature swap of score: 2.15409587173251 instead of 0.715035855107118 -feature swap of score: 1.47994164306661 instead of 0.417255934795064 -feature swap of score: 4.91570803685393 instead of 0.612782191206777 -feature swap of score: 0.527551455366298 instead of 0.495108302468003 -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 * [Thu May 9 19:39:59 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:41:20 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * [Thu May 9 19:41:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 * [Thu May 9 19:41:36 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 * [Thu May 9 19:41:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:41:39 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 83 * [Thu May 9 19:41:41 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3* [Thu May 9 19:41:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.bed * [Thu May 9 19:41:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep * [Thu May 9 19:41:42 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example/pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.* ../../util/cdna_alignment_orf_to_genome_orf.pl pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 pasa_assemblies.gff3 pasa_assemblies.fasta > pasa_assemblies.fasta.transdecoder.genome.gff3 -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 205, 828 -Warning [2], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_117.p2. -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_127.p1. -Warning [4], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 142, 1281 -Warning [5], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_177.p1. -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_198.p3. -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_199.p3. -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_200.p3. -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_243.p1. -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_245.p1. -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p3. -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_278.p1. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_280.p1. -Warning [15], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 107, 466 -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_289.p2. -Warning [17], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_290.p1. -Warning [18], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [19], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [20], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [21], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [22], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [23], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [24], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_420.p1. -Warning [25], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 140, 700 -Warning [26], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 340, 816 -Warning [27], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 93, 1106 -Warning [28], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [29], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [30], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 312, 1253 -Warning [31], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_550.p1. -Warning [32], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_559.p2. -Warning [33], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [34], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_592.p3. -Warning [35], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_593.p3. -Warning [36], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_594.p3. -Warning [37], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [38], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_615.p1. -Warning [39], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 80, 427 -Warning [40], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_682.p1. -Warning [41], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [42], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p3. -Warning [43], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_693.p1. -Warning [44], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_695.p1. -Warning [45], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 112, 447 -Warning [46], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_745.p2. -Warning [47], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_746.p1. -Warning [48], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 108, 452 -Warning [49], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 2, 562 -Warning [50], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [51], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 141, 545 -Warning [52], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 178, 1623 -Warning [53], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry asmbl_855.p1. Done. 765 / 792 transcript orfs could be propagated to the genome ../../util/fasta_prot_checker.pl pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep echo "Done. See pasa_assemblies.fasta.transdecoder.\*" Done. See pasa_assemblies.fasta.transdecoder.\* exit 0 make[4]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/pasa_example' Running example in $... make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target' ./runMe.sh CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir * [Thu May 9 19:41:44 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl Trinity.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. - extracting ORFs from transcripts. -total transcripts to examine: 921 [100/921] = 10.86% done [200/921] = 21.72% done [300/921] = 32.57% done [400/921] = 43.43% done [500/921] = 54.29% done [600/921] = 65.15% done [700/921] = 76.00% done [800/921] = 86.86% done [900/921] = 97.72% done CMD: touch /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. * [Thu May 9 19:41:50 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * [Thu May 9 19:41:50 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: comp847_c0_seq2.p1, not unique enough -skipping training candidate: comp992_c0_seq2.p1, not unique enough -skipping training candidate: comp718_c0_seq2.p1, not unique enough -skipping training candidate: comp1177_c0_seq2.p1, not unique enough -skipping training candidate: comp999_c0_seq2.p1, not unique enough -skipping training candidate: comp989_c0_seq1.p1, not unique enough -skipping training candidate: comp836_c0_seq1.p1, not unique enough -skipping training candidate: comp621_c0_seq2.p1, not unique enough -skipping training candidate: comp844_c0_seq2.p1, not unique enough -skipping training candidate: comp594_c0_seq1.p1, not unique enough -skipping training candidate: comp956_c0_seq2.p1, not unique enough -skipping training candidate: comp1044_c0_seq1.p1, not unique enough -skipping training candidate: comp835_c0_seq2.p2, not unique enough -skipping training candidate: comp1029_c0_seq2.p1, not unique enough -skipping training candidate: comp1016_c0_seq2.p1, not unique enough -skipping training candidate: comp1207_c0_seq2.p1, not unique enough -skipping training candidate: comp862_c0_seq1.p1, not unique enough -skipping training candidate: comp703_c0_seq1.p2, not unique enough -skipping training candidate: comp1191_c0_seq1.p1, not unique enough -skipping training candidate: comp867_c0_seq1.p1, not unique enough -skipping training candidate: comp1207_c0_seq2.p2, not unique enough -skipping training candidate: comp905_c0_seq1.p1, not unique enough -skipping training candidate: comp784_c0_seq2.p1, not unique enough -skipping training candidate: comp674_c0_seq1.p1, not unique enough -skipping training candidate: comp924_c0_seq1.p2, not unique enough -skipping training candidate: comp1174_c0_seq2.p1, not unique enough -skipping training candidate: comp1046_c0_seq2.p1, not unique enough -skipping training candidate: comp1191_c0_seq2.p2, not unique enough -skipping training candidate: comp1044_c0_seq2.p2, not unique enough -skipping training candidate: comp873_c0_seq1.p1, not unique enough -skipping training candidate: comp1177_c0_seq2.p2, not unique enough -skipping training candidate: comp1196_c0_seq2.p1, not unique enough -skipping training candidate: comp999_c0_seq2.p2, not unique enough -skipping training candidate: comp985_c0_seq2.p1, not unique enough -redundancy-minimized set includes 810 / 844 = 95.97% * [Thu May 9 19:41:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 38 * [Thu May 9 19:41:53 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores * [Thu May 9 19:41:57 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores * [Thu May 9 19:42:10 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs * [Thu May 9 19:42:10 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement Training start codon pattern recognition* [Thu May 9 19:42:10 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * [Thu May 9 19:42:12 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:43:37 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * [Thu May 9 19:43:51 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 * [Thu May 9 19:43:53 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 * [Thu May 9 19:43:55 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:43:56 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:43:57 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced num features: 358 num_incorporate: 107 -feature swap of score: 2.01860755745774 instead of -2.43253294753209 -feature swap of score: 2.34732451463516 instead of -2.03515280104856 -feature swap of score: 2.42600756963178 instead of -1.88586714183678 -feature swap of score: 4.04692570560011 instead of -2.07838396233827 -feature swap of score: -2.10349049055208 instead of -2.14357898216183 -feature swap of score: 3.34270681682176 instead of -1.68919591401722 -feature swap of score: 0.785638027271692 instead of -1.75537844488172 -feature swap of score: 0.124937617546208 instead of -1.42423447927029 -feature swap of score: 3.80360939610757 instead of -1.25581956645478 -feature swap of score: 2.22972790847055 instead of -1.43724022198391 -feature swap of score: 1.87223224767761 instead of -1.39134963935408 -feature swap of score: -0.869196741065359 instead of -1.45437592553593 -feature swap of score: 2.61126122082178 instead of -1.4644389491732 -feature swap of score: 0.041614898233897 instead of -1.38236698907653 -feature swap of score: 5.23702512832804 instead of -1.06647647854364 -feature swap of score: 0.489018424262898 instead of -0.95713076184448 -feature swap of score: 1.06810458576389 instead of -0.894284983683669 -feature swap of score: -0.226298629660561 instead of -0.948994050642804 -feature swap of score: 0.450699974271914 instead of -0.959497695240219 -feature swap of score: 4.28695919068754 instead of -0.978907600609435 -feature swap of score: 2.14133448495559 instead of -0.753180766675387 -feature swap of score: 4.12202729113471 instead of -0.76828282708309 -feature swap of score: -0.104946382094106 instead of -0.628776084467911 -feature swap of score: 0.000572807808514326 instead of -0.53263942949094 -feature swap of score: 0.198006134044188 instead of -0.34106805075173 -feature swap of score: 3.6047163749624 instead of -0.51212082035361 -feature swap of score: 0.814286538900709 instead of -0.339061555243772 -feature swap of score: 4.97523538835402 instead of -0.219644205392414 -feature swap of score: 1.97045125499639 instead of -0.113036838336636 -feature swap of score: 4.13053733045551 instead of -0.170052581383971 -feature swap of score: 0.00206436128981199 instead of -0.181062974960661 -feature swap of score: 1.604245252388 instead of 0.0517161275151237 -feature swap of score: 4.3932806981529 instead of 0.0860431565952234 -feature swap of score: 1.72957229182765 instead of 0.221968210457067 -feature swap of score: 1.57263236697426 instead of 0.288968311790631 -feature swap of score: 0.203166281459456 instead of 0.10534662338876 -feature swap of score: 4.38190400149154 instead of 0.196370432457334 -feature swap of score: 5.04613038233112 instead of 0.150614918926321 -feature swap of score: 2.26071953474249 instead of 0.230526386115092 -feature swap of score: 5.13639850152629 instead of 0.252892697647447 -feature swap of score: 1.17098382473728 instead of 0.282995900530861 -feature swap of score: 4.34776268138483 instead of 0.41430990147474 -feature swap of score: 2.15329616437699 instead of 0.429451771590664 -feature swap of score: 5.09229418476461 instead of 0.297828956020416 -feature swap of score: 1.13675328930652 instead of 0.171694593520241 -feature swap of score: 2.02231900226323 instead of 0.206703978994726 -feature swap of score: 2.66734827613583 instead of 0.443525927859022 -feature swap of score: 3.77684820014943 instead of 0.599510264128007 -feature swap of score: 1.29789971226826 instead of 0.51658385615187 -feature swap of score: 3.74256664801257 instead of 0.445260647950643 -feature swap of score: 4.32680419305246 instead of 0.596611075477652 -feature swap of score: 1.77920876164079 instead of 0.52605377488021 -feature swap of score: 1.61583261588263 instead of 0.65317830698915 -feature swap of score: 4.10400531839299 instead of 0.789843632233928 -feature swap of score: 1.83659343125585 instead of 0.716731928502843 -feature swap of score: 1.6438027810344 instead of 0.767790779444299 -feature swap of score: 2.51637019194037 instead of 0.699527206449989 -feature swap of score: 1.60560873858958 instead of 1.07464412670026 -feature swap of score: 2.89883210321421 instead of 1.07157389032513 -feature swap of score: 2.93101514977772 instead of 0.988616846801185 -feature swap of score: 3.72069918320373 instead of 0.868454192870146 -feature swap of score: 1.03519107357972 instead of 0.753010048444791 -feature swap of score: 4.01020820806659 instead of 0.886358064075704 -feature swap of score: 0.879618323769624 instead of 0.61109819149034 -feature swap of score: 7.15234940921215 instead of 1.03360771341683 -feature swap of score: 1.83921458905268 instead of 1.02334035960285 -feature swap of score: 2.23998772164463 instead of 0.834483027752134 -feature swap of score: 2.16522830829353 instead of 1.1968190751818 -feature swap of score: 3.565902255058 instead of 1.04816444694555 -feature swap of score: 1.1156878707122 instead of 0.972785593550388 -feature swap of score: 1.63015648897591 instead of 1.12916093095551 -feature swap of score: 3.15623525707792 instead of 1.19443129843577 -feature swap of score: 1.75064193312005 instead of 1.22439213990375 -feature swap of score: 2.22558017270471 instead of 1.41095670579146 -feature swap of score: 1.69472767650654 instead of 1.47090708539632 -feature swap of score: 5.71675848798316 instead of 1.54417528485585 -feature swap of score: 2.36834513989863 instead of 1.56065511814006 -feature swap of score: 4.72132107671951 instead of 1.39108914413569 -feature swap of score: 2.98996061269645 instead of 1.4726797291019 -feature swap of score: 2.30202014931778 instead of 1.35942459345001 -feature swap of score: 6.94448025054924 instead of 1.53071141968655 -feature swap of score: 2.02147832129674 instead of 1.39293685217156 -feature swap of score: 3.0540382236436 instead of 1.47682791921283 -feature swap of score: 8.35170655675059 instead of 1.54271367706925 -feature swap of score: 2.3591087448739 instead of 1.62983627612991 -feature swap of score: 3.33896220987853 instead of 1.74551832680512 -feature swap of score: 4.47931807129169 instead of 1.65656837994906 -feature swap of score: 6.43889512650897 instead of 1.63523856658065 -feature swap of score: 4.44139726355316 instead of 1.62413947257281 -feature swap of score: 4.3934217091148 instead of 1.5563895897064 -feature swap of score: 2.4178749161712 instead of 1.53540854291086 -feature swap of score: 4.50084537762944 instead of 1.99813615680005 -feature swap of score: 4.36085158331683 instead of 1.81509165074822 -feature swap of score: 3.50540200807125 instead of 1.84763588301182 -feature swap of score: 2.14307301177581 instead of 1.58943578807425 -feature swap of score: 2.80249705432441 instead of 2.03323063135445 -feature swap of score: 2.51995823874979 instead of 1.80649830131556 -feature swap of score: 2.18546699630314 instead of 2.01678734343503 -feature swap of score: 6.02870360838808 instead of 2.11230538713769 -feature swap of score: 4.79559537621424 instead of 1.93041915648434 -feature swap of score: 8.43445355562363 instead of 2.187388349484 -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 * [Thu May 9 19:43:58 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:45:09 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * [Thu May 9 19:45:21 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 * [Thu May 9 19:45:24 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 * [Thu May 9 19:45:26 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:45:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 43 * [Thu May 9 19:45:27 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3* [Thu May 9 19:45:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.bed * [Thu May 9 19:45:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.pep * [Thu May 9 19:45:28 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target/Trinity.fasta.transdecoder.* -Warning [1], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 266, 796 -WARNING, comp1008_c0_seq1 has no genome representation... skipping -Warning [2], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -WARNING, comp1021_c0_seq1 has no genome representation... skipping -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp1026_c0_seq1.p1. -Warning [4], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp1037_c0_seq1.p2. -Warning [5], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 561, 1325 Error, comp1051_c1~~comp1051_c1_seq1.p1 couldn't be fully propagated: $VAR1 = { 'asmbl' => 'comp1051_c1_seq1', 'orient' => '-', 'gene_id' => '', 'contig' => 'III', 'trans_id' => '', 'coords' => [ [ '1642973', '1644586' ] ] }; classification: annotated_genes Model_feat_name: comp1051_c1_seq1.p1 TU_feat_name: comp1051_c1~~comp1051_c1_seq1.p1 strand: + num_exons: 1 mid_pt: 808 is_pseudogene: 0 is_3prime_partial: 0 is_5prime_partial: 0 gene_length: 1616 asmbl_id: comp1051_c1_seq1 com_name: ORF type:5prime_partial (+),score=83.26 source: transdecoder gene_type: protein-coding gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 1616 CDS-exon: 2, 820 gene_span: 1-1616 model_span: 2-820 Error, couldn't localize pt [1615] within coordsets: $VAR1 = [ [ '1642973', '1644586' ] ]; -WARNING, comp1053_c0_seq1 has no genome representation... skipping Error, comp1058_c0~~comp1058_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'contig' => 'I', 'gene_id' => '', 'asmbl' => 'comp1058_c0_seq1', 'orient' => '-', 'coords' => [ [ 5095548, '5095878' ], [ 5095142, '5095301' ] ], 'trans_id' => '' }; classification: annotated_genes Model_feat_name: comp1058_c0_seq1.p1 num_exons: 1 strand: + TU_feat_name: comp1058_c0~~comp1058_c0_seq1.p1 is_pseudogene: 0 is_3prime_partial: 0 mid_pt: 248 is_5prime_partial: 0 com_name: ORF type:5prime_partial (+),score=32.57 asmbl_id: comp1058_c0_seq1 gene_length: 496 gene_type: protein-coding source: transdecoder gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 496 CDS-exon: 3, 422 gene_span: 1-496 model_span: 3-422 Error, couldn't localize pt [494] within coordsets: $VAR1 = [ [ 5095142, '5095301' ], [ 5095548, '5095878' ] ]; -Warning [6], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 3441, 3773 -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0~~comp1112_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ 2380416, '2380466' ], [ 2379717, '2380336' ] ], 'asmbl' => 'comp1112_c0_seq1', 'orient' => '-', 'contig' => 'III', 'gene_id' => '' }; TU_feat_name: comp1112_c0~~comp1112_c0_seq1.p1 num_exons: 1 strand: + is_3prime_partial: 0 is_pseudogene: 0 mid_pt: 1041 classification: annotated_genes Model_feat_name: comp1112_c0_seq1.p1 asmbl_id: comp1112_c0_seq1 com_name: ORF type:complete (+),score=155.28 gene_length: 2081 source: transdecoder gene_type: protein-coding is_5prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 2081 CDS-exon: 365, 1903 gene_span: 1-2081 model_span: 365-1903 Error, couldn't localize pt [1717] within coordsets: $VAR1 = [ [ 2379717, '2380336' ], [ 2380416, '2380466' ] ]; -Warning [7], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0~~comp1198_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'asmbl' => 'comp1198_c0_seq1', 'orient' => '-', 'gene_id' => '', 'contig' => 'II', 'trans_id' => '', 'coords' => [ [ 402195, '402246' ], [ 402017, '402141' ], [ 401844, '401910' ], [ 401352, '401683' ] ] }; com_name: ORF type:internal (+),score=37.56 asmbl_id: comp1198_c0_seq1 gene_length: 597 gene_type: protein-coding source: transdecoder is_5prime_partial: 0 strand: + num_exons: 1 TU_feat_name: comp1198_c0~~comp1198_c0_seq1.p1 is_pseudogene: 0 is_3prime_partial: 0 mid_pt: 299 classification: annotated_genes Model_feat_name: comp1198_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 597 CDS-exon: 2, 595 gene_span: 1-597 model_span: 2-595 Error, couldn't localize pt [596] within coordsets: $VAR1 = [ [ 401352, '401683' ], [ 401844, '401910' ], [ 402017, '402141' ], [ 402195, '402246' ] ]; Error, comp1210_c0~~comp1210_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ 368840, '369008' ], [ 367430, '368790' ] ], 'orient' => '-', 'asmbl' => 'comp1210_c0_seq1', 'gene_id' => '', 'contig' => 'III' }; com_name: ORF type:5prime_partial (+),score=12.16 asmbl_id: comp1210_c0_seq1 gene_length: 1554 gene_type: protein-coding source: transdecoder is_5prime_partial: 0 num_exons: 1 strand: + TU_feat_name: comp1210_c0~~comp1210_c0_seq1.p1 is_3prime_partial: 0 is_pseudogene: 0 mid_pt: 777 classification: annotated_genes Model_feat_name: comp1210_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 1554 CDS-exon: 2, 781 gene_span: 1-1554 model_span: 2-781 Error, couldn't localize pt [1553] within coordsets: $VAR1 = [ [ 367430, '368790' ], [ 368840, '369008' ] ]; -Warning [8], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [9], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). -Warning [10], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 3, 392 -Warning [11], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (+). Error, comp366_c0~~comp366_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'contig' => 'II', 'gene_id' => '', 'asmbl' => 'comp366_c0_seq1', 'orient' => '-', 'coords' => [ [ '3840968', '3841303' ] ], 'trans_id' => '' }; classification: annotated_genes Model_feat_name: comp366_c0_seq1.p1 num_exons: 1 strand: - TU_feat_name: comp366_c0~~comp366_c0_seq1.p1 mid_pt: 170 is_3prime_partial: 0 is_pseudogene: 0 is_5prime_partial: 0 gene_length: 340 com_name: ORF type:internal (-),score=12.83 asmbl_id: comp366_c0_seq1 gene_type: protein-coding source: transdecoder gene_synonyms: mRNA_coords CDS_coords RNA-exon: 340, 1 CDS-exon: 339, 1 gene_span: 340-1 model_span: 339-1 Error, couldn't localize pt [340] within coordsets: $VAR1 = [ [ '3840968', '3841303' ] ]; -Warning [12], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1, 384 -Warning [13], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 3, 347 -Warning [14], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1, 492 -WARNING, comp504_c0_seq1 has no genome representation... skipping -WARNING, comp576_c0_seq1 has no genome representation... skipping -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp583_c0_seq1.p1. -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp591_c0_seq1.p1. Error, comp610_c0~~comp610_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ '5471264', '5472770' ] ], 'orient' => '-', 'asmbl' => 'comp610_c0_seq1', 'contig' => 'I', 'gene_id' => '' }; Model_feat_name: comp610_c0_seq1.p1 classification: annotated_genes is_pseudogene: 0 is_3prime_partial: 0 mid_pt: 755 TU_feat_name: comp610_c0~~comp610_c0_seq1.p1 num_exons: 1 strand: + is_5prime_partial: 0 source: transdecoder gene_type: protein-coding asmbl_id: comp610_c0_seq1 com_name: ORF type:5prime_partial (+),score=50.55 gene_length: 1509 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 1509 CDS-exon: 2, 1210 gene_span: 1-1509 model_span: 2-1210 Error, couldn't localize pt [1508] within coordsets: $VAR1 = [ [ '5471264', '5472770' ] ]; -Warning [17], orf found on opposite strand of single-exon transcript. Reorienting transcribed direction accordingly to match orf orient on genome (-). CDS coords: 1441, 1941 -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp642_c0_seq1.p1. Error, comp645_c0~~comp645_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ '4333088', '4336727' ] ], 'asmbl' => 'comp645_c0_seq1', 'orient' => '-', 'gene_id' => '', 'contig' => 'I' }; Model_feat_name: comp645_c0_seq1.p1 classification: annotated_genes is_pseudogene: 0 is_3prime_partial: 0 mid_pt: 1827 TU_feat_name: comp645_c0~~comp645_c0_seq1.p1 strand: + num_exons: 1 is_5prime_partial: 0 source: transdecoder gene_type: protein-coding asmbl_id: comp645_c0_seq1 com_name: ORF type:5prime_partial (+),score=273.35 gene_length: 3653 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 3653 CDS-exon: 2, 3571 gene_span: 1-3653 model_span: 2-3571 Error, couldn't localize pt [3652] within coordsets: $VAR1 = [ [ '4333088', '4336727' ] ]; Error, comp688_c0~~comp688_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ 380308, '380560' ], [ 380624, '381243' ] ], 'orient' => '+', 'asmbl' => 'comp688_c0_seq1', 'contig' => 'II', 'gene_id' => '' }; gene_type: protein-coding source: transdecoder gene_length: 2784 com_name: ORF type:complete (+),score=172.54 asmbl_id: comp688_c0_seq1 is_5prime_partial: 0 mid_pt: 1392 is_pseudogene: 0 is_3prime_partial: 0 strand: + num_exons: 1 TU_feat_name: comp688_c0~~comp688_c0_seq1.p1 Model_feat_name: comp688_c0_seq1.p1 classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 2784 CDS-exon: 83, 2578 gene_span: 1-2784 model_span: 83-2578 Error, couldn't localize pt [2578] within coordsets: $VAR1 = [ [ 380308, '380560' ], [ 380624, '381243' ] ]; -WARNING, comp701_c0_seq1 has no genome representation... skipping -Warning [19], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp703_c0_seq1.p2. -Warning [20], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp707_c0_seq1.p2. -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0~~comp856_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'orient' => '+', 'asmbl' => 'comp856_c0_seq1', 'gene_id' => '', 'contig' => 'II', 'trans_id' => '', 'coords' => [ [ 3753910, '3754392' ], [ 3754438, '3755057' ] ] }; gene_length: 1569 asmbl_id: comp856_c0_seq1 com_name: ORF type:complete (+),score=71.94 source: transdecoder gene_type: protein-coding is_5prime_partial: 0 TU_feat_name: comp856_c0~~comp856_c0_seq1.p1 strand: + num_exons: 1 mid_pt: 785 is_3prime_partial: 0 is_pseudogene: 0 classification: annotated_genes Model_feat_name: comp856_c0_seq1.p1 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 1569 CDS-exon: 161, 1504 gene_span: 1-1569 model_span: 161-1504 Error, couldn't localize pt [1504] within coordsets: $VAR1 = [ [ 3753910, '3754392' ], [ 3754438, '3755057' ] ]; Error, comp873_c0~~comp873_c0_seq2.p1 couldn't be fully propagated: $VAR1 = { 'orient' => '-', 'asmbl' => 'comp873_c0_seq2', 'gene_id' => '', 'contig' => 'II', 'trans_id' => '', 'coords' => [ [ 3727877, '3728121' ], [ 3727705, '3727810' ], [ 3726988, '3727657' ] ] }; is_5prime_partial: 0 com_name: ORF type:5prime_partial (+),score=8.59 asmbl_id: comp873_c0_seq2 gene_length: 1025 gene_type: protein-coding source: transdecoder classification: annotated_genes Model_feat_name: comp873_c0_seq2.p1 strand: + num_exons: 1 TU_feat_name: comp873_c0~~comp873_c0_seq2.p1 is_3prime_partial: 0 is_pseudogene: 0 mid_pt: 513 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 1025 CDS-exon: 3, 677 gene_span: 1-1025 model_span: 3-677 Error, couldn't localize pt [1023] within coordsets: $VAR1 = [ [ 3726988, '3727657' ], [ 3727705, '3727810' ], [ 3727877, '3728121' ] ]; Error, comp888_c0~~comp888_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ 1268244, '1268583' ], [ 1267938, '1268172' ] ], 'orient' => '-', 'asmbl' => 'comp888_c0_seq1', 'contig' => 'III', 'gene_id' => '' }; is_5prime_partial: 0 source: transdecoder gene_type: protein-coding asmbl_id: comp888_c0_seq1 com_name: ORF type:5prime_partial (+),score=23.94 gene_length: 589 Model_feat_name: comp888_c0_seq1.p1 classification: annotated_genes is_pseudogene: 0 is_3prime_partial: 0 mid_pt: 295 TU_feat_name: comp888_c0~~comp888_c0_seq1.p1 num_exons: 1 strand: + gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 589 CDS-exon: 2, 355 gene_span: 1-589 model_span: 2-355 Error, couldn't localize pt [588] within coordsets: $VAR1 = [ [ 1267938, '1268172' ], [ 1268244, '1268583' ] ]; -Warning [21], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry comp924_c0_seq1.p2. -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0~~comp940_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ 105641, '105736' ], [ 105785, '106404' ] ], 'orient' => '+', 'asmbl' => 'comp940_c0_seq1', 'gene_id' => '', 'contig' => 'III' }; mid_pt: 1065 is_3prime_partial: 0 is_pseudogene: 0 TU_feat_name: comp940_c0~~comp940_c0_seq1.p1 num_exons: 1 strand: + Model_feat_name: comp940_c0_seq1.p1 classification: annotated_genes source: transdecoder gene_type: protein-coding gene_length: 2129 asmbl_id: comp940_c0_seq1 com_name: ORF type:complete (+),score=94.37 is_5prime_partial: 0 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 2129 CDS-exon: 40, 1731 gene_span: 1-2129 model_span: 40-1731 Error, couldn't localize pt [1731] within coordsets: $VAR1 = [ [ 105641, '105736' ], [ 105785, '106404' ] ]; Error, comp983_c0~~comp983_c0_seq1.p1 couldn't be fully propagated: $VAR1 = { 'orient' => '-', 'asmbl' => 'comp983_c0_seq1', 'gene_id' => '', 'contig' => 'I', 'trans_id' => '', 'coords' => [ [ 4100066, '4100163' ], [ 4098246, '4100014' ] ] }; is_5prime_partial: 0 gene_length: 1870 asmbl_id: comp983_c0_seq1 com_name: ORF type:5prime_partial (+),score=143.65 source: transdecoder gene_type: protein-coding classification: annotated_genes Model_feat_name: comp983_c0_seq1.p1 TU_feat_name: comp983_c0~~comp983_c0_seq1.p1 num_exons: 1 strand: + mid_pt: 935 is_3prime_partial: 0 is_pseudogene: 0 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 1870 CDS-exon: 2, 1810 gene_span: 1-1870 model_span: 2-1810 Error, couldn't localize pt [1869] within coordsets: $VAR1 = [ [ 4098246, '4100014' ], [ 4100066, '4100163' ] ]; -WARNING, comp995_c0_seq1 has no genome representation... skipping Done. 646 / 679 transcript orfs could be propagated to the genome make[4]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/simple_transcriptome_target' Running example in $... make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example' ./runMe.sh #!/bin/bash -ve export PERL_HASH_SEED=0 ## generate alignment gff3 formatted output ../../util/gtf_to_alignment_gff3.pl stringtie_merged.gtf > stringtie_merged.gff3 ## generate transcripts fasta file # not including the genome here... too big, but here's how you'd do it. #../../util/gtf_genome_to_cdna_fasta.pl stringtie_merged.gtf genome.fasta > stringtie_merged.transcripts.fasta ## Extract the long ORFs ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir * [Thu May 9 19:45:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. - extracting ORFs from transcripts. -total transcripts to examine: 3501 [100/3501] = 2.86% done [200/3501] = 5.71% done [300/3501] = 8.57% done [400/3501] = 11.43% done [500/3501] = 14.28% done [600/3501] = 17.14% done [700/3501] = 19.99% done [800/3501] = 22.85% done [900/3501] = 25.71% done [1000/3501] = 28.56% done [1100/3501] = 31.42% done [1200/3501] = 34.28% done [1300/3501] = 37.13% done [1400/3501] = 39.99% done [1500/3501] = 42.84% done [1600/3501] = 45.70% done [1700/3501] = 48.56% done [1800/3501] = 51.41% done [1900/3501] = 54.27% done [2000/3501] = 57.13% done [2100/3501] = 59.98% done [2200/3501] = 62.84% done [2300/3501] = 65.70% done [2400/3501] = 68.55% done [2500/3501] = 71.41% done [2600/3501] = 74.26% done [2700/3501] = 77.12% done [2800/3501] = 79.98% done [2900/3501] = 82.83% done [3000/3501] = 85.69% done [3100/3501] = 88.55% done [3200/3501] = 91.40% done [3300/3501] = 94.26% done [3400/3501] = 97.12% done [3500/3501] = 99.97% done CMD: touch /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS * [Thu May 9 19:46:03 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * [Thu May 9 19:46:04 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: NM_198270.p1, not unique enough -skipping training candidate: NR_104391.p1, not unique enough -skipping training candidate: NR_104395.p1, not unique enough -skipping training candidate: NM_001282622.p1, not unique enough -skipping training candidate: MSTRG.376.1.p1, not unique enough -skipping training candidate: MSTRG.839.3.p1, not unique enough -skipping training candidate: NR_104394.p1, not unique enough -skipping training candidate: MSTRG.397.18.p1, not unique enough -skipping training candidate: NM_020717.p1, not unique enough -skipping training candidate: MSTRG.505.14.p1, not unique enough -skipping training candidate: NM_001136024.p1, not unique enough -skipping training candidate: MSTRG.538.2.p1, not unique enough -skipping training candidate: NM_001291868.p1, not unique enough -skipping training candidate: MSTRG.236.1.p1, not unique enough -skipping training candidate: MSTRG.404.8.p1, not unique enough -skipping training candidate: NM_001555.p1, not unique enough -skipping training candidate: NM_001282224.p1, not unique enough -skipping training candidate: NM_001170962.p1, not unique enough -skipping training candidate: NM_001291416.p1, not unique enough -skipping training candidate: NM_021140.p1, not unique enough -skipping training candidate: MSTRG.376.9.p1, not unique enough -skipping training candidate: NM_014710.p1, not unique enough -skipping training candidate: NM_001099411.p1, not unique enough -skipping training candidate: NM_001184727.p1, not unique enough -skipping training candidate: NM_001146702.p1, not unique enough -skipping training candidate: MSTRG.258.8.p1, not unique enough -skipping training candidate: NM_005096.p1, not unique enough -skipping training candidate: MSTRG.258.9.p1, not unique enough -skipping training candidate: MSTRG.502.3.p1, not unique enough -skipping training candidate: NM_001171162.p1, not unique enough -skipping training candidate: MSTRG.502.2.p1, not unique enough -skipping training candidate: MSTRG.502.1.p1, not unique enough -skipping training candidate: NM_001291417.p1, not unique enough -skipping training candidate: NM_001168360.p1, not unique enough -skipping training candidate: NM_032969.p1, not unique enough -skipping training candidate: NM_001168363.p1, not unique enough -skipping training candidate: MSTRG.236.3.p1, not unique enough -skipping training candidate: NM_001168362.p1, not unique enough -skipping training candidate: NM_001291418.p1, not unique enough -skipping training candidate: NM_001169123.p1, not unique enough -skipping training candidate: MSTRG.570.10.p1, not unique enough -skipping training candidate: NR_111960.p1, not unique enough -skipping training candidate: NM_001169122.p1, not unique enough -skipping training candidate: NM_001169124.p1, not unique enough -skipping training candidate: NM_001169125.p1, not unique enough -skipping training candidate: MSTRG.848.14.p1, not unique enough -skipping training candidate: NM_001042749.p1, not unique enough -skipping training candidate: MSTRG.848.13.p1, not unique enough -skipping training candidate: MSTRG.848.7.p1, not unique enough -skipping training candidate: MSTRG.848.12.p1, not unique enough -skipping training candidate: NM_000425.p1, not unique enough -skipping training candidate: NM_024003.p1, not unique enough -skipping training candidate: NM_001143963.p1, not unique enough -skipping training candidate: MSTRG.477.3.p1, not unique enough -skipping training candidate: NM_012310.p1, not unique enough -skipping training candidate: MSTRG.848.11.p1, not unique enough -skipping training candidate: NM_001042751.p1, not unique enough -skipping training candidate: NM_006603.p1, not unique enough -skipping training candidate: MSTRG.848.1.p1, not unique enough -skipping training candidate: MSTRG.848.4.p1, not unique enough -skipping training candidate: MSTRG.848.2.p1, not unique enough -skipping training candidate: NM_001282418.p1, not unique enough -skipping training candidate: MSTRG.848.6.p1, not unique enough -skipping training candidate: NM_004022.p1, not unique enough -skipping training candidate: NM_004013.p1, not unique enough -skipping training candidate: MSTRG.570.9.p1, not unique enough -skipping training candidate: MSTRG.147.2.p1, not unique enough -skipping training candidate: NM_006044.p1, not unique enough -skipping training candidate: MSTRG.331.3.p1, not unique enough -skipping training candidate: MSTRG.331.2.p1, not unique enough -skipping training candidate: MSTRG.331.4.p1, not unique enough -skipping training candidate: NM_001281463.p1, not unique enough -skipping training candidate: NM_001122670.p1, not unique enough -skipping training candidate: MSTRG.147.3.p1, not unique enough -skipping training candidate: NM_021949.p1, not unique enough -skipping training candidate: MSTRG.456.2.p1, not unique enough -skipping training candidate: NM_001130860.p1, not unique enough -skipping training candidate: NM_001172436.p1, not unique enough -skipping training candidate: MSTRG.442.1.p1, not unique enough -skipping training candidate: NM_004023.p1, not unique enough -skipping training candidate: MSTRG.945.2.p1, not unique enough -skipping training candidate: MSTRG.945.3.p1, not unique enough -skipping training candidate: MSTRG.945.8.p1, not unique enough -skipping training candidate: MSTRG.518.1.p1, not unique enough -skipping training candidate: NM_001010986.p1, not unique enough -skipping training candidate: MSTRG.945.1.p1, not unique enough -skipping training candidate: NM_004020.p1, not unique enough -skipping training candidate: NM_153280.p1, not unique enough -skipping training candidate: NM_001291421.p1, not unique enough -skipping training candidate: NM_001105243.p1, not unique enough -skipping training candidate: NM_020766.p1, not unique enough -skipping training candidate: NM_007309.p1, not unique enough -skipping training candidate: NM_005756.p1, not unique enough -skipping training candidate: NM_001113490.p1, not unique enough -skipping training candidate: NM_001079859.p1, not unique enough -skipping training candidate: NM_001184833.p1, not unique enough -skipping training candidate: MSTRG.945.6.p1, not unique enough -skipping training candidate: NM_001168361.p1, not unique enough -skipping training candidate: NM_001079860.p1, not unique enough -skipping training candidate: NM_001184836.p1, not unique enough -skipping training candidate: NM_001184837.p1, not unique enough -skipping training candidate: NM_001257231.p1, not unique enough -skipping training candidate: NM_001184835.p1, not unique enough -skipping training candidate: NM_001282875.p1, not unique enough -skipping training candidate: NM_003069.p1, not unique enough -skipping training candidate: MSTRG.88.1.p1, not unique enough -skipping training candidate: MSTRG.387.2.p1, not unique enough -skipping training candidate: MSTRG.387.1.p1, not unique enough -skipping training candidate: MSTRG.860.6.p1, not unique enough -skipping training candidate: NM_001184834.p1, not unique enough -skipping training candidate: NM_138636.p1, not unique enough -skipping training candidate: NM_181673.p1, not unique enough -skipping training candidate: NM_001271184.p1, not unique enough -skipping training candidate: MSTRG.759.13.p1, not unique enough -skipping training candidate: MSTRG.759.12.p1, not unique enough -skipping training candidate: NM_001037343.p1, not unique enough -skipping training candidate: NM_015107.p1, not unique enough -skipping training candidate: NM_014725.p1, not unique enough -skipping training candidate: NM_001142504.p1, not unique enough -skipping training candidate: MSTRG.945.7.p1, not unique enough -skipping training candidate: NM_001168647.p1, not unique enough -skipping training candidate: NM_001099855.p1, not unique enough -skipping training candidate: NM_004014.p1, not unique enough -skipping training candidate: MSTRG.110.1.p1, not unique enough -skipping training candidate: NM_001282141.p1, not unique enough -skipping training candidate: NM_001666.p1, not unique enough -skipping training candidate: NM_001271183.p1, not unique enough -skipping training candidate: NM_001257237.p1, not unique enough -skipping training candidate: NM_001257230.p1, not unique enough -skipping training candidate: NM_001257234.p1, not unique enough -skipping training candidate: NM_001170628.p1, not unique enough -skipping training candidate: NM_015075.p1, not unique enough -skipping training candidate: NM_001587.p1, not unique enough -skipping training candidate: NM_001184897.p1, not unique enough -skipping training candidate: NM_001171879.p1, not unique enough -skipping training candidate: MSTRG.759.11.p1, not unique enough -skipping training candidate: MSTRG.110.4.p1, not unique enough -skipping training candidate: NM_005676.p1, not unique enough -skipping training candidate: MSTRG.110.5.p1, not unique enough -skipping training candidate: NM_001204467.p1, not unique enough -skipping training candidate: NM_031276.p1, not unique enough -skipping training candidate: NM_005369.p1, not unique enough -skipping training candidate: MSTRG.250.1.p1, not unique enough -skipping training candidate: MSTRG.387.3.p1, not unique enough -skipping training candidate: MSTRG.1005.1.p1, not unique enough -skipping training candidate: NM_001300788.p1, not unique enough -skipping training candidate: MSTRG.508.1.p1, not unique enough -skipping training candidate: NM_001126054.p1, not unique enough -skipping training candidate: NM_003588.p1, not unique enough -skipping training candidate: NM_001126055.p1, not unique enough -skipping training candidate: MSTRG.110.7.p1, not unique enough -skipping training candidate: NM_001184965.p1, not unique enough -skipping training candidate: NM_001085354.p1, not unique enough -skipping training candidate: NM_001168648.p1, not unique enough -skipping training candidate: NM_001079872.p1, not unique enough -skipping training candidate: NM_007325.p1, not unique enough -skipping training candidate: NM_014799.p1, not unique enough -skipping training candidate: MSTRG.110.8.p1, not unique enough -skipping training candidate: MSTRG.855.3.p1, not unique enough -skipping training candidate: NM_001171184.p1, not unique enough -skipping training candidate: MSTRG.110.6.p1, not unique enough -skipping training candidate: NM_001184898.p1, not unique enough -skipping training candidate: MSTRG.276.2.p1, not unique enough -skipping training candidate: NM_024597.p1, not unique enough -skipping training candidate: MSTRG.839.4.p1, not unique enough -skipping training candidate: NM_007156.p1, not unique enough -skipping training candidate: MSTRG.759.1.p1, not unique enough -skipping training candidate: MSTRG.759.21.p1, not unique enough -skipping training candidate: MSTRG.759.22.p1, not unique enough -skipping training candidate: NM_182540.p1, not unique enough -skipping training candidate: NM_001171878.p1, not unique enough -skipping training candidate: NM_152633.p1, not unique enough -skipping training candidate: MSTRG.442.2.p1, not unique enough -skipping training candidate: NM_001173516.p1, not unique enough -skipping training candidate: MSTRG.921.2.p1, not unique enough -skipping training candidate: NM_001204466.p1, not unique enough -skipping training candidate: NM_152856.p1, not unique enough -skipping training candidate: MSTRG.759.20.p1, not unique enough -skipping training candidate: MSTRG.855.4.p1, not unique enough -skipping training candidate: NM_001168649.p1, not unique enough -skipping training candidate: NM_001077445.p1, not unique enough -skipping training candidate: MSTRG.839.6.p1, not unique enough -skipping training candidate: NM_001144004.p1, not unique enough -skipping training candidate: NM_001144010.p1, not unique enough -skipping training candidate: NM_001144003.p1, not unique enough -skipping training candidate: NM_001144009.p1, not unique enough -skipping training candidate: NM_001144005.p1, not unique enough -skipping training candidate: NM_001144006.p1, not unique enough -skipping training candidate: NM_032539.p1, not unique enough -skipping training candidate: NM_139289.p1, not unique enough -skipping training candidate: MSTRG.839.5.p1, not unique enough -skipping training candidate: NM_001173517.p1, not unique enough -skipping training candidate: NM_001184875.p1, not unique enough -skipping training candidate: NM_138437.p1, not unique enough -skipping training candidate: NM_001199818.p1, not unique enough -skipping training candidate: NM_001004051.p1, not unique enough -skipping training candidate: NM_001184874.p1, not unique enough -skipping training candidate: MSTRG.110.11.p1, not unique enough -skipping training candidate: NM_001184749.p1, not unique enough -skipping training candidate: NM_173078.p1, not unique enough -skipping training candidate: MSTRG.759.24.p1, not unique enough -skipping training candidate: NM_018977.p1, not unique enough -skipping training candidate: NM_001184966.p1, not unique enough -skipping training candidate: NM_014735.p1, not unique enough -skipping training candidate: NM_001171877.p1, not unique enough -skipping training candidate: NM_001282146.p1, not unique enough -skipping training candidate: NM_001282145.p1, not unique enough -skipping training candidate: NM_020742.p1, not unique enough -skipping training candidate: NM_001127898.p1, not unique enough -skipping training candidate: NM_001005332.p1, not unique enough -skipping training candidate: NM_001166660.p1, not unique enough -skipping training candidate: MSTRG.189.10.p1, not unique enough -skipping training candidate: NM_001178085.p1, not unique enough -skipping training candidate: MSTRG.189.1.p1, not unique enough -skipping training candidate: NM_001178084.p1, not unique enough -skipping training candidate: NM_003410.p1, not unique enough -skipping training candidate: MSTRG.189.7.p1, not unique enough -skipping training candidate: MSTRG.921.3.p1, not unique enough -skipping training candidate: MSTRG.110.10.p1, not unique enough -skipping training candidate: NM_001287242.p1, not unique enough -skipping training candidate: MSTRG.76.2.p1, not unique enough -skipping training candidate: MSTRG.279.6.p1, not unique enough -skipping training candidate: MSTRG.279.1.p1, not unique enough -skipping training candidate: MSTRG.189.11.p1, not unique enough -skipping training candidate: MSTRG.189.9.p1, not unique enough -skipping training candidate: NM_153380.p1, not unique enough -skipping training candidate: MSTRG.279.11.p1, not unique enough -skipping training candidate: MSTRG.279.2.p1, not unique enough -skipping training candidate: MSTRG.279.3.p1, not unique enough -skipping training candidate: NM_007130.p1, not unique enough -skipping training candidate: MSTRG.279.10.p1, not unique enough -skipping training candidate: NM_006986.p1, not unique enough -skipping training candidate: MSTRG.1005.3.p1, not unique enough -skipping training candidate: NM_001271696.p1, not unique enough -skipping training candidate: MSTRG.279.8.p1, not unique enough -skipping training candidate: MSTRG.279.7.p1, not unique enough -skipping training candidate: NM_024778.p1, not unique enough -skipping training candidate: NM_032591.p1, not unique enough -skipping training candidate: NM_152780.p1, not unique enough -skipping training candidate: NM_013423.p1, not unique enough -skipping training candidate: NM_032512.p1, not unique enough -skipping training candidate: MSTRG.166.5.p1, not unique enough -skipping training candidate: NM_001282163.p1, not unique enough -skipping training candidate: NM_006125.p1, not unique enough -skipping training candidate: MSTRG.604.2.p1, not unique enough -skipping training candidate: NM_001243963.p1, not unique enough -skipping training candidate: NM_001184782.p1, not unique enough -skipping training candidate: NM_001272061_dup1.p1, not unique enough -skipping training candidate: MSTRG.654.4.p1, not unique enough -skipping training candidate: NM_006733.p1, not unique enough -skipping training candidate: MSTRG.654.1.p1, not unique enough -skipping training candidate: MSTRG.925.2.p1, not unique enough -skipping training candidate: NM_001163280.p1, not unique enough -skipping training candidate: NR_033717.p1, not unique enough -skipping training candidate: NM_001177466.p1, not unique enough -skipping training candidate: NM_001271698.p1, not unique enough -skipping training candidate: NM_000084.p1, not unique enough -skipping training candidate: MSTRG.654.3.p1, not unique enough -skipping training candidate: NM_001272062.p1, not unique enough -skipping training candidate: NM_001272063.p1, not unique enough -skipping training candidate: MSTRG.308.3.p1, not unique enough -skipping training candidate: NM_030801_dup1.p1, not unique enough -skipping training 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NM_052817.p1, not unique enough -skipping training candidate: MSTRG.215.2.p1, not unique enough -skipping training candidate: NM_001306193.p1, not unique enough -skipping training candidate: NM_152423.p1, not unique enough -skipping training candidate: NM_001163321.p1, not unique enough -skipping training candidate: MSTRG.572.6.p1, not unique enough -skipping training candidate: NM_001282754.p1, not unique enough -skipping training candidate: NM_001171135.p1, not unique enough -skipping training candidate: NM_001171136.p1, not unique enough -skipping training candidate: NM_001303515.p1, not unique enough -skipping training candidate: MSTRG.922.1.p1, not unique enough -skipping training candidate: MSTRG.279.5.p1, not unique enough -skipping training candidate: NM_022117.p1, not unique enough -skipping training candidate: NM_001178107.p1, not unique enough -skipping training candidate: NM_001173488.p1, not unique enough -skipping training candidate: NM_144657.p1, not unique enough 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NM_001291543_dup2.p1, not unique enough -skipping training candidate: NM_001291543.p1, not unique enough -skipping training candidate: NM_001291543_dup1.p1, not unique enough -skipping training candidate: MSTRG.1025.2.p1, not unique enough -skipping training candidate: NM_004840.p2, not unique enough -skipping training candidate: MSTRG.929.1.p2, not unique enough -skipping training candidate: MSTRG.142.5.p1, not unique enough -skipping training candidate: NM_001037536.p1, not unique enough -skipping training candidate: NM_001037535.p1, not unique enough -skipping training candidate: MSTRG.1025.3.p1, not unique enough -skipping training candidate: MSTRG.1025.6.p1, not unique enough -skipping training candidate: MSTRG.912.5.p2, not unique enough -skipping training candidate: MSTRG.980.6.p1, not unique enough -skipping training candidate: NM_024689.p1, not unique enough -skipping training candidate: MSTRG.405.7.p1, not unique enough -skipping training candidate: MSTRG.405.5.p1, not unique 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NM_004251.p1, not unique enough -skipping training candidate: NM_001178032.p1, not unique enough -skipping training candidate: NR_045044.p1, not unique enough -skipping training candidate: NM_001243804.p1, not unique enough -skipping training candidate: NM_032926.p1, not unique enough -skipping training candidate: NM_001006933.p1, not unique enough -skipping training candidate: MSTRG.232.1.p1, not unique enough -skipping training candidate: MSTRG.232.2.p1, not unique enough -skipping training candidate: MSTRG.337.1.p1, not unique enough -skipping training candidate: MSTRG.305.1.p2, not unique enough -skipping training candidate: NM_003916.p1, not unique enough -skipping training candidate: NM_001139498.p1, not unique enough -skipping training candidate: NM_001666.p2, not unique enough -skipping training candidate: MSTRG.1005.1.p2, not unique enough -skipping training candidate: MSTRG.1024.2.p2, not unique enough -skipping training candidate: NM_001129899.p1, not unique enough -skipping 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NM_001184874.p2, not unique enough -skipping training candidate: MSTRG.143.2.p1, not unique enough -skipping training candidate: MSTRG.1074.2.p2, not unique enough -skipping training candidate: NM_001166420.p1, not unique enough -skipping training candidate: NM_001007088.p2, not unique enough -skipping training candidate: NM_006962.p2, not unique enough -skipping training candidate: MSTRG.294.4.p2, not unique enough -skipping training candidate: MSTRG.1029.2.p2, not unique enough -skipping training candidate: MSTRG.68.18.p1, not unique enough -skipping training candidate: NM_001114377.p3, not unique enough -skipping training candidate: NM_001271186.p1, not unique enough -skipping training candidate: NM_021183.p1, not unique enough -skipping training candidate: MSTRG.216.5.p1, not unique enough -skipping training candidate: NM_001098791.p1, not unique enough -skipping training candidate: NM_021242.p1, not unique enough -skipping training candidate: NM_001098790.p1, not unique enough 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not unique enough -skipping training candidate: NM_017711.p2, not unique enough -skipping training candidate: NM_001171193.p2, not unique enough -skipping training candidate: NM_001171192.p2, not unique enough -skipping training candidate: MSTRG.337.1.p2, not unique enough -skipping training candidate: NM_002025.p3, not unique enough -skipping training candidate: NM_001169125.p3, not unique enough -skipping training candidate: NM_001169122.p3, not unique enough -skipping training candidate: NM_001169124.p3, not unique enough -skipping training candidate: NM_001166448.p1, not unique enough -skipping training candidate: NR_104114.p2, not unique enough -skipping training candidate: MSTRG.664.1.p2, not unique enough -skipping training candidate: MSTRG.664.2.p2, not unique enough -skipping training candidate: NM_001171907.p1, not unique enough -skipping training candidate: NM_182681.p2, not unique enough -skipping training candidate: NR_026710.p1, not unique enough -skipping training candidate: NR_033772_dup1.p1, not unique enough -skipping training candidate: NM_001282302.p1, not unique enough -skipping training candidate: MSTRG.459.2.p1, not unique enough -skipping training candidate: NR_033773_dup1.p1, not unique enough -skipping training candidate: NR_033773.p1, not unique enough -skipping training candidate: MSTRG.1041.6.p2, not unique enough -skipping training candidate: MSTRG.1041.7.p2, not unique enough -skipping training candidate: MSTRG.387.3.p2, not unique enough -skipping training candidate: NM_001184896.p2, not unique enough -skipping training candidate: NM_001170569.p1, not unique enough -skipping training candidate: NR_104121.p1, not unique enough -skipping training candidate: MSTRG.967.1.p1, not unique enough -skipping training candidate: MSTRG.68.7.p1, not unique enough -skipping training candidate: NM_001256789.p2, not unique enough -skipping training candidate: NM_001167992.p1, not unique enough -skipping training candidate: MSTRG.1074.1.p2, not 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NM_024003.p3, not unique enough -skipping training candidate: NM_001143963.p3, not unique enough -skipping training candidate: MSTRG.205.2.p1, not unique enough -skipping training candidate: MSTRG.338.6.p2, not unique enough -skipping training candidate: NM_001136157.p2, not unique enough -skipping training candidate: NM_001136159.p2, not unique enough -skipping training candidate: MSTRG.994.1.p2, not unique enough -skipping training candidate: NR_033772_dup1.p2, not unique enough -skipping training candidate: MSTRG.4.3.p4, not unique enough -skipping training candidate: NM_018390.p4, not unique enough -skipping training candidate: NM_001172672.p1, not unique enough -skipping training candidate: NR_033773_dup1.p2, not unique enough -skipping training candidate: NR_033773.p2, not unique enough -skipping training candidate: MSTRG.17.2.p2, not unique enough -skipping training candidate: MSTRG.668.2.p2, not unique enough -skipping training candidate: MSTRG.759.9.p2, not unique enough 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MSTRG.124.9.p1, not unique enough -skipping training candidate: MSTRG.124.1.p1, not unique enough -skipping training candidate: MSTRG.124.8.p2, not unique enough -skipping training candidate: NM_001256185.p1, not unique enough -skipping training candidate: NM_001282174.p2, not unique enough -skipping training candidate: NM_020717.p2, not unique enough -skipping training candidate: NM_001303545.p1, not unique enough -skipping training candidate: MSTRG.311.2.p1, not unique enough -skipping training candidate: NR_027419.p1, not unique enough -skipping training candidate: NR_033254_dup1.p1, not unique enough -skipping training candidate: NR_033257_dup1.p1, not unique enough -skipping training candidate: NR_033257.p1, not unique enough -skipping training candidate: MSTRG.549.7.p1, not unique enough -skipping training candidate: NM_205856_dup1.p1, not unique enough -skipping training candidate: NM_205856.p1, not unique enough -skipping training candidate: NM_001306188.p1, not unique enough 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NM_001190417.p2, not unique enough -skipping training candidate: NM_001146291.p2, not unique enough -skipping training candidate: MSTRG.266.4.p2, not unique enough -skipping training candidate: NM_001278740.p1, not unique enough -skipping training candidate: NM_001278741.p1, not unique enough -skipping training candidate: MSTRG.324.2.p1, not unique enough -skipping training candidate: NR_104107.p2, not unique enough -skipping training candidate: NM_001184897.p2, not unique enough -skipping training candidate: NM_015107.p3, not unique enough -skipping training candidate: MSTRG.387.3.p3, not unique enough -skipping training candidate: NM_001184896.p3, not unique enough -skipping training candidate: MSTRG.387.1.p2, not unique enough -skipping training candidate: NM_001282462.p1, not unique enough -skipping training candidate: NM_001282461.p1, not unique enough -skipping training candidate: NM_001012755.p2, not unique enough -skipping training candidate: MSTRG.705.2.p2, not unique enough 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NM_001163265.p2, not unique enough -skipping training candidate: NM_001163264.p2, not unique enough -skipping training candidate: NM_001135998.p1, not unique enough -skipping training candidate: MSTRG.961.2.p2, not unique enough -skipping training candidate: MSTRG.961.7.p2, not unique enough -skipping training candidate: MSTRG.961.4.p2, not unique enough -skipping training candidate: MSTRG.68.20.p1, not unique enough -skipping training candidate: NM_001040612.p1, not unique enough -skipping training candidate: MSTRG.925.2.p3, not unique enough -skipping training candidate: NM_001163280.p3, not unique enough -skipping training candidate: NM_175729.p1, not unique enough -skipping training candidate: NM_175729_dup1.p1, not unique enough -skipping training candidate: NR_126093.p2, not unique enough -skipping training candidate: NM_001193417.p2, not unique enough -skipping training candidate: NM_001356.p2, not unique enough -skipping training candidate: NM_005393.p3, not unique enough 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training candidate: MSTRG.131.5.p1, not unique enough -skipping training candidate: NM_001303465.p2, not unique enough -skipping training candidate: MSTRG.1029.3.p2, not unique enough -skipping training candidate: NM_206917.p1, not unique enough -skipping training candidate: NM_031407.p2, not unique enough -skipping training candidate: MSTRG.397.21.p2, not unique enough -skipping training candidate: MSTRG.397.6.p2, not unique enough -skipping training candidate: MSTRG.397.7.p2, not unique enough -skipping training candidate: MSTRG.397.5.p2, not unique enough -skipping training candidate: MSTRG.397.18.p2, not unique enough -skipping training candidate: MSTRG.397.26.p2, not unique enough -skipping training candidate: MSTRG.397.17.p2, not unique enough -skipping training candidate: MSTRG.397.24.p2, not unique enough -skipping training candidate: MSTRG.397.2.p2, not unique enough -skipping training candidate: MSTRG.397.27.p2, not unique enough -skipping training candidate: MSTRG.397.8.p2, 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training candidate: NR_045560.p1, not unique enough -skipping training candidate: MSTRG.268.7.p2, not unique enough -skipping training candidate: NM_001291421.p3, not unique enough -skipping training candidate: NM_001291417.p2, not unique enough -skipping training candidate: NM_021140.p2, not unique enough -skipping training candidate: NM_001291418.p2, not unique enough -skipping training candidate: NM_001291416.p2, not unique enough -skipping training candidate: NM_001291415.p2, not unique enough -skipping training candidate: NM_001256187.p1, not unique enough -skipping training candidate: MSTRG.305.1.p3, not unique enough -skipping training candidate: MSTRG.459.3.p2, not unique enough -skipping training candidate: NM_021783.p2, not unique enough -skipping training candidate: MSTRG.459.1.p3, not unique enough -skipping training candidate: NM_020994.p2, not unique enough -skipping training candidate: NM_001282621.p1, not unique enough -skipping training candidate: NM_001146257.p1, not unique enough -skipping training candidate: MSTRG.109.1.p1, not unique enough -skipping training candidate: NM_001168649.p2, not unique enough -skipping training candidate: NM_014927.p2, not unique enough -skipping training candidate: NM_001168647.p2, not unique enough -skipping training candidate: NM_001242617.p1, not unique enough -skipping training candidate: NM_021029.p1, not unique enough -skipping training candidate: MSTRG.68.10.p3, not unique enough -skipping training candidate: MSTRG.68.8.p2, not unique enough -skipping training candidate: MSTRG.68.2.p1, not unique enough -skipping training candidate: MSTRG.68.16.p2, not unique enough -skipping training candidate: MSTRG.258.8.p2, not unique enough -skipping training candidate: MSTRG.250.5.p1, not unique enough -skipping training candidate: NM_001011658.p1, not unique enough -skipping training candidate: MSTRG.258.9.p2, not unique enough -skipping training candidate: NM_001184898.p2, not unique enough -skipping training candidate: MSTRG.992.7.p2, not unique enough -skipping training candidate: MSTRG.476.2.p1, not unique enough -skipping training candidate: NM_020717.p4, not unique enough -skipping training candidate: NM_001256186.p1, not unique enough -skipping training candidate: NM_017711.p3, not unique enough -skipping training candidate: NM_017883.p2, not unique enough -skipping training candidate: NM_001171192.p3, not unique enough -skipping training candidate: NM_001282621.p2, not unique enough -skipping training candidate: MSTRG.921.1.p2, not unique enough -skipping training candidate: MSTRG.921.3.p2, not unique enough -skipping training candidate: MSTRG.921.2.p2, not unique enough -skipping training candidate: MSTRG.718.1.p1, not unique enough -skipping training candidate: NM_001184819.p2, not unique enough -skipping training candidate: MSTRG.641.8.p1, not unique enough -skipping training candidate: NM_001099857.p2, not unique enough -skipping training candidate: NM_001008534.p1, not unique 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MSTRG.438.2.p1, not unique enough -skipping training candidate: NR_001564.p1, not unique enough -skipping training candidate: MSTRG.531.1.p1, not unique enough -skipping training candidate: MSTRG.531.3.p1, not unique enough -skipping training candidate: MSTRG.275.3.p3, not unique enough -skipping training candidate: NM_001170460.p2, not unique enough -skipping training candidate: MSTRG.275.2.p2, not unique enough -skipping training candidate: MSTRG.275.4.p3, not unique enough -skipping training candidate: MSTRG.275.7.p2, not unique enough -skipping training candidate: MSTRG.275.6.p2, not unique enough -skipping training candidate: NM_006201.p2, not unique enough -skipping training candidate: MSTRG.615.2.p1, not unique enough -skipping training candidate: MSTRG.615.1.p1, not unique enough -skipping training candidate: MSTRG.16.1.p6, not unique enough -skipping training candidate: NM_000495.p2, not unique enough -skipping training candidate: MSTRG.992.3.p1, not unique enough -skipping training candidate: NR_073156.p2, not unique enough -skipping training candidate: MSTRG.62.2.p2, not unique enough -skipping training candidate: MSTRG.62.1.p2, not unique enough -skipping training candidate: NM_006521.p2, not unique enough -skipping training candidate: MSTRG.488.1.p1, not unique enough -skipping training candidate: NR_033212.p1, not unique enough -skipping training candidate: NM_145305.p2, not unique enough -skipping training candidate: NM_001005610.p1, not unique enough -skipping training candidate: NR_001564.p2, not unique enough -skipping training candidate: MSTRG.531.1.p2, not unique enough -skipping training candidate: MSTRG.531.3.p2, not unique enough -skipping training candidate: MSTRG.275.4.p4, not unique enough -skipping training candidate: NM_006201.p3, not unique enough -skipping training candidate: NM_001300788.p3, not unique enough -skipping training candidate: NM_001144003.p2, not unique enough -skipping training candidate: MSTRG.284.1.p3, not unique 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candidate: MSTRG.641.7.p1, not unique enough -skipping training candidate: NM_001145252.p2, not unique enough -skipping training candidate: NM_001143981.p2, not unique enough -skipping training candidate: NM_174951.p2, not unique enough -skipping training candidate: NR_027383.p4, not unique enough -skipping training candidate: MSTRG.32.4.p4, not unique enough -skipping training candidate: MSTRG.327.3.p3, not unique enough -skipping training candidate: NM_003173.p3, not unique enough -skipping training candidate: NR_024048.p2, not unique enough -skipping training candidate: NM_001123385.p2, not unique enough -skipping training candidate: NM_130467.p1, not unique enough -skipping training candidate: NM_005676.p2, not unique enough -skipping training candidate: NM_001204468.p2, not unique enough -skipping training candidate: NR_029427.p3, not unique enough -skipping training candidate: MSTRG.325.4.p2, not unique enough -skipping training candidate: NM_001166426.p2, not unique enough -skipping training candidate: NM_017883.p3, not unique enough -skipping training candidate: NM_001080851.p2, not unique enough -skipping training candidate: NM_001278743.p1, not unique enough -skipping training candidate: MSTRG.822.4.p1, not unique enough -skipping training candidate: NM_033053.p2, not unique enough -skipping training candidate: NM_033053_dup1.p2, not unique enough -skipping training candidate: NM_005647.p3, not unique enough -skipping training candidate: MSTRG.1023.3.p2, not unique enough -skipping training candidate: MSTRG.1023.2.p2, not unique enough -skipping training candidate: NM_001166700.p1, not unique enough -skipping training candidate: MSTRG.1074.8.p2, not unique enough -skipping training candidate: NR_026594.p1, not unique enough -skipping training candidate: NR_110830.p3, not unique enough -skipping training candidate: NM_001080485.p2, not unique enough -skipping training candidate: MSTRG.1025.5.p2, not unique enough -skipping training candidate: NM_001166701.p1, not unique enough -skipping training candidate: NM_138362.p1, not unique enough -skipping training candidate: NM_001256119.p2, not unique enough -skipping training candidate: NM_001256120.p2, not unique enough -skipping training candidate: NM_005676.p3, not unique enough -skipping training candidate: NM_001204466.p2, not unique enough -skipping training candidate: NM_001204468.p3, not unique enough -skipping training candidate: NM_152856.p2, not unique enough -skipping training candidate: NM_021949.p2, not unique enough -skipping training candidate: MSTRG.109.7.p1, not unique enough -skipping training candidate: NM_001168401.p1, not unique enough -skipping training candidate: NM_032621.p1, not unique enough -skipping training candidate: NM_003918.p2, not unique enough -skipping training candidate: MSTRG.913.3.p1, not unique enough -skipping training candidate: NM_001129826_dup1.p1, not unique enough -skipping training candidate: MSTRG.502.3.p2, not unique enough -skipping training candidate: NM_001171162.p2, not unique enough -skipping training candidate: NM_005096.p2, not unique enough -skipping training candidate: MSTRG.502.2.p2, not unique enough -skipping training candidate: MSTRG.502.1.p2, not unique enough -skipping training candidate: MSTRG.9.3.p2, not unique enough -skipping training candidate: MSTRG.654.2.p2, not unique enough -skipping training candidate: MSTRG.654.1.p2, not unique enough -skipping training candidate: MSTRG.654.3.p2, not unique enough -skipping training candidate: MSTRG.794.2.p2, not unique enough -skipping training candidate: NM_001109879.p2, not unique enough -skipping training candidate: MSTRG.230.7.p2, not unique enough -skipping training candidate: NM_001145140_dup1.p2, not unique enough -skipping training candidate: NM_001145139_dup1.p2, not unique enough -skipping training candidate: NM_001145139.p2, not unique enough -skipping training candidate: NM_001303624.p2, not unique enough -skipping training candidate: NM_001114937.p1, not unique enough -skipping training candidate: NM_001291868.p2, not unique enough -skipping training candidate: MSTRG.405.3.p2, not unique enough -skipping training candidate: MSTRG.405.4.p2, not unique enough -skipping training candidate: NM_001291867.p2, not unique enough -skipping training candidate: NM_001136024.p2, not unique enough -skipping training candidate: NM_000166.p2, not unique enough -skipping training candidate: MSTRG.324.2.p2, not unique enough -skipping training candidate: NM_001168302.p2, not unique enough -skipping training candidate: MSTRG.311.2.p2, not unique enough -skipping training candidate: MSTRG.921.5.p3, not unique enough -skipping training candidate: MSTRG.921.6.p3, not unique enough -skipping training candidate: NM_000425.p5, not unique enough -skipping training candidate: NM_024003.p5, not unique enough -skipping training candidate: NM_001143963.p5, not unique enough -skipping training candidate: NM_019863.p2, not unique 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MSTRG.147.4.p2, not unique enough -skipping training candidate: NM_001170931.p2, not unique enough -skipping training candidate: MSTRG.1041.5.p1, not unique enough -skipping training candidate: MSTRG.794.3.p2, not unique enough -skipping training candidate: NM_001356.p3, not unique enough -skipping training candidate: MSTRG.68.1.p2, not unique enough -skipping training candidate: MSTRG.68.18.p3, not unique enough -skipping training candidate: MSTRG.68.10.p4, not unique enough -skipping training candidate: MSTRG.68.8.p3, not unique enough -skipping training candidate: MSTRG.68.5.p2, not unique enough -skipping training candidate: MSTRG.68.3.p2, not unique enough -skipping training candidate: MSTRG.68.6.p2, not unique enough -skipping training candidate: MSTRG.68.16.p3, not unique enough -skipping training candidate: NR_034031.p2, not unique enough -skipping training candidate: MSTRG.68.14.p3, not unique enough -skipping training candidate: MSTRG.68.17.p2, not unique enough -skipping training candidate: NR_027401.p1, not unique enough -skipping training candidate: NM_001303513.p2, not unique enough -skipping training candidate: MSTRG.258.9.p3, not unique enough -skipping training candidate: NM_001037536.p2, not unique enough -skipping training candidate: NM_001037540.p2, not unique enough -skipping training candidate: NM_001037535.p2, not unique enough -skipping training candidate: NM_006746.p2, not unique enough -skipping training candidate: MSTRG.541.3.p2, not unique enough -skipping training candidate: NM_005088.p3, not unique enough -skipping training candidate: NM_001080485.p3, not unique enough -skipping training candidate: NM_020922.p2, not unique enough -skipping training candidate: MSTRG.604.2.p2, not unique enough -skipping training candidate: MSTRG.311.3.p1, not unique enough -skipping training candidate: NM_001080425.p1, not unique enough -skipping training candidate: MSTRG.68.17.p3, not unique enough -skipping training candidate: NR_130733.p1, not 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NM_018390.p5, not unique enough -skipping training candidate: NR_028057.p2, not unique enough -skipping training candidate: MSTRG.109.9.p1, not unique enough -skipping training candidate: NM_001257291.p2, not unique enough -skipping training candidate: NM_001170703.p2, not unique enough -skipping training candidate: MSTRG.889.4.p3, not unique enough -skipping training candidate: MSTRG.889.3.p2, not unique enough -skipping training candidate: MSTRG.889.2.p2, not unique enough -skipping training candidate: NM_133486.p2, not unique enough -skipping training candidate: NM_018388.p2, not unique enough -skipping training candidate: NM_001170701.p2, not unique enough -skipping training candidate: NM_001170702.p2, not unique enough -skipping training candidate: MSTRG.889.1.p2, not unique enough -skipping training candidate: NR_033835.p2, not unique enough -skipping training candidate: NM_178151.p2, not unique enough -skipping training candidate: MSTRG.4.3.p6, not unique enough -skipping 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training candidate: NM_001168399.p2, not unique enough -skipping training candidate: MSTRG.216.5.p4, not unique enough -skipping training candidate: NM_001098791.p3, not unique enough -skipping training candidate: NM_021242.p4, not unique enough -skipping training candidate: NM_001098790.p3, not unique enough -skipping training candidate: NM_001127199_dup3.p1, not unique enough -skipping training candidate: NM_001127199_dup6.p1, not unique enough -skipping training candidate: NM_001127199.p1, not unique enough -skipping training candidate: NM_001127199_dup5.p1, not unique enough -skipping training candidate: NM_001127199_dup2.p1, not unique enough -skipping training candidate: NM_001127199_dup4.p1, not unique enough -skipping training candidate: NM_001127199_dup1.p1, not unique enough -skipping training candidate: NM_001098407.p1, not unique enough -skipping training candidate: NM_001476.p1, not unique enough -skipping training candidate: NM_001476_dup1.p1, not unique enough -skipping training candidate: NM_001476_dup2.p1, not unique enough -skipping training candidate: NM_001098418_dup2.p1, not unique enough -skipping training candidate: NM_001098418_dup3.p1, not unique enough -skipping training candidate: NM_001098418_dup5.p1, not unique enough -skipping training candidate: NM_001098418.p1, not unique enough -skipping training candidate: NM_001098418_dup4.p1, not unique enough -skipping training candidate: NM_001098418_dup1.p1, not unique enough -skipping training candidate: NM_001098409_dup3.p1, not unique enough -skipping training candidate: NM_001098409_dup2.p1, not unique enough -skipping training candidate: NM_001098409.p1, not unique enough -skipping training candidate: NM_001098409_dup1.p1, not unique enough -skipping training candidate: NM_001098409_dup4.p1, not unique enough -skipping training candidate: NM_001098409_dup5.p1, not unique enough -skipping training candidate: MSTRG.68.2.p2, not unique enough -skipping training candidate: MSTRG.68.7.p2, not 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NR_120493.p1, not unique enough -skipping training candidate: NR_120493_dup1.p1, not unique enough -skipping training candidate: NM_002893.p3, not unique enough -skipping training candidate: MSTRG.376.9.p2, not unique enough -skipping training candidate: MSTRG.376.4.p3, not unique enough -skipping training candidate: NM_004187.p2, not unique enough -skipping training candidate: NM_001282622.p2, not unique enough -skipping training candidate: MSTRG.376.2.p3, not unique enough -skipping training candidate: MSTRG.376.8.p3, not unique enough -skipping training candidate: MSTRG.376.1.p2, not unique enough -skipping training candidate: NM_001146702.p2, not unique enough -skipping training candidate: NM_014380.p1, not unique enough -skipping training candidate: MSTRG.799.2.p2, not unique enough -skipping training candidate: NM_001282161.p3, not unique enough -skipping training candidate: NM_022117.p3, not unique enough -skipping training candidate: NM_134445.p2, not unique enough -skipping 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enough -skipping training candidate: NM_001172436.p2, not unique enough -skipping training candidate: MSTRG.306.3.p2, not unique enough -skipping training candidate: NM_001098624.p2, not unique enough -skipping training candidate: MSTRG.128.4.p2, not unique enough -skipping training candidate: MSTRG.1074.5.p3, not unique enough -skipping training candidate: NM_033289.p2, not unique enough -skipping training candidate: NM_001145255.p3, not unique enough -skipping training candidate: MSTRG.1041.6.p4, not unique enough -skipping training candidate: NM_003639.p2, not unique enough -skipping training candidate: NM_001099857.p3, not unique enough -skipping training candidate: MSTRG.1041.7.p3, not unique enough -skipping training candidate: MSTRG.1041.9.p2, not unique enough -skipping training candidate: NM_001099856.p2, not unique enough -skipping training candidate: NM_001303465.p3, not unique enough -skipping training candidate: MSTRG.1029.3.p4, not unique enough -skipping training candidate: NM_001193277.p2, not unique enough -skipping training candidate: NM_147175.p2, not unique enough -skipping training candidate: NM_198450.p2, not unique enough -skipping training candidate: MSTRG.108.1.p4, not unique enough -skipping training candidate: NM_001184835.p2, not unique enough -skipping training candidate: NM_001079859.p2, not unique enough -skipping training candidate: NM_032498.p2, not unique enough -skipping training candidate: NM_001830.p3, not unique enough -skipping training candidate: MSTRG.961.7.p4, not unique enough -skipping training candidate: NM_000202.p2, not unique enough -skipping training candidate: MSTRG.961.3.p2, not unique enough -skipping training candidate: MSTRG.961.4.p4, not unique enough -skipping training candidate: NM_001166550.p2, not unique enough -skipping training candidate: MSTRG.961.1.p3, not unique enough -skipping training candidate: NM_001163278.p2, not unique enough -skipping training candidate: NR_109985.p1, not unique enough -skipping training candidate: NM_001079860.p2, not unique enough -skipping training candidate: NM_007137.p2, not unique enough -skipping training candidate: MSTRG.292.4.p2, not unique enough -skipping training candidate: NM_014253.p2, not unique enough -skipping training candidate: MSTRG.109.9.p2, not unique enough -skipping training candidate: NM_001001994.p2, not unique enough -skipping training candidate: NM_005278.p2, not unique enough -skipping training candidate: NR_027401.p2, not unique enough -skipping training candidate: MSTRG.841.1.p3, not unique enough -skipping training candidate: NM_001079858.p2, not unique enough -skipping training candidate: NM_001184834.p2, not unique enough -skipping training candidate: NM_001449.p3, not unique enough -skipping training candidate: NM_001159703.p3, not unique enough -skipping training candidate: NM_005756.p2, not unique enough -skipping training candidate: NM_001099685.p2, not unique enough -skipping training candidate: NM_001099685_dup1.p2, not unique enough -skipping training candidate: NM_001141920.p3, not unique enough -skipping training candidate: NM_001142529.p2, not unique enough -skipping training candidate: NM_030639.p2, not unique enough -skipping training candidate: NM_001142528.p2, not unique enough -skipping training candidate: NM_001142530.p2, not unique enough -skipping training candidate: NM_001142526.p2, not unique enough -skipping training candidate: NM_001142527.p2, not unique enough -skipping training candidate: NM_001142524.p2, not unique enough -skipping training candidate: NM_001184836.p2, not unique enough -skipping training candidate: NM_175569.p3, not unique enough -skipping training candidate: NR_026594.p2, not unique enough -skipping training candidate: NM_001184837.p2, not unique enough -skipping training candidate: NM_177537_dup1.p4, not unique enough -skipping training candidate: NR_103770.p1, not unique enough -skipping training candidate: MSTRG.945.3.p2, not unique enough -redundancy-minimized set includes 1645 / 4259 = 38.62% * [Thu May 9 19:46:10 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 * [Thu May 9 19:46:10 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores * [Thu May 9 19:46:16 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores * [Thu May 9 19:47:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs * [Thu May 9 19:47:36 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement Training start codon pattern recognition* [Thu May 9 19:47:36 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * [Thu May 9 19:47:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:49:12 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * [Thu May 9 19:49:27 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 * [Thu May 9 19:49:29 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 * [Thu May 9 19:49:32 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:49:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:49:34 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 336 num_incorporate: 100 -feature swap of score: 3.78911079353454 instead of -4.15762669956 -feature swap of score: 4.3075564869904 instead of -3.54241712691985 -feature swap of score: -1.55002091334646 instead of -2.55010664779592 -feature swap of score: 4.83949655109525 instead of -2.24867860418506 -feature swap of score: 0.392270533069581 instead of -2.32345623662297 -feature swap of score: 3.78855323991787 instead of -2.2988029392048 -feature swap of score: 3.99836372804798 instead of -2.19588732342881 -feature swap of score: 3.64835524788969 instead of -2.09663793619562 -feature swap of score: 4.88229074177495 instead of -2.0071137297779 -feature swap of score: -1.8083423728436 instead of -1.93321879934806 -feature swap of score: 3.92879192464595 instead of -1.772614249871 -feature swap of score: -0.465948676008031 instead of -2.00439257184315 -feature swap of score: 0.0546515421473758 instead of -1.60684025496409 -feature swap of score: 0.803622088306608 instead of -1.17227320164039 -feature swap of score: 4.45581598878225 instead of -1.27696269799764 -feature swap of score: 2.07236230159122 instead of -1.40605769767333 -feature swap of score: 4.02245547784082 instead of -1.5805710473436 -feature swap of score: 0.586330906031762 instead of -0.825175240434032 -feature swap of score: 3.96397529913446 instead of -0.871836639747919 -feature swap of score: 1.28205341901886 instead of -0.854499557546068 -feature swap of score: 2.51752465071796 instead of -0.880497045171406 -feature swap of score: 7.60013808606777 instead of -0.651902109016902 -feature swap of score: 5.56752159508171 instead of -0.585113517527429 -feature swap of score: 4.16682533874051 instead of -0.591263924699593 -feature swap of score: 5.98692288702727 instead of -0.550933752346117 -feature swap of score: 2.78461992524222 instead of -0.361642943889318 -feature swap of score: -0.14086687166401 instead of -0.260141330736644 -feature swap of score: 1.30640970749369 instead of -0.208633020456475 -feature swap of score: 0.305536787416525 instead of 0.0104847431676378 -feature swap of score: 3.55759636533095 instead of -0.120486034233916 -feature swap of score: 2.46987628753496 instead of -0.103803542507822 -feature swap of score: 2.0546736913397 instead of 0.0935269368540257 -feature swap of score: 1.31912484703918 instead of 0.229231280733345 -feature swap of score: 1.89359151880524 instead of 0.232351263114116 -feature swap of score: 5.43521751645765 instead of 0.195794099551117 -feature swap of score: 4.33834387795496 instead of -0.054616396540288 -feature swap of score: 6.43704991515938 instead of 0.111124242596921 -feature swap of score: 4.25846830983975 instead of 0.127430589246059 -feature swap of score: 0.771786455336691 instead of 0.285671737045457 -feature swap of score: 6.60911073864081 instead of 0.0418054250163035 -feature swap of score: 6.79809024958936 instead of 0.555671326116825 -feature swap of score: 7.27612094216219 instead of 0.559863976992066 -feature swap of score: 3.36215544495879 instead of 0.702288739001579 -feature swap of score: 4.38866473472805 instead of 0.440911348584446 -feature swap of score: 0.836843797008186 instead of 0.157766373683364 -feature swap of score: 2.13420236534183 instead of 0.949736946003556 -feature swap of score: 1.64354527137561 instead of 0.773162924133292 -feature swap of score: 2.38988424268632 instead of 0.941592652583747 -feature swap of score: 4.91107243910547 instead of 1.09251723189791 -feature swap of score: 2.49264242586391 instead of 0.856412735226522 -feature swap of score: 6.28552706210459 instead of 1.07932791455603 -feature swap of score: 4.67930772689507 instead of 1.27353927782704 -feature swap of score: 7.50973191408739 instead of 1.12100700928058 -feature swap of score: 5.55751937051127 instead of 1.21030026759988 -feature swap of score: 2.60074697345087 instead of 1.47109964978436 -feature swap of score: 3.74655896712747 instead of 1.48225927554747 -feature swap of score: 3.99301668862372 instead of 1.24561259795263 -feature swap of score: 1.72372236527001 instead of 1.02241527158741 -feature swap of score: 6.86300883201794 instead of 1.14563582053961 -feature swap of score: 5.54190533772704 instead of 1.28297492173033 -feature swap of score: 2.51308026289154 instead of 1.4180584754329 -feature swap of score: 3.38846514773249 instead of 1.2857641622143 -feature swap of score: 2.49385651598659 instead of 1.55130322997112 -feature swap of score: 2.65351701617127 instead of 1.23066210648887 -feature swap of score: 2.60425530523188 instead of 1.47665351441682 -feature swap of score: 7.60582369996651 instead of 1.55381032974607 -feature swap of score: 2.9807664000693 instead of 1.59725854839862 -feature swap of score: 4.52648695626297 instead of 1.66034729751211 -feature swap of score: 7.21055045635181 instead of 1.7858663752496 -feature swap of score: 4.25795336260412 instead of 1.84036163713462 -feature swap of score: 9.54168129081765 instead of 1.91931805946798 -feature swap of score: 8.89437210131165 instead of 1.47973460790513 -feature swap of score: 3.3622755750855 instead of 1.94740840499986 -feature swap of score: 6.78489489553093 instead of 1.90264556019824 -feature swap of score: 9.60405031469725 instead of 2.1040236037399 -feature swap of score: 5.57780850222194 instead of 1.85621488376428 -feature swap of score: 3.43303080359017 instead of 0.865435946387495 -feature swap of score: 2.67597182314123 instead of 1.80627212503354 -feature swap of score: 6.43244682385697 instead of 1.78041450678908 -feature swap of score: 3.95962793695356 instead of 1.84794334938432 -feature swap of score: 3.98432173082736 instead of 1.875580806845 -feature swap of score: 3.21236503540814 instead of 2.21808523494257 -feature swap of score: 7.03718379305501 instead of 2.08706655299514 -feature swap of score: 5.90582904633149 instead of 1.87026115503397 -feature swap of score: 5.79478155363706 instead of 1.80883534807753 -feature swap of score: 5.36619160368881 instead of 1.98766010735596 -feature swap of score: 6.07858328906771 instead of 2.06576129141207 -feature swap of score: 5.86937251981998 instead of 1.90511689506347 -feature swap of score: 3.38462816070108 instead of 2.13933881189727 -feature swap of score: 6.37449231938971 instead of 2.82058094033957 -feature swap of score: 6.72646305674668 instead of 2.83352026076865 -feature swap of score: 4.82560543584288 instead of 2.70443214397618 -feature swap of score: 4.42177781286965 instead of 2.8151180947157 -feature swap of score: 8.98279247275997 instead of 2.94679407717209 -feature swap of score: 4.60893969392588 instead of 2.9477877072234 -feature swap of score: 7.85133157245333 instead of 1.91369736378323 -feature swap of score: 5.99853031964839 instead of 2.93641177087966 -feature swap of score: 4.29682354807149 instead of 3.14449015818142 -feature swap of score: 3.52291944162443 instead of 3.13111126617467 -feature swap of score: 4.76551376672987 instead of 3.16811466075655 -num feature swaps: 100 * [Thu May 9 19:49:35 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:50:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * [Thu May 9 19:50:52 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 * [Thu May 9 19:50:54 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 * [Thu May 9 19:50:56 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:50:57 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 247 * [Thu May 9 19:51:00 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3* [Thu May 9 19:51:00 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.bed * [Thu May 9 19:51:02 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.pep * [Thu May 9 19:51:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example/stringtie_merged.transcripts.fasta.transdecoder.* ## convert to genome coordinates ../../util/cdna_alignment_orf_to_genome_orf.pl stringtie_merged.transcripts.fasta.transdecoder.gff3 stringtie_merged.gff3 stringtie_merged.transcripts.fasta > stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 Done. 3037 / 3037 transcript orfs could be propagated to the genome ## make bed files for viewing with GenomeView # covert cufflinks gtf to bed ../../util/gtf_to_bed.pl stringtie_merged.gtf > stringtie_merged.bed # convert the genome-based gene-gff3 file to bed ../../util/gff3_file_to_bed.pl stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 > stringtie_merged.transcripts.fasta.transdecoder.genome.bed ../../util/fasta_prot_checker.pl stringtie_merged.transcripts.fasta.transdecoder.pep # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* exit 0 make[4]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/stringtie_example' Running example in $... make[4]: Entering directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example' ./runMe.sh + ../../util/gtf_to_alignment_gff3.pl supertranscripts.gtf + ../../util/gtf_genome_to_cdna_fasta.pl supertranscripts.gtf supertranscripts.fasta -parsing cufflinks output: supertranscripts.gtf -parsing genome fasta: supertranscripts.fasta -done parsing genome. // processing ADD1 // processing ATPsyn-d // processing AdipoR // processing Aldh-III // processing CG10082 // processing CG10237 // processing CG12581 // processing CG13255 // processing CG13284 // processing CG13887 // processing CG14995 // processing CG15715 // processing CG30438 // processing CG31639 // processing CG31948 // processing CG32082 // processing CG33125 // processing CG33970 // processing CG3530 // processing CG6024 // processing CG6091 // processing CG6145 // processing CG6424 // processing CG6852 // processing CG7564 // processing CG8136 // processing CG8312 // processing Calx // processing CanB2 // processing Cdep // processing Cnx99A // processing Dat // processing Dgk // processing Eno // processing Est-6 // processing Gale // processing Galk // processing His4r // processing Hsc70-1 // processing IP3K1 // processing Irk2 // processing Klp10A // processing Lip4 // processing Mgstl // processing Myo61F // processing Npl4 // processing RpL15 // processing S-Lap3 // processing Sec16 // processing Tm1 // processing bdg // processing bic // processing cdi // processing ctp // processing eIF5B // processing eff // processing gukh // processing hrg // processing kto // processing l(1)G0193 // processing l(3)05822 // processing mGluR // processing mge // processing nmo // processing ogre // processing regucalcin // processing sqd // processing stas // processing trc + ../../TransDecoder.LongOrfs -t transcripts.fasta CMD: mkdir -p /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir * [Thu May 9 19:51:25 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/compute_base_probs.pl transcripts.fasta 0 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. - extracting ORFs from transcripts. -total transcripts to examine: 279 [100/279] = 35.84% done [200/279] = 71.68% done CMD: touch /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/__checkpoints_longorfs/TD.longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. + cmd='../../TransDecoder.Predict -t transcripts.fasta' + '[' ']' + eval ../../TransDecoder.Predict -t transcripts.fasta ++ ../../TransDecoder.Predict -t transcripts.fasta * [Thu May 9 19:51:29 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * [Thu May 9 19:51:29 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/exclude_similar_proteins.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: bdg_i3.p1, not unique enough -skipping training candidate: bdg_i2.p1, not unique enough -skipping training candidate: bdg_i1.p1, not unique enough -skipping training candidate: Dgk_i7.p1, not unique enough -skipping training candidate: Cdep_i1.p1, not unique enough -skipping training candidate: eIF5B_i3.p1, not unique enough -skipping training candidate: eIF5B_i2.p1, not unique enough -skipping training candidate: Dgk_i1.p1, not unique enough -skipping training candidate: eIF5B_i5.p1, not unique enough -skipping training candidate: Dgk_i3.p1, not unique enough -skipping training candidate: Dgk_i6.p1, not unique enough -skipping training candidate: eIF5B_i1.p1, not unique enough -skipping training candidate: Myo61F_i3.p1, not unique enough -skipping training candidate: Myo61F_i2.p1, not unique enough -skipping training candidate: Myo61F_i4.p1, not unique enough -skipping training candidate: ADD1_i3.p1, not unique enough -skipping training candidate: mGluR_i4.p1, not unique enough -skipping training candidate: Calx_i3.p1, not unique enough -skipping training candidate: Calx_i9.p1, not unique enough -skipping training candidate: Calx_i8.p1, not unique enough -skipping training candidate: Calx_i1.p1, not unique enough -skipping training candidate: Calx_i5.p1, not unique enough -skipping training candidate: Calx_i2.p1, not unique enough -skipping training candidate: Calx_i4.p1, not unique enough -skipping training candidate: cdi_i1.p1, not unique enough -skipping training candidate: CG8312_i4.p1, not unique enough -skipping training candidate: CG8312_i2.p1, not unique enough -skipping training candidate: Klp10A_i1.p1, not unique enough -skipping training candidate: Klp10A_i6.p1, not unique enough -skipping training candidate: Klp10A_i4.p1, not unique enough -skipping training candidate: Klp10A_i2.p1, not unique enough -skipping training candidate: Klp10A_i5.p1, not unique enough -skipping training candidate: CG6424_i4.p1, not unique enough -skipping training candidate: CG6424_i3.p1, not unique enough -skipping training candidate: CG6424_i1.p1, not unique enough -skipping training candidate: Dgk_i4.p1, not unique enough -skipping training candidate: CG33970_i1.p1, not unique enough -skipping training candidate: Dgk_i5.p1, not unique enough -skipping training candidate: CG33125_i1.p1, not unique enough -skipping training candidate: CG3530_i2.p1, not unique enough -skipping training candidate: CG10082_i2.p1, not unique enough -skipping training candidate: CG12581_i1.p1, not unique enough -skipping training candidate: CG6091_i3.p1, not unique enough -skipping training candidate: hrg_i1.p1, not unique enough -skipping training candidate: hrg_i3.p1, not unique enough -skipping training candidate: hrg_i4.p1, not unique enough -skipping training candidate: Calx_i7.p1, not unique enough -skipping training candidate: CG32082_i1.p1, not unique enough -skipping training candidate: Npl4_i3.p1, not unique enough -skipping training candidate: Npl4_i1.p1, not unique enough -skipping training candidate: CG3530_i3.p1, not unique enough -skipping training candidate: CG32082_i3.p1, not unique enough -skipping training candidate: CG32082_i2.p1, not unique enough -skipping training candidate: l(3)05822_i3.p1, not unique enough -skipping training candidate: Cnx99A_i4.p1, not unique enough -skipping training candidate: Cnx99A_i3.p1, not unique enough -skipping training candidate: Cnx99A_i2.p1, not unique enough -skipping training candidate: l(3)05822_i1.p1, not unique enough -skipping training candidate: l(3)05822_i4.p1, not unique enough -skipping training candidate: CG6091_i4.p1, not unique enough -skipping training candidate: Aldh-III_i5.p1, not unique enough -skipping training candidate: Aldh-III_i1.p1, not unique enough -skipping training candidate: Aldh-III_i12.p1, not unique enough -skipping training candidate: Aldh-III_i9.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p1, not unique enough -skipping training candidate: Hsc70-1_i3.p1, not unique enough -skipping training candidate: Est-6_i1.p1, not unique enough -skipping training candidate: S-Lap3_i1.p1, not unique enough -skipping training candidate: S-Lap3_i3.p1, not unique enough -skipping training candidate: gukh_i4.p1, not unique enough -skipping training candidate: mGluR_i2.p1, not unique enough -skipping training candidate: CG30438_i2.p1, not unique enough -skipping training candidate: CG30438_i1.p1, not unique enough -skipping training candidate: CG30438_i5.p1, not unique enough -skipping training candidate: CG6145_i4.p1, not unique enough -skipping training candidate: CG33970_i3.p1, not unique enough -skipping training candidate: Aldh-III_i11.p1, not unique enough -skipping training candidate: mGluR_i1.p1, not unique enough -skipping training candidate: Eno_i4.p1, not unique enough -skipping training candidate: Eno_i1.p1, not unique enough -skipping training candidate: Eno_i5.p1, not unique enough -skipping training candidate: CG6091_i2.p1, not unique enough -skipping training candidate: Aldh-III_i4.p1, not unique enough -skipping training candidate: Aldh-III_i6.p1, not unique enough -skipping training candidate: Aldh-III_i7.p1, not unique enough -skipping training candidate: Aldh-III_i3.p1, not unique enough -skipping training candidate: Aldh-III_i10.p1, not unique enough -skipping training candidate: Aldh-III_i8.p1, not unique enough -skipping training candidate: Galk_i3.p1, not unique enough -skipping training candidate: Galk_i4.p1, not unique enough -skipping training candidate: Galk_i1.p1, not unique enough -skipping training candidate: CG6145_i1.p1, not unique enough -skipping training candidate: CG6145_i2.p1, not unique enough -skipping training candidate: Eno_i3.p2, not unique enough -skipping training candidate: Eno_i4.p2, not unique enough -skipping training candidate: Eno_i6.p1, not unique enough -skipping training candidate: Eno_i1.p2, not unique enough -skipping training candidate: Eno_i5.p2, not unique enough -skipping training candidate: CG6424_i3.p2, not unique enough -skipping training candidate: CG6424_i2.p2, not unique enough -skipping training candidate: CG6424_i1.p2, not unique enough -skipping training candidate: Eno_i6.p2, not unique enough -skipping training candidate: Eno_i2.p2, not unique enough -skipping training candidate: trc_i2.p1, not unique enough -skipping training candidate: Irk2_i1.p1, not unique enough -skipping training candidate: Irk2_i4.p1, not unique enough -skipping training candidate: Lip4_i2.p1, not unique enough -skipping training candidate: CG8312_i1.p1, not unique enough -skipping training candidate: AdipoR_i4.p1, not unique enough -skipping training candidate: AdipoR_i2.p1, not unique enough -skipping training candidate: AdipoR_i5.p1, not unique enough -skipping training candidate: Tm1_i5.p1, not unique enough -skipping training candidate: Tm1_i14.p1, not unique enough -skipping training candidate: CG8136_i4.p1, not unique enough -skipping training candidate: kto_i2.p3, not unique enough -skipping training candidate: CG30438_i4.p1, not unique enough -skipping training candidate: Lip4_i1.p1, not unique enough -skipping training candidate: nmo_i6.p1, not unique enough -skipping training candidate: nmo_i3.p1, not unique enough -skipping training candidate: nmo_i7.p1, not unique enough -skipping training candidate: CG8136_i1.p1, not unique enough -skipping training candidate: CG8136_i3.p1, not unique enough -skipping training candidate: CG6145_i3.p1, not unique enough -skipping training candidate: CG7564_i1.p1, not unique enough -skipping training candidate: CG7564_i4.p1, not unique enough -skipping training candidate: CG7564_i3.p1, not unique enough -skipping training candidate: CG14995_i7.p1, not unique enough -skipping training candidate: nmo_i2.p1, not unique enough -skipping training candidate: nmo_i4.p1, not unique enough -skipping training candidate: nmo_i5.p1, not unique enough -skipping training candidate: CG14995_i3.p1, not unique enough -skipping training candidate: Cdep_i4.p1, not unique enough -skipping training candidate: CG14995_i2.p1, not unique enough -skipping training candidate: CG6024_i1.p1, not unique enough -skipping training candidate: gukh_i4.p2, not unique enough -skipping training candidate: AdipoR_i1.p1, not unique enough -skipping training candidate: CG14995_i4.p1, not unique enough -skipping training candidate: ogre_i4.p1, not unique enough -skipping training candidate: ogre_i2.p1, not unique enough -skipping training candidate: ogre_i3.p1, not unique enough -skipping training candidate: ogre_i5.p1, not unique enough -skipping training candidate: ogre_i1.p1, not unique enough -skipping training candidate: IP3K1_i2.p1, not unique enough -skipping training candidate: CG14995_i1.p1, not unique enough -skipping training candidate: Gale_i1.p1, not unique enough -skipping training candidate: CG33125_i1.p2, not unique enough -skipping training candidate: CG13284_i5.p1, not unique enough -skipping training candidate: CG13284_i1.p1, not unique enough -skipping training candidate: CG13284_i2.p1, not unique enough -skipping training candidate: CG13284_i4.p1, not unique enough -skipping training candidate: sqd_i4.p1, not unique enough -skipping training candidate: Klp10A_i1.p2, not unique enough -skipping training candidate: Klp10A_i6.p2, not unique enough -skipping training candidate: Klp10A_i4.p2, not unique enough -skipping training candidate: Klp10A_i2.p2, not unique enough -skipping training candidate: Klp10A_i5.p2, not unique enough -skipping training candidate: Calx_i7.p2, not unique enough -skipping training candidate: sqd_i2.p1, not unique enough -skipping training candidate: sqd_i1.p1, not unique enough -skipping training candidate: CG10237_i4.p1, not unique enough -skipping training candidate: CG10237_i5.p1, not unique enough -skipping training candidate: CG31948_i2.p1, not unique enough -skipping training candidate: regucalcin_i2.p1, not unique enough -skipping training candidate: regucalcin_i4.p1, not unique enough -skipping training candidate: regucalcin_i1.p1, not unique enough -skipping training candidate: CG10237_i1.p1, not unique enough -skipping training candidate: CG10237_i3.p1, not unique enough -skipping training candidate: l(3)05822_i1.p2, not unique enough -skipping training candidate: l(3)05822_i2.p2, not unique enough -skipping training candidate: l(3)05822_i4.p2, not unique enough -skipping training candidate: Tm1_i3.p1, not unique enough -skipping training candidate: Tm1_i4.p1, not unique enough -skipping training candidate: Tm1_i2.p1, not unique enough -skipping training candidate: Tm1_i11.p1, not unique enough -skipping training candidate: Tm1_i9.p1, not unique enough -skipping training candidate: Tm1_i6.p1, not unique enough -skipping training candidate: Npl4_i2.p2, not unique enough -skipping training candidate: Npl4_i1.p2, not unique enough -skipping training candidate: Sec16_i5.p2, not unique enough -skipping training candidate: Sec16_i1.p2, not unique enough -skipping training candidate: Sec16_i2.p2, not unique enough -skipping training candidate: CG8312_i4.p2, not unique enough -skipping training candidate: CG8312_i2.p2, not unique enough -skipping training candidate: Dgk_i7.p2, not unique enough -skipping training candidate: eIF5B_i5.p2, not unique enough -skipping training candidate: eIF5B_i1.p2, not unique enough -skipping training candidate: eIF5B_i3.p2, not unique enough -skipping training candidate: eIF5B_i2.p2, not unique enough -skipping training candidate: Dgk_i3.p2, not unique enough -skipping training candidate: Dgk_i2.p2, not unique enough -skipping training candidate: Dgk_i6.p2, not unique enough -skipping training candidate: l(1)G0193_i2.p2, not unique enough -skipping training candidate: Tm1_i12.p1, not unique enough -skipping training candidate: Dgk_i1.p3, not unique enough -skipping training candidate: Dgk_i7.p3, not unique enough -skipping training candidate: Dat_i1.p1, not unique enough -skipping training candidate: Dgk_i3.p3, not unique enough -skipping training candidate: Dgk_i4.p3, not unique enough -skipping training candidate: Dgk_i2.p3, not unique enough -skipping training candidate: Dgk_i6.p3, not unique enough -skipping training candidate: l(3)05822_i1.p3, not unique enough -skipping training candidate: l(3)05822_i2.p3, not unique enough -skipping training candidate: l(3)05822_i4.p3, not unique enough -skipping training candidate: CG14995_i5.p1, not unique enough -skipping training candidate: CG6024_i1.p2, not unique enough -skipping training candidate: Sec16_i2.p3, not unique enough -skipping training candidate: Sec16_i6.p2, not unique enough -skipping training candidate: CG13887_i4.p1, not unique enough -skipping training candidate: CG13887_i1.p1, not unique enough -skipping training candidate: CG14995_i3.p2, not unique enough -skipping training candidate: Dgk_i5.p3, not unique enough -skipping training candidate: nmo_i6.p2, not unique enough -skipping training candidate: nmo_i2.p2, not unique enough -skipping training candidate: nmo_i4.p2, not unique enough -skipping training candidate: nmo_i3.p2, not unique enough -skipping training candidate: nmo_i7.p2, not unique enough -skipping training candidate: nmo_i5.p2, not unique enough -skipping training candidate: RpL15_i6.p1, not unique enough -skipping training candidate: regucalcin_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i3.p2, not unique enough -skipping training candidate: RpL15_i7.p1, not unique enough -skipping training candidate: regucalcin_i3.p2, not unique enough -skipping training candidate: regucalcin_i2.p2, not unique enough -skipping training candidate: gukh_i3.p2, not unique enough -skipping training candidate: gukh_i4.p3, not unique enough -skipping training candidate: cdi_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p2, not unique enough -skipping training candidate: RpL15_i4.p1, not unique enough -skipping training candidate: RpL15_i5.p1, not unique enough -skipping training candidate: RpL15_i1.p1, not unique enough -skipping training candidate: RpL15_i2.p1, not unique enough -skipping training candidate: RpL15_i3.p1, not unique enough -skipping training candidate: Npl4_i2.p3, not unique enough -skipping training candidate: Npl4_i1.p3, not unique enough -skipping training candidate: trc_i1.p2, not unique enough -skipping training candidate: Hsc70-1_i2.p3, not unique enough -skipping training candidate: Hsc70-1_i3.p3, not unique enough -skipping training candidate: CG14995_i5.p2, not unique enough -skipping training candidate: CG14995_i2.p2, not unique enough -skipping training candidate: CG14995_i4.p2, not unique enough -skipping training candidate: CG14995_i1.p2, not unique enough -skipping training candidate: CG10237_i4.p2, not unique enough -skipping training candidate: CG10237_i5.p2, not unique enough -skipping training candidate: CG10237_i3.p2, not unique enough -skipping training candidate: CG10237_i2.p2, not unique enough -skipping training candidate: Eno_i4.p3, not unique enough -skipping training candidate: Eno_i2.p3, not unique enough -skipping training candidate: Eno_i6.p3, not unique enough -skipping training candidate: Eno_i1.p3, not unique enough -skipping training candidate: Eno_i5.p3, not unique enough -skipping training candidate: Sec16_i4.p3, not unique enough -skipping training candidate: Sec16_i3.p2, not unique enough -skipping training candidate: CG14995_i7.p3, not unique enough -skipping training candidate: CG14995_i3.p3, not unique enough -skipping training candidate: CG13887_i3.p1, not unique enough -skipping training candidate: gukh_i2.p2, not unique enough -skipping training candidate: ATPsyn-d_i1.p1, not unique enough -skipping training candidate: ATPsyn-d_i3.p1, not unique enough -skipping training candidate: CG10082_i2.p2, not unique enough -skipping training candidate: sqd_i5.p1, not unique enough -skipping training candidate: CG14995_i6.p3, not unique enough -skipping training candidate: CG14995_i5.p3, not unique enough -skipping training candidate: CG30438_i2.p2, not unique enough -skipping training candidate: CG30438_i1.p2, not unique enough -skipping training candidate: CG30438_i4.p2, not unique enough -skipping training candidate: CG30438_i5.p2, not unique enough -skipping training candidate: CG14995_i5.p4, not unique enough -skipping training candidate: stas_i1.p1, not unique enough -skipping training candidate: cdi_i1.p3, not unique enough -skipping training candidate: CG14995_i2.p3, not unique enough -skipping training candidate: CG14995_i4.p3, not unique enough -skipping training candidate: CG14995_i1.p3, not unique enough -skipping training candidate: CanB2_i1.p1, not unique enough -skipping training candidate: ADD1_i2.p2, not unique enough -skipping training candidate: Sec16_i4.p4, not unique enough -skipping training candidate: Sec16_i3.p3, not unique enough -skipping training candidate: bic_i1.p1, not unique enough -skipping training candidate: CG12581_i1.p2, not unique enough -skipping training candidate: Mgstl_i1.p1, not unique enough -skipping training candidate: ctp_i1.p1, not unique enough -skipping training candidate: ctp_i3.p1, not unique enough -skipping training candidate: ctp_i4.p1, not unique enough -skipping training candidate: hrg_i3.p2, not unique enough -skipping training candidate: hrg_i4.p2, not unique enough -skipping training candidate: Eno_i4.p4, not unique enough -skipping training candidate: Eno_i2.p4, not unique enough -skipping training candidate: Eno_i6.p4, not unique enough -skipping training candidate: Eno_i1.p4, not unique enough -skipping training candidate: Eno_i5.p4, not unique enough -skipping training candidate: Klp10A_i1.p3, not unique enough -skipping training candidate: Klp10A_i6.p3, not unique enough -skipping training candidate: Klp10A_i4.p3, not unique enough -skipping training candidate: Klp10A_i2.p4, not unique enough -skipping training candidate: Klp10A_i5.p3, not unique enough -skipping training candidate: Calx_i5.p2, not unique enough -skipping training candidate: Calx_i2.p2, not unique enough -skipping training candidate: Calx_i8.p2, not unique enough -skipping training candidate: Calx_i4.p2, not unique enough -skipping training candidate: Calx_i9.p2, not unique enough -skipping training candidate: Calx_i3.p2, not unique enough -skipping training candidate: Calx_i6.p2, not unique enough -skipping training candidate: Calx_i7.p3, not unique enough -skipping training candidate: CG7564_i2.p4, not unique enough -skipping training candidate: CG7564_i1.p2, not unique enough -skipping training candidate: CG7564_i1.p3, not unique enough -skipping training candidate: CG7564_i4.p2, not unique enough -skipping training candidate: CG7564_i4.p3, not unique enough -skipping training candidate: CG7564_i3.p3, not unique enough -skipping training candidate: Gale_i1.p2, not unique enough -skipping training candidate: eIF5B_i5.p3, not unique enough -skipping training candidate: eIF5B_i1.p3, not unique enough -skipping training candidate: eIF5B_i3.p3, not unique enough -skipping training candidate: eIF5B_i2.p3, not unique enough -skipping training candidate: Dgk_i7.p4, not unique enough -skipping training candidate: Mgstl_i3.p2, not unique enough -skipping training candidate: AdipoR_i4.p2, not unique enough -skipping training candidate: CG6424_i3.p3, not unique enough -skipping training candidate: CG6424_i2.p3, not unique enough -skipping training candidate: CG6424_i1.p3, not unique enough -skipping training candidate: CG6424_i1.p4, not unique enough -skipping training candidate: Tm1_i13.p2, not unique enough -skipping training candidate: Tm1_i5.p2, not unique enough -skipping training candidate: Tm1_i14.p2, not unique enough -skipping training candidate: Dgk_i2.p5, not unique enough -skipping training candidate: Dgk_i6.p4, not unique enough -skipping training candidate: Dgk_i1.p4, not unique enough -skipping training candidate: Dgk_i7.p5, not unique enough -skipping training candidate: cdi_i1.p4, not unique enough -skipping training candidate: eff_i2.p1, not unique enough -skipping training candidate: eff_i3.p1, not unique enough -skipping training candidate: CG6852_i2.p1, not unique enough -skipping training candidate: eIF5B_i5.p4, not unique enough -skipping training candidate: eIF5B_i1.p4, not unique enough -skipping training candidate: eIF5B_i3.p4, not unique enough -skipping training candidate: eIF5B_i2.p4, not unique enough -skipping training candidate: Sec16_i1.p5, not unique enough -skipping training candidate: Sec16_i4.p5, not unique enough -skipping training candidate: Sec16_i2.p5, not unique enough -skipping training candidate: Sec16_i6.p3, not unique enough -skipping training candidate: Sec16_i3.p4, not unique enough -skipping training candidate: CG32082_i3.p2, not unique enough -skipping training candidate: CG32082_i1.p2, not unique enough -skipping training candidate: CG32082_i4.p2, not unique enough -skipping training candidate: CG3530_i2.p2, not unique enough -skipping training candidate: CG3530_i3.p2, not unique enough -skipping training candidate: Dgk_i7.p6, not unique enough -skipping training candidate: l(3)05822_i1.p5, not unique enough -skipping training candidate: l(3)05822_i2.p4, not unique enough -skipping training candidate: l(3)05822_i4.p4, not unique enough -skipping training candidate: sqd_i1.p2, not unique enough -skipping training candidate: CG7564_i1.p4, not unique enough -skipping training candidate: CG7564_i4.p4, not unique enough -skipping training candidate: CG7564_i3.p4, not unique enough -skipping training candidate: S-Lap3_i1.p2, not unique enough -skipping training candidate: S-Lap3_i3.p2, not unique enough -skipping training candidate: cdi_i1.p5, not unique enough -skipping training candidate: CG6091_i1.p2, not unique enough -skipping training candidate: CG6091_i3.p2, not unique enough -skipping training candidate: CG6091_i4.p2, not unique enough -skipping training candidate: Cdep_i3.p2, not unique enough -skipping training candidate: Cdep_i1.p2, not unique enough -skipping training candidate: Cnx99A_i1.p2, not unique enough -skipping training candidate: Cnx99A_i4.p2, not unique enough -skipping training candidate: Cnx99A_i3.p2, not unique enough -skipping training candidate: Sec16_i1.p6, not unique enough -skipping training candidate: Sec16_i6.p4, not unique enough -skipping training candidate: Sec16_i3.p5, not unique enough -skipping training candidate: ogre_i3.p2, not unique enough -skipping training candidate: CG6024_i1.p3, not unique enough -skipping training candidate: hrg_i3.p3, not unique enough -skipping training candidate: hrg_i4.p3, not unique enough -skipping training candidate: ATPsyn-d_i3.p2, not unique enough -skipping training candidate: CG6091_i3.p3, not unique enough -skipping training candidate: CG6091_i4.p3, not unique enough -skipping training candidate: ATPsyn-d_i2.p2, not unique enough -skipping training candidate: CG33970_i3.p2, not unique enough -skipping training candidate: CG33970_i1.p2, not unique enough -skipping training candidate: eIF5B_i5.p5, not unique enough -skipping training candidate: eIF5B_i1.p5, not unique enough -skipping training candidate: eIF5B_i3.p5, not unique enough -skipping training candidate: Aldh-III_i10.p2, not unique enough -skipping training candidate: Aldh-III_i8.p2, not unique enough -skipping training candidate: CG13284_i2.p2, not unique enough -skipping training candidate: CG13284_i1.p2, not unique enough -skipping training candidate: CG13284_i4.p2, not unique enough -skipping training candidate: CG13284_i5.p2, not unique enough -skipping training candidate: Lip4_i2.p2, not unique enough -skipping training candidate: Lip4_i1.p2, not unique enough -skipping training candidate: Dgk_i4.p4, not unique enough -skipping training candidate: Dgk_i2.p7, not unique enough -skipping training candidate: Dgk_i6.p5, not unique enough -skipping training candidate: Dgk_i1.p5, not unique enough -skipping training candidate: Dgk_i5.p4, not unique enough -skipping training candidate: Dgk_i7.p7, not unique enough -skipping training candidate: Tm1_i13.p3, not unique enough -skipping training candidate: Tm1_i5.p3, not unique enough -skipping training candidate: Tm1_i14.p3, not unique enough -skipping training candidate: CG8312_i4.p3, not unique enough -skipping training candidate: CG8312_i4.p4, not unique enough -skipping training candidate: CG8312_i1.p2, not unique enough -skipping training candidate: CG8312_i1.p3, not unique enough -skipping training candidate: CG8312_i2.p3, not unique enough -skipping training candidate: CG8312_i2.p4, not unique enough -skipping training candidate: Klp10A_i1.p4, not unique enough -skipping training candidate: Klp10A_i6.p4, not unique enough -skipping training candidate: Klp10A_i4.p4, not unique enough -skipping training candidate: Klp10A_i2.p6, not unique enough -skipping training candidate: Klp10A_i5.p4, not unique enough -skipping training candidate: eff_i2.p2, not unique enough -skipping training candidate: eff_i3.p2, not unique enough -skipping training candidate: CG14995_i3.p4, not unique enough -skipping training candidate: CG14995_i6.p4, not unique enough -skipping training candidate: CG14995_i5.p5, not unique enough -skipping training candidate: CG14995_i4.p4, not unique enough -skipping training candidate: CG14995_i1.p4, not unique enough -skipping training candidate: CG6424_i3.p5, not unique enough -skipping training candidate: CG6424_i2.p4, not unique enough -skipping training candidate: CG6424_i1.p5, not unique enough -skipping training candidate: CG12581_i1.p3, not unique enough -skipping training candidate: CG32082_i3.p3, not unique enough -skipping training candidate: CG32082_i1.p3, not unique enough -skipping training candidate: CG32082_i4.p5, not unique enough -skipping training candidate: Cnx99A_i1.p3, not unique enough -skipping training candidate: Cnx99A_i3.p3, not unique enough -skipping training candidate: Cdep_i4.p2, not unique enough -skipping training candidate: Cdep_i3.p3, not unique enough -skipping training candidate: Sec16_i2.p6, not unique enough -skipping training candidate: CG33970_i3.p3, not unique enough -skipping training candidate: CG33970_i1.p3, not unique enough -skipping training candidate: Sec16_i1.p7, not unique enough -skipping training candidate: Sec16_i4.p6, not unique enough -skipping training candidate: Sec16_i4.p7, not unique enough -skipping training candidate: Sec16_i2.p7, not unique enough -skipping training candidate: Sec16_i6.p5, not unique enough -skipping training candidate: Sec16_i3.p6, not unique enough -skipping training candidate: mge_i3.p1, not unique enough -skipping training candidate: CG6024_i1.p4, not unique enough -skipping training candidate: Myo61F_i2.p2, not unique enough -skipping training candidate: Myo61F_i3.p2, not unique enough -skipping training candidate: Myo61F_i4.p2, not unique enough -skipping training candidate: Cdep_i1.p3, not unique enough -skipping training candidate: Cnx99A_i1.p4, not unique enough -skipping training candidate: Cnx99A_i3.p4, not unique enough -skipping training candidate: CG13887_i4.p2, not unique enough -skipping training candidate: CG13887_i1.p2, not unique enough -skipping training candidate: CG6145_i3.p2, not unique enough -skipping training candidate: CG6145_i1.p2, not unique enough -skipping training candidate: CG6145_i2.p2, not unique enough -skipping training candidate: CG6145_i5.p2, not unique enough -skipping training candidate: Calx_i5.p3, not unique enough -skipping training candidate: Calx_i2.p3, not unique enough -skipping training candidate: Calx_i8.p3, not unique enough -skipping training candidate: Calx_i4.p3, not unique enough -skipping training candidate: Calx_i9.p3, not unique enough -skipping training candidate: Calx_i3.p3, not unique enough -skipping training candidate: Calx_i6.p3, not unique enough -skipping training candidate: Calx_i7.p5, not unique enough -skipping training candidate: mge_i2.p2, not unique enough -skipping training candidate: AdipoR_i4.p3, not unique enough -skipping training candidate: AdipoR_i2.p2, not unique enough -skipping training candidate: AdipoR_i5.p2, not unique enough -skipping training candidate: AdipoR_i1.p2, not unique enough -skipping training candidate: Aldh-III_i4.p2, not unique enough -skipping training candidate: Aldh-III_i6.p2, not unique enough -skipping training candidate: Aldh-III_i10.p3, not unique enough -skipping training candidate: Aldh-III_i7.p2, not unique enough -skipping training candidate: Aldh-III_i2.p2, not unique enough -skipping training candidate: Aldh-III_i9.p2, not unique enough -skipping training candidate: Cdep_i4.p3, not unique enough -skipping training candidate: Cdep_i3.p4, not unique enough -skipping training candidate: Cdep_i1.p4, not unique enough -skipping training candidate: hrg_i1.p4, not unique enough -skipping training candidate: hrg_i3.p4, not unique enough -skipping training candidate: hrg_i4.p4, not unique enough -skipping training candidate: CG33125_i1.p3, not unique enough -skipping training candidate: Calx_i9.p4, not unique enough -skipping training candidate: mge_i3.p2, not unique enough -skipping training candidate: CG12581_i1.p4, not unique enough -skipping training candidate: Sec16_i1.p8, not unique enough -skipping training candidate: Sec16_i1.p9, not unique enough -skipping training candidate: Sec16_i4.p8, not unique enough -skipping training candidate: Sec16_i4.p9, not unique enough -skipping training candidate: Sec16_i2.p8, not unique enough -skipping training candidate: Sec16_i2.p9, not unique enough -skipping training candidate: Sec16_i6.p6, not unique enough -skipping training candidate: Sec16_i6.p7, not unique enough -skipping training candidate: Sec16_i3.p7, not unique enough -skipping training candidate: Sec16_i3.p8, not unique enough -skipping training candidate: Aldh-III_i4.p3, not unique enough -skipping training candidate: l(3)05822_i2.p5, not unique enough -skipping training candidate: CG6091_i1.p4, not unique enough -skipping training candidate: CG6091_i3.p4, not unique enough -skipping training candidate: CG6091_i4.p4, not unique enough -skipping training candidate: CanB2_i1.p2, not unique enough -skipping training candidate: IP3K1_i2.p2, not unique enough -skipping training candidate: Klp10A_i1.p6, not unique enough -skipping training candidate: Klp10A_i6.p5, not unique enough -skipping training candidate: Klp10A_i4.p5, not unique enough -skipping training candidate: Klp10A_i2.p8, not unique enough -skipping training candidate: Klp10A_i5.p5, not unique enough -skipping training candidate: AdipoR_i2.p3, not unique enough -skipping training candidate: Cdep_i4.p4, not unique enough -skipping training candidate: Cdep_i3.p5, not unique enough -skipping training candidate: Cdep_i1.p5, not unique enough -skipping training candidate: Est-6_i1.p2, not unique enough -skipping training candidate: Klp10A_i1.p7, not unique enough -skipping training candidate: Klp10A_i6.p6, not unique enough -skipping training candidate: Klp10A_i4.p6, not unique enough -skipping training candidate: Klp10A_i2.p9, not unique enough -skipping training candidate: Klp10A_i5.p6, not unique enough -skipping training candidate: l(3)05822_i3.p5, not unique enough -skipping training candidate: ADD1_i2.p3, not unique enough -skipping training candidate: AdipoR_i5.p3, not unique enough -skipping training candidate: Cnx99A_i1.p5, not unique enough -skipping training candidate: Cnx99A_i4.p3, not unique enough -skipping training candidate: Cnx99A_i3.p5, not unique enough -skipping training candidate: Myo61F_i2.p3, not unique enough -skipping training candidate: Myo61F_i3.p3, not unique enough -skipping training candidate: Myo61F_i4.p3, not unique enough -skipping training candidate: Myo61F_i2.p4, not unique enough -skipping training candidate: Myo61F_i3.p4, not unique enough -skipping training candidate: Myo61F_i4.p4, not unique enough -skipping training candidate: bic_i1.p3, not unique enough -skipping training candidate: CG10082_i2.p3, not unique enough -skipping training candidate: CG32082_i3.p4, not unique enough -skipping training candidate: CG32082_i1.p4, not unique enough -skipping training candidate: CG32082_i4.p6, not unique enough -skipping training candidate: Eno_i4.p6, not unique enough -skipping training candidate: Eno_i2.p5, not unique enough -skipping training candidate: Eno_i6.p5, not unique enough -skipping training candidate: Eno_i1.p6, not unique enough -skipping training candidate: Eno_i5.p6, not unique enough -skipping training candidate: Sec16_i1.p10, not unique enough -skipping training candidate: Sec16_i4.p10, not unique enough -skipping training candidate: Sec16_i3.p9, not unique enough -skipping training candidate: Dgk_i4.p5, not unique enough -skipping training candidate: Dgk_i2.p8, not unique enough -skipping training candidate: Dgk_i6.p6, not unique enough -skipping training candidate: Dgk_i1.p6, not unique enough -skipping training candidate: Dgk_i5.p5, not unique enough -skipping training candidate: Dgk_i7.p8, not unique enough -skipping training candidate: nmo_i4.p3, not unique enough -skipping training candidate: CG33970_i1.p4, not unique enough -skipping training candidate: sqd_i3.p2, not unique enough -skipping training candidate: Dgk_i6.p7, not unique enough -skipping training candidate: Dgk_i1.p7, not unique enough -skipping training candidate: His4r_i4.p1, not unique enough -skipping training candidate: His4r_i2.p1, not unique enough -skipping training candidate: His4r_i3.p1, not unique enough -skipping training candidate: Hsc70-1_i2.p5, not unique enough -skipping training candidate: Hsc70-1_i3.p4, not unique enough -skipping training candidate: hrg_i3.p5, not unique enough -skipping training candidate: hrg_i4.p6, not unique enough -skipping training candidate: CG8136_i1.p2, not unique enough -skipping training candidate: CG8136_i3.p2, not unique enough -skipping training candidate: CG8136_i4.p2, not unique enough -skipping training candidate: Myo61F_i2.p5, not unique enough -skipping training candidate: Myo61F_i3.p5, not unique enough -skipping training candidate: Myo61F_i4.p5, not unique enough -skipping training candidate: CG6091_i1.p5, not unique enough -skipping training candidate: CG6091_i3.p5, not unique enough -skipping training candidate: CG6091_i4.p5, not unique enough -skipping training candidate: CG6145_i3.p3, not unique enough -skipping training candidate: CG6145_i1.p3, not unique enough -skipping training candidate: CG6145_i2.p3, not unique enough -skipping training candidate: CG6145_i5.p3, not unique enough -skipping training candidate: gukh_i2.p3, not unique enough -skipping training candidate: sqd_i3.p3, not unique enough -skipping training candidate: CG33125_i1.p4, not unique enough -skipping training candidate: gukh_i2.p4, not unique enough -redundancy-minimized set includes 286 / 856 = 33.41% * [Thu May 9 19:51:31 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/get_top_longest_fasta_entries.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 49.4 * [Thu May 9 19:51:31 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/base_freqs.dat > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores * [Thu May 9 19:51:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/score_CDS_likelihood_all_6_frames.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/hexamer.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores * [Thu May 9 19:51:47 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs * [Thu May 9 19:51:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement Training start codon pattern recognition* [Thu May 9 19:51:48 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * [Thu May 9 19:51:49 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:53:20 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * [Thu May 9 19:53:33 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 * [Thu May 9 19:53:36 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc null device 1 * [Thu May 9 19:53:38 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:53:39 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:53:40 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/deplete_feature_noise.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 253 num_incorporate: 75 -feature swap of score: -1.18185682809352 instead of -3.4622525689564 -feature swap of score: -1.71467579077518 instead of -3.18044845838571 -feature swap of score: -1.79394265464109 instead of -2.63874814989372 -feature swap of score: -1.35392651658746 instead of -1.71674254691831 -feature swap of score: -0.59508870500093 instead of -1.418039832083 -feature swap of score: -0.630975576557616 instead of -1.17819733095422 -feature swap of score: 2.02174085842081 instead of -1.07770346628642 -feature swap of score: -0.561880156346374 instead of -1.31865917138723 -feature swap of score: 2.90550498004483 instead of -1.02911674812169 -feature swap of score: -0.185263079691725 instead of -1.05925139747291 -feature swap of score: 2.83347991808692 instead of -1.06953993313952 -feature swap of score: -0.54472952199632 instead of -1.19538174183102 -feature swap of score: 0.641084631180682 instead of -0.941441236384816 -feature swap of score: 2.2375725858748 instead of -1.13771653824959 -feature swap of score: 2.20197329687561 instead of -1.12647354454425 -feature swap of score: -0.800661121254581 instead of -1.12710102163626 -feature swap of score: -0.296716429029973 instead of -1.22971523942985 -feature swap of score: -0.321134459350206 instead of -0.829184932299562 -feature swap of score: -0.270295063528865 instead of -0.997779648649508 -feature swap of score: -0.486216602229743 instead of -2.79216552940938 -feature swap of score: 1.09034017845469 instead of -0.600724521769762 -feature swap of score: 3.59212230860556 instead of -0.331895169434528 -feature swap of score: 1.38835069784522 instead of -0.344420139480721 -feature swap of score: 2.56810886051468 instead of -0.101652294022174 -feature swap of score: -0.273983692436001 instead of -0.357007963129754 -feature swap of score: -0.159504329715206 instead of -0.236094738657556 -feature swap of score: 1.42815133747988 instead of -0.542818733785047 -feature swap of score: 2.42982576520479 instead of -0.0091791842325275 -feature swap of score: 0.334455530723805 instead of -0.0280869708027799 -feature swap of score: 0.589536861904944 instead of 0.170961004687661 -feature swap of score: 1.67033420176975 instead of 0.0400993043541145 -feature swap of score: 0.301535992199674 instead of 0.209110395846244 -feature swap of score: 0.980795350091396 instead of -0.0843496599641954 -feature swap of score: 1.08964271569153 instead of -0.0384425786232236 -feature swap of score: 1.48086292731827 instead of -0.130663942735196 -feature swap of score: 2.85690510715942 instead of -0.376271235855567 -feature swap of score: 1.63395124075004 instead of -0.257710345229121 -feature swap of score: 1.94360588950499 instead of -0.516539159988099 -feature swap of score: 1.17291983996284 instead of -0.256695160788032 -feature swap of score: 0.386278989337483 instead of -0.271885199423381 -feature swap of score: 2.71227646516391 instead of 0.315932400197556 -feature swap of score: 1.82370140986921 instead of 0.182617023689868 -feature swap of score: 1.59234144048307 instead of 0.714241819557537 -feature swap of score: 3.1951661682695 instead of 0.494624764015051 -feature swap of score: 3.18269767987902 instead of 0.511098945973951 -feature swap of score: 2.10127973765731 instead of 0.396590857009673 -feature swap of score: 4.00036004681732 instead of 0.424234348843867 -feature swap of score: 0.472117769393304 instead of 0.387351733443088 -feature swap of score: 0.760597125998812 instead of 0.162274672074256 -feature swap of score: 5.39474693156676 instead of 0.465934164724809 -feature swap of score: 1.74043570645368 instead of 0.623601815488475 -num feature swaps: 51 * [Thu May 9 19:53:41 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scoring.+-.pl --features_plus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * [Thu May 9 19:55:05 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/feature_scores_to_ROC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * [Thu May 9 19:55:19 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/plot_ROC.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 * [Thu May 9 19:55:21 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/compute_AUC.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 * [Thu May 9 19:55:24 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/PWM/make_seqLogo.Rscript /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : Loading required package: grid null device 1 * [Thu May 9 19:55:25 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 12 * [Thu May 9 19:55:25 2024] Running CMD: cp /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 copying output to final output file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3* [Thu May 9 19:55:25 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_bed.pl /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed Making bed file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.bed * [Thu May 9 19:55:26 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep Making pep file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.pep * [Thu May 9 19:55:26 2024] Running CMD: /build/reproducible-path/transdecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS --genetic_code Universal > /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds Making cds file: /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.cds transdecoder is finished. See output files /build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example/transcripts.fasta.transdecoder.* + ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 supertranscripts.gff3 transcripts.fasta -Warning [1], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG10082_i1.p3. -Warning [2], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i1.p3. -Warning [3], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i2.p3. -Warning [4], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i3.p3. -Warning [5], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG32082_i4.p5. -Warning [6], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6091_i4.p2. -Warning [7], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i1.p4. -Warning [8], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG6424_i3.p4. -Warning [9], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i1.p5. -Warning [10], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p2. -Warning [11], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p1. -Warning [12], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG7564_i2.p7. -Warning [13], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry CG8312_i3.p5. -Warning [14], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i1.p5. -Warning [15], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i2.p10. -Warning [16], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i3.p5. -Warning [17], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Cdep_i4.p4. -Warning [18], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Galk_i4.p2. -Warning [19], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Klp10A_i2.p3. -Warning [20], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry Tm1_i14.p4. -Warning [21], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry bic_i2.p3. -Warning [22], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i1.p2. -Warning [23], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i3.p2. -Warning [24], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry hrg_i4.p2. -Warning [25], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i1.p2. -Warning [26], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i2.p2. -Warning [27], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry mge_i3.p2. -Warning [28], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry ogre_i3.p2. -Warning [29], shouldn't have a minus-strand ORF on a plus-strand spliced transcript structure. Skipping entry ogre_i6.p2. Done. 305 / 334 transcript orfs could be propagated to the genome + ../../util/gff3_file_to_bed.pl supertranscripts.wOrfs.gff3 + ../../util/gff3_gene_to_gtf_format.pl supertranscripts.wOrfs.gff3 supertranscripts.fasta -missing faidx file: supertranscripts.fasta.fai, extracting positions directly. -Fasta_retriever:: begin initializing for supertranscripts.fasta -Fasta_retriever:: done initializing for supertranscripts.fasta + echo Done Done make[4]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1/sample_data/supertranscripts_example' make[3]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1/sample_data' make[2]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1' cd ./sample_data && for script in ./*/cleanme.pl; do $($script); done -removing file: blastp.outfmt6 -removing file: mini_Pfam-A.hmm -removing file: mini_Pfam-A.hmm.h3f -removing file: mini_Pfam-A.hmm.h3i -removing file: mini_Pfam-A.hmm.h3m -removing file: mini_Pfam-A.hmm.h3p -removing file: mini_sprot.db.pep -removing file: mini_sprot.db.pep.pdb -removing file: mini_sprot.db.pep.phr -removing file: mini_sprot.db.pep.pin -removing file: mini_sprot.db.pep.pot -removing file: mini_sprot.db.pep.psq -removing file: mini_sprot.db.pep.ptf -removing file: mini_sprot.db.pep.pto -removing file: pfam.domtblout -removing file: test.genome.fasta -removing file: transcripts.bed -removing file: transcripts.fasta -removing file: transcripts.fasta.transdecoder.bed -removing file: transcripts.fasta.transdecoder.cds -removing file: transcripts.fasta.transdecoder.genome.bed -removing file: transcripts.fasta.transdecoder.genome.gff3 -removing file: transcripts.fasta.transdecoder.gff3 -removing file: transcripts.fasta.transdecoder.pep -removing file: transcripts.fasta.transdecoder_dir -removing file: transcripts.gff3 -removing file: transcripts.gtf -removing file: genome.fasta -removing file: pasa.gene_trans_map.txt -removing file: pasa.transdecoder_workdir -removing file: pasa_assemblies.fasta -removing file: pasa_assemblies.fasta.transdecoder.genome.gff3 -removing file: pasa_assemblies.gff3 -removing file: pasa_assemblies_described.txt -removing file: genome_alignments.gmap.gff3 -removing file: Trinity.fasta -removing file: Trinity.fasta.transdecoder.bed -removing file: Trinity.fasta.transdecoder.cds -removing file: Trinity.fasta.transdecoder.genome.gff3 -removing file: Trinity.fasta.transdecoder.gff3 -removing file: Trinity.fasta.transdecoder.pep -removing file: Trinity.fasta.transdecoder_dir -removing file: stringtie_merged.bed -removing file: stringtie_merged.gff3 -removing file: stringtie_merged.transcripts.fasta.transdecoder.bed -removing file: stringtie_merged.transcripts.fasta.transdecoder.cds -removing file: stringtie_merged.transcripts.fasta.transdecoder.genome.bed -removing file: stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 -removing file: stringtie_merged.transcripts.fasta.transdecoder.gff3 -removing file: stringtie_merged.transcripts.fasta.transdecoder.pep -removing file: stringtie_merged.transcripts.fasta.transdecoder_dir -removing file: supertranscripts.gff3 -removing file: supertranscripts.wOrfs.bed -removing file: supertranscripts.wOrfs.gff3 -removing file: supertranscripts.wOrfs.gtf -removing file: transcripts.fasta -removing file: transcripts.fasta.transdecoder.bed -removing file: transcripts.fasta.transdecoder.cds -removing file: transcripts.fasta.transdecoder.gff3 -removing file: transcripts.fasta.transdecoder.pep -removing file: transcripts.fasta.transdecoder_dir make[1]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_install find debian/transdecoder -name '*.p?' | xargs sed -i \ 's=^#!/usr/local/bin/perl=#!/usr/bin/perl=' find debian/*/usr/lib/transdecoder -type d -empty -delete make[1]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1' debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_installdocs for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/transdecoder/usr/lib/transdecoder/util/__pwm_tests/pasa_assemblies.fasta.gz: No such file or directory make[1]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1' dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/transdecoder-5.7.1' dh_fixperms chmod -x debian/transdecoder/usr/lib/transdecoder/PerlLib/Fasta_retriever.pm find debian -name Process_cmd.pm -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/transdecoder-5.7.1' dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'transdecoder-doc' in '../transdecoder-doc_5.7.1-2_all.deb'. dpkg-deb: building package 'transdecoder' in '../transdecoder_5.7.1-2_all.deb'. dpkg-genbuildinfo --build=binary -O../transdecoder_5.7.1-2_amd64.buildinfo dpkg-genchanges --build=binary -O../transdecoder_5.7.1-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2647587 and its subdirectories I: Current time: Thu May 9 19:56:06 -12 2024 I: pbuilder-time-stamp: 1715327766 Fri May 10 07:56:08 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Fri May 10 07:56:08 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Fri May 10 08:07:28 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Fri May 10 08:07:28 UTC 2024 I: transdecoder_5.7.1-2_amd64.changes: Format: 1.8 Date: Thu, 14 Sep 2023 12:37:41 +0200 Source: transdecoder Binary: transdecoder transdecoder-doc Architecture: all Version: 5.7.1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Changes: transdecoder (5.7.1-2) unstable; urgency=medium . * d/tests/control: skip tests when hmmer is not available on that architecture. Checksums-Sha1: 054e82afdac028fe9e98a63880b7b7c2000fb945 14895612 transdecoder-doc_5.7.1-2_all.deb 76832a2920d0a24ea0b46823bb230e6269ca0723 205292 transdecoder_5.7.1-2_all.deb bf6113706928a4c7049f707c00de5c8f99f66407 9074 transdecoder_5.7.1-2_amd64.buildinfo Checksums-Sha256: 4b73abb73d70818e81ace6997791f9b3ff0c8c524590d2adbc85e91e78a8ccdd 14895612 transdecoder-doc_5.7.1-2_all.deb 5614216f0c833cd1556d9db44b376a3a3dffc8de2385575f3fc71ae4bf65ad20 205292 transdecoder_5.7.1-2_all.deb 0d25e59b5f68e1d27dc0773ab2180c619e7d87fe05537e38f0966f83eccd5710 9074 transdecoder_5.7.1-2_amd64.buildinfo Files: ac6550e0ad839d3daeb74b36821e1b51 14895612 doc optional transdecoder-doc_5.7.1-2_all.deb 23ce96a3cae7906459c7ef5e1fc34116 205292 science optional transdecoder_5.7.1-2_all.deb 571fc8e021fd77adb181a3a15ee3098a 9074 science optional transdecoder_5.7.1-2_amd64.buildinfo Fri May 10 08:07:30 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_1-5374.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.XPFKHr3Q/transdecoder_5.7.1-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.XPFKHr3Q/transdecoder_5.7.1-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.XPFKHr3Q/transdecoder_5.7.1-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.XPFKHr3Q/b1/transdecoder_5.7.1-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.XPFKHr3Q/b2/transdecoder_5.7.1-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.571s) 0.571s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.194s) 0.194s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 979ms CPU time consumed: 977ms Fri May 10 08:07:32 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Fri May 10 08:07:32 UTC 2024 I: transdecoder from trixie built successfully and reproducibly on amd64. Fri May 10 08:07:33 UTC 2024 I: Submitting .buildinfo files to external archives: Fri May 10 08:07:33 UTC 2024 I: Submitting 12K b1/transdecoder_5.7.1-2_amd64.buildinfo.asc Fri May 10 08:07:34 UTC 2024 I: Submitting 12K b2/transdecoder_5.7.1-2_amd64.buildinfo.asc Fri May 10 08:07:35 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 10 08:07:35 UTC 2024 I: Done submitting .buildinfo files. Fri May 10 08:07:35 UTC 2024 I: Removing signed transdecoder_5.7.1-2_amd64.buildinfo.asc files: removed './b1/transdecoder_5.7.1-2_amd64.buildinfo.asc' removed './b2/transdecoder_5.7.1-2_amd64.buildinfo.asc'