├── .gitignore ├── .github ├── .gitignore └── workflows │ ├── test-coverage.yaml │ └── check-standard.yaml ├── codecov.yml ├── tests ├── testthat.R └── testthat │ ├── sample-data │ ├── domainless │ │ ├── domainless.faa │ │ ├── tblout │ │ ├── pfamtblout │ │ ├── domtblout │ │ ├── ali.log │ │ └── log │ ├── SLF2_tblout.scan │ ├── five │ │ ├── five.faa │ │ ├── tblout │ │ ├── pfamtblout │ │ ├── domtblout │ │ └── log │ └── slf │ │ ├── SLF1_tblout.scan │ │ └── SLF2_tblout.scan │ └── test-parse.R ├── .Rbuildignore ├── NAMESPACE ├── NEWS.md ├── R ├── rhmmer.R ├── parse_hmmprofile.R └── parse.R ├── cran-comments.md ├── man ├── read_tblout.Rd ├── read_domtblout.Rd ├── read_hmmprofile.Rd └── rhmmer.Rd ├── DESCRIPTION ├── LICENSE ├── vignettes └── domains.Rmd ├── inst └── extdata │ ├── rhino.faa │ ├── rhino.tblout │ ├── example.tblout.txt │ ├── example.hmmprofile.hmm │ ├── rhino.domtblout │ └── example.domtblout.txt └── README.Rmd /.gitignore: -------------------------------------------------------------------------------- 1 | inst/doc 2 | -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- 1 | comment: false 2 | -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- 1 | library(testthat) 2 | library(rhmmer) 3 | 4 | test_check("rhmmer") 5 | -------------------------------------------------------------------------------- /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^codecov\.yml$ 2 | ^cran-comments.md$ 3 | ^README.md$ 4 | ^README.Rmd$ 5 | ^\.github$ 6 | ^LICENSE$ 7 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | export(read_domtblout) 4 | export(read_hmmprofile) 5 | export(read_tblout) 6 | importFrom(magrittr,"%>%") 7 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/domainless/domainless.faa: -------------------------------------------------------------------------------- 1 | >AT2G38544.1 pacid=19638109 transcript=AT2G38544.1 locus=AT2G38544 ID=AT2G38544.1.TAIR10 annot-version=TAIR10 2 | MENWVYLHFRHYRPLHGILVDPALNAFTSASPNHNKLIWMRSIGIW* 3 | -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- 1 | # rhmmer v0.2.0 2 | 3 | * Tests now pass with readr 2.0.0 4 | * Fixed handling of quoted values in `read_tblout` 5 | * Turn off lazy file reading 6 | 7 | # rhmmer v0.1.0 8 | 9 | * Initial release 10 | -------------------------------------------------------------------------------- /R/rhmmer.R: -------------------------------------------------------------------------------- 1 | #' @importFrom magrittr "%>%" 2 | utils::globalVariables(c("%>%", ".")) 3 | NULL 4 | 5 | #' rhmmer: utilities for 'HMMER' 6 | #' 7 | #' Currently rhmmer exports exactly two functions: 8 | #' 9 | #' \describe{ 10 | #' \item{\code{read_tblout}}{Read a file made by HMMER '----tblout'} 11 | #' \item{\code{read_domtblout}}{Read a file made by HMMER '----domtblout'} 12 | #' } 13 | #' 14 | #' @docType package 15 | #' @name rhmmer 16 | NULL 17 | -------------------------------------------------------------------------------- /cran-comments.md: -------------------------------------------------------------------------------- 1 | ## Resubmission 2 | This is a resubmission. In this version I have: 3 | * Fixed handling of quoted values in `read_tblout` 4 | * Fixed warnings generated by readr 5 | * Fixed non-portable file paths in test suite 6 | * Turn off lazy file reading 7 | 8 | ## Test environments 9 | * local manjaro linux 5.10.49-1, R 4.2.0 10 | * win-builder (release and dev) 11 | 12 | ## R CMD check results 13 | 14 | 0 errors | 0 warnings | 0 notes 15 | 16 | ## Reverse dependencies 17 | 18 | * There are no reverse dependencies in CRAN 19 | -------------------------------------------------------------------------------- /man/read_tblout.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/parse.R 3 | \name{read_tblout} 4 | \alias{read_tblout} 5 | \title{Read a file created through the '----tblout' option} 6 | \usage{ 7 | read_tblout(file) 8 | } 9 | \arguments{ 10 | \item{file}{Filename} 11 | } 12 | \value{ 13 | data.frame 14 | } 15 | \description{ 16 | Read a file created through the '----tblout' option 17 | } 18 | \examples{ 19 | file <- system.file('extdata', 'example.tblout.txt', package='rhmmer') 20 | read_tblout(file) 21 | } 22 | -------------------------------------------------------------------------------- /man/read_domtblout.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/parse.R 3 | \name{read_domtblout} 4 | \alias{read_domtblout} 5 | \title{Read a file created through the '----domtblout' option} 6 | \usage{ 7 | read_domtblout(file) 8 | } 9 | \arguments{ 10 | \item{file}{Filename} 11 | } 12 | \value{ 13 | data.frame 14 | } 15 | \description{ 16 | Read a file created through the '----domtblout' option 17 | } 18 | \examples{ 19 | file <- system.file('extdata', 'example.domtblout.txt', package='rhmmer') 20 | read_domtblout(file) 21 | } 22 | -------------------------------------------------------------------------------- /man/read_hmmprofile.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/parse_hmmprofile.R 3 | \name{read_hmmprofile} 4 | \alias{read_hmmprofile} 5 | \title{Read and format a HMMprofile file from HMMbuild into tabular format} 6 | \usage{ 7 | read_hmmprofile(file) 8 | } 9 | \arguments{ 10 | \item{file}{Filename} 11 | } 12 | \value{ 13 | data.frame 14 | } 15 | \description{ 16 | Read and format a HMMprofile file from HMMbuild into tabular format 17 | } 18 | \examples{ 19 | file <- system.file('extdata', 'example.hmmprofile.hmm', package='rhmmer') 20 | read_hmmprofile(file) 21 | } 22 | -------------------------------------------------------------------------------- /man/rhmmer.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rhmmer.R 3 | \docType{package} 4 | \name{rhmmer} 5 | \alias{rhmmer-package} 6 | \alias{rhmmer} 7 | \title{rhmmer: utilities for 'HMMER'} 8 | \description{ 9 | Currently rhmmer exports exactly two functions: 10 | } 11 | \details{ 12 | \describe{ 13 | \item{\code{read_tblout}}{Read a file made by HMMER '----tblout'} 14 | \item{\code{read_domtblout}}{Read a file made by HMMER '----domtblout'} 15 | } 16 | } 17 | \seealso{ 18 | Useful links: 19 | \itemize{ 20 | \item \url{https://github.com/arendsee/rhmmer} 21 | \item Report bugs at \url{https://github.com/arendsee/rhmmer/issues} 22 | } 23 | 24 | } 25 | \author{ 26 | \strong{Maintainer}: Zebulun Arendsee \email{zbwrnz@gmail.com} 27 | 28 | } 29 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/SLF2_tblout.scan: -------------------------------------------------------------------------------- 1 | # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- 2 | # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target 3 | #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- 4 | X x a - 1.7e-06 20.5 0.0 1.8e-06 20.4 0.0 1.0 1 0 0 1 1 1 1 "XXXX" x 5 | Y y a - 2.2e-05 16.8 0.0 2.2e-05 16.7 0.0 1.0 1 0 0 1 1 1 1 XXX x 6 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: rhmmer 2 | Version: 0.2.0 3 | Title: Utilities Parsing 'HMMER' Results 4 | Description: 5 | 'HMMER' is a profile hidden Markov model tool used primarily for sequence 6 | analysis in bioinformatics (). 'rhmmer' provides 7 | utilities for parsing the 'HMMER' output into tidy data frames. 8 | Authors@R: person("Zebulun", "Arendsee", email="zbwrnz@gmail.com", role=c("aut","cre")) 9 | URL: https://github.com/arendsee/rhmmer 10 | BugReports: https://github.com/arendsee/rhmmer/issues 11 | Depends: 12 | R (>= 3.4.0) 13 | Imports: 14 | magrittr, 15 | readr (>= 2.1.0) 16 | Suggests: 17 | testthat, 18 | covr, 19 | knitr, 20 | rmarkdown, 21 | dplyr 22 | LazyData: true 23 | RoxygenNote: 7.3.2 24 | License: MIT + file LICENSE 25 | VignetteBuilder: knitr 26 | Encoding: UTF-8 27 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/domainless/tblout: -------------------------------------------------------------------------------- 1 | # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- 2 | # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target 3 | #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- 4 | # 5 | # Program: hmmscan 6 | # Version: 3.1b2 (February 2015) 7 | # Pipeline mode: SCAN 8 | # Query file: orphan.faa 9 | # Target file: /home/z/db/Pfam-A.hmm 10 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm orphan.faa 11 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 12 | # Date: Fri Dec 15 02:06:38 2017 13 | # [ok] 14 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/domainless/pfamtblout: -------------------------------------------------------------------------------- 1 | # Sequence scores 2 | # --------------- 3 | # 4 | # name bits E-value n exp bias description 5 | # ------------------- ------ --------- --- ----- ----- --------------------- 6 | 7 | # Domain scores 8 | # ------------- 9 | # 10 | # name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description 11 | # ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- 12 | # 13 | # Program: hmmscan 14 | # Version: 3.1b2 (February 2015) 15 | # Pipeline mode: SEARCH 16 | # Query file: orphan.faa 17 | # Target file: /home/z/db/Pfam-A.hmm 18 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm orphan.faa 19 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 20 | # Date: Fri Dec 15 02:06:38 2017 21 | # [ok] 22 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/domainless/domtblout: -------------------------------------------------------------------------------- 1 | # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord 2 | # target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target 3 | #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- 4 | # 5 | # Program: hmmscan 6 | # Version: 3.1b2 (February 2015) 7 | # Pipeline mode: SCAN 8 | # Query file: orphan.faa 9 | # Target file: /home/z/db/Pfam-A.hmm 10 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm orphan.faa 11 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 12 | # Date: Fri Dec 15 02:06:38 2017 13 | # [ok] 14 | -------------------------------------------------------------------------------- /.github/workflows/test-coverage.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | push: 5 | branches: [master] 6 | pull_request: 7 | branches: [master] 8 | 9 | name: test-coverage 10 | 11 | jobs: 12 | test-coverage: 13 | runs-on: ubuntu-latest 14 | env: 15 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 16 | 17 | steps: 18 | - uses: actions/checkout@v3 19 | 20 | - uses: r-lib/actions/setup-r@v2 21 | with: 22 | use-public-rspm: true 23 | 24 | - name: Show testthat output 25 | if: always() 26 | run: | 27 | ## -------------------------------------------------------------------- 28 | find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true 29 | shell: bash 30 | 31 | - name: Upload test results 32 | if: failure() 33 | uses: actions/upload-artifact@v3 34 | with: 35 | name: coverage-test-failures 36 | path: ${{ runner.temp }}/package 37 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | # MIT License 2 | 3 | Copyright (c) 2022 Zebulun Arendsee 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /.github/workflows/check-standard.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | push: 5 | branches: [master] 6 | pull_request: 7 | branches: [master] 8 | 9 | name: R-CMD-check 10 | 11 | jobs: 12 | R-CMD-check: 13 | runs-on: ${{ matrix.config.os }} 14 | 15 | name: ${{ matrix.config.os }} (${{ matrix.config.r }}) 16 | 17 | strategy: 18 | fail-fast: false 19 | matrix: 20 | config: 21 | - {os: macos-latest, r: 'release'} 22 | - {os: windows-latest, r: 'release'} 23 | - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} 24 | - {os: ubuntu-latest, r: 'release'} 25 | - {os: ubuntu-latest, r: 'oldrel-1'} 26 | 27 | env: 28 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 29 | R_KEEP_PKG_SOURCE: yes 30 | 31 | steps: 32 | - uses: actions/checkout@v3 33 | 34 | - uses: r-lib/actions/setup-pandoc@v2 35 | 36 | - uses: r-lib/actions/setup-r@v2 37 | with: 38 | r-version: ${{ matrix.config.r }} 39 | http-user-agent: ${{ matrix.config.http-user-agent }} 40 | use-public-rspm: true 41 | 42 | - uses: r-lib/actions/setup-r-dependencies@v2 43 | with: 44 | extra-packages: any::rcmdcheck 45 | needs: check 46 | 47 | - uses: r-lib/actions/check-r-package@v2 48 | with: 49 | upload-snapshots: true 50 | -------------------------------------------------------------------------------- /R/parse_hmmprofile.R: -------------------------------------------------------------------------------- 1 | #' Read and format a HMMprofile file from HMMbuild into tabular format 2 | #' 3 | #' @param file Filename 4 | #' @return data.frame 5 | #' @export 6 | #' @examples 7 | #' file <- system.file('extdata', 'example.hmmprofile.hmm', package='rhmmer') 8 | #' read_hmmprofile(file) 9 | read_hmmprofile <- function(file){ 10 | text = readLines(file) 11 | 12 | start = grep("HMM", text)[2] 13 | end = grep("//", text) 14 | 15 | if(length(start) == 0 || length(end) == 0) {stop("malformed hmm profile")} 16 | 17 | # parser currently only handles /f formatted .hmm files 18 | if( grepl("HMMER3/f", text[1]) ){ 19 | text = text[start:end] 20 | 21 | 22 | which_emmission = grep(" [0-9]{1,9} ", text) 23 | which_transition = which_emmission + 2 24 | 25 | if(length(start) == 0 || length(end) == 0) {stop("the parser cannot find residue emmission or transition probabilities")} 26 | 27 | df_emmission = read.table(text = text[which_emmission])[,1:21] 28 | df_transition = read.table(text = text[which_transition]) 29 | 30 | df = cbind(df_emmission, 31 | df_transition) 32 | 33 | colnames(df) = c("position", 34 | "A", 35 | "C", 36 | "D", 37 | "E", 38 | "F", 39 | "G", 40 | "H", 41 | "I", 42 | "K", 43 | "L", 44 | "M", 45 | "N", 46 | "P", 47 | "Q", 48 | "R", 49 | "S", 50 | "T", 51 | "V", 52 | "W", 53 | "Y", 54 | "m->m", 55 | "m->i", 56 | "m->d", 57 | "i->m", 58 | "i->i", 59 | "d->m", 60 | "d->d") 61 | } 62 | 63 | return(df) 64 | } 65 | -------------------------------------------------------------------------------- /tests/testthat/test-parse.R: -------------------------------------------------------------------------------- 1 | context("parse") 2 | 3 | tblout_file=file.path('sample-data', 'five', 'tblout') 4 | domtblout_file=file.path('sample-data', 'five', 'domtblout') 5 | 6 | empty_tblout_file=file.path('sample-data', 'domainless', 'tblout') 7 | empty_domtblout_file=file.path('sample-data', 'domainless', 'domtblout') 8 | slf_tblout_file_1=file.path('sample-data', 'slf', 'SLF1_tblout.scan') 9 | slf_tblout_file_2=file.path('sample-data', 'slf', 'SLF2_tblout.scan') 10 | 11 | domtblout_search_file=file.path('sample-data', 'search', 'phytases_domtblout.txt') 12 | 13 | test_that("read_tblout works", { 14 | tblout <- read_tblout(tblout_file) 15 | expect_silent(read_tblout(tblout_file)) 16 | expect_equal(dim(tblout), c(37,19)) 17 | }) 18 | 19 | test_that("read_domtblout works", { 20 | domtblout <- read_domtblout(domtblout_file) 21 | expect_silent(read_domtblout(domtblout_file)) 22 | expect_equal(dim(domtblout), c(70,23)) 23 | }) 24 | 25 | test_that("read_domtblout works with search data", { 26 | expect_silent(read_domtblout(domtblout_search_file)) 27 | }) 28 | 29 | test_that("using the wrong reader fails", { 30 | expect_warning(read_domtblout(tblout_file)) 31 | expect_warning(read_tblout(domtblout_file)) 32 | }) 33 | 34 | test_that("files with no data do not fail", { 35 | expect_silent(read_domtblout(empty_tblout_file)) 36 | expect_silent(read_tblout(empty_domtblout_file)) 37 | expect_equal(dim(read_tblout(empty_tblout_file)), c(0,19)) 38 | expect_equal(dim(read_domtblout(empty_domtblout_file)), c(0,23)) 39 | }) 40 | 41 | test_that("partially quoted descriptions do not fail", { 42 | expect_silent(f1 <- read_tblout(slf_tblout_file_1)) 43 | expect_silent(f2 <- read_tblout(slf_tblout_file_2)) 44 | expect_equal(dim(f1), c(97,19)) 45 | expect_equal(dim(f2), c(97,19)) 46 | expect_equal(f2$description[1], "\"VanR: transcriptional activator regulating VanA, VanH and VanX\" [ARO:3000574]") 47 | }) 48 | 49 | test_that("hmmprofiles with /f format parse", { 50 | file = system.file('extdata', 'example.hmmprofile.hmm', package='rhmmer') 51 | df = read_hmmprofile(file) 52 | expect_true(nrow(df) == 20) 53 | expect_true(ncol(df) == 28) 54 | }) 55 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/domainless/ali.log: -------------------------------------------------------------------------------- 1 | # hmmscan :: search sequence(s) against a profile database 2 | # HMMER 3.1b2 (February 2015); http://hmmer.org/ 3 | # Copyright (C) 2015 Howard Hughes Medical Institute. 4 | # Freely distributed under the GNU General Public License (GPLv3). 5 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 6 | # query sequence file: domainless.faa 7 | # target HMM database: /home/z/db/Pfam-A.hmm 8 | # per-seq hits tabular output: x.tblout 9 | # per-dom hits tabular output: x.domtblout 10 | # pfam-style tabular hit output: x.pfamtblout 11 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 12 | 13 | Query: AT2G38544.1 [L=47] 14 | Description: pacid=19638109 transcript=AT2G38544.1 locus=AT2G38544 ID=AT2G38544.1.TAIR10 annot-version=TAIR10 15 | Scores for complete sequence (score includes all domains): 16 | --- full sequence --- --- best 1 domain --- -#dom- 17 | E-value score bias E-value score bias exp N Model Description 18 | ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 19 | 20 | [No hits detected that satisfy reporting thresholds] 21 | 22 | 23 | Domain annotation for each model (and alignments): 24 | 25 | [No targets detected that satisfy reporting thresholds] 26 | 27 | 28 | Internal pipeline statistics summary: 29 | ------------------------------------- 30 | Query sequence(s): 1 (47 residues searched) 31 | Target model(s): 16712 (2907032 nodes) 32 | Passed MSV filter: 182 (0.0108904); expected 334.2 (0.02) 33 | Passed bias filter: 152 (0.00909526); expected 334.2 (0.02) 34 | Passed Vit filter: 5 (0.000299186); expected 16.7 (0.001) 35 | Passed Fwd filter: 0 (0); expected 0.2 (1e-05) 36 | Initial search space (Z): 16712 [actual number of targets] 37 | Domain search space (domZ): 0 [number of targets reported over threshold] 38 | # CPU time: 0.28u 0.10s 00:00:00.38 Elapsed: 00:00:00.26 39 | # Mc/sec: 525.50 40 | // 41 | [ok] 42 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/domainless/log: -------------------------------------------------------------------------------- 1 | # hmmscan :: search sequence(s) against a profile database 2 | # HMMER 3.1b2 (February 2015); http://hmmer.org/ 3 | # Copyright (C) 2015 Howard Hughes Medical Institute. 4 | # Freely distributed under the GNU General Public License (GPLv3). 5 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 6 | # query sequence file: orphan.faa 7 | # target HMM database: /home/z/db/Pfam-A.hmm 8 | # per-seq hits tabular output: x.tblout 9 | # per-dom hits tabular output: x.domtblout 10 | # pfam-style tabular hit output: x.pfamtblout 11 | # show alignments in output: no 12 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 13 | 14 | Query: AT2G38544.1 [L=47] 15 | Description: pacid=19638109 transcript=AT2G38544.1 locus=AT2G38544 ID=AT2G38544.1.TAIR10 annot-version=TAIR10 16 | Scores for complete sequence (score includes all domains): 17 | --- full sequence --- --- best 1 domain --- -#dom- 18 | E-value score bias E-value score bias exp N Model Description 19 | ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 20 | 21 | [No hits detected that satisfy reporting thresholds] 22 | 23 | 24 | Domain annotation for each model: 25 | 26 | [No targets detected that satisfy reporting thresholds] 27 | 28 | 29 | Internal pipeline statistics summary: 30 | ------------------------------------- 31 | Query sequence(s): 1 (47 residues searched) 32 | Target model(s): 16712 (2907032 nodes) 33 | Passed MSV filter: 182 (0.0108904); expected 334.2 (0.02) 34 | Passed bias filter: 152 (0.00909526); expected 334.2 (0.02) 35 | Passed Vit filter: 5 (0.000299186); expected 16.7 (0.001) 36 | Passed Fwd filter: 0 (0); expected 0.2 (1e-05) 37 | Initial search space (Z): 16712 [actual number of targets] 38 | Domain search space (domZ): 0 [number of targets reported over threshold] 39 | # CPU time: 0.22u 0.13s 00:00:00.35 Elapsed: 00:00:00.25 40 | # Mc/sec: 546.52 41 | // 42 | [ok] 43 | -------------------------------------------------------------------------------- /vignettes/domains.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Protein domain identification" 3 | author: "Zebulun Arendsee" 4 | date: "`r Sys.Date()`" 5 | output: rmarkdown::html_vignette 6 | vignette: > 7 | %\VignetteIndexEntry{Protein domain identification} 8 | %\VignetteEngine{knitr::rmarkdown} 9 | %\VignetteEncoding{UTF-8} 10 | --- 11 | 12 | ```{r setup, include = FALSE} 13 | knitr::opts_chunk$set( 14 | collapse = TRUE, 15 | comment = "#>" 16 | ) 17 | ``` 18 | 19 | One of the main uses of HMMER is identifying protein domains. You can search 20 | individual proteins easily on the HMMER website (http://hmmer.org/). But for 21 | higher throughput analysis, a domain database, such as PFAM, needs to be 22 | downloaded. The PFAM database is freely available from EBI. You can retrieve 23 | the current PFAM release from here: 24 | 25 | ``` 26 | ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz 27 | ``` 28 | 29 | This file can then be unzipped and pressed with `hmmpress` (a tool in the HMMER 30 | suite). Here is a shell script for the process (assuming a UNIX environment): 31 | 32 | ```{sh, eval=FALSE} 33 | wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz 34 | gunzip Pfam-A.hmm.gz 35 | hmmpress Pfam-A.hmm 36 | ``` 37 | 38 | It should only take a few minutes to install and build the database. On 39 | success, the following files are generated: `Pfam-A.hmm`, `Pfam-A.hmm.h3f`, 40 | `Pfam-A.hmm.h3i`, `Pfam-A.hmm.h3m`, and `Pfam-A.hmm.h3p`. 41 | 42 | In this vignette, we we will explore the domains of the rhino mitochondrial 43 | proteins. These sequences are included in the package data. 44 | 45 | 46 | ```{r} 47 | prot <- system.file('extdata', 'rhino.faa', package='rhmmer') 48 | ``` 49 | 50 | Now we can search these proteins against the PFAM database. You could run the 51 | HMMER program from within R through `system2`, but here I will just give the 52 | shell command. 53 | 54 | 55 | ```{sh, eval=FALSE} 56 | hmmscan --tblout rhino.tblout --domtblout rhino.domtblout Pfam-A.hmm rhino.faa 57 | ``` 58 | 59 | This spills a bunch of text to STDOUT and creates two new files: 60 | `rhino.domtblout` and `rhino.tblout`. In case you are not executing all the 61 | installation and database building steps, I've included these outputs in the 62 | package data: 63 | 64 | ```{r} 65 | domtblout_file <- system.file('extdata', 'rhino.domtblout', package='rhmmer') 66 | tblout_file <- system.file('extdata', 'rhino.tblout', package='rhmmer') 67 | ``` 68 | 69 | Now we get to the part `rhmmer` plays, which is to read these files into a tidy 70 | format: 71 | 72 | 73 | ```{r} 74 | library(rhmmer) 75 | domtblout <- read_domtblout(domtblout_file) 76 | tblout <- read_tblout(tblout_file) 77 | ``` 78 | 79 | For a description of all the columns, it is best to go to the [HMMER 80 | manual](http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf). 81 | 82 | Here are a few quick summaries of the results 83 | 84 | ```{r, results="asis"} 85 | library(dplyr) 86 | library(magrittr) 87 | library(knitr) 88 | domtblout %>% 89 | filter(domain_ievalue < 1e-6) %>% 90 | select(domain_name, domain_accession, description) %>% 91 | unique %>% 92 | arrange(domain_name) %>% 93 | kable(caption="Summary of significant domains") 94 | ``` 95 | 96 | ```{r, results="asis"} 97 | tblout %>% 98 | filter(best_domain_evalue < 0.001) %>% 99 | select(query_name, domain_name) %>% 100 | kable(caption="Map of query protein to domain") 101 | ``` 102 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/five/five.faa: -------------------------------------------------------------------------------- 1 | >AT2G18240.1 2 | MEDEPGSENEADTIVASPLAKWRIEFSKSFQNYLDRSAPNIVRRWLVTLVAAVIYIYRVYSVYGYFVISYGLATYILNLL 3 | IGFLSPKVDPELEALDPDSLPVDESDEYKPFVRRLPEFKFWYAATKAFVVAFVMTFFSFLDVPVFWPILLCYWLVLYSLT 4 | MKRLIVHMFKYRYFPFDVRKPVKLLKFLVNSVLTFLRLKKGDGGDDRPSSSNSSQGNEKQD 5 | >AT5G45530.1 6 | MQVIPPAIKKILDKWNIRGLVIMSLLFQTSLIFLAPMRKRTSKKLLAAVLWTAYLLADWTANYAVSQITKNQGKETEPGD 7 | PPKNKKLLALWAPFLLLHLGGPDTITALALEDNALWQRHLFGLVSQALAGVYAVVQSLENVLWPPITLLFITGTIKYVER 8 | TRALYSASLDKFKDRMLQRADAGSNYAKLMEEFASRKMSNLPTEIFLTDEPDKHERPPTLVKPDRDLTDLEIVQYGFKFF 9 | NTFKGLVVDLIFSFRERDESRDFFKELKPGEALRIIETELGFLYESMYTKTAILHTGIGTLFRLISFGSLLSSFFVFHRR 10 | PLKSEDFHGADVVITYVLFIVGIALDLASMVIFLLSDWTFAVLRNLKDDPEEKSTSIDSLFNWFLEFRKPRWKKHTCNGN 11 | QTHEVLSTGFFTRRWSGTIYGFNFIGFCLKAKVSRIHQKRNCNLLVWDYVVSLFDLVIRRIQMMIGWIKNVNRSIRSVLR 12 | QWSKKNPMIRCTVYPLYLVFFAGIPEVFRVLWKYIDRIFSVTSYLDGIRFISREPLTKNQWEFIFNEVKDKSGFAETPEV 13 | AKKVSWARGEWALRDSKLMEVDTLMRYIEKVDYDQSLLLWHIATELCFQKEEGGKMEKLSREGYDDREFSKIISDYMMYL 14 | LIMRPKLMSEVAGIGTIRFRDTKAEAERFFKGRQIKDLRDMKRASETVLLVSNDIEPILVKGDRSKSVLFDASMLAKELQ 15 | NLKESSNEDGKWRVLSKVWVELLCYAASHCKATEHVAQLSRGGELLNFVWLLMAHFGLGDQFQINKGDARAKLVVGEG 16 | >AT1G27880.2 17 | MDFDSDSDGSHVSATPPRDSFPSSPPQLQSPAKHVPPVSRKMTSSSSRSKPKAPTHPPPNPSQEAPVPSPYPPPPPPSPL 18 | FTNLPFRICQSQPARFSSSVSSFSRLCSRASFTSVEKLKSDGVDFVPEPPLVEVIAPPKSVRRKPPNLITDTITSPPVKP 19 | MVFRSNGNGEGNFVKLNLNGKRGKKFPSKYKGVSKSRSSYSFRGKRYKKKEADGDGESLLEEESDLQKQIEDEANGFISS 20 | VEDAILAVKTEASDENLTKLLNLVYGYDSFRDGQLQAIKMILGGSSTMLVLPTGAGKSLCYQIPAMILPGITLVVSPLVS 21 | LMIDQLKHLPSIIKGGLLSSSQRPEEATETLRKLKEGIIKVLFVSPERLLNVEFLSMFRMSLSVSLVVVDEAHCVSEWSH 22 | NFRPSYMRLKASMLFSELKAECILAMTATATTMTLQAVMSSLEIPSTNLIQKSQLRDNFELSVSLSGANRMKDLLILMES 23 | PPYKEIRSIIVYCKFQYETDMISKYLRDNNINAKGYHSGLPAKDRVRIQESFCSNKIRVVVATVAFGMGLDKGDVGAVIH 24 | FSVPGSMEEYVQEIGRAGRDGRLSYCHLFYDNDTYLKLRSLAHSDGVDEYAVGKFLTHVFSTETKQHEKICSLVIESASQ 25 | KFDMKEEVMQTILTHLELGEVQYLRMLPQLNICCTLNFHKSSPNTLAARSAIVAAILKKSHVKQGLHVFDIPAVASSICV 26 | ATTDVLAEIQALKMKGEVTYELKDSAFCYTILKSPKEICSLSSHLTKWLTEIESCKVRKLDIMSSAAVAAISVSNTSELS 27 | SGAKQTRSLQSRIFDYFNGDEKCDSPSKATQNCAFLRADIKVKIQEATLLFILYCFAMYPKNVQLTIVCQNRCFCRVIAK 28 | PNSHQEPSRE 29 | >AT1G56520.1 30 | MASSSSSPRNWRYNVFTSFHGPDVRIKFLSHLRQQFIYNGITMFDDNGIERSQIIAPALKKAIGESRIAILLLSKNYASS 31 | SWSLDELLEILKCKEDIGQIVMTVFYEVDPSDVRNQTGDFGIAFKETCAHKTEEERQKWTQALTYVGNIAGEDFKHWPNE 32 | AKMIEKIARDVSDILNVTPCRDFDGMVGLNDHLREMESLLDLKNDGVKIVGISGPAGIGKSTIATALHGRLSNMFQRTCF 33 | VDNLRESYKIGLDEYRLKLHLQQQLLAYVLNQDKIRVGHLSVMKERLDDLRVLIILDDVEHLYQLEALADIRWFGPGSRV 34 | IVTTENREILLQHGIKDIYHVGFPSEGEALMIFCLSAFRQPSPPYGFLKLTYEVASICGNLPLGLHVLGTLLWGKSQADW 35 | IEELPRLKDCLDGRIESVLKVGYESLYEKDQALFLLIAVYFNYDYVDYVTSMLENTNVLDVRLGLKKLANRCLIQIDIDH 36 | NRKSRVVMNRLLQVMAREVISKQKISKRKILEDPQDICYVLEEAKGKGSALGLSLDVAEIKELVINKKAFKKMCNLLILK 37 | VFNGTDPRDSKLHVPEEMELPSSIRLLHWEAYPRKSFRFGPENLVTLNMEYSELEKLWKGTQPLANLKEMNLCGSSCLKE 38 | LPDLSKAANLERLDVAECNALVEIPSSVANLHKIVNLHMESCESLEVIPTLINLASLKIINIHDCPRLKSFPDVPTSLEE 39 | LVIEKTGVQELPASFRHCTGVTTLYICSNRNLKTFSTHLPMGLRKLDLSNCGIEWVTDSIKDLHNLYYLKLSGCKRLVSL 40 | PELPCSLECLFAEDCTSLERVSDSLNIPNAQFNFIKCFTLDREARRAIIQQSFVHGNVILPAREVLEEVDYRARGNCLTI 41 | PPSAFNRFKVCVVLSIH 42 | >AT3G10370.1 43 | MSLASIRRLAAGAAVIAAASGGAVYLSPSVASSDKGGGPILDSLRRRLGDPTASVPSRSAQESALIAATASDPLDVLVIG 44 | GGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRYLEKAVFNLDYGQLKLVFHALEERKQLIENAPHLCH 45 | ALPCMTPCFDWFEVIYFWMGLKMYDLVAGPRLLHLSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGL 46 | ACTAALAGAAVLNHAEVVSLITDDATKRIIGARIRNNLTGQEFNSYAKVVVNAAGPFCDSIRKMIDEDTKPMICPSSGVH 47 | IVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTDSNTSITSLPEPHEDEIQFILDAISDYLNIKVRRTDVLSAW 48 | SGIRPLAMDPTAKSTESISRDHVVFEENPGLVTITGGKWTTYRSMAEDAVDAAIKSGQLKPTNECVTQKLQLLGSYGWEP 49 | SSFTTLAQQYVRMKKTYGGKVVPGAMDTAAAKHLSHAYGSMADRVATIAQEEGLGKRLAHGHPFLEAEVAYCARHEYCES 50 | AVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDKSRQKQELQKAKEFLETFKSSKNAQFNDGKHN 51 | -------------------------------------------------------------------------------- /R/parse.R: -------------------------------------------------------------------------------- 1 | #' Read a file created through the '----tblout' option 2 | #' 3 | #' @param file Filename 4 | #' @return data.frame 5 | #' @export 6 | #' @examples 7 | #' file <- system.file('extdata', 'example.tblout.txt', package='rhmmer') 8 | #' read_tblout(file) 9 | read_tblout <- function(file){ 10 | .parse_hmmer_output(file, 'tblout') 11 | } 12 | 13 | #' Read a file created through the '----domtblout' option 14 | #' 15 | #' @param file Filename 16 | #' @return data.frame 17 | #' @export 18 | #' @examples 19 | #' file <- system.file('extdata', 'example.domtblout.txt', package='rhmmer') 20 | #' read_domtblout(file) 21 | read_domtblout <- function(file){ 22 | .parse_hmmer_output(file, 'domtblout') 23 | } 24 | 25 | 26 | .parse_hmmer_output <- function(file, type){ 27 | 28 | col_types <- if(type == 'tblout'){ 29 | readr::cols( 30 | domain_name = readr::col_character(), 31 | domain_accession = readr::col_character(), 32 | query_name = readr::col_character(), 33 | query_accession = readr::col_character(), 34 | sequence_evalue = readr::col_double(), 35 | sequence_score = readr::col_double(), 36 | sequence_bias = readr::col_double(), 37 | best_domain_evalue = readr::col_double(), 38 | best_domain_score = readr::col_double(), 39 | best_domain_bis = readr::col_double(), 40 | domain_number_exp = readr::col_double(), 41 | domain_number_reg = readr::col_integer(), 42 | domain_number_clu = readr::col_integer(), 43 | domain_number_ov = readr::col_integer(), 44 | domain_number_env = readr::col_integer(), 45 | domain_number_dom = readr::col_integer(), 46 | domain_number_rep = readr::col_integer(), 47 | domain_number_inc = readr::col_character() 48 | ) 49 | } else if(type == 'domtblout'){ 50 | readr::cols( 51 | domain_name = readr::col_character(), 52 | domain_accession = readr::col_character(), 53 | domain_len = readr::col_integer(), 54 | query_name = readr::col_character(), 55 | query_accession = readr::col_character(), 56 | qlen = readr::col_integer(), 57 | sequence_evalue = readr::col_double(), 58 | sequence_score = readr::col_double(), 59 | sequence_bias = readr::col_double(), 60 | domain_N = readr::col_integer(), 61 | domain_of = readr::col_integer(), 62 | domain_cevalue = readr::col_double(), 63 | domain_ievalue = readr::col_double(), 64 | domain_score = readr::col_double(), 65 | domain_bias = readr::col_double(), 66 | hmm_from = readr::col_integer(), 67 | hmm_to = readr::col_integer(), 68 | ali_from = readr::col_integer(), 69 | ali_to = readr::col_integer(), 70 | env_from = readr::col_integer(), 71 | env_to = readr::col_integer(), 72 | acc = readr::col_double() 73 | ) 74 | } 75 | 76 | N <- length(col_types$cols) 77 | 78 | # the line delimiter should always be just "\n", even on Windows 79 | lines <- readr::read_lines(file, lazy=FALSE, progress=FALSE) 80 | 81 | table <- sub( 82 | pattern = sprintf("(%s).*", paste0(rep('\\S+', N), collapse=" +")), 83 | replacement = '\\1', 84 | x=lines, 85 | perl = TRUE 86 | ) %>% 87 | gsub(pattern=" *", replacement="\t") %>% 88 | paste0(collapse="\n") %>% 89 | readr::read_tsv( 90 | col_names=names(col_types$cols), 91 | comment='#', 92 | na='-', 93 | col_types = col_types, 94 | lazy=FALSE, 95 | progress=FALSE 96 | ) 97 | 98 | if(type == 'domtblout'){ 99 | table$description <- lines[!grepl("^#", lines, perl=TRUE)] %>% 100 | sub( 101 | pattern = sprintf("%s *(.*)", paste0(rep('\\S+', N), collapse=" +")), 102 | replacement = '\\1', 103 | perl = TRUE 104 | ) 105 | } 106 | 107 | table 108 | } 109 | -------------------------------------------------------------------------------- /inst/extdata/rhino.faa: -------------------------------------------------------------------------------- 1 | >YP_002887585.1 NADH dehydrogenase subunit 1 2 | MFTINILLLVIPILLAVAFLTLVERKVLGYMQLRKGPNIVGPYGLLQPIADAIKLFTKEPLQPSTSSTTM 3 | FIIAPILALTLALTMWIPLPMPYPLINMNLGILFMLAMSSLAVYSILWSGWASNSKYALIGALRAVAQTI 4 | SYEVTLAIILLSVLLMNGSFTLSTLITTQEHLWLIFPSWPLTMMWFISTLAETNRAPFDLTEGESELVSG 5 | FNVEYAAGPFALFFMAEYANIIMMNAFTTILFLGAFHNPYMSELYTINFTTKTLLLTTSFLWIRASYPRF 6 | RYDQLMHLLWKNFLPLTLALCMWHVSLPITTSSIPPQT 7 | >YP_002887586.1 NADH dehydrogenase subunit 2 8 | MNPIVFSTILTTAILGTMIVMTSSHWLMIWIGFEMNLLAIIPILMKNFNPRAMEAATKYFLTQTTASMLL 9 | MMAIIINLMFSGQWTITKIFNPTASIIMTSALVMKLGLSPFHFWVPEVTQGISLMSGLILLTWQKLAPMS 10 | VLYQIAPSINPNMLMATALLSILVGGWGGLNQTQLRKIMAYSSIAHMGWMTAILMYNPTMTMLNMLIYIM 11 | MTLTTFMLFMLNSSTTMLSLSLTWNKTPLITSLILITMLSLGGLPPLSGFIPKWMIIQELTKNDSIILPT 12 | SMAIMALLNLYFYMRLTYSTSLTMFPSMNNMKMKWQFENSKRMNFLPTLIIMSTLLLPLTPIMSILN 13 | >YP_002887587.1 cytochrome c oxidase subunit I 14 | MFINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMV 15 | MPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAG 16 | ASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVLITAVLLLLALPVLAAGITMLL 17 | TDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSI 18 | GFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMLWALGFIFLFTV 19 | GGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNQTWAKIHFMIMFVG 20 | VNMTFFPQHFLGLSGMPRRYSDYPDAYTTWNTISSMGSFISLTAVMLMVFMIWEAFASKREVSTVELTTS 21 | NLEWLHGCPPPYHTFEEPVYVNLK 22 | >YP_002887588.1 cytochrome c oxidase subunit II 23 | MAYPLQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPA 24 | IILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLTFDSYMIPTSDLKPGELRLLEVDN 25 | RVVLPMEMTIRMLISSEDVLHSWAIPSLGLKTDAIPGRLNQTTLVSTRPGLYYGQCSEICGSNHSFMPIV 26 | LELVPLKHFEKWSASMI 27 | >YP_002887589.1 ATP synthase F0 subunit 8 28 | MPQLDTSTWSITIMSMIITLFIMFQLKLSKYSYPSNPELKLTKTPAHTMPWESKWTKTYLPLSLPQQL 29 | >YP_002887590.1 ATP synthase F0 subunit 6 30 | MNENLFASFTTPTIMGLPIVILIIMSPSIMFPTSNRLINNRLISIQQWLLQLTSKQMLSIHNNKGQTWAL 31 | MLMSLILFIGSTNLLGLLPHSFTPTTQLSMNLGMAIPLWAGTVFLGFRHNTKTSLAHFLPQGTPIFLIPA 32 | LVIIETISLFIQPVALAVRLTANITAGHLLMYLIGGATLALMNISPTTALVTFIILILLTILEFAVALIQ 33 | AYVFTLLVSLYLHNNT 34 | >YP_002887591.1 cytochrome c oxidase subunit III 35 | MTHQTHAYHMVNPSPWPLTGALSALLMTSGLAMWFHYNSTLLLTLGLTTNLLTMYQWWRDIVRESTFQGH 36 | HTLVVQKGLRYGMILFIISEVFFFSGFFWAFYHSSLAPTPELGGCWPPTGIYPLNPMEVPLLNTSILLAS 37 | GVSITWAHHSLMEGNRKHMLQALFITISLGIYFTLLQASEYYEAPFTISDGIYGSTFFVATGFHGLHVII 38 | GSAFLIVCFLRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS 39 | >YP_002887592.1 NADH dehydrogenase subunit 3 40 | MNLMLTLFINMSLASMLVLIAFWLPQLNIYTEKTSPYECGFDPMGSARLPFSMKFFLVAITFLLFDLEIA 41 | LLLPLPWASQTTNLKTMLTMALALISLLAASLAYEWTQKGLEWAE 42 | >YP_002887593.1 NADH dehydrogenase subunit 4L 43 | MSLIHINIFLAFAASLVGLLMYRSHLMSSLLCLEGMMLSLFIMATMTVLNSNFTLASMMPIILLVFAACE 44 | AALGLSLLVMISNTYGTDYVQNLNLLQC 45 | >YP_002887594.1 NADH dehydrogenase subunit 4 46 | MLKIIIPTLMLIPLTWLSKNNMIWINTTAYSLLISLISLPLLNQFNENSLNMSPMFFSDPLSAPLLVLTT 47 | WLLPLMIMASQHHLSKEPPARKKLYITMLVMLQTFLIMTFTATELISFYILFEATLIPTLIIITRWGNQT 48 | ERLNAGFYFLFYTLTGSLPLLIALTHIQNLTGTLNLLLIQYSTQTLPNSWSNAFLWLACMMAFMVKMPLY 49 | GLHLWLPKAHVEAPIAGSMVLAAILLKLGGYGMLRITMILNPLTSYMAYPFLILSLWGMIMTSSICLRQT 50 | DLKSLIAYSSVSHMALVIVAVLIQTPWSYMGATALMIAHGLTSSVLFCLANSNYERTHSRTMILARGLQT 51 | LLPLMAMWWLLAGLTNLALPPTINLIGELFVVMSSFSWSNITIILMGTNIIITALYSLYMLTTTQRGKYT 52 | HHINNIKPSFTRENTLMALHLLPLLLLSLNPKIILGTLY 53 | >YP_002887595.1 NADH dehydrogenase subunit 5 54 | MNMFPSLMLTSLLMLTLPIITITINTHKNNTYPRYVKNIISYAFITSLIPTMMFIHSGQEMIISNWHWMT 55 | IQTLKLSLSFKLDYFSMIFVPVALFVTWSIMEFSMWYMHSDPHITQFFKYLLMFLITMMILVTANNLFQL 56 | FIGWEGVGIMSFLLISWWYGRTDANTAALQAILYNRIGDIGLIMSMAWFLLNMNSWDLQQIFTLNHSHTN 57 | LPLMGLLLAATGKSAQFGLHPWLPSAMEGPTPVSALLHSSTMVVAGVFLLIRFHPLMENNKTIQTLTLCL 58 | GAITTLFTAICALTQNDIKKIIAFSTSSQLGLMIVTIGINQPYLAFLHICTHAFFKAMLFMCSGSIIHNL 59 | NNEQDIRKMGGLFKVMPFTSTSLIIGSLALTGMPFLTGFYSKDLIIETANMSYTNAWALLITLIATSLTA 60 | AYSTRMIFFTLLGQPRFPTLVTINENNPLLMNSIKRLLIGSIFAGFLISNSIYPTTIPKMTMPYYLKLTA 61 | LTVTILGFALALELSLATYNLKPKHPSSLLKFSSLLGYFPTILHRLPPFMGLSTSQKSASLLLDLTWLES 62 | ILPKSISQFQVKTSTLVSNQKGLIKLYFLSFLITLTLSLLLLMPHE 63 | >YP_002887596.1 NADH dehydrogenase subunit 6 64 | MMTYIGFILSIMFVIGFVGFSSKPSPIYGGLVLIMSGGFGCGIVMSFGGSFLGLMVFLVYLGGMLVVFGY 65 | TTAMATEQYPETWVSNATVLGAFVLGVLMEVMLILYVFKSGEVEVVFKFGGMGDWVVSGSGDFGVFSEEI 66 | VGVSALYSYGVWIIIVTGWSLFVGVLVVLEVTRGA 67 | >YP_002887597.1 cytochrome b 68 | MTNIRKSHPLIKIINHSFIDLPTPSNISAWWNFGSLLGICLILQILTGLFLAMHYTPDTTTAFSSVAHIC 69 | RDVNYGWIIRYLHANGASMFFICLFIHMGRGLYYGSYTFLETWNIGVILLFTLMATAFMGYVLPWGQMSF 70 | WGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAFHFILPFIISALAITHLLFLHETGSNNPSG 71 | IPSNMDKIPFHPYYTIKDILGILLLILTLLTLVLFSPDILGDPDNYTPANPLSTPPHIKPEWYFLFAYAI 72 | LRSIPNKLGGVLALALSILILLIVPFLHTSKQRSMMFRPLSQCMFWLLVADLLTLTWIGGQPVEHPFIII 73 | GQLASILYFSLILVLMPLAGIIENNLLKW 74 | -------------------------------------------------------------------------------- /inst/extdata/rhino.tblout: -------------------------------------------------------------------------------- 1 | # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- 2 | # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target 3 | #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- 4 | NADHdh PF00146.20 YP_002887585.1 - 9.7e-110 366.5 23.1 1.1e-109 366.3 23.1 1.0 1 0 0 1 1 1 1 NADH dehydrogenase 5 | Proton_antipo_M PF00361.19 YP_002887586.1 - 5e-42 144.0 40.7 5e-42 144.0 40.7 1.8 1 1 1 2 2 2 1 Proton-conducting membrane transporter 6 | NADH_dehy_S2_C PF06444.10 YP_002887586.1 - 4.5e-22 78.2 16.2 4.5e-22 78.2 16.2 6.4 6 2 2 8 8 8 1 NADH dehydrogenase subunit 2 C-terminus 7 | COX1 PF00115.19 YP_002887587.1 - 3.8e-144 480.6 65.1 4.8e-144 480.3 65.1 1.1 1 0 0 1 1 1 1 Cytochrome C and Quinol oxidase polypeptide I 8 | COX2 PF00116.19 YP_002887588.1 - 2.1e-64 214.7 0.0 3.3e-64 214.0 0.0 1.3 1 0 0 1 1 1 1 Cytochrome C oxidase subunit II, periplasmic domain 9 | COX2_TM PF02790.14 YP_002887588.1 - 2.3e-28 98.1 7.4 3.6e-28 97.4 7.4 1.3 1 0 0 1 1 1 1 Cytochrome C oxidase subunit II, transmembrane domain 10 | MRAP PF15183.5 YP_002887588.1 - 0.15 11.9 6.0 2.2 8.2 0.2 2.3 2 0 0 2 2 2 0 Melanocortin-2 receptor accessory protein family 11 | ATP-synt_8 PF00895.19 YP_002887589.1 - 2.6e-21 75.7 11.8 3.2e-21 75.4 11.8 1.1 1 0 0 1 1 1 1 ATP synthase protein 8 12 | ATP-synt_A PF00119.19 YP_002887590.1 - 1.2e-40 139.7 27.6 1.4e-40 139.4 27.6 1.0 1 0 0 1 1 1 1 ATP synthase A chain 13 | COX3 PF00510.17 YP_002887591.1 - 1.9e-131 437.5 26.7 2.1e-131 437.3 26.7 1.0 1 0 0 1 1 1 1 Cytochrome c oxidase subunit III 14 | Oxidored_q4 PF00507.18 YP_002887592.1 - 3e-27 94.6 0.9 3.9e-27 94.2 0.9 1.1 1 0 0 1 1 1 1 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 15 | Oxidored_q2 PF00420.23 YP_002887593.1 - 5.7e-17 61.2 13.5 6.5e-17 61.0 13.5 1.1 1 0 0 1 1 1 1 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L 16 | Proton_antipo_M PF00361.19 YP_002887594.1 - 1.7e-77 260.4 36.7 1.7e-77 260.4 36.7 1.7 2 0 0 2 2 2 1 Proton-conducting membrane transporter 17 | Oxidored_q5_N PF01059.16 YP_002887594.1 - 5.9e-34 116.4 21.2 5.9e-34 116.4 21.2 5.4 2 1 2 5 5 5 1 NADH-ubiquinone oxidoreductase chain 4, amino terminus 18 | Birna_RdRp PF04197.11 YP_002887594.1 - 0.32 9.2 0.9 0.45 8.7 0.9 1.1 1 0 0 1 1 1 0 Birnavirus RNA dependent RNA polymerase (VP1) 19 | Proton_antipo_M PF00361.19 YP_002887595.1 - 1.6e-76 257.2 24.6 1.6e-76 257.2 24.6 2.9 3 0 0 3 3 3 1 Proton-conducting membrane transporter 20 | NADH5_C PF06455.10 YP_002887595.1 - 1.3e-53 181.2 17.6 1.3e-53 181.2 17.6 4.9 4 2 0 4 4 4 1 NADH dehydrogenase subunit 5 C-terminus 21 | Proton_antipo_N PF00662.19 YP_002887595.1 - 7e-14 51.5 8.3 7e-14 51.5 8.3 2.9 3 0 0 3 3 3 1 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus 22 | Oxidored_q3 PF00499.19 YP_002887596.1 - 6.7e-18 64.7 16.0 1.1e-17 64.1 16.0 1.3 1 0 0 1 1 1 1 NADH-ubiquinone/plastoquinone oxidoreductase chain 6 23 | Cytochrome_B PF00033.18 YP_002887597.1 - 4e-86 287.6 18.4 4e-86 287.6 18.4 2.0 3 0 0 3 3 3 1 Cytochrome b/b6/petB 24 | Cytochrom_B_N_2 PF13631.5 YP_002887597.1 - 3e-40 137.9 9.8 3e-40 137.9 9.8 2.4 3 0 0 3 3 3 1 Cytochrome b(N-terminal)/b6/petB 25 | Cytochrom_B_C PF00032.16 YP_002887597.1 - 3.1e-37 126.9 1.6 3.1e-37 126.9 1.6 3.0 2 1 0 2 2 2 1 Cytochrome b(C-terminal)/b6/petD 26 | # 27 | # Program: hmmscan 28 | # Version: 3.1b1 (May 2013) 29 | # Pipeline mode: SCAN 30 | # Query file: rhino.faa 31 | # Target file: Pfam-A.hmm 32 | # Option settings: hmmscan --tblout rhino.tblout --domtblout rhino.domtblout Pfam-A.hmm rhino.faa 33 | # Current dir: /home/rnz/Dropbox/data/pfam 34 | # Date: Tue Jan 2 15:13:22 2018 35 | # [ok] 36 | -------------------------------------------------------------------------------- /inst/extdata/example.tblout.txt: -------------------------------------------------------------------------------- 1 | # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- 2 | # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target 3 | #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- 4 | Rer1 PF03248.12 AT2G18240.1 - 2.3e-61 206.4 10.4 7.1e-61 204.8 11.2 1.3 2 0 0 2 2 2 1 Rer1 family 5 | DUF4220 PF13968.5 AT5G45530.1 - 4.6e-78 263.0 0.0 1.3e-77 261.5 0.0 1.7 1 1 0 1 1 1 1 Domain of unknown function (DUF4220) 6 | DUF594 PF04578.12 AT5G45530.1 - 4.7e-24 83.6 1.5 1.1e-23 82.4 1.5 1.7 1 0 0 1 1 1 1 Protein of unknown function, DUF594 7 | DEAD PF00270.28 AT1G27880.2 - 6.7e-20 71.5 0.1 1.9e-19 70.0 0.1 1.8 1 0 0 1 1 1 1 DEAD/DEAH box helicase 8 | Helicase_C PF00271.30 AT1G27880.2 - 3.2e-18 66.0 0.0 3e-17 62.9 0.0 2.5 2 0 0 2 2 2 1 Helicase conserved C-terminal domain 9 | ResIII PF04851.14 AT1G27880.2 - 0.0012 18.8 0.1 0.0084 16.0 0.0 2.4 2 1 0 2 2 2 1 Type III restriction enzyme, res subunit 10 | TIR PF01582.19 AT1G56520.1 - 7.3e-46 156.1 0.0 1.2e-45 155.3 0.0 1.4 1 0 0 1 1 1 1 TIR domain 11 | NB-ARC PF00931.21 AT1G56520.1 - 1.9e-17 63.1 0.0 3.5e-17 62.3 0.0 1.4 1 0 0 1 1 1 1 NB-ARC domain 12 | LRR_3 PF07725.11 AT1G56520.1 - 1e-07 31.4 1.1 1e-07 31.4 1.1 2.7 2 0 0 2 2 2 1 Leucine Rich Repeat 13 | LRR_8 PF13855.5 AT1G56520.1 - 2.3e-07 30.4 7.0 0.0048 16.5 0.0 5.5 3 2 3 6 6 6 4 Leucine rich repeat 14 | LRR_4 PF12799.6 AT1G56520.1 - 2.7e-07 30.6 17.6 0.0047 17.2 0.2 6.1 6 1 1 7 7 5 3 Leucine Rich repeats (2 copies) 15 | TIR_2 PF13676.5 AT1G56520.1 - 2.6e-05 24.4 0.1 9.3e-05 22.6 0.0 1.9 2 0 0 2 2 2 1 TIR domain 16 | AAA_16 PF13191.5 AT1G56520.1 - 0.0002 21.7 0.3 0.00077 19.8 0.3 2.0 1 1 0 1 1 1 1 AAA ATPase domain 17 | AAA_18 PF13238.5 AT1G56520.1 - 0.001 19.5 0.0 0.0024 18.3 0.0 1.7 1 0 0 1 1 1 1 AAA domain 18 | AAA_22 PF13401.5 AT1G56520.1 - 0.0048 17.1 1.0 0.024 14.8 1.0 2.1 1 1 0 1 1 1 1 AAA domain 19 | ATPase_2 PF01637.17 AT1G56520.1 - 0.015 15.1 0.0 0.046 13.5 0.0 1.8 1 1 0 1 1 1 0 ATPase domain predominantly from Archaea 20 | PhoH PF02562.15 AT1G56520.1 - 0.028 13.8 1.1 3.5 6.9 0.2 2.3 1 1 1 2 2 2 0 PhoH-like protein 21 | NACHT PF05729.11 AT1G56520.1 - 0.029 14.2 0.0 0.057 13.2 0.0 1.5 1 0 0 1 1 1 0 NACHT domain 22 | AAA_23 PF13476.5 AT1G56520.1 - 0.039 14.4 0.0 0.34 11.3 0.0 2.3 2 0 0 2 2 2 0 AAA domain 23 | ABC_tran PF00005.26 AT1G56520.1 - 0.044 14.2 0.0 0.095 13.1 0.0 1.5 1 0 0 1 1 1 0 ABC transporter 24 | NTPase_1 PF03266.14 AT1G56520.1 - 0.062 13.1 0.0 0.16 11.8 0.0 1.7 1 1 0 1 1 1 0 NTPase 25 | AAA_29 PF13555.5 AT1G56520.1 - 0.079 12.6 0.1 1.3 8.7 0.1 2.3 2 0 0 2 2 2 0 P-loop containing region of AAA domain 26 | LRR_1 PF00560.32 AT1G56520.1 - 0.15 12.6 14.8 24 5.9 0.0 7.8 8 1 0 8 8 8 0 Leucine Rich Repeat 27 | DAO PF01266.23 AT3G10370.1 - 3.2e-53 181.4 0.1 8.6e-53 180.1 0.0 1.6 2 0 0 2 2 2 1 FAD dependent oxidoreductase 28 | DAO_C PF16901.4 AT3G10370.1 - 9e-39 132.1 0.3 1.6e-38 131.3 0.3 1.4 1 0 0 1 1 1 1 C-terminal domain of alpha-glycerophosphate oxidase 29 | FAD_binding_2 PF00890.23 AT3G10370.1 - 6.3e-07 28.7 1.9 0.0023 17.0 1.2 2.3 2 0 0 2 2 2 2 FAD binding domain 30 | FAD_oxidored PF12831.6 AT3G10370.1 - 0.0001 21.7 1.1 0.00043 19.7 0.3 2.2 2 0 0 2 2 2 1 FAD dependent oxidoreductase 31 | Pyr_redox_2 PF07992.13 AT3G10370.1 - 0.014 14.6 0.0 0.031 13.4 0.0 1.5 1 0 0 1 1 1 0 Pyridine nucleotide-disulphide oxidoreductase 32 | FAD_binding_3 PF01494.18 AT3G10370.1 - 0.015 14.5 0.2 0.39 9.8 0.5 2.1 2 0 0 2 2 2 0 FAD binding domain 33 | GIDA PF01134.21 AT3G10370.1 - 0.036 13.0 0.2 0.23 10.4 0.1 2.0 2 0 0 2 2 2 0 Glucose inhibited division protein A 34 | Pyr_redox PF00070.26 AT3G10370.1 - 0.063 13.8 0.7 0.28 11.7 0.7 2.1 1 0 0 1 1 1 0 Pyridine nucleotide-disulphide oxidoreductase 35 | HI0933_like PF03486.13 AT3G10370.1 - 0.075 11.6 0.2 0.15 10.6 0.2 1.5 1 0 0 1 1 1 0 HI0933-like protein 36 | AAA_30 PF13604.5 AT3G10370.1 - 0.077 12.6 0.6 0.17 11.5 0.0 1.9 2 0 0 2 2 2 0 AAA domain 37 | Pyr_redox_3 PF13738.5 AT3G10370.1 - 0.1 11.7 0.0 0.18 10.9 0.0 1.3 1 0 0 1 1 1 0 Pyridine nucleotide-disulphide oxidoreductase 38 | DUF4179 PF13786.5 AT3G10370.1 - 0.18 12.2 0.9 0.71 10.3 0.0 2.2 2 0 0 2 2 2 0 Domain of unknown function (DUF4179) 39 | 3HCDH_N PF02737.17 AT3G10370.1 - 0.31 10.8 2.0 0.36 10.6 0.2 2.0 2 0 0 2 2 2 0 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 40 | NAD_binding_8 PF13450.5 AT3G10370.1 - 1.4 9.1 5.0 0.32 11.2 0.6 2.3 3 0 0 3 3 2 0 NAD(P)-binding Rossmann-like domain 41 | # 42 | # Program: hmmscan 43 | # Version: 3.1b2 (February 2015) 44 | # Pipeline mode: SCAN 45 | # Query file: five.faa 46 | # Target file: /home/z/db/Pfam-A.hmm 47 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa 48 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 49 | # Date: Fri Dec 15 02:09:00 2017 50 | # [ok] 51 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/five/tblout: -------------------------------------------------------------------------------- 1 | # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- 2 | # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target 3 | #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- 4 | Rer1 PF03248.12 AT2G18240.1 - 2.3e-61 206.4 10.4 7.1e-61 204.8 11.2 1.3 2 0 0 2 2 2 1 Rer1 family 5 | DUF4220 PF13968.5 AT5G45530.1 - 4.6e-78 263.0 0.0 1.3e-77 261.5 0.0 1.7 1 1 0 1 1 1 1 Domain of unknown function (DUF4220) 6 | DUF594 PF04578.12 AT5G45530.1 - 4.7e-24 83.6 1.5 1.1e-23 82.4 1.5 1.7 1 0 0 1 1 1 1 Protein of unknown function, DUF594 7 | DEAD PF00270.28 AT1G27880.2 - 6.7e-20 71.5 0.1 1.9e-19 70.0 0.1 1.8 1 0 0 1 1 1 1 DEAD/DEAH box helicase 8 | Helicase_C PF00271.30 AT1G27880.2 - 3.2e-18 66.0 0.0 3e-17 62.9 0.0 2.5 2 0 0 2 2 2 1 Helicase conserved C-terminal domain 9 | ResIII PF04851.14 AT1G27880.2 - 0.0012 18.8 0.1 0.0084 16.0 0.0 2.4 2 1 0 2 2 2 1 Type III restriction enzyme, res subunit 10 | TIR PF01582.19 AT1G56520.1 - 7.3e-46 156.1 0.0 1.2e-45 155.3 0.0 1.4 1 0 0 1 1 1 1 TIR domain 11 | NB-ARC PF00931.21 AT1G56520.1 - 1.9e-17 63.1 0.0 3.5e-17 62.3 0.0 1.4 1 0 0 1 1 1 1 NB-ARC domain 12 | LRR_3 PF07725.11 AT1G56520.1 - 1e-07 31.4 1.1 1e-07 31.4 1.1 2.7 2 0 0 2 2 2 1 Leucine Rich Repeat 13 | LRR_8 PF13855.5 AT1G56520.1 - 2.3e-07 30.4 7.0 0.0048 16.5 0.0 5.5 3 2 3 6 6 6 4 Leucine rich repeat 14 | LRR_4 PF12799.6 AT1G56520.1 - 2.7e-07 30.6 17.6 0.0047 17.2 0.2 6.1 6 1 1 7 7 5 3 Leucine Rich repeats (2 copies) 15 | TIR_2 PF13676.5 AT1G56520.1 - 2.6e-05 24.4 0.1 9.3e-05 22.6 0.0 1.9 2 0 0 2 2 2 1 TIR domain 16 | AAA_16 PF13191.5 AT1G56520.1 - 0.0002 21.7 0.3 0.00077 19.8 0.3 2.0 1 1 0 1 1 1 1 AAA ATPase domain 17 | AAA_18 PF13238.5 AT1G56520.1 - 0.001 19.5 0.0 0.0024 18.3 0.0 1.7 1 0 0 1 1 1 1 AAA domain 18 | AAA_22 PF13401.5 AT1G56520.1 - 0.0048 17.1 1.0 0.024 14.8 1.0 2.1 1 1 0 1 1 1 1 AAA domain 19 | ATPase_2 PF01637.17 AT1G56520.1 - 0.015 15.1 0.0 0.046 13.5 0.0 1.8 1 1 0 1 1 1 0 ATPase domain predominantly from Archaea 20 | PhoH PF02562.15 AT1G56520.1 - 0.028 13.8 1.1 3.5 6.9 0.2 2.3 1 1 1 2 2 2 0 PhoH-like protein 21 | NACHT PF05729.11 AT1G56520.1 - 0.029 14.2 0.0 0.057 13.2 0.0 1.5 1 0 0 1 1 1 0 NACHT domain 22 | AAA_23 PF13476.5 AT1G56520.1 - 0.039 14.4 0.0 0.34 11.3 0.0 2.3 2 0 0 2 2 2 0 AAA domain 23 | ABC_tran PF00005.26 AT1G56520.1 - 0.044 14.2 0.0 0.095 13.1 0.0 1.5 1 0 0 1 1 1 0 ABC transporter 24 | NTPase_1 PF03266.14 AT1G56520.1 - 0.062 13.1 0.0 0.16 11.8 0.0 1.7 1 1 0 1 1 1 0 NTPase 25 | AAA_29 PF13555.5 AT1G56520.1 - 0.079 12.6 0.1 1.3 8.7 0.1 2.3 2 0 0 2 2 2 0 P-loop containing region of AAA domain 26 | LRR_1 PF00560.32 AT1G56520.1 - 0.15 12.6 14.8 24 5.9 0.0 7.8 8 1 0 8 8 8 0 Leucine Rich Repeat 27 | DAO PF01266.23 AT3G10370.1 - 3.2e-53 181.4 0.1 8.6e-53 180.1 0.0 1.6 2 0 0 2 2 2 1 FAD dependent oxidoreductase 28 | DAO_C PF16901.4 AT3G10370.1 - 9e-39 132.1 0.3 1.6e-38 131.3 0.3 1.4 1 0 0 1 1 1 1 C-terminal domain of alpha-glycerophosphate oxidase 29 | FAD_binding_2 PF00890.23 AT3G10370.1 - 6.3e-07 28.7 1.9 0.0023 17.0 1.2 2.3 2 0 0 2 2 2 2 FAD binding domain 30 | FAD_oxidored PF12831.6 AT3G10370.1 - 0.0001 21.7 1.1 0.00043 19.7 0.3 2.2 2 0 0 2 2 2 1 FAD dependent oxidoreductase 31 | Pyr_redox_2 PF07992.13 AT3G10370.1 - 0.014 14.6 0.0 0.031 13.4 0.0 1.5 1 0 0 1 1 1 0 Pyridine nucleotide-disulphide oxidoreductase 32 | FAD_binding_3 PF01494.18 AT3G10370.1 - 0.015 14.5 0.2 0.39 9.8 0.5 2.1 2 0 0 2 2 2 0 FAD binding domain 33 | GIDA PF01134.21 AT3G10370.1 - 0.036 13.0 0.2 0.23 10.4 0.1 2.0 2 0 0 2 2 2 0 Glucose inhibited division protein A 34 | Pyr_redox PF00070.26 AT3G10370.1 - 0.063 13.8 0.7 0.28 11.7 0.7 2.1 1 0 0 1 1 1 0 Pyridine nucleotide-disulphide oxidoreductase 35 | HI0933_like PF03486.13 AT3G10370.1 - 0.075 11.6 0.2 0.15 10.6 0.2 1.5 1 0 0 1 1 1 0 HI0933-like protein 36 | AAA_30 PF13604.5 AT3G10370.1 - 0.077 12.6 0.6 0.17 11.5 0.0 1.9 2 0 0 2 2 2 0 AAA domain 37 | Pyr_redox_3 PF13738.5 AT3G10370.1 - 0.1 11.7 0.0 0.18 10.9 0.0 1.3 1 0 0 1 1 1 0 Pyridine nucleotide-disulphide oxidoreductase 38 | DUF4179 PF13786.5 AT3G10370.1 - 0.18 12.2 0.9 0.71 10.3 0.0 2.2 2 0 0 2 2 2 0 Domain of unknown function (DUF4179) 39 | 3HCDH_N PF02737.17 AT3G10370.1 - 0.31 10.8 2.0 0.36 10.6 0.2 2.0 2 0 0 2 2 2 0 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 40 | NAD_binding_8 PF13450.5 AT3G10370.1 - 1.4 9.1 5.0 0.32 11.2 0.6 2.3 3 0 0 3 3 2 0 NAD(P)-binding Rossmann-like domain 41 | # 42 | # Program: hmmscan 43 | # Version: 3.1b2 (February 2015) 44 | # Pipeline mode: SCAN 45 | # Query file: five.faa 46 | # Target file: /home/z/db/Pfam-A.hmm 47 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa 48 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 49 | # Date: Fri Dec 15 02:09:00 2017 50 | # [ok] 51 | -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- 1 | [![stable](http://badges.github.io/stability-badges/dist/stable.svg)](http://github.com/badges/stability-badges) 2 | [![Travis-CI Build Status](https://travis-ci.org/arendsee/rhmmer.svg?branch=master)](https://travis-ci.org/arendsee/rhmmer) 3 | [![Coverage Status](https://img.shields.io/codecov/c/github/arendsee/rhmmer/master.svg)](https://codecov.io/github/arendsee/rhmmer?branch=master) 4 | [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/rhmmer)](https://cran.r-project.org/package=rhmmer) 5 | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/rhmmer)](http://cran.rstudio.com/web/packages/rhmmer/index.html) 6 | [![total downloads](http://cranlogs.r-pkg.org/badges/grand-total/rhmmer)](http://cranlogs.r-pkg.org/badges/grand-total/rhmmer) 7 | [![DOI](https://zenodo.org/badge/114339623.svg)](https://zenodo.org/badge/latestdoi/114339623) 8 | 9 | # rhmmer 10 | 11 | [HMMER](http://hmmer.org) is a powerful package for profile HMM analysis. If 12 | you want to interface with the web server through R, for example to search for 13 | domains in a small number of proteins, consider using the 14 | [Bio3D](http://thegrantlab.org/bio3d/index.php) package.`rhmmer` is 15 | specifically designed for working with the standalone HMMER tool. 16 | 17 | ## Installation 18 | 19 | `rhmmer` is available on CRAN 20 | 21 | ```{r, eval=FALSE} 22 | install.packages('rhmmer') 23 | ``` 24 | 25 | Alternatively, you may install the github development version 26 | 27 | ```{r, eval=FALSE} 28 | library(devtools) 29 | install_github('arendsee/rhmmer') 30 | ``` 31 | 32 | ## Examples 33 | 34 | `rhmmer` currently exports exactly two functions: `read_domtblout` and 35 | `read_tblout`. These read the `hmmscan` outputs specified by the `--domtblout` 36 | and `--tblout` arguments, respectively. 37 | 38 | The `domtblout` files have the format: 39 | 40 | ``` 41 | # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord 42 | # target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target 43 | #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- 44 | Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 1 2 4.3e-65 7.1e-61 204.8 11.2 4 168 24 181 21 183 0.96 Rer1 family 45 | Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 2 2 0.43 7.2e+03 -3.6 0.0 55 67 187 199 184 217 0.69 Rer1 family 46 | DUF4220 PF13968.5 352 AT5G45530.1 - 798 4.6e-78 263.0 0.0 1 1 1.5e-81 1.3e-77 261.5 0.0 1 344 51 396 51 427 0.78 Domain of unknown function (DUF4220) 47 | DUF594 PF04578.12 55 AT5G45530.1 - 798 4.7e-24 83.6 1.5 1 1 1.3e-27 1.1e-23 82.4 1.5 3 55 726 778 724 778 0.96 Protein of unknown function, DUF594 48 | DEAD PF00270.28 176 AT1G27880.2 - 890 6.7e-20 71.5 0.1 1 1 3.4e-23 1.9e-19 70.0 0.1 2 171 272 433 271 438 0.83 DEAD/DEAH box helicase 49 | ... 50 | # 51 | # Program: hmmscan 52 | # Version: 3.1b2 (February 2015) 53 | # Pipeline mode: SCAN 54 | # Query file: five.faa 55 | # Target file: /home/z/db/Pfam-A.hmm 56 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa 57 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 58 | # Date: Fri Dec 15 02:09:00 2017 59 | # [ok] 60 | ``` 61 | 62 | This is tricky to parse. It is mostly space delimited, but spaces appear freely 63 | in the `description of target` column. The column names, as given, cannot be 64 | directly used since they 1) contain illegal characters and 2) are not unique 65 | unless information from two rows is considered (e.g. `ali_from` versus 66 | `env_from`). The metadata at the end of the file I do not currently extract, 67 | though I will likely add handling for this in the future. 68 | 69 | ```{r} 70 | library(rhmmer) 71 | domtblout <- system.file('extdata', 'example.domtblout.txt', package='rhmmer') 72 | read_domtblout(domtblout) 73 | ``` 74 | 75 | The `tblout` output is fairly similar and presents the same parsing difficulties: 76 | 77 | ``` 78 | # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- 79 | # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target 80 | #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- 81 | Rer1 PF03248.12 AT2G18240.1 - 2.3e-61 206.4 10.4 7.1e-61 204.8 11.2 1.3 2 0 0 2 2 2 1 Rer1 family 82 | DUF4220 PF13968.5 AT5G45530.1 - 4.6e-78 263.0 0.0 1.3e-77 261.5 0.0 1.7 1 1 0 1 1 1 1 Domain of unknown function (DUF4220) 83 | DUF594 PF04578.12 AT5G45530.1 - 4.7e-24 83.6 1.5 1.1e-23 82.4 1.5 1.7 1 0 0 1 1 1 1 Protein of unknown function, DUF594 84 | DEAD PF00270.28 AT1G27880.2 - 6.7e-20 71.5 0.1 1.9e-19 70.0 0.1 1.8 1 0 0 1 1 1 1 DEAD/DEAH box helicase 85 | Helicase_C PF00271.30 AT1G27880.2 - 3.2e-18 66.0 0.0 3e-17 62.9 0.0 2.5 2 0 0 2 2 2 1 Helicase conserved C-terminal domain 86 | ResIII PF04851.14 AT1G27880.2 - 0.0012 18.8 0.1 0.0084 16.0 0.0 2.4 2 1 0 2 2 2 1 Type III restriction enzyme, res subunit 87 | ... 88 | # 89 | # Program: hmmscan 90 | # Version: 3.1b2 (February 2015) 91 | # Pipeline mode: SCAN 92 | # Query file: five.faa 93 | # Target file: /home/z/db/Pfam-A.hmm 94 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa 95 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 96 | # Date: Fri Dec 15 02:09:00 2017 97 | # [ok] 98 | ``` 99 | 100 | ```{r} 101 | tblout <- system.file('extdata', 'example.tblout.txt', package='rhmmer') 102 | read_tblout(tblout) 103 | ``` 104 | 105 | 106 | ## What `rhmmer` does and doesn't 107 | 108 | What `rhmmer` currently does 109 | 110 | * parse HMMER output (tblout and domtblout) into tidy data frames 111 | 112 | What `rhmmer` may do in the future 113 | 114 | * provide visualization or analysis of HMMER results 115 | 116 | * provide simple wrappers for calling some of the HMMER functions 117 | 118 | * parse metadata from the comments in HMMER output files 119 | 120 | * read pfamtblout and the raw output (with alignments) 121 | 122 | * read the HMM models 123 | 124 | * download databases for you (e.g. PFAM) 125 | 126 | * access precompiled PFAM results 127 | 128 | What `rhmmer` will never do 129 | 130 | * interface with the HMMER web server (use Bio3D) 131 | 132 | * duplicate the whole HMMER api (just use the CLI tool) 133 | 134 | 135 | ## TODO 136 | 137 | [ ] Rewrite the parser in C++ 138 | 139 | [ ] Parse out the file metadata 140 | -------------------------------------------------------------------------------- /inst/extdata/example.hmmprofile.hmm: -------------------------------------------------------------------------------- 1 | HMMER3/f [3.3.2 | Nov 2020] 2 | NAME query_hmm 3 | LENG 20 4 | ALPH amino 5 | RF no 6 | MM no 7 | CONS yes 8 | CS no 9 | MAP yes 10 | DATE Wed Nov 2 17:35:16 2022 11 | NSEQ 33 12 | EFFN 9.671997 13 | CKSUM 3293851812 14 | STATS LOCAL MSV -6.1915 0.72046 15 | STATS LOCAL VITERBI -6.2860 0.72046 16 | STATS LOCAL FORWARD -4.2014 0.72046 17 | HMM A C D E F G H I K L M N P Q R S T V W Y 18 | m->m m->i m->d i->m i->i d->m d->d 19 | COMPO 2.54173 3.27162 2.48425 4.81542 2.88579 2.31958 5.70315 2.96109 4.00368 3.55296 4.13298 4.83967 2.72526 4.01242 5.35720 2.25842 2.87450 2.15120 6.28926 1.93598 20 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 21 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.00000 * 22 | 1 6.27462 7.67753 0.02610 5.40427 7.56604 5.85829 6.99314 7.76193 6.44715 6.97769 8.19287 5.96694 6.54767 6.43128 6.82077 6.25158 6.66458 7.30678 8.12045 7.53106 1 D - - - 23 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 24 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 25 | 2 6.21555 6.97194 6.83757 6.90625 0.21280 6.49094 4.99609 5.71604 6.66631 4.74548 6.19096 5.96659 6.72973 6.18065 6.37052 5.93489 6.39173 5.70228 5.05675 1.95531 2 F - - - 26 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 27 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 28 | 3 4.26553 5.53225 6.25587 5.75426 4.91622 5.69526 6.30346 1.68732 5.61431 3.55170 4.73453 5.85768 6.00636 2.58034 5.74173 5.08509 2.86565 0.53469 6.77189 5.55696 3 V - - - 29 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 30 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 31 | 4 3.42526 3.15263 4.12077 2.61552 4.43926 4.35362 4.58770 1.82197 1.64489 2.60162 4.37461 4.01059 4.73647 1.87718 3.91992 3.58331 2.94881 2.71868 5.84265 4.58283 4 k - - - 32 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 33 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 34 | 5 2.06614 2.75231 5.83126 5.49602 5.49920 2.62672 6.02822 4.88557 5.36605 4.62184 5.48098 5.14923 5.21984 5.52079 5.46139 1.84424 0.89954 2.21484 6.94973 5.81849 5 t - - - 35 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 36 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 37 | 6 1.16438 4.95603 4.95213 4.36629 4.06507 4.58357 4.89508 2.60931 4.24541 2.49837 4.07390 4.57105 2.30326 2.52712 4.42480 3.87176 2.68274 2.02893 5.57651 4.38474 6 a - - - 38 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 39 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 40 | 7 2.53074 5.99961 4.95996 4.80279 6.50138 4.64758 5.83510 5.95532 2.28569 5.50711 6.33972 4.96051 0.32601 5.06295 4.57393 4.19447 4.54636 5.23644 7.54646 6.44245 7 P - - - 41 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 42 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 43 | 8 3.85598 2.94207 5.82063 5.86379 6.60609 0.21583 6.65004 6.19701 6.00922 5.87171 6.61835 2.83857 5.41509 6.09342 6.02353 4.07107 4.45249 5.22505 7.88901 6.89029 8 G - - - 44 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 45 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 46 | 9 1.64978 1.41597 5.53743 4.98224 2.17430 4.59085 5.21094 3.56904 4.78636 3.32280 1.70484 4.90832 5.08439 4.92634 4.81740 2.62742 3.84399 3.36137 5.75489 4.57479 9 c - - - 47 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 48 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 49 | 10 6.16912 7.39410 6.91581 7.00177 7.68046 0.01536 7.67541 7.90793 7.25474 7.13517 8.32427 7.13067 6.72373 7.50036 7.09189 6.43195 6.69659 7.27549 8.12645 7.90529 10 G - - - 50 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 51 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 52 | 11 4.59937 2.81983 6.81970 6.42236 5.36662 6.34830 7.47728 2.13439 6.43992 3.71025 5.02573 6.58051 6.56387 6.78160 6.67316 5.84942 4.87630 0.28523 7.68998 6.39588 11 V - - - 53 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 54 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 55 | 12 0.69625 5.85177 6.05211 6.09940 6.70677 4.62869 6.77931 6.26673 6.16528 5.94401 6.71622 5.52891 0.83471 6.25022 6.13639 4.17579 4.55503 5.31310 7.93726 7.02284 12 a - - - 56 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 57 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 58 | 13 4.32353 2.25485 6.43381 5.93279 4.92165 5.83528 6.42595 0.92341 5.82956 3.55415 4.75169 6.00793 6.10556 6.04755 5.93195 5.23002 4.57812 1.06662 6.81115 2.85040 13 i - - - 59 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 60 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 61 | 14 1.51325 1.78276 5.62645 5.02763 2.49929 4.82493 5.21076 3.20317 4.82259 3.13613 2.72367 5.01010 5.19481 4.95681 4.83691 4.14986 3.88051 1.30850 5.69561 4.51791 14 v - - - 62 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 63 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 64 | 15 4.63132 6.85980 0.45484 4.00089 6.85965 4.81773 5.82248 6.51431 5.14135 6.02835 6.98224 4.54645 5.58843 5.06381 5.81897 4.59885 1.28959 5.87171 8.00843 6.60072 15 D - - - 65 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 66 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 67 | 16 3.74584 5.66372 5.96018 5.99144 6.56595 4.44938 6.64020 6.11207 6.00389 5.80636 6.53891 5.34823 5.33443 6.08428 5.98387 0.27282 1.82428 5.12348 7.89321 6.88367 16 S - - - 68 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 69 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 70 | 17 6.53727 7.33763 6.91904 6.98492 4.37431 6.30090 5.90650 6.54904 6.94552 5.60475 7.03188 6.61601 6.81275 6.82515 6.73618 6.50904 6.83980 6.46719 5.99937 0.04023 17 Y - - - 71 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 72 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 73 | 18 6.53727 7.33763 6.91904 6.98492 4.37431 6.30090 5.90650 6.54904 6.94552 5.60475 7.03188 6.61601 6.81275 6.82515 6.73618 6.50904 6.83980 6.46719 5.99937 0.04023 18 Y - - - 74 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 75 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 76 | 19 4.53023 6.34489 6.20107 6.26653 6.87978 5.08079 7.02772 6.77317 6.44506 6.33706 7.20676 5.95780 5.91844 6.58954 6.42364 0.04932 5.11967 5.86535 7.93338 7.07628 19 S - - - 77 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 78 | 0.00394 5.93478 6.65713 0.61958 0.77255 0.48576 0.95510 79 | 20 5.94726 6.87562 6.80797 6.76881 3.56341 6.41562 5.20896 5.06408 6.50326 1.57569 5.53633 6.08220 6.67119 6.19702 6.29618 5.94224 6.15784 5.23295 5.27108 0.33214 20 Y - - - 80 | 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 81 | 0.00265 5.93349 * 0.61958 0.77255 0.00000 * 82 | // 83 | -------------------------------------------------------------------------------- /inst/extdata/rhino.domtblout: -------------------------------------------------------------------------------- 1 | # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord 2 | # target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target 3 | #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- 4 | NADHdh PF00146.20 299 YP_002887585.1 - 318 9.7e-110 366.5 23.1 1 1 6.6e-114 1.1e-109 366.3 23.1 2 297 5 303 4 305 0.98 NADH dehydrogenase 5 | Proton_antipo_M PF00361.19 293 YP_002887586.1 - 347 5e-42 144.0 40.7 1 2 6e-46 5e-42 144.0 40.7 1 284 23 279 23 289 0.92 Proton-conducting membrane transporter 6 | Proton_antipo_M PF00361.19 293 YP_002887586.1 - 347 5e-42 144.0 40.7 2 2 0.13 1.1e+03 -1.5 0.4 61 87 301 330 279 342 0.38 Proton-conducting membrane transporter 7 | NADH_dehy_S2_C PF06444.10 55 YP_002887586.1 - 347 4.5e-22 78.2 16.2 1 8 0.54 4.5e+03 -1.8 1.6 29 41 7 19 1 29 0.52 NADH dehydrogenase subunit 2 C-terminus 8 | NADH_dehy_S2_C PF06444.10 55 YP_002887586.1 - 347 4.5e-22 78.2 16.2 2 8 0.27 2.3e+03 -0.9 1.1 38 49 61 72 47 81 0.52 NADH dehydrogenase subunit 2 C-terminus 9 | NADH_dehy_S2_C PF06444.10 55 YP_002887586.1 - 347 4.5e-22 78.2 16.2 3 8 2 1.7e+04 -3.9 5.1 21 47 77 103 66 112 0.53 NADH dehydrogenase subunit 2 C-terminus 10 | NADH_dehy_S2_C PF06444.10 55 YP_002887586.1 - 347 4.5e-22 78.2 16.2 4 8 0.85 7.1e+03 -2.5 0.3 33 46 150 163 139 164 0.61 NADH dehydrogenase subunit 2 C-terminus 11 | NADH_dehy_S2_C PF06444.10 55 YP_002887586.1 - 347 4.5e-22 78.2 16.2 5 8 0.42 3.5e+03 -1.5 10.6 28 50 196 220 179 223 0.69 NADH dehydrogenase subunit 2 C-terminus 12 | NADH_dehy_S2_C PF06444.10 55 YP_002887586.1 - 347 4.5e-22 78.2 16.2 6 8 0.59 4.9e+03 -2.0 6.4 20 49 226 255 220 261 0.60 NADH dehydrogenase subunit 2 C-terminus 13 | NADH_dehy_S2_C PF06444.10 55 YP_002887586.1 - 347 4.5e-22 78.2 16.2 7 8 1 8.4e+03 -2.7 0.2 34 46 275 285 263 288 0.45 NADH dehydrogenase subunit 2 C-terminus 14 | NADH_dehy_S2_C PF06444.10 55 YP_002887586.1 - 347 4.5e-22 78.2 16.2 8 8 5.4e-26 4.5e-22 78.2 16.2 1 54 290 343 290 344 0.98 NADH dehydrogenase subunit 2 C-terminus 15 | COX1 PF00115.19 426 YP_002887587.1 - 514 3.8e-144 480.6 65.1 1 1 2.9e-148 4.8e-144 480.3 65.1 1 426 14 460 14 460 0.97 Cytochrome C and Quinol oxidase polypeptide I 16 | COX2 PF00116.19 120 YP_002887588.1 - 227 2.1e-64 214.7 0.0 1 1 6e-68 3.3e-64 214.0 0.0 1 120 95 214 95 214 0.99 Cytochrome C oxidase subunit II, periplasmic domain 17 | COX2_TM PF02790.14 89 YP_002887588.1 - 227 2.3e-28 98.1 7.4 1 1 6.4e-32 3.6e-28 97.4 7.4 1 89 1 83 1 83 0.98 Cytochrome C oxidase subunit II, transmembrane domain 18 | MRAP PF15183.5 89 YP_002887588.1 - 227 0.15 11.9 6.0 1 2 0.00039 2.2 8.2 0.2 23 70 13 60 2 78 0.76 Melanocortin-2 receptor accessory protein family 19 | MRAP PF15183.5 89 YP_002887588.1 - 227 0.15 11.9 6.0 2 2 0.002 11 5.9 1.2 7 24 101 117 96 122 0.82 Melanocortin-2 receptor accessory protein family 20 | ATP-synt_8 PF00895.19 55 YP_002887589.1 - 68 2.6e-21 75.7 11.8 1 1 1.9e-25 3.2e-21 75.4 11.8 1 55 1 55 1 55 1.00 ATP synthase protein 8 21 | ATP-synt_A PF00119.19 211 YP_002887590.1 - 226 1.2e-40 139.7 27.6 1 1 8.6e-45 1.4e-40 139.4 27.6 6 210 19 222 13 223 0.86 ATP synthase A chain 22 | COX3 PF00510.17 258 YP_002887591.1 - 261 1.9e-131 437.5 26.7 1 1 1.3e-135 2.1e-131 437.3 26.7 1 258 6 261 6 261 1.00 Cytochrome c oxidase subunit III 23 | Oxidored_q4 PF00507.18 99 YP_002887592.1 - 115 3e-27 94.6 0.9 1 1 2.3e-31 3.9e-27 94.2 0.9 3 99 16 113 14 113 0.90 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 24 | Oxidored_q2 PF00420.23 105 YP_002887593.1 - 98 5.7e-17 61.2 13.5 1 1 3.9e-21 6.5e-17 61.0 13.5 2 103 4 93 3 98 0.94 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L 25 | Proton_antipo_M PF00361.19 293 YP_002887594.1 - 459 1.7e-77 260.4 36.7 1 2 0.99 5.5e+03 -3.9 2.5 72 106 37 73 8 81 0.61 Proton-conducting membrane transporter 26 | Proton_antipo_M PF00361.19 293 YP_002887594.1 - 459 1.7e-77 260.4 36.7 2 2 3.1e-81 1.7e-77 260.4 36.7 1 293 112 403 112 403 0.98 Proton-conducting membrane transporter 27 | Oxidored_q5_N PF01059.16 110 YP_002887594.1 - 459 5.9e-34 116.4 21.2 1 5 1.1e-37 5.9e-34 116.4 21.2 1 110 1 109 1 109 0.97 NADH-ubiquinone oxidoreductase chain 4, amino terminus 28 | Oxidored_q5_N PF01059.16 110 YP_002887594.1 - 459 5.9e-34 116.4 21.2 2 5 3 1.7e+04 -4.2 6.8 25 70 169 213 117 217 0.55 NADH-ubiquinone oxidoreductase chain 4, amino terminus 29 | Oxidored_q5_N PF01059.16 110 YP_002887594.1 - 459 5.9e-34 116.4 21.2 3 5 0.076 4.3e+02 0.9 8.3 1 76 200 271 197 285 0.70 NADH-ubiquinone oxidoreductase chain 4, amino terminus 30 | Oxidored_q5_N PF01059.16 110 YP_002887594.1 - 459 5.9e-34 116.4 21.2 4 5 0.48 2.7e+03 -1.6 5.0 9 72 294 358 287 369 0.59 NADH-ubiquinone oxidoreductase chain 4, amino terminus 31 | Oxidored_q5_N PF01059.16 110 YP_002887594.1 - 459 5.9e-34 116.4 21.2 5 5 0.63 3.5e+03 -2.0 6.9 11 75 383 448 368 450 0.45 NADH-ubiquinone oxidoreductase chain 4, amino terminus 32 | Birna_RdRp PF04197.11 872 YP_002887594.1 - 459 0.32 9.2 0.9 1 1 8e-05 0.45 8.7 0.9 323 361 15 53 13 77 0.87 Birnavirus RNA dependent RNA polymerase (VP1) 33 | Proton_antipo_M PF00361.19 293 YP_002887595.1 - 606 1.6e-76 257.2 24.6 1 3 0.88 4.9e+03 -3.7 4.4 76 106 78 108 8 132 0.67 Proton-conducting membrane transporter 34 | Proton_antipo_M PF00361.19 293 YP_002887595.1 - 606 1.6e-76 257.2 24.6 2 3 2.9e-80 1.6e-76 257.2 24.6 1 292 134 418 134 419 0.95 Proton-conducting membrane transporter 35 | Proton_antipo_M PF00361.19 293 YP_002887595.1 - 606 1.6e-76 257.2 24.6 3 3 0.1 5.7e+02 -0.6 0.4 54 100 426 474 422 502 0.79 Proton-conducting membrane transporter 36 | NADH5_C PF06455.10 181 YP_002887595.1 - 606 1.3e-53 181.2 17.6 1 4 3 1.7e+04 -16.7 21.4 54 111 70 128 1 143 0.52 NADH dehydrogenase subunit 5 C-terminus 37 | NADH5_C PF06455.10 181 YP_002887595.1 - 606 1.3e-53 181.2 17.6 2 4 1.2 6.8e+03 -3.6 0.3 76 90 182 196 179 217 0.49 NADH dehydrogenase subunit 5 C-terminus 38 | NADH5_C PF06455.10 181 YP_002887595.1 - 606 1.3e-53 181.2 17.6 3 4 0.34 1.9e+03 -1.8 4.8 60 117 276 336 241 361 0.44 NADH dehydrogenase subunit 5 C-terminus 39 | NADH5_C PF06455.10 181 YP_002887595.1 - 606 1.3e-53 181.2 17.6 4 4 2.3e-57 1.3e-53 181.2 17.6 1 180 422 601 422 602 0.99 NADH dehydrogenase subunit 5 C-terminus 40 | Proton_antipo_N PF00662.19 58 YP_002887595.1 - 606 7e-14 51.5 8.3 1 3 1.3e-17 7e-14 51.5 8.3 1 57 65 121 65 122 0.98 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus 41 | Proton_antipo_N PF00662.19 58 YP_002887595.1 - 606 7e-14 51.5 8.3 2 3 3 1.7e+04 -4.9 1.3 23 30 126 133 126 134 0.82 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus 42 | Proton_antipo_N PF00662.19 58 YP_002887595.1 - 606 7e-14 51.5 8.3 3 3 2.7 1.5e+04 -3.9 0.2 25 40 408 423 403 424 0.53 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus 43 | Oxidored_q3 PF00499.19 137 YP_002887596.1 - 175 6.7e-18 64.7 16.0 1 1 6.3e-22 1.1e-17 64.1 16.0 2 135 17 169 16 171 0.81 NADH-ubiquinone/plastoquinone oxidoreductase chain 6 44 | Cytochrome_B PF00033.18 189 YP_002887597.1 - 379 4e-86 287.6 18.4 1 3 7.1e-90 4e-86 287.6 18.4 2 189 19 204 18 204 0.99 Cytochrome b/b6/petB 45 | Cytochrome_B PF00033.18 189 YP_002887597.1 - 379 4e-86 287.6 18.4 2 3 1.3 7.3e+03 -3.5 0.7 164 182 224 242 215 245 0.56 Cytochrome b/b6/petB 46 | Cytochrome_B PF00033.18 189 YP_002887597.1 - 379 4e-86 287.6 18.4 3 3 0.82 4.6e+03 -2.9 0.1 85 85 313 313 290 342 0.49 Cytochrome b/b6/petB 47 | Cytochrom_B_N_2 PF13631.5 169 YP_002887597.1 - 379 3e-40 137.9 9.8 1 3 0.093 5.2e+02 0.4 0.2 27 53 30 56 26 86 0.74 Cytochrome b(N-terminal)/b6/petB 48 | Cytochrom_B_N_2 PF13631.5 169 YP_002887597.1 - 379 3e-40 137.9 9.8 2 3 5.4e-44 3e-40 137.9 9.8 2 168 89 252 88 253 0.96 Cytochrome b(N-terminal)/b6/petB 49 | Cytochrom_B_N_2 PF13631.5 169 YP_002887597.1 - 379 3e-40 137.9 9.8 3 3 1.9 1.1e+04 -3.8 0.1 150 157 297 304 284 316 0.51 Cytochrome b(N-terminal)/b6/petB 50 | Cytochrom_B_C PF00032.16 103 YP_002887597.1 - 379 3.1e-37 126.9 1.6 1 2 0.51 2.8e+03 -1.5 2.8 32 49 115 135 20 224 0.70 Cytochrome b(C-terminal)/b6/petD 51 | Cytochrom_B_C PF00032.16 103 YP_002887597.1 - 379 3.1e-37 126.9 1.6 2 2 5.6e-41 3.1e-37 126.9 1.6 1 103 258 359 258 359 1.00 Cytochrome b(C-terminal)/b6/petD 52 | # 53 | # Program: hmmscan 54 | # Version: 3.1b1 (May 2013) 55 | # Pipeline mode: SCAN 56 | # Query file: rhino.faa 57 | # Target file: Pfam-A.hmm 58 | # Option settings: hmmscan --tblout rhino.tblout --domtblout rhino.domtblout Pfam-A.hmm rhino.faa 59 | # Current dir: /home/rnz/Dropbox/data/pfam 60 | # Date: Tue Jan 2 15:13:22 2018 61 | # [ok] 62 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/five/pfamtblout: -------------------------------------------------------------------------------- 1 | # Sequence scores 2 | # --------------- 3 | # 4 | # name bits E-value n exp bias description 5 | # ------------------- ------ --------- --- ----- ----- --------------------- 6 | Rer1 206.4 2.3e-61 2 1.3 10.4 Rer1 family 7 | 8 | # Domain scores 9 | # ------------- 10 | # 11 | # name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description 12 | # ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- 13 | Rer1 204.8 7.1e-61 1 11.2 21 183 24 181 4 168 Rer1 family 14 | Rer1 -3.6 7.2e+03 2 0.0 184 217 187 199 55 67 Rer1 family 15 | # Sequence scores 16 | # --------------- 17 | # 18 | # name bits E-value n exp bias description 19 | # ------------------- ------ --------- --- ----- ----- --------------------- 20 | DUF4220 263.0 4.6e-78 1 1.7 0.0 Domain of unknown function (DUF4220) 21 | DUF594 83.6 4.7e-24 1 1.7 1.5 Protein of unknown function, DUF594 22 | 23 | # Domain scores 24 | # ------------- 25 | # 26 | # name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description 27 | # ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- 28 | DUF4220 261.5 1.3e-77 1 0.0 51 427 51 396 1 344 Domain of unknown function (DUF4220) 29 | DUF594 82.4 1.1e-23 1 1.5 724 778 726 778 3 55 Protein of unknown function, DUF594 30 | # Sequence scores 31 | # --------------- 32 | # 33 | # name bits E-value n exp bias description 34 | # ------------------- ------ --------- --- ----- ----- --------------------- 35 | DEAD 71.5 6.7e-20 1 1.8 0.1 DEAD/DEAH box helicase 36 | Helicase_C 66.0 3.2e-18 2 2.5 0.0 Helicase conserved C-terminal domain 37 | ResIII 18.8 0.0012 2 2.4 0.1 Type III restriction enzyme, res subunit 38 | 39 | # Domain scores 40 | # ------------- 41 | # 42 | # name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description 43 | # ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- 44 | DEAD 70.0 1.9e-19 1 0.1 271 438 272 433 2 171 DEAD/DEAH box helicase 45 | Helicase_C 62.9 3e-17 2 0.0 470 581 485 580 15 110 Helicase conserved C-terminal domain 46 | ResIII 16.0 0.0084 2 0.0 268 432 270 430 4 169 Type III restriction enzyme, res subunit 47 | Helicase_C -0.7 1.7e+03 1 0.0 307 367 314 364 21 72 Helicase conserved C-terminal domain 48 | ResIII -3.7 9.4e+03 1 0.1 188 256 214 232 102 123 Type III restriction enzyme, res subunit 49 | # Sequence scores 50 | # --------------- 51 | # 52 | # name bits E-value n exp bias description 53 | # ------------------- ------ --------- --- ----- ----- --------------------- 54 | TIR 156.1 7.3e-46 1 1.4 0.0 TIR domain 55 | NB-ARC 63.1 1.9e-17 1 1.4 0.0 NB-ARC domain 56 | LRR_3 31.4 1e-07 2 2.7 1.1 Leucine Rich Repeat 57 | LRR_8 30.4 2.3e-07 6 5.5 7.0 Leucine rich repeat 58 | LRR_4 30.6 2.7e-07 7 6.1 17.6 Leucine Rich repeats (2 copies) 59 | TIR_2 24.4 2.6e-05 2 1.9 0.1 TIR domain 60 | AAA_16 21.7 0.0002 1 2.0 0.3 AAA ATPase domain 61 | AAA_18 19.5 0.001 1 1.7 0.0 AAA domain 62 | AAA_22 17.1 0.0048 1 2.1 1.0 AAA domain 63 | ATPase_2 15.1 0.015 1 1.8 0.0 ATPase domain predominantly from Archaea 64 | PhoH 13.8 0.028 2 2.3 1.1 PhoH-like protein 65 | NACHT 14.2 0.029 1 1.5 0.0 NACHT domain 66 | AAA_23 14.4 0.039 2 2.3 0.0 AAA domain 67 | ABC_tran 14.2 0.044 1 1.5 0.0 ABC transporter 68 | NTPase_1 13.1 0.062 1 1.7 0.0 NTPase 69 | AAA_29 12.6 0.079 2 2.3 0.1 P-loop containing region of AAA domain 70 | LRR_1 12.6 0.15 8 7.8 14.8 Leucine Rich Repeat 71 | 72 | # Domain scores 73 | # ------------- 74 | # 75 | # name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description 76 | # ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- 77 | TIR 155.3 1.2e-45 1 0.0 12 189 13 179 2 164 TIR domain 78 | NB-ARC 62.3 3.5e-17 1 0.0 189 456 192 440 4 262 NB-ARC domain 79 | LRR_3 31.4 1e-07 1 1.1 603 622 603 622 1 20 Leucine Rich Repeat 80 | TIR_2 22.6 9.3e-05 1 0.0 15 120 15 101 1 85 TIR domain 81 | AAA_16 19.8 0.00077 1 0.3 186 319 187 243 3 63 AAA ATPase domain 82 | AAA_18 18.3 0.0024 1 0.0 210 332 210 274 1 69 AAA domain 83 | LRR_4 17.2 0.0047 5 0.2 762 805 763 804 3 42 Leucine Rich repeats (2 copies) 84 | LRR_8 16.5 0.0048 5 0.0 716 773 717 772 2 60 Leucine rich repeat 85 | AAA_22 14.8 0.024 1 1.0 204 324 209 312 7 113 AAA domain 86 | ATPase_2 13.5 0.046 1 0.0 190 311 193 265 8 82 ATPase domain predominantly from Archaea 87 | NACHT 13.2 0.057 1 0.0 208 336 210 304 3 95 NACHT domain 88 | ABC_tran 13.1 0.095 1 0.0 200 276 208 232 12 36 ABC transporter 89 | NTPase_1 11.8 0.16 1 0.0 209 303 210 293 2 87 NTPase 90 | AAA_23 11.3 0.34 1 0.0 192 284 208 238 20 50 AAA domain 91 | AAA_29 8.7 1.3 1 0.1 194 232 201 227 18 42 P-loop containing region of AAA domain 92 | LRR_8 8.8 1.3 2 0.3 602 661 603 657 2 58 Leucine rich repeat 93 | LRR_4 9.1 1.6 4 0.0 716 760 716 756 1 39 Leucine Rich repeats (2 copies) 94 | LRR_8 8.2 2 6 0.1 760 795 763 794 27 59 Leucine rich repeat 95 | PhoH 6.9 3.5 1 0.2 192 251 206 227 18 39 PhoH-like protein 96 | LRR_8 6.6 6.2 3 0.2 625 683 626 682 2 59 Leucine rich repeat 97 | LRR_4 7.2 6.5 2 0.1 625 671 626 658 2 33 Leucine Rich repeats (2 copies) 98 | LRR_4 6.6 10 3 0.3 649 715 684 711 12 38 Leucine Rich repeats (2 copies) 99 | PhoH 5.3 11 2 0.0 240 341 257 332 87 161 PhoH-like protein 100 | LRR_1 5.9 24 6 0.0 762 783 763 773 2 12 Leucine Rich Repeat 101 | LRR_8 2.6 1.1e+02 4 0.1 648 706 649 703 2 57 Leucine rich repeat 102 | LRR_1 3.3 1.6e+02 7 0.3 785 818 785 800 1 16 Leucine Rich Repeat 103 | LRR_1 3.1 1.9e+02 4 0.0 696 738 696 728 1 13 Leucine Rich Repeat 104 | AAA_29 0.9 3.5e+02 2 0.0 582 608 583 606 3 25 P-loop containing region of AAA domain 105 | LRR_1 1.4 7e+02 3 0.0 649 671 649 669 1 21 Leucine Rich Repeat 106 | LRR_8 -0.6 1.1e+03 1 0.0 535 561 544 560 15 31 Leucine rich repeat 107 | LRR_3 -0.6 1.3e+03 2 0.5 626 641 626 640 1 14 Leucine Rich Repeat 108 | AAA_23 -0.5 1.4e+03 2 0.0 811 864 818 843 118 143 AAA domain 109 | LRR_1 0.1 1.9e+03 2 0.1 626 647 626 637 1 12 Leucine Rich Repeat 110 | LRR_1 -1.0 4.3e+03 8 0.0 866 888 874 886 8 21 Leucine Rich Repeat 111 | TIR_2 -2.5 6e+03 2 0.1 256 296 257 295 16 55 TIR domain 112 | LRR_1 -1.5 6.2e+03 5 0.0 741 760 742 752 3 13 Leucine Rich Repeat 113 | LRR_4 -2.6 8.3e+03 1 0.0 535 566 550 563 19 33 Leucine Rich repeats (2 copies) 114 | LRR_1 -1.9 8.5e+03 1 0.0 603 621 603 615 1 13 Leucine Rich Repeat 115 | # Sequence scores 116 | # --------------- 117 | # 118 | # name bits E-value n exp bias description 119 | # ------------------- ------ --------- --- ----- ----- --------------------- 120 | DAO 181.4 3.2e-53 2 1.6 0.1 FAD dependent oxidoreductase 121 | DAO_C 132.1 9e-39 1 1.4 0.3 C-terminal domain of alpha-glycerophosphate oxidase 122 | FAD_binding_2 28.7 6.3e-07 2 2.3 1.9 FAD binding domain 123 | FAD_oxidored 21.7 0.0001 2 2.2 1.1 FAD dependent oxidoreductase 124 | Pyr_redox_2 14.6 0.014 1 1.5 0.0 Pyridine nucleotide-disulphide oxidoreductase 125 | FAD_binding_3 14.5 0.015 2 2.1 0.2 FAD binding domain 126 | GIDA 13.0 0.036 2 2.0 0.2 Glucose inhibited division protein A 127 | Pyr_redox 13.8 0.063 1 2.1 0.7 Pyridine nucleotide-disulphide oxidoreductase 128 | HI0933_like 11.6 0.075 1 1.5 0.2 HI0933-like protein 129 | AAA_30 12.6 0.077 2 1.9 0.6 AAA domain 130 | Pyr_redox_3 11.7 0.1 1 1.3 0.0 Pyridine nucleotide-disulphide oxidoreductase 131 | DUF4179 12.2 0.18 2 2.2 0.9 Domain of unknown function (DUF4179) 132 | 3HCDH_N 10.8 0.31 2 2.0 2.0 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 133 | NAD_binding_8 9.1 1.4 3 2.3 5.0 NAD(P)-binding Rossmann-like domain 134 | 135 | # Domain scores 136 | # ------------- 137 | # 138 | # name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description 139 | # ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- 140 | DAO 180.1 8.6e-53 1 0.0 75 443 75 442 1 351 FAD dependent oxidoreductase 141 | DAO_C 131.3 1.6e-38 1 0.3 465 601 465 600 1 125 C-terminal domain of alpha-glycerophosphate oxidase 142 | FAD_oxidored 19.7 0.00043 1 0.3 75 142 75 114 1 40 FAD dependent oxidoreductase 143 | FAD_binding_2 17.0 0.0023 1 1.2 75 124 75 115 1 41 FAD binding domain 144 | Pyr_redox_2 13.4 0.031 1 0.0 59 151 75 108 2 36 Pyridine nucleotide-disulphide oxidoreductase 145 | HI0933_like 10.6 0.15 1 0.2 74 109 75 105 2 32 HI0933-like protein 146 | AAA_30 11.5 0.17 2 0.0 455 559 484 533 32 81 AAA domain 147 | Pyr_redox_3 10.9 0.18 1 0.0 58 151 75 128 166 220 Pyridine nucleotide-disulphide oxidoreductase 148 | GIDA 10.4 0.23 1 0.1 75 134 75 103 1 29 Glucose inhibited division protein A 149 | Pyr_redox 11.7 0.28 1 0.7 75 111 76 106 2 32 Pyridine nucleotide-disulphide oxidoreductase 150 | FAD_binding_2 10.1 0.29 2 0.0 226 320 247 307 154 213 FAD binding domain 151 | NAD_binding_8 11.2 0.32 1 0.6 78 145 78 122 1 42 NAD(P)-binding Rossmann-like domain 152 | 3HCDH_N 10.6 0.36 1 0.2 75 131 76 106 2 32 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 153 | FAD_binding_3 9.8 0.39 1 0.5 73 131 75 124 3 51 FAD binding domain 154 | DUF4179 10.3 0.71 1 0.0 2 63 5 40 5 37 Domain of unknown function (DUF4179) 155 | FAD_binding_3 2.2 83 2 0.0 228 401 240 306 117 179 FAD binding domain 156 | GIDA 0.0 3.3e+02 2 0.0 249 311 257 305 110 159 Glucose inhibited division protein A 157 | FAD_oxidored -0.1 4.1e+02 2 0.0 214 296 247 294 100 143 FAD dependent oxidoreductase 158 | DAO -1.8 1.7e+03 2 0.1 538 626 554 590 68 106 FAD dependent oxidoreductase 159 | DUF4179 -0.6 1.8e+03 2 0.1 235 300 243 290 10 57 Domain of unknown function (DUF4179) 160 | 3HCDH_N -1.8 2.2e+03 2 0.1 560 623 578 613 30 65 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 161 | AAA_30 -2.7 3.7e+03 1 0.1 58 98 60 94 5 39 AAA domain 162 | NAD_binding_8 -2.4 5.5e+03 2 0.0 420 454 435 444 31 40 NAD(P)-binding Rossmann-like domain 163 | # 164 | # Program: hmmscan 165 | # Version: 3.1b2 (February 2015) 166 | # Pipeline mode: SEARCH 167 | # Query file: five.faa 168 | # Target file: /home/z/db/Pfam-A.hmm 169 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa 170 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 171 | # Date: Fri Dec 15 02:09:00 2017 172 | # [ok] 173 | -------------------------------------------------------------------------------- /inst/extdata/example.domtblout.txt: -------------------------------------------------------------------------------- 1 | # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord 2 | # target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target 3 | #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- 4 | Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 1 2 4.3e-65 7.1e-61 204.8 11.2 4 168 24 181 21 183 0.96 Rer1 family 5 | Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 2 2 0.43 7.2e+03 -3.6 0.0 55 67 187 199 184 217 0.69 Rer1 family 6 | DUF4220 PF13968.5 352 AT5G45530.1 - 798 4.6e-78 263.0 0.0 1 1 1.5e-81 1.3e-77 261.5 0.0 1 344 51 396 51 427 0.78 Domain of unknown function (DUF4220) 7 | DUF594 PF04578.12 55 AT5G45530.1 - 798 4.7e-24 83.6 1.5 1 1 1.3e-27 1.1e-23 82.4 1.5 3 55 726 778 724 778 0.96 Protein of unknown function, DUF594 8 | DEAD PF00270.28 176 AT1G27880.2 - 890 6.7e-20 71.5 0.1 1 1 3.4e-23 1.9e-19 70.0 0.1 2 171 272 433 271 438 0.83 DEAD/DEAH box helicase 9 | Helicase_C PF00271.30 111 AT1G27880.2 - 890 3.2e-18 66.0 0.0 1 2 0.31 1.7e+03 -0.7 0.0 21 72 314 364 307 367 0.74 Helicase conserved C-terminal domain 10 | Helicase_C PF00271.30 111 AT1G27880.2 - 890 3.2e-18 66.0 0.0 2 2 5.4e-21 3e-17 62.9 0.0 15 110 485 580 470 581 0.91 Helicase conserved C-terminal domain 11 | ResIII PF04851.14 171 AT1G27880.2 - 890 0.0012 18.8 0.1 1 2 1.7 9.4e+03 -3.7 0.1 102 123 214 232 188 256 0.54 Type III restriction enzyme, res subunit 12 | ResIII PF04851.14 171 AT1G27880.2 - 890 0.0012 18.8 0.1 2 2 1.5e-06 0.0084 16.0 0.0 4 169 270 430 268 432 0.74 Type III restriction enzyme, res subunit 13 | TIR PF01582.19 176 AT1G56520.1 - 897 7.3e-46 156.1 0.0 1 1 1.3e-48 1.2e-45 155.3 0.0 2 164 13 179 12 189 0.95 TIR domain 14 | NB-ARC PF00931.21 288 AT1G56520.1 - 897 1.9e-17 63.1 0.0 1 1 3.6e-20 3.5e-17 62.3 0.0 4 262 192 440 189 456 0.78 NB-ARC domain 15 | LRR_3 PF07725.11 20 AT1G56520.1 - 897 1e-07 31.4 1.1 1 2 1e-10 1e-07 31.4 1.1 1 20 603 622 603 622 0.98 Leucine Rich Repeat 16 | LRR_3 PF07725.11 20 AT1G56520.1 - 897 1e-07 31.4 1.1 2 2 1.3 1.3e+03 -0.6 0.5 1 14 626 640 626 641 0.79 Leucine Rich Repeat 17 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 1 6 1.1 1.1e+03 -0.6 0.0 15 31 544 560 535 561 0.88 Leucine rich repeat 18 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 2 6 0.0013 1.3 8.8 0.3 2 58 603 657 602 661 0.90 Leucine rich repeat 19 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 3 6 0.0064 6.2 6.6 0.2 2 59 626 682 625 683 0.88 Leucine rich repeat 20 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 4 6 0.11 1.1e+02 2.6 0.1 2 57 649 703 648 706 0.66 Leucine rich repeat 21 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 5 6 4.9e-06 0.0048 16.5 0.0 2 60 717 772 716 773 0.87 Leucine rich repeat 22 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 6 6 0.002 2 8.2 0.1 27 59 763 794 760 795 0.70 Leucine rich repeat 23 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 1 5 8.4 8.3e+03 -2.6 0.0 19 33 550 563 535 566 0.71 Leucine Rich repeats (2 copies) 24 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 2 5 0.0066 6.5 7.2 0.1 2 33 626 658 625 671 0.81 Leucine Rich repeats (2 copies) 25 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 3 5 0.01 10 6.6 0.3 12 38 684 711 649 715 0.56 Leucine Rich repeats (2 copies) 26 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 4 5 0.0017 1.6 9.1 0.0 1 39 716 756 716 760 0.88 Leucine Rich repeats (2 copies) 27 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 5 5 4.8e-06 0.0047 17.2 0.2 3 42 763 804 762 805 0.90 Leucine Rich repeats (2 copies) 28 | TIR_2 PF13676.5 102 AT1G56520.1 - 897 2.6e-05 24.4 0.1 1 2 9.5e-08 9.3e-05 22.6 0.0 1 85 15 101 15 120 0.79 TIR domain 29 | TIR_2 PF13676.5 102 AT1G56520.1 - 897 2.6e-05 24.4 0.1 2 2 6.1 6e+03 -2.5 0.1 16 55 257 295 256 296 0.80 TIR domain 30 | AAA_16 PF13191.5 170 AT1G56520.1 - 897 0.0002 21.7 0.3 1 1 7.8e-07 0.00077 19.8 0.3 3 63 187 243 186 319 0.74 AAA ATPase domain 31 | AAA_18 PF13238.5 130 AT1G56520.1 - 897 0.001 19.5 0.0 1 1 2.4e-06 0.0024 18.3 0.0 1 69 210 274 210 332 0.69 AAA domain 32 | AAA_22 PF13401.5 137 AT1G56520.1 - 897 0.0048 17.1 1.0 1 1 2.4e-05 0.024 14.8 1.0 7 113 209 312 204 324 0.64 AAA domain 33 | ATPase_2 PF01637.17 233 AT1G56520.1 - 897 0.015 15.1 0.0 1 1 4.7e-05 0.046 13.5 0.0 8 82 193 265 190 311 0.64 ATPase domain predominantly from Archaea 34 | PhoH PF02562.15 205 AT1G56520.1 - 897 0.028 13.8 1.1 1 2 0.0036 3.5 6.9 0.2 18 39 206 227 192 251 0.82 PhoH-like protein 35 | PhoH PF02562.15 205 AT1G56520.1 - 897 0.028 13.8 1.1 2 2 0.011 11 5.3 0.0 87 161 257 332 240 341 0.85 PhoH-like protein 36 | NACHT PF05729.11 166 AT1G56520.1 - 897 0.029 14.2 0.0 1 1 5.8e-05 0.057 13.2 0.0 3 95 210 304 208 336 0.81 NACHT domain 37 | AAA_23 PF13476.5 200 AT1G56520.1 - 897 0.039 14.4 0.0 1 2 0.00035 0.34 11.3 0.0 20 50 208 238 192 284 0.80 AAA domain 38 | AAA_23 PF13476.5 200 AT1G56520.1 - 897 0.039 14.4 0.0 2 2 1.4 1.4e+03 -0.5 0.0 118 143 818 843 811 864 0.84 AAA domain 39 | ABC_tran PF00005.26 137 AT1G56520.1 - 897 0.044 14.2 0.0 1 1 9.6e-05 0.095 13.1 0.0 12 36 208 232 200 276 0.89 ABC transporter 40 | NTPase_1 PF03266.14 168 AT1G56520.1 - 897 0.062 13.1 0.0 1 1 0.00016 0.16 11.8 0.0 2 87 210 293 209 303 0.79 NTPase 41 | AAA_29 PF13555.5 61 AT1G56520.1 - 897 0.079 12.6 0.1 1 2 0.0013 1.3 8.7 0.1 18 42 201 227 194 232 0.80 P-loop containing region of AAA domain 42 | AAA_29 PF13555.5 61 AT1G56520.1 - 897 0.079 12.6 0.1 2 2 0.36 3.5e+02 0.9 0.0 3 25 583 606 582 608 0.86 P-loop containing region of AAA domain 43 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 1 8 8.6 8.5e+03 -1.9 0.0 1 13 603 615 603 621 0.83 Leucine Rich Repeat 44 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 2 8 1.9 1.9e+03 0.1 0.1 1 12 626 637 626 647 0.70 Leucine Rich Repeat 45 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 3 8 0.71 7e+02 1.4 0.0 1 21 649 669 649 671 0.73 Leucine Rich Repeat 46 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 4 8 0.19 1.9e+02 3.1 0.0 1 13 696 728 696 738 0.61 Leucine Rich Repeat 47 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 5 8 6.4 6.2e+03 -1.5 0.0 3 13 742 752 741 760 0.71 Leucine Rich Repeat 48 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 6 8 0.024 24 5.9 0.0 2 12 763 773 762 783 0.82 Leucine Rich Repeat 49 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 7 8 0.17 1.6e+02 3.3 0.3 1 16 785 800 785 818 0.75 Leucine Rich Repeat 50 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 8 8 4.4 4.3e+03 -1.0 0.0 8 21 874 886 866 888 0.77 Leucine Rich Repeat 51 | DAO PF01266.23 352 AT3G10370.1 - 629 3.2e-53 181.4 0.1 1 2 7.2e-56 8.6e-53 180.1 0.0 1 351 75 442 75 443 0.80 FAD dependent oxidoreductase 52 | DAO PF01266.23 352 AT3G10370.1 - 629 3.2e-53 181.4 0.1 2 2 1.4 1.7e+03 -1.8 0.1 68 106 554 590 538 626 0.61 FAD dependent oxidoreductase 53 | DAO_C PF16901.4 126 AT3G10370.1 - 629 9e-39 132.1 0.3 1 1 1.3e-41 1.6e-38 131.3 0.3 1 125 465 600 465 601 0.98 C-terminal domain of alpha-glycerophosphate oxidase 54 | FAD_binding_2 PF00890.23 417 AT3G10370.1 - 629 6.3e-07 28.7 1.9 1 2 1.9e-06 0.0023 17.0 1.2 1 41 75 115 75 124 0.94 FAD binding domain 55 | FAD_binding_2 PF00890.23 417 AT3G10370.1 - 629 6.3e-07 28.7 1.9 2 2 0.00024 0.29 10.1 0.0 154 213 247 307 226 320 0.82 FAD binding domain 56 | FAD_oxidored PF12831.6 433 AT3G10370.1 - 629 0.0001 21.7 1.1 1 2 3.6e-07 0.00043 19.7 0.3 1 40 75 114 75 142 0.93 FAD dependent oxidoreductase 57 | FAD_oxidored PF12831.6 433 AT3G10370.1 - 629 0.0001 21.7 1.1 2 2 0.34 4.1e+02 -0.1 0.0 100 143 247 294 214 296 0.85 FAD dependent oxidoreductase 58 | Pyr_redox_2 PF07992.13 292 AT3G10370.1 - 629 0.014 14.6 0.0 1 1 2.6e-05 0.031 13.4 0.0 2 36 75 108 59 151 0.78 Pyridine nucleotide-disulphide oxidoreductase 59 | FAD_binding_3 PF01494.18 356 AT3G10370.1 - 629 0.015 14.5 0.2 1 2 0.00033 0.39 9.8 0.5 3 51 75 124 73 131 0.84 FAD binding domain 60 | FAD_binding_3 PF01494.18 356 AT3G10370.1 - 629 0.015 14.5 0.2 2 2 0.069 83 2.2 0.0 117 179 240 306 228 401 0.67 FAD binding domain 61 | GIDA PF01134.21 392 AT3G10370.1 - 629 0.036 13.0 0.2 1 2 0.00019 0.23 10.4 0.1 1 29 75 103 75 134 0.87 Glucose inhibited division protein A 62 | GIDA PF01134.21 392 AT3G10370.1 - 629 0.036 13.0 0.2 2 2 0.27 3.3e+02 0.0 0.0 110 159 257 305 249 311 0.58 Glucose inhibited division protein A 63 | Pyr_redox PF00070.26 81 AT3G10370.1 - 629 0.063 13.8 0.7 1 1 0.00023 0.28 11.7 0.7 2 32 76 106 75 111 0.96 Pyridine nucleotide-disulphide oxidoreductase 64 | HI0933_like PF03486.13 409 AT3G10370.1 - 629 0.075 11.6 0.2 1 1 0.00012 0.15 10.6 0.2 2 32 75 105 74 109 0.94 HI0933-like protein 65 | AAA_30 PF13604.5 192 AT3G10370.1 - 629 0.077 12.6 0.6 1 2 3.1 3.7e+03 -2.7 0.1 5 39 60 94 58 98 0.57 AAA domain 66 | AAA_30 PF13604.5 192 AT3G10370.1 - 629 0.077 12.6 0.6 2 2 0.00014 0.17 11.5 0.0 32 81 484 533 455 559 0.88 AAA domain 67 | Pyr_redox_3 PF13738.5 305 AT3G10370.1 - 629 0.1 11.7 0.0 1 1 0.00015 0.18 10.9 0.0 166 220 75 128 58 151 0.73 Pyridine nucleotide-disulphide oxidoreductase 68 | DUF4179 PF13786.5 88 AT3G10370.1 - 629 0.18 12.2 0.9 1 2 0.00059 0.71 10.3 0.0 5 37 5 40 2 63 0.82 Domain of unknown function (DUF4179) 69 | DUF4179 PF13786.5 88 AT3G10370.1 - 629 0.18 12.2 0.9 2 2 1.5 1.8e+03 -0.6 0.1 10 57 243 290 235 300 0.50 Domain of unknown function (DUF4179) 70 | 3HCDH_N PF02737.17 180 AT3G10370.1 - 629 0.31 10.8 2.0 1 2 0.0003 0.36 10.6 0.2 2 32 76 106 75 131 0.85 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 71 | 3HCDH_N PF02737.17 180 AT3G10370.1 - 629 0.31 10.8 2.0 2 2 1.9 2.2e+03 -1.8 0.1 30 65 578 613 560 623 0.45 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 72 | NAD_binding_8 PF13450.5 68 AT3G10370.1 - 629 1.4 9.1 5.0 1 2 0.00027 0.32 11.2 0.6 1 42 78 122 78 145 0.83 NAD(P)-binding Rossmann-like domain 73 | NAD_binding_8 PF13450.5 68 AT3G10370.1 - 629 1.4 9.1 5.0 2 2 4.6 5.5e+03 -2.4 0.0 31 40 435 444 420 454 0.73 NAD(P)-binding Rossmann-like domain 74 | # 75 | # Program: hmmscan 76 | # Version: 3.1b2 (February 2015) 77 | # Pipeline mode: SCAN 78 | # Query file: five.faa 79 | # Target file: /home/z/db/Pfam-A.hmm 80 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa 81 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 82 | # Date: Fri Dec 15 02:09:00 2017 83 | # [ok] 84 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/five/domtblout: -------------------------------------------------------------------------------- 1 | # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord 2 | # target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target 3 | #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- 4 | Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 1 2 4.3e-65 7.1e-61 204.8 11.2 4 168 24 181 21 183 0.96 Rer1 family 5 | Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 2 2 0.43 7.2e+03 -3.6 0.0 55 67 187 199 184 217 0.69 Rer1 family 6 | DUF4220 PF13968.5 352 AT5G45530.1 - 798 4.6e-78 263.0 0.0 1 1 1.5e-81 1.3e-77 261.5 0.0 1 344 51 396 51 427 0.78 Domain of unknown function (DUF4220) 7 | DUF594 PF04578.12 55 AT5G45530.1 - 798 4.7e-24 83.6 1.5 1 1 1.3e-27 1.1e-23 82.4 1.5 3 55 726 778 724 778 0.96 Protein of unknown function, DUF594 8 | DEAD PF00270.28 176 AT1G27880.2 - 890 6.7e-20 71.5 0.1 1 1 3.4e-23 1.9e-19 70.0 0.1 2 171 272 433 271 438 0.83 DEAD/DEAH box helicase 9 | Helicase_C PF00271.30 111 AT1G27880.2 - 890 3.2e-18 66.0 0.0 1 2 0.31 1.7e+03 -0.7 0.0 21 72 314 364 307 367 0.74 Helicase conserved C-terminal domain 10 | Helicase_C PF00271.30 111 AT1G27880.2 - 890 3.2e-18 66.0 0.0 2 2 5.4e-21 3e-17 62.9 0.0 15 110 485 580 470 581 0.91 Helicase conserved C-terminal domain 11 | ResIII PF04851.14 171 AT1G27880.2 - 890 0.0012 18.8 0.1 1 2 1.7 9.4e+03 -3.7 0.1 102 123 214 232 188 256 0.54 Type III restriction enzyme, res subunit 12 | ResIII PF04851.14 171 AT1G27880.2 - 890 0.0012 18.8 0.1 2 2 1.5e-06 0.0084 16.0 0.0 4 169 270 430 268 432 0.74 Type III restriction enzyme, res subunit 13 | TIR PF01582.19 176 AT1G56520.1 - 897 7.3e-46 156.1 0.0 1 1 1.3e-48 1.2e-45 155.3 0.0 2 164 13 179 12 189 0.95 TIR domain 14 | NB-ARC PF00931.21 288 AT1G56520.1 - 897 1.9e-17 63.1 0.0 1 1 3.6e-20 3.5e-17 62.3 0.0 4 262 192 440 189 456 0.78 NB-ARC domain 15 | LRR_3 PF07725.11 20 AT1G56520.1 - 897 1e-07 31.4 1.1 1 2 1e-10 1e-07 31.4 1.1 1 20 603 622 603 622 0.98 Leucine Rich Repeat 16 | LRR_3 PF07725.11 20 AT1G56520.1 - 897 1e-07 31.4 1.1 2 2 1.3 1.3e+03 -0.6 0.5 1 14 626 640 626 641 0.79 Leucine Rich Repeat 17 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 1 6 1.1 1.1e+03 -0.6 0.0 15 31 544 560 535 561 0.88 Leucine rich repeat 18 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 2 6 0.0013 1.3 8.8 0.3 2 58 603 657 602 661 0.90 Leucine rich repeat 19 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 3 6 0.0064 6.2 6.6 0.2 2 59 626 682 625 683 0.88 Leucine rich repeat 20 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 4 6 0.11 1.1e+02 2.6 0.1 2 57 649 703 648 706 0.66 Leucine rich repeat 21 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 5 6 4.9e-06 0.0048 16.5 0.0 2 60 717 772 716 773 0.87 Leucine rich repeat 22 | LRR_8 PF13855.5 61 AT1G56520.1 - 897 2.3e-07 30.4 7.0 6 6 0.002 2 8.2 0.1 27 59 763 794 760 795 0.70 Leucine rich repeat 23 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 1 5 8.4 8.3e+03 -2.6 0.0 19 33 550 563 535 566 0.71 Leucine Rich repeats (2 copies) 24 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 2 5 0.0066 6.5 7.2 0.1 2 33 626 658 625 671 0.81 Leucine Rich repeats (2 copies) 25 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 3 5 0.01 10 6.6 0.3 12 38 684 711 649 715 0.56 Leucine Rich repeats (2 copies) 26 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 4 5 0.0017 1.6 9.1 0.0 1 39 716 756 716 760 0.88 Leucine Rich repeats (2 copies) 27 | LRR_4 PF12799.6 43 AT1G56520.1 - 897 2.7e-07 30.6 17.6 5 5 4.8e-06 0.0047 17.2 0.2 3 42 763 804 762 805 0.90 Leucine Rich repeats (2 copies) 28 | TIR_2 PF13676.5 102 AT1G56520.1 - 897 2.6e-05 24.4 0.1 1 2 9.5e-08 9.3e-05 22.6 0.0 1 85 15 101 15 120 0.79 TIR domain 29 | TIR_2 PF13676.5 102 AT1G56520.1 - 897 2.6e-05 24.4 0.1 2 2 6.1 6e+03 -2.5 0.1 16 55 257 295 256 296 0.80 TIR domain 30 | AAA_16 PF13191.5 170 AT1G56520.1 - 897 0.0002 21.7 0.3 1 1 7.8e-07 0.00077 19.8 0.3 3 63 187 243 186 319 0.74 AAA ATPase domain 31 | AAA_18 PF13238.5 130 AT1G56520.1 - 897 0.001 19.5 0.0 1 1 2.4e-06 0.0024 18.3 0.0 1 69 210 274 210 332 0.69 AAA domain 32 | AAA_22 PF13401.5 137 AT1G56520.1 - 897 0.0048 17.1 1.0 1 1 2.4e-05 0.024 14.8 1.0 7 113 209 312 204 324 0.64 AAA domain 33 | ATPase_2 PF01637.17 233 AT1G56520.1 - 897 0.015 15.1 0.0 1 1 4.7e-05 0.046 13.5 0.0 8 82 193 265 190 311 0.64 ATPase domain predominantly from Archaea 34 | PhoH PF02562.15 205 AT1G56520.1 - 897 0.028 13.8 1.1 1 2 0.0036 3.5 6.9 0.2 18 39 206 227 192 251 0.82 PhoH-like protein 35 | PhoH PF02562.15 205 AT1G56520.1 - 897 0.028 13.8 1.1 2 2 0.011 11 5.3 0.0 87 161 257 332 240 341 0.85 PhoH-like protein 36 | NACHT PF05729.11 166 AT1G56520.1 - 897 0.029 14.2 0.0 1 1 5.8e-05 0.057 13.2 0.0 3 95 210 304 208 336 0.81 NACHT domain 37 | AAA_23 PF13476.5 200 AT1G56520.1 - 897 0.039 14.4 0.0 1 2 0.00035 0.34 11.3 0.0 20 50 208 238 192 284 0.80 AAA domain 38 | AAA_23 PF13476.5 200 AT1G56520.1 - 897 0.039 14.4 0.0 2 2 1.4 1.4e+03 -0.5 0.0 118 143 818 843 811 864 0.84 AAA domain 39 | ABC_tran PF00005.26 137 AT1G56520.1 - 897 0.044 14.2 0.0 1 1 9.6e-05 0.095 13.1 0.0 12 36 208 232 200 276 0.89 ABC transporter 40 | NTPase_1 PF03266.14 168 AT1G56520.1 - 897 0.062 13.1 0.0 1 1 0.00016 0.16 11.8 0.0 2 87 210 293 209 303 0.79 NTPase 41 | AAA_29 PF13555.5 61 AT1G56520.1 - 897 0.079 12.6 0.1 1 2 0.0013 1.3 8.7 0.1 18 42 201 227 194 232 0.80 P-loop containing region of AAA domain 42 | AAA_29 PF13555.5 61 AT1G56520.1 - 897 0.079 12.6 0.1 2 2 0.36 3.5e+02 0.9 0.0 3 25 583 606 582 608 0.86 P-loop containing region of AAA domain 43 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 1 8 8.6 8.5e+03 -1.9 0.0 1 13 603 615 603 621 0.83 Leucine Rich Repeat 44 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 2 8 1.9 1.9e+03 0.1 0.1 1 12 626 637 626 647 0.70 Leucine Rich Repeat 45 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 3 8 0.71 7e+02 1.4 0.0 1 21 649 669 649 671 0.73 Leucine Rich Repeat 46 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 4 8 0.19 1.9e+02 3.1 0.0 1 13 696 728 696 738 0.61 Leucine Rich Repeat 47 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 5 8 6.4 6.2e+03 -1.5 0.0 3 13 742 752 741 760 0.71 Leucine Rich Repeat 48 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 6 8 0.024 24 5.9 0.0 2 12 763 773 762 783 0.82 Leucine Rich Repeat 49 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 7 8 0.17 1.6e+02 3.3 0.3 1 16 785 800 785 818 0.75 Leucine Rich Repeat 50 | LRR_1 PF00560.32 23 AT1G56520.1 - 897 0.15 12.6 14.8 8 8 4.4 4.3e+03 -1.0 0.0 8 21 874 886 866 888 0.77 Leucine Rich Repeat 51 | DAO PF01266.23 352 AT3G10370.1 - 629 3.2e-53 181.4 0.1 1 2 7.2e-56 8.6e-53 180.1 0.0 1 351 75 442 75 443 0.80 FAD dependent oxidoreductase 52 | DAO PF01266.23 352 AT3G10370.1 - 629 3.2e-53 181.4 0.1 2 2 1.4 1.7e+03 -1.8 0.1 68 106 554 590 538 626 0.61 FAD dependent oxidoreductase 53 | DAO_C PF16901.4 126 AT3G10370.1 - 629 9e-39 132.1 0.3 1 1 1.3e-41 1.6e-38 131.3 0.3 1 125 465 600 465 601 0.98 C-terminal domain of alpha-glycerophosphate oxidase 54 | FAD_binding_2 PF00890.23 417 AT3G10370.1 - 629 6.3e-07 28.7 1.9 1 2 1.9e-06 0.0023 17.0 1.2 1 41 75 115 75 124 0.94 FAD binding domain 55 | FAD_binding_2 PF00890.23 417 AT3G10370.1 - 629 6.3e-07 28.7 1.9 2 2 0.00024 0.29 10.1 0.0 154 213 247 307 226 320 0.82 FAD binding domain 56 | FAD_oxidored PF12831.6 433 AT3G10370.1 - 629 0.0001 21.7 1.1 1 2 3.6e-07 0.00043 19.7 0.3 1 40 75 114 75 142 0.93 FAD dependent oxidoreductase 57 | FAD_oxidored PF12831.6 433 AT3G10370.1 - 629 0.0001 21.7 1.1 2 2 0.34 4.1e+02 -0.1 0.0 100 143 247 294 214 296 0.85 FAD dependent oxidoreductase 58 | Pyr_redox_2 PF07992.13 292 AT3G10370.1 - 629 0.014 14.6 0.0 1 1 2.6e-05 0.031 13.4 0.0 2 36 75 108 59 151 0.78 Pyridine nucleotide-disulphide oxidoreductase 59 | FAD_binding_3 PF01494.18 356 AT3G10370.1 - 629 0.015 14.5 0.2 1 2 0.00033 0.39 9.8 0.5 3 51 75 124 73 131 0.84 FAD binding domain 60 | FAD_binding_3 PF01494.18 356 AT3G10370.1 - 629 0.015 14.5 0.2 2 2 0.069 83 2.2 0.0 117 179 240 306 228 401 0.67 FAD binding domain 61 | GIDA PF01134.21 392 AT3G10370.1 - 629 0.036 13.0 0.2 1 2 0.00019 0.23 10.4 0.1 1 29 75 103 75 134 0.87 Glucose inhibited division protein A 62 | GIDA PF01134.21 392 AT3G10370.1 - 629 0.036 13.0 0.2 2 2 0.27 3.3e+02 0.0 0.0 110 159 257 305 249 311 0.58 Glucose inhibited division protein A 63 | Pyr_redox PF00070.26 81 AT3G10370.1 - 629 0.063 13.8 0.7 1 1 0.00023 0.28 11.7 0.7 2 32 76 106 75 111 0.96 Pyridine nucleotide-disulphide oxidoreductase 64 | HI0933_like PF03486.13 409 AT3G10370.1 - 629 0.075 11.6 0.2 1 1 0.00012 0.15 10.6 0.2 2 32 75 105 74 109 0.94 HI0933-like protein 65 | AAA_30 PF13604.5 192 AT3G10370.1 - 629 0.077 12.6 0.6 1 2 3.1 3.7e+03 -2.7 0.1 5 39 60 94 58 98 0.57 AAA domain 66 | AAA_30 PF13604.5 192 AT3G10370.1 - 629 0.077 12.6 0.6 2 2 0.00014 0.17 11.5 0.0 32 81 484 533 455 559 0.88 AAA domain 67 | Pyr_redox_3 PF13738.5 305 AT3G10370.1 - 629 0.1 11.7 0.0 1 1 0.00015 0.18 10.9 0.0 166 220 75 128 58 151 0.73 Pyridine nucleotide-disulphide oxidoreductase 68 | DUF4179 PF13786.5 88 AT3G10370.1 - 629 0.18 12.2 0.9 1 2 0.00059 0.71 10.3 0.0 5 37 5 40 2 63 0.82 Domain of unknown function (DUF4179) 69 | DUF4179 PF13786.5 88 AT3G10370.1 - 629 0.18 12.2 0.9 2 2 1.5 1.8e+03 -0.6 0.1 10 57 243 290 235 300 0.50 Domain of unknown function (DUF4179) 70 | 3HCDH_N PF02737.17 180 AT3G10370.1 - 629 0.31 10.8 2.0 1 2 0.0003 0.36 10.6 0.2 2 32 76 106 75 131 0.85 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 71 | 3HCDH_N PF02737.17 180 AT3G10370.1 - 629 0.31 10.8 2.0 2 2 1.9 2.2e+03 -1.8 0.1 30 65 578 613 560 623 0.45 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 72 | NAD_binding_8 PF13450.5 68 AT3G10370.1 - 629 1.4 9.1 5.0 1 2 0.00027 0.32 11.2 0.6 1 42 78 122 78 145 0.83 NAD(P)-binding Rossmann-like domain 73 | NAD_binding_8 PF13450.5 68 AT3G10370.1 - 629 1.4 9.1 5.0 2 2 4.6 5.5e+03 -2.4 0.0 31 40 435 444 420 454 0.73 NAD(P)-binding Rossmann-like domain 74 | # 75 | # Program: hmmscan 76 | # Version: 3.1b2 (February 2015) 77 | # Pipeline mode: SCAN 78 | # Query file: five.faa 79 | # Target file: /home/z/db/Pfam-A.hmm 80 | # Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa 81 | # Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data 82 | # Date: Fri Dec 15 02:09:00 2017 83 | # [ok] 84 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/slf/SLF1_tblout.scan: -------------------------------------------------------------------------------- 1 | # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- 2 | # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target 3 | #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- 4 | gene_2396|GeneMark.hmm|810_aa|+|4897|7329 - AAC3-I RF0003 7e-07 29.4 0.1 2.8e-06 27.4 0.0 1.9 2 0 0 2 2 2 1 >k141_17650 flag=0 multi=10.9753 len=9041 5 | gene_11365|GeneMark.hmm|148_aa|+|172|618 - AAC3-I RF0003 0.00011 22.2 0.0 0.00014 21.9 0.0 1.2 1 0 0 1 1 1 1 >k141_33670 flag=1 multi=4.0000 len=2669 6 | gene_2949|GeneMark.hmm|149_aa|-|737|1186 - AAC3-I RF0003 0.00068 19.7 0.1 0.00092 19.3 0.1 1.1 1 0 0 1 1 1 1 >k141_27916 flag=1 multi=4.0000 len=1916 7 | gene_14069|GeneMark.hmm|167_aa|+|3933|4436 - AAC3-I RF0003 0.0022 18.0 0.0 0.0026 17.8 0.0 1.2 1 0 0 1 1 1 1 >k141_29979 flag=0 multi=29.9947 len=136896 8 | gene_14358|GeneMark.hmm|146_aa|-|21121|21561 - AAC3-I RF0003 0.0025 17.8 0.0 0.0036 17.3 0.0 1.2 1 0 0 1 1 1 1 >k141_54625 flag=0 multi=46.9983 len=1190833 9 | gene_2086|GeneMark.hmm|394_aa|+|33811|34995 - AAC3-I RF0003 0.007 16.4 0.1 0.022 14.8 0.1 1.8 1 1 1 2 2 2 1 >k141_21140 flag=0 multi=12.9869 len=40545 10 | gene_13593|GeneMark.hmm|143_aa|-|1198|1629 - AAC3-I RF0003 0.018 15.1 0.0 0.022 14.8 0.0 1.2 1 0 0 1 1 1 0 >k141_6690 flag=0 multi=6.9681 len=4280 11 | gene_4891|GeneMark.hmm|238_aa|+|1329|2045 - AAC3-I RF0003 0.031 14.3 0.0 0.069 13.2 0.0 1.5 1 0 0 1 1 1 0 >k141_42387 flag=0 multi=6.8730 len=2219 12 | gene_4772|GeneMark.hmm|184_aa|+|21702|22256 - AAC3-I RF0003 0.086 12.8 0.0 0.17 11.8 0.0 1.3 1 1 0 1 1 1 0 >k141_21989 flag=1 multi=10.0000 len=30961 13 | gene_14446|GeneMark.hmm|157_aa|+|104299|104772 - AAC3-I RF0003 0.12 12.4 0.0 0.16 12.0 0.0 1.2 1 0 0 1 1 1 0 >k141_54625 flag=0 multi=46.9983 len=1190833 14 | gene_8221|GeneMark.hmm|148_aa|+|619720|620166 - AAC3-I RF0003 0.13 12.3 0.0 0.18 11.8 0.0 1.2 1 0 0 1 1 1 0 >k141_27970 flag=0 multi=44.2885 len=699727 15 | gene_6501|GeneMark.hmm|156_aa|+|34217|34687 - AAC6-I RF0004 2.3e-05 23.7 5.1 0.00015 21.0 0.5 2.1 1 1 1 2 2 2 2 >k141_8450 flag=0 multi=34.7298 len=74281 16 | gene_1084|GeneMark.hmm|187_aa|+|30103|30666 - AAC6-I RF0004 0.0004 19.6 0.2 0.0009 18.5 0.1 1.6 2 1 0 2 2 2 1 >k141_24195 flag=0 multi=39.8376 len=72305 17 | gene_13593|GeneMark.hmm|143_aa|-|1198|1629 - AAC6-I RF0004 0.00045 19.4 0.1 0.00047 19.4 0.1 1.1 1 0 0 1 1 1 1 >k141_6690 flag=0 multi=6.9681 len=4280 18 | gene_8221|GeneMark.hmm|148_aa|+|619720|620166 - AAC6-I RF0004 0.00047 19.4 0.9 0.0012 18.1 0.1 1.7 1 1 1 2 2 2 1 >k141_27970 flag=0 multi=44.2885 len=699727 19 | gene_6830|GeneMark.hmm|167_aa|+|91330|91833 - AAC6-I RF0004 0.0013 17.9 0.2 0.0067 15.6 0.2 2.1 1 1 0 1 1 1 1 >k141_45260 flag=0 multi=36.7967 len=102807 20 | gene_4624|GeneMark.hmm|293_aa|-|1347|2228 - AAC6-I RF0004 0.0043 16.2 0.0 0.0094 15.1 0.0 1.6 1 0 0 1 1 1 1 >k141_42230 flag=0 multi=6.9574 len=3239 21 | gene_1785|GeneMark.hmm|105_aa|-|22781|23098 - AAC6-I RF0004 0.018 14.2 0.1 0.023 13.8 0.1 1.1 1 0 0 1 1 1 0 >k141_24243 flag=0 multi=33.8017 len=34139 22 | gene_10213|GeneMark.hmm|140_aa|-|77837|78259 - AAC6-I RF0004 0.021 14.0 0.6 0.059 12.5 0.2 1.8 1 1 1 2 2 2 0 >k141_43348 flag=0 multi=35.0000 len=98294 23 | gene_9509|GeneMark.hmm|176_aa|+|36473|37003 - AAC6-I RF0004 0.03 13.5 0.0 0.05 12.8 0.0 1.5 1 0 0 1 1 1 0 >k141_19026 flag=0 multi=35.8537 len=37451 24 | gene_10051|GeneMark.hmm|217_aa|+|19133|19786 - AAC6-I RF0004 0.032 13.4 0.0 0.047 12.8 0.0 1.2 1 0 0 1 1 1 0 >k141_26048 flag=1 multi=10.0000 len=45677 25 | gene_14724|GeneMark.hmm|164_aa|+|426279|426773 - AAC6-I RF0004 0.036 13.2 0.0 0.055 12.6 0.0 1.3 1 1 0 1 1 1 0 >k141_54625 flag=0 multi=46.9983 len=1190833 26 | gene_6989|GeneMark.hmm|170_aa|-|131131|131643 - AAC6-I RF0004 0.051 12.7 0.0 0.13 11.4 0.0 1.6 1 1 0 1 1 1 0 >k141_42596 flag=1 multi=23.0000 len=191289 27 | gene_7017|GeneMark.hmm|169_aa|-|161031|161540 - AAC6-I RF0004 0.098 11.8 0.1 0.17 11.1 0.1 1.4 1 1 0 1 1 1 0 >k141_42596 flag=1 multi=23.0000 len=191289 28 | gene_11365|GeneMark.hmm|148_aa|+|172|618 - AAC6-I RF0004 0.1 11.7 0.0 0.16 11.1 0.0 1.3 1 0 0 1 1 1 0 >k141_33670 flag=1 multi=4.0000 len=2669 29 | gene_7017|GeneMark.hmm|169_aa|-|161031|161540 - AAC6-Ib RF0005 0.00024 20.5 0.0 0.00037 19.9 0.0 1.2 1 0 0 1 1 1 1 >k141_42596 flag=1 multi=23.0000 len=191289 30 | gene_8392|GeneMark.hmm|157_aa|-|3|473 - AAC6-Ib RF0005 0.017 14.6 0.0 0.034 13.5 0.0 1.5 2 0 0 2 2 2 0 >k141_35651 flag=1 multi=4.0000 len=1528 31 | gene_7017|GeneMark.hmm|169_aa|-|161031|161540 - AAC6-II RF0006 0.014 14.9 0.0 0.021 14.3 0.0 1.2 1 0 0 1 1 1 0 >k141_42596 flag=1 multi=23.0000 len=191289 32 | gene_8392|GeneMark.hmm|157_aa|-|3|473 - AAC6-II RF0006 0.022 14.2 0.0 0.038 13.4 0.0 1.3 1 0 0 1 1 1 0 >k141_35651 flag=1 multi=4.0000 len=1528 33 | gene_9704|GeneMark.hmm|292_aa|-|6069|6947 - AAC6-II RF0006 0.084 12.3 0.0 0.32 10.4 0.0 1.9 1 1 1 2 2 2 0 >k141_35856 flag=1 multi=13.0000 len=16195 34 | gene_1898|GeneMark.hmm|566_aa|+|59297|60997 - ABC_efflux RF0007 6.4e-101 338.3 0.2 7.7e-101 338.1 0.2 1.0 1 0 0 1 1 1 1 >k141_51779 flag=0 multi=38.9884 len=72037 35 | gene_2179|GeneMark.hmm|579_aa|-|16481|18220 - ABC_efflux RF0007 5.4e-99 332.0 0.8 6.6e-99 331.7 0.8 1.0 1 0 0 1 1 1 1 >k141_38215 flag=0 multi=13.9921 len=36174 36 | gene_3854|GeneMark.hmm|566_aa|+|30172|31872 - ABC_efflux RF0007 8.1e-99 331.4 0.1 9.6e-99 331.2 0.1 1.0 1 0 0 1 1 1 1 >k141_45111 flag=1 multi=29.9959 len=149652 37 | gene_4256|GeneMark.hmm|618_aa|+|12331|14187 - ABC_efflux RF0007 1.5e-94 317.4 4.2 1.7e-94 317.2 4.2 1.0 1 0 0 1 1 1 1 >k141_21848 flag=0 multi=36.8784 len=39057 38 | gene_11249|GeneMark.hmm|584_aa|+|23334|25088 - ABC_efflux RF0007 2.9e-94 316.4 3.3 3.2e-94 316.2 3.3 1.0 1 0 0 1 1 1 1 >k141_5620 flag=0 multi=9.9881 len=33305 39 | gene_4357|GeneMark.hmm|617_aa|+|28933|30786 - ABC_efflux RF0007 2.8e-93 313.1 8.4 3.4e-93 312.8 8.4 1.0 1 0 0 1 1 1 1 >k141_52305 flag=0 multi=23.9842 len=61181 40 | gene_9945|GeneMark.hmm|590_aa|+|46122|47894 - ABC_efflux RF0007 4.5e-92 309.2 0.0 5.5e-92 308.8 0.0 1.0 1 0 0 1 1 1 1 >k141_28317 flag=0 multi=11.9960 len=60070 41 | gene_6178|GeneMark.hmm|598_aa|+|20415|22211 - ABC_efflux RF0007 5.3e-90 302.3 6.2 6.5e-90 302.0 6.2 1.0 1 0 0 1 1 1 1 >k141_32020 flag=0 multi=13.5044 len=128229 42 | gene_4629|GeneMark.hmm|543_aa|-|634|2265 - ABC_efflux RF0007 6.2e-89 298.8 3.0 7.3e-89 298.6 3.0 1.0 1 0 0 1 1 1 1 >k141_35114 flag=1 multi=3.0000 len=2265 43 | gene_7539|GeneMark.hmm|601_aa|-|10456|12261 - ABC_efflux RF0007 2e-86 290.5 0.0 2.4e-86 290.3 0.0 1.0 1 0 0 1 1 1 1 >k141_22684 flag=1 multi=9.0000 len=20310 44 | gene_7005|GeneMark.hmm|589_aa|-|146375|148144 - ABC_efflux RF0007 2.7e-85 286.8 6.2 3.1e-85 286.6 6.2 1.1 1 0 0 1 1 1 1 >k141_42596 flag=1 multi=23.0000 len=191289 45 | gene_15198|GeneMark.hmm|582_aa|+|924562|926310 - ABC_efflux RF0007 2.8e-83 280.2 4.5 3.3e-83 279.9 4.5 1.0 1 0 0 1 1 1 1 >k141_54625 flag=0 multi=46.9983 len=1190833 46 | gene_10400|GeneMark.hmm|641_aa|+|409|2334 - ABC_efflux RF0007 1.1e-82 278.2 0.1 1.4e-82 277.9 0.1 1.0 1 0 0 1 1 1 1 >k141_33358 flag=1 multi=9.2583 len=10214 47 | gene_14581|GeneMark.hmm|610_aa|-|252654|254486 - ABC_efflux RF0007 4.8e-82 276.1 3.9 1.4e-80 271.3 3.8 2.0 1 1 0 1 1 1 1 >k141_54625 flag=0 multi=46.9983 len=1190833 48 | gene_3426|GeneMark.hmm|578_aa|+|33334|35070 - ABC_efflux RF0007 1.1e-80 271.6 0.0 1.4e-80 271.2 0.0 1.0 1 0 0 1 1 1 1 >k141_31414 flag=0 multi=15.1565 len=53008 49 | gene_12962|GeneMark.hmm|672_aa|+|22823|24841 - ABC_efflux RF0007 1.6e-80 271.1 0.0 6.7e-64 216.2 0.0 2.0 2 0 0 2 2 2 2 >k141_6238 flag=1 multi=10.8561 len=46090 50 | gene_3108|GeneMark.hmm|639_aa|+|4905|6824 - ABC_efflux RF0007 7.3e-79 265.6 0.0 8.2e-60 202.7 0.1 2.0 1 1 0 2 2 2 2 >k141_14706 flag=1 multi=12.0000 len=6961 51 | gene_5410|GeneMark.hmm|500_aa|-|7|1509 - ABC_efflux RF0007 2.3e-78 263.9 0.0 2.9e-78 263.6 0.0 1.0 1 0 0 1 1 1 1 >k141_42562 flag=1 multi=4.0000 len=1511 52 | gene_11876|GeneMark.hmm|372_aa|+|2|1120 - ABC_efflux RF0007 9e-76 255.4 0.0 9.8e-76 255.2 0.0 1.0 1 0 0 1 1 1 1 >k141_9122 flag=1 multi=3.0000 len=1642 53 | gene_641|GeneMark.hmm|491_aa|-|319|1794 - ABC_efflux RF0007 2.5e-75 253.9 0.0 2.9e-75 253.7 0.0 1.0 1 0 0 1 1 1 1 >k141_13961 flag=1 multi=6.0000 len=1794 54 | gene_8366|GeneMark.hmm|601_aa|-|51555|53360 - ABC_efflux RF0007 1.3e-73 248.2 0.0 1.6e-73 247.9 0.0 1.1 1 0 0 1 1 1 1 >k141_18765 flag=0 multi=9.9973 len=73986 55 | gene_9061|GeneMark.hmm|581_aa|-|235|1980 - ABC_efflux RF0007 1.8e-73 247.8 1.0 2.1e-73 247.5 1.0 1.0 1 0 0 1 1 1 1 >k141_15998 flag=0 multi=11.1779 len=6482 56 | gene_7081|GeneMark.hmm|562_aa|+|10324|12012 - ABC_efflux RF0007 2.9e-71 240.5 1.8 3.7e-71 240.1 1.8 1.0 1 0 0 1 1 1 1 >k141_35439 flag=0 multi=47.0000 len=64673 57 | gene_3831|GeneMark.hmm|451_aa|-|692|2047 - ABC_efflux RF0007 1.4e-70 238.3 0.0 1.9e-70 237.8 0.0 1.1 1 0 0 1 1 1 1 >k141_7746 flag=1 multi=5.0000 len=2047 58 | gene_9964|GeneMark.hmm|538_aa|-|2|1615 - ABC_efflux RF0007 1.4e-69 235.0 0.0 1.7e-69 234.7 0.0 1.0 1 0 0 1 1 1 1 >k141_40231 flag=1 multi=2.7356 len=2123 59 | gene_14582|GeneMark.hmm|594_aa|-|254486|256270 - ABC_efflux RF0007 3.4e-69 233.7 4.7 4e-69 233.4 4.7 1.0 1 0 0 1 1 1 1 >k141_54625 flag=0 multi=46.9983 len=1190833 60 | gene_6971|GeneMark.hmm|581_aa|-|107399|109144 - ABC_efflux RF0007 4.1e-69 233.4 0.0 5.7e-69 232.9 0.0 1.1 1 0 0 1 1 1 1 >k141_42596 flag=1 multi=23.0000 len=191289 61 | gene_8829|GeneMark.hmm|280_aa|-|819|1661 - ABC_efflux RF0007 7.1e-69 232.6 0.5 8.5e-69 232.3 0.5 1.0 1 0 0 1 1 1 1 >k141_8748 flag=1 multi=7.0000 len=1663 62 | gene_9062|GeneMark.hmm|588_aa|-|1981|3747 - ABC_efflux RF0007 2.6e-68 230.7 0.0 3.5e-68 230.3 0.0 1.0 1 0 0 1 1 1 1 >k141_15998 flag=0 multi=11.1779 len=6482 63 | gene_3427|GeneMark.hmm|578_aa|+|35063|36799 - ABC_efflux RF0007 3.3e-68 230.4 0.0 4e-68 230.1 0.0 1.0 1 0 0 1 1 1 1 >k141_31414 flag=0 multi=15.1565 len=53008 64 | gene_7080|GeneMark.hmm|591_aa|+|8548|10323 - ABC_efflux RF0007 3.6e-68 230.3 2.6 4.7e-68 229.9 2.6 1.0 1 0 0 1 1 1 1 >k141_35439 flag=0 multi=47.0000 len=64673 65 | gene_487|GeneMark.hmm|586_aa|-|10123|11883 - ABC_efflux RF0007 3.5e-67 227.0 0.0 5.9e-67 226.3 0.0 1.3 1 1 0 1 1 1 1 >k141_44596 flag=0 multi=12.0901 len=26050 66 | gene_2180|GeneMark.hmm|577_aa|-|18217|19950 - ABC_efflux RF0007 3.4e-66 223.8 0.5 4.4e-66 223.4 0.5 1.0 1 0 0 1 1 1 1 >k141_38215 flag=0 multi=13.9921 len=36174 67 | gene_5656|GeneMark.hmm|552_aa|+|266767|268425 - ABC_efflux RF0007 7.1e-66 222.7 0.0 8.3e-66 222.5 0.0 1.0 1 0 0 1 1 1 1 >k141_11001 flag=0 multi=46.3091 len=526625 68 | gene_4356|GeneMark.hmm|752_aa|+|26682|28940 - ABC_efflux RF0007 8.5e-66 222.5 5.6 1.6e-65 221.5 5.6 1.4 1 0 0 1 1 1 1 >k141_52305 flag=0 multi=23.9842 len=61181 69 | gene_9129|GeneMark.hmm|584_aa|+|15373|17127 - ABC_efflux RF0007 1.4e-65 221.8 6.4 1.6e-65 221.5 6.4 1.0 1 0 0 1 1 1 1 >k141_35731 flag=0 multi=24.9960 len=130800 70 | gene_6970|GeneMark.hmm|580_aa|-|105676|107418 - ABC_efflux RF0007 1.5e-65 221.7 1.5 1.7e-65 221.4 1.5 1.0 1 0 0 1 1 1 1 >k141_42596 flag=1 multi=23.0000 len=191289 71 | gene_6504|GeneMark.hmm|638_aa|-|37124|39040 - ABC_efflux RF0007 1.7e-65 221.4 20.2 5e-38 130.8 0.2 4.7 1 1 3 4 4 4 4 >k141_8450 flag=0 multi=34.7298 len=74281 72 | gene_4340|GeneMark.hmm|585_aa|+|9362|11119 - ABC_efflux RF0007 2.5e-65 220.9 8.7 3.3e-65 220.5 8.7 1.1 1 0 0 1 1 1 1 >k141_52305 flag=0 multi=23.9842 len=61181 73 | gene_1298|GeneMark.hmm|643_aa|+|2734|4665 - ABC_efflux RF0007 5.2e-65 219.9 12.6 1.2e-33 116.3 0.5 4.5 3 1 2 5 5 5 4 >k141_44794 flag=0 multi=35.2980 len=40597 74 | gene_488|GeneMark.hmm|591_aa|-|11880|13655 - ABC_efflux RF0007 5.9e-65 219.7 0.0 9.1e-65 219.1 0.0 1.2 1 0 0 1 1 1 1 >k141_44596 flag=0 multi=12.0901 len=26050 75 | gene_3413|GeneMark.hmm|552_aa|+|21730|23388 - ABC_efflux RF0007 6.6e-65 219.5 0.0 8e-65 219.2 0.0 1.0 1 0 0 1 1 1 1 >k141_31414 flag=0 multi=15.1565 len=53008 76 | gene_3423|GeneMark.hmm|589_aa|+|28997|30766 - ABC_efflux RF0007 7e-65 219.4 0.0 9.2e-65 219.0 0.0 1.0 1 0 0 1 1 1 1 >k141_31414 flag=0 multi=15.1565 len=53008 77 | gene_11844|GeneMark.hmm|596_aa|-|2084|3874 - ABC_efflux RF0007 1.2e-64 218.7 0.8 3.1e-64 217.3 0.8 1.5 1 1 0 1 1 1 1 >k141_12574 flag=0 multi=25.8883 len=9993 78 | gene_3107|GeneMark.hmm|626_aa|+|3032|4912 - ABC_efflux RF0007 1.2e-64 218.7 0.0 1.6e-64 218.3 0.0 1.1 1 0 0 1 1 1 1 >k141_14706 flag=1 multi=12.0000 len=6961 79 | gene_10241|GeneMark.hmm|580_aa|+|9271|11013 - ABC_efflux RF0007 3.3e-64 217.2 0.0 4.5e-64 216.8 0.0 1.1 1 0 0 1 1 1 1 >k141_16384 flag=1 multi=10.0000 len=15240 80 | gene_13318|GeneMark.hmm|638_aa|+|24941|26857 - ABC_efflux RF0007 3.9e-64 217.0 11.7 3.8e-38 131.2 0.2 4.3 2 2 1 3 3 3 2 >k141_37049 flag=0 multi=10.4617 len=82240 81 | gene_5569|GeneMark.hmm|576_aa|+|164899|166629 - ABC_efflux RF0007 5e-64 216.6 0.1 6.2e-64 216.3 0.1 1.0 1 0 0 1 1 1 1 >k141_11001 flag=0 multi=46.3091 len=526625 82 | gene_15030|GeneMark.hmm|578_aa|-|736596|738332 - ABC_efflux RF0007 9e-64 215.8 0.3 1.1e-63 215.5 0.3 1.0 1 0 0 1 1 1 1 >k141_54625 flag=0 multi=46.9983 len=1190833 83 | gene_4255|GeneMark.hmm|765_aa|+|10041|12338 - ABC_efflux RF0007 2.2e-63 214.5 6.7 3.1e-63 214.0 6.7 1.1 1 0 0 1 1 1 1 >k141_21848 flag=0 multi=36.8784 len=39057 84 | gene_5568|GeneMark.hmm|580_aa|+|163154|164896 - ABC_efflux RF0007 5e-63 213.3 1.9 1.1e-61 208.9 1.9 2.0 1 1 0 1 1 1 1 >k141_11001 flag=0 multi=46.3091 len=526625 85 | gene_8964|GeneMark.hmm|328_aa|+|3|989 - ABC_efflux RF0007 8.4e-63 212.6 0.5 1e-62 212.3 0.5 1.0 1 0 0 1 1 1 1 >k141_11616 flag=1 multi=3.0000 len=1824 86 | gene_10042|GeneMark.hmm|589_aa|-|5299|7068 - ABC_efflux RF0007 5e-62 210.0 0.0 5.9e-62 209.8 0.0 1.0 1 0 0 1 1 1 1 >k141_26048 flag=1 multi=10.0000 len=45677 87 | gene_15029|GeneMark.hmm|560_aa|-|734910|736592 - ABC_efflux RF0007 5.1e-62 210.0 1.1 6.3e-62 209.7 1.1 1.1 1 0 0 1 1 1 1 >k141_54625 flag=0 multi=46.9983 len=1190833 88 | gene_12829|GeneMark.hmm|618_aa|+|1|1857 - ABC_efflux RF0007 6.9e-62 209.6 7.3 8.8e-62 209.2 7.3 1.1 1 0 0 1 1 1 1 >k141_20242 flag=1 multi=5.0000 len=2280 89 | gene_9196|GeneMark.hmm|599_aa|+|83935|85734 - ABC_efflux RF0007 9.1e-62 209.2 2.9 2.2e-61 207.9 2.9 1.5 1 1 0 1 1 1 1 >k141_35731 flag=0 multi=24.9960 len=130800 90 | gene_3424|GeneMark.hmm|577_aa|+|30750|32483 - ABC_efflux RF0007 1.1e-61 208.9 5.1 7.5e-61 206.1 5.1 1.9 1 1 0 1 1 1 1 >k141_31414 flag=0 multi=15.1565 len=53008 91 | gene_11314|GeneMark.hmm|417_aa|-|485|1738 - ABC_efflux RF0007 1.1e-61 208.9 2.1 1.5e-61 208.4 2.1 1.1 1 0 0 1 1 1 1 >k141_43700 flag=1 multi=5.0000 len=1739 92 | gene_3412|GeneMark.hmm|578_aa|+|19993|21729 - ABC_efflux RF0007 1.9e-61 208.1 0.1 2.4e-61 207.8 0.1 1.0 1 0 0 1 1 1 1 >k141_31414 flag=0 multi=15.1565 len=53008 93 | gene_11843|GeneMark.hmm|571_aa|-|376|2091 - ABC_efflux RF0007 2.4e-61 207.8 0.5 4.1e-61 207.0 0.5 1.3 1 1 0 1 1 1 1 >k141_12574 flag=0 multi=25.8883 len=9993 94 | gene_10041|GeneMark.hmm|589_aa|-|3524|5293 - ABC_efflux RF0007 7.2e-61 206.2 0.0 8.7e-61 205.9 0.0 1.0 1 0 0 1 1 1 1 >k141_26048 flag=1 multi=10.0000 len=45677 95 | gene_10240|GeneMark.hmm|633_aa|+|7377|9278 - ABC_efflux RF0007 2.7e-60 204.3 0.0 3e-56 190.9 0.0 2.1 2 0 0 2 2 2 2 >k141_16384 flag=1 multi=10.0000 len=15240 96 | gene_15112|GeneMark.hmm|629_aa|+|824646|826535 - ABC_efflux RF0007 1.2e-59 202.1 10.9 5.6e-27 94.4 0.0 5.0 1 1 2 4 4 4 4 >k141_54625 flag=0 multi=46.9983 len=1190833 97 | gene_9197|GeneMark.hmm|579_aa|+|85700|87439 - ABC_efflux RF0007 4e-59 200.4 4.6 4e-59 200.4 4.6 2.0 2 0 0 2 2 2 1 >k141_35731 flag=0 multi=24.9960 len=130800 98 | gene_9130|GeneMark.hmm|576_aa|+|17127|18857 - ABC_efflux RF0007 4.1e-58 197.1 0.2 5.2e-58 196.8 0.2 1.1 1 0 0 1 1 1 1 >k141_35731 flag=0 multi=24.9960 len=130800 99 | gene_7006|GeneMark.hmm|577_aa|-|148131|149864 - ABC_efflux RF0007 2.3e-57 194.6 1.2 1.8e-56 191.7 1.2 1.9 1 1 0 1 1 1 1 >k141_42596 flag=1 multi=23.0000 len=191289 100 | gene_6177|GeneMark.hmm|699_aa|+|18332|20431 - ABC_efflux RF0007 3e-57 194.3 8.9 1.3e-56 192.2 8.9 1.8 1 1 0 1 1 1 1 >k141_32020 flag=0 multi=13.5044 len=128229 101 | # 102 | # Program: hmmsearch 103 | # Version: 3.3.2 (Nov 2020) 104 | # Pipeline mode: SEARCH 105 | # Query file: /datos/vberrios/resfams_db/Resfams.hmm 106 | # Target file: clean_proteins.fasta 107 | # Option settings: hmmsearch --tblout SLF1_tblout.scan /datos/vberrios/resfams_db/Resfams.hmm clean_proteins.fasta 108 | # Current dir: /datos/vberrios/sea_lions/filtered/refiltered/assemblies/FP.SLF1/protein_fasta 109 | # Date: Sun Jul 18 03:05:10 2021 110 | # [ok] 111 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/slf/SLF2_tblout.scan: -------------------------------------------------------------------------------- 1 | # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- 2 | # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target 3 | #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- 4 | vanR RF0154 gene_6|GeneMark.hmm|54_aa|+|2238|2399 - 1.7e-06 20.5 0.0 1.8e-06 20.4 0.0 1.0 1 0 0 1 1 1 1 "VanR: transcriptional activator regulating VanA, VanH and VanX" [ARO:3000574] 5 | baeR RF0035 gene_6|GeneMark.hmm|54_aa|+|2238|2399 - 2.2e-05 16.8 0.0 2.2e-05 16.7 0.0 1.0 1 0 0 1 1 1 1 baeR: subunit of gene modulating antibiotic efflux [ARO:3000828] 6 | macB RF0089 gene_24|GeneMark.hmm|906_aa|-|3|2720 - 4.5e-05 14.9 3.1 7.1e-05 14.2 2.0 1.9 2 0 0 2 2 2 1 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 7 | msbA RF0107 gene_31|GeneMark.hmm|262_aa|+|233|1021 - 8.2e-36 116.1 0.1 1.2e-35 115.5 0.1 1.2 1 1 0 1 1 1 1 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 8 | macB RF0089 gene_31|GeneMark.hmm|262_aa|+|233|1021 - 2.4e-33 108.2 0.2 2.7e-33 108.0 0.2 1.0 1 0 0 1 1 1 1 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 9 | ABC_efflux RF0007 gene_31|GeneMark.hmm|262_aa|+|233|1021 - 2.6e-28 91.8 0.1 3.7e-28 91.3 0.1 1.2 1 0 0 1 1 1 1 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 10 | msbA RF0107 gene_32|GeneMark.hmm|244_aa|+|1021|1755 - 2.1e-36 118.1 0.6 6.5e-22 70.2 0.1 2.0 2 0 0 2 2 2 2 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 11 | macB RF0089 gene_32|GeneMark.hmm|244_aa|+|1021|1755 - 7.8e-33 106.5 0.5 3.2e-31 101.2 0.5 2.0 1 1 0 1 1 1 1 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 12 | ABC_efflux RF0007 gene_32|GeneMark.hmm|244_aa|+|1021|1755 - 1.2e-29 96.2 0.4 4.8e-29 94.2 0.4 1.7 1 1 0 1 1 1 1 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 13 | msbA RF0107 gene_45|GeneMark.hmm|524_aa|+|3|1577 - 6.6e-55 179.2 0.9 7.6e-33 106.3 0.0 2.2 2 0 0 2 2 2 2 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 14 | macB RF0089 gene_45|GeneMark.hmm|524_aa|+|3|1577 - 4.3e-40 130.5 1.2 1.1e-27 89.5 0.1 2.1 1 1 1 2 2 2 2 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 15 | ABC_efflux RF0007 gene_45|GeneMark.hmm|524_aa|+|3|1577 - 3.3e-38 124.5 2.3 1.4e-24 79.5 0.2 2.8 2 1 0 2 2 2 2 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 16 | emrB RF0065 gene_93|GeneMark.hmm|548_aa|-|241|1887 - 1.3e-12 40.1 21.9 3.4e-12 38.6 21.7 1.6 1 1 0 1 1 1 1 emrB: subunit of efflux pump conferring antibiotic resistance [ARO:3000074] 17 | MFS_efflux RF0104 gene_93|GeneMark.hmm|548_aa|-|241|1887 - 0.00029 12.6 61.9 0.02 6.5 61.9 2.6 1 1 0 1 1 1 1 major facilitator superfamily (MFS) antibiotic efflux pump [ARO:0010002] 18 | Chlor_Efflux_Pump RF0051 gene_93|GeneMark.hmm|548_aa|-|241|1887 - 0.0066 8.3 54.8 0.15 3.9 54.8 2.4 1 1 0 1 1 1 1 chloramphenicol efflux pump [ARO:3001212] 19 | MFS_efflux RF0104 gene_96|GeneMark.hmm|536_aa|-|5607|7217 - 1.8e-21 69.3 47.9 3.6e-21 68.3 47.9 1.4 1 1 0 1 1 1 1 major facilitator superfamily (MFS) antibiotic efflux pump [ARO:0010002] 20 | emrB RF0065 gene_96|GeneMark.hmm|536_aa|-|5607|7217 - 7e-16 50.8 24.8 1e-15 50.3 24.8 1.3 1 0 0 1 1 1 1 emrB: subunit of efflux pump conferring antibiotic resistance [ARO:3000074] 21 | tet_MFS_efflux RF0134 gene_96|GeneMark.hmm|536_aa|-|5607|7217 - 9.1e-13 40.6 48.6 1.5e-12 39.9 48.0 1.6 2 1 0 2 2 2 1 tetracycline resistance MFS efflux pump: selectively pump out tetracycline or tetracycline derivatives [ARO:3000239] 22 | norA RF0109 gene_96|GeneMark.hmm|536_aa|-|5607|7217 - 0.014 7.6 27.9 0.0026 10.0 18.0 3.2 2 2 0 2 2 2 0 norA: major facilitator superfamily (MFS) antibiotic efflux pump [ARO:3000391] 23 | macB RF0089 gene_103|GeneMark.hmm|243_aa|-|12095|12826 - 3e-50 164.0 0.0 3.5e-50 163.8 0.0 1.0 1 0 0 1 1 1 1 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 24 | msbA RF0107 gene_103|GeneMark.hmm|243_aa|-|12095|12826 - 1.9e-49 161.2 0.0 2.2e-49 160.9 0.0 1.0 1 0 0 1 1 1 1 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 25 | ABC_efflux RF0007 gene_103|GeneMark.hmm|243_aa|-|12095|12826 - 1.4e-41 135.6 0.0 1.7e-41 135.3 0.0 1.0 1 0 0 1 1 1 1 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 26 | ClassB RF0054 gene_106|GeneMark.hmm|394_aa|-|15671|16855 - 8.2e-12 37.8 0.5 4.2e-11 35.4 0.1 2.0 1 1 1 2 2 2 1 Class B beta-lactamase [ARO:3000004] 27 | SubclassB1 RF0123 gene_106|GeneMark.hmm|394_aa|-|15671|16855 - 1.3e-06 20.7 0.4 3.7e-06 19.2 0.0 1.8 2 0 0 2 2 2 1 "Subclass B1 (metallo-) beta-lactamase hydrolize penicillins, cephalosporins and carbapenems" [ARO:3000568] 28 | msbA RF0107 gene_128|GeneMark.hmm|958_aa|-|3684|6560 - 2.8e-29 94.6 9.1 2.1e-14 45.4 0.0 4.1 4 0 0 4 4 4 4 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 29 | ABC_efflux RF0007 gene_128|GeneMark.hmm|958_aa|-|3684|6560 - 4.4e-28 91.1 2.2 5.3e-13 41.3 0.0 4.1 4 0 0 4 4 4 4 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 30 | macB RF0089 gene_128|GeneMark.hmm|958_aa|-|3684|6560 - 3.6e-25 81.2 3.7 4.4e-11 34.7 0.0 4.1 4 0 0 4 4 4 4 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 31 | TE_Inactivator RF0168 gene_132|GeneMark.hmm|551_aa|+|10023|11678 - 0.0012 10.7 0.0 0.0017 10.2 0.0 1.1 1 0 0 1 1 1 1 Legionella_TE_Inactivator 32 | vanS RF0155 gene_160|GeneMark.hmm|230_aa|+|3|695 - 1.2e-31 102.9 0.0 1.4e-31 102.7 0.0 1.0 1 0 0 1 1 1 1 VanS: trasncriptional regulator of van glycopeptide resistance genes [ARO:3000071] 33 | baeS RF0036 gene_160|GeneMark.hmm|230_aa|+|3|695 - 2.9e-25 81.4 0.1 3.4e-25 81.2 0.1 1.0 1 0 0 1 1 1 1 baeS: subunit of gene modulating antibiotic efflux [ARO:3000829] 34 | phoQ RF0112 gene_160|GeneMark.hmm|230_aa|+|3|695 - 7.6e-18 57.2 0.0 9.1e-18 56.9 0.0 1.0 1 0 0 1 1 1 1 phoQ: subunit of gene modulating antibiotic efflux [ARO:3000835] 35 | adeS RF0023 gene_160|GeneMark.hmm|230_aa|+|3|695 - 5.5e-13 41.6 0.1 6.5e-13 41.3 0.1 1.0 1 0 0 1 1 1 1 adeS: gene modulating antibiotic efflux regulating AdeABC [ARO:3000549] 36 | tet_ribosomoal_protect RF0135 gene_174|GeneMark.hmm|536_aa|-|4396|6006 - 2.1e-66 217.3 0.0 5.6e-41 133.3 0.0 1.9 2 0 0 2 2 2 2 tetracycline resistance ribosomal protection protein: protect RNA-polymerase from tetracycline inhibition [ARO:0000002] 37 | TetM-TetW-TetO-TetS RF0133 gene_174|GeneMark.hmm|536_aa|-|4396|6006 - 5e-45 146.7 0.0 3e-31 101.1 0.0 2.0 2 0 0 2 2 2 2 "tetM, tetW, tetO, and tetS: tetracycline resistance ribosomal protection protein" [ARO:3000186;ARO:3000194;ARO:3000190;ARO:3000192] 38 | macA RF0088 gene_206|GeneMark.hmm|435_aa|-|225|1532 - 0.002 9.7 2.1 0.002 9.6 0.1 1.8 2 0 0 2 2 2 1 macA: subunit of efflux pump conferring antibiotic resistance [ARO:3000533] 39 | msbA RF0107 gene_207|GeneMark.hmm|731_aa|-|1537|3732 - 3e-96 315.7 17.6 3.8e-96 315.3 17.6 1.0 1 0 0 1 1 1 1 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 40 | ABC_efflux RF0007 gene_207|GeneMark.hmm|731_aa|-|1537|3732 - 9.3e-64 208.8 7.3 1.2e-63 208.4 7.3 1.1 1 0 0 1 1 1 1 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 41 | macB RF0089 gene_207|GeneMark.hmm|731_aa|-|1537|3732 - 3.9e-26 84.4 0.4 5.5e-26 83.9 0.4 1.1 1 0 0 1 1 1 1 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 42 | ABC_efflux RF0007 gene_312|GeneMark.hmm|204_aa|-|1|612 - 1.4e-26 86.1 0.0 1.5e-26 86.0 0.0 1.0 1 0 0 1 1 1 1 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 43 | msbA RF0107 gene_312|GeneMark.hmm|204_aa|-|1|612 - 2e-25 81.8 0.0 3e-25 81.3 0.0 1.3 1 1 0 1 1 1 1 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 44 | macB RF0089 gene_312|GeneMark.hmm|204_aa|-|1|612 - 8.8e-17 53.5 0.0 1.5e-16 52.8 0.0 1.4 1 1 0 1 1 1 1 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 45 | tet_ribosomoal_protect RF0135 gene_322|GeneMark.hmm|356_aa|-|2299|3369 - 1.7e-20 65.7 0.0 2.2e-20 65.3 0.0 1.0 1 0 0 1 1 1 1 tetracycline resistance ribosomal protection protein: protect RNA-polymerase from tetracycline inhibition [ARO:0000002] 46 | TetM-TetW-TetO-TetS RF0133 gene_322|GeneMark.hmm|356_aa|-|2299|3369 - 4.2e-08 24.7 0.0 5.8e-08 24.2 0.0 1.1 1 0 0 1 1 1 1 "tetM, tetW, tetO, and tetS: tetracycline resistance ribosomal protection protein" [ARO:3000186;ARO:3000194;ARO:3000190;ARO:3000192] 47 | blaR1 RF0043 gene_416|GeneMark.hmm|320_aa|-|987|1949 - 0.00082 10.8 1.7 0.0014 10.1 1.7 1.3 1 0 0 1 1 1 1 "blaR1: gene modulating beta-lactam resistance, regulates PC1 beta-lactamase (blaZ)" [ARO:3000217] 48 | msbA RF0107 gene_425|GeneMark.hmm|80_aa|-|1|240 - 4e-05 14.8 0.0 4.4e-05 14.7 0.0 1.0 1 0 0 1 1 1 1 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 49 | macB RF0089 gene_425|GeneMark.hmm|80_aa|-|1|240 - 0.00076 10.8 0.0 0.00076 10.8 0.0 1.0 1 0 0 1 1 1 1 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 50 | msbA RF0107 gene_435|GeneMark.hmm|587_aa|-|219|1982 - 9.7e-67 218.2 1.1 8.3e-35 112.8 0.0 2.6 2 1 0 2 2 2 2 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 51 | ABC_efflux RF0007 gene_435|GeneMark.hmm|587_aa|-|219|1982 - 9.5e-56 182.3 0.1 1.4e-28 92.7 0.4 2.9 2 1 0 2 2 2 2 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 52 | macB RF0089 gene_435|GeneMark.hmm|587_aa|-|219|1982 - 3.8e-55 180.2 1.1 2.9e-30 98.0 0.2 2.0 2 0 0 2 2 2 2 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 53 | ClassA RF0053 gene_444|GeneMark.hmm|368_aa|-|8629|9735 - 1.2e-06 20.6 0.0 1.1e-05 17.4 0.0 1.9 1 1 1 2 2 2 1 Class A beta-lactamase [ARO:3000078] 54 | MoxA RF0105 gene_444|GeneMark.hmm|368_aa|-|8629|9735 - 2.7e-05 16.3 1.5 5.5e-05 15.3 1.5 1.6 1 1 0 1 1 1 1 MoxA beta-lactamase (class a) [ARO:3001215] 55 | macB RF0089 gene_494|GeneMark.hmm|1061_aa|-|9480|12665 - 0.0001 13.7 0.0 0.0012 10.1 0.0 2.2 2 0 0 2 2 2 2 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 56 | macB RF0089 gene_500|GeneMark.hmm|511_aa|-|18828|20363 - 1.1e-50 165.4 2.7 1.6e-29 95.6 0.3 2.0 1 1 0 2 2 2 2 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 57 | msbA RF0107 gene_500|GeneMark.hmm|511_aa|-|18828|20363 - 2.1e-46 151.1 1.8 1.5e-25 82.3 0.1 2.0 2 0 0 2 2 2 2 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 58 | ABC_efflux RF0007 gene_500|GeneMark.hmm|511_aa|-|18828|20363 - 1.4e-34 112.5 4.4 4.1e-18 58.2 0.5 2.0 2 0 0 2 2 2 2 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 59 | macB RF0089 gene_520|GeneMark.hmm|249_aa|-|37433|38182 - 8e-49 159.3 0.1 9.6e-49 159.0 0.1 1.0 1 0 0 1 1 1 1 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 60 | msbA RF0107 gene_520|GeneMark.hmm|249_aa|-|37433|38182 - 2e-41 134.6 0.0 2.7e-41 134.2 0.0 1.0 1 0 0 1 1 1 1 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 61 | ABC_efflux RF0007 gene_520|GeneMark.hmm|249_aa|-|37433|38182 - 1.8e-30 98.9 0.0 2.2e-30 98.6 0.0 1.0 1 0 0 1 1 1 1 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 62 | soxR RF0121 gene_551|GeneMark.hmm|289_aa|-|256|1125 - 5.4e-11 35.5 0.6 8e-11 34.9 0.6 1.3 1 0 0 1 1 1 1 soxR: mutant efflux regulatory protein conferring antibiotic resistance [ARO:3000836] 63 | macA RF0088 gene_556|GeneMark.hmm|605_aa|+|3980|5797 - 3e-05 15.7 0.7 6.4e-05 14.6 0.7 1.5 1 1 0 1 1 1 1 macA: subunit of efflux pump conferring antibiotic resistance [ARO:3000533] 64 | MFS_efflux RF0104 gene_599|GeneMark.hmm|420_aa|+|558|1820 - 2.1e-11 36.1 19.4 3.6e-11 35.3 19.4 1.4 1 0 0 1 1 1 1 major facilitator superfamily (MFS) antibiotic efflux pump [ARO:0010002] 65 | tet_MFS_efflux RF0134 gene_599|GeneMark.hmm|420_aa|+|558|1820 - 8.3e-10 30.9 27.2 2.1e-09 29.5 27.2 1.5 1 1 0 1 1 1 1 tetracycline resistance MFS efflux pump: selectively pump out tetracycline or tetracycline derivatives [ARO:3000239] 66 | TetA RF0127 gene_599|GeneMark.hmm|420_aa|+|558|1820 - 7.8e-07 21.0 19.6 8.9e-06 17.5 19.8 1.9 1 1 0 1 1 1 1 tetA: tetracycline resistance MFS efflux pump [ARO:3000165] 67 | norA RF0109 gene_599|GeneMark.hmm|420_aa|+|558|1820 - 3.2e-05 16.3 30.9 5.6e-05 15.5 15.7 2.1 1 1 1 2 2 2 2 norA: major facilitator superfamily (MFS) antibiotic efflux pump [ARO:3000391] 68 | tet_ribosomoal_protect RF0135 gene_600|GeneMark.hmm|652_aa|+|1804|3762 - 4.6e-284 936.4 5.0 5.4e-284 936.2 5.0 1.0 1 0 0 1 1 1 1 tetracycline resistance ribosomal protection protein: protect RNA-polymerase from tetracycline inhibition [ARO:0000002] 69 | TetM-TetW-TetO-TetS RF0133 gene_600|GeneMark.hmm|652_aa|+|1804|3762 - 5.5e-163 536.3 1.1 6.2e-163 536.2 1.1 1.0 1 0 0 1 1 1 1 "tetM, tetW, tetO, and tetS: tetracycline resistance ribosomal protection protein" [ARO:3000186;ARO:3000194;ARO:3000190;ARO:3000192] 70 | vanS RF0155 gene_618|GeneMark.hmm|409_aa|-|8572|9801 - 9.1e-55 179.0 19.7 3.9e-53 173.6 19.7 2.3 1 1 0 1 1 1 1 VanS: trasncriptional regulator of van glycopeptide resistance genes [ARO:3000071] 71 | adeS RF0023 gene_618|GeneMark.hmm|409_aa|-|8572|9801 - 2.7e-27 88.6 4.1 3.7e-27 88.2 1.2 2.1 1 1 1 2 2 2 1 adeS: gene modulating antibiotic efflux regulating AdeABC [ARO:3000549] 72 | baeS RF0036 gene_618|GeneMark.hmm|409_aa|-|8572|9801 - 2.8e-26 84.7 0.0 4.9e-26 83.9 0.0 1.3 1 0 0 1 1 1 1 baeS: subunit of gene modulating antibiotic efflux [ARO:3000829] 73 | phoQ RF0112 gene_618|GeneMark.hmm|409_aa|-|8572|9801 - 2.4e-08 25.9 0.3 6.3e-08 24.5 0.0 1.7 2 0 0 2 2 2 1 phoQ: subunit of gene modulating antibiotic efflux [ARO:3000835] 74 | vanR RF0154 gene_619|GeneMark.hmm|222_aa|-|9815|10483 - 1.9e-69 226.5 1.1 2.2e-69 226.3 1.1 1.0 1 0 0 1 1 1 1 "VanR: transcriptional activator regulating VanA, VanH and VanX" [ARO:3000574] 75 | baeR RF0035 gene_619|GeneMark.hmm|222_aa|-|9815|10483 - 4.6e-49 159.7 0.3 6e-49 159.3 0.3 1.0 1 0 0 1 1 1 1 baeR: subunit of gene modulating antibiotic efflux [ARO:3000828] 76 | adeR RF0022 gene_619|GeneMark.hmm|222_aa|-|9815|10483 - 1e-39 129.4 1.6 1.1e-39 129.3 1.6 1.0 1 0 0 1 1 1 1 adeR: positive regulator of AdeABC efflux system [ARO:3000553] 77 | tet_ribosomoal_protect RF0135 gene_625|GeneMark.hmm|611_aa|+|17999|19834 - 2.7e-51 167.4 0.1 3.6e-39 127.3 0.1 3.1 2 1 1 3 3 3 3 tetracycline resistance ribosomal protection protein: protect RNA-polymerase from tetracycline inhibition [ARO:0000002] 78 | TetM-TetW-TetO-TetS RF0133 gene_625|GeneMark.hmm|611_aa|+|17999|19834 - 5.8e-34 110.1 0.0 4.8e-31 100.4 0.0 2.9 2 1 1 3 3 3 3 "tetM, tetW, tetO, and tetS: tetracycline resistance ribosomal protection protein" [ARO:3000186;ARO:3000194;ARO:3000190;ARO:3000192] 79 | vanR RF0154 gene_631|GeneMark.hmm|253_aa|-|23774|24535 - 1.2e-18 60.3 9.1 1.6e-18 59.9 9.1 1.1 1 0 0 1 1 1 1 "VanR: transcriptional activator regulating VanA, VanH and VanX" [ARO:3000574] 80 | baeR RF0035 gene_631|GeneMark.hmm|253_aa|-|23774|24535 - 5.8e-16 51.4 2.3 7e-16 51.1 2.3 1.1 1 0 0 1 1 1 1 baeR: subunit of gene modulating antibiotic efflux [ARO:3000828] 81 | adeR RF0022 gene_631|GeneMark.hmm|253_aa|-|23774|24535 - 1.1e-10 34.3 15.0 1.4e-10 34.0 15.0 1.1 1 0 0 1 1 1 1 adeR: positive regulator of AdeABC efflux system [ARO:3000553] 82 | vanS RF0155 gene_646|GeneMark.hmm|431_aa|+|35911|37206 - 2.3e-12 39.4 0.5 2.3e-12 39.4 0.5 2.1 2 0 0 2 2 2 1 VanS: trasncriptional regulator of van glycopeptide resistance genes [ARO:3000071] 83 | phoQ RF0112 gene_646|GeneMark.hmm|431_aa|+|35911|37206 - 3e-08 25.5 0.1 2.2e-05 16.1 0.0 2.1 2 0 0 2 2 2 2 phoQ: subunit of gene modulating antibiotic efflux [ARO:3000835] 84 | vanR RF0154 gene_647|GeneMark.hmm|280_aa|+|37208|38050 - 3.6e-12 39.1 0.9 5.2e-12 38.6 0.9 1.2 1 0 0 1 1 1 1 "VanR: transcriptional activator regulating VanA, VanH and VanX" [ARO:3000574] 85 | baeR RF0035 gene_647|GeneMark.hmm|280_aa|+|37208|38050 - 3e-08 26.2 0.1 3.7e-08 25.8 0.1 1.3 1 0 0 1 1 1 1 baeR: subunit of gene modulating antibiotic efflux [ARO:3000828] 86 | tet_ribosomoal_protect RF0135 gene_656|GeneMark.hmm|394_aa|-|10530|11714 - 7.6e-23 73.4 0.1 9.9e-23 73.0 0.1 1.1 1 0 0 1 1 1 1 tetracycline resistance ribosomal protection protein: protect RNA-polymerase from tetracycline inhibition [ARO:0000002] 87 | TetM-TetW-TetO-TetS RF0133 gene_656|GeneMark.hmm|394_aa|-|10530|11714 - 3.6e-22 71.1 0.0 4.7e-22 70.7 0.0 1.1 1 0 0 1 1 1 1 "tetM, tetW, tetO, and tetS: tetracycline resistance ribosomal protection protein" [ARO:3000186;ARO:3000194;ARO:3000190;ARO:3000192] 88 | vanT RF0156 gene_692|GeneMark.hmm|387_aa|-|246|1409 - 2.5e-68 224.0 5.4 3e-68 223.7 5.4 1.0 1 0 0 1 1 1 1 "VanT: membrane bound serine racemase, converting L-serine to D-serine" [ARO:3000372] 89 | RND_efflux RF0115 gene_696|GeneMark.hmm|155_aa|+|1366|1833 - 0.00043 11.2 0.8 0.00046 11.1 0.8 1.0 1 0 0 1 1 1 1 resistance-nodulation-cell division (RND) antibiotic efflux pump [ARO:0010004] 90 | TetX RF0136 gene_735|GeneMark.hmm|75_aa|-|3|227 - 0.00025 13.0 0.0 0.00025 13.0 0.0 1.0 1 0 0 1 1 1 1 tetX: tetracycline inactivation enzyme [ARO:3000205] 91 | TE_Inactivator RF0168 gene_736|GeneMark.hmm|560_aa|-|220|1902 - 0.00013 13.9 0.0 0.00024 13.0 0.0 1.3 1 0 0 1 1 1 1 Legionella_TE_Inactivator 92 | TetX RF0136 gene_736|GeneMark.hmm|560_aa|-|220|1902 - 0.00033 12.6 0.0 0.00057 11.8 0.0 1.3 1 0 0 1 1 1 1 tetX: tetracycline inactivation enzyme [ARO:3000205] 93 | ABC_efflux RF0007 gene_741|GeneMark.hmm|515_aa|-|4400|5947 - 3.4e-39 127.7 4.4 6.7e-22 70.6 0.2 3.4 2 2 0 2 2 2 2 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 94 | msbA RF0107 gene_741|GeneMark.hmm|515_aa|-|4400|5947 - 2.3e-28 91.5 1.2 1.8e-09 29.1 0.1 4.1 4 0 0 4 4 4 4 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 95 | macB RF0089 gene_741|GeneMark.hmm|515_aa|-|4400|5947 - 1.9e-17 55.8 0.8 2.8e-06 18.9 0.0 4.1 3 1 1 4 4 4 4 macB: subunit of efflux pump conferring antibiotic resistance [ARO:3000535] 96 | msbA RF0107 gene_757|GeneMark.hmm|198_aa|-|2|595 - 3.2e-15 48.1 10.3 3.8e-15 47.9 10.3 1.0 1 0 0 1 1 1 1 msbA: ATP-binding cassette (ABC) antibiotic efflux pump [ARO:3000460] 97 | ABC_efflux RF0007 gene_757|GeneMark.hmm|198_aa|-|2|595 - 2.7e-09 29.1 5.7 3.3e-09 28.8 5.7 1.0 1 0 0 1 1 1 1 ATP-binding cassette (ABC) antibiotic efflux pump [ARO:0010001] 98 | marA RF0091 gene_766|GeneMark.hmm|290_aa|-|1378|2250 - 2.5e-08 27.1 0.1 4.9e-08 26.2 0.1 1.4 1 0 0 1 1 1 1 marA: transcription factor induces MDR efflux pump AcrAB [ARO:3000263] 99 | robA RF0116 gene_766|GeneMark.hmm|290_aa|-|1378|2250 - 2.6e-08 26.5 0.0 4.1e-08 25.8 0.0 1.2 1 0 0 1 1 1 1 robA: transcriptional activator of AcrAB antibiotic efflux pump [ARO:3000825] 100 | ramA RF0114 gene_766|GeneMark.hmm|290_aa|-|1378|2250 - 2.8e-07 23.6 0.0 5.3e-07 22.7 0.0 1.4 1 0 0 1 1 1 1 ramA: gene modulating antibiotic efflux [ARO:3000823] 101 | # 102 | # Program: hmmscan 103 | # Version: 3.3.2 (Nov 2020) 104 | # Pipeline mode: SCAN 105 | # Query file: clean_protein.fasta 106 | # Target file: /datos/vberrios/resfams_db/Resfams.hmm 107 | # Option settings: hmmscan --tblout SLF2_tblout.scan /datos/vberrios/resfams_db/Resfams.hmm clean_protein.fasta 108 | # Current dir: /datos/vberrios/sea_lions/filtered/refiltered/assemblies/FP.SLF2/protein_fasta 109 | # Date: Mon Jul 19 02:38:51 2021 110 | # [ok] 111 | -------------------------------------------------------------------------------- /tests/testthat/sample-data/five/log: -------------------------------------------------------------------------------- 1 | # hmmscan :: search sequence(s) against a profile database 2 | # HMMER 3.1b2 (February 2015); http://hmmer.org/ 3 | # Copyright (C) 2015 Howard Hughes Medical Institute. 4 | # Freely distributed under the GNU General Public License (GPLv3). 5 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 6 | # query sequence file: five.faa 7 | # target HMM database: /home/z/db/Pfam-A.hmm 8 | # per-seq hits tabular output: x.tblout 9 | # per-dom hits tabular output: x.domtblout 10 | # pfam-style tabular hit output: x.pfamtblout 11 | # show alignments in output: no 12 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 13 | 14 | Query: AT2G18240.1 [L=221] 15 | Scores for complete sequence (score includes all domains): 16 | --- full sequence --- --- best 1 domain --- -#dom- 17 | E-value score bias E-value score bias exp N Model Description 18 | ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 19 | 2.3e-61 206.4 10.4 7.1e-61 204.8 11.2 1.3 2 Rer1 Rer1 family 20 | 21 | 22 | Domain annotation for each model: 23 | >> Rer1 Rer1 family 24 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 25 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 26 | 1 ! 204.8 11.2 4.3e-65 7.1e-61 4 168 .. 24 181 .. 21 183 .. 0.96 27 | 2 ? -3.6 0.0 0.43 7.2e+03 55 67 .. 187 199 .. 184 217 .. 0.69 28 | 29 | 30 | 31 | Internal pipeline statistics summary: 32 | ------------------------------------- 33 | Query sequence(s): 1 (221 residues searched) 34 | Target model(s): 16712 (2907032 nodes) 35 | Passed MSV filter: 613 (0.0366802); expected 334.2 (0.02) 36 | Passed bias filter: 260 (0.0155577); expected 334.2 (0.02) 37 | Passed Vit filter: 14 (0.000837721); expected 16.7 (0.001) 38 | Passed Fwd filter: 1 (5.98372e-05); expected 0.2 (1e-05) 39 | Initial search space (Z): 16712 [actual number of targets] 40 | Domain search space (domZ): 1 [number of targets reported over threshold] 41 | # CPU time: 0.27u 0.17s 00:00:00.44 Elapsed: 00:00:00.26 42 | # Mc/sec: 2470.98 43 | // 44 | Query: AT5G45530.1 [L=798] 45 | Scores for complete sequence (score includes all domains): 46 | --- full sequence --- --- best 1 domain --- -#dom- 47 | E-value score bias E-value score bias exp N Model Description 48 | ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 49 | 4.6e-78 263.0 0.0 1.3e-77 261.5 0.0 1.7 1 DUF4220 Domain of unknown function (DUF4220) 50 | 4.7e-24 83.6 1.5 1.1e-23 82.4 1.5 1.7 1 DUF594 Protein of unknown function, DUF594 51 | 52 | 53 | Domain annotation for each model: 54 | >> DUF4220 Domain of unknown function (DUF4220) 55 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 56 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 57 | 1 ! 261.5 0.0 1.5e-81 1.3e-77 1 344 [. 51 396 .. 51 427 .. 0.78 58 | 59 | >> DUF594 Protein of unknown function, DUF594 60 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 61 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 62 | 1 ! 82.4 1.5 1.3e-27 1.1e-23 3 55 .] 726 778 .. 724 778 .. 0.96 63 | 64 | 65 | 66 | Internal pipeline statistics summary: 67 | ------------------------------------- 68 | Query sequence(s): 1 (798 residues searched) 69 | Target model(s): 16712 (2907032 nodes) 70 | Passed MSV filter: 574 (0.0343466); expected 334.2 (0.02) 71 | Passed bias filter: 439 (0.0262685); expected 334.2 (0.02) 72 | Passed Vit filter: 36 (0.00215414); expected 16.7 (0.001) 73 | Passed Fwd filter: 2 (0.000119674); expected 0.2 (1e-05) 74 | Initial search space (Z): 16712 [actual number of targets] 75 | Domain search space (domZ): 2 [number of targets reported over threshold] 76 | # CPU time: 0.41u 0.13s 00:00:00.54 Elapsed: 00:00:00.22 77 | # Mc/sec: 10544.60 78 | // 79 | Query: AT1G27880.2 [L=890] 80 | Scores for complete sequence (score includes all domains): 81 | --- full sequence --- --- best 1 domain --- -#dom- 82 | E-value score bias E-value score bias exp N Model Description 83 | ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 84 | 6.7e-20 71.5 0.1 1.9e-19 70.0 0.1 1.8 1 DEAD DEAD/DEAH box helicase 85 | 3.2e-18 66.0 0.0 3e-17 62.9 0.0 2.5 2 Helicase_C Helicase conserved C-terminal domain 86 | 0.0012 18.8 0.1 0.0084 16.0 0.0 2.4 2 ResIII Type III restriction enzyme, res subunit 87 | 88 | 89 | Domain annotation for each model: 90 | >> DEAD DEAD/DEAH box helicase 91 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 92 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 93 | 1 ! 70.0 0.1 3.4e-23 1.9e-19 2 171 .. 272 433 .. 271 438 .. 0.83 94 | 95 | >> Helicase_C Helicase conserved C-terminal domain 96 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 97 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 98 | 1 ? -0.7 0.0 0.31 1.7e+03 21 72 .. 314 364 .. 307 367 .. 0.74 99 | 2 ! 62.9 0.0 5.4e-21 3e-17 15 110 .. 485 580 .. 470 581 .. 0.91 100 | 101 | >> ResIII Type III restriction enzyme, res subunit 102 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 103 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 104 | 1 ? -3.7 0.1 1.7 9.4e+03 102 123 .. 214 232 .. 188 256 .. 0.54 105 | 2 ! 16.0 0.0 1.5e-06 0.0084 4 169 .. 270 430 .. 268 432 .. 0.74 106 | 107 | 108 | 109 | Internal pipeline statistics summary: 110 | ------------------------------------- 111 | Query sequence(s): 1 (890 residues searched) 112 | Target model(s): 16712 (2907032 nodes) 113 | Passed MSV filter: 650 (0.0388942); expected 334.2 (0.02) 114 | Passed bias filter: 380 (0.0227382); expected 334.2 (0.02) 115 | Passed Vit filter: 26 (0.00155577); expected 16.7 (0.001) 116 | Passed Fwd filter: 4 (0.000239349); expected 0.2 (1e-05) 117 | Initial search space (Z): 16712 [actual number of targets] 118 | Domain search space (domZ): 3 [number of targets reported over threshold] 119 | # CPU time: 0.45u 0.11s 00:00:00.56 Elapsed: 00:00:00.22 120 | # Mc/sec: 11760.27 121 | // 122 | Query: AT1G56520.1 [L=897] 123 | Scores for complete sequence (score includes all domains): 124 | --- full sequence --- --- best 1 domain --- -#dom- 125 | E-value score bias E-value score bias exp N Model Description 126 | ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 127 | 7.3e-46 156.1 0.0 1.2e-45 155.3 0.0 1.4 1 TIR TIR domain 128 | 1.9e-17 63.1 0.0 3.5e-17 62.3 0.0 1.4 1 NB-ARC NB-ARC domain 129 | 1e-07 31.4 1.1 1e-07 31.4 1.1 2.7 2 LRR_3 Leucine Rich Repeat 130 | 2.3e-07 30.4 7.0 0.0048 16.5 0.0 5.5 6 LRR_8 Leucine rich repeat 131 | 2.7e-07 30.6 17.6 0.0047 17.2 0.2 6.1 5 LRR_4 Leucine Rich repeats (2 copies) 132 | 2.6e-05 24.4 0.1 9.3e-05 22.6 0.0 1.9 2 TIR_2 TIR domain 133 | 0.0002 21.7 0.3 0.00077 19.8 0.3 2.0 1 AAA_16 AAA ATPase domain 134 | 0.001 19.5 0.0 0.0024 18.3 0.0 1.7 1 AAA_18 AAA domain 135 | 0.0048 17.1 1.0 0.024 14.8 1.0 2.1 1 AAA_22 AAA domain 136 | ------ inclusion threshold ------ 137 | 0.015 15.1 0.0 0.046 13.5 0.0 1.8 1 ATPase_2 ATPase domain predominantly from Archaea 138 | 0.028 13.8 1.1 3.5 6.9 0.2 2.3 2 PhoH PhoH-like protein 139 | 0.029 14.2 0.0 0.057 13.2 0.0 1.5 1 NACHT NACHT domain 140 | 0.039 14.4 0.0 0.34 11.3 0.0 2.3 2 AAA_23 AAA domain 141 | 0.044 14.2 0.0 0.095 13.1 0.0 1.5 1 ABC_tran ABC transporter 142 | 0.062 13.1 0.0 0.16 11.8 0.0 1.7 1 NTPase_1 NTPase 143 | 0.079 12.6 0.1 1.3 8.7 0.1 2.3 2 AAA_29 P-loop containing region of AAA domain 144 | 0.15 12.6 14.8 24 5.9 0.0 7.8 8 LRR_1 Leucine Rich Repeat 145 | 146 | 147 | Domain annotation for each model: 148 | >> TIR TIR domain 149 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 150 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 151 | 1 ! 155.3 0.0 1.3e-48 1.2e-45 2 164 .. 13 179 .. 12 189 .. 0.95 152 | 153 | >> NB-ARC NB-ARC domain 154 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 155 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 156 | 1 ! 62.3 0.0 3.6e-20 3.5e-17 4 262 .. 192 440 .. 189 456 .. 0.78 157 | 158 | >> LRR_3 Leucine Rich Repeat 159 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 160 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 161 | 1 ! 31.4 1.1 1e-10 1e-07 1 20 [] 603 622 .. 603 622 .. 0.98 162 | 2 ? -0.6 0.5 1.3 1.3e+03 1 14 [. 626 640 .. 626 641 .. 0.79 163 | 164 | >> LRR_8 Leucine rich repeat 165 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 166 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 167 | 1 ? -0.6 0.0 1.1 1.1e+03 15 31 .. 544 560 .. 535 561 .. 0.88 168 | 2 ! 8.8 0.3 0.0013 1.3 2 58 .. 603 657 .. 602 661 .. 0.90 169 | 3 ! 6.6 0.2 0.0064 6.2 2 59 .. 626 682 .. 625 683 .. 0.88 170 | 4 ? 2.6 0.1 0.11 1.1e+02 2 57 .. 649 703 .. 648 706 .. 0.66 171 | 5 ! 16.5 0.0 4.9e-06 0.0048 2 60 .. 717 772 .. 716 773 .. 0.87 172 | 6 ! 8.2 0.1 0.002 2 27 59 .. 763 794 .. 760 795 .. 0.70 173 | 174 | >> LRR_4 Leucine Rich repeats (2 copies) 175 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 176 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 177 | 1 ? -2.6 0.0 8.4 8.3e+03 19 33 .. 550 563 .. 535 566 .. 0.71 178 | 2 ! 7.2 0.1 0.0066 6.5 2 33 .. 626 658 .. 625 671 .. 0.81 179 | 3 ? 6.6 0.3 0.01 10 12 38 .. 684 711 .. 649 715 .. 0.56 180 | 4 ! 9.1 0.0 0.0017 1.6 1 39 [. 716 756 .. 716 760 .. 0.88 181 | 5 ! 17.2 0.2 4.8e-06 0.0047 3 42 .. 763 804 .. 762 805 .. 0.90 182 | 183 | >> TIR_2 TIR domain 184 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 185 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 186 | 1 ! 22.6 0.0 9.5e-08 9.3e-05 1 85 [. 15 101 .. 15 120 .. 0.79 187 | 2 ? -2.5 0.1 6.1 6e+03 16 55 .. 257 295 .. 256 296 .. 0.80 188 | 189 | >> AAA_16 AAA ATPase domain 190 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 191 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 192 | 1 ! 19.8 0.3 7.8e-07 0.00077 3 63 .. 187 243 .. 186 319 .. 0.74 193 | 194 | >> AAA_18 AAA domain 195 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 196 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 197 | 1 ! 18.3 0.0 2.4e-06 0.0024 1 69 [. 210 274 .. 210 332 .. 0.69 198 | 199 | >> AAA_22 AAA domain 200 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 201 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 202 | 1 ! 14.8 1.0 2.4e-05 0.024 7 113 .. 209 312 .. 204 324 .. 0.64 203 | 204 | >> ATPase_2 ATPase domain predominantly from Archaea 205 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 206 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 207 | 1 ? 13.5 0.0 4.7e-05 0.046 8 82 .. 193 265 .. 190 311 .. 0.64 208 | 209 | >> PhoH PhoH-like protein 210 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 211 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 212 | 1 ? 6.9 0.2 0.0036 3.5 18 39 .. 206 227 .. 192 251 .. 0.82 213 | 2 ? 5.3 0.0 0.011 11 87 161 .. 257 332 .. 240 341 .. 0.85 214 | 215 | >> NACHT NACHT domain 216 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 217 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 218 | 1 ? 13.2 0.0 5.8e-05 0.057 3 95 .. 210 304 .. 208 336 .. 0.81 219 | 220 | >> AAA_23 AAA domain 221 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 222 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 223 | 1 ? 11.3 0.0 0.00035 0.34 20 50 .. 208 238 .. 192 284 .. 0.80 224 | 2 ? -0.5 0.0 1.4 1.4e+03 118 143 .. 818 843 .. 811 864 .. 0.84 225 | 226 | >> ABC_tran ABC transporter 227 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 228 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 229 | 1 ? 13.1 0.0 9.6e-05 0.095 12 36 .. 208 232 .. 200 276 .. 0.89 230 | 231 | >> NTPase_1 NTPase 232 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 233 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 234 | 1 ? 11.8 0.0 0.00016 0.16 2 87 .. 210 293 .. 209 303 .. 0.79 235 | 236 | >> AAA_29 P-loop containing region of AAA domain 237 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 238 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 239 | 1 ? 8.7 0.1 0.0013 1.3 18 42 .. 201 227 .. 194 232 .. 0.80 240 | 2 ? 0.9 0.0 0.36 3.5e+02 3 25 .. 583 606 .. 582 608 .. 0.86 241 | 242 | >> LRR_1 Leucine Rich Repeat 243 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 244 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 245 | 1 ? -1.9 0.0 8.6 8.5e+03 1 13 [. 603 615 .. 603 621 .. 0.83 246 | 2 ? 0.1 0.1 1.9 1.9e+03 1 12 [. 626 637 .. 626 647 .. 0.70 247 | 3 ? 1.4 0.0 0.71 7e+02 1 21 [. 649 669 .. 649 671 .. 0.73 248 | 4 ? 3.1 0.0 0.19 1.9e+02 1 13 [. 696 728 .. 696 738 .. 0.61 249 | 5 ? -1.5 0.0 6.4 6.2e+03 3 13 .. 742 752 .. 741 760 .. 0.71 250 | 6 ? 5.9 0.0 0.024 24 2 12 .. 763 773 .. 762 783 .. 0.82 251 | 7 ? 3.3 0.3 0.17 1.6e+02 1 16 [. 785 800 .. 785 818 .. 0.75 252 | 8 ? -1.0 0.0 4.4 4.3e+03 8 21 .. 874 886 .. 866 888 .. 0.77 253 | 254 | 255 | 256 | Internal pipeline statistics summary: 257 | ------------------------------------- 258 | Query sequence(s): 1 (897 residues searched) 259 | Target model(s): 16712 (2907032 nodes) 260 | Passed MSV filter: 446 (0.0266874); expected 334.2 (0.02) 261 | Passed bias filter: 384 (0.0229775); expected 334.2 (0.02) 262 | Passed Vit filter: 71 (0.00424844); expected 16.7 (0.001) 263 | Passed Fwd filter: 17 (0.00101723); expected 0.2 (1e-05) 264 | Initial search space (Z): 16712 [actual number of targets] 265 | Domain search space (domZ): 17 [number of targets reported over threshold] 266 | # CPU time: 0.47u 0.14s 00:00:00.61 Elapsed: 00:00:00.22 267 | # Mc/sec: 11852.76 268 | // 269 | Query: AT3G10370.1 [L=629] 270 | Scores for complete sequence (score includes all domains): 271 | --- full sequence --- --- best 1 domain --- -#dom- 272 | E-value score bias E-value score bias exp N Model Description 273 | ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 274 | 3.2e-53 181.4 0.1 8.6e-53 180.1 0.0 1.6 2 DAO FAD dependent oxidoreductase 275 | 9e-39 132.1 0.3 1.6e-38 131.3 0.3 1.4 1 DAO_C C-terminal domain of alpha-glycerophosphate ox 276 | 6.3e-07 28.7 1.9 0.0023 17.0 1.2 2.3 2 FAD_binding_2 FAD binding domain 277 | 0.0001 21.7 1.1 0.00043 19.7 0.3 2.2 2 FAD_oxidored FAD dependent oxidoreductase 278 | ------ inclusion threshold ------ 279 | 0.014 14.6 0.0 0.031 13.4 0.0 1.5 1 Pyr_redox_2 Pyridine nucleotide-disulphide oxidoreductase 280 | 0.015 14.5 0.2 0.39 9.8 0.5 2.1 2 FAD_binding_3 FAD binding domain 281 | 0.036 13.0 0.2 0.23 10.4 0.1 2.0 2 GIDA Glucose inhibited division protein A 282 | 0.063 13.8 0.7 0.28 11.7 0.7 2.1 1 Pyr_redox Pyridine nucleotide-disulphide oxidoreductase 283 | 0.075 11.6 0.2 0.15 10.6 0.2 1.5 1 HI0933_like HI0933-like protein 284 | 0.077 12.6 0.6 0.17 11.5 0.0 1.9 2 AAA_30 AAA domain 285 | 0.1 11.7 0.0 0.18 10.9 0.0 1.3 1 Pyr_redox_3 Pyridine nucleotide-disulphide oxidoreductase 286 | 0.18 12.2 0.9 0.71 10.3 0.0 2.2 2 DUF4179 Domain of unknown function (DUF4179) 287 | 0.31 10.8 2.0 0.36 10.6 0.2 2.0 2 3HCDH_N 3-hydroxyacyl-CoA dehydrogenase, NAD binding d 288 | 1.4 9.1 5.0 0.32 11.2 0.6 2.3 2 NAD_binding_8 NAD(P)-binding Rossmann-like domain 289 | 290 | 291 | Domain annotation for each model: 292 | >> DAO FAD dependent oxidoreductase 293 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 294 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 295 | 1 ! 180.1 0.0 7.2e-56 8.6e-53 1 351 [. 75 442 .. 75 443 .. 0.80 296 | 2 ? -1.8 0.1 1.4 1.7e+03 68 106 .. 554 590 .. 538 626 .. 0.61 297 | 298 | >> DAO_C C-terminal domain of alpha-glycerophosphate oxidase 299 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 300 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 301 | 1 ! 131.3 0.3 1.3e-41 1.6e-38 1 125 [. 465 600 .. 465 601 .. 0.98 302 | 303 | >> FAD_binding_2 FAD binding domain 304 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 305 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 306 | 1 ! 17.0 1.2 1.9e-06 0.0023 1 41 [. 75 115 .. 75 124 .. 0.94 307 | 2 ! 10.1 0.0 0.00024 0.29 154 213 .. 247 307 .. 226 320 .. 0.82 308 | 309 | >> FAD_oxidored FAD dependent oxidoreductase 310 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 311 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 312 | 1 ! 19.7 0.3 3.6e-07 0.00043 1 40 [. 75 114 .. 75 142 .. 0.93 313 | 2 ? -0.1 0.0 0.34 4.1e+02 100 143 .. 247 294 .. 214 296 .. 0.85 314 | 315 | >> Pyr_redox_2 Pyridine nucleotide-disulphide oxidoreductase 316 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 317 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 318 | 1 ? 13.4 0.0 2.6e-05 0.031 2 36 .. 75 108 .. 59 151 .. 0.78 319 | 320 | >> FAD_binding_3 FAD binding domain 321 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 322 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 323 | 1 ? 9.8 0.5 0.00033 0.39 3 51 .. 75 124 .. 73 131 .. 0.84 324 | 2 ? 2.2 0.0 0.069 83 117 179 .. 240 306 .. 228 401 .. 0.67 325 | 326 | >> GIDA Glucose inhibited division protein A 327 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 328 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 329 | 1 ? 10.4 0.1 0.00019 0.23 1 29 [. 75 103 .. 75 134 .. 0.87 330 | 2 ? 0.0 0.0 0.27 3.3e+02 110 159 .. 257 305 .. 249 311 .. 0.58 331 | 332 | >> Pyr_redox Pyridine nucleotide-disulphide oxidoreductase 333 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 334 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 335 | 1 ? 11.7 0.7 0.00023 0.28 2 32 .. 76 106 .. 75 111 .. 0.96 336 | 337 | >> HI0933_like HI0933-like protein 338 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 339 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 340 | 1 ? 10.6 0.2 0.00012 0.15 2 32 .. 75 105 .. 74 109 .. 0.94 341 | 342 | >> AAA_30 AAA domain 343 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 344 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 345 | 1 ? -2.7 0.1 3.1 3.7e+03 5 39 .. 60 94 .. 58 98 .. 0.57 346 | 2 ? 11.5 0.0 0.00014 0.17 32 81 .. 484 533 .. 455 559 .. 0.88 347 | 348 | >> Pyr_redox_3 Pyridine nucleotide-disulphide oxidoreductase 349 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 350 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 351 | 1 ? 10.9 0.0 0.00015 0.18 166 220 .. 75 128 .. 58 151 .. 0.73 352 | 353 | >> DUF4179 Domain of unknown function (DUF4179) 354 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 355 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 356 | 1 ? 10.3 0.0 0.00059 0.71 5 37 .. 5 40 .. 2 63 .. 0.82 357 | 2 ? -0.6 0.1 1.5 1.8e+03 10 57 .. 243 290 .. 235 300 .. 0.50 358 | 359 | >> 3HCDH_N 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 360 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 361 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 362 | 1 ? 10.6 0.2 0.0003 0.36 2 32 .. 76 106 .. 75 131 .. 0.85 363 | 2 ? -1.8 0.1 1.9 2.2e+03 30 65 .. 578 613 .. 560 623 .. 0.45 364 | 365 | >> NAD_binding_8 NAD(P)-binding Rossmann-like domain 366 | # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc 367 | --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 368 | 1 ? 11.2 0.6 0.00027 0.32 1 42 [. 78 122 .. 78 145 .. 0.83 369 | 2 ? -2.4 0.0 4.6 5.5e+03 31 40 .. 435 444 .. 420 454 .. 0.73 370 | 371 | 372 | 373 | Internal pipeline statistics summary: 374 | ------------------------------------- 375 | Query sequence(s): 1 (629 residues searched) 376 | Target model(s): 16712 (2907032 nodes) 377 | Passed MSV filter: 741 (0.0443394); expected 334.2 (0.02) 378 | Passed bias filter: 596 (0.035663); expected 334.2 (0.02) 379 | Passed Vit filter: 63 (0.00376975); expected 16.7 (0.001) 380 | Passed Fwd filter: 14 (0.000837721); expected 0.2 (1e-05) 381 | Initial search space (Z): 16712 [actual number of targets] 382 | Domain search space (domZ): 14 [number of targets reported over threshold] 383 | # CPU time: 0.45u 0.08s 00:00:00.53 Elapsed: 00:00:00.22 384 | # Mc/sec: 8311.47 385 | // 386 | [ok] 387 | --------------------------------------------------------------------------------