| Next changeset 1:7fdfbf042ec6 (2020-04-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 69cfb20d049ddeccef197865cc07eac5363ea8ea |
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added:
meta_proteome_analyzer.xml test-data/Test416Ebendorf.mgf test-data/searchdb.fa |
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| diff -r 000000000000 -r bea389f80d87 meta_proteome_analyzer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meta_proteome_analyzer.xml Sat Mar 04 07:00:01 2017 -0500 |
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| b'@@ -0,0 +1,181 @@\n+<tool id="meta_proteome_analyzer" name="MetaProteomeAnalyzer" version="1.4.1">\n+ <description>\n+ functional and taxonomic characterization of proteins\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="1.4.1">mpa-portable</requirement>\n+ </requirements>\n+ <command>\n+<![CDATA[\n+ #set $temp_stderr = "mpa_stderr"\n+\n+ cwd=`pwd` &&\n+ mkdir -p output_dir &&\n+ ## copy mpa conf dir to working dir\n+ jar_dir=`mpa-portable -get_jar_dir` &&\n+ cp -R \\$jar_dir/conf . &&\n+\n+ ## echo the search engines to run\n+ #set $search_engines = str($search_engines_options.engines).split(\',\')\n+ echo "$search_engines_options.engines" &&\n+ echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}" &&\n+\n+ #for $mgf in $peak_lists:\n+ #set $input_name = $mgf.display_name.split(\'/\')[-1].replace(".mgf", "") + ".mgf"\n+ ln -s -f \'${mgf}\' \'${input_name}\' &&\n+ #set $encoded_id = $__app__.security.encode_id($mgf.id)\n+ echo "Spectrums:${mgf.display_name}(API:${encoded_id}) " &&\n+ #end for\n+ cp "${input_database}" input_database.fasta &&\n+\n+ ######################\n+ ## MPA ##\n+ ######################\n+ (mpa-portable de.mpa.cli.CmdLineInterface -Djava.awt.headless=true -Xmx2048m\n+ -spectrum_files \\$cwd\n+ -database input_database.fasta\n+ -missed_cleav $missed_cleavages\n+ -prec_tol ${precursor_options.prec_tol}${precursor_options.prec_tol_units}\n+ -frag_tol ${precursor_options.frag_tol}Da\n+ -xtandem #if \'X!Tandem\' in $search_engines then 1 else 0#\n+ -comet #if \'Comet\' in $search_engines then 1 else 0#\n+ -msgf #if \'MSGF\' in $search_engines then 1 else 0#\n+ -output_folder output_dir\n+ -threads "\\${GALAXY_SLOTS:-12}"\n+ 2> $temp_stderr) &&\n+ mv ./output_dir/*_metaproteins.csv metaproteins.csv &&\n+ mv ./output_dir/*_metaprotein_taxa.csv metaprotein_taxa.csv &&\n+ mv ./output_dir/*_peptides.csv peptides.csv &&\n+ mv ./output_dir/*_proteins.csv proteins.csv &&\n+ mv ./output_dir/*_psms.csv psms.csv &&\n+ mv ./output_dir/*_spectrum_ids.csv spectrum_ids.csv &&\n+ exit_code_for_galaxy=\\$? &&\n+ cat $temp_stderr 2>&1 &&\n+ (exit \\$exit_code_for_galaxy)\n+ \n+]]>\n+ </command>\n+ <inputs>\n+ <param format="fasta" name="input_database" type="data" label="Protein Database"\n+ help="Select FASTA database from history"/>\n+ <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"\n+ help="Select appropriate MGF dataset(s) from history" />\n+ <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"\n+ help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>\n+ <section name="precursor_options" expanded="false" title="Precursor Options">\n+ <param name="prec_tol_units" type="select" label="Precursor Ion Tolerance Units"\n+ help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">\n+ <option value="ppm">Parts per million (ppm)</option>\n+ <option value="Da">Daltons</option>\n+ </param>\n+ <param name="prec_tol" type="float" value="10" label="Percursor Ion Tolerance"\n+ help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>\n+ <param name="frag_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"\n+ help="Provide error value for fragment ions, based on instrument used"/>\n+ </section>\n+ <!-- Search Engine Selection -->\n+ '..b',Sequence_Coverage,Peptide_Count,NSAF,emPAI,Spectral_Count,Isoelectric_Point,Molecular_Weight,Protein_Sequence,Peptides" />\n+ </actions>\n+ </data>\n+ <data format="tabular" name="output_peptides" from_work_dir="peptides.csv" label="${tool.name} on ${on_string}: peptides">\n+ <actions>\n+ <action name="comment_lines" type="metadata" default="1" />\n+ <action name="column_names" type="metadata" default="Peptide_Num,Protein_Accessions,Peptide_Sequence,Protein_Count,Spectral_Count,Taxonomic_Group,Taxonomic_Rank,NCBI_Taxonomy_ID" />\n+ </actions>\n+ </data>\n+ <data format="tabular" name="output_PSMs" from_work_dir="psms.csv" label="${tool.name} on ${on_string}: PSMs">\n+ <actions>\n+ <action name="comment_lines" type="metadata" default="1" />\n+ <action name="column_names" type="metadata" default="PSM_Num,Protein_Accessions,Peptide_Sequence,Spectrum_Title,Charge,Search_Engine,q-value,Score" />\n+ </actions>\n+ </data>\n+ <data format="tabular" name="output_spectrum_ids" from_work_dir="spectrum_ids.csv" label="${tool.name} on ${on_string}: spectrum_ids">\n+ <actions>\n+ <action name="comment_lines" type="metadata" default="1" />\n+ <action name="column_names" type="metadata" default="Spectrum_Number,Spectrum_ID,Spectrum_Title,Peptides,Protein_Accessions" />\n+ </actions>\n+ </data>\n+ <data format="tabular" name="output_metaproteins" from_work_dir="metaproteins.csv" label="${tool.name} on ${on_string}: metaproteins">\n+ <actions>\n+ <action name="comment_lines" type="metadata" default="1" />\n+ <action name="column_names" type="metadata" default="Meta-Protein_Num,Meta-Protein_Accession,Meta-Protein_Description,Meta-Protein_Taxonomy,Meta-Protein_UniRef100,Meta-Protein_UniRef90,Meta-Protein_UniRef50,Meta-Protein_KO,Meta-Protein_EC,Peptide_Count,Spectral_Count,Proteins,Peptides" />\n+ </actions>\n+ </data>\n+ <data format="tabular" name="output_metaprotein_taxa" from_work_dir="metaprotein_taxa.csv" label="${tool.name} on ${on_string}: metaprotein_taxa">\n+ <actions>\n+ <action name="comment_lines" type="metadata" default="1" />\n+ <action name="column_names" type="metadata" default="Unclassified,Superkingdom,Kingdom,Phylum,Class,Order,Family,Genus,Species,Subspecies,Num_Peptides,Spectral_Count" />\n+ </actions>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="peak_lists" value="Test416Ebendorf.mgf" ftype="mgf"/>\n+ <param name="input_database" value="searchdb.fa" ftype="fasta"/>\n+ <param name="missed_cleavages" value="2"/>\n+ <param name="prec_tol" value="ppm"/>\n+ <param name="prec_tol" value="10"/>\n+ <param name="frag_tol" value="0.5"/>\n+ <param name="engines" value="X!Tandem,MSGF,Comet"/>\n+ <output name="output_PSMs">\n+ <assert_contents>\n+ <has_text text="A2SPK1" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+=======\n+\n+MetaProteomeAnalyzer (MPA) performs identification of proteins and in-depth analysis of metaproteomics (and also proteomics) data. The MPA software currently supports the database search engines Comet, MS-GF+ and X!Tandem taking MGF spectrum files as input data. User-provided FASTA databases (preferably downloaded from UniProtKB) are formatted automatically. \n+\n+https://github.com/compomics/meta-proteome-analyzer\n+\n+----\n+\n+Outputs\n+=======\n+\n+MPA generates 6 tabular outputs:\n+\n+* psms\n+* peptides\n+* proteins\n+* spectrum_ids\n+* metaproteins\n+* metaprotein_taxa\n+\n+\n+------\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1021/pr501246w</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r bea389f80d87 test-data/Test416Ebendorf.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Test416Ebendorf.mgf Sat Mar 04 07:00:01 2017 -0500 |
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34.4394\r\n+1053.4780 18.9945\r\n+1054.2530 35.4295\r\n+1055.8990 87.4507\r\n+1056.6800 130.8600\r\n+1057.6160 1118.1800\r\n+1058.6380 715.1370\r\n+1059.6690 108.6100\r\n+1060.6360 94.6484\r\n+1061.7340 50.5902\r\n+1062.7120 72.8667\r\n+1063.7680 28.2457\r\n+1064.3690 34.6721\r\n+1065.6770 93.7793\r\n+1067.2990 87.9193\r\n+1069.6610 70.5419\r\n+1070.6310 66.9707\r\n+1071.6420 85.0818\r\n+1072.9720 100.9660\r\n+1073.6550 82.2976\r\n+1074.7200 83.1554\r\n+1075.7500 107.8660\r\n+1076.6430 34.3568\r\n+1077.7500 73.2019\r\n+1079.9890 18.8490\r\n+1080.6510 17.7130\r\n+1081.6430 39.9129\r\n+1082.8020 75.3783\r\n+1084.0780 38.9081\r\n+1084.6890 482.6040\r\n+1085.6850 144.2260\r\n+1087.1310 63.7397\r\n+1087.7660 114.8700\r\n+1088.6750 157.4850\r\n+1090.6200 61.9661\r\n+1092.0050 33.6174\r\n+1092.7090 10.7122\r\n+1093.9420 6.1712\r\n+1097.8880 31.5140\r\n+1098.6080 8.5990\r\n+1099.7730 152.5440\r\n+1100.8700 81.6861\r\n+1102.6580 7809.6300\r\n+1103.6360 2766.3300\r\n+1104.7550 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366.1310\r\n+1160.8830 10.7310\r\n+1161.7090 17.9758\r\n+1164.8120 28.6674\r\n+1166.9510 12.4283\r\n+1168.6400 7.4822\r\n+1169.6940 55.9301\r\n+1171.0510 64.8479\r\n+1171.7120 12.8208\r\n+1172.7480 29.3517\r\n+1173.7510 30.7463\r\n+1174.5980 72.9392\r\n+1175.7190 113.6670\r\n+1183.7390 28.5900\r\n+1185.5520 27.4424\r\n+1187.8010 7.7254\r\n+1188.5560 27.4763\r\n+1192.4620 18.4626\r\n+1195.8300 16.1276\r\n+1197.4540 17.7246\r\n+1200.8910 6.8054\r\n+1202.8010 9.3713\r\n+1203.6970 78.2725\r\n+1210.9860 13.9996\r\n+1211.7700 29.9811\r\n+1215.9500 17.9569\r\n+1225.8050 9.0460\r\n+1227.4520 20.0955\r\n+1235.9080 12.5488\r\n+1238.3670 36.0598\r\n+1244.7140 23.4732\r\n+1248.4010 12.1899\r\n+1249.7480 10.9310\r\n+1252.9010 23.5073\r\n+1256.9030 26.0421\r\n+1260.8570 13.5420\r\n+1262.7970 8.1450\r\n+1273.7870 22.3611\r\n+1280.7030 19.7096\r\n+1296.6290 12.5164\r\n+END IONS\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r bea389f80d87 test-data/searchdb.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchdb.fa Sat Mar 04 07:00:01 2017 -0500 |
| b |
| b'@@ -0,0 +1,34 @@\n+>sp|Q46G04|ACDA1_METBF Acetyl-CoA decarbonylase/synthase complex subunit alpha 1 OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=cdhA1 PE=1 SV=1\n+MSKLTTGSFSIEDLESVQITINNIVGAAKEAAEEKAKELVNAGPTLFAGLESYRDDWNFKLLDRYEPVITPMCDQCCYCTYGPCDLSGNKRGACGIDMLGHNGREFFLRVITGTACHAAHGRHLLDHLIETFGEDLPLNLGQSNVLTPNITISTGLSPKTLGEVKPAMEYVEEQLTQLLATVHAGQESAEIDYDSKALFSGSLDHVGMEISDIVQVTAYDFPRADPEAPLIEIGMGTIDKSKPFLCVIGHNVAGVTYMMDYMEDHDLTDKMEIAGLCCTAIDLTRYKEADRRPPYAKVIGSMSKELKVIRSGMPDVIVVDEQCVRGDIVPEAQKLMIPVIASNPKIMYGLPNRTDADVDETIEELRSGKIPGCVMLDYDKLGEICIRLTMEMAPIRDASGITAIPTDEEFTNWVMKCADCGACMIACPEELDIPEAMGFAKEGDYSYLDILHDQCIGCRRCEQVCKKEIPILNIIEKAAQKQISEEKGLMRAGRGQVSDAEIRAEGLNLVMGTTPGIIAIIGCPNYPEGTKDVYYIAEEFLKRNFIVVTTGCGAMDIGMFKDEDGKTLYERFPGGFECGGLANIGSCVSNAHITGAAEKVAAIFAQRTLEGNLAEIGDYVLNRVGACGLAWGAFSQKASSIGTGCNILGIPAVLGPHSSKYRRALIAKNYEEDKWKVYDARNGQEMAIPPAPEFLLTTAETWQEAIPMMAKACIRPSDNNMGRSIKLTHWMELHKKYLGSKPEDWWKFVRNEADLPLATREALLKELEKEHGWEIDWKRKKVISGPKIKFDVSAQPTNLKRLCKEA\n+>sp|Q8TJC6|ACDA2_METAC Acetyl-CoA decarbonylase/synthase complex subunit alpha 2 OS=Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) GN=cdhA2 PE=3 SV=1\n+MSKLTTGSFSIEDLESVQITINNIVGAAKEAAEEKAKELGPMGPTAMAGLASYRSWNLLLLDRYEPVLTPMCDQCCYCTYGPCDLSGNKRGACGIDMAGQTGREFFLRVITGTACHAAHGRHLLDHVIEVFGEDLPLNLGESNVLTPNVTICTGLSPKTLGECRAPMEYVEEQLTQLLATIHAGQESAEIDYDSKALFSGSLDHVGMEVSDIAQVSAYDFPKADPEAPLIEIGMGSIDKSKPLIVAIGHNVAGVTYIMDYMEENNLTDKMEIAGLCCTAFDMTRYKEADRRAPYAKIVGSLAKELKVIRSGMPDVIVVDEQCVRGDVLSESQKLKIPVIASNEKIMMGLPDRTDADVDSIVEEIKSGAIPGCVMLDYDKLGELIPKIAEVMAPIRDAEGITAIPTDEEFKVYIDKCVKCGECMLACPEELDIPEALEYAAKGSYEYLEALHDVCIGCRRCEQVCKKEIPILNVLEKAAQKSISEEKGWVRSGRGQASDAEIRKEGLNLVMGTTPGIIAIIGCPNYPAGTKDVYLIAEEFLKRNYLLAVSGCSAMDIGMFKDEDGKTLYEKYPGTFAGGGLLNTGSCVSNAHISGAAEKVAGIFAQRTLAGNLAEIADYTLNRVGACGLAWGAYSQKAASIGTGCNIYGIPAVLGPHSSKYRRALIAKNYDESKWKVYDGRDGSEMTIPPAPEFLLTTAETWQEAIPMMAKACIRPSDNNMGRSIKLTHWMELSKKYLGVEPEDWWKFVRNEADLPLAKREELLKRLEAEHGWEIDWKRKKIISGPKIKFDVSAQPTNLKRLCKEA\n+>sp|Q8THW2|ACDA3_METAC Acetyl-CoA decarbonylase/synthase complex subunit alpha 3 OS=Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) GN=cdhA3 PE=3 SV=1\n+MSKLTTGSFSIEDLESVQITINNIVGAAKEAAEEKAKELGPMGPTAMAGLASYRSWNLLLLDRYEPVLTPMCDQCCYCTYGPCDLSGNKRGACGIDMAGQTGREFFLRVITGTACHAAHGRHLLDHVIEVFGEDLPLNLGESNVLTPNVTICTGLSPKTLGECRAPMEYVEEQLTQLLATIHAGQESAEIDYDSKALFSGSLDHVGMEVSDIAQVSAYDFPKADPEAPLIEIGMGSIDKSKPLIVAIGHNVAGVTYIMDYMEENNLTDKMEIAGLCCTAFDMTRYKEADRRAPYAKIVGSLAKELKVIRSGMPDVIVVDEQCVRGDVLSESMKLKIPVIASNEKIMMGLPDRTDADVDSIVEEIKSGAIPGCVMLDYDKLGELIPKIAEVMAPIRDAEGITAIPTDEEFKVYIDKCVKCGECMLACPEELDIPEALEYAAKGSYEYLEALHDVCIGCRRCEQVCKKEIPILNVLEKAAQKSISEEKGWVRSGRGQASDAEIRAEGLNLVMGTTPGIIAIIGCPNYPAGTKDVYNIAEEFLKRNYLVVVSGCSAMDIGMYKDDDGKTLYERYPGTFSGGGLLNTGSCVSNAHITGAAEKVAGIFAQRTLAGNLAEVADYTLNRVGACGLAWGAYSQKAASIGTGCNIYGIPAVLGPHSSKYRRALIAKTYEEDKWKVFDARDGSEMNIPPAPEFLLTTAETWQEALPMMAKACIRPSDNNMGRSIKLTHWMELSKKYLGVEPEDWWKFVRNEADLPLAKREELLKRLEAEQGWEIDWKRKKIISGPKIKFDVSAQPTNLKRLCKEA\n+>sp|Q9C4Z4|ACDA2_METTE Acetyl-CoA decarbonylase/synthase complex subunit alpha 2 OS=Methanosarcina thermophila GN=cdhA2 PE=1 SV=1\n+MAKLTTGSFSIEDLESVQITINNIVGAAKEAAEKAEEELGPMGPTPFPTAATVRDWSFTLFDRYEPVYTPMCDQCCYCTFGPCNLEGNRRGACGLDMKGQAAREFFLRCITGCACHSAHGRHLLDHIISIFGEDMPINMGASNVIAPNIQLITGRQPKTLGDLKPIMEYVEEELGQLLATVHAGQEGAAIDYDNKAMLAGILDHVGMEVSDIAQVTALGFPKSDPEAPLVEVGMGTLDASKPVIIAIGHNVAGVTYIMDYMEDNNLTDKMEIGGLCCTAFDMTRYKREDRKPPYAKIVGTISKELKVVRSGIPDVIVIDEQCVRADLVEEGKKLKIPVIASNEKVMYGLPDRTNDDVDAIIEDIKTGKIPGCVMLDYEKLGELVPRLAMEMAPLREGISAIPSDEEMASLVAKCVACGECALACPEELDIPDAIQAAKEGDFTALDFLHDLCVGCRRCEQVCNKEIPILSVIDKAAQKAIAEEKGLVRAGRGQVSDAEIRAEGLNLVMGTTPGVIAIIGCANYPAGSKDVYRIAEEFLNRNYIVAVSGCSAMDIGMYKDADGKTLYERFPGRFERGNILNTGSCVSNSHISGTCHKVAAIFAGRNLSGNLAEIADYTLNRVGAVGLAWGAYSQKAAAIGTGCNMYGIPAVLGPHSGKYRRALIAKTYDENKWKVYDSRNGSELDIPPSPEFLITTAETWQEACVLLAKNCIRPSDNNMGRSIKLTHWIELSEKYLGVLPEDWWKFVRHEADLPLSRREELLKKLETEHGWEIDWKKKKIISGPKIKFDVSSQPTNLKRLCKEA\n+>sp|Q8PV87|ACDG2_METMA Acetyl-CoA decarbonylase/synthase complex subunit gamma 2 OS=Methanosarcina mazei (stra'..b'FVEPWNDHLGEMRGDLIRCTDKVVLTTGRIGMKYSHMLFPDYTVVMVGSRISEGLDNASGDIIICGLPGLVLKWGNPKMLEGSGYATVVEMLEKAPEHERLKEAFEMAVEKGKGARIVVIDRDGSVLMDSKSGK\n+>sp|Q8PYH6|DPO41_METMA DNA polymerase IV 1 OS=Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) GN=dbh1 PE=3 SV=1\n+MMQRVVLHIDMDYFFAAIEERENPELREKAVVVCMLSGRSELSGSVSTCNYVAREFGIRSGMPCSRAKKLNPEAVFLPVRKDFYTSVSDRIMEILRSYADPGNGDSFEQISVDEAFLESSERTGGDFRLAFEVGMQIKKEIKEKENLTCSIGIGPNKLISKMASSAKKPDGITVVSPQDLEAFLWPLNVSKLWGIGSVTAGKLQEMGIVTVKDLAERDVIELISIFGKSRGTWLKQAASGIDDSPLKERDGSEQIGRIATLPEDSLDKKLISSLIERLAGDVIEKLDSRELSFRIVTVTVINSNFRMYTKSRTLSHPVSSKEVLLQVSGEILDEFLSENRTEFRRVGVRVGGLQKKKGQKSLFDY\n+>sp|P07962|MCRA_METBF Methyl-coenzyme M reductase subunit alpha OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=mcrA PE=1 SV=3\n+MAADIFSKFKKDMEVKFAQEFGSNKQTGGDITDKTAKFLRLGPEQDPRKVEMIKAGKEIAEKRGIAFYNPMMHSGAPLGQRAITPYTISGTDIVCEPDDLHYVNNAAMQQMWDDIRRTCIVGLDMAHETLEKRLGKEVTPETINHYLEVLNHAMPGAAVVQEMMVETHPALVDDCYVKVFTGDDALADEIDKQFLIDINKEFSEEQAAQIKASIGKTSWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFISAYAMCAGEAAVADLSFAAKHAALVSMGEMLPARRARGPNEPGGLSFGHLSDIVQTSRVSEDPAKIALEVVGAGCMLYDQIWLGSYMSGGVGFTQYATAAYTDDILDNNTYYDVDYINDKYNGAATVGKDNKVKASLEVVKDIATESTLYGIETYEKFPTALEDHFGGSQRATVLAAAAGVACSLATGNANAGLSGWYLSMYLHKEAWGRLGFFGFDLQDQCGATNVLSYQGDEGLPDELRGPNYPNYAMNVGHQGGYAGIAQAAHSGRGDAFTVNPLLKVCFADDLLPFNFAEPRREFGRGAIREFVPAGERSLVIPAK\n+>sp|P07955|MCRB_METBF Methyl-coenzyme M reductase subunit beta OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=mcrB PE=1 SV=3\n+MSDTVDIYDDRGKLLESNVDIMSLAPTRNAAIQSIIMDTKRSVAVNLAGIQGALASGKMGGKGRQILGRGLNYDIVGNADAIAENVKKLVQVDEGDDTNVIKVKGGKSLLIQSPKSRIIAGADFMSATTVGAAAVTQTIMDMFGTDPYDAPIVKSAVWGSYPQTMDLMGGQVQGILSIPQNNEGLGFSLRNIMANHVAAISNRNAMNASALSSIYEQSGIFEMGGAVGMFERHQLLGLAYQGLNANNLLYDIVKENGKDGTIGTVIESVVRRAIEAGIISVDKTAPSGYNFYKANDVPKWNACAAVGTLAATLVNCGAGRAAQNVSSTLLYFNDILEKETGLPGCDYGKVEGTAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFAIPCVCAAVALDAGTQMFSIESTSGLIGDVFGAIPEFREPIKAVAGVL\n+>sp|P07964|MCRG_METBF Methyl-coenzyme M reductase subunit gamma OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=mcrG PE=1 SV=3\n+MAYERQYYPGATSVAANRRKHMSGKLEKLREISDEDLTAVLGHRAPGSDYPSTHPPLAEMGEPACSTRENVAATPGAAAGDRVRYIQFADSMYNAPATPYFRSYFAAINFRGVDPGTLSGRQIVEARERDMEQCAKVQMETEITDHALAGVRGATVHGHSVRLQEDGVMFDMLDRRRLENGTIIMDKDQVAIPLDRKVDLGKPMSSEEAAKRTTIYRVDNVAFRDDAEVVEWVHRIFDQRTKFGFQPK\n+>sp|A2SPK1|MTD_METLZ F420-dependent methylenetetrahydromethanopterin dehydrogenase OS=Methanocorpusculum labreanum (strain ATCC 43576 / DSM 4855 / Z) GN=mtd PE=3 SV=1\n+MVVKVGVAKLGNIAAGVMAELLLDERADREDMMTFMATSGTKLQKEDVDRVVSNLKAWQPDFAIVVSPNGVLEGPVGAREDLKAAGIPTIVITDDVTTKKEGWEALKASGFGYIIVKADAMIGARREFLDPVEMADYNGNLVKVLALTGAFRKLQLELDKVIDQVKAGKKGAELELPKLVLNSDNSTKGEFTNPYALAKARAAYEIAQAVAGVNVKGCFMTKEWTDYVPIVASAHEMMRAAANLCDQARELEKGCDGVIRKPHKKTGEIVSKVALISKPE\n+>sp|B8GJQ7|MTD_METPE F420-dependent methylenetetrahydromethanopterin dehydrogenase OS=Methanosphaerula palustris (strain ATCC BAA-1556 / DSM 19958 / E1-9c) GN=mtd PE=3 SV=1\n+MVVKVGIAKLGNIASGVMAELLLDERADREDMQTFMATSGTKLQPEDIDRVVSTMKAWEPDFCIVVSPNGVLPGPVGARDELLKAGIPCVVITDDITTKKEGWEALKASSFGYIIMKADAMIGARREFLDPVEMADFNGNLVKVLALTGAFRKLQTELDKVIDQVKEGKKGADLVLPKVVMTSDKAVDGEFSNPYALAKARAAYEIAQAVAGVNVKGCFMTKEWEKYIPIVASAHEMMRQAAALGDEAREIEKAGNGIIRKPHKKDGTIVSKITLISKPE\n+>sp|Q2FRN2|MTRA_METHJ Tetrahydromethanopterin S-methyltransferase subunit A OS=Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1) GN=mtrA PE=3 SV=1\n+MANKKSPASGWPIVQGDFHTGDPNSPVAVVTMGSHLDEGAICSAGAAIAGSCKTENLGLEKVIANVISNPNIRFVITCGTEVKGHLSGQSLIALHQNGVDGGKIVGSKGAIPFIENLSADNIKRFQEQVELVDIMESEDLGAISAKIKELTARDPGAFDAEAMIVEIKEEGGGAAEEGGEVRPMSAEVALIHARMKTIQRTITDIGFYDKYAAGVYGGKVEGLMIGLIVSFVIIGLLLVGHGVS\n+>sp|Q12TU6|Y2269_METBU Maf-like protein Mbur_2269 OS=Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 / ACE-M) GN=Mbur_2269 PE=3 SV=1\n+MRKVVLASASPRRKELLSKLIGNNFEVCVSSYEETPLQEMNVEELVVFHSLEKAKDVALRFDSGIIISADTVVFCDGAILGKPHTLNNAKEMLENISGKSVLAITGMTILDMDSGKCVSEYVSTDVNMKQMSSDEIASYVNSGEPLDKAGAFAIQGKGAVLVESINGDFFNVVGLPLFRLGTILEEMGISIFDDC\n' |