# HG changeset patch # User galaxyp # Date 1488571079 18000 # Node ID b41e6d379c5f367b9edb24f80fb797571626eb25 # Parent c0abf055f6f13b1bbadafd9cd0ad0223ac68d8cf Uploaded diff -r c0abf055f6f1 -r b41e6d379c5f meta_proteome_analyzer.xml --- a/meta_proteome_analyzer.xml Fri Mar 03 11:44:29 2017 -0500 +++ b/meta_proteome_analyzer.xml Fri Mar 03 14:57:59 2017 -0500 @@ -13,9 +13,10 @@ mkdir -p output_dir; ## copy mpa conf dir to working dir jar_dir=`mpa-portable -get_jar_dir`; - cp -R jar_dir/conf .; + cp -R \$jar_dir/conf .; ## echo the search engines to run + #set $search_engines = str($search_engines_options.engines).split(',') echo "$search_engines_options.engines"; echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}"; @@ -36,10 +37,10 @@ -database input_database.fasta -missed_cleav $missed_cleavages -prec_tol ${precursor_options.prec_tol}${precursor_options.prec_tol_units} - -frag_tol ${precursor_options.frag_tol} - -xtandem #if 'X!Tandem' in $search_engines_options.engines 1 else 0# - -comet #if 'Comet' in $search_engines_options.engines 1 else 0# - -msgf #if 'MSGF' in $search_engines_options.engines 1 else 0# + -frag_tol ${precursor_options.frag_tol}Da + -xtandem #if 'X!Tandem' in $search_engines then 1 else 0# + -comet #if 'Comet' in $search_engines then 1 else 0# + -msgf #if 'MSGF' in $search_engines then 1 else 0# -output_folder output_dir -threads "\${GALAXY_SLOTS:-12}" 2> $temp_stderr) && @@ -83,6 +84,16 @@ + + + @@ -123,163 +134,47 @@ + + + + + + + + + + + + + + **What it does** -Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results. +======= -http://compomics.github.io/projects/peptide-shaker.html -http://compomics.github.io/projects/searchgui.html +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. + +https://github.com/compomics/meta-proteome-analyzer ---- -Reports +Outputs ======= - -PSM Report ----------- - -* Protein(s): Protein(s) to which the peptide can be attached -* Sequence: Sequence of the peptide -* Variable Modifications: The variable modifications -* D-score: D-score for variable PTM localization -* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. -* Localization Confidence: The confidence in variable PTM localization. -* Fixed Modifications: The fixed modifications. -* Spectrum File: The spectrum file. -* Spectrum Title: The title of the spectrum. -* Spectrum Scan Number: The spectrum scan number. -* RT: Retention time -* m/z: Measured m/z -* Measured Charge: The charge as given in the spectrum file. -* Identification Charge: The charge as inferred by the search engine. -* Theoretical Mass: The theoretical mass of the peptide. -* Isotope Number: The isotope number targetted by the instrument. -* Precursor m/z Error: The precursor m/z matching error. -* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). -* Confidence: Confidence in percent associated to the retained PSM. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Protein Report --------------- - -* Main Accession: Main accession of the protein group. -* Description: Description of the protein designed by the main accession. -* Gene Name: The gene names of the Ensembl gene ID associated to the main accession. -* Chromosome: The chromosome of the Ensembl gene ID associated to the main accession. -* PI: Protein Inference status of the protein group. -* Secondary Accessions: Other accessions in the protein group (alphabetical order). -* Protein Group: The complete protein group (alphabetical order). -* #Peptides: Total number of peptides. -* #Validated Peptides: Number of validated peptides. -* #Unique: Total number of peptides unique to this protein group. -* #PSMs: Number of PSMs -* #Validated PSMs: Number of validated PSMs -* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. -* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. -* MW (kDa): Molecular Weight. -* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) -* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) -* Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized. -* Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized. -* Score: Score of the protein group. -* Confidence: Confidence in percent associated to the protein group. -* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Peptide Report --------------- - +MPA generates 6 tabular outputs: -* Protein(s): Protein(s) to which this peptide can be attached. -* AAs Before: The amino-acids before the sequence. -* Sequence: Sequence of the peptide. -* AAs After: The amino-acids after the sequence. -* Modified Sequence: The peptide sequence annotated with variable modifications. -* Variable Modifications: The variable modifications. -* Localization Confidence: The confidence in PTMs localization. -* Fixed Modifications: The fixed modifications. -* #Validated PSMs: Number of validated PSMs. -* #PSMs: Number of PSMs. -* Score: Score of the peptide. -* Confidence: Confidence in percent associated to the peptide. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Hierachical Report ------------------- - -* Main Accession: Main accession of the protein group. -* Description: Description of the protein designed by the main accession. -* PI: Protein Inference status of the protein group. -* Secondary Accessions: Other accessions in the protein group (alphabetical order). -* Protein Group: The complete protein group (alphabetical order). -* #Peptides: Total number of peptides. -* #Validated Peptides: Number of validated peptides. -* #Unique: Total number of peptides unique to this protein group. -* #PSMs: Number of PSMs -* #Validated PSMs: Number of validated PSMs -* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. -* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. -* MW (kDa): Molecular Weight. -* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) -* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) -* Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized. -* Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized. -* Score: Score of the protein group. -* Confidence: Confidence in percent associated to the protein group. -* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. -* Protein(s): Protein(s) to which this peptide can be attached. -* AAs Before: The amino-acids before the sequence. -* Sequence: Sequence of the peptide. -* AAs After: The amino-acids after the sequence. -* Variable Modifications: The variable modifications. -* Localization Confidence: The confidence in PTMs localization. -* Fixed Modifications: The fixed modifications. -* #Validated PSMs: Number of validated PSMs. -* #PSMs: Number of PSMs. -* Score: Score of the peptide. -* Confidence: Confidence in percent associated to the peptide. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. -* Protein(s): Protein(s) to which the peptide can be attached. -* Sequence: Sequence of the peptide. -* Modified Sequence: The peptide sequence annotated with variable modifications. -* Variable Modifications: The variable modifications. -* D-score: D-score for variable PTM localization. -* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. -* Localization Confidence: The confidence in variable PTM localization. -* Fixed Modifications: The fixed modifications. -* Spectrum File: The spectrum file. -* Spectrum Title: The title of the spectrum. -* Spectrum Scan Number: The spectrum scan number. -* RT: Retention time -* m/z: Measured m/z -* Measured Charge: The charge as given in the spectrum file. -* Identification Charge: The charge as inferred by the search engine. -* Theoretical Mass: The theoretical mass of the peptide. -* Isotope Number: The isotope number targetted by the instrument. -* Precursor m/z Error: The precursor m/z matching error. -* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). -* Confidence: Confidence in percent associated to the retained PSM. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. +* psms +* peptides +* proteins +* spectrum_ids +* metaproteins +*metaprotein_taxa ------ -**Citation** - -To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io - -If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. 10.1021/pr501246w diff -r c0abf055f6f1 -r b41e6d379c5f test-data/searchdb.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchdb.fa Fri Mar 03 14:57:59 2017 -0500 @@ -0,0 +1,34 @@ +>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 +MSKLTTGSFSIEDLESVQITINNIVGAAKEAAEEKAKELVNAGPTLFAGLESYRDDWNFKLLDRYEPVITPMCDQCCYCTYGPCDLSGNKRGACGIDMLGHNGREFFLRVITGTACHAAHGRHLLDHLIETFGEDLPLNLGQSNVLTPNITISTGLSPKTLGEVKPAMEYVEEQLTQLLATVHAGQESAEIDYDSKALFSGSLDHVGMEISDIVQVTAYDFPRADPEAPLIEIGMGTIDKSKPFLCVIGHNVAGVTYMMDYMEDHDLTDKMEIAGLCCTAIDLTRYKEADRRPPYAKVIGSMSKELKVIRSGMPDVIVVDEQCVRGDIVPEAQKLMIPVIASNPKIMYGLPNRTDADVDETIEELRSGKIPGCVMLDYDKLGEICIRLTMEMAPIRDASGITAIPTDEEFTNWVMKCADCGACMIACPEELDIPEAMGFAKEGDYSYLDILHDQCIGCRRCEQVCKKEIPILNIIEKAAQKQISEEKGLMRAGRGQVSDAEIRAEGLNLVMGTTPGIIAIIGCPNYPEGTKDVYYIAEEFLKRNFIVVTTGCGAMDIGMFKDEDGKTLYERFPGGFECGGLANIGSCVSNAHITGAAEKVAAIFAQRTLEGNLAEIGDYVLNRVGACGLAWGAFSQKASSIGTGCNILGIPAVLGPHSSKYRRALIAKNYEEDKWKVYDARNGQEMAIPPAPEFLLTTAETWQEAIPMMAKACIRPSDNNMGRSIKLTHWMELHKKYLGSKPEDWWKFVRNEADLPLATREALLKELEKEHGWEIDWKRKKVISGPKIKFDVSAQPTNLKRLCKEA +>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 +MSKLTTGSFSIEDLESVQITINNIVGAAKEAAEEKAKELGPMGPTAMAGLASYRSWNLLLLDRYEPVLTPMCDQCCYCTYGPCDLSGNKRGACGIDMAGQTGREFFLRVITGTACHAAHGRHLLDHVIEVFGEDLPLNLGESNVLTPNVTICTGLSPKTLGECRAPMEYVEEQLTQLLATIHAGQESAEIDYDSKALFSGSLDHVGMEVSDIAQVSAYDFPKADPEAPLIEIGMGSIDKSKPLIVAIGHNVAGVTYIMDYMEENNLTDKMEIAGLCCTAFDMTRYKEADRRAPYAKIVGSLAKELKVIRSGMPDVIVVDEQCVRGDVLSESQKLKIPVIASNEKIMMGLPDRTDADVDSIVEEIKSGAIPGCVMLDYDKLGELIPKIAEVMAPIRDAEGITAIPTDEEFKVYIDKCVKCGECMLACPEELDIPEALEYAAKGSYEYLEALHDVCIGCRRCEQVCKKEIPILNVLEKAAQKSISEEKGWVRSGRGQASDAEIRKEGLNLVMGTTPGIIAIIGCPNYPAGTKDVYLIAEEFLKRNYLLAVSGCSAMDIGMFKDEDGKTLYEKYPGTFAGGGLLNTGSCVSNAHISGAAEKVAGIFAQRTLAGNLAEIADYTLNRVGACGLAWGAYSQKAASIGTGCNIYGIPAVLGPHSSKYRRALIAKNYDESKWKVYDGRDGSEMTIPPAPEFLLTTAETWQEAIPMMAKACIRPSDNNMGRSIKLTHWMELSKKYLGVEPEDWWKFVRNEADLPLAKREELLKRLEAEHGWEIDWKRKKIISGPKIKFDVSAQPTNLKRLCKEA +>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 +MSKLTTGSFSIEDLESVQITINNIVGAAKEAAEEKAKELGPMGPTAMAGLASYRSWNLLLLDRYEPVLTPMCDQCCYCTYGPCDLSGNKRGACGIDMAGQTGREFFLRVITGTACHAAHGRHLLDHVIEVFGEDLPLNLGESNVLTPNVTICTGLSPKTLGECRAPMEYVEEQLTQLLATIHAGQESAEIDYDSKALFSGSLDHVGMEVSDIAQVSAYDFPKADPEAPLIEIGMGSIDKSKPLIVAIGHNVAGVTYIMDYMEENNLTDKMEIAGLCCTAFDMTRYKEADRRAPYAKIVGSLAKELKVIRSGMPDVIVVDEQCVRGDVLSESMKLKIPVIASNEKIMMGLPDRTDADVDSIVEEIKSGAIPGCVMLDYDKLGELIPKIAEVMAPIRDAEGITAIPTDEEFKVYIDKCVKCGECMLACPEELDIPEALEYAAKGSYEYLEALHDVCIGCRRCEQVCKKEIPILNVLEKAAQKSISEEKGWVRSGRGQASDAEIRAEGLNLVMGTTPGIIAIIGCPNYPAGTKDVYNIAEEFLKRNYLVVVSGCSAMDIGMYKDDDGKTLYERYPGTFSGGGLLNTGSCVSNAHITGAAEKVAGIFAQRTLAGNLAEVADYTLNRVGACGLAWGAYSQKAASIGTGCNIYGIPAVLGPHSSKYRRALIAKTYEEDKWKVFDARDGSEMNIPPAPEFLLTTAETWQEALPMMAKACIRPSDNNMGRSIKLTHWMELSKKYLGVEPEDWWKFVRNEADLPLAKREELLKRLEAEQGWEIDWKRKKIISGPKIKFDVSAQPTNLKRLCKEA +>sp|Q9C4Z4|ACDA2_METTE Acetyl-CoA decarbonylase/synthase complex subunit alpha 2 OS=Methanosarcina thermophila GN=cdhA2 PE=1 SV=1 +MAKLTTGSFSIEDLESVQITINNIVGAAKEAAEKAEEELGPMGPTPFPTAATVRDWSFTLFDRYEPVYTPMCDQCCYCTFGPCNLEGNRRGACGLDMKGQAAREFFLRCITGCACHSAHGRHLLDHIISIFGEDMPINMGASNVIAPNIQLITGRQPKTLGDLKPIMEYVEEELGQLLATVHAGQEGAAIDYDNKAMLAGILDHVGMEVSDIAQVTALGFPKSDPEAPLVEVGMGTLDASKPVIIAIGHNVAGVTYIMDYMEDNNLTDKMEIGGLCCTAFDMTRYKREDRKPPYAKIVGTISKELKVVRSGIPDVIVIDEQCVRADLVEEGKKLKIPVIASNEKVMYGLPDRTNDDVDAIIEDIKTGKIPGCVMLDYEKLGELVPRLAMEMAPLREGISAIPSDEEMASLVAKCVACGECALACPEELDIPDAIQAAKEGDFTALDFLHDLCVGCRRCEQVCNKEIPILSVIDKAAQKAIAEEKGLVRAGRGQVSDAEIRAEGLNLVMGTTPGVIAIIGCANYPAGSKDVYRIAEEFLNRNYIVAVSGCSAMDIGMYKDADGKTLYERFPGRFERGNILNTGSCVSNSHISGTCHKVAAIFAGRNLSGNLAEIADYTLNRVGAVGLAWGAYSQKAAAIGTGCNMYGIPAVLGPHSGKYRRALIAKTYDENKWKVYDSRNGSELDIPPSPEFLITTAETWQEACVLLAKNCIRPSDNNMGRSIKLTHWIELSEKYLGVLPEDWWKFVRHEADLPLSRREELLKKLETEHGWEIDWKKKKIISGPKIKFDVSSQPTNLKRLCKEA +>sp|Q8PV87|ACDG2_METMA Acetyl-CoA decarbonylase/synthase complex subunit gamma 2 OS=Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) GN=cdhE2 PE=3 SV=1 +MKINSPLEAYKYLPQTNCGECGQPTCMAFASTLIDRSGKTTDCPPLIKEKKFAKKLAELDRLLAPEIRQVTIGVGERAANIGGDDVLYRHKLTFFNKTKMFFDVADNMDEAAIVERVKKISDYKKFYVGRNLLLDGVAIRAASNDPAKFATAVKKVIENTELPVILCSFNPAVLKAGLEVAKGKNPLLYAANKDNWKEVGELALEYNVPVVVSAFNDLDGLKTLAKTFAEAGIKDIVLDPGTYPTGKGLKDTFTNFLKIRRAGIMGDTEIAYPIMAMPLTAWMAGIADPVSASYWETVLSSIFTIRYGDIMLLHSMEPYATMPEVHLAETIYTDPRSPVAVDSKMYKVGNPTADSPVLFTTNFALTYYTVESDLASNGIDCWLLAVNTDGIGVEAAAAGGQLTADKVKDAFEKSGFDLKSDVTHNSVVIPGLAARLQGDIEDKLNVKVMVGPMDSGRLPGWMEKNWPPKK +>sp|Q8TRZ6|ACDB1_METAC Acetyl-CoA decarbonylase/synthase complex subunit beta 1 OS=Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) GN=cdhC1 PE=3 SV=1 +MVEFPFEISPMFEGERVRKEGMFVELGGPKSLGLELVRAKPMDEIEDDKVTIVGPDLKEMEEGKTYPWAMIFNIGGELVEPDLESVVERRVHDFINYCQGIMHLNQRYDVWMRVSKDTAAKMDSFEPFGQAVMMLFKTELPFIEKMQVTFYTEQAEVEKQMETAKEIFKARDERTKDLHDEDVDVFYGCTLCQSFAPTNVCVVSPDRVSLCGAINWFDGRAAAKVDPEGPQFEIAKGDLLDANTGEYTGVNDIAKKLSAGEFDKIKLHSFFDSPHTSCGCFEVVGFYIPEVDGIGWVNREYQGMAPNGIGFSTMAGQTGGGKQIVGFLGIGINYFYSPKFIQADGGWNRVVWLPSMLKDKIIDTIPEDLKDKIATENDSTDIESLKAFLQEKGHPVVATWAAEEEEEEEEEEEEEVAVAAAPMMMPAAGFQMPAMPMMSGGSSGGIKLTFKNAKITIDKMIISEKKEKK +>sp|Q50539|ACDG1_METTE Acetyl-CoA decarbonylase/synthase complex subunit gamma 1 OS=Methanosarcina thermophila GN=cdhE1 PE=1 SV=1 +MKINSPLEAYKYLPQTNCGECGEPTCMAFASKLIDRSGKTSDCPPLVKEKKYAKKLAELDRLLAPEIRQVTIGVGEKAANIGGDDVLYRHKLTFFNKTKMFFDVSDNMEEDALIERVKKIADFKKFYVGRNLLLDGVAIKATSNDPAKFAAAVKKVAEIGLPMIFCSFNPAVLKAGLEVAKDKNPLLYAANKDNWKEVGELALEYKVPVVVSVFNDLDGLKSLAKTFAEAGIKDIVLDPGTYPSGKGLKDTFTNFLKIRRAGIMGDTEIAYPIMALPLTAWMAGISDPVSASYWETVIASVFTIRYGDIMILHSLEPYAALPEMHLAETIYTDPRTPVSVDGGMYKVGEPDKDSPVFFTTNFALTYYTVESDISANGIVCWLLAVDTDGIGVEAAVAGGQLTSAKVKDAFEKAGFDLKTDTNHNTLIIPGLSARLQGDLEDTLGANVKVGPMDSGRIPGWVEKNWPPK +>sp|Q9C4Z0|ACDG2_METTE Acetyl-CoA decarbonylase/synthase complex subunit gamma 2 OS=Methanosarcina thermophila GN=cdhE2 PE=3 SV=1 +MKINSPLEAYKYLPQTNCGECGEATCMAFASKLIDRSGKPTQCPPLVKEKKFAKKLAELERLLAPEIREITIGVGDRAVKIGGDDVLYRHKLTFFNKTKMFYDVTDTMDEAALLERTKKVADFRKFYVGRNLLLDGVAIRSVSNDPEKFAAAVKKVSEVGIPMILCSFNPAVLKAGLEVAKDKNPLIYAANKDNWKEVGELALEYNVPVVVSAFNDLDGLKTLAKTFAEAGIKDIVLDPGTYPSGQGLKDSFTNFLKIRRAGIMGDTEIAYPIMALPITAWMAGISDPVSAAYWETAMAAIFTIRYGDIMILHSLEPYATLPEVHLAETIYTDPRTPVAVDSKMYKVGEPDENSPVLFTTNFALTYYTVESDLSSNGITCWLLAVDTDGIGVEAAAAGGQLTADKVKDAFEKSGFDLKKDVTHNTVIIPGLAARLQGDLEDKLGARVLVGPMDSGRLPGWFEKNWPPK +>sp|Q8TTB6|CBID_METAC Cobalt-precorrin-5B C(1)-methyltransferase OS=Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) GN=cbiD PE=3 SV=1 +MIDPVNNFKIPEEWIARSGLPREELEKNVASGMIVILSDGSVLKRGYTTGTTASAAAKAAVLSLKKTVDSVSVPTPVGLRAYLEVSKSSPGRAVVKKIPNDHESDVTRGLEFVGEAREAEGISILGGKGIGIVKRDGLQVPKGKPAINPKPMEQIRAAVQEAVEELGLKGAEVTILIPEGERIGKETLNSRIGVEGGISVLGSTGFVEPWNDHLGEMRGDLIRCTDKVVLTTGRIGMKYSHMLFPDYTVVMVGSRISEGLDNASGDIIICGLPGLVLKWGNPKMLEGSGYATVVEMLEKAPEHERLKEAFEMAVEKGKGARIVVIDRDGSVLMDSKSGK +>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 +MMQRVVLHIDMDYFFAAIEERENPELREKAVVVCMLSGRSELSGSVSTCNYVAREFGIRSGMPCSRAKKLNPEAVFLPVRKDFYTSVSDRIMEILRSYADPGNGDSFEQISVDEAFLESSERTGGDFRLAFEVGMQIKKEIKEKENLTCSIGIGPNKLISKMASSAKKPDGITVVSPQDLEAFLWPLNVSKLWGIGSVTAGKLQEMGIVTVKDLAERDVIELISIFGKSRGTWLKQAASGIDDSPLKERDGSEQIGRIATLPEDSLDKKLISSLIERLAGDVIEKLDSRELSFRIVTVTVINSNFRMYTKSRTLSHPVSSKEVLLQVSGEILDEFLSENRTEFRRVGVRVGGLQKKKGQKSLFDY +>sp|P07962|MCRA_METBF Methyl-coenzyme M reductase subunit alpha OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=mcrA PE=1 SV=3 +MAADIFSKFKKDMEVKFAQEFGSNKQTGGDITDKTAKFLRLGPEQDPRKVEMIKAGKEIAEKRGIAFYNPMMHSGAPLGQRAITPYTISGTDIVCEPDDLHYVNNAAMQQMWDDIRRTCIVGLDMAHETLEKRLGKEVTPETINHYLEVLNHAMPGAAVVQEMMVETHPALVDDCYVKVFTGDDALADEIDKQFLIDINKEFSEEQAAQIKASIGKTSWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFISAYAMCAGEAAVADLSFAAKHAALVSMGEMLPARRARGPNEPGGLSFGHLSDIVQTSRVSEDPAKIALEVVGAGCMLYDQIWLGSYMSGGVGFTQYATAAYTDDILDNNTYYDVDYINDKYNGAATVGKDNKVKASLEVVKDIATESTLYGIETYEKFPTALEDHFGGSQRATVLAAAAGVACSLATGNANAGLSGWYLSMYLHKEAWGRLGFFGFDLQDQCGATNVLSYQGDEGLPDELRGPNYPNYAMNVGHQGGYAGIAQAAHSGRGDAFTVNPLLKVCFADDLLPFNFAEPRREFGRGAIREFVPAGERSLVIPAK +>sp|P07955|MCRB_METBF Methyl-coenzyme M reductase subunit beta OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=mcrB PE=1 SV=3 +MSDTVDIYDDRGKLLESNVDIMSLAPTRNAAIQSIIMDTKRSVAVNLAGIQGALASGKMGGKGRQILGRGLNYDIVGNADAIAENVKKLVQVDEGDDTNVIKVKGGKSLLIQSPKSRIIAGADFMSATTVGAAAVTQTIMDMFGTDPYDAPIVKSAVWGSYPQTMDLMGGQVQGILSIPQNNEGLGFSLRNIMANHVAAISNRNAMNASALSSIYEQSGIFEMGGAVGMFERHQLLGLAYQGLNANNLLYDIVKENGKDGTIGTVIESVVRRAIEAGIISVDKTAPSGYNFYKANDVPKWNACAAVGTLAATLVNCGAGRAAQNVSSTLLYFNDILEKETGLPGCDYGKVEGTAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFAIPCVCAAVALDAGTQMFSIESTSGLIGDVFGAIPEFREPIKAVAGVL +>sp|P07964|MCRG_METBF Methyl-coenzyme M reductase subunit gamma OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=mcrG PE=1 SV=3 +MAYERQYYPGATSVAANRRKHMSGKLEKLREISDEDLTAVLGHRAPGSDYPSTHPPLAEMGEPACSTRENVAATPGAAAGDRVRYIQFADSMYNAPATPYFRSYFAAINFRGVDPGTLSGRQIVEARERDMEQCAKVQMETEITDHALAGVRGATVHGHSVRLQEDGVMFDMLDRRRLENGTIIMDKDQVAIPLDRKVDLGKPMSSEEAAKRTTIYRVDNVAFRDDAEVVEWVHRIFDQRTKFGFQPK +>sp|A2SPK1|MTD_METLZ F420-dependent methylenetetrahydromethanopterin dehydrogenase OS=Methanocorpusculum labreanum (strain ATCC 43576 / DSM 4855 / Z) GN=mtd PE=3 SV=1 +MVVKVGVAKLGNIAAGVMAELLLDERADREDMMTFMATSGTKLQKEDVDRVVSNLKAWQPDFAIVVSPNGVLEGPVGAREDLKAAGIPTIVITDDVTTKKEGWEALKASGFGYIIVKADAMIGARREFLDPVEMADYNGNLVKVLALTGAFRKLQLELDKVIDQVKAGKKGAELELPKLVLNSDNSTKGEFTNPYALAKARAAYEIAQAVAGVNVKGCFMTKEWTDYVPIVASAHEMMRAAANLCDQARELEKGCDGVIRKPHKKTGEIVSKVALISKPE +>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 +MVVKVGIAKLGNIASGVMAELLLDERADREDMQTFMATSGTKLQPEDIDRVVSTMKAWEPDFCIVVSPNGVLPGPVGARDELLKAGIPCVVITDDITTKKEGWEALKASSFGYIIMKADAMIGARREFLDPVEMADFNGNLVKVLALTGAFRKLQTELDKVIDQVKEGKKGADLVLPKVVMTSDKAVDGEFSNPYALAKARAAYEIAQAVAGVNVKGCFMTKEWEKYIPIVASAHEMMRQAAALGDEAREIEKAGNGIIRKPHKKDGTIVSKITLISKPE +>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 +MANKKSPASGWPIVQGDFHTGDPNSPVAVVTMGSHLDEGAICSAGAAIAGSCKTENLGLEKVIANVISNPNIRFVITCGTEVKGHLSGQSLIALHQNGVDGGKIVGSKGAIPFIENLSADNIKRFQEQVELVDIMESEDLGAISAKIKELTARDPGAFDAEAMIVEIKEEGGGAAEEGGEVRPMSAEVALIHARMKTIQRTITDIGFYDKYAAGVYGGKVEGLMIGLIVSFVIIGLLLVGHGVS +>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 +MRKVVLASASPRRKELLSKLIGNNFEVCVSSYEETPLQEMNVEELVVFHSLEKAKDVALRFDSGIIISADTVVFCDGAILGKPHTLNNAKEMLENISGKSVLAITGMTILDMDSGKCVSEYVSTDVNMKQMSSDEIASYVNSGEPLDKAGAFAIQGKGAVLVESINGDFFNVVGLPLFRLGTILEEMGISIFDDC