GapMind for catabolism of small carbon sources

 

Protein AO356_28220 in Pseudomonas fluorescens FW300-N2C3

Annotation: AO356_28220 non-ribosomal peptide synthetase

Length: 8596 amino acids

Source: pseudo5_N2C3_1 in FitnessBrowser

Candidate for 1 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism amaB lo L-2-aminoadipate reductase; Alpha-aminoadipate reductase; Alpha-AR; L-aminoadipate-semialdehyde dehydrogenase; EC 1.2.1.31; EC 1.2.1.95 (characterized) 31% 50% 261.9 non-ribosomal peptide synthetase OfaA 50% 1556.6

Sequence Analysis Tools

View AO356_28220 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNQFLQLSTSYPLTTAQRDIWLDQMTKGDSPLYNIGGYLHIQGAVDPERFQRAVDLLIEK
YDALRTVLHYGADGVPMQTMAETLEARVPVLDFSDRPDPEAAVHAWMQQRMAVAIRLDES
PLFRFYLAKLGDASFYFVMHLHHIILDGWGVGLVLTSLGELYDALENDQPPDLSAPSYVG
FIDEDARYRDSPRFKLDEAYWLDKYQDVPDPLFIARHHDQPPGVLAPSAQALYRFAHTLS
DRIDVLAQAHQASRFSVLLAALYVFFIRTTQRDELVIGLPILNRPNATFKKTAGLFTQVS
AVRFKFASDLSFGELIRGVTRTLKQDYRNQRFPLSEMNRSLELRRDNRAQLFDVSFSYEQ
EDRRFMFGQAPAHFVMGSNGQEQMPLSIHIRSNPHDDNAWLHWIYNESYFQADEIESMAD
RFMHVLEQGLRDDTLPIEGFVLPTAAEADMLQAWNASDARTYEHDHTIHGLFEAQVRARP
DAVAVLHEDRCLTYGELNARANQVAHRLLILGVHPDDRVAICVERGLDMIIGLLGILKSG
AGYVPLDPAYPQERLAFMLDDSAPVALLTQSTLQVQLPALQVPVLLLDQAEAAGITAQSR
YNPDVRTLASHHLAYVIYTSGSTGLPKGVMVEHRNVARLFSATQPWFEFGPQDVWALFHS
FAFDFSVWEIWGALTHGGRLLVVPQLVSRSPQDCYALLCEAGVTVLNQTPSAFRQLIAAQ
GDSDLCHSLRQVIFGGEALETSMLKPWYARATNAGTQLVNMYGITETTVHVTYRALCAAD
AQLTGVSPIGKRIPDLRLYLLDKYGQPVPVGVEGELYVGGAGVARGYLNRPQLDETRFLA
DPFDGGAHARMYRTGDLGRWLKNGELEYLGRNDEQVKIRGFRIELGEIEAKLAVCAQVRE
AVVIAREDNPGDKRLVAYVVADAGRQLSVADLRDQLLGLLADYMVPSAFVLLDALPLTTN
GKLDRKALPAPDSQAYARRSYEAPEGEVETVLARLWAELLGVEQVGRHDRFFELGGHSLL
AVKLIERMRQVKLHADVGVLFGQPTLASLAAATGVSKGIVVPDNMIAHGVECITSDMLPL
ATLTQDEIDRVVAAVPGGVDNVQDIYGLVPLQEGILYHHLATEEGDPYLLQILLRIDSRE
QLDAIVQALQVAIERHDILRTSVAWEGLGEPVQVVWRQAQLMVEELGLDVAEGDIAGQMQ
RRFDPRHTRFDLRQAPMMRLHFTEDVAHGNWVAVLLFHHLIDDATSLGMLGKEIEAHLEG
RSAELPVSVPYRNYVAQVRLAGNQEHHEAFFSEMLGDIDEPTLPFGLRDVQGDGVGVEET
VLPLAADLAQRLRTQARRLGVSTASLHHLAWGQVVGRLSGRQDVVFGTVLMGRLHSGQEA
GHALGMFVNTLPLRVEAGGQGVLAALKATHARLATLLRHEHAPLSLAQRCSGVAAPTPLF
SALMNYRQTAVAAQAPKAVGEGRRWAGAQILSGEERTNYPLTLSVDDLGDGFSLTVQAVV
EIGARRIGAYMEAALTSLAAALERAVESPLADLTILPALEREQLLVAFNATEADYPQQQM
VHGLFEEQAQRTPDAVAVIRGEQRLTYHELNERANRLAHYLRKQGVEPDSRVAICVERGI
DMVVGLLAILKAGGGYVPLDPAYPLDRIAYMLDDSAPAAVLAQTATLELLAEASMPVINL
DSGDWQDESVQNPEVTELTSSHLAYVIYTSGSTGLPKGVMIEHRNTVNFLTWAHRSFDAQ
TLSKTLFSTSLNFDLAVYECFAPLTSGGSIEVVTNVLELQQGEHDITLINTVPSALKALL
ESGGLGEGVDTVNVAGEALKRSLVETLFEQTQVKRLCNLYGPSETTTYSSWVSMAREDGF
AAHIGKPVANTQFYLLDEHKQPVPLGVPGEIYIGGAGVARGYLNRDDLTAERFLKDPFST
TPNARMYKTGDLGRYLPDGNIEYLGRNDDQVKIRGFRIELGEIEAKLAQAPNIKETVVLA
REDVPGDKRLVAYFTQHSPDETVEIEALRTHLQAQLPAYMVPVAYVRLDALPLTPNGKLD
RKALPAPDLDAVITRGYEAPQGETETTLAQIWQDVLKVERVGRHDHFFELGGHSLLAVSL
IERMRQAGLSADVRILFNQPTLAALAAAVGTGNEVTVPANLIPLGCEHITPAMLPLAKLS
QEAIDRIVSTVPGGARNVQDIYPLAPLQEGILYHHLAAEQGDPYVLQAQFTFDSRERLDD
FTQALQGVIDRHDILRSSMAWEGLDEPVQVVWRKAVLGVEHVIPHDEEGDILAQLKASFD
VSHHRLDIRQAPLMRVRFAQDAVNQRWLATLLVHHMALDHTALEVMRHEIQMHLQGHAGQ
LGDAVPYRNYVAQVCLGVSREEHETFFRAMLGDIDEPTLPFGLQDVRGDGSSIEEAQQAI
STELSRRLRLQARQLGVSAASLYHLAWAQVLGRVSGREDVVLGTVLMGRMQGGEGADRAL
GMFINTLPISVQVGAQSVRDGVLTTHARLSGLLGHEHASLALAQRCSGVVAPTPLFSALL
NYRHSVAEPNALQASSTWEGIEEVGGEERTNYPLVLSVDDLGEGFSLTVQAVAEIGARRI
GAYMEAALTSLVVALECAAGTSLSDLTILPAQERDRLLVTFNATEIDYPQQQTIHGLFEE
QVQRTPDAVAVIRGEQRLTYHELNERANRLAHYLRKQGVEPDSRVAICVERGIDMVVGLL
AILKAGGGYVPLDPAYPLDRIAYMLDDSAPAVVLAQTATLELLAAASMPVIDLDSGLWQD
ESVQNPEVAELTSSHLAYVIYTSGSTGLPKGVMIEHRNTVNFLTWAHRSFDSQTLAKTLF
STSLNFDLAVYECFAPLTSGGSIEVVTNVLELQQGEHDITLINTVPSALKALLESGGLGE
GVDTVNVAGEALKRSLVETLFEQTQVKRLCNLYGPSETTTYSSWVSMAREDGFAAHIGKP
VANTQFYLLDEHKQPVPLGVPGEIYIGGAGVARGYLNRDDLTAERFLKDPFSAVPNARMY
KTGDLGRYLPDGNIEYLGRNDDQVKIRGFRIELGEIEAKLAQHAALNETVVLAREDVPGD
KRLVAYFTQHSPDESVDIEALRAYLQALLPSYMVPVAYVRLDALPLTPNGKLDRKALPAP
DLDAVISRGYEAPQGETETTLAQIWQDLLGLQQVGRHDHFFELGGHSLLAVTLIERMRQA
GLSADVRILFGQPTLAALAAAVGGSNEIVVPVNRIALDCERITPDMLTLTSLDQDAIDRI
VSTVPGGARNVQDIYPLAPLQEGILYHHLASEQGDPYVLQTQFAFDNRERLDAFIQALQS
VVDRHDILRSSMAWEGLDEPVQVVWRKAVLGVEHVIPHDEEGDILAQLKASFDVSHHRLD
IRQAPLMCVRFAEDAVNQRWLATLLFHHMALDHTALEVVRHEMQAHLSGQAGQLGDAVPY
RNYVAQVCLGVSREEHEAFFRAMLGDIDEPTLPFGLQDVRGDGSGIEEARQAIATDLSRR
LRTQARRLGVSAAALHHLAWAQVLGRVSGREDVVFGTVLMGRMQGGEGADRALGMFINTL
PIGVQVGAQSVRDAVLATHTRLSGLLGHEHASLALAQRCSGVIAPTPLFSALLNYRHSVA
EPIALQTSSAWQGIEILGSEERTNYPLTMSVDDLGKDFSLTVLVESRVGAQRICGYMQVA
LESLVEALEHAPQTPMCSLAILPLAERKQLLETWNATAAIYAHDPLIHRQFEAQAAAHPQ
AVAVVHAGQTLTYCELNARANQVAHRLLALGVCPDDRVAICVERSLEMVVGLLGVLKAGA
GYVPVDPAYPAERIAYLLQDSAPVAVLVQAVTQGLLAAGAVPVINLDNAGWQDESVSNPA
VPGLEARHLAYVIYTSGSTGLPKGVMVEHRNLSNLVGWHCQAFNVKRGSRTSSVAGFGFD
AAAWEIWPSLCAGATLLLPPAHAGSEDVGALLDWWQAQALDVCFLPTPIAEYAFGRNLGH
DQLRTLLIGGDRLRKLPADLPFELINNYGPTETTVVATSGRIDASQAVLHIGKPVANTQV
YLLDAHLQPVPVGVAGELYIGGAGVARGYLNRGQLTAERFVKDPFSLVQDARMYRTGDLG
RYLPDGNIDYLGRNDSQLKIRGLRIELGEIEARLGACAGVREAVVVAVGEAPDDQRLVAY
YTAHDTLDQALTADSLREQLQVHLPSHMVPAAYMCLDALPLTPNGKLDHRALPVPDSEAY
SGRGYAAPQGEVETALARIWSELLKVEQVGRYDNFFELGGHSLMAVSLIERMRQVGLSAD
VRVLFSQPTLAALAAAVGSGSEVSVPANLIPLDCEHITPAMLPLVALDPHAIERIVSTVP
GGARNVQDIYPLAPLQEGILYHHLSAEQGDPYLLQTLFAFETQDRLEDFARALQQVIDRH
DILRTSIRWEGFEQPLQIVWRKALLRRQEVALDPVDGDAAAQLYERFDSRHHRLDITQAP
MLRLVHAHDTDNDRWLAMLLFHHMTLDHTALDVMQHEIQACLSGEAAQLGAAMPYRNYVA
QARLGVSGEAHERFFRDMLGDVDEPTLPFGLQDVQGDGSDIEEVRQDVAADLSRRLRGQA
RQLGVSAASLYHLVWAQVLGQVSGKDDVVFGTVLMGRMQGGEGADRALGMFINTLPLRVS
VAQAGVRAGVKETHARLTALLAHEHASLALAQRSSGVQAPTPLFSALLNYRHTGATTAIE
LLPAWDGIQILSSEERTNYPLTLSVDDQGEAFSFTVMTPARIGAQRLCGYVQHTLENLVG
MLEQTPDQPLQHLSILPALEREQLLVTFNATEADYPQQQTVHGLFEDQAQRTPEAVAVIR
GEQRLTYHELNERANRLAHYLRKQGVEPDSRVAICVERGIDMVVGLLAILKAGGGYVPLD
PAYPLDRIAYMLDDSAPAAVLAQTATLELLAEASMPVINLDSGDWQDESVQNPEVAELTS
SHLAYVIYTSGSTGLPKGVMIEHRNTVNFLTWAHRSFDDATLSKTLFSTSLNFDLAVYEC
FAPLTSGGSIEVVTNVLELQQGEHDITLINTVPSALKALLESGGLGEGVDTVNVAGEALK
RSLVETLFEQTQVKRLCNLYGPSETTTYSSWVSMAREDGFAAHIGKPVANTQFYLLDEHK
QPVPLGVPGEIYIGGAGVARGYLNRDDLTAERFLKDPFRTAPNARMYKTGDLGRYLPDGN
IEYLGRNDDQVKIRGFRIELGEIEAKLAQHAALNETVVLAREDVPGDKRLVAYFTQHSPD
ESVDIEALRIYLQALLPSYMVPVAYVRLDALPLTPNGKLDRKALPAPDLDALITRGYEAP
QGEVEISLAQIWQDVLKVERVGRHDHFFELGGHSLLAVTLIERMRQAGLSADVRVLFGQP
TLAALAAAVGGGSEIDVPVNGIPFGCERITPDMLTLTSLDQDAIDRIVSTVPGGARNVQE
IYPVAPLQEGILYHHLSAEQGDPYVLHAQFAFDSRERLDGFTQALQSVIDRHDILRTAIL
WEGLDGPRQVVWREARLGLEELVLDPQAGAIAQQLQHRFDVRHYALDMTQAPLMRLAFAQ
DKPNQRWVAMLLFHHIALDHAALKVVQSEMQAYLLGQAGQLDVPVPYRNYVAQACLGVDR
EAQEGFFREMLGDVDEPTLPFGLQQVQGDSHDIEDASLVLDGDLSRRLRRLARQSGVGVA
SLHHLAWAQVLGQASGKQDVVFGTVLMGRMQGGQGADRALGMFINTLPLRVSVGDQAVKA
GVKAVHGQLTALLGHEHASLAVAQRCSGVAAPLPLFSALLNYRNSSEQADTEAAQLAWHG
IETLGGEARTNYPLTLCIDDLGEDFALTVLATSGVGAQRVCAYMATALQSLATALESDPT
SRLQTLAVLPQAERHQVLTGFNTTARRYPQDRTVHGLFEAQANERPQAVAAVHNEHSLTY
AELNHRANRLARHLVGLGVRPGDRVAIALERSLELLVSQLAILKCAAVYVPLDVSAPLER
QQFMVQDSGAQVVLTSGTAVAPEASQRVDLDTLVFNEAADNLHLTQSGESVAYIMYTSGS
TGTPKGVLVPHRAINRLVINNGYAEFNAQDRVAFASNPAFDASTLDVWAPLLNGGCVVVV
DQDVLLTQERFAALLQEQSVSVLWMTAGLFHQYAAGLMSVFAQLRYLIVGGDVLDPAVIG
RVLKEGAPLHLLNGYGPTEATTFTTTHEIKSVGEGGIPIGRPIGNTRVYVLDANQQPVPI
GVAGELYIGGDGVAKGYLNRPELSAEKFVADPFNADPGALLYRTGDLARWRADGTVDYLG
RNDDQVKIRGFRIELGEIEARLGQHDEVKDVVVLVREDVPGEKRLVAYFTPRDLDVAPHI
ETLRTHLQGQLPDYMIPVAYIRLDTLPLTANGKLDRRALPAPDSEAYVSREYEAPQGEVE
QLLAQLWAELLRVEQVGRHDNFFELGGHSLLAVTLIERMRQVGLSADVRVLFGQPTLAAL
AAAIGSGREVSVPANVIPLHCEHITPDLLPLVNLSQAAIDRLVATVPGGARNVQDIYPLA
PLQDGILYHHLAAEQGDPYVLKTVFELQSRDRLAAFVDALQYVIDRHDILRTSVVWQGFD
APIQVVWREAKLHLEEIALDIAKGEITAQLQERFDPQRYRLDITQAPLMRLVFAEDALNQ
RWVAVLLFHHMALDHTALEVVQQEMQAHLLGQTDQLPVAMPYRAYVAQARLGVSQQEHEG
FFREMLADVDEPTLPFGLQDVSGDGQAIEQARQVVEATLSLRLRAQARQLGVSAASLVHL
AWAQVLGRVSGKDDVVFGTVLLGRMQSGDGADRALGMFINTLPLRIDVSSQGVREGVKAT
HARLTGLLGHEHASLALAQRCSGVVAPLPLFSALLNYRHSASAAAEVSNETQAAWQGIEF
LSNEERTNYPLTLSVDDLGDGFLLSALVVQGIGAARICAYMHTALESLVQALEHAPQTPL
NRLEILPQSERNQLLEDFNATQRTYPHEQTVLALFEAQATYLPQAIAAVHGQRQVSYAQL
NEQANRLAHHLIGLGVQPDDCVAILLPRSIELLASQLAILKCAAAYVPLDRNASLERQGF
MLDDCQAKCLLTFSTETVPEGASRIDLDTLDSQGPVHNPALAQSSESIAYIMYTSGSTGQ
PKGVLVPHRAINRLVINNGYADFNAQDRIAFASNPAFDASTMDVWGALLNGGQVVVIDHE
TLLEPSRFAQVLQDSGVTVLFVTTAIFNQYVQLIPQALGGLRILLCGGERADVASFRRLL
DLAPGLRLVHCYGPTETTTYATTLEVKAVALDAECVPIGGPIGNTQVYVLDARQQLAPLG
VVGEMYIGGQGVAKGYLNRPDLTAEKFIADPFSHEPDALLYRTGDLGRWLPEGSLECLGR
NDDQVKIRGFRIELGEIEAKLVACDGVRDAVVLVRADETGEKRLVAYVIAQPQVTLSVAG
LREQLSSTLSEYMVPAAFVMLPAFPLTLNGKVDRKALPAPDAEAYASQAYAAPQGEIEQV
LAGMWAELLKVERIGRHDHFFELGGHSLLAVTLIERMRQAGLSADVRVLFSQPTLAALAA
AIGSGREVRVPANLIPLDCEHITPDLLPLINLSQEAIDRLVATVPGGARNVQDIYPLAPL
QEGILYHHLAAEQGDPYVLQSQFAFDNRERLDAFIGALQVVIDRHDILRTSVVWEGLDEP
VQVVWRQVVLAPQCIVLDATAGDIATQLASRFDARHSRLDLGRAPLLHLAYARDEAQDRW
IAILLFHHMALDHTALDVMQHEMQMHLLGQDEHLVASVPYRNYVAQARLGTSEQEHETFF
REMLGDIDEPTLPFGLAQVQGDGHGIEEVKAFVDDTLSQRLRTQARQLGVSAASLVHLAW
AQVLAVASGQENVVFGTVLLGRMQGGDGADRALGMFINTLPICVPVNEQNVRDAVKTTHA
RLTGLLGHEHASLALAQRCSEVASPAPLFSALLNFRHSSLQVTDEGLSAWNGMQMLSSEE
RTNYPLTLNVDDLGEGFSLTVQVESRIGAQRICDYVQVALQSLVDSLEHAPQTAVHNLAV
LPSAERKHLLETWNAPEATYAHDALIHRQFEAQVATQSDAVAVVFEDQVLTYGELNAQAN
QLAHRLLSLGIRPDDRVAICVERGLDMLVGLLGILKSGAGYVPLDPASPAERIAYMLEDS
APVAIVVHAATQALLAEESVRLIELDSPALRSQSTANPQVPGQTSSQLAYVIYTSGSTGL
PKGVMVEHRNVARLFSATQPWFEFGQQDVWALFHSFAFDFSVWEIWGALIHGGRLLVVPQ
LVSRSPQECYALLCQAGVTVLNQTPSAFRQLIVAQGESDLRHSLRQVIFGGEALETAMLK
PWYARVANAGTQLVNMYGITETTVHVTYRPLEAADAQLTGVSPIGKRIPDLQLYVLDARR
EPVPVGVVGEMYVGGAGVARGYLNRPELTQERFIADTFSGGEGARLYRTGDLGRWLADGS
IEYLGRNDDQVKIRGFRIELGEIEATLAACEGVSDALVIAREDAPGDKRLVGYVIAADGA
QLLAAELRAQLLASLADYMVPSAFVVLEAFPLTTNGKLDRKALPAPDQSAVATREYEAPQ
GETETVIAAIWQDLLDLERIGRHDNFFELGGHSLLAVKLLERMRHVGLSADVRVLFGQPT
LAALAAAVGGHTEVVV

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory