Annotation: FitnessBrowser__pseudo5_N2C3_1:AO356_28220
Length: 8596 amino acids
Source: pseudo5_N2C3_1 in FitnessBrowser
| 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 |
View AO356_28220 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
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.
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:
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 paper from 2022 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