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:
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