Annotation: FitnessBrowser__pseudo5_N2C3_1:AO356_28210
Length: 10307 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% | 51% | 261.9 |
View AO356_28210 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...
MQFSELMAALSQHPIRLQQDGDNLVILGDDERMDHALWESLTVHKQELLDLVERNGGDWL SPAFRITPDMLPLADLTQEEIDRIVDTVPGGAGNVQDIYPLAPLQEGILYHHLAAEQGDP YVLQSLFGADRRTRLDDFAQALQGVIDRHDILRTSVVWEGLDEPVQVVWHEATLALEEVV LDPAAGDAVWQLQQRFDTRHHRLDVGQAPLMRLICAQDRDNDRWVAILLFHHMAIDHTAL ELVQGEMQAFLLGQAHQLPDPVPYRNYVAQVRLGVGGDSHEGFFREMLADVDEPTLPLGF AEVPEGQSVIEEAHLPIDASLSRRLRAQARQLGVSAASLHHLAWARVVGGLSGKQDVVFG TVLMGRMQGGDGADRALGMFINTLPLRVKLAGHGAREGVKNTHASLTALLGHEHASLALA QRCSGVAAPAPLFGALLNYRHSSTAQALSSQTLEAWEGLHALGGAEGTNYPLTLSVDDLG EGFSLSVLALAGMGAQRIAGYMRQALENLVWMLEQQPDMPLQRLSILPASEREQLLVTFN ATEADYPRQQTVHGLFEEQVQRTPDAVAVIRGEQRLSYRELNERANRQAHYLRKQGVEPD SRVAICVERSIDMVVGLLAILKAGGGYVPLDPAYPLDRIAYMLEDSAPAAVLTQTATLEL LAAASMPVINLESGDWQDESVQNPEVTELTSSHLAYVIYTSGSTGLPKGVMIEHRNTVNF LTWAHRSFDAQTLSKTLFSTSLNFDLAVYECFAPLTSGGSIEVVTNVLELQQGEHDITLI NTVPSALKALLESGGLGEGVDTVNVAGEALKRSLVETLFEQTQVKRLCNLYGPSETTTYS SWVSMAREDGFAAHIGKPVANTQFYLLDEHKQPVPLGVPGEIYIGGAGVARGYLNRDDLT AERFLKDPFSTAPNARMYRTGDLGRYLPDGNIEYLGRNDDQVKIRGFRIELGEIEAKLSQ HDALKEAVVVAREDVPGDKRLVAYFTQHSPVDIETLRTHLQAQLPAYMVPVAYVRLEALP LTPNGKLDRKALPAPDLDAVITRGYEAPQGETETTLAQIWQDLLKVERVGRHDHFFELGG HSLLAVTLIERMRQAGLSADVRVLFGQPTLAALAAAVGSGKEISVPANLIALDCERITPE LLPLANLSQTTIDRLVATVPGGVRNVQDIYPLAPLQEGILYHHLAAEQGDPYVLQSQFAF DNREHLDAFIGALQVVIDRHDILRTSIVWEGLDEPMQVVRREARLHLETLDLDPVAGDVA EQLRQRFDSRHYRLDIAQAPLMRLAYGRDEANHRLVATLLFHHLALDHTALEVVQHEMQA YLLGEAGQLAEAVPYRNYVAQARLGVNREEHEAFFRDMLGDIDEPTLPFNLQDVQAGGHD IEEAHQALDDALDQRLRAQARQLGVSAASLVHLAWAQVLAKVSGKQEVVFGTVLMGRMQG GEGADRALGMFINTLPLRVTLGEQGVKAGVKAVHGQLTALLGHEHASLALAQRCSGVAAP LPLFSALLNYRHAATTTSNEVSSAWSGMQALGGEERTNYPLTLNVDDLGTGFNLTVLVGQ EIGAQRICAYMHAALQTLVLALEQTPQAALHRLSILPAAEIEQLLVTFNATEADYPQQQT IHGLFEEQVQRTPEAVAVIRGEQRLSYGELNERANRLAHYLRKQGVKPDSRVAICVERGI DMVVGLLAILKAGGGYVPLDPAYPLDRIAYMLEDSAPAAVLAQDATVGLLSDASMAVINL DSGDWQDESVQNPEVTELTSSHLAYVIYTSGSTGLPKGVMIEHRNTVNFLTWAHRSFDSQ TLAKTLFSTSLNFDLAVYECFAPLTSGGSIEVVTNVLELQQGEHDITLINTVPSALKALL ESGGLGEGVDTVNVAGEALKRSLVETLFEQTQVKRLCNLYGPSETTTYSSWVSMAREDGF AAHIGKPVANTQFYLLDEHKQPVPLGVPGEIYIGGAGVARGYLNRDDLTAERFLKDPFST APNARMYKTGDLGRYLPDGNIEYLGRNDDQVKIRGFRIELGEIEAKLAQAPNIKETVVLA REDVPGDKRLVAYFTQHSPVDIEALRTHLQAQLPAYMVPVAYVRLEALPLTPNGKLDRKA LPAPDLDAVITRGYEAPQGEVEISLAQIWQDLLKVERVGRHDHFFELGGHSLLAVSLIGR MRQLGLSADVRVLFSQPTLAALAAAVGSGGEVVVPDNGILLGCTRITPSMLPLVALDQQD IDRLVETVPGGARNVQDIYPLAPLQEGILYHHIAAHTGDPYVLQATFTVADRERLEAFAQ ALQGVIDRHDILRTSVVWEGLDEPVQVVWRKAQLAVEELVLSAEAGDIAGQLRERFDTLH YRLDMQQAPLMRIAFAHDPANQRWVAMLLFHHMVLDHTALEVVQHEMQAHLLGQADQLGQ AVPFRNYVAQARLGVSREEHEGFFRDMLSDVDEPTLPFGLLDVRGDGSDIEEAGLSLPAD LSRRLRAQARQLGVSAASLHHLAWAQVLGQVSGKQDVVFGTVLMGRMQGGDGAEHALGMF INTLPLRVGVGAQGVRDGVKATHARLTGLLGHEHASLALAQRCSGVVAPMPLFNALLNYR HSAAGVASNEALVAWDGIQLLSNEERTNYPLTLSVDDLGEAFHLSALAVPQVGAQRICAY MNIALEHLVEALEQAPQTPLHSLSILPPAERRQLLVDFNATTRSYPQDRTVHGLFEARAK ELPEATAVVHNGHSLTYAELNRRANCLTRHLIGLGVQPGDRVAILLERSVGLLVSQLAIL KCAAVYVPLDVSAPLERQDFMVRDSGARTLLTLSAMAVPEGIARVDLDSVVLETEADHDL RLIQSTESVAYIMYTSGSTGTPKGVLVPHRAINRLVINNGYAEFNAQDRVAFASNPAFDA STLDVWAPLLNGGCVVVVDQDVLLTQERFAALLQEQSVSVLWMTAGLFHQYAAGLMSVFA QLRYLIVGGDVLDPAVIGRVLKEGAPQHLLNGYGPTEATTFTTTHEIKSVGEGGIPIGRP IGNTRVYVLDANRQPVPIGVAGELYIGGDGVAKGYLNRPELSAEKFVADPFNADPGALLY RTGDLARWRADGAVDYLGRNDDQVKIRGFRIELGEIEARLGECPGVKDAVVLARQDDAGP KRLVGYVIPEPGVTLSVHALREQLSSVLADYMLPSAFVVLPAFPLTANGKLDRRELPAPD AEAYASREYEAPLGKVEQTLAQIWADVLKVEQVGRHDHFFELGGHSLLAVTLIERMRQAG LSADVRVLFSQPTLAALAAAIGSGREVSVPPNLIPLHCEHITPDLLPLINLSQDAIDRLV ATVPGGARNVQDIYPLAPLQEGILYHHLAAEQGDPYVLQSQFAFDNRERLDAFIGALQMV IDRHDILRTSVLWEGLDEPVQVVWRQVLLESQCIVPDATAGDVATQLANRFDARHYRLDL GRAPLLQLAYARDEAQDRWVAILLFHHMALDHTALDVMQHEMQMHLLGQGEQLGAAMPYR NYVAQARLGTSEQEHETFFREMLGDIDEPTLPFGLQDVQGEGHGIDEDRQPVDLALSRRL RVQARHLGVSAASLVHLAWAQVLGKVSGKQEVVFGTVLLGRMQGGDGADRALGMFINTLP LRVDVGTQDVRSGVKATHGRLTALLGHEHASLALAQRCSGVVAPTPLFSALLNYRHSAVQ VTQDALSAWSGINALGGDERTNYPLTLNVDDLGDGFFLTVMVDTAIGAQRICGYMQVALE NLVMALEQAPQTPLHALAILPSAERRQLLETWNTTDVTYADDALIHRQFEGWAASQPDTV AVVHEEQALTYGELNARANQLAHSLVALGVRPDDRVAICVERGLDMIIGLLGILKAGAGY VPLDPTYPPERIAYMLHDSSPVAVVTQSQWRDSLPVLPVPTLVLDPTDAGEMNQQPRHNP DVADLNASHLAYVIYTSGSTGLPKGVMVEHRNVARLFSATQPWFEFGPQDVWALFHSFAF DFSVWEIWGALTHGGRLLVVPQLVSRSPQYCYALLCEAGVTILNQTPSAFRQLIAAQGES DLSHSLRQVIFGGEALETGILKPWYARQANARTQLVNMYGITETTVHVTYRPLDAADAQL AGVSPIGKRIPDLQLYVLDTQREPVPVGVTGEMYVGGGGVSRGYLNRDELTAERFLDNPF SPEPNARMYRTGDLGRWLADGSIEYLGRNDDQVKIRGFRIELGEIEAKLAACNGVREAVV VARQDTPGDQRLVAYVIAEEGEPPSAAELRDELLGSLAEYMVPSAFVMLTVFPLTTNGKL DRKALPVPDQSSVVTREYEAPQGEVEIAIARIWQDLLHVERVGRHDHFFEMGGHSLLAVK LVERMRQIDLAADVRVLFGQPTLAALAAAVGGCQEVQVPANLIPDDCSRITPDLLPLATL SQDEIDRVVATVPGGVGNVQDIYALTPLQEGILYHHVAAAKGDPYLQYILFAFDSRARLD LFAKALQSTVSRHDILRTGVVWEGIDEPVQVVWREARLGFDEIMLDPAAGDIARQLRERL DPRHYRLDIRQAPMMRIGYAQDVANDRWVGMLLFHHMVDDATSLAMLAAEIGAHMSGGEQ ALAASVPYRNFVAQARLGVSREEHEAFFHEMLGDVAEPTLPFGLQDVQGDGHDIEEVRQR VDAELGQRLRVQARQLGVSAASLYHLAWALVLGKVSGKEDVVFGTVLLGRMQGGEGADRA LGMFINTLPLRVSLGAQGVRAAVKSTHARLTALLGHEHASLVLAQRCSGVAAPTPLFSAL LNYRHLGAQAPSSEVIAAWEGIQTLEGEERTNYPLTLSVDDLGEGFNLTVMAQAPIGAER VCNYVQCVVENLVQALEQSPLAPLSGLKILPPAERRQLLESWNGTGVAFAQDALIHAQFE VWAAAQPEAMAVMFEERTLTYSELNARANQVAHRLLAQGIRPDDRVAICVERGLDMIVGL LGILKAGAGYVPVDPAYPTERIAYMLRDSMPVALLAHAATHRLLAGVSMPVLQLDDGSWQ DESVANPQVPGLDSSHLAYVIYTSGSTGLPKGVMVEHRNVARLFSATQPWFDFGQQDVWA LFHSFAFDFSVWEIWGALTHGGRLLVVPQLVSRSPQDCYALLCETGVTVLNQTPSAFRQL IVAQGESDLRHSLRQVIFGGEALETGMLKPWYARVGNAGTQLVNMYGITETTVHVTYRAL EAADAQSTGVSPIGKRIPDLQLYVLDAQREPAPVGVVGEMYVGGAGVSRGYLNRDELTAE RFLDNPFSPEPNARMYRTGDLGRWLADGSIEYLGRNDDQVKIRGFRIELGEIEATLAACE GVSEAVVIAREDEPGDKRLVAYVIATEGAQPSAVDLRTQLLRSLAEHMVPSAFVILDAFP LTTNGKLDRKALPAPDQSAVISREYEAPQGEVETTIARIWQDLLKLGRVGRHDNFFELGG HSLLAVKLIERMRQVDLAADVRVLFGQPTLAALAAAVGGVREVVVPGNAIADGCTRITPD MLPLADLDQDAIDRIVATVQGGVTNVQDIYALAPLQEGILYHHLAAEQGDPYVLQVLFGF DNRERLQAFAQALQSVVSRNDILRTSMVWQGLEAPVQVVWRHATLGLEEIEVDPAGGEVV QQLHGRFDPRHYRLDIAQAPLMRFAFAQDVANQRWVGMLLFHHMALDHTALEVVVHEMQA SLLGQAHLLSPAVPYRNHVAQARLGVSREQHEAFFREMLGDIDEPTLPFGLQDVQGDGSG IEEAHQDVDAALAQRLRAQARQLGVSAASLVHLAWGHVVGRVSGREEVVFGTVLMGRMQG GDGADRALGMFINTLPLRVSVGAQGARAGVKATHGRLSALLGHEHASLSLAQRCSGVPTS LPLFSTLLNYRHSAAEAVSDQAISAWQGMQTLHMEERTNYPLCLNVDDLGEGFRFTAQAV VEVGAQRVCGYMHTALESLVAALEQTPERALRELPIVPAAEREQLLVDFNATHADYPQEQ TIHGLFEAQVLRTPDAVAVRHGRHQLNYRELNGLSNRLAHYLRKQGVEPDSRVAICVERG IEMVVGLLAILKAGGGYVPLDPAYPLDRIAYMLEDSAPAAILVQGTTRNLLGETAIPVID LDKGIWQDEAAPNPQVPGLSSSHLAYVIYTSGSTGLPKGVMIEHRNTVNFLTWAHRSFDA QILSKTLFSTSLNFDLAVYECFAPLTSGGSIEVVTNVLELQQGEHDITLINTVPSALKAL LESGGLGEGVDTVNVAGEALKRSLVETLFEQTQVKRLCNLYGPSETTTYSSWVSMAREDG FAAHIGKPVANTQFYLLDEHKQPVPLGVPGEIYIGGAGVARGYLNRDDLTAERFLKNPFS TAPNARMYRTGDLGRYLPDGNIEYLGRNDDQVKIRGFRIELGEIEAKLAQHDALKEAVVV AREDVPGDKRLVAYFTQHSPDETVEIEALRTHLQTQLPAYMVPAVYVRLDALPLTPNGKL DRKALPAPDLDAVISRGYEAPQGEVETTLAQIWQDLLDLQQVGRHDQFFELGGHSLLAIQ LISQVRLRLGVELGLTELFAQPQLMGLAQAVALAGRSTLPEIVRVSRKDDLPLSFAQQRL WFLAQMEGASAAYHIPAGLRLRGVLDRLALQRALDRIVARHEALRTTFVQVRGQEARQCI APVDVGFALLHHDFCGLADAEGQLHALAAQEATDTFSLEQGPLIRGRLVRLGSEDHVLLL TMHHIVSDGWSIGVLIKELTALYEAFRHDLDDPLPALTVQYSDYAVWQRRWLSGEVLQTQ SDYWRQALADAPALLMLPTDRARPAQQDYAGATLPVVFDADLTASLKALSQRHGVTLYMT MMAAWGALLSRLSGQDEVVIGSPVANRTRSEVEGLIGFFVNTLAVRIDLSGAPTVETLLA RVKAQALGAQAHQDLPFEQVVEVLKPVRSLAHSPLFQAMLSWQTHDNTELVLGDLKLEGL GAASNVAKFDVSLELSEIQGQMFGALEYATALFDEGTVQRYLGYFQRLLRAMVASDQTRI ERIALLDNAEREHLLAGLNATQAAYPREQTIHQLFEAQVEARPDAIAVAFGDERLSYAEL NRQANQMAHHLIGLGIRPDDRVAICVERGADMLIGLLAILKAGAGYVPLDPAFPAERLAY MLADSAPVALLSQGELLDRLPAFTVPVVLLDRAERVRCGIAAGRDDNPLVASLGVRHLAY VIYTSGSTGNPKGVMIEHRGLVNYCVDAVRLFGLTPDDTVLQQNTLNFDLSVEEIFPALL AGATLAPTRQLFGSAELQQNGDIRPTFLHLTAAHWHTLAAEWHNSPAQARDYLRDVRLIN VTGDALSTQKLQMWDAVRPAHTRLVNTYGPTEATVSCTAAYMEHDAVDGILGNASIGRPM ANTRIYLLDAHRQPVPFGVAGEIFIGGDGVARGYLNLDAINAERFLADPFSDQPDARLYK TGDLARYRPDGRLEYLGRNDFQVKVRGFRIELGEIEARLGDCAGVKEAAVIVREDTPGDK RLVAYVVPQAGVNLNAASLRAQLAVQLAEYMLPGAFVSLAALPLTPNRKLDRQALPAPDA EAYASRTHEAPQGHTEIVLAQIWQSLLKVESVGRHDHFFELGGHSLLVMRLIAQVREQLG VELNLRDVFAQPQLSALAQVLSQAAHSTRPGIVPVSREQALPLSFAQQRLWFLAQLDGTS AAYHIPTGLRLRGALDTSALTRALDRIVARHEALRTTFVQAQGQEVEQRIAPVDVGFALR LQALAGRADAETELMALAEEEARQAFDLAHGPLVRGRLVRMADDDHVLVVTLHHIVSDGW SADLLTHELGVLYEAFRQGQDDPLPALPIQYADYALWQRRWLTGEVLDQQERFWRQTLAD APALLTLPTDRPRPAQQDHAGAAVGIVLDETLTQGLKALSQRHGATLFMTVMAAWATVLS RLSGQHDVVIGTPVANRMQAEVEGLIGLFVNTLALRVDVADELTVQALLQQVKVRTLDAQ AHQDLPFEQVVEVVRPLRSLSHSPVFQAMLSWQNNEATGLELGDMSLQGLGVTSRTAKFD VLLDMALIDGRLFGALEYATALFDSATMERYLGYLESVLRAMVADEQTLVAQIPLLGDNE RQNLLETLNATAVDYPQGLTLHGLFEARVVASPDAVAVVSGEAQLSYAQLNERANQIAHR LLELGIRPDDRVAICADRSLDMVAGLLGILKAGAAYVPLDPDYPHERLAYMLENSAPMVV LTQRALQASLPATQARTLLLDEAQGFSTQPTDNPQVEGLHAHHLAYVIYTSGSTGLPKGV MNEHGGVVNRLLWMQDEYGLTATDAVLQKTPFSFDVSVWEFFWPLFSGARLVMARPGGHR DPAYLREVIQAQGITTLHFVPSMLDVFLAHGEASQCAGLVRVMCSGEALPGHLVRRFKAQ LPHTGLYNLYGPTEAAVDVTAWDCAGTDTPDSTPIGKPIANTRIYLLDGHQQPVPMGVAG EIYIGGVQVARGYLNRPELTVERFLRDLFSRAANARMYRTGDLGRYLPDGNIEYLGRNDD QVKIRGFRIELGEIEAKLAQHEAIKEAVVLALEDVPGAKRLVAYFTVHGDEHSVEIENLR TQLQAQLPEYMVPAAYVRLQALPLTPNGKLDRKALPAPDLASVITREYEAPQGAVETTLA QLWAELLKVEKVGRHDHFFELGGHSLLAVTLIERMRQAGLSADVRVLFGQPTLAALAAAV GGTTEIVVPDNGIVPGCERITPQMLPLADLTQQEVDAIVAWVPGGVSNVQDIYALAPLQE GILYHHLVSSQGDLYVQQAMFNLEDRARLDAFVSALQGVIDRHDILRTAVLWEGLREPVQ VVLREAPLAVQTCTVEPGEDVATQLRERFDPRHSRLDVRQAPMMRLACAYDDEHQRWVAL LLFHHIALDHTALEVIQHDMQAYLLGQQAQLGDAVPYRNYVAQARLGVTQSAHEAFFRDM LQDIQEPTLPFGLQDVQGDSHVIEQARLGVDDSLNRRLRTQSRLLGVSAASLHHLAWARV VGAVSGRENVVFGTVLMGRMQGGEGADRALGLFINTLPLRVDVGVDGARAGVKATHARLT ALLGHEHASLALAQRCSGVATSTPLFSALLNYRHTATQVTEEAQSAWNGIEGLGGEEWSN YPLSLNIDDLGEAFVLTALAESRIGAERICGYMHTALESLVDALERTPEAPVRELAILPA AERRQLLVDFNATDTVYPREETVHGLFEAQVRARPDAIALQHGAQQLTYRELHERANHLA HCLLERGVQPGSRVAIMLNRSFELIISELAILKCAAVYVPLDHHAPEERQRFMLQDSAAV LVLTTRDRALPEDMPRLDLDTLQLIQAARPAVFPGQTSDTPAYIMYTSGSTGHPKGVIVP HLAIGRLAINNGYADFGVQDRVAFASNPAFDASTMEVWGALLNGGRVVIIDHETLLSPTQ FAQALTEAEVSVLFVTTAMFNQYLVLIPDALAGLRILLCGGERGDPASFRRLLAHAPSLR LVHCYGPTETTTFATTHVVSAVPHGATSVPIGRPIANTRVYILDAARQPVPVGVAGEIHI GGVGVALGYLNRPDLTEERFIADPFSDSGSARLYRSGDLGRWLPDGTIEYLDRNDGQVKI RGFRIELGEIEARLHECHGVREALVVAREDSPGDKCLIAYYTEHENGGDLDADVLRAQLR SVLPEYMIPAAYVRLTALPLTLNGKVNTGALPVPEMHAYGSQDYEAPQGDLEVTLAGLWA DVLKLEQIGRHDNFFELGGHSLLAIRLVGLLAQANLTVSLAELFQHESVASMASMLLART EDARVKEAIVPVRTTGQQNPLFLVHEFSGLDLYFPMLGKHIDPDIPVYGLPAVEWGEPQL QTMECMASRLVGIIRSVQPKGPYRLAGWSFGGVLAYETAIQLIGLDEEVEFVGLIDSYLP RLVDQGRSRWALDEAHKLHLLDRCDVFWRAALPGEEVLAVMLENLADLQGQLDRFDFTGL VQHCRDEALLPAELAVYSAEQLWQYLDREVAHGHALAHYAVYPISVPVHLLVAEERKDDA PEHSGYLGWDAVLPTSKLHCIKVPGNHQSMMQAPHVKALGQAITAALHTAASRPAPSPKS GYQPLLTIQGGRTDRAPIFCVPGAGDSVTGFIGLTDAFGPDWPIHGLQHRGLDGSTEPFS LVETAAQVYLDAIDKVQPEGPVHLLGHSFGGWIVFEMAARLHARGRKVASLTLIDSESPG GNGVVGKPYTATGVLNRLIEAMQLASGKSLGIDATVFGTQDDTAQMRLLHAGMVRAGMLP QRSAVDSMRGPARAFGTALRTVYQPQHRYTGPVRLVLADDPTLDTAGNKREQEQMIEGWR KHIPDLSIWYGPGNHFTILKAPHVHNLAAWWQDGLPMLDEEAASDYV
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