Align Phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_013088370.1 BC1002_RS01835 FAD-linked oxidase
Query= reanno::BFirm:BPHYT_RS03150 (1364 letters) >NCBI__GCF_000092885.1:WP_013088370.1 Length = 1368 Score = 2645 bits (6855), Expect = 0.0 Identities = 1306/1368 (95%), Positives = 1343/1368 (98%), Gaps = 4/1368 (0%) Query: 1 MNAPQVFDPHGAAATVAADPEARLREIPYNYTSFSDREIVIRLLGDEAWAVLAELRAERR 60 MNAPQVFDPHGAAA VAADPEARLREIPYNYTSFSDREIVIRLLG++AW LAELRAERR Sbjct: 1 MNAPQVFDPHGAAAAVAADPEARLREIPYNYTSFSDREIVIRLLGNDAWDALAELRAERR 60 Query: 61 TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAMLIEALHHRLSEIEKRRRADLTEH 120 TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRA+LIEAL+HRL+EIEKRRRADL+EH Sbjct: 61 TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRALLIEALNHRLAEIEKRRRADLSEH 120 Query: 121 GDEAGVDRAARVETLVQAARRAVDEFASEFQKTYDLRKRATKVLGKVTEKDNIKFDGLSR 180 GDEAGVDRAARVE LVQAARRA+D+FASEFQ+TYDLR+R T+VLGKVT+KDNIKFDGLSR Sbjct: 121 GDEAGVDRAARVEKLVQAARRAIDQFASEFQQTYDLRRRTTRVLGKVTQKDNIKFDGLSR 180 Query: 181 VSHVTDATDWRVEYPFVVLTPDTEAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF 240 VSHVTDATDWRVEYPFVVLTPD+EAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF Sbjct: 181 VSHVTDATDWRVEYPFVVLTPDSEAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF 240 Query: 241 SAVINTEKLEQLGAVEMTELPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD 300 SAVINTEKLEQLG VEMT+LPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD Sbjct: 241 SAVINTEKLEQLGPVEMTQLPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD 300 Query: 301 ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNMGKIHDIEVARF 360 ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRL+HNMGKIHDIEVARF Sbjct: 301 ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLEHNMGKIHDIEVARF 360 Query: 361 RLDWFDGNYAPGEKLMRTEALDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA 420 L WFDGNYAPGEKL+RTE+LDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA Sbjct: 361 ELKWFDGNYAPGEKLLRTESLDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA 420 Query: 421 RWVLHKMPAHTRTVCLEFFGQARDAIPSIVEIKDYLFETSKQGGAILAGLEHLDERYLRA 480 RWVLHKMPAHTRTVCLEFFGQAR+AIPSIVEIKDYLFETS+QGGAILAGLEHLDERYLRA Sbjct: 421 RWVLHKMPAHTRTVCLEFFGQAREAIPSIVEIKDYLFETSRQGGAILAGLEHLDERYLRA 480 Query: 481 VGYATKSKRNAFPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAVNAEARKRFW 540 VGYATKSKRNAFPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAV+AEARKRFW Sbjct: 481 VGYATKSKRNAFPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAVSAEARKRFW 540 Query: 541 LDRSRTAAIAKHTNAFKINEDVVIPLDRMGEYTDGIERINIELSIKNKLQLVDALEAFFK 600 LDRSRTAAIAKHTNAFKINEDVVIPLDRM EYTDGIERINIELS+KNKLQLVDALEAFFK Sbjct: 541 LDRSRTAAIAKHTNAFKINEDVVIPLDRMDEYTDGIERINIELSLKNKLQLVDALEAFFK 600 Query: 601 GGKLPLGKSDDANEIPSAELLEDRVQQALDLLKRVRTRWEFLRDKLDLSLREAQHYLVGL 660 GGKLPLGKSDDANEIPSAELLEDRVQQALDLL RVRTRWEF+RDKLDLSLREAQHYLVGL Sbjct: 601 GGKLPLGKSDDANEIPSAELLEDRVQQALDLLARVRTRWEFVRDKLDLSLREAQHYLVGL 660 Query: 661 GYEAMAEKFADRVDAQPDVNVFHVTQDRTIRVSWKQEIRAELRQIFNGGEFKPILDEAQA 720 GYE++AEKFADRVDAQPD VFH+ QDRTIRVSWKQEIRAELRQIFNGGEFKPILDEAQA Sbjct: 661 GYESLAEKFADRVDAQPDATVFHLAQDRTIRVSWKQEIRAELRQIFNGGEFKPILDEAQA 720 Query: 721 IHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAHTAVARIMKLARSLDGVISG 780 IHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAH AVARIMKLARSLDGVISG Sbjct: 721 IHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAHAAVARIMKLARSLDGVISG 780 Query: 781 EHGIGITKLEFLTEDEISEFRQYKQRVDPHGRFNAGKLLEGADLRNAYTPSFGLMGYESL 840 EHGIGITKLEFLT+DEI EFR+YKQRVDPHGRFNAGKLLEGADLRNAYTPSFGLMGYESL Sbjct: 781 EHGIGITKLEFLTDDEIGEFRKYKQRVDPHGRFNAGKLLEGADLRNAYTPSFGLMGYESL 840 Query: 841 IMQQSDIGAISESIKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQT 900 IMQQSDIGAISESIKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQT Sbjct: 841 IMQQSDIGAISESIKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQT 900 Query: 901 RRGVSIKHWDEFNDVADHCTVCHKCVTPCPVKIDFGDVTMNMRNLLRKMGKKKFNPGNAA 960 RRGVSIKHWDEFNDVADHCTVCHKCVTPCPVKIDFGDV+MNMRNLLRKMGKKKFNPGNAA Sbjct: 901 RRGVSIKHWDEFNDVADHCTVCHKCVTPCPVKIDFGDVSMNMRNLLRKMGKKKFNPGNAA 960 Query: 961 GMFFLNATNPQTINLARTAMMGVGYKAQRLGNEVLKKFTKKQTAHPPATVGKPPVTQQVI 1020 GMFFLNATNPQTINLARTAMMGVGYKAQRLGNEVLKKFTKKQTAHPPATVGKP +TQQVI Sbjct: 961 GMFFLNATNPQTINLARTAMMGVGYKAQRLGNEVLKKFTKKQTAHPPATVGKPAITQQVI 1020 Query: 1021 HFMNKKMPGNLPKKTARALLDIEDNKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVG 1080 HFMNKKMPGNLPKKTARALLDIEDNKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVG Sbjct: 1021 HFMNKKMPGNLPKKTARALLDIEDNKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVG 1080 Query: 1081 LATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQFDKAEQIVTDNRVLFHRVANTLNYLDIK 1140 LATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQ+DKAEQIVTDNRVLFHRVANTLNYLDIK Sbjct: 1081 LATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQYDKAEQIVTDNRVLFHRVANTLNYLDIK 1140 Query: 1141 TVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHEFLLEKGMKLDGVNGVRYMYHDPCHTPIK 1200 TVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHE+LLEKG+KLDGVNGVRYMYHDPCH+PIK Sbjct: 1141 TVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHEYLLEKGIKLDGVNGVRYMYHDPCHSPIK 1200 Query: 1201 TMDPIKLVNQLMGSEKDGYKIEKNDRCCGESGTLAVTRPDISTQVRFRKEEEIRKGAAKL 1260 TMDP+KLVNQLMGSE+DGYKIEKNDRCCGESGTLAVTRPDISTQVRFRKEEEIRKGAAKL Sbjct: 1201 TMDPVKLVNQLMGSEQDGYKIEKNDRCCGESGTLAVTRPDISTQVRFRKEEEIRKGAAKL 1260 Query: 1261 RGIPLVAEAGANGINPANASAGSAGAPEGSVLKAGDGPQP----KGATDVKILTSCPSCL 1316 RGIPLVAEAGAN INPANASAGSAGAP GSVLKAGDGPQP G+TDVKILTSCPSCL Sbjct: 1261 RGIPLVAEAGANAINPANASAGSAGAPNGSVLKAGDGPQPGNGNAGSTDVKILTSCPSCL 1320 Query: 1317 QGLSRYNEDAGIEADYIVVEMARHVLGEDWMVDYVQRANNGGIERVLV 1364 QGLSRYNEDAG EADYIVVEMARHVLGE+WM DYVQRANNGGIERVLV Sbjct: 1321 QGLSRYNEDAGTEADYIVVEMARHVLGENWMADYVQRANNGGIERVLV 1368 Lambda K H 0.320 0.136 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 4928 Number of extensions: 186 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 1364 Length of database: 1368 Length adjustment: 49 Effective length of query: 1315 Effective length of database: 1319 Effective search space: 1734485 Effective search space used: 1734485 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 60 (27.7 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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