Align Phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate RR42_RS02380 RR42_RS02380 FAD-linked oxidase
Query= reanno::BFirm:BPHYT_RS03150 (1364 letters) >FitnessBrowser__Cup4G11:RR42_RS02380 Length = 1324 Score = 2237 bits (5796), Expect = 0.0 Identities = 1101/1365 (80%), Positives = 1198/1365 (87%), Gaps = 42/1365 (3%) Query: 1 MNAPQVFDPHGAAATVAADPEARLREIPYNYTSFSDREIVIRLLGDEAWAVLAELRAERR 60 MNAP V D A A D ARLREIPYNYTSFSDREIVIRLLG+EAW +LAELR ERR Sbjct: 1 MNAPLVLD----AKLAAQDAPARLREIPYNYTSFSDREIVIRLLGEEAWRILAELRGERR 56 Query: 61 TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAMLIEALHHRLSEIEKRRRADLTEH 120 TGRSARMLYEVLGDIWVVRRNPYLQDDLL+NPKRR ML+ ALHHRLSE+EKRR AD EH Sbjct: 57 TGRSARMLYEVLGDIWVVRRNPYLQDDLLENPKRRQMLVTALHHRLSEVEKRRAADRAEH 116 Query: 121 GDEAGVDRAARVETLVQAARRAVDEFASEFQKTYDLRKRATKVLGKVTEKDNIKFDGLSR 180 + A DR+ RVE LV A++A+++F EF YDLRKR +VLG++T+KDNIKFDGLSR Sbjct: 117 AEPAAEDRSHRVEQLVSFAKQAIEDFKQEFAHAYDLRKRTQRVLGRITQKDNIKFDGLSR 176 Query: 181 VSHVTDATDWRVEYPFVVLTPDTEAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF 240 VSHVTDATDWRVEYPFVVLTPDTE EIAGM+K CFELGLT+IPRGGGTGYTGGAVPLTP Sbjct: 177 VSHVTDATDWRVEYPFVVLTPDTEEEIAGMVKGCFELGLTIIPRGGGTGYTGGAVPLTPM 236 Query: 241 SAVINTEKLEQLGAVEMTELPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD 300 SAVINTEKLEQLG VE T+LPGV KV TIFSGAGVVTRRV +AA++AG VFAVDPTS+D Sbjct: 237 SAVINTEKLEQLGPVEQTDLPGVSHKVGTIFSGAGVVTRRVADAADKAGLVFAVDPTSID 296 Query: 301 ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNMGKIHDIEVARF 360 ASC+GGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHN+GKIHD+ VA F Sbjct: 297 ASCIGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNLGKIHDVAVATF 356 Query: 361 RLDWFDGNYAPGEKLMRTEALDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA 420 L W DGN APGEK +RTE L I+GR FRKEGLGKDVTDKFLAGLPG+QKEGCDG+ITSA Sbjct: 357 ELKWSDGNRAPGEKPLRTETLAIEGRKFRKEGLGKDVTDKFLAGLPGIQKEGCDGIITSA 416 Query: 421 RWVLHKMPAHTRTVCLEFFGQARDAIPSIVEIKDYL-FETSKQGGAILAGLEHLDERYLR 479 RW+LH+MPAH RTVCLEFFGQARDAIPSIVEIKDYL E+ GGAILAGLEHLDERYLR Sbjct: 417 RWILHRMPAHVRTVCLEFFGQARDAIPSIVEIKDYLDAESRTPGGAILAGLEHLDERYLR 476 Query: 480 AVGYATKSKRNAFPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAVNAEARKRF 539 AVGYATKSKRNAFPKMVLIGDIVGDD DAVA+ATSEV+RMANGKSGEGFVAV+ EARK+F Sbjct: 477 AVGYATKSKRNAFPKMVLIGDIVGDDQDAVARATSEVIRMANGKSGEGFVAVSPEARKKF 536 Query: 540 WLDRSRTAAIAKHTNAFKINEDVVIPLDRMGEYTDGIERINIELSIKNKLQLVDALEAFF 599 WLDRSRTAAIA+HTNAFKINEDVVIPL RMGEYTDGIERINIELSIKNKLQL DALEAFF Sbjct: 537 WLDRSRTAAIARHTNAFKINEDVVIPLPRMGEYTDGIERINIELSIKNKLQLTDALEAFF 596 Query: 600 KGGKLPLGKSDDANEIPSAELLEDRVQQALDLLKRVRTRWEFLRDKLDLSLREAQHYLVG 659 G LPLG+SDDANEIPSAELLEDRVQ AL LL+ +R+RW +L+D LD L A+ L+G Sbjct: 597 ARGNLPLGRSDDANEIPSAELLEDRVQHALQLLREIRSRWTYLQDHLDTPLATARASLIG 656 Query: 660 LGYEAMAEKFADRVDAQPDVNVFHVTQDRTIRVSWKQEIRAELRQIFNGGEFKPILDEAQ 719 G + + F R++ QPD VFH+ QDRTIRVSWK E+RAELR IFNGGEFKPILDEAQ Sbjct: 657 HGLGLLGQAFEARLEQQPDATVFHLLQDRTIRVSWKSEVRAELRNIFNGGEFKPILDEAQ 716 Query: 720 AIHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAHTAVARIMKLARSLDGVIS 779 IHKQVLRGRVFVALHMHAGDGNVHTN+PVNSD+Y+MLQDAH AVARIM LARSLDGVIS Sbjct: 717 KIHKQVLRGRVFVALHMHAGDGNVHTNIPVNSDDYDMLQDAHRAVARIMALARSLDGVIS 776 Query: 780 GEHGIGITKLEFLTEDEISEFRQYKQRVDPHGRFNAGKLLEGADLRNAYTPSFGLMGYES 839 GEHGIGITKLEFLTEDEI EFR+YKQRVDP GRFN GKLL GADLRNAYTPSFGLMG+ES Sbjct: 777 GEHGIGITKLEFLTEDEIGEFREYKQRVDPQGRFNKGKLLPGADLRNAYTPSFGLMGHES 836 Query: 840 LIMQQSDIGAISESIKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQ 899 +IMQQSDIGAI++S+KDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQ Sbjct: 837 IIMQQSDIGAIADSVKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQ 896 Query: 900 TRRGVSIKHWDEFNDVADHCTVCHKCVTPCPVKIDFGDVTMNMRNLLRKMGKKKFNPGNA 959 TRRG+SIKHWDEF+DVADHCTVCHKCVTPCPVKIDFGDV+MNMRNLLRKMG+KKFNPG A Sbjct: 897 TRRGISIKHWDEFSDVADHCTVCHKCVTPCPVKIDFGDVSMNMRNLLRKMGQKKFNPGTA 956 Query: 960 AGMFFLNATNPQTINLARTAMMGVGYKAQRLGNEVLKKFTKKQTAHPPATVGKPPVTQQV 1019 A MFFLNATNPQTIN+ R M+ GYKAQRLGN+VLKKF +KQTAHPPATVG+ PV +QV Sbjct: 957 ASMFFLNATNPQTINMTRKVMIDWGYKAQRLGNDVLKKFARKQTAHPPATVGRAPVQEQV 1016 Query: 1020 IHFMNKKMPGNLPKKTARALLDIEDNKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQV 1079 IHF+NKKMPGNLPKKTARALLDIEDN+IVPIIR+PK T+ +TEAVFYFPGCGSERLFSQV Sbjct: 1017 IHFINKKMPGNLPKKTARALLDIEDNEIVPIIRDPKRTSPETEAVFYFPGCGSERLFSQV 1076 Query: 1080 GLATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQFDKAEQIVTDNRVLFHRVANTLNYLDI 1139 GLATQAMLW GVQTVLPPGYLCCGYPQRG+GQFDKAE++VTDNRVLFHRVANTLNYLDI Sbjct: 1077 GLATQAMLWHVGVQTVLPPGYLCCGYPQRGNGQFDKAEKMVTDNRVLFHRVANTLNYLDI 1136 Query: 1140 KTVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHEFLLEKGMKLDGVNGVRYMYHDPCHTPI 1199 KTVVVSCGTCYDQLAGYEF+KIFPGCRIIDIHE+LLEKG+KL+GV G RYMYHDPCHTPI Sbjct: 1137 KTVVVSCGTCYDQLAGYEFDKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHTPI 1196 Query: 1200 KTMDPIKLVNQLMGSEKDGYKIEKNDRCCGESGTLAVTRPDISTQVRFRKEEEIRKGAAK 1259 KTMDP KLVN+LMG + G KIEKN+RCCGESGTLAV+RPD+STQ+RFRKEEE+ KGA K Sbjct: 1197 KTMDPTKLVNELMGGNEGGSKIEKNERCCGESGTLAVSRPDVSTQIRFRKEEEMTKGADK 1256 Query: 1260 LRGIPLVAEAGANGINPANASAGSAGAPEGSVLKAGDGPQPKGATDVKILTSCPSCLQGL 1319 LR + G G DVKILTSCPSCLQGL Sbjct: 1257 LR------------------TDGFVG-------------------DVKILTSCPSCLQGL 1279 Query: 1320 SRYNEDAGIEADYIVVEMARHVLGEDWMVDYVQRANNGGIERVLV 1364 SRY EDA + ADYIVVEMA+H+LGE+WM DYV +AN+GGIERVLV Sbjct: 1280 SRYKEDATVTADYIVVEMAKHLLGENWMPDYVAKANSGGIERVLV 1324 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: 4578 Number of extensions: 159 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 1364 Length of database: 1324 Length adjustment: 49 Effective length of query: 1315 Effective length of database: 1275 Effective search space: 1676625 Effective search space used: 1676625 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: 59 (27.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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