Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_051623281.1 P166_RS0101595 FAD-linked oxidase
Query= reanno::HerbieS:HSERO_RS19500 (1333 letters) >NCBI__GCF_000711315.1:WP_051623281.1 Length = 1292 Score = 1432 bits (3708), Expect = 0.0 Identities = 722/1318 (54%), Positives = 932/1318 (70%), Gaps = 44/1318 (3%) Query: 22 RLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNP 81 R+REIPYNYTSFSD+EI +R +G E W ++ LR R TGRSARML+EVLGD+WVV RNP Sbjct: 13 RIREIPYNYTSFSDKEIALRFVGMEGWKCIESLRDSRNTGRSARMLFEVLGDMWVVSRNP 72 Query: 82 YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141 Y+QDDL++NPKRR ALI+AL HRL +V+ R +AE LL + + Sbjct: 73 YIQDDLIENPKRRDALIKALEHRLKQVESRLNGNQKAEE--------------LLSSIRG 118 Query: 142 AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201 A+ F E F +LR + K L + T DNI F GL+RVSH TDATDWRVE P VV++P Sbjct: 119 AVNKFTEWFPHQIELRSKVRKKLSKHTRLDNIDFGGLARVSHATDATDWRVELPLVVVSP 178 Query: 202 DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261 DTE+E+A LV CI+LGLTIIPRGGGTGYTGGAIPL S VINTEKLE + VE LP Sbjct: 179 DTEEEVAYLVDGCIQLGLTIIPRGGGTGYTGGAIPLYQDSVVINTEKLEYMSLVEHVDLP 238 Query: 262 GLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVLWG 321 G+ K TI +GAGVVT+RVS+ AE+ G+ FAVDPTS +ASCIGGN+AMNAGGKKAVLWG Sbjct: 239 GIGK-VPTIQTGAGVVTRRVSEQAERFGYAFAVDPTSQDASCIGGNIAMNAGGKKAVLWG 297 Query: 322 TALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFKTEI 381 T LDNLASW+MV P +WLEV R++HNLGK+ D +F++ + EK KT V KTE Sbjct: 298 TTLDNLASWKMVTPDAEWLEVERINHNLGKLQDQNTVKFRI---NRYEKDGKTPVGKTET 354 Query: 382 LEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFFG 441 LE+ G FR GLGKDVTDKFLSGLPG+QKEGCDGLITSAR+++H+MP RTVCLEFFG Sbjct: 355 LEMPGSAFRHAGLGKDVTDKFLSGLPGIQKEGCDGLITSARFVVHRMPSHIRTVCLEFFG 414 Query: 442 -QARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLIG 500 A+P+IVEI DY++++ K G +L+GLEHLDERY++AV Y TK+ R LPKM+L+ Sbjct: 415 TDLSKAVPAIVEITDYIESK-KAHGILLSGLEHLDERYIKAVNYNTKANRKGLPKMILLA 473 Query: 501 DIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFKIN 560 DI G++ VA A E++ +A R EGF+AVS EARK+FW DRSRTAAI+KHTNAFKIN Sbjct: 474 DIAGENGFEVANTAQEIVELAKKRDAEGFIAVSEEARKRFWADRSRTAAISKHTNAFKIN 533 Query: 561 EDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLP-LGKSDDAEGDDIP 619 EDVVIPL + EY IERINIE SIKNKLQ+L +L+++F G +P DD E + Sbjct: 534 EDVVIPLENLNEYNTEIERINIEESIKNKLQILDQLNAYFA-GEIPEYTLEDDFENSEGQ 592 Query: 620 AAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVDQ 679 A +D+V + +T ARW +L NLD + K EL G + L Sbjct: 593 PASYFKDKVAATLGHIGKTKARWEGILQNLDVQV-LTKPELLLEG---------EALKLS 642 Query: 680 PEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALHM 739 + ++ R ++IS+K E+ L+++F G F+ + + +H + R+FVALHM Sbjct: 643 ADDTFVSLLLKREIKISYKSEMVTFLQEVFMGHDFEALHTRLKKLHFEIRNARLFVALHM 702 Query: 740 HAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTEDE 799 HAGDGN+HTNIPV+S++YEM+ A V V RIM++A+ LNGVISGEHGIG+TK ++L +D+ Sbjct: 703 HAGDGNIHTNIPVHSNNYEMIHQAEVIVDRIMEIAKRLNGVISGEHGIGLTKFQYLDKDK 762 Query: 800 IGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIAS 859 I F +YK +VDP G FNKGKL+ PG + L NAYTPS L+ E+LI++ +D+ + Sbjct: 763 IQAFVDYKNKVDPHGHFNKGKLM--PG--SGLQNAYTPSLHLVEQEALILEANDLDLLNK 818 Query: 860 SVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEEF 919 +KDCLRCGKCKPVC TH+PRANLLYSPRNKILAT ++EAFLYEEQTRRG+S+ H++ Sbjct: 819 DIKDCLRCGKCKPVCQTHIPRANLLYSPRNKILATGQVIEAFLYEEQTRRGISLHHFDAM 878 Query: 920 EDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPAT 979 DVADHCT CHKC TPCPVDIDFGDVS++MR +L MG+K + A++FLN P T Sbjct: 879 NDVADHCTTCHKCETPCPVDIDFGDVSIHMRTILTNMGQKRSSIMVKLALYFLNTKHPFT 938 Query: 980 INATRKVMTQWGFKAQRLGNDLMKKFA--KKQTQKPPATVGKPPVKEQVIHFINKKMPGN 1037 IN RK M WG A +G+ + F +++ P +T P+++ VI+F+ K + Sbjct: 939 INFLRKTMIGWGAVAMTIGHRFARLFGLVERKNALPASTSEPAPIQQHVINFVRKPLDTG 998 Query: 1038 LPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWNV 1097 + + R++L +ED VPI+R+P TT DTEAVFYFPGCGSERLFS +GLAT + L++ Sbjct: 999 PNQSSYRSVLGLEDATQVPIVRDPNKTTEDTEAVFYFPGCGSERLFSDIGLATISSLYDA 1058 Query: 1098 GVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTCY 1157 GVQTVLPPGYLCCGYPQ G +K +I T+NR LFHR+ANTLNY+DI TV+VSCGTCY Sbjct: 1059 GVQTVLPPGYLCCGYPQAAAGLAQKSSQITTENRALFHRVANTLNYMDINTVIVSCGTCY 1118 Query: 1158 DQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVNS 1217 DQL YEFE+IFPGCR++DIHE+L E+G+ LE TG +Y+YH PCH PMK+ D Sbjct: 1119 DQLTKYEFERIFPGCRLMDIHEFLTERGMGLESPTGKQYLYHTPCHDPMKKMDGTTVAKD 1178 Query: 1218 LITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRADG--FTGDV 1275 L+ + ++ +DRCC E+GT SRPD++ Q+RFRKEEE+ KG ++ + G+V Sbjct: 1179 LLQS----EVLFSDRCCAEAGTLATSRPDIANQLRFRKEEELTKGIVELTGESKVKNGEV 1234 Query: 1276 KILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERILV 1333 K+LTSCP+C QGL+RY+++ G DYIVVE+ ++ G W E+ E+ NGG+E++L+ Sbjct: 1235 KLLTSCPACQQGLNRYHDNTGLDTDYIVVELMKNRYGNTWNKEFYEKLKNGGVEKVLL 1292 Lambda K H 0.319 0.136 0.402 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: 3877 Number of extensions: 164 Number of successful extensions: 13 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: 1333 Length of database: 1292 Length adjustment: 48 Effective length of query: 1285 Effective length of database: 1244 Effective search space: 1598540 Effective search space used: 1598540 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 (21.7 bits) S2: 59 (27.3 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