Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_009238667.1 ALIDE2_RS09920 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000204645.1:WP_009238667.1 Length = 336 Score = 165 bits (417), Expect = 2e-45 Identities = 117/334 (35%), Positives = 171/334 (51%), Gaps = 21/334 (6%) Query: 1 MRPKVGVLLKMKREALEELKKYADVEIILYPSGEEL--KGVIGRF---DGIIVSPTTKIT 55 M+PKV + + E +E L ADV I + E L VI R D ++ I Sbjct: 1 MKPKVVLTHWVHPEIIELLSASADV--IPNTTRETLPRSEVIARAKDADALMAFMPDSID 58 Query: 56 REVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRK 115 LE +L+VI GYDN D+ T+ G+++T V LL+ AE T+GL++ L R Sbjct: 59 SAFLEECPKLRVIGAALKGYDNFDVNACTRHGVWLTIVPDLLTIPTAELTIGLLLGLTRH 118 Query: 116 IHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYW 175 + D+ IR G H + W L GK +GI+GMGA+G+AIA+RL F + L Y Sbjct: 119 MLEGDRQIRSG----HFQGWRPTLYGSGLTGKTLGIIGMGAVGRAIAQRLAGFEMNLLYC 174 Query: 176 SR-HRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE-GKYLVN 233 EK + + +DELLEK D V+ +P+ +T H+I+ + K++ G YL+N Sbjct: 175 DPIPLNAEQEKAWHVQRVTLDELLEKCDYVVPMVPMAAETLHLIDATALAKMKTGSYLIN 234 Query: 234 IGRGALVDEKAVTEAIKQGKLKGYATDVFEKEP-VREHE-------LFKYEWETVLTPHY 285 RG++VDE AV A+ GKL GYA DVFE E +R L +T TPH Sbjct: 235 ACRGSVVDENAVIAALASGKLAGYAADVFEMEEWIRADRPQAIPKALLDNTAQTFFTPHL 294 Query: 286 AGLALEAQEDVGFRAVENLLKVLRGEVPEDLVNK 319 E + ++ +A N+++ L GE P +N+ Sbjct: 295 GSAVKEVRLEIERQAAMNIIQALAGEKPMGAINQ 328 Lambda K H 0.319 0.139 0.393 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: 258 Number of extensions: 17 Number of successful extensions: 4 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: 333 Length of database: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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: 49 (23.5 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