Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_068169361.1 HTA01S_RS08640 3-phosphoglycerate dehydrogenase
Query= BRENDA::Q972A9 (313 letters) >NCBI__GCF_001592305.1:WP_068169361.1 Length = 335 Score = 115 bits (288), Expect = 1e-30 Identities = 84/273 (30%), Positives = 141/273 (51%), Gaps = 16/273 (5%) Query: 49 IIVVRSRTKVTKDVIEKGKKLKIIARAGIGLDNIDTEEAEKRNIKVVYAPGASTDSAVEL 108 ++++R RT++T+ ++EK KLK+IA+ G +ID +R I V GA +A EL Sbjct: 50 LVLIRERTQITRQLVEKLPKLKLIAQTGRVGGHIDVNACTERGIAVAEGVGAPFATA-EL 108 Query: 109 TIGLMIAAARKMYTSMALAKSGIFKKIE------------GLELAGKTIGIVGFGRIGTK 156 T L++A+ R++ +A K G +++ G+ L GKT+G+ +GRIG Sbjct: 109 TWALIMASMRRIPQYVANLKHGAWQQAGLKSSSMPVNFGVGMVLRGKTLGVWSYGRIGQL 168 Query: 157 VGIIANAMGMKVLAYDILDIREKAEKINAK-AVSLEELLKNSDVISLHVTVSKDAKPIID 215 V A GM+V+ + R++A + A +L ++SDV+SLH+ + + + Sbjct: 169 VAGYGRAFGMRVIVWGSEASRQRASADGYEIAKDKIDLFESSDVLSLHLRLGETNACSVT 228 Query: 216 YPQFELMKDNVIIVNTSRAVAVNGKALLDYIKKGKVYAYATDVFWNEPPKEEWELELLKH 275 MK ++VNTSRA + +ALL + +G+ A DVF +EP + LL+ Sbjct: 229 LEDLSRMKPTSLLVNTSRAELLEPEALLAALNRGRPGMAAVDVFESEPILQGH--ALLRL 286 Query: 276 ERVIVTTHIGAQTKEAQKRVAEMTTQNLLNAMK 308 E I T HIG +E+ + N++N +K Sbjct: 287 ENCICTPHIGYVEQESYETYFSSAFDNVVNYIK 319 Lambda K H 0.317 0.134 0.361 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: 210 Number of extensions: 9 Number of successful extensions: 3 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: 313 Length of database: 335 Length adjustment: 28 Effective length of query: 285 Effective length of database: 307 Effective search space: 87495 Effective search space used: 87495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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