Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 6936424 Sama_0612 D-lactate dehydrogenase (RefSeq)
Query= curated2:O29445 (527 letters) >FitnessBrowser__SB2B:6936424 Length = 329 Score = 150 bits (379), Expect = 7e-41 Identities = 95/279 (34%), Positives = 142/279 (50%), Gaps = 19/279 (6%) Query: 42 YEAIVVRSQTKVDAEVIQA--AKNLKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTIS 99 +E I ++ AEV+ ++I G +N+D+ A G+ VVN P + S Sbjct: 45 FEVICAFVNDELSAEVLNELHGNGTRVIAMRCAGFNNVDLEEAKHLGMTVVNVPAYSPES 104 Query: 100 TAEHAIALMLAAARKIPQADRSVKEGKWERKKFMGIELRGKTAGVIGLGRVGFEVAKRCK 159 AEH +ALML RKI +A + ++ + + +G + GKT GVIG G++G + Sbjct: 105 VAEHTVALMLTLNRKIHKAYQRTRDANFSLEGLVGFNMHGKTVGVIGTGKIGLATIRILL 164 Query: 160 ALEMNVLAYDPFVSKERAEQIGVKLVDFDTLLASSDVITVHVPRTKETIGLIGKGQFEKM 219 V+A+DPF S E +GV ++ D LL DV+++H P TKE L+ F KM Sbjct: 165 GFGCKVVAFDPFPS-PAVEALGVPYLELDELLKLCDVVSLHCPLTKENHHLLRAETFAKM 223 Query: 220 KDGVIVVNAARGGIVDEAALYEAIKAGKVAAAALDVYEKEP----PSPDNPLLKLD---- 271 K GV+V+N +RGG+++ EA+K G++ A LDVYE E N +++ D Sbjct: 224 KPGVMVINTSRGGLLNAFDAMEALKVGQIGALGLDVYENEKELFFEDKSNEVIQDDVFRR 283 Query: 272 -----NVVTTPHIAASTREAQLNVGMIIAEDIVNMAKGL 305 NVV T H A T EA +G I + N+ K L Sbjct: 284 LSACHNVVFTGHQAFLTEEA---LGAIATTTLTNVQKAL 319 Lambda K H 0.317 0.136 0.376 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: 350 Number of extensions: 22 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: 527 Length of database: 329 Length adjustment: 31 Effective length of query: 496 Effective length of database: 298 Effective search space: 147808 Effective search space used: 147808 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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