Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 206855 DVU1412 D-isomer specific 2-hydroxyacid dehydrogenase family protein
Query= curated2:O29445 (527 letters) >MicrobesOnline__882:206855 Length = 326 Score = 171 bits (433), Expect = 4e-47 Identities = 99/274 (36%), Positives = 149/274 (54%), Gaps = 8/274 (2%) Query: 45 IVVRSQTKVDAEVIQAAKNLKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTISTAEHA 104 +V+ ++ +D +QA L+ + G D +D+ AA GI V N PG T S A+H Sbjct: 47 VVLTNKVPLDMSALQALPGLRFVSVLATGYDKVDVAAAGVLGIPVSNVPGYGTDSVAQHV 106 Query: 105 IALMLAAARKIPQADRSVKEGKWERKKFMGI------ELRGKTAGVIGLGRVGFEVAKRC 158 AL+L R+ D ++ G W + EL GKT G++G G G V + Sbjct: 107 FALLLELCRRTALHDHRIRAGAWTQSPDWCFWDSTQEELTGKTMGIVGFGNTGRRVGRIA 166 Query: 159 KALEMNVLAYDPFVSKERAEQIGVKLVDFDTLLASSDVITVHVPRTKETIGLIGKGQFEK 218 AL MNV+AY P S+ + + V D L S+DV+++H P T ET GL+ + Sbjct: 167 NALGMNVIAYAPR-SRFDPDYRPFEHVGLDELFTSADVVSLHCPLTPETEGLVDARRLAS 225 Query: 219 MKDGVIVVNAARGGIVDEAALYEAIKAGKVAAAALDVYEKEPPSPDNPLLKLDNVVTTPH 278 M+ G ++N ARG ++DE A+ EA+ +G++A A LDV +EPP+ DNPLL N + TPH Sbjct: 226 MRPGSYLINTARGPLLDERAVAEALDSGRLAGAGLDVLSQEPPAADNPLLSAKNCLITPH 285 Query: 279 IAASTREAQLNVGMIIAEDIVNMAKGLPVRNAVN 312 +A ++R A+ + A +I + +G PV N VN Sbjct: 286 LAWASRTARRTLMDSTAANIRSFIEGTPV-NVVN 318 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: 345 Number of extensions: 19 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: 527 Length of database: 326 Length adjustment: 31 Effective length of query: 496 Effective length of database: 295 Effective search space: 146320 Effective search space used: 146320 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