Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate CA265_RS17230 CA265_RS17230 D-glycerate dehydrogenase
Query= curated2:O29445 (527 letters) >FitnessBrowser__Pedo557:CA265_RS17230 Length = 319 Score = 185 bits (470), Expect = 2e-51 Identities = 108/306 (35%), Positives = 175/306 (57%), Gaps = 7/306 (2%) Query: 1 MKVLVAEPISEEAIDYMRKNGLEV---EVKTGMSREELIREVPKYEAIVVRSQTKVDAEV 57 MKV ++ I+ I + +N + + + ++ EELI +A++ K++A Sbjct: 1 MKVFISGNIASVGIKELEENNITITQWKENRQITAEELIAACQDQDALISVGPNKINAAF 60 Query: 58 IQAAKNLKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTISTAEHAIALMLAAARKIPQ 117 ++A +LK+I VG D +D+ AA + I + N PG + +TA+ A LMLA +RK Sbjct: 61 LKACSHLKVIALHSVGYDQVDVAAAKKLNIPIGNTPGVLSKATADTAFLLMLAVSRKAFF 120 Query: 118 ADRSVKEGKW---ERKKFMGIELRGKTAGVIGLGRVGFEVAKRC-KALEMNVLAYDPFVS 173 A + + +G+W E +GIE+ GKT G+ GLG++G E+AK+C A +M V+ ++ + Sbjct: 121 AHKKIIKGEWKNYEPTPELGIEVNGKTLGIFGLGKIGLEMAKKCIGAYQMPVIYHNRSRN 180 Query: 174 KERAEQIGVKLVDFDTLLASSDVITVHVPRTKETIGLIGKGQFEKMKDGVIVVNAARGGI 233 +E ++IG K V F+TLLA SDV++VH T ET F++MK I +N ARG I Sbjct: 181 EEAEKEIGAKYVSFETLLAQSDVLSVHTALTPETKDKFTLDVFKQMKANSIFINTARGAI 240 Query: 234 VDEAALYEAIKAGKVAAAALDVYEKEPPSPDNPLLKLDNVVTTPHIAASTREAQLNVGMI 293 +E L +A++ + A LDV EP +NPLL ++NV PHI ++T E + + I Sbjct: 241 HNEKDLIKALEKKIIWGAGLDVTNPEPMDKNNPLLSMENVAVLPHIGSATEETRAAMAQI 300 Query: 294 IAEDIV 299 I ++I+ Sbjct: 301 IVKNII 306 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: 344 Number of extensions: 17 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: 319 Length adjustment: 31 Effective length of query: 496 Effective length of database: 288 Effective search space: 142848 Effective search space used: 142848 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