Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_072908752.1 BUB13_RS10730 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_900142125.1:WP_072908752.1 Length = 318 Score = 176 bits (446), Expect = 1e-48 Identities = 104/301 (34%), Positives = 167/301 (55%), Gaps = 10/301 (3%) Query: 20 LEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNV 79 L+E+ V PEE+ + + I++ ++ + E+I+ P+LK I G + V Sbjct: 21 LKELGTYAVYPRTAPEEICQRAESAE-IILTNKVVLDAEIIDQLPKLKYIGVLATGYNVV 79 Query: 80 DVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGI-- 137 D+ AA+ RGI+V N P ++ +V++ L+L +++++ R V+EG W Sbjct: 80 DLDAASARGIVVTNIPGYSTDSVSQMVFALLLEMSQQVGHHARLVQEGAWSNCEDFSFHD 139 Query: 138 ----ELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLL 193 EL GKT+GI+G G+IG +V AFGM ++V + K + ++ V TD++ + Sbjct: 140 RPLFELAGKTIGIVGYGQIGRRVAQIANAFGMKVLVNTAHPEKYSCDK-SVEFTDIDRIF 198 Query: 194 RESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGA 253 +SDI++++ PLT ETRHL + +K ++N RG +IDEDA+ AL +G + G Sbjct: 199 DDSDIISLNCPLTGETRHLANTARLMRVKQGTLLINTGRGDLIDEDAVAEALNEGYLGGF 258 Query: 254 ALDVFEEEPP-EGSPLLELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRNVL 312 A DV EPP E +PLL N +TPHI +T+EA++ I IK FQ G P+N + Sbjct: 259 AADVLSSEPPDEDNPLLSTPNTFITPHIAWATAEARQRLLDIAIANIK-AFQDGTPQNQV 317 Query: 313 N 313 N Sbjct: 318 N 318 Lambda K H 0.316 0.135 0.366 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: 371 Number of extensions: 18 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: 525 Length of database: 318 Length adjustment: 31 Effective length of query: 494 Effective length of database: 287 Effective search space: 141778 Effective search space used: 141778 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 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