Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_028950807.1 Q385_RS0106035 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000619805.1:WP_028950807.1 Length = 319 Score = 157 bits (398), Expect = 4e-43 Identities = 101/287 (35%), Positives = 159/287 (55%), Gaps = 18/287 (6%) Query: 31 TITPEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIM 90 T T EE ++ +KD + IV+ ++ + ++V+ A LK+I A G +NVD+ A +GI Sbjct: 32 TKTKEETIERVKDKN-IVITNKVVIDKDVMNNAHYLKLICVAATGYNNVDIDYAKQKGIA 90 Query: 91 VINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGI------ELNGKTL 144 V N ++ +V +H+ ++ L + D VK G++ K+ ELNGKT Sbjct: 91 VANVAGYSTNSVVQHTFAMLFYLLENLRYYDDYVKLGEYSKSPIFTHLDRPFWELNGKTW 150 Query: 145 GIIGMGRIGSQVVVRTKAFGMDIMVYDPYISK--EAAEEMGVTVTDLETLLRESDIVTIH 202 GIIG+G IG +V ++FG D++ Y +A G L+ LL SD+V+IH Sbjct: 151 GIIGLGTIGKRVAQVAESFGCDVIYYSTSGKNINQAYPHKG-----LDELLSISDVVSIH 205 Query: 203 VPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEP 262 PL T++LI+ D+ KLMK TA ++N RGGI++E L +AL +G IAGA LDV E+EP Sbjct: 206 APLNEYTKNLITYDKIKLMKKTAILLNLGRGGIVNEKDLAKALDEGLIAGAGLDVLEKEP 265 Query: 263 PEGSPLL----ELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQG 305 LL + +++TPHI ++ EA++ + I+ +G Sbjct: 266 ISPDNLLLHIKNKDRLLITPHIAWTSIEARQTLVKEIYLNIEAFIRG 312 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: 330 Number of extensions: 14 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: 525 Length of database: 319 Length adjustment: 31 Effective length of query: 494 Effective length of database: 288 Effective search space: 142272 Effective search space used: 142272 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