Align D-3-phosphoglycerate dehydrogenase 2; 3-PGDH 2; 2-oxoglutarate reductase; EC 1.1.1.95; EC 1.1.1.399 (characterized)
to candidate WP_012048703.1 SWIT_RS12620 2-hydroxyacid dehydrogenase
Query= SwissProt::P40510 (469 letters) >NCBI__GCF_000016765.1:WP_012048703.1 Length = 309 Score = 111 bits (277), Expect = 4e-29 Identities = 78/269 (28%), Positives = 134/269 (49%), Gaps = 15/269 (5%) Query: 88 SLPEDELIEKIKDVHAIGIRSKTRLTEKILQHARNLVCIGCFCIGTNQVDLKYAASKGIA 147 +L E++ ++ +V A+ + + RL ++++ L I CF +G + VD+ ++GI Sbjct: 29 ALWEEKDPPRLAEVSALIMAGEFRLPPELVERMPKLGLIACFTVGYDGVDVAAVRARGIQ 88 Query: 148 VFNSPFSNSRSVAELVIGEIISLARQLGDRSIELHTGTWNKVAARCW-EVRGKTLGIIGY 206 V ++ +N+ VA+ IG I++ R++ L G W A + G +GI+G Sbjct: 89 VCHAHDANNEDVADHAIGMILAERRRIFSGDRMLRAGEWKPGAKLITGSLDGARIGIVGL 148 Query: 207 GHIGSQLSVLAEAMGLHVLYYDIVTIMALGTARQVSTLDELLNKSDFVTLHVPATPETEK 266 G IG+ ++ A+ M + ++ R + TL++L SD + + A + EK Sbjct: 149 GSIGAAVARRADVMRMETRWWGPNPKPDAAWPR-METLEDLAAWSDILVVAARAHHDNEK 207 Query: 267 MLSAPQFAAMKDGAYVINASRGTVVDIPSLIQAVKANKIAGAALDVYPHEPAKNGEGSFN 326 M+SA A+ ++N +RG VVD +LI A++ ++ AALDVY EP G Sbjct: 208 MISAAVIDALGPDGLLVNVARGQVVDEDALIAALRDGRLGAAALDVYAQEPTPAGR---- 263 Query: 327 DELNSWTSELVSLPNIILTPHIGGSTEEA 355 W +PN ILTPH G+T+ A Sbjct: 264 -----W----ADVPNTILTPHTSGATDAA 283 Lambda K H 0.315 0.131 0.367 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: 254 Number of extensions: 9 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: 469 Length of database: 309 Length adjustment: 30 Effective length of query: 439 Effective length of database: 279 Effective search space: 122481 Effective search space used: 122481 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