Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_028584590.1 G494_RS0111035 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000429965.1:WP_028584590.1 Length = 314 Score = 167 bits (423), Expect = 5e-46 Identities = 110/320 (34%), Positives = 183/320 (57%), Gaps = 24/320 (7%) Query: 7 LIADSINEKGISELEEVAEVVVNTTITP-EELLDAIKDFDAIVVRSRTKVTREVIEAAPR 65 L A+S+ + +S L E + TP +E+ I + + ++V ++ ++T ++ APR Sbjct: 6 LDAESLADLDLSALAGCFEDLAVYQQTPSKEVAQRIAEAEVVIV-NKVRLTAALLRGAPR 64 Query: 66 LKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVK 125 L+++ G DNVD AA + GI V N + +V +H ++LAL + R+V Sbjct: 65 LRLVCLVATGTDNVDCAAARELGITVCNCQAYGTDSVVQHVFTMILALHTSLLPYTRAVA 124 Query: 126 EGKWEKNR------FMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYD-PYISKEA 178 EG+W+++ F +EL G+TLGI+G G +G V +AF M++++ + P + +E Sbjct: 125 EGRWQQSSQFCLLDFPIVELKGRTLGIMGYGTLGRGVARMAEAFEMEVLLGERPGVRQEG 184 Query: 179 AEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDE 238 LE LL + DI+T+H PL+ +TR+LI +LM+ ++F++N ARGGI++E Sbjct: 185 R-------IPLEELLPQVDILTLHCPLSEQTRNLIDARALELMRPSSFLINAARGGIVEE 237 Query: 239 DALYRALKDGEIAGAALDVFEEEPP-EGSPLL--ELENVVLTPHIGASTSEAQRDAAIIV 295 AL AL+ G IAGAA DV EPP + +PLL ++ N+++TPH + +A+ A IV Sbjct: 238 QALADALRRGTIAGAASDVLTTEPPGDDNPLLAADIPNLIVTPHCAWGSYQAR---ARIV 294 Query: 296 ANEIKTV--FQGGAPRNVLN 313 A ++ + F AP V+N Sbjct: 295 AQTVENIEGFVRQAPLRVVN 314 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: 334 Number of extensions: 15 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: 314 Length adjustment: 31 Effective length of query: 494 Effective length of database: 283 Effective search space: 139802 Effective search space used: 139802 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