Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate SMc02849 SMc02849 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >FitnessBrowser__Smeli:SMc02849 Length = 334 Score = 191 bits (486), Expect = 3e-53 Identities = 120/305 (39%), Positives = 175/305 (57%), Gaps = 14/305 (4%) Query: 18 SELEEVAEVVVNTTITPE---ELLDAIKDFDAIVVRSRTKVTREVIE-AAPRLKIIARAG 73 + + E+ + +N TP EL+ A+K D +V ++ +IE A P+LK+IA Sbjct: 21 TRMRELFDAELNIDDTPRSQPELVAAVKRADVLVPTVTDRIDAALIEQAGPQLKLIAAFS 80 Query: 74 VGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA-----IADRSVKEGK 128 GVDN+DV AA +GI V N P + A+ ++ L+LA+ R++A + DR + Sbjct: 81 NGVDNIDVDAAARKGITVTNTPNVLTEDTADMTMALILAVPRRLAEGAQVLTDRKGEWAG 140 Query: 129 WEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEM-GVTVT 187 W +G + GK +GI+GMGRIG+ V R KAFG+ I ++ + K EEM T Sbjct: 141 WSPTWMLGRRIAGKRIGIVGMGRIGTAVARRAKAFGLSIHYHNRHRVKPETEEMLEATYW 200 Query: 188 D-LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALK 246 D L+ +L DIV+++ P TP T HL+S LM+ ++IVN ARGGIIDE AL ++L+ Sbjct: 201 DSLDQMLARVDIVSVNCPSTPATYHLLSARRLALMRPDSYIVNTARGGIIDEAALIKSLR 260 Query: 247 DGEIAGAALDVFEEEPPEGSPLLELE---NVVLTPHIGASTSEAQRDAAIIVANEIKTVF 303 +G+IAGA LDVFE EP L++L VVL PH+ ++T E + D V I+T F Sbjct: 261 EGKIAGAGLDVFENEPCVNPKLIKLAGEGKVVLLPHMSSATLEGRIDMGEKVVINIRTFF 320 Query: 304 QGGAP 308 G P Sbjct: 321 DGHRP 325 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: 408 Number of extensions: 16 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: 334 Length adjustment: 32 Effective length of query: 493 Effective length of database: 302 Effective search space: 148886 Effective search space used: 148886 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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