Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_005817430.1 DHAF_RS06735 glyoxylate reductase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000021925.1:WP_005817430.1 Length = 338 Score = 211 bits (537), Expect = 3e-59 Identities = 118/319 (36%), Positives = 189/319 (59%), Gaps = 7/319 (2%) Query: 2 SRMKVLIADSINEKGISELEEVAEVVVNTTI---TPEELLDAIKDFDAIVVRSRTKVTRE 58 +R KV I I L + +V ++ + + EE++ +K DA++ + ++ Sbjct: 8 NRKKVFITGRIPSLAYEILSKEFDVTMHDDLRLLSKEEIIAGLKGKDALLCLLSDAIDKD 67 Query: 59 VIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA 118 +IEA P+LK+IA G G +N+D+ AA + I V N P+ ++ A+ + GL+LA+AR+I Sbjct: 68 IIEANPQLKVIANYGAGYNNIDIAAAGEANIPVTNTPDVSTDATADLTFGLILAIARRIV 127 Query: 119 IADRSVKEGK---WEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYD-PYI 174 D+ + G+ W +G+++ GKTLGIIGMG IG + R K F M I+ + Sbjct: 128 EGDKETRAGRFKGWAPLYHLGVDVTGKTLGIIGMGNIGKAIARRAKGFDMKIVYTSRTRL 187 Query: 175 SKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGG 234 S++ +E+G T LE +L+ +D V++ + +P T H+I E E + MK +A+++N ARG Sbjct: 188 SEQQEKELGFTYMSLEGVLKTADFVSLSLSYSPATHHMIGERELETMKPSAYLINTARGP 247 Query: 235 IIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAII 294 ++DE AL +AL++ IAGAALDV+E EP + L +L+ V+LTPHIG +T E + A I Sbjct: 248 LVDEKALLKALENKSIAGAALDVYEFEPQITAGLEKLDQVILTPHIGNATVETRDAMAEI 307 Query: 295 VANEIKTVFQGGAPRNVLN 313 A I V +G AP +N Sbjct: 308 AAGNIAAVLRGEAPLTCVN 326 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: 377 Number of extensions: 19 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: 338 Length adjustment: 32 Effective length of query: 493 Effective length of database: 306 Effective search space: 150858 Effective search space used: 150858 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