Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011319416.1 AVA_RS13470 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000204075.1:WP_011319416.1 Length = 341 Score = 148 bits (373), Expect = 3e-40 Identities = 95/298 (31%), Positives = 151/298 (50%), Gaps = 18/298 (6%) Query: 44 FDAIVVRSRTKVTREVIE--AAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSIT 101 F A+ V +V +E A+ ++I G +NVD+KAA G+ V+ P + Sbjct: 45 FPAVCVFVHDQVDAATLEILASRGTRLIVLRCAGFNNVDLKAANKLGVNVVRVPAYSPYG 104 Query: 102 VAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTK 161 VAEH++GL+L+L RKI A V+EG + + +G +NG+T+GIIG G+IG + K Sbjct: 105 VAEHAVGLILSLNRKIHRAYNRVREGNFALDGLLGFNINGRTVGIIGTGKIGLILGQIMK 164 Query: 162 AFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLM 221 FG ++ YD Y + E +G +L L SDI+++H PL P+T HLI+ + + + Sbjct: 165 GFGCRLLAYDVYHNPEML-ALGGEYVELPELFANSDIISLHCPLMPQTHHLINAEAIEQV 223 Query: 222 KDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPP------EG--------SP 267 K ++N +RG +I A+ LK G+I +DV+E+E G Sbjct: 224 KPGVMLINTSRGALIHTQAVIEGLKTGKIGSLGVDVYEQESELFFEDLSGEIIQDDIFQR 283 Query: 268 LLELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQG-GAPRNVLNMPVMDSETYKS 324 L NV++T H T +A R+ A N I + QG P + P ++++ S Sbjct: 284 LTTFPNVLITGHQAFFTEDALRNIAETTLNNIADIEQGRSCPNEIRYQPEVEAKVLVS 341 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: 367 Number of extensions: 17 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: 341 Length adjustment: 32 Effective length of query: 493 Effective length of database: 309 Effective search space: 152337 Effective search space used: 152337 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 09 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