Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_086509103.1 BZY95_RS06210 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_002151265.1:WP_086509103.1 Length = 328 Score = 180 bits (456), Expect = 8e-50 Identities = 113/281 (40%), Positives = 161/281 (57%), Gaps = 9/281 (3%) Query: 48 VVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSI 107 +V S + E+I+ AP+L+ +A VG DN V+A T RGI++ N P+ + T A+ Sbjct: 49 LVGSSLVIAPELIDLAPQLEAVATISVGYDNYPVEALTRRGILLCNTPDVLTETTADTGF 108 Query: 108 GLMLALARK-IAIADRSVKEGKWEKN---RFMGIELNGKTLGIIGMGRIGSQVVVR-TKA 162 L++A AR+ I +AD VK G W + G +++GKTLG++G GRIG+ V R Sbjct: 109 LLIMATARRAIELADL-VKRGDWTASIGEPHFGTDVHGKTLGMVGFGRIGAGVARRGALG 167 Query: 163 FGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMK 222 FGM ++ +E+G +L+ LL ++D V + VPLT ET HLI EF LMK Sbjct: 168 FGMRVLYACSSPKPALEQELGAVRCELDELLSQADFVCVTVPLTAETTHLIGRREFGLMK 227 Query: 223 DTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEP--PEGSPLLELENVVLTPHI 280 +A VN ARG ++DE AL AL+ GEI A LDVFE+EP PE SPL + NVV PH+ Sbjct: 228 PSAIFVNIARGKVVDEAALIAALETGEIHAAGLDVFEQEPLSPE-SPLPHMANVVALPHV 286 Query: 281 GASTSEAQRDAAIIVANEIKTVFQGGAPRNVLNMPVMDSET 321 G++T E + A + I +G P +++N ET Sbjct: 287 GSATHETRDAMAQRAVDNITLALEGKRPLSLVNEVAWRGET 327 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: 369 Number of extensions: 18 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: 328 Length adjustment: 31 Effective length of query: 494 Effective length of database: 297 Effective search space: 146718 Effective search space used: 146718 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