Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate BWI76_RS27925 BWI76_RS27925 D-isomer specific 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >FitnessBrowser__Koxy:BWI76_RS27925 Length = 314 Score = 131 bits (330), Expect = 2e-35 Identities = 83/272 (30%), Positives = 141/272 (51%), Gaps = 10/272 (3%) Query: 34 EELKGVIGRFDGIIVSPTTKITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKV 93 EEL + +F +I + +TR+++ + L++I+ GYD +D+ A + V+ Sbjct: 34 EELAVLAEQFTIMITNGEATVTRQLISSLPSLELIAVFGVGYDGVDVRAAADHRVAVSHT 93 Query: 94 SGLLSEAVAEFTVGLIINLMRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILG 153 G+L++ VA+ +GL++ R+I A KFI G W WT + G +VGI+G Sbjct: 94 PGVLTDDVADLAMGLMLATSRQIVSAQKFIEAGGWRQGGFQWT-----RKVSGSRVGIVG 148 Query: 154 MGAIGKAIARRLIPFGVKLYYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRD 213 MG IG+AIARR F +++ Y R ++ DI L ++D +++ P + + Sbjct: 149 MGRIGQAIARRCEGFAMQIAYSDRKAIPGLDYPW---IEDISTLASQTDFLVICTPGSAE 205 Query: 214 TYHIINEERVKKLEGK-YLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHEL 272 +I+E + L L+NI RG++VDE A+ +A++QG + G DVF +EP L Sbjct: 206 NQALIDERVLSALGASGILINISRGSVVDEFALIKALEQGIIAGAGLDVFSQEPEVPQAL 265 Query: 273 FKYEWETVLTPHYAGLALEAQEDVGFRAVENL 304 + V+TPH A +E + +EN+ Sbjct: 266 LR-RANVVVTPHMASATWSTREAMSRLVLENV 296 Lambda K H 0.319 0.139 0.393 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: 250 Number of extensions: 10 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: 333 Length of database: 314 Length adjustment: 28 Effective length of query: 305 Effective length of database: 286 Effective search space: 87230 Effective search space used: 87230 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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