Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate AO356_06935 AO356_06935 glycerate dehydrogenase
Query= BRENDA::H9JRZ9 (432 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_06935 Length = 321 Score = 140 bits (352), Expect = 7e-38 Identities = 91/253 (35%), Positives = 129/253 (50%), Gaps = 13/253 (5%) Query: 163 VTKEVLDAGVKLKVVGRAGAGVDNIDVDSAGKKGVGVINAPGANALSACELTCTLMLVLA 222 + + + A +LK++ + G +N+D+ +A G+ V N G S + T L+L LA Sbjct: 60 IDAQAMAASPELKLILISATGTNNVDLAAARHHGITVCNCQGYGTPSVAQHTLMLLLNLA 119 Query: 223 RHVVPASTALKAGRWDRAL------YTGSELAGKTLAILGLGRVGREVATRMYAFGMNII 276 + A+ GRW +A Y EL GKTL +LG G +G V AFGM ++ Sbjct: 120 TRLADYQNAVGEGRWQQASQFCLLDYPIVELEGKTLGLLGHGELGSAVGRLAEAFGMRVL 179 Query: 277 -GFDPFVSADQCAQFHCTKMELEDIWPLADYITLHTPLIESTRNFINADVLKQCKKGVKI 335 G P A ++ LE + P D +TLH PL E TRNFI A L K G + Sbjct: 180 LGQIPGRPARP------DRLPLEQLLPQVDALTLHCPLNEHTRNFIGARELALLKPGAFV 233 Query: 336 INVGRGGLIQETDFLQALKSGKVGGAALDVFEQEPPTDPVTLEIIQQPAVIATPHLGAST 395 +N RGGLI E +AL+SG +GGAA DV EPPT L P +I TPH + Sbjct: 234 VNTARGGLIDEQALAEALRSGHLGGAATDVLSVEPPTQGNPLLAGDIPRLIVTPHNAWGS 293 Query: 396 KEAQVRVGQEIAE 408 +EA+ R+ +++E Sbjct: 294 REARQRIVGQMSE 306 Lambda K H 0.320 0.135 0.387 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: 253 Number of extensions: 8 Number of successful extensions: 2 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: 432 Length of database: 321 Length adjustment: 30 Effective length of query: 402 Effective length of database: 291 Effective search space: 116982 Effective search space used: 116982 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 (21.8 bits) S2: 49 (23.5 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