Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Pf1N1B4_2954 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= BRENDA::H9JRZ9 (432 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2954 Length = 321 Score = 136 bits (342), Expect = 1e-36 Identities = 89/262 (33%), Positives = 131/262 (50%), Gaps = 13/262 (4%) Query: 154 ALVVRSATQVTKEVLDAGVKLKVVGRAGAGVDNIDVDSAGKKGVGVINAPGANALSACEL 213 ++ + + + + A +LK++ G +N+D+ +A G+ V N G S + Sbjct: 51 SVAISNKIVIDAAAMAASPELKLILITATGTNNVDLAAARAHGITVCNCQGYGTPSVAQH 110 Query: 214 TCTLMLVLARHVVPASTALKAGRWDRAL------YTGSELAGKTLAILGLGRVGREVATR 267 T L+L LA + A+ GRW +A Y EL GKTL +LG G +G VA Sbjct: 111 TIMLLLNLATRLADYQKAVAEGRWQQAKQFCLLDYPIVELEGKTLGLLGHGELGSAVARL 170 Query: 268 MYAFGMNI-IGFDPFVSADQCAQFHCTKMELEDIWPLADYITLHTPLIESTRNFINADVL 326 AFGM + +G P A ++ L+++ P D +TLH PL E TR+FI A L Sbjct: 171 AEAFGMRVMLGQIPGRPARP------DRLPLDELLPQIDALTLHCPLNEHTRHFIGAREL 224 Query: 327 KQCKKGVKIINVGRGGLIQETDFLQALKSGKVGGAALDVFEQEPPTDPVTLEIIQQPAVI 386 K G ++N RGGLI E AL++G +GGAA DV EPPT L P +I Sbjct: 225 ASMKPGAFVVNTARGGLIDEQALADALRNGHLGGAATDVLSVEPPTAGNPLLAQDIPRLI 284 Query: 387 ATPHLGASTKEAQVRVGQEIAE 408 TPH ++EA+ R+ ++ E Sbjct: 285 VTPHNAWGSREARQRIVGQLTE 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: 248 Number of extensions: 9 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