Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 8499437 DvMF_0209 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= curated2:O29445 (527 letters) >FitnessBrowser__Miya:8499437 Length = 322 Score = 173 bits (438), Expect = 1e-47 Identities = 106/289 (36%), Positives = 147/289 (50%), Gaps = 8/289 (2%) Query: 34 ELIREVPKYEAIVVRSQTKVDAEVIQAAKNLKIIGRAGVGVDNIDINAATQRGIVVVNAP 93 E IRE +V+ ++T +DA+ I A +L IG G D +DI AA R I V N P Sbjct: 36 EAIRERAAGAHMVLTNKTPLDADTIAALPDLAYIGVLATGYDVVDIRAAAARSIPVCNVP 95 Query: 94 GGNTISTAEHAIALMLAAARKIPQADRSVKEGKWERKK------FMGIELRGKTAGVIGL 147 G T + A+H A +L R+I + D SVK G W K IEL GK G++G Sbjct: 96 GYGTEAVAQHVFAFLLELCRRIARHDASVKVGNWSANKDWCFWETTQIELTGKAMGIVGF 155 Query: 148 GRVGFEVAKRCKALEMNVLAYDPFVSKERAEQIGVKLVDFDTLLASSDVITVHVPRTKET 207 G +G V + A M VLAY P + V D L A SDV+T+H P T T Sbjct: 156 GNMGKRVGQIANAFGMKVLAYSPNTRTMPGYE-PFAYVSLDELFARSDVVTLHCPLTDAT 214 Query: 208 IGLIGKGQFEKMKDGVIVVNAARGGIVDEAALYEAIKAGKVAAAALDVYEKEPPSPDNPL 267 G++ + + MK G I++N ARG ++DEAA+ A+ + +DV EP PDNPL Sbjct: 215 RGMVNRVRLASMKQGAILINTARGPLLDEAAVAAALNDNHLGGLGVDVVAVEPIRPDNPL 274 Query: 268 LKLDNVVTTPHIAASTREAQLNVGMIIAEDIVNMAKGLPVRNAVNLPSI 316 L N + TPH+A +T A+ + + A +I G P N V P++ Sbjct: 275 LTAKNCLITPHLAWATLTARQTLMRVTAGNIRAFLAGAPT-NVVKAPTV 322 Lambda K H 0.317 0.136 0.376 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: 327 Number of extensions: 18 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: 527 Length of database: 322 Length adjustment: 31 Effective length of query: 496 Effective length of database: 291 Effective search space: 144336 Effective search space used: 144336 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