Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 3609257 Dshi_2643 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= curated2:O29445 (527 letters) >FitnessBrowser__Dino:3609257 Length = 316 Score = 167 bits (424), Expect = 4e-46 Identities = 108/319 (33%), Positives = 172/319 (53%), Gaps = 11/319 (3%) Query: 1 MKVLVAEPISEEAIDYMRK--NGLEVEVKTGMSREELIREVPKYEAIVVRSQTKVDAEVI 58 MK+L++ P+ E + R + E M EEL + Y+ ++ AEV Sbjct: 1 MKLLISRPLPEAVLARARARFDCTLRETTQPMRAEELRGALRDYDLVLPTLGDAFSAEVF 60 Query: 59 QAAKN--LKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTISTAEHAIALMLAAARKIP 116 +++ GVG ++ID AA G+ V N PG T +TA+ A+ L+L AAR+ Sbjct: 61 ADVPEPRARLLANFGVGYNHIDAVAARAAGVAVTNTPGAVTDATADTALTLILMAARRAG 120 Query: 117 QADRSVKEGKW---ERKKFMGIELRGKTAGVIGLGRVGFEVAKRCK-ALEMNVLAYDPFV 172 + +R V+ G W + +G+ + GKT GVIG+GR+G +A RC M V+ Y+ Sbjct: 121 EGERLVRAGTWTGWHPTQMLGLHVTGKTLGVIGMGRIGQAIAARCHHGFGMEVVFYNR-- 178 Query: 173 SKERAEQIGVKLVDFDTLLASSDVITVHVPRTKETIGLIGKGQFEKMKDGVIVVNAARGG 232 S + + +L ++A++D++ V VP ET LIG F M+ + VN ARG Sbjct: 179 SPKTPDLPARQLASVAEVMAAADIVVVAVPGGAETHHLIGAEAFAAMQPHAVFVNIARGD 238 Query: 233 IVDEAALYEAIKAGKVAAAALDVYEKEPPSPDNPLLKLDNVVTTPHIAASTREAQLNVGM 292 +VDEAAL A++AG++ AA LDVYE EP P+ L+ ++NVV PH+ + E + +G Sbjct: 239 VVDEAALIAALQAGQLGAAGLDVYEFEPAVPE-ALIGMENVVLLPHLGTAALEVREAMGH 297 Query: 293 IIAEDIVNMAKGLPVRNAV 311 + ++++ A+G P+ N V Sbjct: 298 MALDNLIACAEGAPLPNPV 316 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: 354 Number of extensions: 22 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: 527 Length of database: 316 Length adjustment: 31 Effective length of query: 496 Effective length of database: 285 Effective search space: 141360 Effective search space used: 141360 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