Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_034995987.1 DL88_RS11255 hydroxyacid dehydrogenase
Query= curated2:O29445 (527 letters) >NCBI__GCF_000745425.1:WP_034995987.1 Length = 330 Score = 192 bits (488), Expect = 2e-53 Identities = 111/305 (36%), Positives = 176/305 (57%), Gaps = 5/305 (1%) Query: 3 VLVAEPISEEAIDYMRKN-GLEVEVKTGMSREELIREVPKYEAIVVRSQTKVDAEVIQAA 61 +LVA I E +D +R G+ +++ ++ E + V K +AI++R+Q +A VI A Sbjct: 4 ILVAGRIHEAGLDILRNAPGVSLDLVDEVTMESYVPFVEKADAILIRTQPLPEA-VIAKA 62 Query: 62 KNLKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTISTAEHAIALMLAAARKIPQADRS 121 K L+ + R GVG D +D+ A T+R I + N+ S AEHA+ L+LA A+++ D + Sbjct: 63 KKLRFVSRHGVGYDAVDVEALTRRSIPLSIVGDVNSRSVAEHAMTLLLAVAKRVCAYDHA 122 Query: 122 VKEGKWE-RKKFMGIELRGKTAGVIGLGRVGFEVAKRCKALEMNVLAYDPFVSKERAEQI 180 + GKW R ++ GKT +IG GR+G VA + +M VLAYDPF+ + E+ Sbjct: 123 TRSGKWGLRNDLSATDVFGKTLLLIGFGRIGRLVATMARGFDMTVLAYDPFLDEASIEKA 182 Query: 181 G-VKLVDFDTLLASSDVITVHVPRTKETIGLIGKGQFEKMKDGVIVVNAARGGIVDEAAL 239 G + D L +D +++H+P + L+G+ + +K G I++N ARGG+VDE AL Sbjct: 183 GAIPARDLAGALHIADFVSLHMPPPRGG-PLLGENELAALKPGAILINTARGGVVDELAL 241 Query: 240 YEAIKAGKVAAAALDVYEKEPPSPDNPLLKLDNVVTTPHIAASTREAQLNVGMIIAEDIV 299 A+ G +A A LDV+ EPP P++PLL+ D V+ TPH A TRE + + + +I+ Sbjct: 242 AHALAEGTIAGAGLDVFSAEPPPPEHPLLQSDRVILTPHSAGLTRECAARMAVSASRNIL 301 Query: 300 NMAKG 304 + G Sbjct: 302 DYFAG 306 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: 386 Number of extensions: 22 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: 330 Length adjustment: 31 Effective length of query: 496 Effective length of database: 299 Effective search space: 148304 Effective search space used: 148304 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