Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate GFF2436 PGA1_c24680 glyoxylate reductase GyaR
Query= curated2:O29445 (527 letters) >FitnessBrowser__Phaeo:GFF2436 Length = 318 Score = 150 bits (379), Expect = 7e-41 Identities = 96/321 (29%), Positives = 171/321 (53%), Gaps = 17/321 (5%) Query: 2 KVLVAEPISEEAIDYMRKNGLEVEVK---TGMSREELIREVPKYEAIVVRSQTKVDAEVI 58 K+ + P++ A++ ++ E++ T ++ E R + +++ ++ + DA Sbjct: 4 KLWITRPMTA-AVEARARSEFGAEIRQETTPLTAGERQRALREFDVVMPTLGDQFDAASF 62 Query: 59 Q--AAKNLKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTISTAEHAIALMLAAARKIP 116 +A +++ GVG ++ID++AA GI V N PG T +TA+ A+ LML AR+ Sbjct: 63 AGVSAPRCRLLANFGVGYNHIDVDAAKTAGIAVSNTPGAVTDATADTALTLMLMTARRAG 122 Query: 117 QADRSVKEGKWER---KKFMGIELRGKTAGVIGLGRVGFEVAKRCK---ALEMNVLAYDP 170 + +R V+ G+W+ + +G+ L GK G++G GR+G +A+RC + ++ LA Sbjct: 123 EGERLVRSGQWQGWHPTQMLGLHLTGKHVGIVGFGRIGEAIARRCHFGFGMSVSYLAR-- 180 Query: 171 FVSKERAEQIGVKLVDFDTLLASSDVITVHVPRTKETIGLIGKGQFEKMKDGVIVVNAAR 230 S++ V+ L AS DV+ + VP ET LI M+ +++N AR Sbjct: 181 --SEKSPGFPAVRADSLTALAASVDVLVLAVPGGAETRHLINAEVLAAMRPEALLINIAR 238 Query: 231 GGIVDEAALYEAIKAGKVAAAALDVYEKEPPSPDNPLLKLDNVVTTPHIAASTREAQLNV 290 G +VDEAAL A++ G++A A LDVYE EP P L +++ V PH+ +T E + ++ Sbjct: 239 GEVVDEAALISALQTGQIAGAGLDVYEFEPEVP-LALQQMEQVTLLPHLGTATEEVRSDM 297 Query: 291 GMIIAEDIVNMAKGLPVRNAV 311 G + +++ G P+ + V Sbjct: 298 GHLALDNVAAFLAGKPLISPV 318 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: 324 Number of extensions: 13 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: 318 Length adjustment: 31 Effective length of query: 496 Effective length of database: 287 Effective search space: 142352 Effective search space used: 142352 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