Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_012589279.1 MSIL_RS01175 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000021745.1:WP_012589279.1 Length = 324 Score = 182 bits (461), Expect = 2e-50 Identities = 112/295 (37%), Positives = 170/295 (57%), Gaps = 18/295 (6%) Query: 21 EEVAEVVVNTTIT-PEELLDAIKDFDAI-VVRSRTKVTREVIEAAPRLKIIARAGVGVDN 78 E A V N + PE + + FD + V+R RT + R ++E PRLK+I G + Sbjct: 31 ERAAITVFNDHLADPEAVALRLAPFDILCVMRERTPLPRALLERLPRLKLIVTTGRRNAS 90 Query: 79 VDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGIE 138 +D+ AA +RGI+V + S++ T+ E + L+LA R IA + S++ G W+++ +G Sbjct: 91 IDLTAAAERGIVVAHTGYSSTPTI-EFAFSLILASVRNIASENASLRAGGWQRS--LGGS 147 Query: 139 LNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDI 198 L G TLG++G+G IG+++ AFGM I+ + ++ E A G T+ L SDI Sbjct: 148 LRGATLGVMGLGNIGAEMARLGLAFGMTIIAWSQNLTPERAAAAGATLVSKTELFEHSDI 207 Query: 199 VTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVF 258 ++IH+ L+ TR L+ E LMK TA +VN +RG I+DE AL AL++G+IAGAA+DVF Sbjct: 208 LSIHLVLSGRTRGLVGAQELALMKPTARLVNSSRGPIVDESALIEALREGQIAGAAIDVF 267 Query: 259 EEEP-PEGSPLLELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRNVL 312 + EP P+ P L NV+ TPHIG V+ ++ VF G +N+L Sbjct: 268 DCEPLPQDHPFRTLPNVLATPHIG------------YVSKDMYRVFYGDTVKNIL 310 Lambda K H 0.316 0.135 0.366 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: 342 Number of extensions: 16 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: 525 Length of database: 324 Length adjustment: 31 Effective length of query: 494 Effective length of database: 293 Effective search space: 144742 Effective search space used: 144742 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 10 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