Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_020174531.1 A3OQ_RS0106350 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000385335.1:WP_020174531.1 Length = 331 Score = 179 bits (454), Expect = 1e-49 Identities = 111/304 (36%), Positives = 171/304 (56%), Gaps = 9/304 (2%) Query: 14 EKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIEAA-PRLKIIARA 72 E + EL + + + ++ E+++A+K+ D +V ++ +I AA ++K+IA Sbjct: 19 ETRMCELFDTRLNIDDRPMSAAEIIEAVKNADVLVPTVTDRIDAALIAAAGDKMKLIANF 78 Query: 73 GVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKW--- 129 G GVDN+DV AA +RG+ V N P + A+ ++ L+LA+AR++ + + G+W Sbjct: 79 GNGVDNIDVLAAYERGMTVTNTPGVLTEDTADMTMALILAVARRLVEGAQVIPGGEWGGW 138 Query: 130 EKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPY-ISKEAAEEMGVTVTD 188 +G + GK LGI+GMGRIG V R KAFG+ I ++ +S EE+ T D Sbjct: 139 SPTWMLGRRITGKRLGIVGMGRIGQAVARRAKAFGLQIHYHNRRRLSATVEEELEATYWD 198 Query: 189 -LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKD 247 L+ +L DIV+++ P TP T HL+S K ++ A +VN ARG +IDE L + L Sbjct: 199 SLDQMLARMDIVSVNCPHTPATYHLLSARRLKYLRPHAILVNTARGEVIDEVTLTKMLDA 258 Query: 248 GEIAGAALDVFEEEPPEGSPLLELE---NVVLTPHIGASTSEAQRDAAIIVANEIKTVFQ 304 GEIAGA LDVFE EP + L++L V L PH+G++T+E + D V +K Sbjct: 259 GEIAGAGLDVFEHEPAVSTKLVKLAQAGKVTLLPHMGSATTEGRVDMGEKVIINVKAFMD 318 Query: 305 GGAP 308 G P Sbjct: 319 GHRP 322 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: 383 Number of extensions: 21 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: 525 Length of database: 331 Length adjustment: 31 Effective length of query: 494 Effective length of database: 300 Effective search space: 148200 Effective search space used: 148200 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