Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_005455045.1 SACCYDRAFT_RS07500 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000244975.1:WP_005455045.1 Length = 321 Score = 211 bits (536), Expect = 4e-59 Identities = 129/318 (40%), Positives = 185/318 (58%), Gaps = 16/318 (5%) Query: 3 RMKVLIADSINEKGISELEEVAEVVV---NTTITPEELLDAIKDFDAIVVRSRTKVTREV 59 R ++++ I E + L E EV V + + EEL A+ DA+V +V Sbjct: 2 RPRIVVTRKIAEPALELLRETGEVWVPEPDRALPTEELHAAVAGADAVVSALHDQVDGAF 61 Query: 60 IEAA-PRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA 118 +AA P+LK+++ VG DN+DV A R ++V N P + A+ + GL+L++ R++ Sbjct: 62 ADAAGPQLKVVSTVAVGYDNIDVPALHARDVVVTNTPGVLTDATADLAFGLLLSVTRRLG 121 Query: 119 IADRSVK-EGKWEKN-RFM-GIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYIS 175 A+R ++ W + RFM G L GKTLGI+G+G+IG + R AFGMDI+ Y Sbjct: 122 EAERLLRARTPWMFHPRFMLGTGLQGKTLGIVGLGQIGRAMARRALAFGMDIV----YTG 177 Query: 176 KEAAE-----EMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNC 230 + A+ E+ L+ LLR SD+V++H PLTP+TRHLI D MK TAF+VN Sbjct: 178 RRRADPGVERELDARYVTLDELLRTSDVVSLHCPLTPQTRHLIDADALATMKPTAFLVNT 237 Query: 231 ARGGIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRD 290 RG ++DE AL ALK G IAGAALDVFE+EP LLEL+NV L PH+G++T+E + Sbjct: 238 TRGPVVDEAALADALKRGAIAGAALDVFEKEPEVHPTLLELDNVALAPHLGSATTETRTA 297 Query: 291 AAIIVANEIKTVFQGGAP 308 A++ A V +G P Sbjct: 298 MAVLAARNAIAVLRGEEP 315 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: 381 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: 321 Length adjustment: 31 Effective length of query: 494 Effective length of database: 290 Effective search space: 143260 Effective search space used: 143260 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