Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_012568277.1 RC1_RS14980 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000016185.1:WP_012568277.1 Length = 329 Score = 203 bits (517), Expect = 7e-57 Identities = 123/301 (40%), Positives = 176/301 (58%), Gaps = 6/301 (1%) Query: 14 EKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIEAA-PRLKIIARA 72 E + EL E + +T +T E LLDA D +V ++ EVI AA PRLK+IA Sbjct: 20 ETRMMELFETRLNLDDTPLTREHLLDAAAQADVLVPTVTDRIDAEVIAAAGPRLKLIANF 79 Query: 73 GVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWE-- 130 G GVD++D+KAA +RGI V N P + A+ ++ L+LA+AR++ +R V+ G+W Sbjct: 80 GNGVDHIDLKAARERGISVTNTPGVLTEDTADMTMALILAVARRLTEGERLVRSGRWTGW 139 Query: 131 -KNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPY-ISKEAAEEMGVTVTD 188 +G L GK LGI+GMGRIG + R + FG+ I ++ + E E+ T + Sbjct: 140 GPTNMLGSRLGGKRLGIVGMGRIGQALARRARGFGLSIHYHNRRRVHPEIEAELDATYWE 199 Query: 189 -LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKD 247 L+ +L DIV+I+ P TP T HL++ KL+K +A +VN +RG IDE L L+ Sbjct: 200 SLDQMLARVDIVSINCPRTPATYHLLNARRLKLLKPSAIVVNTSRGEAIDEGTLAGMLQR 259 Query: 248 GEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGA 307 EIAGA LDVFE+EP LL+L+NVVL PH+G++T E++ D V +KT G Sbjct: 260 REIAGAGLDVFEQEPDVDPKLLKLDNVVLLPHLGSATYESRVDMGEKVIVNVKTFVDGHP 319 Query: 308 P 308 P Sbjct: 320 P 320 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: 405 Number of extensions: 20 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: 329 Length adjustment: 31 Effective length of query: 494 Effective length of database: 298 Effective search space: 147212 Effective search space used: 147212 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