Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_036260473.1 DL86_RS08935 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000746085.1:WP_036260473.1 Length = 313 Score = 174 bits (440), Expect = 5e-48 Identities = 109/289 (37%), Positives = 161/289 (55%), Gaps = 19/289 (6%) Query: 33 TPEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVI 92 T +E++D + D I + ++ + + P LK+IA A G D VD A GI+V Sbjct: 33 TVDEIVDRLGDA-TIAIINKVPMREATLAKLPNLKLIAVAATGTDVVDKGYAKAHGIIVS 91 Query: 93 NAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEK-NRFMGIE-----LNGKTLGI 146 N TV EH L AL R I V+ G+W++ ++F + + G T+GI Sbjct: 92 NIRNYAFNTVPEHVFALAFALRRNILAYRDDVRAGRWQECDQFCFFDHPIHDMRGSTIGI 151 Query: 147 IGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLT 206 IG G IG V +AF M ++ YD + + DLETLLRESDI+T+H PLT Sbjct: 152 IGYGAIGKAVARIAEAFEMKVLPYDAFPQPG--------LVDLETLLRESDIITLHAPLT 203 Query: 207 PETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPP-EG 265 ET+++I E E KLMK A ++N RGG++DE+AL +AL G I GA DV EPP +G Sbjct: 204 AETKNMIGERELKLMKPGAILINTGRGGLVDEEALAQALTQGVIGGAGFDVLTTEPPKQG 263 Query: 266 SPLLELE--NVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRNVL 312 + LL+L+ N ++TPH+ ++ EA + A + + ++ F G P+NV+ Sbjct: 264 NILLDLKLPNFIITPHVAWASREAMQILADQLIDNVE-AFVAGKPQNVV 311 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: 26 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: 313 Length adjustment: 31 Effective length of query: 494 Effective length of database: 282 Effective search space: 139308 Effective search space used: 139308 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