Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011764560.1 AZO_RS04165 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000061505.1:WP_011764560.1 Length = 316 Score = 174 bits (442), Expect = 3e-48 Identities = 109/287 (37%), Positives = 165/287 (57%), Gaps = 15/287 (5%) Query: 35 EELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINA 94 E++++ ++D + ++ ++ ++ I A PRL+++A A G DNVD++A RGI+V N Sbjct: 35 EQVVERLRDAEVAII-NKLRLGASEIAALPRLQMVAVAATGSDNVDLEACRARGIVVSNV 93 Query: 95 PESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGI------ELNGKTLGIIG 148 TV EH++ LMLAL R++ V+ G+W ++ +L+G TL IIG Sbjct: 94 RGYAVHTVPEHALMLMLALRRRLFDYVADVRAGRWARSDNFCFFDHPIGDLHGATLAIIG 153 Query: 149 MGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPE 208 G +G V AFGM ++ Y + + T E +L E+D++++H PLTP Sbjct: 154 RGGLGDGVARLGAAFGMRVI----YAEHKGVAGVREGYTAFERVLAEADVLSLHCPLTPA 209 Query: 209 TRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPP-EGSP 267 TR LI E MK A +VN ARGG++DE AL AL+ G IAGAA DV EPP EG+P Sbjct: 210 TRGLIGASELASMKREAVLVNTARGGVVDEPALAAALRAGVIAGAATDVLSSEPPREGNP 269 Query: 268 LL--ELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRNVL 312 LL ++ N+++TPH+ ++ +A + A V + I F GAPRN L Sbjct: 270 LLAADIPNLIVTPHVAWASRQAMQTLADQVIDNI-DAFAAGAPRNRL 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: 368 Number of extensions: 17 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: 316 Length adjustment: 31 Effective length of query: 494 Effective length of database: 285 Effective search space: 140790 Effective search space used: 140790 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