Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_012101301.1 CKL_RS04525 NAD(P)-dependent oxidoreductase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000016505.1:WP_012101301.1 Length = 329 Score = 162 bits (410), Expect = 2e-44 Identities = 110/327 (33%), Positives = 167/327 (51%), Gaps = 17/327 (5%) Query: 4 MKVLIADSINE-----KGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTRE 58 MK+LI S + I +++ +V + + E+LD K+ +AI++ + K+ + Sbjct: 1 MKILIIGSKDRYLKYMPNIKFVQDCEKVYIPRDYSQTEILDQAKNVNAIIIDAIAKLPEK 60 Query: 59 VIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA 118 +I P LKII GV + +D +AA RGI V N + + +VAE +I LMLAL R + Sbjct: 61 IIVQMPNLKIIQSEGVAYNGIDCRAAKQRGIYVCNCKGANASSVAEQTILLMLALLRSMV 120 Query: 119 IADRSVKEGKW----EKNRFMGI-ELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPY 173 IADR +EG E GI EL +G+IG G I R FG I Y Sbjct: 121 IADRIEREGYQIELKEHLMLEGITELGDCRIGLIGFGDIAKATAKRLAPFGCKIFYYTKR 180 Query: 174 ISKEAAE-EMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCAR 232 E E V+ + L+ DIV+IH P+TPET +++ + MK +++++N AR Sbjct: 181 PKSHYVEKEFQVSYLGRKELISSCDIVSIHCPVTPETTGMVNTEFLSHMKHSSYLINTAR 240 Query: 233 GGIIDEDALYRALKDGEIAGAALD-VFEEEPPEGSPLLEL-----ENVVLTPHIGASTSE 286 G I+D ALY A+ +I+GA LD V+ E + + LL L E ++ +PHIG T+ Sbjct: 241 GEIVDNQALYNAIVSEQISGAGLDTVYPEPTTKDNVLLNLPGKYAERIIFSPHIGGITTS 300 Query: 287 AQRDAAIIVANEIKTVFQGGAPRNVLN 313 R A V N + +G P ++N Sbjct: 301 FFRRAHAFVWNNVAKALKGERPEFIVN 327 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: 331 Number of extensions: 17 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: 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 09 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