Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_012620277.1 CKL_RS04525 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000016505.1:WP_012620277.1 Length = 346 Score = 160 bits (406), Expect = 5e-44 Identities = 105/309 (33%), Positives = 160/309 (51%), Gaps = 12/309 (3%) Query: 17 ISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGV 76 I +++ +V + + E+LD K+ +AI++ + K+ ++I P LKII GV Sbjct: 36 IKFVQDCEKVYIPRDYSQTEILDQAKNVNAIIIDAIAKLPEKIIVQMPNLKIIQSEGVAY 95 Query: 77 DNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKW----EKN 132 + +D +AA RGI V N + + +VAE +I LMLAL R + IADR +EG E Sbjct: 96 NGIDCRAAKQRGIYVCNCKGANASSVAEQTILLMLALLRSMVIADRIEREGYQIELKEHL 155 Query: 133 RFMGI-ELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAE-EMGVTVTDLE 190 GI EL +G+IG G I R FG I Y E E V+ + Sbjct: 156 MLEGITELGDCRIGLIGFGDIAKATAKRLAPFGCKIFYYTKRPKSHYVEKEFQVSYLGRK 215 Query: 191 TLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEI 250 L+ DIV+IH P+TPET +++ + MK +++++N ARG I+D ALY A+ +I Sbjct: 216 ELISSCDIVSIHCPVTPETTGMVNTEFLSHMKHSSYLINTARGEIVDNQALYNAIVSEQI 275 Query: 251 AGAALD-VFEEEPPEGSPLLEL-----ENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQ 304 +GA LD V+ E + + LL L E ++ +PHIG T+ R A V N + + Sbjct: 276 SGAGLDTVYPEPTTKDNVLLNLPGKYAERIIFSPHIGGITTSFFRRAHAFVWNNVAKALK 335 Query: 305 GGAPRNVLN 313 G P ++N Sbjct: 336 GERPEFIVN 344 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: 341 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: 346 Length adjustment: 32 Effective length of query: 493 Effective length of database: 314 Effective search space: 154802 Effective search space used: 154802 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: 51 (24.3 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