Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011736035.1 PPRO_RS10760 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000015045.1:WP_011736035.1 Length = 357 Score = 221 bits (564), Expect = 3e-62 Identities = 126/294 (42%), Positives = 188/294 (63%), Gaps = 8/294 (2%) Query: 4 MKVLIADSINEKGISELEEVAEVVVNTTITPEELLDA-IKDFDAIVVRSRTKVTREVIEA 62 M VLIA SI+ + I LE+ +V+ + EE L A I+D +A+V RS +V+ +++ Sbjct: 23 MNVLIASSIDGEAIERLEQEHQVIRAFPNSSEESLHALIRDCEALVFRSGIRVSADLMGC 82 Query: 63 APRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADR 122 APRLK++ RAG G+DN+DV+ A RG+ ++ P+ ++ VAE + MLAL+R++ ADR Sbjct: 83 APRLKLLVRAGSGMDNLDVEYARKRGVQLVRIPQPSARAVAEMAFAFMLALSRRLLEADR 142 Query: 123 SVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAE-- 180 S++ G+WEK+ F G L KTLG++G+G GS V A+GM ++ + S+E E Sbjct: 143 SMRNGRWEKHEFSGYLLRDKTLGVVGIGNTGSCVAQMGVAWGMRVIGCVQHPSREREEGF 202 Query: 181 -EMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDED 239 E G+ + + + ++ +D ++IHVPL TR L+ D MK A+++N ARGGI+DE Sbjct: 203 CEKGIQMLEFDQVIANADYLSIHVPLKDNTRRLLDADALSRMKPGAYLINLARGGIVDEQ 262 Query: 240 ALYRAL-KDGEIAGAALDVFEEEPPEG--SPLLELENVVLTPHIGASTSEAQRD 290 ALY +L +G + GAALDV E E +G SPL L NV+LTPHIGA +AQR+ Sbjct: 263 ALYESLTHNGGLRGAALDVHEHE-GQGCMSPLAMLNNVILTPHIGAMAIDAQRE 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: 376 Number of extensions: 15 Number of successful extensions: 5 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: 357 Length adjustment: 32 Effective length of query: 493 Effective length of database: 325 Effective search space: 160225 Effective search space used: 160225 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