Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_029933667.1 N746_RS0101860 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000711195.1:WP_029933667.1 Length = 331 Score = 165 bits (417), Expect = 3e-45 Identities = 101/284 (35%), Positives = 149/284 (52%), Gaps = 19/284 (6%) Query: 22 EVAEVVVNTTITPEELLDA--IKDFDAIVVRSRTKVTREVIE--AAPRLKIIARAGVGVD 77 EV E+ + P + A + FDA+ ++ IE A KIIA G + Sbjct: 20 EVTEIAMQYFEVPLNVATAHYAQGFDAVSAFVNDELNEATIEILADGGCKIIALRCAGFN 79 Query: 78 NVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGI 137 NVD+KAA + G+ ++ P + VAEH+IGLMLAL+RK+ + V+EG + N +G Sbjct: 80 NVDLKAAENLGVKIVRVPAYSPYAVAEHTIGLMLALSRKLYKSYNRVREGNFSLNGLLGF 139 Query: 138 ELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESD 197 + GKT+GIIG G+IG V R KAFG ++VYDPY+ K +E G L+ L ES Sbjct: 140 DFYGKTVGIIGAGKIGLLVAERMKAFGCHVLVYDPYLCK-TCKEQGFEQVPLDQLYEESH 198 Query: 198 IVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDV 257 ++++H PL +T +I++ + M+ ++N RG +ID AL ALK ++ LDV Sbjct: 199 VISLHCPLNNDTHRMINQASIEKMRGGVMLINTGRGALIDTQALIYALKSRKVGYVGLDV 258 Query: 258 FEEEPP--------------EGSPLLELENVVLTPHIGASTSEA 287 +EEE P L+ NV++T H T EA Sbjct: 259 YEEEGPLFFEDHSNDIILDDNFERLMTFPNVLVTGHQAYFTKEA 302 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: 377 Number of extensions: 18 Number of successful extensions: 2 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: 331 Length adjustment: 31 Effective length of query: 494 Effective length of database: 300 Effective search space: 148200 Effective search space used: 148200 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