Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_008805143.1 KVAR_RS14490 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000025465.1:WP_008805143.1 Length = 329 Score = 130 bits (327), Expect = 5e-35 Identities = 89/273 (32%), Positives = 143/273 (52%), Gaps = 23/273 (8%) Query: 55 TREVLEN--AERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINL 112 +R VLE A +K I+ AG++N+DLE A + G+ V +V EAVAE +G++++L Sbjct: 57 SRPVLEELKAHGVKYIALRCAGFNNVDLEAAKELGLRVVRVPAYSPEAVAEHAIGMMMSL 116 Query: 113 MRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKL 172 R+IH A + R + TGF ++YGK G++G G IG A+ R L FG++L Sbjct: 117 NRRIHRAYQRTRDANFSLEG--LTGF----TMYGKTAGVIGTGKIGVAMLRILKGFGMRL 170 Query: 173 YYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKL-EGKYL 231 + + EL Y+D+ L ++SD++ L PLT + YH++N E ++ +G + Sbjct: 171 LAFDPYPSA-AALELGVEYVDLATLYKESDVISLHCPLTDENYHLLNREAFDQMKDGVMV 229 Query: 232 VNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKE----------PVREHELFKYE---WE 278 +N RGAL+D +A +A+K K+ DV+E E V + ++F+ Sbjct: 230 INTSRGALIDSQAAIDALKHQKIGALGLDVYENERDLFFEDKSNDVIQDDVFRRLSACHN 289 Query: 279 TVLTPHYAGLALEAQEDVGFRAVENLLKVLRGE 311 + T H A L EA + + NL +V GE Sbjct: 290 VLFTGHQAFLTAEALISISETTLGNLQQVANGE 322 Lambda K H 0.319 0.139 0.393 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: 230 Number of extensions: 13 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: 333 Length of database: 329 Length adjustment: 28 Effective length of query: 305 Effective length of database: 301 Effective search space: 91805 Effective search space used: 91805 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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