Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Echvi_3936 Echvi_3936 Lactate dehydrogenase and related dehydrogenases
Query= BRENDA::O58256 (333 letters) >FitnessBrowser__Cola:Echvi_3936 Length = 330 Score = 122 bits (306), Expect = 1e-32 Identities = 88/280 (31%), Positives = 142/280 (50%), Gaps = 28/280 (10%) Query: 44 DGIIVSPTTKITREVLENAER--LKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAV 101 D + + T +R VLE ++ +K ++ SAG++++DL A + G+ V +V A+ Sbjct: 44 DAVAIFVTDNGSRPVLEKLQQFGVKYLALRSAGFNHVDLSAAEELGLKVARVPEYSPAAI 103 Query: 102 AEFTVGLIINLMRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAI 161 AE TV L++ L RK+ A +R + + GF + GK +GI G G IG + Sbjct: 104 AEHTVALMLALNRKLVKAHNRVRDLNFSLDGLV--GF----DMEGKTIGIAGTGKIGSKV 157 Query: 162 ARRLIPFGVKLYYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEE 221 A+ L FG +L + + +++ EL+ Y+D L +SDI+ L LPL+ + ++IN Sbjct: 158 AKTLSGFGCRLLAYDPYINESLKAELEIEYVDFKTLCTESDIITLHLPLSSSSQYMINSS 217 Query: 222 RVKKL-EGKYLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWETV 280 ++ + +G L+N RGALV+ K V EA+K GK+ + DV+E+E E F+ E + Sbjct: 218 SMEDMKKGVMLINTSRGALVNTKEVIEALKTGKIGSFGMDVYEEE---EDLFFEDHSEDI 274 Query: 281 L----------------TPHYAGLALEAQEDVGFRAVENL 304 L T H A L EA E + NL Sbjct: 275 LQDDVIARLLTFQNVLITSHQAFLTKEALEKIAGVTAFNL 314 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: 259 Number of extensions: 13 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: 333 Length of database: 330 Length adjustment: 28 Effective length of query: 305 Effective length of database: 302 Effective search space: 92110 Effective search space used: 92110 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 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