Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate GFF3991 Psest_4064 Lactate dehydrogenase and related dehydrogenases
Query= BRENDA::O58256 (333 letters) >FitnessBrowser__psRCH2:GFF3991 Length = 329 Score = 127 bits (320), Expect = 3e-34 Identities = 78/201 (38%), Positives = 119/201 (59%), Gaps = 8/201 (3%) Query: 66 KVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADKFIRR 125 ++I+ SAGY+++DL A + G+ V +V AVAE TV LI+ L R++ A IR Sbjct: 70 RLIALRSAGYNHVDLPCAKRLGLPVVRVPAYSPHAVAEHTVALILALNRRLPRAYNRIRE 129 Query: 126 GEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYWSRHRKVNVEK 185 G + TGF L GK+VG++G G IG AR ++ FG ++ + + +E+ Sbjct: 130 GNFSLQG--LTGF----DLVGKRVGVVGSGQIGAVFARIMLGFGCEVQLYDPYPNPELER 183 Query: 186 ELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLEGK-YLVNIGRGALVDEKA 244 L RY+ +DELL SDIV L PLT T+H+IN++ + ++ + L+N GRGAL+D A Sbjct: 184 -LGMRYVALDELLASSDIVSLHCPLTAQTHHLINQQSLATMKPRAMLINTGRGALIDTPA 242 Query: 245 VTEAIKQGKLKGYATDVFEKE 265 + A+K G+L DV+E+E Sbjct: 243 LIGALKSGQLGYLGLDVYEEE 263 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: 209 Number of extensions: 15 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 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