Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate GFF427 Psest_0431 Lactate dehydrogenase and related dehydrogenases
Query= BRENDA::O58256 (333 letters) >FitnessBrowser__psRCH2:GFF427 Length = 336 Score = 151 bits (381), Expect = 3e-41 Identities = 95/276 (34%), Positives = 145/276 (52%), Gaps = 13/276 (4%) Query: 53 KITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINL 112 ++ + L+ L+V+ C G+DN D++ T RG+++T V LL+ AE +GL + L Sbjct: 56 RVDADFLQACPELRVVGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGL 115 Query: 113 MRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKL 172 R + AD F+R G+++ + G L VGILGMGAIG A+A RL +G L Sbjct: 116 GRHLRAADAFVRSGKFQGWQPQFYG----TGLDNATVGILGMGAIGLAMADRLQGWGATL 171 Query: 173 -YYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE-GKY 230 Y+ ++ E+ L R + EL SD ++LALPL DT H++N E + + G Sbjct: 172 QYHEAKALDTQTEQRLGLRRVACSELFASSDFILLALPLNADTQHLVNAELLALVRPGAL 231 Query: 231 LVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKE-------PVREHELFKYEWETVLTP 283 LVN RG++VDE AV A+++G+L GYA DVFE E P T+ TP Sbjct: 232 LVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPRLIDPALLAHPNTLFTP 291 Query: 284 HYAGLALEAQEDVGFRAVENLLKVLRGEVPEDLVNK 319 H + ++ A +N+++ L G P + N+ Sbjct: 292 HIGSAVRAVRLEIERCAAQNIIQALAGARPINAANR 327 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: 238 Number of extensions: 10 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: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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