Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_086511882.1 BZY95_RS21230 hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_002151265.1:WP_086511882.1 Length = 331 Score = 150 bits (379), Expect = 4e-41 Identities = 90/276 (32%), Positives = 143/276 (51%), Gaps = 18/276 (6%) Query: 51 TTKITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLII 110 T ++ E+L NA RLK+I+C GYDN D E + G++++ V LL+ AE V L + Sbjct: 54 TDRVDTELLTNAPRLKIIACALKGYDNYDAEACAQAGVWLSIVPDLLTAPTAELAVALAL 113 Query: 111 NLMRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGV 170 L R + D F+R+G + + G+ L+ V +LG+G +G A+ RL FG Sbjct: 114 GLARHVRAGDAFVRQGNYRGWRPHFYGY----GLHNSTVAVLGLGRLGSALVERLQGFGC 169 Query: 171 KLYYWSRHRKVNVEKELKARY-MDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE-G 228 +R V+ L + + L ++D V LPL+ +T+H+++ ++ + G Sbjct: 170 -----ARILGVDTHASLPGVVNCSLQDALAQADFVFSLLPLSEETWHLLDAAHLRACKPG 224 Query: 229 KYLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFK-------YEWETVL 281 + L+N+GRG++VDE AV + + +G+L GYA DVF E E + T+ Sbjct: 225 QLLINVGRGSVVDELAVADVLAEGRLGGYAADVFSCEDWAYLERLRKIPDALLLAENTLF 284 Query: 282 TPHYAGLALEAQEDVGFRAVENLLKVLRGEVPEDLV 317 TPH A+ + RA +N+L VL G PED V Sbjct: 285 TPHLGSAVHSARRAIEHRAADNILAVLAGRAPEDAV 320 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: 242 Number of extensions: 11 Number of successful extensions: 5 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: 331 Length adjustment: 28 Effective length of query: 305 Effective length of database: 303 Effective search space: 92415 Effective search space used: 92415 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