Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_011517523.1 Q392_RS32360 NAD(P)-dependent oxidoreductase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000745855.1:WP_011517523.1 Length = 327 Score = 160 bits (404), Expect = 5e-44 Identities = 113/331 (34%), Positives = 167/331 (50%), Gaps = 34/331 (10%) Query: 4 KVGVLLKMKREALEELKKYADVEIILYP-----SGEELKGVIGRFDGIIVSPTTKITREV 58 K+ V + E L +L+ A+ E+I+ P S +L+ + D ++ T +T+E Sbjct: 5 KIVVTQPVHEEVLRKLQ--AEGEVIMNPGPDPWSPSQLREYLVDADAMMAFMTDSVTKES 62 Query: 59 LENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHY 118 L NA RLK ISC GYDN DL + G+ VT V LL+E AE +GL I R + Sbjct: 63 LLNAPRLKTISCALKGYDNFDLRACAQAGVSVTFVPDLLTEPTAELAIGLAIAAGRNVLQ 122 Query: 119 ADKFIRRG--EWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYWS 176 D R G W A TG L+G ++G+G +G+AI RL FG Sbjct: 123 GDAATRAGYSGWRP-ALYGTG------LHGSVASVIGLGKVGQAILARLAGFGCA----- 170 Query: 177 RHRKVNVEKELK---ARYMDIDELLEKSDIVILALPLTRDTYHIINEERVK-KLEGKYLV 232 R + V+ ++ + +DE + SD V LA+PL DT H+++ ++ +G+ LV Sbjct: 171 --RLLGVDPSVRLDQVELVTLDEAVSTSDYVFLAVPLVSDTRHLVDSRMLQLSKKGQILV 228 Query: 233 NIGRGALVDEKAVTEAIKQGKLKGYATDVFEKE-------PVREHELFKYEWETVLTPHY 285 N+GRG++VDE+AV +A+ +L YA DV+E E P H TVLTPH Sbjct: 229 NVGRGSVVDERAVVDALANEQLGAYAADVYEMEDWLLPDRPREIHPGLTNNARTVLTPHI 288 Query: 286 AGLALEAQEDVGFRAVENLLKVLRGEVPEDL 316 + ++ RA ENL++ LRGE D+ Sbjct: 289 GSAVRRVRFEIEMRAAENLVRSLRGESLSDV 319 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: 234 Number of extensions: 14 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: 327 Length adjustment: 28 Effective length of query: 305 Effective length of database: 299 Effective search space: 91195 Effective search space used: 91195 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 Jul 25 2024. The underlying query database was built on Jul 25 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