Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate WP_025272362.1 HALAL_RS0101795 3-oxoacyl-ACP reductase FabG
Query= curated2:P37079 (267 letters) >NCBI__GCF_000527155.1:WP_025272362.1 Length = 236 Score = 115 bits (289), Expect = 7e-31 Identities = 79/256 (30%), Positives = 129/256 (50%), Gaps = 30/256 (11%) Query: 11 VIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDRHHNGDNYHFWSTDISSATEVQQTI 70 V+++TGG GIG A L G V + D + D +H+ D+S + I Sbjct: 5 VVLITGGTRGIGRAAAQRLKDDGFTVAVASRSIPDAENRLDVHHY-QVDVSDGNACKDLI 63 Query: 71 DAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQKGVFFMSQAV 130 + ID L+N+AG+ L+ + + ++ N G + M +++ Sbjct: 64 TTVEDEVGDIDVLINSAGIVRDSPLLT---------MTGDDWNDVIRTNLDGTYNMCRSM 114 Query: 131 ARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKYGIRVVGVAP 190 A M+K++ G I+N+SS +G++G+ QS Y+A+KA + F+++ SKELG++ IRV VAP Sbjct: 115 AFSMMKRKNGSIINLSSVAGIQGNPTQSNYSASKAGIIGFSKALSKELGRFNIRVNVVAP 174 Query: 191 GILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNA---IPIGRAGKLSEVADFVCYLLS 247 G +E ++T + L E K A IP+GR G + +VA V +L S Sbjct: 175 GFIE----------------TDMTAD-LAESVKKKAVENIPLGRMGSVDDVAHLVGFLAS 217 Query: 248 ARASYITGVTTNIAGG 263 RA+Y+TG + GG Sbjct: 218 PRATYMTGAVVPVDGG 233 Lambda K H 0.316 0.133 0.386 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: 140 Number of extensions: 6 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: 267 Length of database: 236 Length adjustment: 24 Effective length of query: 243 Effective length of database: 212 Effective search space: 51516 Effective search space used: 51516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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