Align D-chiro-inositol 1-dehydrogenase (EC 1.1.1.369) (characterized)
to candidate SMc04139 SMc04139 oxidoreductase
Query= BRENDA::Q9WYP5 (334 letters) >FitnessBrowser__Smeli:SMc04139 Length = 357 Score = 96.3 bits (238), Expect = 1e-24 Identities = 72/229 (31%), Positives = 113/229 (49%), Gaps = 17/229 (7%) Query: 3 IGVIGLGRIGTIH-AENLKMIDDAI-LYAISDVREDRLREMKEKLGVEKAYKDPHELIED 60 + +IG G IG H E + D + A+ D+ E+RL E+ ++ G+E+ + +EL++D Sbjct: 6 VAIIGCG-IGRSHIVEGYQPHPDKFRVQALCDLNEERLNEVGDEFGIEQRTRSFNELLDD 64 Query: 61 PNVDAVLVCSSTNTHSELVIACAKAKKHVFCEKPLSLNLADVDRMIEETKKADVILFTGF 120 ++D + +C+ H E V+A A KHV CEKPL+ +L VD ++E K+A +L F Sbjct: 65 DSIDIIDICTPPGIHLEQVLAALAAGKHVICEKPLTGSLEGVDAIMEAEKEARGVLMPIF 124 Query: 121 NRRFDRNFKKLKEAVENGTIGKPHV-------LRITSRDPAPPPLDYIRVSGGIFLDMTI 173 R+ +K K +E G GKP+V LR P + GG+ + + Sbjct: 125 QYRYGDGIEKAKRIIEAGIAGKPYVGSVETFWLRTPEYYSVPWRGKWATELGGVLVTHAL 184 Query: 174 HDFDMARYIMGEEVEEVFADGSVLV-DEEIGKAGDVDTAVVVLRFKSGA 221 H DM ++ G V VF + V D E+ D A L K+GA Sbjct: 185 HLHDMMLHLFG-PVARVFGRVATRVNDIEV-----EDCASASLLMKNGA 227 Lambda K H 0.319 0.139 0.390 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: 243 Number of extensions: 9 Number of successful extensions: 1 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: 334 Length of database: 357 Length adjustment: 29 Effective length of query: 305 Effective length of database: 328 Effective search space: 100040 Effective search space used: 100040 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 Sep 17 2021. 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