Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate SMc01698 SMc01698 oxidoreductase
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__Smeli:SMc01698 Length = 251 Score = 142 bits (359), Expect = 5e-39 Identities = 83/261 (31%), Positives = 129/261 (49%), Gaps = 15/261 (5%) Query: 1 MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60 M GK+ +VTGAG IG A + +L EG + + D + +A A +R G AR Sbjct: 1 MKLGLEGKIAIVTGAGSGIGAAVSRQLGGEGAEVIVADRDADAARSVAAEIRSAGGRARD 60 Query: 61 YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120 + DVT AV V VR+ G + NNAG +G DYP +D+ R++ +N+ G Sbjct: 61 FTVDVTDAGAVEQMVAFTVRECGGLHLAVNNAGIEGPRQATADYPLEDWRRLIEVNLNGV 120 Query: 121 FHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNI 180 F+ +K M+ + G IVN +S+ G P +AY +K ++ LT+ A ++ A I Sbjct: 121 FYCMKYEIAAMLGKGGGAIVNMSSILGAVALPTASAYTAAKHGVVGLTKAAGIEYARMGI 180 Query: 181 RVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGV 240 R+NA+ PG+ +E G + ++ A Q P+ R G E+ + Sbjct: 181 RINAVGPGW----------IETPLLSGHSELAKTRRLEALQ-----PLGRRGKPEEVAAL 225 Query: 241 VAFLLGDDSSFMTGVNLPIAG 261 V FLL + +SF+TG P+ G Sbjct: 226 VCFLLSEQASFITGSYHPVDG 246 Lambda K H 0.318 0.135 0.384 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: 158 Number of extensions: 9 Number of successful extensions: 2 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: 262 Length of database: 251 Length adjustment: 24 Effective length of query: 238 Effective length of database: 227 Effective search space: 54026 Effective search space used: 54026 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 (21.7 bits) S2: 47 (22.7 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