Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 7026324 Shewana3_3466 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__ANA3:7026324 Length = 292 Score = 115 bits (288), Expect = 1e-30 Identities = 80/257 (31%), Positives = 129/257 (50%), Gaps = 7/257 (2%) Query: 7 GKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYV--CD 64 GKV L+TG+ IGLATA LAE+G + L + EA + A+ + +Y D Sbjct: 36 GKVGLITGSTSGIGLATAHVLAEQGCHLILHGLMPEAEGRRLAAEFAEQYHIHTYFSNAD 95 Query: 65 VTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVL 124 + E++ +D+ V+ G ID L NNAG Q V +P D + ++ IN++ AFH + Sbjct: 96 LRDPESIHAFMDAGVKALGSIDILVNNAGIQHT-ENVAHFPIDKWNDIIAINLSSAFHTI 154 Query: 125 KAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNA 184 + M + +GRI+N AS+ G+ N AAY +K I+ LT+ A++ A I VNA Sbjct: 155 QQAVPAMAEKRWGRIINIASVHGLVASVNKAAYCAAKHGIVGLTKVVAIECAEQGITVNA 214 Query: 185 ISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFL 244 I PG++ + ++ + + G Y ++V + P+ D +I V FL Sbjct: 215 ICPGWVDTPLINKQIEAIASNKGLSYDEAKYQLVTAKQ----PLPEMLDPRQIGEFVLFL 270 Query: 245 LGDDSSFMTGVNLPIAG 261 + +TG +L + G Sbjct: 271 CSSAARGITGASLAMDG 287 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: 165 Number of extensions: 11 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: 292 Length adjustment: 25 Effective length of query: 237 Effective length of database: 267 Effective search space: 63279 Effective search space used: 63279 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