Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate N515DRAFT_1253 N515DRAFT_1253 2-dehydro-3-deoxy-L-fuconate dehydrogenase (EC 1.1.1.-)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__Dyella79:N515DRAFT_1253 Length = 248 Score = 120 bits (301), Expect = 3e-32 Identities = 90/263 (34%), Positives = 126/263 (47%), Gaps = 19/263 (7%) Query: 1 MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60 MS + GK LVT AG IG ATAL A EG + D++ +AL A++ + E R+ Sbjct: 1 MSGRLAGKHALVTAAGAGIGRATALAFAREGARVLATDIDEQAL----AALSAEAPELRT 56 Query: 61 YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120 DVT + D +V D LFN AGY A + D + R INV Sbjct: 57 ERLDVTDPVQI----DRLVASHPPFDVLFNCAGYVHA-GTILDTDDAAWKRSFAINVDSM 111 Query: 121 FHVLKAVSRQMITQNYGRIVNTASMAG-VKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179 FH+ + V M+ + G IVN +S+A +KG PN AY T+K A+I LT++ A D Sbjct: 112 FHLCQRVLPAMLERGGGSIVNMSSVASSIKGVPNRFAYSTTKAAVIGLTKSVAADFVGRG 171 Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239 IR NAI PG + + +R L D V + + PM R G+ EI Sbjct: 172 IRCNAICPGTVKTPSLGDRVRAL---------GGDEDAVWRGFVERQPMGRLGNPEEIAM 222 Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262 + +L D+++F TG + GG Sbjct: 223 LALYLASDEAAFTTGTVHIVDGG 245 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: 151 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: 262 Length of database: 248 Length adjustment: 24 Effective length of query: 238 Effective length of database: 224 Effective search space: 53312 Effective search space used: 53312 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