Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__Caulo:CCNA_01892 Length = 546 Score = 130 bits (327), Expect = 6e-35 Identities = 87/263 (33%), Positives = 128/263 (48%), Gaps = 17/263 (6%) Query: 1 MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60 M+ K +V LVTG IG A R A G + + D N +E+A G + + Sbjct: 26 MTSKAQSRVVLVTGGADGIGWAACQRFARAGDQVLVADRN---VERARERADSLGPDHHA 82 Query: 61 YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQ-DYPSDDFARVLTINVTG 119 DV+SE + + + R+FG++D L NNAG D +++ AR+ INVTG Sbjct: 83 IAMDVSSEAQIREGFEQLHREFGRLDVLVNNAGVTDPQPTATLDQTAEEVARLQAINVTG 142 Query: 120 AFHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179 AF + R MI Q +G I+N AS AG+ +Y SK A+I+LT T A + A Sbjct: 143 AFLAAREAGRLMIEQGHGAIINLASGAGLVALAKRTSYSASKAAVISLTRTLACEWAAKG 202 Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239 +RVNA+ PGY + V+ Q G DP +V + +P+ R G+ E+ Sbjct: 203 VRVNAVLPGYTR-----TQMVQDQIDAG----LLDPSIV----LSRIPLGRMGEPEEMAE 249 Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262 FL D +S++ G L + GG Sbjct: 250 GAFFLASDAASYVVGATLVVDGG 272 Score = 96.7 bits (239), Expect = 9e-25 Identities = 67/255 (26%), Positives = 114/255 (44%), Gaps = 18/255 (7%) Query: 8 KVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVTS 67 +V +TG G IG G + +++ + E + ++ ++ + ++ + DV + Sbjct: 296 RVSAITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALAEALGDEHIVVQADITDVAA 355 Query: 68 EEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKAV 127 EA + +G++D L NNAG F P + + DF V +N +G KA Sbjct: 356 VEAAFAQAQA---RWGRLDVLINNAGAADVFKPSLEQTAQDFTSVYDLNFSGPLATAKAA 412 Query: 128 SRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAISP 187 +R M G IVN S+AG+ P AY +K A+ ++ + A + A IRVN ++P Sbjct: 413 ARLM--SQGGVIVNLGSIAGLGALPQRNAYCAAKAAVTMMSRSLACEWASAGIRVNTVAP 470 Query: 188 GYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLGD 247 GY+ E L K + ++ P+ R GD E+ +AFL Sbjct: 471 GYI------ETPAVLALKSAG-------RAQFDKIRRRAPIGRLGDPMEVARTIAFLASP 517 Query: 248 DSSFMTGVNLPIAGG 262 +S++ G L + GG Sbjct: 518 AASYVAGATLTVDGG 532 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: 309 Number of extensions: 12 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 262 Length of database: 546 Length adjustment: 30 Effective length of query: 232 Effective length of database: 516 Effective search space: 119712 Effective search space used: 119712 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: 50 (23.9 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