Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Ac3H11_1922 Citronellol and citronellal dehydrogenase
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1922 Length = 309 Score = 136 bits (343), Expect = 5e-37 Identities = 88/258 (34%), Positives = 130/258 (50%), Gaps = 17/258 (6%) Query: 5 FNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCD 64 F G+V +VTG G IG TA LA G + L+ E L + G VCD Sbjct: 18 FQGQVVVVTGGGSGIGRCTAHELAHLGAHVVLVGRKPEKLLAVAEEITADGGRVSCQVCD 77 Query: 65 VTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVL 124 + SEE V+ V +V G+ID L NNAG Q AP++ + + VL N+TG F + Sbjct: 78 IRSEEGVVALVQQIVAAQGRIDALVNNAGGQ-FMAPLESISAKGWEAVLHTNLTGGFLMA 136 Query: 125 KAVSRQMITQNYGRIVN-TASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVN 183 + RQ + Q+ G IVN A M G P M G ++ +++LTETAAL+ A +RVN Sbjct: 137 REFYRQWMAQHGGSIVNIVADMWG--SMPGMGHSGAARAGMVSLTETAALEWAHSGVRVN 194 Query: 184 AISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAF 243 A++PGY+ A G + + + + M +VP+ R+G+ E+ + F Sbjct: 195 AVAPGYI-------------ASSGMDNYPPEAADMLRAMPRTVPLGRFGNEAEVSAAITF 241 Query: 244 LLGDDSSFMTGVNLPIAG 261 LL +SF++G L + G Sbjct: 242 LLSPAASFISGTTLRVDG 259 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: 213 Number of extensions: 13 Number of successful extensions: 4 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: 309 Length adjustment: 26 Effective length of query: 236 Effective length of database: 283 Effective search space: 66788 Effective search space used: 66788 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