Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate 5208224 Shew_0736 aldo/keto reductase (RefSeq)
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__PV4:5208224 Length = 346 Score = 101 bits (252), Expect = 2e-26 Identities = 78/228 (34%), Positives = 111/228 (48%), Gaps = 37/228 (16%) Query: 33 IGGWMWGGTDDDA-SIKTIHRAIDLGINIIDTAPAYG-------RGHAEEVVGKAIK--G 82 +G WG + A + + + AI GIN IDTA Y +G E ++G +K G Sbjct: 18 LGTMTWGEQNTQAQAFEQLDYAIGQGINFIDTAEMYPVPPKAETQGETERILGNYLKARG 77 Query: 83 QRDNLIIATKVGLDWTLTPDQSMRRNSSAS--RIKKEIEDSLRRLGTDYIDLYQVHWPD- 139 +RD+LIIATKV + +R+N + I + + DSL RL + IDLYQ+HWPD Sbjct: 78 KRDDLIIATKVAAPGGKS--DYIRQNMALDWRNIHQAVNDSLERLQIETIDLYQLHWPDR 135 Query: 140 ----------------PLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAE-- 181 L PI +T L L K GKIR IGVSN + + ++ + AE Sbjct: 136 NTNFFGELFYEQQDDEKLTPIIDTLEALADLIKAGKIRYIGVSNETPWGLMKYLQLAEKH 195 Query: 182 ----LAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGR 225 + Q+PYNL R + + A + +L +L Y L G LSG+ Sbjct: 196 GLPRIISVQNPYNLLNRSFEVGMAEIAHREELPLLAYSPLAFGALSGK 243 Lambda K H 0.317 0.136 0.407 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: 287 Number of extensions: 17 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: 340 Length of database: 346 Length adjustment: 29 Effective length of query: 311 Effective length of database: 317 Effective search space: 98587 Effective search space used: 98587 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 (21.6 bits) S2: 49 (23.5 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