Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate 7026237 Shewana3_3379 aldo/keto reductase (RefSeq)
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__ANA3:7026237 Length = 346 Score = 99.4 bits (246), Expect = 1e-25 Identities = 74/228 (32%), 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+ IK G Sbjct: 18 LGTMTWGEQNTQAEAFAQLDYAIGSGINFIDTAEMYPVPPKPETQGETERILGQYIKARG 77 Query: 83 QRDNLIIATKVGLDWTLTPDQSMRRNSSA--SRIKKEIEDSLRRLGTDYIDLYQVHWPD- 139 RD+L+IATK+ + +R+N + + I + ++ SL RL D IDLYQVHWPD Sbjct: 78 NRDDLVIATKIAAPGGKS--DYIRKNMALDWNNIHQAVDASLERLQIDTIDLYQVHWPDR 135 Query: 140 ----------------PLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAE-- 181 PI ET L + ++GK+R IGVSN + + ++ + AE Sbjct: 136 NTNFFGELFYDEQEIEQQTPILETLEALAEVIRQGKVRYIGVSNETPWGLMKYLQLAEKH 195 Query: 182 ----LAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGR 225 + Q+PYNL R + + + + +L +L Y L G LSG+ Sbjct: 196 GLPRIVTVQNPYNLLNRSFEVGMSEISHREELPLLAYSPLAFGALSGK 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: 275 Number of extensions: 18 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