Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate CA265_RS00525 CA265_RS00525 aldo/keto reductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Pedo557:CA265_RS00525 Length = 323 Score = 140 bits (354), Expect = 3e-38 Identities = 97/278 (34%), Positives = 145/278 (52%), Gaps = 12/278 (4%) Query: 37 MWGGT--DDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATKVG 94 +WGG ++ SI TIH A+D GIN ++T YG GH E ++GKAIK + D I+ K G Sbjct: 29 IWGGATPNEAESIATIHEALDRGINFLNTGDFYGAGHNEMLIGKAIKDRLDEAFISVKFG 88 Query: 95 LDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILEAL 154 Q + + IK I SL RLG + IDLYQ D VP+E+ + L Sbjct: 89 A--IFHNGQWLGLDLRPLAIKNFINYSLTRLGIETIDLYQPCRMDDSVPVEDIIGTVADL 146 Query: 155 RKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGY 214 KEGK+R IGVS + Q+ + ++ + Y+L +R+I+ ++LP AK+ + V+ + Sbjct: 147 IKEGKVRHIGVSEITADQLRKANNTHPISALEIGYSLADRQIESELLPAAKELGIAVVAF 206 Query: 215 GALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLAL 274 GLL+G M A A +D +FQ H L VE LK++A++ + L Sbjct: 207 ANTAEGLLTGEMKAPLA--ANDYHSHFSRFQGENLVHNLEKVEVLKQMARDK-GCTPTQL 263 Query: 275 AIRWMLEQG----PTLALWGACK-PEQIDGIDEVFGWQ 307 AI W+ EQG P +++ + PE + +D VF Q Sbjct: 264 AIAWVKEQGDHIMPLVSMSRRSRLPENLKAMDIVFSPQ 301 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: 241 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 323 Length adjustment: 28 Effective length of query: 312 Effective length of database: 295 Effective search space: 92040 Effective search space used: 92040 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