Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate SMa0563 SMa0563 aldehyde or keto oxidase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Smeli:SMa0563 Length = 329 Score = 148 bits (374), Expect = 2e-40 Identities = 92/279 (32%), Positives = 153/279 (54%), Gaps = 3/279 (1%) Query: 42 DDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATKVGLDWTL-T 100 D I+ + RA+DLG++ DTA YG EE+VG+A G RD + IATK G D T Sbjct: 30 DRPQMIELLRRAVDLGMDFFDTAEVYGPWTNEEMVGEAFAGMRDKVKIATKFGWDIDQST 89 Query: 101 PDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILEALRKEGKI 160 + NS ++I+ +E SL+RL TD+IDL H DP VP+E+ A ++ L EGK+ Sbjct: 90 GEHGGGVNSKPTQIRSAVEGSLKRLRTDFIDLLYQHRVDPDVPMEDVAGTVKDLIAEGKV 149 Query: 161 RSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRG 220 R G+S + + +A QS Y+L+ RE + +I+P ++ + ++ + L +G Sbjct: 150 RYFGLSEAGAESIRRAHAVQPVAALQSEYSLWTREPEAEIIPTLEELGIGLVPFSPLGKG 209 Query: 221 LLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWML 280 L+G++ A AF +D R P+F E A V+ ++ + E + + +A+ W++ Sbjct: 210 FLAGKIDASTAFAANDFRSQIPRFAPEAREANQALVDLIRSVG-ERRSATPAQVALAWLM 268 Query: 281 EQGPTLA-LWGACKPEQIDGIDEVFGWQISDEDLKQIDA 318 Q P + L+G K E+++ +SD+DL+QI++ Sbjct: 269 AQKPWIVPLFGTRKLERLEENLGALSVTLSDDDLEQIES 307 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: 314 Number of extensions: 20 Number of successful extensions: 3 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: 329 Length adjustment: 28 Effective length of query: 312 Effective length of database: 301 Effective search space: 93912 Effective search space used: 93912 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