Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate N515DRAFT_3546 N515DRAFT_3546 Predicted oxidoreductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Dyella79:N515DRAFT_3546 Length = 330 Score = 154 bits (388), Expect = 4e-42 Identities = 95/296 (32%), Positives = 159/296 (53%), Gaps = 4/296 (1%) Query: 27 ALGTWAIG-GWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRD 85 ALG +G +G DD SI TIH A+D G+ ++DTA YG EE+VGKAI+ +R Sbjct: 15 ALGLGCMGMSEFYGARDDAESIATIHHALDRGLTLLDTADIYGPYINEELVGKAIRARRG 74 Query: 86 NLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIE 145 + +ATK G+ QS + +++ ++ SL+RLG + IDLY H DP PIE Sbjct: 75 QVFLATKFGIVRDPANPQSRAVSGRPEYVRESVDGSLKRLGVEQIDLYYQHRLDPRTPIE 134 Query: 146 ETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKD-ILPYA 204 +T + L + GK+R +G+S S + ++ +A QS ++L+ R+ ++ +L Sbjct: 135 DTVGAMAELVQAGKVRYLGLSEVSAETLERAHAVHPIAAVQSEFSLWTRDPQENGVLAMC 194 Query: 205 KKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAK 264 +K ++ Y L RG L+G + F DD R++ P+F F L V+++ +LA+ Sbjct: 195 RKLGTALVAYSPLGRGFLTGAYKSPDDFAADDYRRSSPRFLGENFTRNLQLVDKVTELAR 254 Query: 265 EHYNKSVLALAIRWMLEQG-PTLALWGACKPEQIDGIDEVFGWQISDEDLKQIDAI 319 + + LA+ W+L QG + + G + +++D ++S +L+ IDAI Sbjct: 255 DK-GCTPAQLALAWVLAQGDDVIGIPGTKRRDRLDENLGALDVKLSGAELEAIDAI 309 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: 288 Number of extensions: 14 Number of successful extensions: 2 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: 330 Length adjustment: 28 Effective length of query: 312 Effective length of database: 302 Effective search space: 94224 Effective search space used: 94224 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