Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate PfGW456L13_2937 Oxidoreductase, aldo/keto reductase family
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2937 Length = 336 Score = 128 bits (322), Expect = 2e-34 Identities = 93/304 (30%), Positives = 151/304 (49%), Gaps = 15/304 (4%) Query: 28 LGTWAIGGWMWGG-TDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDN 86 + T +G M+G T + S++ I +A D GIN IDTA Y G +EE+VG+AI +R Sbjct: 13 VSTLTLGTMMFGEQTSTEDSLRIIDKAWDQGINFIDTADVYTNGRSEEIVGEAIASRRHE 72 Query: 87 LIIATKVGLDWTLTPDQSMRRNSSASR--IKKEIEDSLRRLGTDYIDLYQVHWPDPLVPI 144 ++ATKVG P + S SR + I+ SL RLGTDY+D+Y +H D P+ Sbjct: 73 WVLATKVGFG----PVDGVPNRSGLSRKHLFNGIDASLTRLGTDYLDIYYLHREDHNTPL 128 Query: 145 EETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAEL------AVSQSPYNLFEREIDK 198 E T + + L ++GKIR G+SNY ++ E + A+ +SQ YN+ R+ + Sbjct: 129 EVTVSAIGDLIRQGKIRYWGLSNYRGWRIAEVIRVADKLGVDRPVISQPLYNIVNRQAET 188 Query: 199 DILPYAKKNDLVVLGYGALCRGLLSGRMTAD-RAFTGDDLRKTDPKFQKPRFEHYLAAVE 257 + + A+ L V+ Y L RG+LSG+ D + + D + + + + Sbjct: 189 EQITAAQSYGLGVVPYSPLARGVLSGKYAPDVKPDANSRAGRQDKRILETEWRVESLRIA 248 Query: 258 ELKKLAKEHYNKSVLALAIRWMLEQGP-TLALWGACKPEQIDGIDEVFGWQISDEDLKQI 316 + + + ++ AI W+L T A+ G EQ D + +I+ ED I Sbjct: 249 QQIQQYTQQRGVGIVEFAIAWVLNNSAVTSAIVGPRTEEQWDAYTKAQAVKITAEDEAFI 308 Query: 317 DAIL 320 D+++ Sbjct: 309 DSLV 312 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: 285 Number of extensions: 14 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: 336 Length adjustment: 28 Effective length of query: 312 Effective length of database: 308 Effective search space: 96096 Effective search space used: 96096 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