Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_047212629.1 PATSB16_RS03325 aldo/keto reductase
Query= BRENDA::F2YCN5 (340 letters) >NCBI__GCF_001931675.1:WP_047212629.1 Length = 331 Score = 139 bits (350), Expect = 1e-37 Identities = 101/300 (33%), Positives = 154/300 (51%), Gaps = 29/300 (9%) Query: 18 GIDKSATRVALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYG-------RG 70 G + +R+ LGT G T++ AS + +A D G+N IDTA Y G Sbjct: 8 GTGLTVSRLCLGTMTFGLQ----TEEAASHAILDKAADAGVNFIDTADVYPLGGTEQLAG 63 Query: 71 HAEEVVGKAIKGQRDNLIIATK-VGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDY 129 EE+VGK +KG+R+ I+ATK VG DQ +S + I+ SLRRLGTDY Sbjct: 64 RTEEIVGKWLKGKRERFILATKAVGKVGPSLWDQG----ASRKHLLDAIDVSLRRLGTDY 119 Query: 130 IDLYQVHWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQM------DEFKKYAELA 183 +DLYQ+H D P++ET L+ + ++GK R IGVSN+ ++ + + A Sbjct: 120 VDLYQLHADDAQTPLDETLEALDTIVRQGKARYIGVSNFLAYRLARALGRADVLRVARFV 179 Query: 184 VSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTAD-----RAFTGDDLR 238 Q YNL R+I++++LP A++ L V+ Y L GLL+G+ D FT + Sbjct: 180 SVQPRYNLLFRQIERELLPLAQEEQLAVIPYNPLAGGLLTGKHRHDVTPTEGRFTATVGK 239 Query: 239 KTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLEQGP-TLALWGACKPEQI 297 + Q+ E +E+LK++A + K + A+ W+L T A+ GA + EQ+ Sbjct: 240 AGEMYTQRYWHEREFHTIEKLKEIAAQ-TGKPLTQTALAWVLANPTVTSAIIGASRAEQL 298 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: 276 Number of extensions: 16 Number of successful extensions: 4 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: 331 Length adjustment: 28 Effective length of query: 312 Effective length of database: 303 Effective search space: 94536 Effective search space used: 94536 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 24 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