Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate 3607117 Dshi_0539 aldo/keto reductase (RefSeq)
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Dino:3607117 Length = 312 Score = 107 bits (266), Expect = 5e-28 Identities = 96/317 (30%), Positives = 140/317 (44%), Gaps = 45/317 (14%) Query: 34 GGWMWGGT-DDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATK 92 G +GGT D AS GIN DTA Y G +E +G+ + Q D+L+IATK Sbjct: 18 GCMQFGGTADKPASAAMFEACRAAGINFFDTAHVYTEGRSETWLGEMVTDQADDLLIATK 77 Query: 93 VGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILE 152 VG S + I+ ++SLRRLG D +D+ +H D P+EET L Sbjct: 78 VGYVG----------GSGRANIRTTFDESLRRLGLDAVDILYLHRWDAETPLEETFEALA 127 Query: 153 ALRKEGKIRSIGVSNYSVQQMDEFKKYAE-----LAVSQSPYNLFEREIDKDILPYAKKN 207 L+ G+ R IGVSN++ Q+ + + AE + + Q Y+L +R+ + +ILP A Sbjct: 128 DLQSAGRFRYIGVSNFAAWQVMKAQAVAEQFGTRIDILQPMYSLIKRQAEVEILPMALSE 187 Query: 208 DLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHY 267 + V Y L GLL+G+ + K + ++ P A L+ LA E Sbjct: 188 GIAVAPYSPLGGGLLTGKYAEGGTGRLTENEKYEMRYSMPWMHE---AAVALRVLAAE-I 243 Query: 268 NKSVLALAIRWMLEQGPTLALWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAKN---I 324 + LA+ W A P G+ IS D+ Q+DA LA + Sbjct: 244 GAAPATLAV-----------AWAAAHP----GVKAPI---ISARDVAQLDASLAARDMAL 285 Query: 325 PNPIGAEFMA----PPP 337 P + A A PPP Sbjct: 286 PPDLYARITALSQTPPP 302 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: 247 Number of extensions: 12 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: 312 Length adjustment: 28 Effective length of query: 312 Effective length of database: 284 Effective search space: 88608 Effective search space used: 88608 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: 48 (23.1 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