Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate Ga0059261_3340 Ga0059261_3340 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases)
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Korea:Ga0059261_3340 Length = 351 Score = 138 bits (348), Expect = 2e-37 Identities = 98/315 (31%), Positives = 161/315 (51%), Gaps = 16/315 (5%) Query: 24 TRVALGTWAI--GGWMWG--GTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKA 79 +R++LGT GG + TD + + A+ GIN IDTA Y +EE++GK Sbjct: 14 SRLSLGTMTFTRGGGLKAIAKTDLKDAAALVDHALAAGINFIDTADVYSDFESEEMLGKI 73 Query: 80 IKGQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPD 139 + G+RD L+IATK G W T R SA+ + I+ SL+RLGTD++D+Y H D Sbjct: 74 VAGRRDELVIATKAG--WR-TGQPLNRSGLSAAHLHWSIDHSLKRLGTDHVDVYIAHRDD 130 Query: 140 PLVPIEETATILEALRKEGKIRSIGVSNY------SVQQMDEFKKYAELAVSQSPYNLFE 193 P+EET L+A+ + GK R +GVSN+ + ++ +A +Q Y+L Sbjct: 131 RNTPLEETLQALDAIVRAGKARYLGVSNWPAWKVAAAIELQRANGWAPFTHAQMLYSLMH 190 Query: 194 REIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYL 253 R+I+++ LP A++ L + + L G L+G+ T D A DD + R Y Sbjct: 191 RDIEQEFLPMARRYGLGITPWSPLGGGFLTGKYTRDNAGGADDRLASHDDIPLDREMGY- 249 Query: 254 AAVEELKKLAKEHYNKSVLALAIRWMLEQGPTLA-LWGACKPEQIDGIDEVFGWQISDED 312 ++ ++ +A H S+ +A+ W+L + + L GA K Q+D ++SD++ Sbjct: 250 KLIDTMRGIADGH-GVSIAQIALAWLLSKDQVSSILLGATKLHQLDDNLAAVNVKLSDDE 308 Query: 313 LKQIDAILAKNIPNP 327 + ++ I A+ P Sbjct: 309 IAAMEEISAQRRAYP 323 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: 319 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: 351 Length adjustment: 29 Effective length of query: 311 Effective length of database: 322 Effective search space: 100142 Effective search space used: 100142 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