Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate SM_b20500 SM_b20500 aldoketo reductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Smeli:SM_b20500 Length = 331 Score = 250 bits (638), Expect = 4e-71 Identities = 138/314 (43%), Positives = 184/314 (58%), Gaps = 10/314 (3%) Query: 22 SATRVALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIK 81 +A+ V LGTWAIGGWMWGGTD+ S+ I ++D G+ +IDTAPAYG G AEE+VGKA+ Sbjct: 16 AASAVGLGTWAIGGWMWGGTDERESVAAIQASLDAGVTLIDTAPAYGLGRAEEIVGKALS 75 Query: 82 GQRDNLIIATKVGLDWTLTP-----DQSMR---RNSSASRIKKEIEDSLRRLGTDYIDLY 133 G+RD +IATK GL W DQ R R+ I E+E SLRRLGTDYIDLY Sbjct: 76 GRRDKAVIATKCGLVWHTQQGNHFFDQDGRPVHRHLGRESIFHEVEQSLRRLGTDYIDLY 135 Query: 134 QVHWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFE 193 HW DP PIEET LE LR GKIR+IG SN +++++ + + L Q +++ + Sbjct: 136 ITHWQDPTTPIEETMRALEDLRAAGKIRAIGASNVNLEELQIYVQIGGLDAIQERFSMLD 195 Query: 194 REIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYL 253 REI+ +LP N + L Y +L GLLSG + +R F+GDD R+ +P+F E Sbjct: 196 REIEAQLLPVTMANGVATLSYSSLALGLLSGSIGPERVFSGDDQRRNNPRFSVANREKVT 255 Query: 254 AAVEELKKLAKEHYNKSVLALAIRWMLEQ-GPTLALWGACKPEQIDGIDEVFGWQISDED 312 E ++ +A+E Y S+ + I W L Q G T AL GA P Q ++S E Sbjct: 256 RFAEAIRPIAQE-YEGSIAQIVIAWTLAQPGITFALCGARNPAQALDNAGAGTIRLSAEA 314 Query: 313 LKQIDAILAKNIPN 326 L IDA +A + N Sbjct: 315 LSAIDAAIAAELAN 328 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: 294 Number of extensions: 12 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: 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 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