Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate Echvi_3882 Echvi_3882 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases)
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Cola:Echvi_3882 Length = 328 Score = 139 bits (349), Expect = 1e-37 Identities = 95/292 (32%), Positives = 150/292 (51%), Gaps = 19/292 (6%) Query: 18 GIDKSATRVALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVG 77 G D + V+LGTW +GG GG D+ A+ K +H A+D G+N IDTA Y G +E VG Sbjct: 8 GTDIEVSEVSLGTWQVGGGWGGGFDEKAAAKILHEAVDGGVNFIDTADVYDDGKSEAAVG 67 Query: 78 KAIKGQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHW 137 + +K + + L +A+K G + P S + ++K +E SL+ +G + +DL Q+H Sbjct: 68 RLLKERSEQLYVASKCGRQ--INPHVS--EGYTPEALRKYVEASLKNIGIETLDLIQLHC 123 Query: 138 PDPLV-PIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREI 196 P V +E + + L++EGKI+ +GVS V + + Y + Q +N+F ++ Sbjct: 124 PPTAVYRRDEIFELFDRLKEEGKIKHLGVSVEKVTEAELALNYPNVKTVQIIFNMFRQKP 183 Query: 197 DKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPK---------FQKP 247 AK D+ V+ L GLLSG+M +R F +D R + + F Sbjct: 184 ADSFFELAKAKDVGVIVRVPLASGLLSGKMDRERVFDKNDHRHFNREGQAFDKGETFSGV 243 Query: 248 RFEHYLAAVEELKKLAKEHYNKSVLALAIRW--MLEQGPTLALWGACKPEQI 297 FE L AV LK + E + + A A+RW M +Q T+ + GA +P Q+ Sbjct: 244 DFEKGLEAVAALKDVLGE--EEPLAAWALRWILMFDQVSTV-IPGASRPSQV 292 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: 19 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: 328 Length adjustment: 28 Effective length of query: 312 Effective length of database: 300 Effective search space: 93600 Effective search space used: 93600 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