Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate Echvi_4177 Echvi_4177 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases)
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Cola:Echvi_4177 Length = 327 Score = 146 bits (368), Expect = 8e-40 Identities = 101/285 (35%), Positives = 150/285 (52%), Gaps = 6/285 (2%) Query: 41 TDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATKVGLDWTLT 100 T+ +A+IK I A + GI DTA YG EE+VG+AI R ++IATK G Sbjct: 31 TEKNAAIKLIRSAFEQGITFFDTAECYGPFTNEELVGEAIAPFRKEVVIATKFGFK---D 87 Query: 101 PDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILEALRKEGKI 160 D +SS RI++ E SLRRL TD+IDL+ H DP VP+E+ A + L KEGKI Sbjct: 88 GDSKKGLDSSPKRIREVAESSLRRLNTDHIDLFYQHRVDPSVPMEDVAGTMSDLIKEGKI 147 Query: 161 RSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRG 220 G+S + + LA QS Y+LF RE +K+I+P ++ + + + L +G Sbjct: 148 GHWGLSEAGATTIRKAHAIQPLAALQSEYSLFYREPEKEIIPLLEEFGIGFVPFSPLGKG 207 Query: 221 LLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWML 280 L+G ++ F +D R T P+F K + A V+ +KK+A + + +A+ W+L Sbjct: 208 FLTGAISESTQFDPNDFRNTVPRFSKENRKANQALVDLVKKIAVQK-QATPGQIALGWLL 266 Query: 281 EQGP-TLALWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAKNI 324 Q P L + G K ++ +SD+DL Q+ L KNI Sbjct: 267 AQKPFILPIPGTTKQHRLTENVGSTKINLSDDDLFQVSTAL-KNI 310 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: 297 Number of extensions: 13 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: 327 Length adjustment: 28 Effective length of query: 312 Effective length of database: 299 Effective search space: 93288 Effective search space used: 93288 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