Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate Echvi_3562 Echvi_3562 Aldo/keto reductases, related to diketogulonate reductase
Query= BRENDA::O74237 (322 letters) >FitnessBrowser__Cola:Echvi_3562 Length = 319 Score = 230 bits (587), Expect = 3e-65 Identities = 127/314 (40%), Positives = 186/314 (59%), Gaps = 11/314 (3%) Query: 8 IKLSSGHLMPSIGFGCWKLANATAGEQVYQAIKAGYRLFDGAEDYGNEKEVGDGVKRAID 67 + S+G MP IG G W+ V +AI+ GYR FD A Y NEKE+GD +A Sbjct: 4 LTFSNGDTMPIIGLGTWQSKPGEVYNAVLKAIEIGYRHFDCAYIYKNEKEIGDAFAKAFA 63 Query: 68 EGLVKREEIFLTSKLWNNYHDPKNVETALNKTLADLKVDYVDLFLIHFPIAFKFVPIEEK 127 +G +KRE+I++TSKLWN+ H P++V AL TL DL++DY+DL+L+H+P+A K Sbjct: 64 DGTIKREDIWVTSKLWNDSHKPEHVLPALESTLKDLQLDYLDLYLVHWPLAL-------K 116 Query: 128 YPPGFYCGDGNNFVYEDVPILETWKALEKLVAAGKIKSIGVSNFPGALLLDLLRGATIKP 187 + F +G+ +++P+ TW A+E L+ GK+K IGVSNF L ++L A KP Sbjct: 117 HGVDFPEENGDFEHLDNIPLSTTWAAMEGLLETGKVKHIGVSNFKIEKLKEILASAKSKP 176 Query: 188 AVLQVEHHPYLQQPKLIEFAQKAGVTITAYSSFGPQSFVEMNQGRALNTPTLFAHDTIKA 247 V QVE HP+L Q L+++ +K G+ +TAY+ G + G ++ P L +D +K Sbjct: 177 EVNQVEMHPFLPQQGLVDYCKKEGIHLTAYAPLGAAYRTQGQDG--VDLPILLENDQVKN 234 Query: 248 IAAKYNKTPAEVLLRWAAQRGIAVIPKSNLPERLVQNRSFNTFDLTKEDFEEIAKLDIGL 307 IA K N T A+V+L W QR IAVIPKS P R+ +N N L++E+ +++ +L+ Sbjct: 235 IANKLNATTAQVVLAWNIQRDIAVIPKSVTPSRIEENFKSNLLTLSQEEMDQLNQLEGPY 294 Query: 308 RFNDP--WDWDNIP 319 RF D W N P Sbjct: 295 RFTDGKLWTTHNSP 308 Lambda K H 0.319 0.138 0.418 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: 318 Number of extensions: 17 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: 322 Length of database: 319 Length adjustment: 28 Effective length of query: 294 Effective length of database: 291 Effective search space: 85554 Effective search space used: 85554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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