Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate SMc00101 SMc00101 oxidoreductase
Query= BRENDA::A0MTG4 (323 letters) >FitnessBrowser__Smeli:SMc00101 Length = 275 Score = 145 bits (365), Expect = 1e-39 Identities = 92/294 (31%), Positives = 156/294 (53%), Gaps = 44/294 (14%) Query: 12 NNGLEMPSIGFGCWKLGKSTAADQVYNAIKAGYRLFDGAEDYGNEQEVGEGVKRAIDEGI 71 +NG +P++GFG +++ + + A+K G+R D A+ YGNE EVGE AI + Sbjct: 6 SNGANIPALGFGTFRMSGAEVLRILPQALKLGFRHVDTAQIYGNEAEVGE----AIQKSG 61 Query: 72 VTREEIFLTSKLWNNYHDPKNVETALNKTLKDLKVDYVDLFLIHFPIAFKFVPIEEKYPP 131 + R ++FLT+K+W + + +++++L+ L+ D+VDL L+H+P + Sbjct: 62 IPRADVFLTTKVWVDNYRHDAFIASVDESLRKLRTDHVDLLLLHWPGS------------ 109 Query: 132 GFYCGDGDNFVYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLFRGATIKPAVL 191 DVP+ E AL ++ AGK+R IG+SNF + + R + A Sbjct: 110 -------------DVPMAERIGALNEVRNAGKVRHIGISNFNTTQMEEAARLSDAPIATN 156 Query: 192 QVEHHPYLQQPKLIEYAQKVGITVTAYSSFGPQSFVEMNQGRALNTPTLFEHDVIKAIAA 251 QVE+HPYL Q K+++ A+++G+++T+Y + M G+ P L E I Sbjct: 157 QVEYHPYLDQTKVLQTARRLGMSLTSYYA--------MANGKVPADPLLTE------IGG 202 Query: 252 KHNKVPAEVLLRWSA-QRGIAVIPKSNLPERLVQNRSFNDFELTKEDFEEISKL 304 +H K A+V LRW Q+ + V+ K+ RL +N + DF LT+E+ + +L Sbjct: 203 RHGKTAAQVALRWLVQQQDVIVLSKTATEARLKENFAIFDFALTREEMAAVREL 256 Lambda K H 0.319 0.139 0.422 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: 210 Number of extensions: 11 Number of successful extensions: 5 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: 323 Length of database: 275 Length adjustment: 26 Effective length of query: 297 Effective length of database: 249 Effective search space: 73953 Effective search space used: 73953 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