Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_000621325.1:WP_211248857.1 Length = 255 Score = 103 bits (256), Expect = 5e-27 Identities = 75/256 (29%), Positives = 114/256 (44%), Gaps = 15/256 (5%) Query: 7 GKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVT 66 GKV ++TGA IG A A EG + L E E A++R G EA DV Sbjct: 11 GKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIRATGGEAVFVCTDVL 70 Query: 67 SEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKA 126 E + V + + FG +D LFNNAG +G + + + ++ + NV ++ Sbjct: 71 QEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSVLWGMQH 130 Query: 127 VSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAIS 186 R M + G I+N AS+ G N A Y SK A++ +T AA++ IR+NA+ Sbjct: 131 AIRAMQSAG-GAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGIRINAVC 189 Query: 187 PGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLG 246 PG Q +G + D + + + P R G EI V FL Sbjct: 190 PGITYTPMS-------QRLLGGE----DEQ---NAFMATTPAGRTGQPEEIAAAVVFLAS 235 Query: 247 DDSSFMTGVNLPIAGG 262 ++S+++G L + GG Sbjct: 236 GNASYISGQCLNVDGG 251 Lambda K H 0.318 0.135 0.384 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: 143 Number of extensions: 9 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: 262 Length of database: 255 Length adjustment: 24 Effective length of query: 238 Effective length of database: 231 Effective search space: 54978 Effective search space used: 54978 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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