Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_037458219.1 N825_RS25105 SDR family oxidoreductase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_000576635.1:WP_037458219.1 Length = 249 Score = 150 bits (379), Expect = 2e-41 Identities = 90/259 (34%), Positives = 133/259 (51%), Gaps = 19/259 (7%) Query: 4 KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVC 63 ++ G+ ++TG IG A RL EG ++ L D+N +++ KA A + +K + + V Sbjct: 6 RYKGRRAVITGGASGIGFGVASRLVAEGASVCLWDVNPDSIAKATAELGDKAMGVQVNVA 65 Query: 64 DVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHV 123 D + E V G ID L AG G + DYP D + +V+ INV G FH Sbjct: 66 DWDTVERA---ASETVAKLGGIDVLVACAGITGPNTTLWDYPVDSWRQVMDINVNGIFHC 122 Query: 124 LKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVN 183 +AV M++ YGRIVN AS+AG +G PN +AY TSK A+I LT++ +LA NI VN Sbjct: 123 NRAVVPHMMSGGYGRIVNIASVAGKEGNPNASAYSTSKAAVIGLTKSLGKELAKTNITVN 182 Query: 184 AISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAF 243 A++P A V + F + M+ +PM R+G + EI +V + Sbjct: 183 AVTP----------------AAVKTAIFDQMTQQHIDFMLSKIPMGRFGLVEEITSLVCW 226 Query: 244 LLGDDSSFMTGVNLPIAGG 262 + D+ SF TG +GG Sbjct: 227 IASDECSFTTGSVFDASGG 245 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: 167 Number of extensions: 10 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: 262 Length of database: 249 Length adjustment: 24 Effective length of query: 238 Effective length of database: 225 Effective search space: 53550 Effective search space used: 53550 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 Sep 24 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