Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_057507496.1 ABB28_RS04570 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_001431535.1:WP_057507496.1 Length = 253 Score = 136 bits (342), Expect = 5e-37 Identities = 85/258 (32%), Positives = 128/258 (49%), Gaps = 18/258 (6%) Query: 5 FNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCD 64 FN K +VTGAG IG ATA + G + L D R+ + A + + D Sbjct: 3 FNAKTVIVTGAGSGIGAATARAFSNAGANVVLAD--RDHPDVAALAGELAAERTLVHDVD 60 Query: 65 VTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVL 124 V+ E V VD+ V+ FG +D +FNNAG P +D +D+ R++ +N+TG F Sbjct: 61 VSDEAQVQALVDATVKRFGGLDVIFNNAGIL-VEGPAEDTSLEDWNRIVAVNLTGVFLGC 119 Query: 125 KAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNA 184 +A ++ + G IVNTAS++G+ NM AY KGA+ LT A+D + +RVNA Sbjct: 120 RAALPEL-RKRKGCIVNTASVSGLAADRNMPAYNAVKGAVANLTRALAIDNGRHGVRVNA 178 Query: 185 ISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFL 244 + P + E++ + K + + +PM R G+ +I V L Sbjct: 179 VCPTFTRTSMTAEKEKD--------------KALVTNFLNRIPMGRLGEPEDIANAVLLL 224 Query: 245 LGDDSSFMTGVNLPIAGG 262 D + F+TGVNLP+ GG Sbjct: 225 ASDHAGFITGVNLPVDGG 242 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: 148 Number of extensions: 9 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: 262 Length of database: 253 Length adjustment: 24 Effective length of query: 238 Effective length of database: 229 Effective search space: 54502 Effective search space used: 54502 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