Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_017547482.1 C792_RS0100525 SDR family oxidoreductase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_000330705.1:WP_017547482.1 Length = 257 Score = 167 bits (422), Expect = 3e-46 Identities = 95/263 (36%), Positives = 141/263 (53%), Gaps = 10/263 (3%) Query: 1 MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60 MS +F G+V ++TG G IG TAL+ +EG + ++D+N E+L A + +G E + Sbjct: 1 MSNRFEGQVVIITGGSGGIGKQTALQFLQEGAKVTIVDINEESLTSAREELSRQG-EVLA 59 Query: 61 YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120 DV+ E V + + V FGK+D LFNNAG G + D D+F V +N+ G Sbjct: 60 VQADVSDEADVENYIRATVEKFGKVDVLFNNAGIIGKVGSLVDQEYDNFKAVTGVNMNGV 119 Query: 121 FHVLKAVSRQMITQNY-GRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179 F LK +QMI Q G I+NT S+ +G P +AY +K A++ LT+TAA++ A +N Sbjct: 120 FLGLKHAIKQMIKQGTPGSIINTGSVDSFRGSPEQSAYSATKHAVVGLTKTAAVEAAGHN 179 Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239 IRVN+I P + + A V + V ++ +P+ RY D ++I Sbjct: 180 IRVNSIHPAPV--------DTPMMAHVEESRDKKNSASVREKFTSGIPLNRYADSSDIAD 231 Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262 +V FL DDS F+TG I GG Sbjct: 232 LVLFLASDDSKFVTGSQYSIDGG 254 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: 183 Number of extensions: 14 Number of successful extensions: 4 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: 257 Length adjustment: 24 Effective length of query: 238 Effective length of database: 233 Effective search space: 55454 Effective search space used: 55454 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