Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 3607950 Dshi_1358 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__Dino:3607950 Length = 258 Score = 129 bits (325), Expect = 5e-35 Identities = 82/256 (32%), Positives = 130/256 (50%), Gaps = 21/256 (8%) Query: 7 GKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVT 66 GK L+TGA IG AL L + G + L + LE ++R +G+ A++ DVT Sbjct: 18 GKRALITGASSGIGAHLALTLGQAGAEVILAARRADRLEAVAETLRAEGIVAQTAALDVT 77 Query: 67 SEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKA 126 +V V +V G +D L NN+G G + D D+ RVL N+ GA+ V +A Sbjct: 78 DAASVAAAVTTV----GPLDILINNSGVSGQDMVI-DTTEADWDRVLDTNLKGAWRVSRA 132 Query: 127 VSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAIS 186 + +I + G I+N AS+ G+ + Y SK +I LT AL+LA +RVNA++ Sbjct: 133 FAPGLIARQ-GTILNVASILGIGVLKTVGPYAASKAGLIQLTRAMALELARDGVRVNALA 191 Query: 187 PGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLG 246 PGY ++ + +++F+++ Q+M+ VP RR G ++ V LLG Sbjct: 192 PGY------------IETPINTEFFASE---AGQKMLRGVPQRRLGQPGDLDAAVLMLLG 236 Query: 247 DDSSFMTGVNLPIAGG 262 + F+TG + + GG Sbjct: 237 PGAGFVTGATVVVDGG 252 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: 147 Number of extensions: 11 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: 258 Length adjustment: 24 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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 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