Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 6936328 Sama_0517 D-beta-hydroxybutyrate dehydrogenase (RefSeq)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__SB2B:6936328 Length = 266 Score = 113 bits (283), Expect = 4e-30 Identities = 81/263 (30%), Positives = 131/263 (49%), Gaps = 9/263 (3%) Query: 3 KKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYV 62 + GKV L+TG+ IGLATA LAE+G + L + E ++ A+ R++ Sbjct: 6 RSLEGKVGLITGSTSGIGLATAQVLAEQGCNLILHGLLPEDEGQSMAADFAAQYRIRTFF 65 Query: 63 --CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120 D+ E++ + + G ID L NNAG Q + V +P + + ++ IN++ A Sbjct: 66 SNADLRQPESIHRFMAEGTKALGSIDILINNAGIQHTDS-VASFPIEKWNDIIAINLSSA 124 Query: 121 FHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNI 180 FH ++ M + +GRI+N AS+ G+ N AAY +K I+ LT+ A++ A I Sbjct: 125 FHTMQQAVPAMAQKRWGRIINIASVHGLVASVNKAAYCAAKHGIVGLTKVVAIECAEQGI 184 Query: 181 RVNAISPGYMGPGFMWERQVELQAKV-GSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239 VNAI PG++ + +Q+E A G Y ++V + P+ D +I Sbjct: 185 TVNAICPGWVDTPLI-NKQIEAVANTKGLDYHEARYQLVTAKQ----PLPEMLDPRQIGE 239 Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262 FL GD + +TG +L + GG Sbjct: 240 FALFLCGDAARGITGASLAMDGG 262 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: 152 Number of extensions: 6 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: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 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