Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 5210113 Shew_2557 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__PV4:5210113 Length = 306 Score = 114 bits (286), Expect = 2e-30 Identities = 66/194 (34%), Positives = 104/194 (53%), Gaps = 11/194 (5%) Query: 4 KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNR----------EALEKAEASVRE 53 +F+ +V +VTGAG +G A A+ LAE G +A++D L K ++ E Sbjct: 3 RFDEQVAVVTGAGAGLGRAYAIALAERGARLAIIDSGSGDSRCQSYAGAGLNKTARTLAE 62 Query: 54 KGVEARSYVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVL 113 G + S+ DVT +A+ +++V++ +G+ID NNAG + + + R L Sbjct: 63 LGADCLSFQLDVTDSQALKSAIETVLKRWGRIDIAINNAGIHTPVS-FDSLSFEQWQRQL 121 Query: 114 TINVTGAFHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAAL 173 +++ G+FH+ K V QM QNYGRIV TA +G+ G + Y TSK A++ L + A Sbjct: 122 DVDLNGSFHLTKLVWPQMKRQNYGRIVMTAGASGLYGDMHETPYSTSKMALVGLVNSLAK 181 Query: 174 DLAPYNIRVNAISP 187 + YNI VN + P Sbjct: 182 EGRDYNISVNTLVP 195 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: 173 Number of extensions: 17 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: 306 Length adjustment: 26 Effective length of query: 236 Effective length of database: 280 Effective search space: 66080 Effective search space used: 66080 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