Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Synpcc7942_0684 Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__SynE:Synpcc7942_0684 Length = 249 Score = 129 bits (324), Expect = 6e-35 Identities = 84/257 (32%), Positives = 133/257 (51%), Gaps = 22/257 (8%) Query: 8 KVCLVTGAGGNIGLATALRLAEEGTAIAL-LDMNREALEKAEASVREKGVEARSYVCDVT 66 ++ LVTGA IG A AL LA G +A+ + A ++ A++ G EA + DV+ Sbjct: 9 RIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVS 68 Query: 67 SEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKA 126 E V +V+ +G++D L NNAG ++ DD+ VL +N+ G F +A Sbjct: 69 QESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLR-MKRDDWQSVLDLNLGGVFLCSRA 127 Query: 127 VSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAIS 186 ++ M+ Q GRI+N AS+ G G P A Y +K +I LT+T A +LA I VNA++ Sbjct: 128 AAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVA 187 Query: 187 PGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLG 246 PG++ E + A++++ +P+ RYG+ E+ GVV FL Sbjct: 188 PGFIATDMTSE-------------------LAAEKLLEVIPLGRYGEAAEVAGVVRFLAA 228 Query: 247 DD-SSFMTGVNLPIAGG 262 D ++++TG + I GG Sbjct: 229 DPAAAYITGQVINIDGG 245 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: 12 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: 249 Length adjustment: 24 Effective length of query: 238 Effective length of database: 225 Effective search space: 53550 Effective search space used: 53550 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