Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate GFF2840 HP15_2784 3-ketoacyl-(acyl-carrier-protein) reductase
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__Marino:GFF2840 Length = 247 Score = 136 bits (342), Expect = 5e-37 Identities = 91/257 (35%), Positives = 132/257 (51%), Gaps = 19/257 (7%) Query: 7 GKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREAL-EKAEASVREKGVEARSYVCDV 65 GKV LVTGA IG AL+LA+ G +A+ +R++ E+ + GV A S+ D+ Sbjct: 6 GKVALVTGASRGIGRHIALQLAQRGADVAINYRSRQSEGEEVAKEIEATGVRALSFKADL 65 Query: 66 TSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLK 125 + V V +G+ID L NNAG + ++ DD+ VL N+ + Sbjct: 66 SKMPEARSLVRQVQEQWGRIDILVNNAGITKDKS-MKKLTDDDWNDVLDTNLGSVYATCS 124 Query: 126 AVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAI 185 V + M+ Q YGRI+N S G G A Y SKG IIA T+T AL++A YNI VNAI Sbjct: 125 EVLKIMMDQKYGRIINITSFVGQAGNFGQANYAASKGGIIAFTKTLALEMAKYNITVNAI 184 Query: 186 SPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLL 245 +PG+ + E+ A+V P+ + +Q+I VPM R+G EI V FL Sbjct: 185 APGF--------TETEMLAQV--------PENIREQIIARVPMGRFGKPEEIARAVVFLA 228 Query: 246 GDDSSFMTGVNLPIAGG 262 + ++TG + + GG Sbjct: 229 A-EGDYITGQQINVNGG 244 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: 166 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: 247 Length adjustment: 24 Effective length of query: 238 Effective length of database: 223 Effective search space: 53074 Effective search space used: 53074 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