Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 6937211 Sama_1381 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__SB2B:6937211 Length = 252 Score = 106 bits (265), Expect = 4e-28 Identities = 77/263 (29%), Positives = 120/263 (45%), Gaps = 27/263 (10%) Query: 8 KVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVTS 67 KV ++TG G +GLA A LA G +AL+D+++E LE+A A + + E + Y D+T Sbjct: 6 KVIVITGGAGGLGLAMAKDLAAHGAKLALIDVDQERLERACADIGD-ATEVQGYALDITD 64 Query: 68 EEAVIGTVDSVVRDFGKIDFLFNNAGY--QGAFAPVQD------YPSDDFARVLTINVTG 119 EE V+ ++ DFG I L NNAG G +D D F V+ +N+TG Sbjct: 65 EEDVVAGFRYILEDFGVIHGLVNNAGILRDGLLIKAKDGVVTDRMSLDQFQSVINVNLTG 124 Query: 120 AFHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179 F + + MI G ++ S G Y SK + + A +LA +N Sbjct: 125 TFLCGREAAAAMIESGQGGVIVNISSLARAGNMGQTNYAASKAGVATMAVGWAKELARFN 184 Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239 IR A++PG + E+ A + + +++ VP+ R G EI Sbjct: 185 IRAAAVAPGVIA--------TEMTAAMKPE--------ALERLEKMVPVGRLGQAEEIAS 228 Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262 V F++ +D ++ G I GG Sbjct: 229 TVRFIMEND--YVNGRVFEIDGG 249 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: 144 Number of extensions: 9 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: 252 Length adjustment: 24 Effective length of query: 238 Effective length of database: 228 Effective search space: 54264 Effective search space used: 54264 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