Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate Synpcc7942_0684 Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__SynE:Synpcc7942_0684 Length = 249 Score = 140 bits (354), Expect = 2e-38 Identities = 85/241 (35%), Positives = 132/241 (54%), Gaps = 10/241 (4%) Query: 11 RCAIVTGGASGLGKQVAARIIAEGGAVALWDLNG-----DALAATQAEIDATHVVALDVS 65 R A+VTG + G+G+ +A + A G VA+ + + +AA A V DVS Sbjct: 9 RIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVS 68 Query: 66 DHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNRE 125 + V A G++D+L+ +AGIT T+ + D +Q V+D+NL G+F C+R Sbjct: 69 QESEVEALFAAVIERWGRLDVLVNNAGITRDTL-LLRMKRDDWQSVLDLNLGGVFLCSRA 127 Query: 126 VVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALT 185 ML+ GRI+N+ASV G+ GNP + YSA+KAGVIG TK++ KELA +G+ NA+ Sbjct: 128 AAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVA 187 Query: 186 PATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASE-ECSFTTASTFDTSG 244 P + + +L + + IP+GR G E A +V F+A++ ++ T + G Sbjct: 188 PGFIATDMTSEL---AAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDG 244 Query: 245 G 245 G Sbjct: 245 G 245 Lambda K H 0.318 0.132 0.381 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: 7 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: 249 Length of database: 249 Length adjustment: 24 Effective length of query: 225 Effective length of database: 225 Effective search space: 50625 Effective search space used: 50625 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: 46 (22.3 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