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 5209125 Shew_1603 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__PV4:5209125 Length = 248 Score = 144 bits (363), Expect = 2e-39 Identities = 82/238 (34%), Positives = 136/238 (57%), Gaps = 4/238 (1%) Query: 10 GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEI--DATHVVALDVSDH 67 G+ A+VTG + G+G+ VA ++ E GA+ + + AA E D H + L+V+D Sbjct: 9 GKVALVTGASRGIGRAVAETLV-EAGALVIGTATSERGAAAIQEYLGDKGHGLVLNVTDS 67 Query: 68 AAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVV 127 ++ +G+VDIL+ +AGIT + + D + +ID NL L+ +++V+ Sbjct: 68 ESIDHLFASIKEKVGEVDILVNNAGITRDNL-LMRMKEDEWTDIIDTNLTSLYRTSKQVL 126 Query: 128 PFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPA 187 M++ GRI+N+ SV G GN + Y A+KAG+IGFTKSL +E+A + + NA+ P Sbjct: 127 RAMMKKRSGRIINIGSVVGTMGNAGQTNYCAAKAGLIGFTKSLAREVASRQITVNAIAPG 186 Query: 188 TFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGG 245 ++ + D+L + Q + S++PM RLG +E A V F+AS+ ++ T T +GG Sbjct: 187 FIQTDMTDELTEEQQKGIMSQVPMERLGQPQEIANAVLFLASDSAAYITGETLHVNGG 244 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: 143 Number of extensions: 6 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: 249 Length of database: 248 Length adjustment: 24 Effective length of query: 225 Effective length of database: 224 Effective search space: 50400 Effective search space used: 50400 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