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 WP_012043651.1 BBTA_RS16605 NAD(P)-dependent oxidoreductase
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_000015165.1:WP_012043651.1 Length = 248 Score = 245 bits (625), Expect = 7e-70 Identities = 127/243 (52%), Positives = 171/243 (70%), Gaps = 3/243 (1%) Query: 9 AGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVAL--DVSD 66 A RCA+VTGGA G G+ + R A G VA+WD + ALA A+ V+AL DV+D Sbjct: 7 AHRCAVVTGGAQGFGRAITERFKASGAKVAIWD-HDIALAEKTAKEIGPEVLALQVDVTD 65 Query: 67 HAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREV 126 AAV A + AA G +DIL+ +AGI G VWE ++ +++V+ INL+G F C + + Sbjct: 66 PAAVEKARDATLAAFGTIDILVNNAGIAGVNKTVWETDLEEWRKVLRINLDGPFICAKAI 125 Query: 127 VPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTP 186 VP ML+ GYGRIVN+AS+AGKEGNPNA+ YSASKAG+I TKSLGKELA + + NA+TP Sbjct: 126 VPVMLKQGYGRIVNIASIAGKEGNPNAAHYSASKAGLIALTKSLGKELAQQNITVNAVTP 185 Query: 187 ATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGGR 246 A ++ I DQ+ ++ +++M SKIP GR LVEE AA+V ++AS+ECSF+T + FD SGGR Sbjct: 186 AAAKTAIFDQMTEAHINFMLSKIPKGRFVLVEELAALVAWLASDECSFSTGAVFDISGGR 245 Query: 247 TTF 249 T+ Sbjct: 246 ATY 248 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: 183 Number of extensions: 8 Number of successful extensions: 2 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 24 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