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_009566244.1 RSPH17029_RS09145 SDR family oxidoreductase
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_000015985.1:WP_009566244.1 Length = 246 Score = 139 bits (349), Expect = 7e-38 Identities = 89/248 (35%), Positives = 132/248 (53%), Gaps = 14/248 (5%) Query: 5 AGRYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVALDV 64 AGR G+ A+VT G+G+ A + EG V DLN AL AE V LDV Sbjct: 2 AGRLEGKRALVTAAGQGIGRASALAMAREGARVLATDLNAAALEGLAAE--GLEVQPLDV 59 Query: 65 SDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNR 124 D A++AAA AA G +D+L AG A+ + + + + + +NL G++ R Sbjct: 60 RDPASIAAAV----AAAGPLDVLFNCAGFV-ASGTILDCDEEDWAFSVGLNLTGMYRMCR 114 Query: 125 EVVPFMLENGYGRIVNLASVAGKE-GNPNASAYSASKAGVIGFTKSLGKELAGKGVIANA 183 +P M+ G G I+N+ASV PN Y +KAGV+G TKS+ + G+G+ NA Sbjct: 115 AFLPGMIAGGGGSIINMASVVSAAIAAPNRFVYGTTKAGVVGLTKSIAADFIGQGIRCNA 174 Query: 184 LTPATFESPILDQLPQSQVDY------MRSKIPMGRLGLVEESAAMVCFMASEECSFTTA 237 + P T ESP L++ ++ DY ++ P+GR+G EE AA+V ++AS+E ++TT Sbjct: 175 ICPGTVESPSLEERLRATGDYEAARRAFVARQPIGRIGRPEEIAALVVYLASDESAYTTG 234 Query: 238 STFDTSGG 245 GG Sbjct: 235 VAHVIDGG 242 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: 165 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: 249 Length of database: 246 Length adjustment: 24 Effective length of query: 225 Effective length of database: 222 Effective search space: 49950 Effective search space used: 49950 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 Apr 10 2024. 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