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_011840077.1 RSPH17029_RS20910 SDR family oxidoreductase
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_000015985.1:WP_011840077.1 Length = 248 Score = 258 bits (660), Expect = 6e-74 Identities = 131/242 (54%), Positives = 171/242 (70%), Gaps = 1/242 (0%) Query: 9 AGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVV-ALDVSDH 67 AGR A+VTGGA G+G+ VA R+IA G V LWD + + AAT AE+ +D D Sbjct: 7 AGRVAVVTGGAQGIGRAVAERLIASGARVCLWDRDAERAAATAAELGGNSFFQVVDQVDF 66 Query: 68 AAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVV 127 AV AA + A G++DILI +AGI G+ PV ++PV+ + R+IDINLNG+F+C + VV Sbjct: 67 TAVKAATDATEATGGRIDILIANAGIAGSNAPVADYPVEEWHRIIDINLNGVFHCCKAVV 126 Query: 128 PFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPA 187 P M GYGRIV +AS+AGKEGNPNA+AYSASKAGVI TKSLGKE+AG+ + N +TPA Sbjct: 127 PGMKARGYGRIVTVASIAGKEGNPNAAAYSASKAGVIALTKSLGKEVAGQDIAVNCVTPA 186 Query: 188 TFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGGRT 247 + I DQ+ QS +DYM S+IP GR ++E+AAM+ ++AS E SFTT + FD SGGR Sbjct: 187 AARTQIFDQMAQSHIDYMLSRIPRGRFLDLDEAAAMIAWLASAENSFTTGAVFDLSGGRA 246 Query: 248 TF 249 T+ Sbjct: 247 TY 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: 230 Number of extensions: 11 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 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