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 CCNA_01747 CCNA_01747 3-oxoacyl-(acyl-carrier protein) reductase
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__Caulo:CCNA_01747 Length = 246 Score = 141 bits (355), Expect = 1e-38 Identities = 85/238 (35%), Positives = 129/238 (54%), Gaps = 3/238 (1%) Query: 10 GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEI-DATHVVALDVSDHA 68 G+ A+VTG G+G +A + A+G V L ALA +AE+ + V ++SD Sbjct: 6 GKTALVTGATGGIGGAIARALHAQGAHVVLSGTRESALAELKAELGERASTVVANLSDAE 65 Query: 69 AV-AAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVV 127 V AK AA +DI+I +AG+T + V + + VI +NL G F +R Sbjct: 66 QVDGLVAKAEEAAGAPLDIVIANAGVTRDGLIV-RMKDEDWDTVIKVNLEGYFRLSRAAA 124 Query: 128 PFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPA 187 M++ GRI+ + S+ G GNP + Y+ASKAG+IGF+K+L +ELA +GV N + P Sbjct: 125 KGMMKRRAGRIIGITSIVGVTGNPGQTNYAASKAGMIGFSKALAQELASRGVTVNCVAPG 184 Query: 188 TFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGG 245 SP+ D L + Q + S IP G+LG + AA ++AS++ + T T +GG Sbjct: 185 FIASPMTDALNEQQKAGILSTIPAGKLGEGADIAAACVYLASDQAGYVTGQTLHVNGG 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: 173 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: 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 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