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 Ga0059261_0364 Ga0059261_0364 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100)
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__Korea:Ga0059261_0364 Length = 245 Score = 154 bits (389), Expect = 2e-42 Identities = 84/237 (35%), Positives = 136/237 (57%), Gaps = 2/237 (0%) Query: 10 GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVAL-DVSDHA 68 G A+VTG + GLG +A + A+G +A+ N + L A +AE+ HV + ++SD A Sbjct: 6 GMTALVTGASGGLGTAIAKGLAAQGARLAISGSNAEKLEAFRAELGGDHVALVCNLSDGA 65 Query: 69 AVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVVP 128 V + ALGK+DIL+ +AG+T + + + + +VI +NL F R Sbjct: 66 EVDGLVPRAVEALGKLDILVNNAGVTRDNLAM-RMKDEEWDQVIRVNLEAAFRLMRAAAK 124 Query: 129 FMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPAT 188 M++ YGR++++ SV G+ GNP + Y+ASKAG++G +K+L +ELA + + N + P Sbjct: 125 PMMKARYGRMISITSVVGQTGNPGQANYAASKAGLVGMSKALAQELASRNITVNCVAPGF 184 Query: 189 FESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGG 245 S + D LP++Q + +KIP G LG E+ A V ++AS+E + T T +GG Sbjct: 185 MRSAMTDVLPEAQKAALLTKIPAGDLGTGEDIGAAVVYLASKEAGYVTGQTLHVNGG 241 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: 135 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: 245 Length adjustment: 24 Effective length of query: 225 Effective length of database: 221 Effective search space: 49725 Effective search space used: 49725 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