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_007689819.1 C447_RS00650 glucose 1-dehydrogenase
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_000336675.1:WP_007689819.1 Length = 245 Score = 128 bits (321), Expect = 1e-34 Identities = 81/240 (33%), Positives = 122/240 (50%), Gaps = 5/240 (2%) Query: 11 RCAIVTGGASGLGKQVAARIIAEGGAVALWDL----NGDALAATQAEIDATHVVALDVSD 66 + AIVTG +SG+G+ A R EG +V + DL D + + E V DV++ Sbjct: 4 KSAIVTGASSGIGRATARRFAEEGASVVVADLVEEGGNDTVDIIEDEGGEAMFVQTDVTN 63 Query: 67 HAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREV 126 V+ + G +D++ +AGI P+ + + ++++NL G++ + Sbjct: 64 DDDVSKMVDAAVENYGSLDVVHNNAGILTGFDPLTDLDESDWDALLNVNLKGVWLGLKHE 123 Query: 127 VPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTP 186 +P MLE+G G IVN AS AG G P + Y ASK GVIG T++ G E A G+ NA+ P Sbjct: 124 IPAMLEDGGGAIVNTASEAGLVGFPGIANYVASKHGVIGLTRAAGLEYAEDGIRVNAVCP 183 Query: 187 ATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGGR 246 E+P+ D P + PM R+G EE A V ++ S+E S+ TA GGR Sbjct: 184 GPIETPMTDD-PSVDSKEVVEYTPMRRMGQPEEVANAVVWLCSDEASYVTAHPLSVDGGR 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: 10 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 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