Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_041751350.1 BBTA_RS09870 Zn-dependent oxidoreductase
Query= SwissProt::P0DOW0 (331 letters) >NCBI__GCF_000015165.1:WP_041751350.1 Length = 336 Score = 113 bits (282), Expect = 8e-30 Identities = 66/207 (31%), Positives = 107/207 (51%), Gaps = 5/207 (2%) Query: 1 MKTLTWTAKETMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRKPPLVMGHE 60 MK+L +SI + P P G I ++V GICGS++ G N + P V+GHE Sbjct: 1 MKSLVVERPGRLSIETRAIPEPASGEIRIKVERAGICGSDIHILHGSNPFARYPRVIGHE 60 Query: 61 FSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGIDFPGAYAER 120 F G ++++G GV + ++G + +P+V CG C C G C ++G+ G ++E Sbjct: 61 FFGRIDKLGDGV-HARLGARIVVDPVVACGTCYPCSVGRPNVCAQLAVLGVHRDGGFSEY 119 Query: 121 VLVPSNQCYAVKDAI---DGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLL 177 VP+ + + D++ LVEP + A + D A+V GAG IGL +++L Sbjct: 120 ACVPAENAHLLPDSVGDDQAPLVEPFSIAANITDHTSVFASDIALVYGAGPIGLTVIQVL 179 Query: 178 -GLSGAKRIAVVDPNDERLKISQLWGA 203 + G K + V D D+RL+ ++ GA Sbjct: 180 KHVYGVKELIVTDRIDQRLEAARNNGA 206 Lambda K H 0.322 0.139 0.424 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: 293 Number of extensions: 16 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: 331 Length of database: 336 Length adjustment: 28 Effective length of query: 303 Effective length of database: 308 Effective search space: 93324 Effective search space used: 93324 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 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