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_007693551.1 C447_RS10170 zinc-dependent alcohol dehydrogenase family protein
Query= SwissProt::P0DOW0 (331 letters) >NCBI__GCF_000336675.1:WP_007693551.1 Length = 358 Score = 140 bits (353), Expect = 5e-38 Identities = 105/340 (30%), Positives = 157/340 (46%), Gaps = 13/340 (3%) Query: 1 MKTLTWTAKETMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRKPPLVMGHE 60 M+ TA + + P P + +RV G+C ++ Y G E PLV+GHE Sbjct: 16 MRASVLTAVGEVEVQDRPRPTVADDDVLIRVGACGVCMTDYHMYHGSFEA-PTPLVLGHE 74 Query: 61 FSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIG----IDFPGA 116 +G V EVG VTNV +GD VT NP V C C C RGE C IG G+ Sbjct: 75 TAGEVVEVGENVTNVTVGDRVTLNPTVPCNACPACKRGETNLCADNTSIGGAGNTIRDGS 134 Query: 117 YAERVLVPSNQCYAVKD--AIDGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTV 174 +AE V P++ D AL EPLAC V AV A + GDT VIGAG IGL+ V Sbjct: 135 FAEYVAAPASVVVDCGDLPVRTAALAEPLACCVHAVDRADVTTGDTVAVIGAGPIGLLMV 194 Query: 175 RLLGLSGAKRIAVVDPNDERLKISQLWG---ATEMAPNLGALLTDNHPQSFDCVIDAVGL 231 + ++GA + V + + +R +++ G A + A D + VG Sbjct: 195 QSFRVAGAGEVIVSELDADRRELALELGADHAVDPADGDAVEQVTAVDGPVDVAAEVVGQ 254 Query: 232 STTRRDSLNALIRGGRAVWIGL--HEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSL 289 + T + +GGR + G+ +A + DE+ + G+F T + F RAV+L Sbjct: 255 TATIEQARAMTGKGGRTLVAGVPPQDATMEFSPFDLYFDEVSMVGTFALTQESFERAVTL 314 Query: 290 INSQKFLPVDRQWLDVRSLEEGPAAFKELVNGSPFSKIIL 329 + + + + VD + L+ AF+ + N K+++ Sbjct: 315 LRNDR-IDVDPLVTEEIGLDGLEGAFERMGNTEGLKKLVV 353 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: 331 Number of extensions: 23 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: 358 Length adjustment: 29 Effective length of query: 302 Effective length of database: 329 Effective search space: 99358 Effective search space used: 99358 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