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 15892 b1774 predicted oxidoreductase, Zn-dependent and NAD(P)-binding (NCBI)
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__Keio:15892 Length = 347 Score = 128 bits (321), Expect = 2e-34 Identities = 99/326 (30%), Positives = 158/326 (48%), Gaps = 21/326 (6%) Query: 11 TMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRKPP------LVMGHEFSGV 64 TM I+SA PVP+ + ++V VGICGS++ G+ + PP + +GHE +G Sbjct: 13 TMKIISAEIPVPKEDEVLIKVEYVGICGSDVHGFESGPFI--PPKDPNQEIGLGHECAGT 70 Query: 65 VEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGI--DFPGAYAERVL 122 V VG V K GD V P V CG C +CL G+ C + ++ GA + Sbjct: 71 VVAVGSRVRKFKPGDRVNIEPGVPCGHCRYCLEGKYNICPDVDFMATQPNYRGALTHYLC 130 Query: 123 VPSNQCYAVKDAID---GALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGL 179 P + Y + D +D GALVEP A + A LA +K G +++GAG IGLMT++ Sbjct: 131 HPESFTYKLPDNMDTMEGALVEPAAVGMHAAMLADVKPGKKIIILGAGCIGLMTLQACKC 190 Query: 180 SGAKRIAVVDPNDERLKISQLWGATEM-----APNLGALLTDNHPQSFDCVIDAVGLSTT 234 GA IAVVD ++RL +++ GAT + + D V + G + T Sbjct: 191 LGATEIAVVDVLEKRLAMAEQLGATVVINGAKEDTIARCQQFTEDMGADIVFETAGSAVT 250 Query: 235 RRDSLNALIRGGRAVWIGLHEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSLINSQK 294 + + ++RGG+ + +G + ++ +I R E+ ++ F Y + + + I+S + Sbjct: 251 VKQAPYLVMRGGKIMIVGTVPGDSAINFLKINR-EVTIQTVFRYA-NRYPVTIEAISSGR 308 Query: 295 FLPVDRQWLDVRSLEEGPAAFKELVN 320 F V + + AF+E VN Sbjct: 309 F-DVKSMVTHIYDYRDVQQAFEESVN 333 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: 305 Number of extensions: 14 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: 331 Length of database: 347 Length adjustment: 28 Effective length of query: 303 Effective length of database: 319 Effective search space: 96657 Effective search space used: 96657 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 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