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 3608643 Dshi_2036 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__Dino:3608643 Length = 327 Score = 156 bits (394), Expect = 8e-43 Identities = 112/339 (33%), Positives = 166/339 (48%), Gaps = 24/339 (7%) Query: 1 MKTLTWTAKETMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRKPPLVMGHE 60 MK L +T ++ P PVP G +R+ VGICGS++ YLGH++ R PL++GHE Sbjct: 1 MKALVYTGVAQLAFRDVPEPVPAAGDHLIRIDSVGICGSDMHAYLGHDDRRPAPLILGHE 60 Query: 61 FSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGI-DFPGAYAE 119 +GV+ + + G+ VT NPLVTCG C C+ G C +R+II + GA+A+ Sbjct: 61 GAGVI------IGGPRDGERVTINPLVTCGTCPACVSGRDNLCATRQIISMPPRDGAFAQ 114 Query: 120 RVLVPSNQCYAVKDAI---DGALVEPLACAVRAVGLARIKVG----DTAVVIGAGIIGLM 172 V +P+ V D + AL EP+A + AV L + D+A+VIG G IG+ Sbjct: 115 YVAMPARNLVTVPDDVPLEKAALAEPVAVSWHAVRLGLASMADARRDSALVIGGGAIGVA 174 Query: 173 TVRLLGLSGAKRIAVVDPNDERLK-ISQLWGATEMAPNLGALLTDNHPQSFDCVIDAVGL 231 L G + +V+PN R + +++ T P A + FD +D VG Sbjct: 175 AAISLQAQGVADVTLVEPNAMRREYLARDANYTIATPEQVA------GRVFDITVDGVGY 228 Query: 232 STTRRDSLNALIRGGRAVWIGLHEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSLIN 291 TR + A GG + IGL LD +I E+ V G++ YT +F + + Sbjct: 229 DATRAAASAATRPGGLLLHIGLGGGSAGLDIRRITLQEITVIGTYTYTAQDFRDTCAAMF 288 Query: 292 SQKFLPVDRQWLDVRSLEEGPAAFKELVNGS-PFSKIIL 329 + +D W + R L G AF ++ G P KIIL Sbjct: 289 DGRLGGLD--WTESRPLSAGADAFADIRAGRVPAPKIIL 325 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: 327 Number of extensions: 22 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: 327 Length adjustment: 28 Effective length of query: 303 Effective length of database: 299 Effective search space: 90597 Effective search space used: 90597 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