Align 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase; EC 1.1.1.368 (characterized)
to candidate RR42_RS34260 RR42_RS34260 alcohol dehydrogenase
Query= SwissProt::O87871 (368 letters) >FitnessBrowser__Cup4G11:RR42_RS34260 Length = 342 Score = 113 bits (283), Expect = 7e-30 Identities = 100/345 (28%), Positives = 147/345 (42%), Gaps = 25/345 (7%) Query: 27 GAPMVRAEFEIGELSADQVVVAVAGCGVCHTDLGYYYDSVRTNHALPLALGHEISGRVVQ 86 GAP+ E + + Q+ V + GVCHTDL LP GHE G V Sbjct: 14 GAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLPFIPGHEGVGYVSA 73 Query: 87 AGANAAQWL-GRAVIVPAVMP-CGTCELCTSGHGTICRDQVMPGNDIQGGFASHVVVPAR 144 GA ++ G V VP + CG CE C G T+C Q G + GG+ +VV Sbjct: 74 VGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSVNGGYGEYVVADPN 133 Query: 145 --GLCPVDEARLAAAGLQLADVSVVADAVTTPYQAVLQAGVEPGDVAVVIGVGGVGGYAV 202 GL P + A + A V+V Y+ + PG V+ G+GG+G AV Sbjct: 134 YVGLLPDSVGFVEIAPILCAGVTV--------YKGLKVTDTRPGQWVVISGIGGLGHVAV 185 Query: 203 QIANAFGASVVAIDVDPAKLEMMSKHGAALTLNAREISG-RDLKKAIEAHAKANGLRLTR 261 Q A A G V A+D+D KLE+ K GA +T+NAR L+K I A+G +T Sbjct: 186 QYARAMGLRVAAVDIDDKKLELARKLGAEVTVNARTTDPVAFLQKEI---GGAHGALVT- 241 Query: 262 WKIFECSGTGAGQTSAYGLLTHGATLAVVGFTMDKVEVRLSNLMAFHARALGNWGCLPEY 321 S GQ A G++ G T+A+ G + +++ G+ Sbjct: 242 ----AVSPKAFGQ--AIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSD 295 Query: 322 YPAALDLVLDKKIDLASFIERHPLDQIGEVFAAAHAHKLTRRAIL 366 +LD + + + PL++I E+F A + R ++ Sbjct: 296 LQESLDFAAHGAV--KATVSTAPLEKINEIFTRMRAGDIEGRVVM 338 Lambda K H 0.320 0.134 0.406 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: 18 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: 368 Length of database: 342 Length adjustment: 29 Effective length of query: 339 Effective length of database: 313 Effective search space: 106107 Effective search space used: 106107 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 (21.8 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