Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate Echvi_2990 Echvi_2990 Acyl-CoA dehydrogenases
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__Cola:Echvi_2990 Length = 402 Score = 159 bits (402), Expect = 1e-43 Identities = 111/374 (29%), Positives = 180/374 (48%), Gaps = 8/374 (2%) Query: 5 TEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMG 64 T E L +RD +E++P E + + FP F ++G P +PA YGG + Sbjct: 29 TAEHLLIRQSLRDFVKKEVSPYIEEWAQDAHFPSEIVPKFGEIGAFGPQIPAKYGGGGLD 88 Query: 65 VLTLALILEELGRVCASTALLLIAQTDGMLPIIHG-GSPELKERYLRRFAGESTLLTALA 123 ++ LI++E+ R + + Q ++ IH GS E +E++L + A L Sbjct: 89 YISYGLIMQEIERGDSGMRSTVSVQGSLVMYPIHAFGSEEQREKFLPKLAS-GEWLGCFG 147 Query: 124 ATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAF 183 TEP GS+ + T GD Y++NG K +I+N AD+ VV+A + + I Sbjct: 148 LTEPDHGSNPGGLTTSFKDNGDHYLLNGAKMWISNAPEADIAVVWAKDENGR----IHGL 203 Query: 184 VVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRV 243 +VE+G G K +R S EL F+N++VP EN++ + +G + + L R Sbjct: 204 IVERGMEGFTTPTTHHKWSLRASCTGELVFDNVKVPKENLLPGK-SGLSAPLMCLDAARY 262 Query: 244 FCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAE 303 A A+G A + A R+ +R+QF KPIA VQ +A+M T + ++LL + Sbjct: 263 GIAWGAIGAAMDCYESAKRYAMERIQFDKPIAAFQLVQKKLAEMLTEITKAQLLAWRLGT 322 Query: 304 LLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYT 363 L D G K SMAK A+ + +A Q+ GG G + + R M + + Y Sbjct: 323 LKDQG-KATSAQISMAKRNNVAMALEIAREARQIHGGMGITGDYPIMRHMMNLESVITYE 381 Query: 364 GTNQITRMVTGRAL 377 GT+ I ++ G+ + Sbjct: 382 GTHDIHLLILGQEI 395 Lambda K H 0.319 0.134 0.371 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: 16 Number of successful extensions: 5 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: 380 Length of database: 402 Length adjustment: 31 Effective length of query: 349 Effective length of database: 371 Effective search space: 129479 Effective search space used: 129479 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 (21.7 bits) S2: 50 (23.9 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