Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate GFF814 PS417_04135 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__WCS417:GFF814 Length = 378 Score = 261 bits (667), Expect = 2e-74 Identities = 156/372 (41%), Positives = 217/372 (58%), Gaps = 4/372 (1%) Query: 40 EQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDIT 99 E +L E VR ++ AP ++ + + G+L +P EYGG G D Sbjct: 10 EHELFRESVRTFLEKDAAPFHGHWEKQGYIDRRLWNKAGEAGMLCSHLPEEYGGLGADFL 69 Query: 100 TFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAFAAT 158 A+V+EEI ++ T + +D + IL GS ALK KYLP+ ++TA A T Sbjct: 70 YSAVVIEEISRL-GLTGIGFSLHSDIVAPYILHYGSEALKHKYLPKL-ISGEMVTAIAMT 127 Query: 159 EPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTFVV 218 EPGAGSDL +KT AV GD+YVING K FITNG +A+++ V A TDP GAKG S F+V Sbjct: 128 EPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGYLAELVIVVAKTDPKAGAKGTSLFLV 187 Query: 219 ERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVFC 278 E TPG G +K+GM+ SELFF+D+ VP ENL+G+ G GFAYLM L R+ Sbjct: 188 EADTPGFDKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQERLTV 247 Query: 279 ASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTLL 338 A A+ A+ ALE +++TRER+ FGK IA +F +A+MATE++ R+ V K L Sbjct: 248 AIGALSSAEAALEWTLEYTRERKAFGKAIADFQNTRFKLAEMATEIQIGRVFVDKCMA-L 306 Query: 339 DAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYTGT 398 + K MAK +A+D KV + VQ+ GG G+M EY + R +A++ +IY GT Sbjct: 307 HLEGKLDVPTAAMAKYWATDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYAGT 366 Query: 399 NQITRMVTGRSL 410 N+I + + R+L Sbjct: 367 NEIMKEIIARAL 378 Lambda K H 0.318 0.133 0.375 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: 352 Number of extensions: 14 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: 414 Length of database: 378 Length adjustment: 31 Effective length of query: 383 Effective length of database: 347 Effective search space: 132901 Effective search space used: 132901 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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