Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate CCNA_00436 CCNA_00436 acyl-CoA dehydrogenase, short-chain specific
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Caulo:CCNA_00436 Length = 382 Score = 233 bits (593), Expect = 1e-65 Identities = 138/377 (36%), Positives = 211/377 (55%), Gaps = 8/377 (2%) Query: 39 EEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDI 98 E ++ L++ V + P ++ EN + P + LGL +P E+GG G+ + Sbjct: 6 ETREQLIDTVARFVAERLRPIEAQVAENDAVPDDVIEEMKGLGLFGLTIPEEFGGLGLTM 65 Query: 99 TTFAMVLEEIGKVCASTALMLLAQAD---GMLSIILDGSPALKEKYLPRFGEKSTLMTAF 155 A+V E+G+ AS A + + G +++ G+ K K+LP ++T+F Sbjct: 66 EEEALVAIELGR--ASPAFRSVFGTNVGIGSQGLVMFGNDEQKAKWLPGIAS-GAVITSF 122 Query: 156 AATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDP-SKGAKGMS 214 A TEP AGSD A++TRA + GD Y++NG K +ITN A + TV A T+P +KG G+S Sbjct: 123 ALTEPEAGSDSAAVQTRATRDGDDYILNGSKRYITNAGKASLFTVMARTNPDAKGGAGVS 182 Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274 F+V R PGL G EKKMG +G ++ F+++ VPA N +G EG+GF M L Sbjct: 183 AFLVPRDLPGLTVGKPEKKMGQQGAHIHDVTFDNVRVPAWNRLGAEGEGFKVAMQVLDRG 242 Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334 R+ A+ VG+A+ + + + ER+QFG+PIA IQ MIAD TE AA+ LV + Sbjct: 243 RLHIAAVCVGVAERLIADCVAYASERKQFGQPIASFQLIQAMIADSKTEALAAKALVLET 302 Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 DA L +K FAS+ +V AVQV GG+GY+ +Y +ER+ R+ ++ +I Sbjct: 303 ARKRDA-GVNVTLEAASSKLFASEMVGRVADRAVQVFGGAGYVADYGIERLYRDVRIFRI 361 Query: 395 YTGTNQITRMVTGRSLL 411 Y GT+Q+ +++ R L Sbjct: 362 YEGTSQVQQLIIARETL 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: 326 Number of extensions: 16 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: 382 Length adjustment: 31 Effective length of query: 383 Effective length of database: 351 Effective search space: 134433 Effective search space used: 134433 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