Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate CA265_RS22715 CA265_RS22715 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Pedo557:CA265_RS22715 Length = 379 Score = 300 bits (768), Expect = 5e-86 Identities = 171/382 (44%), Positives = 240/382 (62%), Gaps = 13/382 (3%) Query: 36 ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95 EL+EEQ ++ + R+ A +E+ P IE DE+ FP +LG L +V +Y G+G Sbjct: 4 ELSEEQLMIRQAARDFAQQELKPGVIERDEHQKFPAEQVKKLGELGFLGMMVSEKYNGSG 63 Query: 96 MDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD--GSPALKEKYLPRF--GEKSTL 151 +D ++ +V+EE+ K+ AS ++++ + ++ L+ GS A KEKYL GEK Sbjct: 64 LDAISYVLVMEELSKIDASASVVVSVN-NSLVCYGLEAYGSEAQKEKYLKPLAAGEK--- 119 Query: 152 MTAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAK 211 + AF +EP AGSD + +T A KGD Y++NG K +ITNGS A V A T P K Sbjct: 120 IGAFCLSEPEAGSDATSQRTTAEDKGDYYLLNGTKNWITNGSTASTYLVIAQTHPELRHK 179 Query: 212 GMSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGAL 271 G++ F+VE+G G G E K+G+RG L F D++VP EN +GE+G GF + M L Sbjct: 180 GINAFIVEKGMEGFTVGPKENKLGIRGSDTHSLMFNDVKVPKENRIGEDGFGFKFAMKTL 239 Query: 272 SINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLV 331 R+ A+QA+GIAQGA E A Q+ +ER+ FGKPI+ I F +ADMAT++EAARLLV Sbjct: 240 EGGRIGIAAQALGIAQGAFELATQYAKERKSFGKPISEHQAIAFKLADMATQIEAARLLV 299 Query: 332 RKATTLLDAKDKRGPL--IGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREA 389 KA L KD+ P G MAK +AS AM VT +AVQV GG G+++EY VER+MR+A Sbjct: 300 YKAAWL---KDQGLPYTQAGSMAKLYASKVAMDVTIEAVQVHGGYGFVKEYHVERLMRDA 356 Query: 390 KLTQIYTGTNQITRMVTGRSLL 411 K+TQIY GT++I +MV R ++ Sbjct: 357 KITQIYEGTSEIQKMVISREVI 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: 354 Number of extensions: 16 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: 414 Length of database: 379 Length adjustment: 31 Effective length of query: 383 Effective length of database: 348 Effective search space: 133284 Effective search space used: 133284 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