Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_003939784.1 C1M55_RS25280 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_002893965.1:WP_003939784.1 Length = 385 Score = 319 bits (818), Expect = 8e-92 Identities = 169/375 (45%), Positives = 235/375 (62%), Gaps = 2/375 (0%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 L EE L +R L+ +EIAP A ++DEN FP A G + VP Y G G Sbjct: 12 LNEEHDELRAAIRGLSEKEIAPYAKDVDENARFPEEALTALNASGFNAIHVPEAYDGQGA 71 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156 D +V+EE+ +VC S++L+ G + +IL GS LK K LP M ++A Sbjct: 72 DSVATCIVIEEVARVCGSSSLIPAVNKLGTMGLILKGSEELKSKVLPDLVNGG--MASYA 129 Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216 +E AGSD +M+TRA GD +++NG KC+ITNG + TV A TDP KGA G+S+F Sbjct: 130 LSEREAGSDAASMRTRAKADGDDWILNGSKCWITNGGKSTWYTVMAVTDPDKGANGISSF 189 Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276 +V + G + G EKK+G++G P +EL+FE+ +P + ++GE G GF + L R Sbjct: 190 MVHKDDEGFVVGPKEKKLGIKGSPTAELYFENCRIPGDRIIGEPGTGFKTALETLDHTRP 249 Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336 +QAVG+AQGAL+ A+ +T++R+QFGK I+ +QFM+ADMA +VEAARL+V + Sbjct: 250 TIGAQAVGLAQGALDAALAYTKDRKQFGKSISDFQAVQFMLADMAMKVEAARLMVYTSAA 309 Query: 337 LLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYT 396 + +K I AK FASD AM+VTTDAVQ+ GG+GY ++ VERMMR+AK+TQIY Sbjct: 310 RAERGEKNLGFISAAAKCFASDVAMEVTTDAVQLFGGAGYTTDFPVERMMRDAKITQIYE 369 Query: 397 GTNQITRMVTGRSLL 411 GTNQI R+V R+LL Sbjct: 370 GTNQIQRVVMSRALL 384 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: 393 Number of extensions: 17 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: 385 Length adjustment: 31 Effective length of query: 383 Effective length of database: 354 Effective search space: 135582 Effective search space used: 135582 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 24 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