Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_097070176.1 CRO22_RS10865 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_900217815.1:WP_097070176.1 Length = 381 Score = 231 bits (589), Expect = 3e-65 Identities = 132/377 (35%), Positives = 207/377 (54%), Gaps = 6/377 (1%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 L+EE + + EM + EIAP A + + P A LGL V E+GG+G+ Sbjct: 5 LSEESRAIFEMAQAFGQEEIAPHARAWEAAGTIPRALWAKVAALGLGGLYVSEEHGGSGL 64 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQ--ADGMLSIILDGSPALKEKYLPRFGEKSTLMTA 154 +V E + C S + L GM+ G+P LK+++LP+ T+ + Sbjct: 65 SRLDATLVFEALAMACPSVSAFLSIHNMCGGMIEKF--GAPDLKDRFLPKLCTMETVFS- 121 Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214 + TEPG+GSD A++TRA + +NG K FI+ G +D T G KG+S Sbjct: 122 YCLTEPGSGSDAAALRTRAEAVPQGWKLNGTKAFISGGGYSDAYITMVRTG-EPGPKGIS 180 Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274 T +VE GTPGL +G E KMG R P +++ F+D +PAENLVG G+GF+Y M L Sbjct: 181 TVIVEAGTPGLSFGAKEDKMGWRAQPTAQVQFDDCIIPAENLVGAPGRGFSYAMAGLDGG 240 Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334 R+ A+ A+G AQ A+ + + ER+ FG+ + +QF +A+M ++++AR+ +R+A Sbjct: 241 RLNIAASALGGAQAAMNATLAYMGERKAFGQSLDQFQALQFRLAEMEVKLQSARIFLRQA 300 Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 LD MAK + +D A V +Q+ GG GY+ +Y +E+++R+ ++ QI Sbjct: 301 AWKLDQGAPDATKFCAMAKLYVTDAAFDVANQCLQLHGGYGYLADYGIEKILRDLRVHQI 360 Query: 395 YTGTNQITRMVTGRSLL 411 GTN+I R++ GR++L Sbjct: 361 LEGTNEIMRLIIGRAVL 377 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: 334 Number of extensions: 18 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: 414 Length of database: 381 Length adjustment: 31 Effective length of query: 383 Effective length of database: 350 Effective search space: 134050 Effective search space used: 134050 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