Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate CCNA_01412 CCNA_01412 acyl-CoA dehydrogenase, short-chain specific
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Caulo:CCNA_01412 Length = 381 Score = 270 bits (689), Expect = 7e-77 Identities = 151/376 (40%), Positives = 224/376 (59%), Gaps = 6/376 (1%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 L E+Q + + R A ++AP + + DEN FPV A+LG V + GG+G+ Sbjct: 7 LNEDQVAIQDAARAFAEGQLAPHSADWDENKHFPVDVLRQAAELGFAGIYVNEDVGGSGL 66 Query: 97 DITTFAMVLEEI--GKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTA 154 +++ E + G V + L + A M+ GS L+++YLPR L+ + Sbjct: 67 SRLDASIIFEALSYGDVPVAAYLTIHNMASWMIDRF--GSDDLRQRYLPRLTTME-LIAS 123 Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214 + TEPG+GSD AM+T A GD YV+NG K FI+ G V+DI V A T +GAKG+S Sbjct: 124 YCLTEPGSGSDAAAMRTTAKLDGDHYVLNGGKAFISGGGVSDIYVVMARTG-GEGAKGVS 182 Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274 FVVE+G GL +G NE+KMG P +++ F++ VP N +G+EG+GF + M L Sbjct: 183 AFVVEKGMEGLSFGANERKMGWNAQPTAQVNFDNCRVPVANRIGQEGEGFRFAMMGLDGG 242 Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334 R+ AS ++G AQ AL+ A + R QFG+P+ +QF +ADMATE+EAARL+VR+A Sbjct: 243 RLNIASCSLGGAQFALDTAKAYLETRNQFGRPLKDFQALQFKLADMATELEAARLMVRRA 302 Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 LD+K + MAK FA+D +V DA+Q+ GG GY+Q+Y +ER++R+ ++ QI Sbjct: 303 AHALDSKHPEATKLCAMAKRFATDAGFQVANDALQLHGGYGYLQDYPLERLVRDLRVHQI 362 Query: 395 YTGTNQITRMVTGRSL 410 GTN+I R++ R + Sbjct: 363 LEGTNEIMRVIIAREM 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: 362 Number of extensions: 15 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: 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 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