Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate AZOBR_RS17455 AZOBR_RS17455 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__azobra:AZOBR_RS17455 Length = 387 Score = 208 bits (529), Expect = 3e-58 Identities = 128/362 (35%), Positives = 197/362 (54%), Gaps = 19/362 (5%) Query: 63 IDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDITTFAMVLEEIGKVCASTALMLLAQ 122 IDE +P D G ++ L+P EYGG+G+ +T ++++EEI + ++ Q Sbjct: 31 IDEERGYPEAFVDALTKAGWMAALIPEEYGGSGLGLTEASVIMEEINRSGGNSGACH-GQ 89 Query: 123 ADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVI 182 M +++ GS + +YLP+ + + TEP G+D +KTRA KKGD+YVI Sbjct: 90 MYNMNTLVRHGSEEQRRRYLPKIAAGELRLQSMGVTEPTTGTDTTRIKTRAEKKGDRYVI 149 Query: 183 NGQKCFITNGSVADILTVWAYTDP----SKGAKGMSTFVVERGTPGLIYGHNEKKMGMRG 238 NGQK +I+ +D++ + A T P K ++GMS F+V+ I +K M ++ Sbjct: 150 NGQKVWISRVQHSDLMILLARTTPLDQVRKKSEGMSIFIVD------IKEAMQKGMTVQP 203 Query: 239 CPN------SELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVFCASQAVGIAQGALER 292 N +ELFF++LE+PAENL+GEEG+GF Y++ L+ RV A++ +G +++ Sbjct: 204 IRNMVNHETNELFFDNLEIPAENLIGEEGQGFKYILTGLNAERVLIAAECIGDGYWFIDK 263 Query: 293 AMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTLLDAKDKRGPLIGGMA 352 +TR+R+ FG+PIA +QF IA+ EVEAA L+ +A L DA + G MA Sbjct: 264 VCDYTRDRQVFGRPIAQNQGVQFPIAESFIEVEAANLMRFEACRLYDAGEPCGAQ-ANMA 322 Query: 353 KTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIY-TGTNQITRMVTGRSLL 411 K A+ + + +Q GG G+ EY VER RE +L Q+ TN I V L Sbjct: 323 KYLAAKASWEAANACLQFHGGFGFASEYDVERKFRETRLYQVAPVSTNLILAYVAEHVLD 382 Query: 412 FP 413 P Sbjct: 383 LP 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: 344 Number of extensions: 18 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: 387 Length adjustment: 31 Effective length of query: 383 Effective length of database: 356 Effective search space: 136348 Effective search space used: 136348 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