Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate AZOBR_RS22365 AZOBR_RS22365 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__azobra:AZOBR_RS22365 Length = 379 Score = 272 bits (696), Expect = 1e-77 Identities = 155/379 (40%), Positives = 223/379 (58%), Gaps = 12/379 (3%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 L+EEQ+ + R+ A +E+AP A DEN FPV A LG V E+GG+G+ Sbjct: 5 LSEEQQAFRDTARDFAQQEMAPNAAHWDENSVFPVDTLRQAAALGFAGIYVGEEFGGSGL 64 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD--GSPALKEKYLPRFGEKSTLMTA 154 A++ EE+ C STA + M S ++D G+ +E++LP K T M Sbjct: 65 GRLDAALIFEELSAACPSTAAYI--SIHNMASWMIDRFGNAEQRERFLP----KLTTMEH 118 Query: 155 FAA---TEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAK 211 FA+ TEPGAGSD +++TRA + GD YV+NG K FI+ G +D+ T G K Sbjct: 119 FASYCLTEPGAGSDAASLRTRAERVGDHYVLNGSKAFISGGGTSDVYVCMVRTG-EPGPK 177 Query: 212 GMSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGAL 271 G+S VE+GTPGL +G E K+G + P S + FE+ VP N +GEEG+GF M L Sbjct: 178 GISCIAVEKGTPGLSFGKQEHKLGWKSQPTSAVIFENCRVPVANRIGEEGEGFRIAMKGL 237 Query: 272 SINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLV 331 R+ A+ +VG A+ LE+A+ +T ER+QFGKP+ +QF +ADMATE++AARL++ Sbjct: 238 DGGRLNIAACSVGGARFCLEQAVAYTTERKQFGKPLNAFQALQFKLADMATELDAARLML 297 Query: 332 RKATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKL 391 +A LDA MAK FA+D +V +A+Q+ GG GY++EY +ER+ R+ ++ Sbjct: 298 HRAAASLDAGSPEATAHCAMAKRFATDAGFQVVNEALQLHGGYGYIKEYPIERIFRDLRV 357 Query: 392 TQIYTGTNQITRMVTGRSL 410 QI GTN+I R++ R L Sbjct: 358 HQILEGTNEIMRVIIARHL 376 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: 361 Number of extensions: 11 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