Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate CA265_RS09630 CA265_RS09630 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Pedo557:CA265_RS09630 Length = 396 Score = 185 bits (470), Expect = 2e-51 Identities = 122/374 (32%), Positives = 185/374 (49%), Gaps = 12/374 (3%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 LT+E KL+ R+ +E++P + + FP H AD+G P +PVEYGG G+ Sbjct: 22 LTDEHKLIRATARDWVKKEVSPIIEDYAQKAEFPKHLIKGLADIGAFGPTIPVEYGGAGL 81 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADG---MLSIILDGSPALKEKYLPRFGEKSTLMT 153 D T + ++++EI + + + A G M I GS ++KYLP+ +M Sbjct: 82 DYTAYGILMQEIER--GDSGIRSTASVQGSLVMYPIYAYGSEEQRKKYLPKLA-SGEMMG 138 Query: 154 AFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGM 213 F TEP GS+ M T G Y++NG K +I+N ADI VWA D S +G+ Sbjct: 139 CFGLTEPDHGSNPGGMVTNIKDAGSHYILNGAKMWISNAPFADIAVVWA-KDESGKIRGL 197 Query: 214 STFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSI 273 +VERG G K +R EL F++++VP EN+ E G +G L+ Sbjct: 198 ---IVERGMEGFSTPETHHKWSLRASATGELVFDNVKVPKENIF-PEISGLKGPLGCLNQ 253 Query: 274 NRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRK 333 R A A+G A + A+++++ER QFGKPI Q +A+M TE+ +LLV + Sbjct: 254 ARYGIAWGALGAAMDCYDTALRYSKERVQFGKPIGGFQLQQKKLAEMVTEITKGQLLVWR 313 Query: 334 ATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQ 393 L I MAK + + A+ + +A Q++GG G EY + R M + Sbjct: 314 LGVLKSENRASAEQI-SMAKRNSVEIALDIARNARQMLGGMGITGEYSIMRHMMNLESVV 372 Query: 394 IYTGTNQITRMVTG 407 Y GT+ I ++TG Sbjct: 373 TYEGTHDIHLLITG 386 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: 360 Number of extensions: 21 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: 396 Length adjustment: 31 Effective length of query: 383 Effective length of database: 365 Effective search space: 139795 Effective search space used: 139795 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