Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate GFF1190 PGA1_c12060 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Phaeo:GFF1190 Length = 383 Score = 212 bits (539), Expect = 2e-59 Identities = 139/383 (36%), Positives = 211/383 (55%), Gaps = 18/383 (4%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 +T+E ++L +M RE AP+ + + LGLL P VP EYGG G Sbjct: 10 MTDEHQMLADMTAQFITREWAPKFETWRKQGMMDRSTWNEAGALGLLCPSVPEEYGGVGG 69 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLS--IILDGSPALKEKYLPRF--GEKSTLM 152 D A +L E + A+ A G+++ ++ G+ K+++LP+ GE L+ Sbjct: 70 DFGHEAAILIEGSR--ANLASWGHGIHSGIVAHYVLSYGTEEQKQRWLPKMITGE---LV 124 Query: 153 TAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKG 212 A A TEP GSD+ +KT+AVK G+ Y ++GQK FITNG A+++ V A TDPS+G+KG Sbjct: 125 GALAMTEPSTGSDVQRIKTKAVKDGNAYRLSGQKTFITNGQHANLILVAAKTDPSQGSKG 184 Query: 213 MSTFVVER-GTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLV-GEEGKGFAYLMGA 270 +S VE G G G N K+G+ SELFF+++E+ EN++ G EG+GF +M Sbjct: 185 ISLVAVETDGADGFSRGRNLDKIGLHAADTSELFFDNVEIAPENILGGTEGQGFYQMMQQ 244 Query: 271 LSINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLL 330 L R+ A AVG +GA+ER + + +ERE FG P+ +F + + T+ + AR Sbjct: 245 LPQERLIIACGAVGAMEGAVERTITYCKEREAFGGPLTQFQNTRFKLVECQTKTKVARAF 304 Query: 331 VRKATTLLDAKDKRGPLI---GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMR 387 + + + +G L MAK + +DT V + VQ+ GG G+MQEY V M Sbjct: 305 LDECM----VEHLQGKLTVEKAAMAKYWITDTQGDVLDECVQLHGGYGFMQEYAVAEMWT 360 Query: 388 EAKLTQIYTGTNQITRMVTGRSL 410 +A++ +IY GTN+I + + RSL Sbjct: 361 DARVQRIYGGTNEIMKELIARSL 383 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: 368 Number of extensions: 20 Number of successful extensions: 6 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: 383 Length adjustment: 31 Effective length of query: 383 Effective length of database: 352 Effective search space: 134816 Effective search space used: 134816 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