Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate CA265_RS17575 CA265_RS17575 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Pedo557:CA265_RS17575 Length = 597 Score = 192 bits (488), Expect = 2e-53 Identities = 120/395 (30%), Positives = 200/395 (50%), Gaps = 30/395 (7%) Query: 36 ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLF--ADLGLLSPLVPVEYGG 93 E EEQ+++ + R+ E+ P +ID+ + L +LG+L VP EYGG Sbjct: 29 EFDEEQQMIAQTCRDFLAAEVYPNLDKIDKQEDPELMPTLLTKAGELGILGVSVPEEYGG 88 Query: 94 TGMDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMT 153 G + T +V + +G + + G L I+ G+ A K KY+P+ G Sbjct: 89 FGKNFNTSMLVADVVGAGHSFAVALSAHTGIGTLPILYYGNEAQKAKYIPKLGS-GEWKA 147 Query: 154 AFAATEPGAGSDLLAMKTRAV--KKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAK 211 A+ TEP +GSD + KT+A + G Y+I GQK +ITNG ADI V+A D K Sbjct: 148 AYCLTEPNSGSDANSGKTKATLSEDGKHYIITGQKMWITNGGFADIFIVFAKIDDDKN-- 205 Query: 212 GMSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGAL 271 ++ F+VE+ G+ E KMG++G ++FF D VP EN++ + GF + L Sbjct: 206 -LTAFIVEKDFGGITMNPEEHKMGIKGSSTRQVFFNDCPVPVENMLSDRENGFKIAVNIL 264 Query: 272 SINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLV 331 +I R+ ++ A+G ++ L A+ ++ ER QFG+PI+ I+F IA++A+++ A Sbjct: 265 NIGRIKLSAAAIGASKATLNTAINYSNERIQFGRPISKYGAIRFKIAEIASKLYAVDAAN 324 Query: 332 RKATTLLDAKDKRGPLIGG--------------------MAKTFASDTAMKVTTDAVQVM 371 +A +D D L+ G + K + S+ + VQ+ Sbjct: 325 YRAGQNID--DTYDQLVAGGMESGKARLKSVEQFAVECAILKVWGSEALDYTVDEGVQIY 382 Query: 372 GGSGYMQEYQVERMMREAKLTQIYTGTNQITRMVT 406 GG G+ + ++R R+A++ +I+ GTN+I R++T Sbjct: 383 GGMGFSADAPMDRAYRDARINRIFEGTNEINRLLT 417 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: 505 Number of extensions: 30 Number of successful extensions: 7 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: 597 Length adjustment: 34 Effective length of query: 380 Effective length of database: 563 Effective search space: 213940 Effective search space used: 213940 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: 52 (24.6 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