Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_054255950.1 BN2503_RS07075 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_001298675.1:WP_054255950.1 Length = 376 Score = 254 bits (648), Expect = 4e-72 Identities = 142/377 (37%), Positives = 220/377 (58%), Gaps = 7/377 (1%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 LT++Q ++ + VR+ +I P A D+ H FP A LG VP +YGG G+ Sbjct: 3 LTQDQTMVRDAVRDFVREQITPHAARWDKEHHFPRDVHQGLAQLGAYGICVPEQYGGAGL 62 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAF 155 D T A+VLEEI T+ + + +I++ GS A K+++L + ++ AF Sbjct: 63 DYVTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGSEAQKQQWLAPLA-RGEMLGAF 121 Query: 156 AATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMST 215 TEP GSD A++T A ++GD YVING K FIT+G + V A TD + G KGMS Sbjct: 122 CLTEPHVGSDASALRTTATREGDDYVINGVKQFITSGKNGHVAIVIAVTDKAAGKKGMSA 181 Query: 216 FVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINR 275 F+V PG E+K+G +++ F++ +PA NL+G EG+G+ + AL R Sbjct: 182 FLVPTSNPGYQVARLEEKLGQHSSDTAQINFDNCRIPAANLIGAEGEGYKIALSALEGGR 241 Query: 276 VFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKAT 335 + A+Q+VG+A+ A E A+Q+++ERE FG+PI + + F +AD AT++EAAR L+ A Sbjct: 242 IGIAAQSVGMARAAFECALQYSKERESFGQPIFNHQAVGFRLADCATQLEAARQLIWHAA 301 Query: 336 TLLDAKDKRGPLI--GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQ 393 +L DA P + MAK FAS+ A +V + A+Q +GG G + ++ VER R+ ++ Q Sbjct: 302 SLRDAGQ---PCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERFYRDVRVCQ 358 Query: 394 IYTGTNQITRMVTGRSL 410 IY GT+ + +++ R+L Sbjct: 359 IYEGTSDVQKIIIQRAL 375 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: 330 Number of extensions: 15 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: 376 Length adjustment: 31 Effective length of query: 383 Effective length of database: 345 Effective search space: 132135 Effective search space used: 132135 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 24 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