Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate SMa1400 SMa1400 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Smeli:SMa1400 Length = 380 Score = 252 bits (644), Expect = 1e-71 Identities = 151/375 (40%), Positives = 216/375 (57%), Gaps = 3/375 (0%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 LTE Q + +M R A I P A +D FP A LGL VP GG G Sbjct: 3 LTEIQGQVRDMARAFADEVIRPMAESLDREERFPAELYGEMAKLGLFGIGVPEHLGGPGF 62 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156 D T+A+V+EE+ + AS A + + ++++ +++ LP S + A+ Sbjct: 63 DTLTYAVVMEELSRGYASVADQC-GLVELISTLLVRHGTEGQQRMLPDVLNMSAKV-AYC 120 Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216 TEP AG+D+ ++T A + GD +++NG K +I N VAD+ V A TD G +GMS F Sbjct: 121 ITEPEAGTDVSGIRTTAERDGDGWMLNGGKIWIHNAPVADVGFVLARTDKEAGNRGMSIF 180 Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276 +V+ + G+ G E KMG R L F D+ +P L+G+EG+GF +M L RV Sbjct: 181 IVDLNSAGVERGPKEHKMGQRASQVGALTFTDVRLPGGALLGQEGRGFHMMMSVLDKGRV 240 Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336 A+ AVGIAQ LE A+ + R+QFGK I+ +Q+++ADMA ++EAARLLV A + Sbjct: 241 GIAALAVGIAQAGLEAAVDYAGTRKQFGKAISDFQGVQWLLADMAKDIEAARLLVHSAAS 300 Query: 337 LLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYT 396 +D + +AK FA D A++ T DAVQV GGSGY++ ++VER+ R+AK+TQIY Sbjct: 301 KID-RGLDATKACSIAKCFAGDMAVQRTADAVQVFGGSGYIRGFEVERLYRDAKITQIYE 359 Query: 397 GTNQITRMVTGRSLL 411 GTNQI RM+ R LL Sbjct: 360 GTNQIQRMIIARELL 374 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: 14 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: 380 Length adjustment: 31 Effective length of query: 383 Effective length of database: 349 Effective search space: 133667 Effective search space used: 133667 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