Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate Echvi_1473 Echvi_1473 Acyl-CoA dehydrogenases
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__Cola:Echvi_1473 Length = 380 Score = 249 bits (637), Expect = 7e-71 Identities = 153/378 (40%), Positives = 213/378 (56%), Gaps = 7/378 (1%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 LTE Q + M+RD +EI P E D+ FP +LGL+ L+P+ YGG+ Sbjct: 6 LTENQSMIAQMIRDFGAKEITPFRKEWDDHQTFPLPLFKKLGELGLMGVLIPSEYGGSGF 65 Query: 64 GVLTLALILEELGRVCASTALLLIAQTD---GMLPIIHGGSPELKERYLRRFAGESTLLT 120 G L + EL ++ L + A G + + GS E K++YL + A L Sbjct: 66 GYLEYVTAILELAKLDPGIGLSMAAHNSLCSGHIMLF--GSEEQKQKYLPKLAS-CEFLG 122 Query: 121 ALAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGI 180 A TEP GSD MKT A +GD +V+NG K FIT+G DV VV A T G+ Sbjct: 123 AWGLTEPNTGSDAANMKTTATAEGDYFVLNGAKNFITHGVSGDVAVVIARTGEVGDKHGM 182 Query: 181 SAFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLST 240 +AFVVEKGT G GR E K+GMR S +EL FE+ V I+G G GF M+ L Sbjct: 183 TAFVVEKGTEGFRGGRKEDKLGMRTSETAELIFEDCRVHKSQILGEVGEGFIQSMKVLDG 242 Query: 241 NRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRK 300 R+ AA ++GIA+GA + A+ ++++R QF KPI+ + F +ADMAT +EA++LLT K Sbjct: 243 GRISIAALSLGIAEGAFEAALSYSKERQQFQKPISAYQGISFKLADMATKLEAAKLLTFK 302 Query: 301 AAELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQ 360 AA+L + G+ L + AK AS+ A+ + +AVQV GG G+ K+ VE+ RD KL Sbjct: 303 AADLKNRGE-YVTLASAQAKYYASEIAVELANEAVQVYGGYGFTKDYPVEKYYRDVKLCT 361 Query: 361 IYTGTNQITRMVTGRALL 378 I GT++I ++V R LL Sbjct: 362 IGEGTSEIQKIVISRELL 379 Lambda K H 0.319 0.134 0.371 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: 344 Number of extensions: 17 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: 380 Length of database: 380 Length adjustment: 30 Effective length of query: 350 Effective length of database: 350 Effective search space: 122500 Effective search space used: 122500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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