Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate AZOBR_RS22300 AZOBR_RS22300 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__azobra:AZOBR_RS22300 Length = 377 Score = 275 bits (704), Expect = 1e-78 Identities = 161/377 (42%), Positives = 224/377 (59%), Gaps = 5/377 (1%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 LTEEQ++ DM RD A +AP A E D FP+ +LGL+ L+P + G Sbjct: 3 LTEEQRMVRDMARDFAAERLAPTAAERDRTGAFPKEELAEMGRLGLMGMLVPEEFDGAGT 62 Query: 64 GVLTLALILEELGRVC-ASTALLLIAQTDGMLPIIHGGSPELKERYLRRFA-GESTLLTA 121 + AL +EE+ A + ++ + + G +PI+ GS E KER+L+ A GE L Sbjct: 63 DHIAYALAIEEIAAGDGAISTIMSVHNSVGCMPILKFGSAEQKERFLKPMARGEQ--LGC 120 Query: 122 LAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGIS 181 TEP AGSD A+KTRA R G+ +V+NG K FIT+G ADV +V+A +DPE G KGI+ Sbjct: 121 FCLTEPQAGSDAAAIKTRARRDGNHWVLNGTKQFITSGKNADVAIVFAVSDPEAGKKGIT 180 Query: 182 AFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTN 241 AFVV TPG R E K+G S ++ E+ +PA+ ++GAEG G+ + L Sbjct: 181 AFVVPTDTPGFQVARVEEKLGQSCSDTCQIVLEDCRIPADLMLGAEGGGYRVALANLEGG 240 Query: 242 RVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKA 301 R+ A+Q+VG+A+ ALD A R+ Q+R G PI V F +ADMAT VEA+R L A Sbjct: 241 RIGIASQSVGMARAALDHATRYAQERQSMGLPIIQHQAVAFRLADMATKVEAARQLVLHA 300 Query: 302 AELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQI 361 A L D G+ + +MAK AS+ A RV +DA+Q+ GG GY+ + VER+ RD ++ QI Sbjct: 301 ASLRDAGE-PCLKEAAMAKLFASEIAERVCSDAIQIHGGYGYLNDFPVERIYRDVRVCQI 359 Query: 362 YTGTNQITRMVTGRALL 378 Y GT+ I R+V RAL+ Sbjct: 360 YEGTSDIQRLVISRALM 376 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: 345 Number of extensions: 14 Number of successful extensions: 4 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: 377 Length adjustment: 30 Effective length of query: 350 Effective length of database: 347 Effective search space: 121450 Effective search space used: 121450 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