Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_097069413.1 CRO22_RS07005 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_900217815.1:WP_097069413.1 Length = 391 Score = 216 bits (549), Expect = 1e-60 Identities = 141/384 (36%), Positives = 225/384 (58%), Gaps = 17/384 (4%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEK-SLFPEYARDLFAK---LGLLNPLLPAAYG 59 L+ EQ L + VRD E+AP E+++ +L PE+A +F + LGL +P A+G Sbjct: 5 LSHEQTLLVQTVRDFIAAELAPLEAEVEDTGALAPEHAARIFDRSRGLGLYAMNIPEAFG 64 Query: 60 GTEMGVLTLALILEELGRVCASTALLLIAQTDG-MLPIIHGGSPELKERYLR-RFAGEST 117 G + L L+ E+ GR T+ +L+ + G + ++ E +R+L GE Sbjct: 65 GGGLSALDTMLVEEQFGR----TSDILVRRAFGNVYEVLLACEGEQIDRWLTPTVRGER- 119 Query: 118 LLTALAATEPAAGSDLLAMKTRAVRQGDK-YVINGQKCFITNGSVADVIVVYAYTDPEKG 176 + ++A TEP AGSD +++T+AV G+ + + G K FI++G V+D VV A TDP+KG Sbjct: 120 -VCSIAITEPGAGSDAASIRTKAVEDGEGGWRLTGTKHFISDGLVSDFFVVSAVTDPDKG 178 Query: 177 SKGISAFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQ 236 +KGIS F+V+KG PG GR++ MG+RG+ + EL F+++ + ++GA G GF + Sbjct: 179 AKGISLFLVDKGAPGFTIGRDQPMMGLRGTSHVELSFDDVPLAPVTMLGARGMGFRMALG 238 Query: 237 TLSTNRVF-CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASR 295 L R+ A+++G A LD+ + + ++R QFG+PI V M+AD A + A+R Sbjct: 239 VLGRVRLAQVGARSIGKATKVLDLMLDYARERRQFGQPIGEFQLVAQMLADSALEINAAR 298 Query: 296 LLTRKAAELLDDG-DKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMR 354 L + A +D G D ++ + S+ K A++T RV AVQV GG G+ K+ +ER R Sbjct: 299 LALWQTALEIDAGRDPRSRI--SLVKVQAAETLGRVADRAVQVFGGMGFCKDLPIERYYR 356 Query: 355 DAKLTQIYTGTNQITRMVTGRALL 378 DA++ +I+ GT++I R V GRAL+ Sbjct: 357 DARIYRIFDGTSEIHRTVMGRALM 380 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: 329 Number of extensions: 14 Number of successful extensions: 5 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: 391 Length adjustment: 30 Effective length of query: 350 Effective length of database: 361 Effective search space: 126350 Effective search space used: 126350 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 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