Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_011913061.1 PST_RS09700 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_000013785.1:WP_011913061.1 Length = 379 Score = 247 bits (630), Expect = 4e-70 Identities = 146/374 (39%), Positives = 213/374 (56%), Gaps = 5/374 (1%) Query: 6 EEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGV 65 E+Q +M R A + P A + + +P A A LG L+P +GG++ G Sbjct: 5 EDQCAIAEMARQFARERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTGY 64 Query: 66 LTLALILEELGRVC-ASTALLLIAQTDGMLPIIHGGSPELKERYLRRFA-GESTLLTALA 123 L A+ LEE+ A + ++ + + G +PI+ G+ + K +L A GE + A A Sbjct: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNDQQKRDFLGPLARGEQ--IGAFA 122 Query: 124 ATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAF 183 TEP AGSD +++TRA R GD YV+NG K FIT+G A ++V+A TDP+ G +GISAF Sbjct: 123 LTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKRGISAF 182 Query: 184 VVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRV 243 +V +PG R E K+G S ++ FE++ VP N +G EG G+ + L R+ Sbjct: 183 IVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRI 242 Query: 244 FCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAE 303 AAQAVG+A+ A + A + +R FGKPI V F +ADMAT + +R + AA Sbjct: 243 GIAAQAVGMARAAFEAARDYAGERETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAA 302 Query: 304 LLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYT 363 L + G + A++ SMAK AS+ A RV + A+Q LGG GY+ + VER+ RD ++ QIY Sbjct: 303 LREAG-RPALVEASMAKLFASEMAERVCSAAIQTLGGYGYLSDFPVERIYRDVRVCQIYE 361 Query: 364 GTNQITRMVTGRAL 377 GT+ I R+V R L Sbjct: 362 GTSDIQRLVISRNL 375 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: 300 Number of extensions: 13 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: 379 Length adjustment: 30 Effective length of query: 350 Effective length of database: 349 Effective search space: 122150 Effective search space used: 122150 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 Apr 09 2024. 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