Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate BPHYT_RS28040 BPHYT_RS28040 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__BFirm:BPHYT_RS28040 Length = 377 Score = 263 bits (673), Expect = 5e-75 Identities = 145/372 (38%), Positives = 222/372 (59%), Gaps = 3/372 (0%) Query: 5 TEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMG 64 T+EQ++ D RD AT ++AP A + D ++ P +LG L ++PA +GG+ Sbjct: 6 TDEQRMIRDAARDFATEQLAPHAGQWDREAQLPAEVVRQMGELGFLGMIVPAEWGGSYTD 65 Query: 65 VLTLALILEELGRVCASTALLL-IAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTALA 123 + AL LEE+ CA+ A L+ + + G PI++ G+ K+RYL+ A + A Sbjct: 66 YVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGTEAQKDRYLQDLA-TGRRIGAFC 124 Query: 124 ATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAF 183 TEP AGS+ ++TRAV + K+++NG K F+TNGS AD+ +V+A TDP++G +G++AF Sbjct: 125 LTEPQAGSEANNLRTRAVLRDGKWILNGSKQFVTNGSRADLAIVFAVTDPDRGKRGLTAF 184 Query: 184 VVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRV 243 +V TPG G+ E K+G+R S + ++ VP N++G G G + L R+ Sbjct: 185 IVPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPEANLLGEPGEGLRIALSNLEGGRI 244 Query: 244 FCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAE 303 AAQAVGIA+ A D A + +R+QFGK + + M+ADMAT + A+RLL AA Sbjct: 245 GIAAQAVGIARAAFDAARLYANERIQFGKALKEHQTIANMLADMATRLNAARLLVHHAAR 304 Query: 304 LLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYT 363 L G K + S AK AS+ A + ++A+Q+ GG GY+++ VER RDA++TQIY Sbjct: 305 LRTAG-KPCLSEASQAKLFASELAEEICSNAIQIHGGYGYLEDYAVERHYRDARITQIYE 363 Query: 364 GTNQITRMVTGR 375 GT+++ RM+ R Sbjct: 364 GTSEVQRMLIAR 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: 335 Number of extensions: 16 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