Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate GFF2713 PS417_13840 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__WCS417:GFF2713 Length = 383 Score = 242 bits (618), Expect = 1e-68 Identities = 149/374 (39%), Positives = 210/374 (56%), Gaps = 3/374 (0%) Query: 5 TEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMG 64 TEEQ + DM RD A EIAP A ++ + +LGLL ++P +GGT + Sbjct: 7 TEEQVMIRDMARDFARGEIAPYAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYVD 66 Query: 65 VLTLALILEELGRVCAST-ALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTALA 123 + AL +EE+ +T AL+ I + G PI++ G+ K+ +L A + Sbjct: 67 YVAYALAVEEISAGDGATGALMSIHNSVGCGPILNYGTESQKQTWLADLASGQAI-GCFC 125 Query: 124 ATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAF 183 TEP AGS+ ++TRA + +VI G K F++NG A + +V+A TDPE G KGISAF Sbjct: 126 LTEPQAGSEAHNLRTRAELRDGHWVITGAKQFVSNGKRAKLAIVFAITDPELGKKGISAF 185 Query: 184 VVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRV 243 +V TPG V R E KMG+R S + VP N++G G G A + L R+ Sbjct: 186 LVPTATPGFVVDRTEHKMGIRASDTCAVTLNQCTVPEANLLGERGKGLAIALSNLEGGRI 245 Query: 244 FCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAE 303 AAQA+GIA+ A + A+ + +DRVQF K I V ++ADM T + A+RLL AA Sbjct: 246 GIAAQALGIARAAFEAALAYARDRVQFDKAIIEHQSVANLLADMQTQLNAARLLILHAAR 305 Query: 304 LLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYT 363 L G K + S AK AS+ A +V + A+Q+ GG GY+++ VER RDA++TQIY Sbjct: 306 LRSAG-KPCLSEASQAKLFASEMAEKVCSSAMQIHGGYGYLEDYPVERYYRDARITQIYE 364 Query: 364 GTNQITRMVTGRAL 377 GT++I RMV R L Sbjct: 365 GTSEIQRMVIAREL 378 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: 338 Number of extensions: 9 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: 383 Length adjustment: 30 Effective length of query: 350 Effective length of database: 353 Effective search space: 123550 Effective search space used: 123550 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