Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate PP_3492 PP_3492 short-chain acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__Putida:PP_3492 Length = 383 Score = 251 bits (640), Expect = 3e-71 Identities = 148/375 (39%), Positives = 219/375 (58%), Gaps = 3/375 (0%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 L+EEQ + DM RD A EIAP A ++ + +LGLL ++P +GG+ Sbjct: 6 LSEEQIMIRDMARDFARGEIAPHAQAWEKAGWIDDGVVRKMGELGLLGMVVPEDFGGSYT 65 Query: 64 GVLTLALILEELGRVCAST-ALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTAL 122 + AL +EE+ C +T A++ I + G P++ G+ E ++++L R A ++ Sbjct: 66 DYVAYALAVEEISAGCGATGAMMSIHNSVGCGPLLAYGTAEQQQQWLPRLAS-GEVIGCF 124 Query: 123 AATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISA 182 TEP AGS+ ++TRA ++VING K F++N A + +V+A TDPE G KG+SA Sbjct: 125 CLTEPQAGSEAHNLRTRAELVDGQWVINGAKQFVSNARRAGLAIVFAVTDPELGKKGLSA 184 Query: 183 FVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNR 242 F+V PG R+E KMG+R S + F+N +PA NI+G G G A + L R Sbjct: 185 FLVPTDNPGFKVDRSEHKMGIRASDTCAVTFDNCRIPAANILGERGKGLAIALSNLEGGR 244 Query: 243 VFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAA 302 + AAQA+GIA+ A + A+ +++DR+QFGKPI + ++ADM V A+RLL AA Sbjct: 245 IGIAAQALGIARAAFEAALVYSRDRIQFGKPINEHQSIANLLADMQVQVNAARLLILHAA 304 Query: 303 ELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIY 362 L G K + S AK AS+ A RV + A+QV GG GY+++ VER RDA++TQIY Sbjct: 305 RLRSAG-KPCLSEASQAKLFASEMAERVCSMAIQVHGGYGYLEDYPVERYYRDARITQIY 363 Query: 363 TGTNQITRMVTGRAL 377 G+++I RM+ R L Sbjct: 364 EGSSEIQRMLIAREL 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: 329 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