Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate PP_3725 PP_3725 putative Acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__Putida:PP_3725 Length = 386 Score = 210 bits (535), Expect = 5e-59 Identities = 144/386 (37%), Positives = 210/386 (54%), Gaps = 16/386 (4%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEK-SLFPEYARDLFAKL---GLLNPLLPAAYG 59 LT+EQ++ ++ VR +E+ P +D ++ PE A + K G +P G Sbjct: 5 LTQEQEMLVEAVRSFVAKELLPHEEAVDRADAVSPELAAQIRGKAIAAGFYAFNMPEEVG 64 Query: 60 GTEMGVLTLALILEELGRVCASTAL-LLIAQTDGMLPIIHGGSPELKERYLRRFAGESTL 118 G + L+ ALI EL +V S AL + +A+ +L ++ + L GE Sbjct: 65 GGGLDYLSQALIERELSKV--SWALHVFVARPSKILMACK--DEQINDYLLPCVQGEK-- 118 Query: 119 LTALAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDP--EKG 176 + A TEP AGSD A+KTRAVRQGD +VING K FI++ AD +V+A TD G Sbjct: 119 VDCFALTEPGAGSDANAIKTRAVRQGDDFVINGSKHFISHAGHADFAIVFAVTDTYEHNG 178 Query: 177 SK--GISAFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANL 234 K ++A +V++GTPG+ R + RG ELFF++ VPA ++G G G+ Sbjct: 179 RKRNAVTALLVDRGTPGMTIRRGPKCVSNRGYHTYELFFDDCRVPASKVLGEVGKGWEVA 238 Query: 235 MQTLSTNRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEAS 294 L+ RV AA VG AQ ALD++++ DR QFG+ I V F +ADMAT + A+ Sbjct: 239 NAWLTAGRVMVAANCVGQAQRALDLSLQWAADRKQFGQAIGSYQGVSFKLADMATQIRAA 298 Query: 295 RLLTRKAAELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMR 354 +LT A +D G+ G MAK AS+ +V +AVQ+ GG G M E VER+ R Sbjct: 299 EMLTLHTAWKMDQGNMTDGEAG-MAKLFASEVLGKVADEAVQIFGGMGLMDEGPVERIWR 357 Query: 355 DAKLTQIYTGTNQITRMVTGRALLFP 380 +A++ +I+ GT++I R + R LL P Sbjct: 358 NARIERIWEGTSEIQRHIIARELLRP 383 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: 284 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: 386 Length adjustment: 30 Effective length of query: 350 Effective length of database: 356 Effective search space: 124600 Effective search space used: 124600 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