Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate PP_2216 PP_2216 short-chain acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__Putida:PP_2216 Length = 375 Score = 271 bits (694), Expect = 2e-77 Identities = 152/375 (40%), Positives = 226/375 (60%), Gaps = 3/375 (0%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 + +EQ+ D VR A + P A + D+ FP+ A D A+LGL L+P +GG++ Sbjct: 3 VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 Query: 64 GVLTLALILEELGRVC-ASTALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTAL 122 G + A+ LEE+ A + ++ + + G +PI+ G+ + KE++L A +L A Sbjct: 63 GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLA-TGAMLGAF 121 Query: 123 AATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISA 182 A TEP AGSD ++KTRA +GD YV+NG K FIT+G A V++V+A TDPE G +GISA Sbjct: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181 Query: 183 FVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNR 242 F+V +PG R E K+G S ++ F+N++VP N +GAEG G+ + L R Sbjct: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241 Query: 243 VFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAA 302 + A+QAVG+A+ A ++A + +R FGKP+ V F +ADMAT + +R + AA Sbjct: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 Query: 303 ELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIY 362 L D G + A++ SMAK AS+ A +V +DA+Q LGG GY+ + +ER+ RD ++ QIY Sbjct: 302 ALRDAG-RPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 Query: 363 TGTNQITRMVTGRAL 377 GT+ I RMV R L Sbjct: 361 EGTSDIQRMVIARNL 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: 308 Number of extensions: 12 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: 375 Length adjustment: 30 Effective length of query: 350 Effective length of database: 345 Effective search space: 120750 Effective search space used: 120750 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