Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_055435174.1 ASC41_RS03050 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_001418085.1:WP_055435174.1 Length = 390 Score = 202 bits (515), Expect = 1e-56 Identities = 125/380 (32%), Positives = 204/380 (53%), Gaps = 7/380 (1%) Query: 2 KHLTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGT 61 ++ TEE L + D +E+ P + ++ + + F ++G P AYGG Sbjct: 4 RYFTEEHNLFRQSLADFLQKEVVPHIDKWEKTGHIERFIWEKFGEMGFFGIAYPEAYGGM 63 Query: 62 EMGVLTLALILEELGRVCAS--TALLLIAQTDGMLPIIHGGSPELKERYLRR-FAGESTL 118 ++ + + LEEL +V + A + M + GS E+K++YL + GE Sbjct: 64 DLDLFYTVIFLEELQKVNSGGFAAAMWAHAYLAMTHVNAEGSEEIKQKYLTKSITGE--F 121 Query: 119 LTALAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSK 178 + A+A TEP GSD+ M+T AV++G+ YV+NG K FITNG +D IVV A T PE G+K Sbjct: 122 IGAMAVTEPFGGSDVAGMRTTAVKEGNTYVLNGSKTFITNGVYSDYIVVAAKTSPELGNK 181 Query: 179 GISAFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTL 238 GIS F+V++ T G V K+G R S E+ F+N+ +PA +++G EG GF +MQ Sbjct: 182 GISMFIVDRDTKG-VSATKLDKLGWRASDTGEIAFDNVVIPASHLMGEEGKGFPYIMQHF 240 Query: 239 STNRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLT 298 + R+ A A+ AL+ AV++ +R FGK I ++ +AD +E + Sbjct: 241 AFERLIMGVNAHARAEFALEYAVKYMGERQAFGKSIDKFQALRHTMADCYADMEVCKEFN 300 Query: 299 RKAAELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKL 358 A LD ++ V +++K ++ A V +Q+LGG GYM+E + R++RD++L Sbjct: 301 YTVAARLDK-NEYVVKEATISKLRSTKMADDVIYQCLQMLGGYGYMEEYPMARLLRDSRL 359 Query: 359 TQIYTGTNQITRMVTGRALL 378 I GT++I R + + ++ Sbjct: 360 GPIGGGTSEILREIIAKMVI 379 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: 322 Number of extensions: 23 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: 390 Length adjustment: 30 Effective length of query: 350 Effective length of database: 360 Effective search space: 126000 Effective search space used: 126000 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 24 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