Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_025764976.1 X939_RS0119550 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_000566685.1:WP_025764976.1 Length = 387 Score = 234 bits (596), Expect = 4e-66 Identities = 137/384 (35%), Positives = 206/384 (53%), Gaps = 3/384 (0%) Query: 29 QRRDTMNELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVP 88 Q ++ E +L+ E VR+ A++ I P +E DE+ FP +LGL+ LVP Sbjct: 5 QHTESGEHREENCRLIQETVRDFALKNIQPHIMEWDESQHFPTEVFHSLGELGLMGMLVP 64 Query: 89 VEYGGTGMDITTFAMVLEEIGKVCASTALMLLAQADGMLS-IILDGSPALKEKYLPRFGE 147 +YGG G+ + + + KV S L + A + I++ G+ K KYLP+ Sbjct: 65 EQYGGAGLGYQEYITAIIALSKVDPSIGLSMAAHNSLCTNHILMFGNEDQKNKYLPKLAS 124 Query: 148 KSTLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPS 207 + A+ TEP GSD MKT AV+ G+ +++NG K FITNG + V T Sbjct: 125 GEWI-GAWGLTEPNTGSDAGNMKTTAVRDGEDWILNGAKNFITNGQSGRVAVVITRTGEP 183 Query: 208 KGAKGMSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYL 267 G + F+VE GT G G E K+GMR EL FED + +G+ G+GF Sbjct: 184 GDKHGATAFIVEHGTHGFTSGRKENKLGMRASETVELLFEDCRISDSQRLGQIGEGFIQS 243 Query: 268 MGALSINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAA 327 + L R+ A+ VG A GA E A+ +++ER QFGK I+ I F +ADM T+++A+ Sbjct: 244 LKILDGGRISIAALGVGTALGAYEAALAYSKERHQFGKAISSFQGIAFKLADMYTDIQAS 303 Query: 328 RLLVRKATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMR 387 LL +A D K L G +AK +S+TA++V T+AVQ+ GG G+ ++Y E+ R Sbjct: 304 TLLTFQAGKEKDLGQKVS-LSGAVAKYHSSETAVRVATEAVQIYGGYGFTKDYPAEKFYR 362 Query: 388 EAKLTQIYTGTNQITRMVTGRSLL 411 ++KL I GT++I +MV + +L Sbjct: 363 DSKLCTIGEGTSEIQKMVISKEIL 386 Lambda K H 0.318 0.133 0.375 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: 336 Number of extensions: 17 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: 414 Length of database: 387 Length adjustment: 31 Effective length of query: 383 Effective length of database: 356 Effective search space: 136348 Effective search space used: 136348 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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