Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate PfGW456L13_1630 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1630 Length = 378 Score = 259 bits (661), Expect = 1e-73 Identities = 153/375 (40%), Positives = 216/375 (57%), Gaps = 4/375 (1%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 L+ E +L + VR +E P + ++ + + G+L +P EYGG G Sbjct: 7 LSPEHELFRDSVRTFLEKEAVPFHGQWEKQGYIDRKLWNKAGEAGMLCSHLPEEYGGLGA 66 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAF 155 D A+V+EE+G++ T + +D + IL GS LK KYLP+ ++TA Sbjct: 67 DFLYSAVVIEEVGRL-GLTGIGFSLHSDIVAPYILHYGSETLKHKYLPKL-VSGEMVTAI 124 Query: 156 AATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMST 215 A TEPGAGSDL +KT AV GD+YVING K FITNG +AD++ V A TDP GAKG S Sbjct: 125 AMTEPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGYLADLVIVVAKTDPKAGAKGTSL 184 Query: 216 FVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINR 275 F+VE TPG G +K+GM+ SELFF+D+ VP ENL+G+ G GFAYLM L R Sbjct: 185 FLVEANTPGFDKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQER 244 Query: 276 VFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKAT 335 + A + A+ AL+ + +TRER+ FGK IA +F +A+MATE++ R+ V + Sbjct: 245 LTVAIGGLASAEAALQWTLDYTRERKAFGKSIADFQNTRFKLAEMATEIQIGRVFVDRCL 304 Query: 336 TLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIY 395 L + K MAK + +D KV + VQ+ GG G+M EY + R +A++ +IY Sbjct: 305 E-LHLQGKLDVPTAAMAKYWGTDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIY 363 Query: 396 TGTNQITRMVTGRSL 410 GTN+I + + RSL Sbjct: 364 AGTNEIMKEIIARSL 378 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: 364 Number of extensions: 15 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: 414 Length of database: 378 Length adjustment: 31 Effective length of query: 383 Effective length of database: 347 Effective search space: 132901 Effective search space used: 132901 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 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