Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Dino:3607424 Length = 382 Score = 234 bits (597), Expect = 3e-66 Identities = 148/381 (38%), Positives = 211/381 (55%), Gaps = 12/381 (3%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 +T+E ++L EM RN E AP + +LGLL P VP YGG G Sbjct: 7 MTDEHRMLAEMTRNFITTEWAPHFERWRDQGEMDREIWQQAGELGLLCPSVPEAYGGPGG 66 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLS--IILDGSPALKEKYLPRFGEKSTLMTA 154 D A +L EI + S G+++ I+ GS K+K+LP+ ++ A Sbjct: 67 DFGHEAAILIEIARANLSAWGAGHGIHSGIVAHYILAYGSEEQKQKWLPKM-VSGEMVGA 125 Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214 A TEPGAGSDL +KTRAVK G+ Y ++G K FITNG A+++ V A TDPS GAKG+S Sbjct: 126 LAMTEPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKTDPSAGAKGVS 185 Query: 215 TFVVE-RGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLV-GEEGKGFAYLMGALS 272 V+E G G G N K+GM SELFF+++ +P ENL+ GE GKGF +M L Sbjct: 186 LVVLETEGAEGFSRGRNLHKVGMHASDTSELFFDNVAIPPENLLGGEVGKGFYQMMTQLP 245 Query: 273 INRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVR 332 R+ A+ AVG +GA+ER + + +ER+ FG PI +F +A+ T+ AR + Sbjct: 246 QERLIIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKLAECQTKTTVARAFLN 305 Query: 333 KATTLLDAKDKRGPLI---GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREA 389 + A+ G L MAK + +DT +V + VQ+ GG GYM EY + +M +A Sbjct: 306 ECM----AEHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGGYGYMAEYDIAQMWSDA 361 Query: 390 KLTQIYTGTNQITRMVTGRSL 410 ++ +IY GTN+I + + GR+L Sbjct: 362 RVQRIYGGTNEIMKELIGRAL 382 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: 384 Number of extensions: 20 Number of successful extensions: 6 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: 382 Length adjustment: 31 Effective length of query: 383 Effective length of database: 351 Effective search space: 134433 Effective search space used: 134433 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