Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 5209191 Shew_1669 butyryl-CoA dehydrogenase (RefSeq)
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__PV4:5209191 Length = 385 Score = 258 bits (660), Expect = 2e-73 Identities = 145/375 (38%), Positives = 208/375 (55%), Gaps = 2/375 (0%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 L E+Q+ E+ A E+AP A + DE H FP +LG S P GG G+ Sbjct: 5 LNEDQRQFAELATQFAQEELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGL 64 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156 +++ E++ C +T ML + GS L++++ + L ++ Sbjct: 65 SRLDSSIIFEQLAMGCTATTAMLTIHNMATWMVTSFGSQTLRDEWSEALTTGNKL-ASYC 123 Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216 TE GAGSD ++KT+AV++GD+YVI+G K FI+ ++L V T + G KG+S Sbjct: 124 LTEAGAGSDAASLKTKAVREGDEYVISGAKMFISGAGSTELLVVMCRTGDA-GPKGISAI 182 Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276 + G+ YG E KMG P E+ F+ + VP NL+GEEG+GF + M L R+ Sbjct: 183 AIPADAAGISYGKAEDKMGWNAQPTREITFDKVRVPVTNLLGEEGQGFTFAMKGLDGGRI 242 Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336 A+ +VG AQ ALERA Q+ ER+QFGKPIA +QF +ADMATE+ AAR +VR A Sbjct: 243 NIATCSVGTAQAALERAQQYMNERQQFGKPIAAFQALQFKLADMATELVAARQMVRLAAF 302 Query: 337 LLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYT 396 LD+ D MAK FA+D V A+Q+ GG GY++EY +ER R+ ++ QI Sbjct: 303 KLDSGDPEATAYCAMAKRFATDVGFNVCDSALQLHGGYGYIREYPLERHFRDVRVHQILE 362 Query: 397 GTNQITRMVTGRSLL 411 GTN+I R++ R LL Sbjct: 363 GTNEIMRLIIARRLL 377 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: 337 Number of extensions: 9 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: 385 Length adjustment: 31 Effective length of query: 383 Effective length of database: 354 Effective search space: 135582 Effective search space used: 135582 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