Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ga0059261_2668 Ga0059261_2668 Enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__Korea:Ga0059261_2668 Length = 256 Score = 94.0 bits (232), Expect = 3e-24 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 7/247 (2%) Query: 12 ERVARIKIANPP-VNVLDMETMKEII---SAIDEVEGVDVIVFSGEG-KSFSAGAEIKEH 66 + VA I + P +N L E +I SA + + V +V +G G K+FSAG++I Sbjct: 11 DHVATITLNRPAKLNALTPEMAAALIASVSACNSSDAVRCVVITGAGEKAFSAGSDITTL 70 Query: 67 FPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLGVPE 126 P R D + C+ VAA+ G+ALGGG E A+A D +AS NA+ PE Sbjct: 71 DGYATPWDFRNRDDYCDALRACRKPVVAAINGYALGGGLETAMAADIRIASTNARFAAPE 130 Query: 127 ITLAHYPPVAIAL-LPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEESVND 185 I L +A L +G NA ++ TG+ I AE+A GLV++V + + Sbjct: 131 IKLGWIGGGGMAAGLTYSMGASNAALMLFTGDMIDAEKALAWGLVSEVVAPDALLARAQE 190 Query: 186 FVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKAFLEKR 245 ++ ++ +A K L + + + D+ + ++DA EG AF EKR Sbjct: 191 IARTIASRAPIAAETAKLNLRAAHTMPWDKAIEYERDLQ-AICFATDDAKEGRAAFAEKR 249 Query: 246 KPEWKGR 252 P ++ R Sbjct: 250 APVFRRR 256 Lambda K H 0.318 0.136 0.382 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: 137 Number of extensions: 8 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: 252 Length of database: 256 Length adjustment: 24 Effective length of query: 228 Effective length of database: 232 Effective search space: 52896 Effective search space used: 52896 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: 47 (22.7 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