Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.

ABSTRACT: Data mining methods in bioinformatics and comparative genomics commonly rely on working definitions of protein families from prior computation. Partial phylogenetic profiling (PPP), by contrast, optimizes family sizes during its searches for the cooccurring protein families that serve different roles in the same biological system. In a large-scale investigation of the incredibly diverse radical S-adenosylmethionine (SAM) enzyme superfamily, PPP aided in building a collection of 68 TIGRFAMs hidden Markov models (HMMs) that define nonoverlapping and functionally distinct subfamilies. Many identify radical SAM enzymes as molecular markers for multicomponent biological systems; HMMs defining their partner proteins also were constructed. Newly found systems include five groupings of protein fam

SUBMITTER: Haft DH 

PROVIDER: S-EPMC3133131 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature