Despite decades of work by structural biologists, there are still ~5,200 protein families with unknown structure outside the range of comparative modeling. It has recently been shown that this gap can be largely reduced if Rosetta structure prediction pipeline is augmented with residue-residue contacts inferred from evolutionary information. Such significant boost in the number of… [Read More]

Comparative sequence analysis, be it between genomes or metagenomes can significantly expand our biological knowledge by letting us ask questions directly of ecosystems and their inhabitants. The team proposes calculating signatures for the approximately 5,200 private microbial genomes and all of private and public metagenomes in the IMG/M database. Having the MinHash signatures will allow… [Read More]

A functionally diverse enzyme superfamily is a collection of enzymes that share a common ancestor and fold, as well as active site architectures and a partial reaction or other chemical capability. Putting enzymes into their superfamily context has proved to be a powerful way to understand their sequence-structure-function relationships. Metagenomic profiling of enzyme superfamilies can… [Read More]

Microbial sRNAs are untranslated short transcripts that generally reside within intergenic regions on microbial genomes. Most microbial sRNAs function as regulators, and many are currently known to be involved in environmentally significant processes including amino acid and vitamin biosynthesis, quorum sensing, and photosynthesis. Using publicly available metatranscriptomes and metagenomes, as well as metagenomes and metatranscriptomes… [Read More]

Microbial communities drive matter and energy transformations through distributed networks of metabolite exchange that can be reprogrammed though viral infection. In this light, individual microorganisms function as information processing units implementing a distributed genetic algorithm manifested in biologically driven redox reactions on a planetary scale. A core set of genes that evolved early in the… [Read More]

How microbial communities contrast with respect to taxonomic and functional composition within and between soil ecosystems remains an unresolved question that is central to modeling soil functioning and services. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared… [Read More]