SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts

Summary

SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.

Availability and implementation

SpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS: https://github.com/soedinglab/spacepharer.

Supplementary information

Supplementary data are available at Bioinformatics online.

Fast and sensitive taxonomic assignment to metagenomic contigs

SUMMARY

MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig's taxonomic identity by weighted voting. Its fragment extraction step is suitable for the analysis of all domains of life. MMseqs2 taxonomy is 2-18× faster than state-of-the-art tools and also contains new modules for creating and manipulating taxonomic reference databases as well as reporting and visualizing taxonomic assignments.

AVAILABILITY AND IMPLEMENTATION

MMseqs2 taxonomy is part of the MMseqs2 free open-source software package available for Linux, macOS and Windows at https://mmseqs.com.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin

Outer membrane beta-barrels (OMBBs) are the major class of outer membrane proteins from Gram-negative bacteria, mitochondria, and plastids. Their transmembrane domains consist of 8-24 beta-strands forming a closed, barrel-shaped beta-sheet around a central pore. Despite their obvious structural regularity, evidence for an origin by duplication or for a common ancestry has not been found. We use three complementary approaches to show that all OMBBs from Gram-negative bacteria evolved from a single, ancestral beta beta hairpin. First, we link almost all families of known single-chain bacterial OMBBs with each other through transitive profile searches. Second, we identify a clear repeat signature in the sequences of many OMBBs in which the repeating sequence unit coincides with the structural beta beta hairpin repeat. Third, we show that the observed sequence similarity between OMBB hairpins cannot be explained by structural or membrane constraints on their sequences. The third approach addresses a longstanding problem in protein evolution: how to distinguish between a very remotely homologous relationship and the opposing scenario of "sequence convergence." The origin of a diverse group of proteins from a single hairpin module supports the hypothesis that, around the time of transition from the RNA to the protein world, proteins arose by amplification and recombination of short peptide modules that had previously evolved as cofactors of RNAs.

Prediction of protein functional residues from sequence by probability density estimation

MOTIVATION

The prediction of ligand-binding residues or catalytically active residues of a protein may give important hints that can guide further genetic or biochemical studies. Existing sequence-based prediction methods mostly rank residue positions by evolutionary conservation calculated from a multiple sequence alignment of homologs. A problem hampering more wide-spread application of these methods is the low per-residue precision, which at 20% sensitivity is around 35% for ligand-binding residues and 20% for catalytic residues.

RESULTS

We combine information from the conservation at each site, its amino acid distribution, as well as its predicted secondary structure (ss) and relative solvent accessibility (rsa). First, we measure conservation by how much the amino acid distribution at each site differs from the distribution expected for the predicted ss and rsa states. Second, we include the conservation of neighboring residues in a weighted linear score by analytically optimizing the signal-to-noise ratio of the total score. Third, we use conditional probability density estimation to calculate the probability of each site to be functional given its conservation, the observed amino acid distribution, and the predicted ss and rsa states. We have constructed two large data sets, one based on the Catalytic Site Atlas and the other on PDB SITE records, to benchmark methods for predicting functional residues. The new method FRcons predicts ligand-binding and catalytic residues with higher precision than alternative methods over the entire sensitivity range, reaching 50% and 40% precision at 20% sensitivity, respectively.

AVAILABILITY

Server: http://frpred.tuebingen.mpg.de. Data sets: ftp://ftp.tuebingen.mpg.de/pub/protevo/FRpred/.

Coherent beam splitter for atoms based on a bichromatic standing light wave

We propose a new coherent atomic beam splitter that is based on the induced redistribution of photons in the intense field of two collinear standing waves with different frequencies. In the dressed-atom approach, we show that this scheme can provide a clear large-angle splitting into two components without being restricted to the Raman-Nath regime.