Estimating statistical significance of local protein profile-profile alignments

Silva C, Pedersen AG, Agger JW. Classification of polyphenol oxidases shows ancient gene duplication leading to two distinct enzyme types

Polyphenol oxidases (PPOs) are coupled binuclear copper proteins that catalyze the oxidation of phenols. New functions of PPOs are continuously being discovered, latest with several fungal o-methoxy phenolases, which are active on lignin-derived compounds. Here, we perform a comprehensive phylogenetic analysis of PPOs from a wide taxonomic origin and define 12 PPO groups. We find that a deep gene duplication has led to two distinct PPO types. Type 1 includes PPOs from chordates and molluscs, as well as the fungal o-methoxy phenolases. Type 2 includes plant PPOs, molluscan hemocyanins, and fungal tyrosinases. Most of the type 2 proteins have a C-terminal shielding domain and a thioether bond in the copper-binding site. We also find that most ascomycetes contain high numbers of the PPO type 1 that includes the o-methoxy phenolases, which may indicate a role in the lignin conversion strategy of these fungi.

The COMER web server for protein analysis by homology

SUMMARY

Sequence homology is a basic concept in protein evolution, structure and function studies. However, there are not many different tools and services for homology searches being sensitive, accurate and fast at the same time. We present a new web server for protein analysis based on COMER2, a sequence alignment and homology search method that exhibits these characteristics. COMER2 has been upgraded since its last publication to improve its alignment quality and ease of use. We demonstrate how the user can benefit from using it by providing examples of extensive annotation of proteins of unknown function. Among the distinctive features of the web server is the user's ability to submit multiple queries with one click of a button. This and other features allow for transparently running homology searches-in a command-line, programmatic or graphical environment-across multiple databases with multiple queries. They also promote extensive simultaneous protein analysis at the sequence, structure and function levels.

AVAILABILITY AND IMPLEMENTATION

The COMER web server is available at https://bioinformatics.lt/comer.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

COMER2: GPU-accelerated sensitive and specific homology searches

Summary

Searching for homology in the vast amount of sequence data has a particular emphasis on its speed. We present a completely rewritten version of the sensitive homology search method COMER based on alignment of protein sequence profiles, which is capable of searching big databases even on a lightweight laptop. By harnessing the power of CUDA-enabled graphics processing units, it is up to 20 times faster than HHsearch, a state-of-the-art method using vectorized instructions on modern CPUs.

Availability and implementation

COMER2 is cross-platform open-source software available at https://sourceforge.net/projects/comer2 and https://github.com/minmarg/comer2. It can be easily installed from source code or using stand-alone installers.

Contact

mindaugas.margelevicius@bti.vu.lt

Supplementary information

Supplementary data are available at Bioinformatics online.