BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes

Abstract

With the recent progress in complete genome sequencing, mining the increasing amount of genomic information available should in theory provide the means to discover new classes of peptides. However, annotation pipelines often do not consider small reading frames likely to be expressed. BactPepDB, available online at http://bactpepdb.rpbs.univ-paris-diderot.fr, is a database that aims at providing an exhaustive re-annotation of all complete prokaryotic genomes—chromosomal and plasmid DNA—available in RefSeq for coding sequences ranging between 10 and 80 amino acids. The identified peptides are classified as (i) previously identified in RefSeq, (ii) entity-overlapping (intragenic) or intergenic, and (iii) potential pseudogenes—intergenic sequences corresponding to a portion of a previously annotated larger gene. Additional information is related to homologs within order, predicted signal sequence, transmembrane segments, disulfide bonds, secondary structure, and the existence of a related 3D structure in the Protein Databank. As a result, BactPepDB provides insights about candidate peptides, and provides information about their conservation, together with some of their expected biological/structural features. The BactPepDB interface allows to search for candidate peptides in the database, or to search for peptides similar to a query, according to the multiple properties predicted or related to genomic localization.Database URL: http://www.yeastgenome.org/

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

“…Firstly, RiPP “gene clusters” can be as small as two genes: a precursor peptide and a tailoring protein, especially when further hydrolytic processing can be carried out by endogenous peptidases [ 120 ]. The prevalence of putative small peptides encoded throughout genomes [ 160 ] make it difficult to predict which of these are post-translationally processed, and some small genes are overlooked by automated gene annotation software, which means that some putative RiPP precursors are not even listed in databases. Furthermore, novel classes are difficult to identify precisely due to their novelty compared to known pathways.…”

PEP-FOLD3: fasterde novostructure prediction for linear peptides in solution and in complex

“…Owing to the progress of sequencing techniques, an increasing number of peptide sequences, validated or hypothetical is available. Over 1 800 000 candidate sequences are identified among all prokaryotes ( 2 ), and several millions of new sequences are expected from venom analyses ( 3 ), but their structures remain largely unknown. The rational design of peptides at protein/protein ( 4 – 6 ) and protein/membrane ( 7 ) interfaces is also raising interest ( 8 , 9 ).…”

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

“…Pseudogenes are also a problem in metagenome functional annotation, and they could represent up to 35% in prokaryotic genomes (Liu et al, 2004 ). To address this annotation challenge, there are databases like BactPepDB (Rey et al, 2014 ) and Pseudogene.org for short sequences and pseudogenes of prokaryotic and eukaryotic organisms (Karro et al, 2007 ). A search in such databases before further analysis could be useful to discard non-coding sequences.…”