dbAPIS: a database of anti-prokaryotic immune system genes

Authors

• Yuchen Yan, University of Nebraska - LincolnFollow
• Jinfang Zheng, Zhejiang Lab
• Xinpeng Zhang, University of Nebraska - LincolnFollow
• Yanbin Yin, University of Nebraska – LincolnFollow

Document Type

Article

Date of this Version

10-10-2023

Citation

Nucleic Acids Research , 2024, 52 , D419–D425 https://doi.org/10.1093/nar/gkad932

Comments

Open access.

Abstract

Anti-prokaryotic immune system (APIS) proteins, typically encoded b y phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, to xin-antito xin, CRISPR-Cas). A growing number of APIS genes have been characterized and dispersed in the literature. Here we developed dbAPIS ( https:// bcb.unl.edu/ dbAPIS ), as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include: (i) experimentally verified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted structures, genomic context, sequence and structural homologs from different microbiome / virome databases; (ii) classification of APIS proteins into sequence-based families and construction of hidden Markov models (HMMs); (iii) user-friendly web interface for data browsing by the inhibited immune system types or by the hosts, and functions for searching and batch downloading of pre-computed data; (iv) Inclusion of all types of APIS proteins (except f or anti-CRISPRs) that inhibit a variety of prokaryotic defense systems (e.g. RM, TA, CB A SS , Thoeris, Gabija). The current release of dbAPIS contains 41 verified APIS proteins and ∼4400 sequence homologs of 92 families and 38 clans. dbAPIS will facilitate the discovery of novel anti-defense genes and genomic islands in phages, by providing a user-friendly data repository and a web resource for an easy homology search against known APIS proteins.