Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
Zhejiang Lab, Hangzhou, Zhejiang 311121, China.
Nucleic Acids Res. 2024 Jan 5;52(D1):D419-D425. doi: 10.1093/nar/gkad932.
Anti-prokaryotic immune system (APIS) proteins, typically encoded by phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, toxin-antitoxin, 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 for anti-CRISPRs) that inhibit a variety of prokaryotic defense systems (e.g. RM, TA, CBASS, 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.
抗原核免疫系统 (APIS) 蛋白通常由噬菌体、前噬菌体和质粒编码，可抑制原核免疫系统（如限制修饰、毒素-抗毒素、CRISPR-Cas）。越来越多的 APIS 基因已在文献中得到描述和分散。在这里，我们开发了 dbAPIS（https://bcb.unl.edu/dbAPIS），这是第一个针对经实验验证的 APIS 基因及其相关蛋白家族的文献 curated 数据存储库。dbAPIS 的主要特点包括：(i) 具有蛋白质序列、功能注释、PDB 或 AlphaFold 预测结构、基因组上下文、来自不同微生物组/病毒组数据库的序列和结构同源物的经实验验证的 APIS 基因；(ii) 将 APIS 蛋白分类为基于序列的家族，并构建隐马尔可夫模型 (HMM)；(iii) 用户友好的网络界面，可按抑制的免疫系统类型或宿主浏览数据，以及搜索和批量下载预计算数据的功能；(iv) 包含抑制各种原核防御系统（如 RM、TA、CBASS、Thoeris、Gabija）的所有类型的 APIS 蛋白（抗 CRISPRs 除外）。dbAPIS 当前版本包含 41 种已验证的 APIS 蛋白和 92 个家族和 38 个族的约 4400 个序列同源物。dbAPIS 将通过提供用户友好的数据存储库和易于针对已知 APIS 蛋白进行同源搜索的网络资源，促进噬菌体中新型抗防御基因和基因组岛的发现。
