dbAPIS: a database of anti-prokaryotic immune systems

dbAPIS serves as a comprehensive data repository for experimentally validated viral anti-prokaryotic immune system (APIS) proteins and their associated protein families. APIS proteins, typically encoded by phages, prophages, and other mobile genetic elements like plasmids, play a key role in inhibiting prokaryotic immune or defense mechanisms. Notably, our database does not include anti-CRISPR proteins due to their extensive coverage in existing databases such as Anti-CRISPRdb, AcrDB , CRISPRminer, AcrCatalog , etc.

1. Experimentally verified APIS genes are manually curated from literature, with their protein sequences, protein families, functional description, PDB or AlphaFold predicted structures, genomic context, metadata, sequence and structural homologs (Foldseek against AlphaFoldDB and ESMAtlas) in various phage and microbiome/virome databases.

2. APIS proteins are classified into sequence-based protein families and construction of hidden Markov models (HMMs), and a job submission page is provided to allow automated annotation of phage/prophage/plasmid genomes for APIS proteins using HMMER and BLAST against our APIS protein family HMMdb and FASTA sequence database.

3. A user-friendly web interface is provided for easy browsing APIS genes and families by: (i) their inhibited prokaryotic immune or defense system types and (ii) by host taxonomy, and for searching, and batch downloading of pre-computed data.

4. All types of APIS proteins (except for anti-CRISPRs) are included that inhibit a variety of prokaryotic defense systems (e.g., RM, TA, BREX, CBASS, Thoeris, Gabija).

dbAPIS aims to routinely curate literature and collect all experimentally characterized APIS genes, and to facilitate the research in phage anti-prokaryotic immune mechanisms and aid in the discovery of novel APIS proteins by providing a comprehensive web resource.

restriction-modification (RM) (30)	Gabija (13)	pyrimidine cyclase system for antiphage resistance (Pycsar) (11)
toxin-antitoxin (TA) (10)	Thoeris (8)	broad-spectrum counter-defense (7)
bacteriophage exclusion (BREX) (6)	RecBCD (5)	cyclic oligonucleotide-based antiphage signaling system (CBASS) (4)
O-antigen-based barrier (3)	superinfection exclusion (2)	Hachiman (1)
defence-associated sirtuin (DSR) (1)

Enterobacterales (48)	Unknown (29)	Bacillales (8)
Pseudomonadales (3)	Burkholderiales (3)	Bacillales_D (1)
Bacteroidales (1)	Peptostreptococcales (1)	Mycobacteriales (1)

Introduction to dbAPIS

dbAPIS will be updated once a year to include new experimentally validated APIS genes from literature curation.

6/1/2023: first release of dbAPIS with 41 experimentally characterized APIS proteins.