Table 2.

Overview of databases and tools for microbial effectors

Microbial effector		Name	Description	Source
Virulence factors	Database	VFDB	- Virulence factors of bacterial pathogens	[12]
	Tool	PATHOFact	- Prediction of AMR genes, virulence factors, toxins, and BGCs	[13]
		MetaVF	- Identification of pathobiont-carried VFGs at the species level	[14]
Toxins	Database	Toxinome	- Bacterial protein toxin	[15]
		TADB	- Bacterial types I to VIII toxin-antitoxin loci	[16]
	Tool	PathoFact	- Prediction of AMR genes, virulence factors, toxins and BGCs	[13]
Antimicrobials	Database	AntibioticDB	- Antibacterial compounds (incl. discontinued agents and drugs under pre-clinical development or in clinical trials)	[17]
		DrugBank	- Drugs, drug targets, and related pharmaceutical information	[18]
		PubChem	- Chemical information on e.g., small molecules, siRNA, miRNA, lipids or carbohydrates	[19]
		ChEMBL	- Bioactive molecules with drug-like properties	[20]
		CARD	- Antibiotic resistance ontologies with curated AMR gene sequences and resistance-conferring mutations	[21]
	Tool	antiSMASH	- Detecting and characterizing biosynthetic gene clusters (BGCs)	[22]
		ResFinder	- Identification of AMR genes in NGS-data	[23]
Antimicrobial/non-ribosomal peptides	Database	CAMPR4	- Natural and synthetic AMPs	[24]
		dbAMP	- Annotations on AMPs (incl. sequence information, functional activity data, or physicochemical properties)	[25]
		DBAASP	- Sequences, chemical modifications, structures, bioactivities and toxicities of AMPs	[26]
		DRAMP	- Antimicrobial, antifungal, antiviral, anticancer, antitumor, antiprotozoal, and insecticidal peptides	[27]
	Tool	Macrel	- Prediction of AMP sequences from genomes and metagenomes	[28]
		SPEQ	- Identification of high-quality, not identified LC–MS spectra	[29]
		Ensemble-AMPPred	- AMP prediction and recognition from sequence data	[30]
		Deep-AmPEP30	- Prediction of short-length (≤ 30 aa) AMP	[31]
		SBSPKSv3	- Prediction of macrocyclized structures of non-ribosomal peptide synthetase and polyketide synthase	[32]
		NRPminer	- NRP discovery from (meta)genomic and mass spectrometry datasets	[33]
		BiG-MEx	- Identification of BGC protein domains and assessment of diversity and novelty	[34]
		BiG-SCAPE	- Analysis of sequence similarity networks of biosynthetic gene clusters and gene cluster families	[35]
		NaPDos	- Assessment of secondary metabolite biosynthetic gene diversity and novelty of in organisms and environments	[36]
Bacteriophages/Archeophages	Database	PhageDive	- Experimental data (e.g., host range) and metadata (e.g., geographical origin) on bacteriophages	[37]
		Gut Phage Database (GPD)	- Non-redundant viral genomes obtained by mining human gut metagenomes and reference genomes of cultured gut bacteria	[38]
		Microbe Versus Phage (MVP)	- Phage–microbe interactions	[39]
		PhagesDB	- Interactive website for discovery, characterization, and genomics of viruses that infect Actinobacteria	[40]
		PhaLP	- Phage lytic proteins	[41]
	Tool	phageAI	- Lifecycle prediction tasks based on bacteriophage nucleotide sequences	[42]
		What the Phage	- Identification and analysis of phage sequences	[43]
		PHASTEST	- Identification, interactive visualization, and annotation of prophage sequences within bacterial genomes or plasmids	[44]
		PEPGM	- Taxonomic inference of viral proteome samples	[45]
		VirHostMatcher	- Prediction of virus-prokaryote interactions	[46]