Experimentally validated data were obtained from experimental literatures.
In silico predicted data were identified by BLASTp.

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Natural transformation-associated genes
Category	Experimentally validated	In silico predicted	All
All genes	DNA Protein	DNA Protein	DNA Protein
Machinery genes	DNA Protein	DNA Protein	DNA Protein
Regulatory genes	DNA Protein	DNA Protein	DNA Protein
Auxiliary factors	DNA Protein	DNA Protein	DNA Protein
Genes with unclear function	DNA Protein	DNA Protein	DNA Protein

DNA Uptake Sequences (DUS)/Uptake Signal Sequences (USS)
Known DUS	DNA	Known USS	DNA
Detailed table of predicted DUS in Neisseriaceae	CSV	Detailed table of predicted USS in Pasteurellaceae	CSV

MGEs associate with natural transformation machinery and regulatory genes
MGE-gene association table	CSV	MGE information table	TSV

HMM profiles of natural transformation machinery and regulatory genes
37 curated HMM profiles from Pfam	HMM