Table 2. Intact and incomplete phages predicted in L. lactis subsp. lactis NCDO 2118.

Phages	Genes	Proteins
Region 1 –Intact phage	rusA e arsC1	Integrase, Prophage, Phage antirepressor, Transcriptional regulator, Recombinase, Endodeoxyribonuclease, Aminotransferase, Phage terminase small subunit, Peptidase, Bacteriophage lysine, Arsenate reductase
Region 2 –Intact phage	amtB, kinA, llra, rpmE2, arsC3, carA, pyrB, pyrP	Ammonium transporter, Sensor protein kinase, Two-component system regulator, 50S ribosomal protein L31 type B, Universal stress protein, Arsenate reductase, Bacteriophage lysine, Phage tail protein, Head-tail joining protein, Capsid protein, Phage ATP-dependent endopeptidase, Phage terminase small subunit, Endonuclease, Terminase, Replisome organizer, BRO-like protein, DNA binding protein, Phage integrase, Carbamoyl-phosphate synthase small chain, Aspartate carbamoyltransferase, Uracil transporter
Region 3 –Intact phage	pepT, ppaC, pflA, ysiA, ysiB	Amino Acid permease, Peptidase T, Manganese-dependent inorganic pyrophosphatase, Pyruvate-formate lyase activating enzyme, Permease, Phage protein, Integrase
Region 4 –Incomplete phage	ardA, ecfA1, ecfA2, ecfT, dapH, yciA	Peptidoglycan hydrolase, Antirestriction protein, Integrase, ATPase, Energy-coupling factor transporter, Thiol-disulfide isomerase, N-acetyldiaminopimelate deacetylase
Region 5 –Incomplete phage	glnA	Integrase, Bacteriocin, DNA primase, Glutamine synthetase

Phage locations were predicted using the software PHAST.