Table 2.

Protospacer identity: origin of protospacer sequences matched against plasmids, phage and prophage

	Spacer	Target species	Organism	Protein target	Protein ID	Nucleotide ID	Nucleotide ID (percentage)
CRISPR1	19	Plasmid	Rhizobium leguminosarum bv. viciae plasmid pRL8	Aminotransferase class V-fold PLP-dependent	WP_011654699.1	25/33	75.76
		Plasmid	Azospirillum brasilense strain Az39 plasmid	Helix–turn–helix domain-containing protein	WP_040134386.1	26/33	78.79
		Plasmid	Arthrobacter sp. ERGS1 : 01 plasmid unnamed2	DUF3416 domain-containing protein	WP_082368864.1	24/33	72.73
		Plasmid	Neorhizobium galegae chromid pHAMBI540a	DUF1211 domain-containing protein	WP_035996019.1	25/33	75.76
	16	Phage	AJ564013_AJ564013 bacteriophage PY54	Immunity repressor Icd	CAD91791.1	28/33	84.85
	10	Plasmid	Escherichia coli strain 08–00022 plasmid pCFSAN004179G	Conjugative transfer relaxase/helicase trai	WP_047088735.1	27/33	81.82
	7	Plasmid	Enterococcus faecium strain E1 plasmid	Glycoside hydrolase family 1 protein	WP_002289584.1	26/33	78.79
		Plasmid	Burkholderia caribensis MBA4 plasmid	DUF1211 domain-containing protein	WP_035996019.1	25/33	75.76
		Plasmid	Enterococcus faecium DO plasmid 3	Beta-glucosidase	YP_006377528.1	26/33	78.79
	5	Plasmid	Cupriavidus metallidurans CH34 megaplasmid	Anion permease	WP_011518338.1	26/33	78.79
	1	Plasmid	Sinorhizobium fredii NGR234 plasmid	Hypothetical protein	NP_443999.1	24/33	72.73
CRISPR2.1	26	Phage*	Klebsiella pneumoniae strain Kp_Goe_149832 plasmid	Phage tail tape measure protein	WP_048292313.1	24/32	75.00
		Plasmid	Shigella boydii CDC 3083–94 plasmid	Type II toxin–antitoxin system	WP_000604847.1	25/32	78.13
		Plasmid	Methylobacterium radiotolerans JCM 2831 plasmid	MFS transporter	WP_012329600.1	24/32	75.00
		Phage	AF226852_AF226852 Pseudomonas phage phi8	P10	AAF63303.1	24/32	75.00
	26	Prophage	Serratia plymuthica 4r×13	Phage tail tape measure protein	WP_041417117.1	28/32	87.50
	25	Phage*	Anoxybacillus amylolyticus strain DSM 15939 plasmid	DNA primase	WP_084256491.1	25/32	78.13
	24	Prophage	Yersinia mollaretii strain IP25089	Baseplate protein	WP_049611672.1	30/32	93.75
	23	Prophage	Serratia marcescens strain 907_SMAR 425_37092_653157	Recombinase	WP_049202623.1	29/32	90.63
	21	Phage	KT898134_KT898134 Aeromonas phage phiARM81mr	Terminase large subunit	ALN97629.1	31/32	96.88
		Plasmid	Synechococcus sp. PCC 7117 plasmid unnamed5	Type I-D CRISPR-associated endonuclease Cas1	WP_065712013.1	26/32	81.25
		Prophage	Aeromonas hydrophila strain Ah-HSP	Terminase	WP_077096195.1	31/32	96.88
		Plasmid	Rhodobacter sphaeroides ATCC 17025 plasmid	Gluconate : proton symporter	WP 011910413.1	25/32	78.13
	18	Phage	EU307292_EU307292 Burkholderia phage Bups phi1	Putative PAPS reductase/sulfotransferase	ABY40518.1	27/32	84.38
		Plasmid	Klebsiella oxytoca strain 2880STDY5682598	Hypothetical protein	WP_064405428.1	29/32	90.63
	17	Plasmid	Shigella flexneri 1 a strain 0228 plasmid	Hypothetical protein	NZ_CP012733.1	26/32	81.25
		Prophage	Cronobacter sakazakii strain 699	Phage protein	WP_007882954.1	30/32	93.75
	16	Phage*	Streptomyces sp. F2 plasmid	Hypothetical protein	YP_008996313.1	26/32	81.25
	12	Phage	KY709687_KY709687 Salmonella phage 29 485	Hypothetical protein	arb10913.1	27/32	84.38
	9	Plasmid	Yersinia pseudotuberculosis IP 32953 plasmid	Type IA DNA topoisomerase	WP_011191426.1	26/32	81.25
	7	Prophage	Serratia marcescens 2880STDY5682985	Hypothetical protein	WP_060433331.1	29/32	90.63
		Prophage	Klebsiella oxytoca strain 2880STDY5682691	Transcriptional regulator	NZ_FKZE01000009	29/32	90.63
		Prophage	Sodalis glossinidius str. morsitans	Hypothetical protein	WP_041867073.1	29/32	90.63
		Plasmid	Sphingomonas sanxanigenens DSM 19645	Hypothetical protein	WP_075153410.1	24/32	75.00
	5	Prophage	Serratia sp. S4	DUF968 domain-containing protein	WP_017892522.1	31/32	96.88
		Phage	JQ182729 JQ182729 Enterobacterial phage mEp390	Hypothetical protein	AFM76141.1	27/32	84.38
		Plasmid	Dinoroseobacter shibae DFL 12 plasmid	FAD-dependent oxidoreductase	WP_012187434.1	24/32	75.00
CRISPR2.2	15	Plasmid	Alteromonas mediterranea strain CP48 plasmid	Single-stranded DNA-binding protein	WP_071960856.1	27/32	84.38
		Plasmid	Kangiella geojedonensis strain YCS-5	Single-stranded DNA-binding protein	WP_046560643.1	29/32	90.63
	13	Phage*	Methylomonas sp. DH-1 plasmid	Atp/GTP-binding protein	NP_639742.1	26/32	81.25
		Prophage	Yersinia aldovae strain IP23238	Phage capsid protein	WP_049687658.1	29/32	90.63
	8	Phage*	Klebsiella pneumoniae strain Kp_Goe_827024 plasmid	Histidine kinase	WP_064023699.1	26/32	81.25
		Prophage	Klebsiella pneumoniae strain CHS159	Tail assembly protein	WP_016530340.1	30/32	93.75
	7	Phage*	Pantoea sp. At-9b plasmid	Hypothetical protein	WP_013511365.1	29/32	90.63
		Prophage	Pantoea sp. At-9b plasmid pPAT9B01	Hypothetical protein	WP_013511365.1	29/32	90.63
	6	Phage*	Streptomyces coelicolor A3(2) plasmid	Atp/GTP-binding protein	NP_639742.1	26/32	81.25
	5	Prophage	Serratia marcescens strain 2880STDY5682949	Phage head protein	WP_060427589.1	29/32	90.63
	4	Plasmid	Microscilla sp. pre1 plasmid	Ms149	NP_116837.1	26/32	81.25
	1	Plasmid	Rahnella sp. J11-6	Noncoding		31/32	96.88

*Denotes that the organism is listed as a plasmid in the NCBI database but is suspected to be a phage due to protein content.