CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Prophage number
CP025800	Yersinia ruckeri strain SC09 chromosome, complete genome	0 crisprs	DEDDh,c2c9_V-U4,cas3,csa3,DinG	5
CP025802	Yersinia ruckeri strain SC09 plasmid pLT, complete sequence	0 crisprs	NA	0
CP025801	Yersinia ruckeri strain SC09 plasmid pWKY, complete sequence	0 crisprs	NA	0

Results visualization

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CRISPR-Cas detection and classification

Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1621877 : 1657446

Prochlorococcus_phage(25.0%)

tail,plate,tRNA

The bacterium proteins that are colored denote the protein is present at specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin' and 'tRNA')

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AUQ41778.1\|1621877_1622825_-\|tRNA	methionyl-tRNA formyltransferase	E3SNR5	Prochlorococcus_phage	1.9e-06	35.0
AUQ41779.1\|1622849_1623362_-	peptide deformylase	NA	NA	NA	NA
AUQ41780.1\|1623494_1624616_+	DNA-protecting protein DprA	NA	NA	NA	NA
AUQ41781.1\|1624587_1625061_+	DUF494 domain-containing protein	NA	NA	NA	NA
AUQ43682.1\|1625102_1625639_+	hypothetical protein	NA	NA	NA	NA
AUQ41782.1\|1625645_1626215_+	L-threonylcarbamoyladenylate synthase type 1 TsaC	S4VW33	Pandoravirus	5.4e-09	30.4
AUQ41783.1\|1626224_1627046_+	shikimate dehydrogenase	NA	NA	NA	NA
AUQ41784.1\|1627122_1627665_-	gamma carbonic anhydrase family protein	NA	NA	NA	NA
AUQ41785.1\|1634582_1635512_+	homoserine O-succinyltransferase	NA	NA	NA	NA
AUQ41786.1\|1635896_1637495_+	malate synthase A	NA	NA	NA	NA
AUQ41787.1\|1637525_1638833_+	isocitrate lyase	NA	NA	NA	NA
AUQ41788.1\|1638909_1640637_+	bifunctional isocitrate dehydrogenase kinase/phosphatase	NA	NA	NA	NA
AUQ41789.1\|1640904_1641744_-	acetate operon transcriptional repressor IclR	NA	NA	NA	NA
AUQ41790.1\|1641992_1645673_+	methionine synthase	A0A140XBC7	Dickeya_phage	1.8e-25	84.1
AUQ41791.1\|1645851_1646241_+	hypothetical protein	NA	NA	NA	NA
AUQ41792.1\|1646378_1647503_-	hypothetical protein	NA	NA	NA	NA
AUQ41793.1\|1647817_1648630_-	LysR family transcriptional regulator	NA	NA	NA	NA
AUQ41794.1\|1648616_1648865_-	hypothetical protein	A0A0U2RK18	Escherichia_phage	1.1e-09	61.0
AUQ43683.1\|1649780_1650230_+\|tail	phage tail protein	NA	NA	NA	NA
AUQ41795.1\|1650267_1651338_+\|tail	phage tail sheath family protein	NA	NA	NA	NA
AUQ41796.1\|1651361_1652762_+\|tail	phage tail sheath family protein	NA	NA	NA	NA
AUQ41797.1\|1652829_1654059_+\|tail	phage tail sheath family protein	NA	NA	NA	NA
AUQ41798.1\|1654074_1654533_+\|tail	phage tail protein	NA	NA	NA	NA
AUQ41799.1\|1654529_1654712_+	hypothetical protein	NA	NA	NA	NA
AUQ41800.1\|1654708_1655401_+	hypothetical protein	NA	NA	NA	NA
AUQ41801.1\|1655397_1657014_+	hypothetical protein	NA	NA	NA	NA
AUQ41802.1\|1657023_1657446_+\|plate	phage baseplate protein	NA	NA	NA	NA

DBSCAN-SWA_2

2592315 : 2638098

Salmonella_phage(32.56%)

tail,head,holin,portal,protease,terminase,capsid,plate

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AUQ42535.1\|2592315_2593461_-	D-alanyl-D-alanine- carboxypeptidase/endopeptidase AmpH	A0A2H4JAN9	uncultured_Caudovirales_phage	5.6e-05	26.8
AUQ42536.1\|2593865_2594858_+	MBL fold metallo-hydrolase	NA	NA	NA	NA
AUQ42537.1\|2594967_2595210_-	DinI family protein	K7PKR6	Enterobacteria_phage	1.2e-23	69.7
AUQ42538.1\|2595706_2595910_-	DUF1883 domain-containing protein	NA	NA	NA	NA
AUQ42539.1\|2596398_2597577_-	recombinase	A0A2D1GN00	Marinobacter_phage	3.2e-32	30.4
AUQ42540.1\|2597580_2597799_-	hypothetical protein	NA	NA	NA	NA
AUQ42541.1\|2597856_2598426_-	3'-5' exoribonuclease	A0A192Y6E0	Salmonella_phage	1.7e-66	67.2
AUQ42542.1\|2598426_2598609_-	hypothetical protein	NA	NA	NA	NA
AUQ42543.1\|2598605_2599142_-	hypothetical protein	A5LH62	Enterobacteria_phage	1.6e-55	60.8
AUQ42544.1\|2599226_2600054_-	DUF2303 domain-containing protein	A0A0P0ZBZ4	Stx2-converting_phage	2.0e-89	60.0
AUQ42545.1\|2600112_2600487_-	hypothetical protein	Q8HAA1	Salmonella_phage	6.8e-45	73.9
AUQ42546.1\|2600771_2601005_+	hypothetical protein	NA	NA	NA	NA
AUQ42547.1\|2601001_2601262_-	hypothetical protein	NA	NA	NA	NA
AUQ42548.1\|2601457_2602090_-	LexA family transcriptional repressor	K7PLZ5	Enterobacterial_phage	1.4e-42	44.9
AUQ42549.1\|2602189_2602390_+	cell division protein	NA	NA	NA	NA
AUQ42550.1\|2602427_2602964_+	DNA-binding protein	NA	NA	NA	NA
AUQ42551.1\|2602960_2603143_+	hypothetical protein	NA	NA	NA	NA
AUQ42552.1\|2603144_2603324_+	DUF4222 domain-containing protein	NA	NA	NA	NA
AUQ42553.1\|2603320_2604340_+	helix-turn-helix domain-containing protein	U5P0A0	Shigella_phage	9.6e-33	73.1
AUQ42554.1\|2604336_2605056_+	phage N-6-adenine-methyltransferase	K7PGU4	Enterobacteria_phage	4.3e-88	70.3
AUQ42555.1\|2605046_2605424_+	RusA family crossover junction endodeoxyribonuclease	A0A1C9IIA0	Salmonella_phage	6.7e-40	65.3
AUQ42556.1\|2605517_2606216_+	phage regulatory protein/antirepressor Ant	A0A1P8DTE1	Proteus_phage	8.8e-54	54.6
AUQ42557.1\|2606305_2607127_+	DNA-binding protein	Q8HA92	Salmonella_phage	2.1e-91	61.7
AUQ42558.1\|2607123_2608125_+	DUF968 domain-containing protein	A0A1C9IHZ5	Salmonella_phage	1.1e-89	47.9
AUQ42559.1\|2608182_2609001_+	antitermination protein	A0A286N2Q2	Klebsiella_phage	2.0e-57	43.9
AUQ42560.1\|2609368_2610457_+	site-specific DNA-methyltransferase	A0A0N7KZF8	Stx2-converting_phage	1.6e-131	63.4
AUQ42561.1\|2610735_2611614_+	alpha/beta hydrolase	NA	NA	NA	NA
AUQ42562.1\|2611862_2612420_+	hypothetical protein	NA	NA	NA	NA
AUQ43733.1\|2612633_2612978_+\|holin	phage holin, lambda family	Q8HA87	Salmonella_phage	5.9e-27	61.0
AUQ42563.1\|2612981_2613605_+	endolysin	Q8HA86	Salmonella_phage	6.6e-69	64.7
AUQ42564.1\|2613601_2613946_+	DUF2570 domain-containing protein	NA	NA	NA	NA
AUQ42565.1\|2613920_2614148_+	hypothetical protein	NA	NA	NA	NA
AUQ42566.1\|2614531_2615056_+	hypothetical protein	G8C7W4	Escherichia_phage	2.4e-48	54.6
AUQ42567.1\|2615177_2615528_+	HNH endonuclease	A0A1W6JP27	Morganella_phage	1.9e-44	68.1
AUQ42568.1\|2615663_2616119_+\|terminase	phage terminase small subunit P27 family	A0A1J0GV10	Halomonas_phage	2.1e-24	52.9
AUQ42569.1\|2616121_2617852_+\|terminase	terminase large subunit	A0A1J0GUY5	Halomonas_phage	9.1e-209	58.9
AUQ42570.1\|2617999_2619229_+\|portal	phage portal protein	A0A1W6JP33	Morganella_phage	4.8e-196	82.2
AUQ42571.1\|2619221_2619821_+\|head,protease	HK97 family phage prohead protease	Q8SBH9	Shigella_phage	9.2e-84	76.5
AUQ43734.1\|2619839_2621066_+\|capsid	phage major capsid protein	Q8SBH8	Shigella_phage	1.5e-152	66.3
AUQ43735.1\|2621149_2621467_+\|head,tail	phage gp6-like head-tail connector protein	S5FKK6	Shigella_phage	6.4e-28	59.4
AUQ42572.1\|2621463_2621856_+\|head,tail	head-tail adaptor protein	NA	NA	NA	NA
AUQ42573.1\|2621855_2622374_+	hypothetical protein	Q8HAC8	Salmonella_phage	2.2e-49	56.8
AUQ42574.1\|2622370_2622943_+	hypothetical protein	M1FQV7	Enterobacteria_phage	1.8e-57	56.3
AUQ42575.1\|2622949_2623156_+	DUF2635 domain-containing protein	Q8SBH3	Shigella_phage	3.9e-10	71.4
AUQ42576.1\|2623152_2624652_+\|tail	phage tail protein	A0A192Y7L1	Salmonella_phage	3.3e-183	68.5
AUQ42577.1\|2624652_2625009_+\|tail	phage tail protein	U5P076	Shigella_phage	9.1e-55	85.6
AUQ42578.1\|2625005_2625278_+\|tail	phage tail assembly protein	Q8W621	Enterobacteria_phage	2.8e-16	48.9
AUQ42579.1\|2625410_2627291_+\|tail	phage tail tape measure protein	Q8HAC2	Salmonella_phage	5.3e-170	52.5
AUQ42580.1\|2627303_2627792_+	hypothetical protein	NA	NA	NA	NA
AUQ42581.1\|2627851_2629156_+	DNA circularization protein	S5FUX4	Shigella_phage	1.4e-129	54.3
AUQ42582.1\|2629152_2630226_+\|plate	baseplate protein	U5P0H6	Shigella_phage	1.9e-132	65.2
AUQ42583.1\|2630225_2630792_+\|plate	phage baseplate assembly protein V	A0A192Y8K5	Salmonella_phage	2.2e-31	46.4
AUQ42584.1\|2630795_2631209_+	hypothetical protein	Q8HAB8	Salmonella_phage	6.0e-42	58.4
AUQ42585.1\|2631201_2632260_+\|plate	phage baseplate protein	U5P424	Shigella_phage	6.3e-128	61.6
AUQ42586.1\|2632250_2632832_+	DUF2313 domain-containing protein	O22003	Shigella_phage	9.2e-73	65.8
AUQ43736.1\|2633039_2633816_+	hypothetical protein	A0A0M3ULD8	Salmonella_phage	2.1e-40	44.2
AUQ42587.1\|2633819_2634167_+\|tail	phage tail protein	A0A0M4S6V4	Salmonella_phage	3.1e-15	36.8
AUQ42588.1\|2634204_2634426_-\|tail	phage tail protein	G4KKN7	Yersinia_phage	2.0e-07	41.1
AUQ42589.1\|2634424_2634655_+	hypothetical protein	NA	NA	NA	NA
AUQ42590.1\|2634861_2636655_-	DUF3413 domain-containing protein	NA	NA	NA	NA
AUQ42591.1\|2636682_2636910_-	hypothetical protein	NA	NA	NA	NA
AUQ42592.1\|2637087_2638098_+	nucleoid-associated protein YejK	A0A1V0E8C0	Vibrio_phage	5.7e-86	47.7

DBSCAN-SWA_3

2847980 : 2885725

Erwinia_phage(47.06%)

tail,integrase,head,portal,capsid,plate

attL 2846355:2846371|attR 2895821:2895837

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
2846355:2846371	attL	NA	NA	NA	NA
AUQ42777.1\|2847980_2848199_-\|integrase	integrase	B6SD78	Bacteriophage	3.2e-26	69.4
AUQ42778.1\|2848774_2849530_+	3-oxoacyl-ACP reductase	NA	NA	NA	NA
AUQ42779.1\|2849964_2850189_-	DUF2594 domain-containing protein	NA	NA	NA	NA
AUQ42780.1\|2850922_2851579_+	two-component system response regulator UvrY	NA	NA	NA	NA
AUQ42781.1\|2851550_2853404_+	excinuclease ABC subunit UvrC	NA	NA	NA	NA
AUQ42782.1\|2853462_2854011_+	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	NA	NA	NA	NA
AUQ42783.1\|2854706_2854922_-	transcriptional regulator	Q37973	Salmonella_virus	9.7e-20	62.5
AUQ42784.1\|2855013_2856180_-	hypothetical protein	A0A218M4J7	Erwinia_phage	3.7e-137	64.8
AUQ42785.1\|2856176_2856662_-\|tail	phage tail protein	F1BUT6	Erwinia_phage	2.3e-48	62.9
AUQ42786.1\|2856673_2859127_-\|tail	phage tail tape measure protein	Q7Y4C8	Escherichia_virus	4.7e-134	38.9
AUQ42787.1\|2859119_2859242_-\|tail	GpE family phage tail protein	Q858U8	Yersinia_virus	2.8e-08	72.2
AUQ42788.1\|2859268_2859565_-\|tail	phage tail assembly protein	F1BUU0	Erwinia_phage	5.6e-26	62.6
AUQ42789.1\|2859620_2860136_-\|tail	phage major tail tube protein	A0A218M4J0	Erwinia_phage	1.5e-63	71.9
AUQ42790.1\|2860150_2861320_-\|tail	phage tail protein	F1BUU3	Erwinia_phage	2.0e-183	79.9
AUQ42791.1\|2861447_2862116_-\|tail	phage tail protein	Q9MCR5	Enterobacteria_phage	4.8e-33	51.6
AUQ42792.1\|2862115_2863498_-\|tail	phage tail protein	M1TAS6	Escherichia_phage	4.3e-100	45.6
AUQ42793.1\|2863487_2864105_-\|tail	phage tail protein I	F1BUP2	Erwinia_phage	3.6e-83	72.3
AUQ42794.1\|2864097_2865006_-\|plate	baseplate assembly protein	A0A1J0I2M3	Salmonella_phage	4.1e-120	75.2
AUQ42795.1\|2865010_2865361_-\|plate	baseplate assembly protein	F1BUP4	Erwinia_phage	8.4e-37	65.5
AUQ42796.1\|2865357_2865996_-\|plate	phage baseplate assembly protein V	A0A0M4S6F6	Salmonella_phage	1.1e-58	56.1
AUQ42797.1\|2866150_2866894_+	rod shape-determining protein MreC	NA	NA	NA	NA
AUQ42798.1\|2866894_2867437_+	ImmA/IrrE family metallo-endopeptidase	Q854W5	Mycobacterium_virus	3.6e-10	34.2
AUQ43743.1\|2867442_2868474_+	beta family protein	NA	NA	NA	NA
AUQ42799.1\|2868459_2869083_-	protein cII	NA	NA	NA	NA
AUQ42800.1\|2869169_2869634_-	phage virion morphogenesis protein	O80313	Escherichia_phage	5.7e-49	69.4
AUQ42801.1\|2869630_2870095_-\|tail	phage tail protein	F1BUP9	Erwinia_phage	2.6e-54	67.8
AUQ42802.1\|2870190_2870607_-	LysB family transcriptional regulator	F1BUQ1	Erwinia_phage	7.9e-26	48.9
AUQ42803.1\|2870608_2871115_-	lysozyme	A0A218M4K3	Erwinia_phage	1.1e-56	64.3
AUQ42804.1\|2871098_2871308_-	hypothetical protein	A0A218M4L5	Erwinia_phage	1.5e-09	47.8
AUQ42805.1\|2871310_2871514_-\|tail	phage tail protein	Q858W3	Yersinia_virus	2.4e-20	68.7
AUQ43744.1\|2871513_2871987_-\|head	head completion/stabilization protein	F1BUQ6	Erwinia_phage	3.0e-45	56.7
AUQ42806.1\|2872078_2872732_-	hypothetical protein	F1BUQ7	Erwinia_phage	1.3e-70	66.7
AUQ42807.1\|2872735_2873938_-\|capsid	phage major capsid protein, P2 family	F1BUQ8	Erwinia_phage	2.4e-152	76.1
AUQ42808.1\|2874000_2874855_-\|capsid	phage capsid protein	Q01088	Escherichia_phage	5.1e-88	58.9
AUQ42809.1\|2875009_2876773_+	oxidoreductase	F1BUR2	Erwinia_phage	8.8e-292	82.7
AUQ42810.1\|2876772_2877810_+\|portal	phage portal protein	F1BUR7	Erwinia_phage	3.1e-156	75.4
AUQ42811.1\|2878215_2878410_-	hypothetical protein	NA	NA	NA	NA
AUQ42812.1\|2878558_2878909_-	hypothetical protein	Q858C6	Salmonella_phage	2.4e-15	42.6
AUQ42813.1\|2878901_2881211_-	replication endonuclease	A0A0F7LBQ2	Escherichia_phage	3.9e-239	56.6
AUQ42814.1\|2881197_2881446_-	DUF2732 domain-containing protein	NA	NA	NA	NA
AUQ42815.1\|2881511_2881823_-	hypothetical protein	NA	NA	NA	NA
AUQ42816.1\|2881834_2882020_-	hypothetical protein	NA	NA	NA	NA
AUQ42817.1\|2882029_2882539_-	hypothetical protein	E5G6L3	Salmonella_phage	7.1e-45	53.0
AUQ42818.1\|2882593_2882791_-	DNA-binding protein	Q1I116	Pasteurella_virus	2.8e-05	39.3
AUQ42819.1\|2882861_2883473_+	Cro/Cl family transcriptional regulator	Q6K1G0	Salmonella_virus	3.4e-25	37.9
AUQ42820.1\|2883513_2884398_+	NAD-dependent DNA ligase	NA	NA	NA	NA
AUQ42821.1\|2884696_2885725_+\|integrase	integrase	Q1I119	Pasteurella_virus	5.4e-116	62.1
2895821:2895837	attR	NA	NA	NA	NA

DBSCAN-SWA_4

3045017 : 3056760

Tupanvirus(22.22%)

plate,tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AUQ42962.1\|3045017_3046946_+\|tRNA	threonine--tRNA ligase	A0A2K9L297	Tupanvirus	1.0e-128	37.2
AUQ42963.1\|3046949_3047501_+	translation initiation factor IF-3	A0A2L0UZ54	Agrobacterium_phage	2.6e-16	33.7
AUQ42964.1\|3047599_3047797_+	50S ribosomal protein L35	NA	NA	NA	NA
AUQ42965.1\|3047834_3048191_+	50S ribosomal protein L20	NA	NA	NA	NA
AUQ42966.1\|3048671_3049655_+\|tRNA	phenylalanine--tRNA ligase subunit alpha	A0A2K9L3A8	Tupanvirus	1.2e-35	39.0
AUQ42967.1\|3049669_3052057_+\|tRNA	phenylalanine--tRNA ligase subunit beta	A0A1L3IZU3	BeAn_58058_virus	5.1e-08	27.8
AUQ42968.1\|3052061_3052358_+	integration host factor subunit alpha	A0A0H3UZA0	Geobacillus_virus	4.2e-13	40.0
AUQ42969.1\|3052571_3052868_-	TM2 domain-containing protein	M4ZS56	Bacillus_phage	6.2e-17	70.3
AUQ42970.1\|3053994_3054654_-\|plate	phage baseplate assembly protein V	A0A0F7LDY9	Escherichia_phage	2.5e-42	47.2
AUQ42971.1\|3054767_3055355_-	cell filamentation protein Fic	NA	NA	NA	NA
AUQ43755.1\|3055351_3055540_-	hypothetical protein	NA	NA	NA	NA
AUQ42972.1\|3055633_3056251_-	phage virion morphogenesis protein	A0A0A7NV60	Enterobacteria_phage	3.0e-37	42.5
AUQ42973.1\|3056472_3056760_+	tyrosine recombinase XerS	A0A0F7LBR0	Escherichia_phage	2.6e-28	62.0

DBSCAN-SWA_5

3665072 : 3674625

Brazilian_cedratvirus(16.67%)

protease,tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AUQ43467.1\|3665072_3666797_+	thiol reductant ABC exporter subunit CydC	A0A2R8FG22	Brazilian_cedratvirus	2.0e-14	29.5
AUQ43468.1\|3666896_3667607_+\|tRNA	leucyl/phenylalanyl-tRNA--protein transferase	NA	NA	NA	NA
AUQ43469.1\|3667770_3667989_+	translation initiation factor IF-1	NA	NA	NA	NA
AUQ43470.1\|3668243_3670520_-\|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	A0A223W0B1	Agrobacterium_phage	4.3e-166	42.3
AUQ43471.1\|3670547_3670868_-\|protease	ATP-dependent Clp protease adapter ClpS	A0A1B1IT64	uncultured_Mediterranean_phage	1.8e-14	42.7
AUQ43472.1\|3671227_3671449_+	cold shock domain protein CspD	A0A2H4N7Y6	Lake_Baikal_phage	4.6e-17	59.7
AUQ43473.1\|3671560_3673510_-	macrolide ABC transporter ATP-binding protein/permease MacB	G9BWD6	Planktothrix_phage	7.2e-37	39.3
AUQ43474.1\|3673509_3674625_-	macrolide transporter subunit MacA	A0A140XAI1	Dickeya_phage	1.9e-10	39.8

Anti-CRISPR protein detection

Acr ID	Acr position	Acr size	Homology with known anti	Neighbor HTH/AcRanker	Neighbor Aca	In prophage	Protospacer in prophage