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
CP025562	Listeria monocytogenes strain PIR00544 plasmid p1PIR00544, complete sequence	0 crisprs	csa3	0
CP025564	Listeria monocytogenes strain PIR00544 plasmid p3PIR00544, complete sequence	0 crisprs	NA	0
CP025563	Listeria monocytogenes strain PIR00544 plasmid p2PIR00544, complete sequence	0 crisprs	NA	0
CP025565	Listeria monocytogenes strain PIR00544 chromosome, complete genome	0 crisprs	DinG,cas3,WYL,casR,DEDDh,csa3	4

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

130449 : 136976

Listeria_phage(33.33%)

tail

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
AVU85598.1\|130449_130902_-	ImmA/IrrE family metallo-endopeptidase	A0A059T7S0	Listeria_phage	4.0e-31	47.9
AVU85599.1\|130907_131243_-	XRE family transcriptional regulator	A0A2H4JAR9	uncultured_Caudovirales_phage	4.0e-20	52.5
AVU85600.1\|131459_131888_+	hypothetical protein	NA	NA	NA	NA
AVU85601.1\|131899_132316_+	hypothetical protein	A8ASQ1	Listeria_phage	3.2e-19	37.9
AVU85602.1\|132595_132985_+	DUF5072 domain-containing protein	NA	NA	NA	NA
AVU85603.1\|132997_133510_+\|tail	phage major tail protein, TP901-1 family	A0A097PBF4	Streptococcus_pyogenes_phage	1.2e-47	62.7
AVU85604.1\|133557_133860_+	segregation and condensation protein B	NA	NA	NA	NA
AVU85605.1\|133901_134306_+	phenylalanine racemase	NA	NA	NA	NA
AVU85606.1\|134292_136161_+	hypothetical protein	A0A097PAU2	Streptococcus_pyogenes_phage	3.5e-20	45.8
AVU85607.1\|136157_136976_+\|tail	phage tail family protein	A0A060AFE1	Staphylococcus_phage	7.2e-39	35.0

DBSCAN-SWA_2

1831811 : 1840097

Synechococcus_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVU87204.1\|1831811_1832378_-	phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	8.3e-26	36.4
AVU87205.1\|1832374_1833424_-	phosphoribosylformylglycinamidine cyclo-ligase	Q58MH8	Prochlorococcus_phage	3.2e-63	44.4
AVU87206.1\|1833442_1834870_-	amidophosphoribosyltransferase	A0A0M3SGR2	Mollivirus	1.1e-53	34.6
AVU87207.1\|1834854_1837074_-	phosphoribosylformylglycinamidine synthase subunit PurL	A6N228	Microbacterium_phage	6.5e-159	40.8
AVU87208.1\|1837066_1837750_-	phosphoribosylformylglycinamidine synthase subunit PurQ	NA	NA	NA	NA
AVU87209.1\|1837753_1837999_-	phosphoribosylformylglycinamidine synthase subunit PurS	NA	NA	NA	NA
AVU87210.1\|1838010_1838724_-	phosphoribosylaminoimidazolesuccinocarboxamide synthase	A0A0E3F9V5	Synechococcus_phage	6.7e-41	38.3
AVU87211.1\|1838804_1840097_-	adenylosuccinate lyase	A0A1B3B081	Gordonia_phage	2.5e-17	33.0

DBSCAN-SWA_3

2405885 : 2448884

Listeria_phage(93.65%)

capsid,tail,portal,coat,holin,terminase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVU87739.1\|2405885_2406083_-	hypothetical protein	A8ATC6	Listeria_phage	1.7e-15	66.1
AVU87740.1\|2406079_2406313_-	hypothetical protein	A8ATC5	Listeria_phage	1.2e-34	92.2
AVU87741.1\|2406545_2406938_-	hypothetical protein	A8ATC1	Listeria_phage	5.1e-67	100.0
AVU87742.1\|2406934_2407438_-	DUF4065 domain-containing protein	A8ATC0	Listeria_phage	7.0e-93	100.0
AVU87743.1\|2407840_2408767_-	N-acetylmuramoyl-L-alanine amidase	R4ICC5	Listeria_phage	9.9e-170	92.2
AVU87744.1\|2408768_2409002_-	hypothetical protein	R4IBI3	Listeria_phage	1.7e-33	92.2
AVU87745.1\|2408998_2409283_-\|holin	holin	R4IDW2	Listeria_phage	5.7e-44	98.9
AVU87746.1\|2409295_2409661_-	hypothetical protein	A8ASL3	Listeria_phage	1.3e-11	100.0
AVU87747.1\|2409697_2409856_-	hypothetical protein	Q9T1A1	Listeria_phage	7.1e-12	76.9
AVU87748.1\|2409860_2410139_-	hypothetical protein	A8ATB3	Listeria_phage	2.9e-16	55.7
AVU87749.1\|2410135_2411212_-	hypothetical protein	Q9T1A3	Listeria_phage	6.9e-90	75.5
AVU87750.1\|2411208_2412243_-	hypothetical protein	Q9T1A4	Listeria_phage	3.1e-148	77.6
AVU87751.1\|2412243_2413269_-	hypothetical protein	Q9T1A5	Listeria_phage	6.4e-186	90.6
AVU87752.1\|2413277_2414096_-\|tail	phage tail family protein	Q9T1A6	Listeria_phage	9.8e-145	90.8
AVU87753.1\|2414097_2419461_-\|tail	tail tape measure protein	A8ASK6	Listeria_phage	0.0e+00	90.7
AVU87754.1\|2419471_2420074_-	hypothetical protein	A8ASK5	Listeria_phage	3.7e-109	100.0
AVU87755.1\|2420079_2420502_-	hypothetical protein	Q9T1A9	Listeria_phage	5.9e-69	97.9
AVU87756.1\|2420554_2420887_-	Ig-like virion protein	Q9T1B0	Listeria_phage	1.5e-30	70.9
AVU87757.1\|2420816_2421251_-\|tail	phage tail protein	Q9T1B1	Listeria_phage	3.0e-76	97.2
AVU87758.1\|2421253_2421661_-\|capsid	minor capsid protein	A8ASK1	Listeria_phage	2.0e-66	99.3
AVU87759.1\|2421660_2421999_-\|capsid	minor capsid protein	A0A0B5CTV8	Listeria_phage	5.4e-57	95.5
AVU87760.1\|2421998_2422361_-\|capsid	minor capsid protein	A8ASJ9	Listeria_phage	2.1e-59	93.3
AVU87761.1\|2422360_2422756_-	hypothetical protein	A0A059T5E3	Listeria_phage	1.1e-64	96.2
AVU87762.1\|2422774_2423776_-\|coat	coat protein	A0A059T6D4	Listeria_phage	6.3e-186	99.4
AVU87763.1\|2423775_2424366_-	scaffolding protein	A0A059T7N8	Listeria_phage	2.5e-86	100.0
AVU87764.1\|2424444_2425584_-\|capsid	minor capsid protein	A0A059T7W2	Listeria_phage	6.6e-208	99.7
AVU87765.1\|2425589_2427080_-\|portal	portal protein	A0A0B5D0F2	Listeria_phage	2.4e-282	99.0
AVU87766.1\|2427092_2428424_-\|terminase	PBSX family phage terminase large subunit	A8ASJ2	Listeria_phage	4.3e-259	98.2
AVU87767.1\|2428392_2428935_-\|terminase	terminase small subunit	A8ASJ1	Listeria_phage	7.8e-90	97.2
AVU87768.1\|2428974_2429274_-	hypothetical protein	A0A2H4JBC0	uncultured_Caudovirales_phage	3.8e-14	40.7
AVU87769.1\|2429838_2430273_-	hypothetical protein	A8ASQ1	Listeria_phage	9.6e-75	98.6
AVU87770.1\|2430291_2430456_-	hypothetical protein	A8ASQ0	Listeria_phage	2.5e-20	92.6
AVU87771.1\|2430584_2430968_-	hypothetical protein	A8ASP8	Listeria_phage	7.4e-63	96.1
AVU87772.1\|2430971_2431376_-	DUF1064 domain-containing protein	A8ASP7	Listeria_phage	5.4e-64	94.0
AVU87773.1\|2431320_2431512_-	hypothetical protein	A8ASP6	Listeria_phage	2.6e-24	93.7
AVU87774.1\|2431530_2432013_-	single-stranded DNA-binding protein	A8ATZ7	Listeria_phage	2.4e-74	90.0
AVU87775.1\|2432012_2432414_-	hypothetical protein	A8ATZ6	Listeria_phage	1.3e-54	83.5
AVU87776.1\|2432424_2432652_-	DUF3850 domain-containing protein	A0A059T7N3	Listeria_phage	1.9e-34	96.0
AVU87777.1\|2432652_2432838_-	hypothetical protein	NA	NA	NA	NA
AVU87778.1\|2432837_2433128_-	hypothetical protein	Q8W5X0	Listeria_phage	5.0e-43	90.6
AVU87779.1\|2433124_2433310_-	hypothetical protein	A0A059T5G1	Listeria_phage	1.2e-26	98.4
AVU87780.1\|2433306_2433576_-	hypothetical protein	A0A059T7S7	Listeria_phage	5.8e-38	89.5
AVU87781.1\|2433588_2434290_-	hypothetical protein	NA	NA	NA	NA
AVU87782.1\|2434289_2434793_-	hypothetical protein	A0A0B5CYR4	Listeria_phage	9.3e-29	44.8
AVU87783.1\|2434971_2435151_-	hypothetical protein	A0A059T5G0	Listeria_phage	3.5e-23	93.2
AVU87784.1\|2435147_2435777_-	hypothetical protein	A8ATY9	Listeria_phage	7.0e-50	53.1
AVU87785.1\|2435779_2436010_-	hypothetical protein	A0A059T7Z5	Listeria_phage	3.8e-38	96.1
AVU87786.1\|2436006_2437269_-	DNA (cytosine-5-)-methyltransferase	A0A141E1L1	Streptococcus_phage	2.5e-123	55.5
AVU87787.1\|2437265_2438180_-	DnaD domain protein	A0A0B5D175	Listeria_phage	5.2e-139	89.2
AVU87788.1\|2438199_2439015_-	recombinase RecT	A8ATY6	Listeria_phage	1.0e-149	98.5
AVU87789.1\|2439014_2439974_-	hypothetical protein	A8ATY5	Listeria_phage	8.1e-175	98.1
AVU87790.1\|2440206_2440395_-	hypothetical protein	A0A0B5CU43	Listeria_phage	4.5e-29	100.0
AVU87791.1\|2440503_2440719_-	hypothetical protein	Q9T176	Listeria_phage	1.8e-26	90.1
AVU87792.1\|2440715_2441249_-	hypothetical protein	A8ATY1	Listeria_phage	1.8e-78	87.9
AVU87793.1\|2441371_2442148_-	phage antirepressor Ant	A0A0B5D0I2	Listeria_phage	2.7e-136	95.3
AVU87794.1\|2442289_2442754_+	hypothetical protein	A8ATX9	Listeria_phage	1.4e-79	99.4
AVU87795.1\|2442731_2443085_-	hypothetical protein	A8ATX8	Listeria_phage	1.8e-50	93.2
AVU87796.1\|2443081_2443318_-	hypothetical protein	A0A059T5E9	Listeria_phage	4.8e-36	97.4
AVU87797.1\|2443382_2443742_+	DUF2513 domain-containing protein	A0A2H4J4K9	uncultured_Caudovirales_phage	2.1e-06	26.3
AVU87798.1\|2443700_2443895_-	hypothetical protein	A0A059T6E5	Listeria_phage	4.1e-25	95.3
AVU87799.1\|2444118_2444385_-	hypothetical protein	A0A059T7Q1	Listeria_phage	4.7e-40	97.7
AVU87800.1\|2444403_2444688_-	hypothetical protein	A0A0B5D168	Listeria_phage	8.0e-38	83.0
AVU87801.1\|2444707_2444908_-	XRE family transcriptional regulator	NA	NA	NA	NA
AVU87802.1\|2445079_2445565_+	transcriptional regulator	A8ASM2	Listeria_phage	8.0e-38	61.2
AVU87803.1\|2445721_2445889_+	hypothetical protein	NA	NA	NA	NA
AVU87804.1\|2445943_2446594_+	hypothetical protein	NA	NA	NA	NA
AVU87805.1\|2446656_2448015_+	recombinase family protein	Q9T193	Listeria_phage	3.6e-253	97.6
AVU87806.1\|2448005_2448482_+	competence protein ComK	NA	NA	NA	NA
AVU87807.1\|2448536_2448884_-	XRE family transcriptional regulator	A0A0A7RTK4	Clostridium_phage	9.9e-06	40.7

DBSCAN-SWA_4

2606022 : 2613867

Streptococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVU87951.1\|2606022_2606994_-	DNA-binding protein WhiA	Q7AWZ3	Streptococcus_phage	5.2e-52	39.4
AVU87952.1\|2607001_2607970_-	YvcK family protein	A1IMD5	Streptococcus_phage	1.8e-68	43.6
AVU87953.1\|2607971_2608847_-	RNase adaptor protein RapZ	A0A0R8VB27	Thermobifida_phage	1.9e-08	29.7
AVU87954.1\|2608954_2610685_-	phospho-sugar mutase	A0A1X9I671	Streptococcus_phage	7.3e-174	53.3
AVU87955.1\|2610726_2611788_-	galactose-1-epimerase	NA	NA	NA	NA
AVU87956.1\|2611804_2612788_-	UDP-glucose 4-epimerase GalE	A0A2K9L5H6	Tupanvirus	4.0e-52	38.1
AVU87957.1\|2612907_2613867_-	thioredoxin-disulfide reductase	G3MA85	Bacillus_virus	2.0e-88	53.7

Anti-CRISPR protein detection

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