CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
NZ_CP018802	Histophilus somni strain USDA-ARS-USMARC-63250 chromosome, complete genome	0 crisprs	cas14j,cas3,DEDDh,DinG	0	0	4	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

365732 : 419440

Mannheimia_phage(41.38%)

integrase,protease,transposase,terminase,capsid

attL 369881:369898|attR 399390:399407

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
WP_075293630.1\|365732_366977_-\|protease	ATP-dependent protease ATP-binding subunit ClpX	G3M9Z9	Bacillus_virus	6.3e-127	57.0
WP_075293629.1\|366992_367574_-	ATP-dependent Clp endopeptidase proteolytic subunit ClpP	A0A223W000	Agrobacterium_phage	9.0e-60	62.9
WP_075293628.1\|367659_368958_-	trigger factor	NA	NA	NA	NA
WP_075293701.1\|369340_370732_+	type II/IV secretion system protein	NA	NA	NA	NA
369881:369898	attL	NA	NA	NA	NA
WP_012341088.1\|370765_372025_-	HlyC/CorC family transporter	NA	NA	NA	NA
WP_075293627.1\|372094_372892_-	ABC transporter permease	NA	NA	NA	NA
WP_075293626.1\|373041_374418_+	signal recognition particle protein	NA	NA	NA	NA
WP_075293625.1\|374460_376200_-	C4-dicarboxylic acid transporter DauA	A0A2H4J153	uncultured_Caudovirales_phage	5.1e-34	27.9
WP_075293624.1\|376656_377898_+\|integrase	tyrosine-type recombinase/integrase	A0A1V0E8G8	Vibrio_phage	8.8e-89	41.5
WP_011609578.1\|377859_378045_-	AlpA family transcriptional regulator	A0A2H4J8C8	uncultured_Caudovirales_phage	1.7e-09	43.6
WP_075293623.1\|378057_378852_-	hypothetical protein	NA	NA	NA	NA
WP_075293622.1\|378883_380071_-	DNA cytosine methyltransferase	A0A2I7R2G4	Vibrio_phage	1.6e-95	46.5
WP_075293621.1\|380099_380828_-	hypothetical protein	A0A0M3LPL3	Mannheimia_phage	9.0e-17	60.2
WP_087449173.1\|380833_381874_-	hypothetical protein	A0A0M3LPL3	Mannheimia_phage	2.8e-11	68.6
WP_075293619.1\|381923_382592_-	translocation protein TolB precursor	A0A0M3LP90	Mannheimia_phage	6.4e-94	74.0
WP_075293618.1\|382584_383520_-	recombinase	A0A0M3LNU3	Mannheimia_phage	7.0e-131	76.9
WP_011609572.1\|383531_383831_-	hypothetical protein	NA	NA	NA	NA
WP_075293617.1\|383827_384265_-	hypothetical protein	A0A0M3LSK4	Mannheimia_phage	3.6e-05	45.6
WP_075293616.1\|384261_384546_-	hypothetical protein	NA	NA	NA	NA
WP_087437307.1\|384632_385340_-	KilA-N domain-containing protein	K7PH30	Enterobacteria_phage	2.9e-20	46.6
WP_087437242.1\|386320_386743_-	hypothetical protein	NA	NA	NA	NA
WP_075293616.1\|386739_387024_-	hypothetical protein	NA	NA	NA	NA
WP_087449174.1\|387110_387770_-	hypothetical protein	B6SCX2	Bacteriophage	1.0e-27	53.2
WP_075293614.1\|388420_388639_+	hypothetical protein	A0A0M3LQV3	Mannheimia_phage	8.1e-22	79.2
WP_075293613.1\|388662_389685_-	hypothetical protein	NA	NA	NA	NA
WP_075293612.1\|389825_390314_-	hypothetical protein	NA	NA	NA	NA
WP_075293611.1\|390443_390860_-	hypothetical protein	NA	NA	NA	NA
WP_075293610.1\|390856_391036_-	hypothetical protein	NA	NA	NA	NA
WP_075293609.1\|391267_391459_+	hypothetical protein	NA	NA	NA	NA
WP_075293608.1\|391866_392424_-	hypothetical protein	NA	NA	NA	NA
WP_075293607.1\|392435_393380_-	hypothetical protein	NA	NA	NA	NA
WP_011609560.1\|393688_394324_-	LexA family transcriptional repressor	G9L676	Escherichia_phage	7.8e-41	45.6
WP_011609559.1\|394462_394669_+	helix-turn-helix transcriptional regulator	A0A0N7C2U7	Escherichia_phage	4.9e-13	50.0
WP_011609558.1\|394713_395166_+	hypothetical protein	NA	NA	NA	NA
WP_087449175.1\|395208_395457_+	hypothetical protein	A0A0M3LR73	Mannheimia_phage	3.5e-21	72.2
WP_075293605.1\|396241_396934_+	replication protein P	A0A077KCC8	Edwardsiella_phage	1.9e-24	34.6
WP_075293604.1\|396943_397474_+	phage N-6-adenine-methyltransferase	A0A0M3LNW2	Mannheimia_phage	4.8e-68	67.2
WP_075293603.1\|397510_398137_+	DUF1367 family protein	K7PKS6	Enterobacteria_phage	3.1e-18	28.1
WP_075293602.1\|398149_398428_+	hypothetical protein	NA	NA	NA	NA
WP_075293601.1\|398506_399094_+	recombination protein NinG	A0A0M3LTG3	Mannheimia_phage	1.7e-50	55.1
WP_075293600.1\|399083_399488_+	hypothetical protein	NA	NA	NA	NA
399390:399407	attR	NA	NA	NA	NA
WP_075293599.1\|399638_400478_+	KilA-N domain-containing protein	Q4ZC41	Staphylococcus_virus	1.6e-73	52.6
WP_075319826.1\|400746_401163_-\|transposase	IS200/IS605 family transposase	A0A1S5RHE3	Helicobacter_phage	7.4e-48	63.5
WP_075319827.1\|401209_402346_+\|transposase	IS200/IS605 family element transposase accessory protein TnpB	A0A1B0VCD8	Salmonella_phage	2.6e-119	56.4
WP_012341704.1\|402634_402871_+	hypothetical protein	A0A0M3LR95	Mannheimia_phage	2.7e-23	70.5
WP_075294024.1\|402860_403400_+	lysozyme	Q19UR6	Mannheimia_phage	9.9e-45	49.7
WP_075294034.1\|403372_403699_+	DUF2570 domain-containing protein	NA	NA	NA	NA
WP_041604566.1\|403727_403871_+	hypothetical protein	A0A0M3LNX0	Mannheimia_phage	9.9e-13	69.8
WP_075294025.1\|403895_404591_+\|terminase	terminase	NA	NA	NA	NA
WP_011609539.1\|404590_406138_+	hypothetical protein	A0A1B1IVN4	uncultured_Mediterranean_phage	6.4e-97	42.0
WP_075294026.1\|406139_408317_+	hypothetical protein	S4S2T1	Puniceispirillum_phage	3.4e-43	25.9
WP_011609534.1\|416895_417198_+	XRE family transcriptional regulator	NA	NA	NA	NA
WP_011609533.1\|417295_417478_+	hypothetical protein	NA	NA	NA	NA
WP_012341716.1\|417555_418419_+	hypothetical protein	NA	NA	NA	NA
WP_075294028.1\|418444_419440_+\|capsid	N4-gp56 family major capsid protein	NA	NA	NA	NA

DBSCAN-SWA_2

464052 : 521009

Escherichia_phage(16.67%)

protease,integrase,transposase

attL 489494:489510|attR 508040:508056

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_075319814.1\|464052_464469_-\|transposase	IS200/IS605 family transposase	A0A1S5RHE3	Helicobacter_phage	1.5e-48	64.2
WP_075319813.1\|464515_465652_+\|transposase	IS200/IS605 family element transposase accessory protein TnpB	A0A1B0VCD8	Salmonella_phage	5.2e-112	53.7
WP_075293400.1\|465907_466837_+	hypothetical protein	NA	NA	NA	NA
WP_075293401.1\|466855_467302_-	hypothetical protein	NA	NA	NA	NA
WP_075293402.1\|467519_467852_-	hypothetical protein	NA	NA	NA	NA
WP_157665519.1\|468004_468145_-	hypothetical protein	NA	NA	NA	NA
WP_075293403.1\|468221_468869_-	DUF3560 domain-containing protein	NA	NA	NA	NA
WP_075293405.1\|469451_469868_-	hypothetical protein	NA	NA	NA	NA
WP_075293406.1\|469966_470185_-	hypothetical protein	NA	NA	NA	NA
WP_075293407.1\|470308_470773_-	DUF3577 domain-containing protein	NA	NA	NA	NA
WP_075293408.1\|471535_473566_-	DNA topoisomerase III	A0A1X9I6W8	Streptococcus_phage	1.2e-47	31.2
WP_041604434.1\|473567_473855_-	hypothetical protein	NA	NA	NA	NA
WP_011609878.1\|473949_474672_+	hypothetical protein	NA	NA	NA	NA
WP_075293409.1\|474957_475209_+	hypothetical protein	NA	NA	NA	NA
WP_075293410.1\|475205_476102_-	hypothetical protein	NA	NA	NA	NA
WP_075293411.1\|476213_476693_-	hypothetical protein	NA	NA	NA	NA
WP_075293412.1\|477593_478808_+	hypothetical protein	NA	NA	NA	NA
WP_075293413.1\|478920_479313_+	hypothetical protein	NA	NA	NA	NA
WP_075293458.1\|480160_481000_+	ThiF family adenylyltransferase	NA	NA	NA	NA
WP_075293414.1\|480983_481988_+	patatin-like phospholipase family protein	A0A1B2LRS3	Wolbachia_phage	1.2e-19	27.6
WP_075293415.1\|482609_483032_-	DUF805 domain-containing protein	NA	NA	NA	NA
WP_075293416.1\|483084_483585_-	hypothetical protein	NA	NA	NA	NA
WP_075293417.1\|483587_483785_-	hypothetical protein	NA	NA	NA	NA
WP_075293459.1\|483958_484420_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_075293418.1\|484782_485193_-	hypothetical protein	NA	NA	NA	NA
WP_075293419.1\|485194_487222_-\|integrase	integrase	NA	NA	NA	NA
WP_075293460.1\|487224_488547_-\|integrase	site-specific integrase	NA	NA	NA	NA
489494:489510	attL	NA	NA	NA	NA
WP_075293420.1\|490629_490824_+	hypothetical protein	NA	NA	NA	NA
WP_011609870.1\|490827_491037_-	hypothetical protein	NA	NA	NA	NA
WP_081376608.1\|491040_491838_-	hypothetical protein	NA	NA	NA	NA
WP_011609868.1\|491985_492498_-	DUF3158 family protein	NA	NA	NA	NA
WP_075293421.1\|492538_492808_-	DUF1845 domain-containing protein	NA	NA	NA	NA
WP_081376609.1\|493004_494192_+\|integrase	site-specific integrase	A0A1B5FPC6	Escherichia_phage	6.8e-46	32.1
WP_081376610.1\|494163_495003_+	nucleoside triphosphate hydrolase	H7BWC4	unidentified_phage	1.6e-38	38.5
WP_041604971.1\|495528_495732_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_135026463.1\|495847_496129_-	hypothetical protein	NA	NA	NA	NA
WP_075293423.1\|496097_496319_-	hypothetical protein	NA	NA	NA	NA
WP_075293424.1\|496622_496805_-	ribbon-helix-helix protein, CopG family	Q19US2	Mannheimia_phage	2.2e-12	67.8
WP_012341117.1\|497101_497320_-	hypothetical protein	NA	NA	NA	NA
WP_012341122.1\|498274_498574_+	putative addiction module antidote protein	NA	NA	NA	NA
WP_075293425.1\|498784_499303_-	hypothetical protein	NA	NA	NA	NA
WP_081376612.1\|500209_501439_-	hypothetical protein	NA	NA	NA	NA
WP_011609865.1\|501601_502153_-	DUF2857 domain-containing protein	NA	NA	NA	NA
WP_075293427.1\|502163_503870_-	chromosome partitioning protein ParB	NA	NA	NA	NA
WP_135026467.1\|503859_505164_-	replicative DNA helicase	A0A077SK18	Escherichia_phage	3.1e-84	44.8
WP_075293428.1\|506354_507464_+	methionine biosynthesis PLP-dependent protein	A0A1V0SL56	Klosneuvirus	3.6e-17	25.0
WP_011609498.1\|507628_507952_+	thioredoxin	A0A1J0GW78	Streptomyces_phage	4.3e-19	49.0
WP_012341146.1\|508069_508765_-	DnaA regulatory inactivator Hda	NA	NA	NA	NA
508040:508056	attR	NA	NA	NA	NA
WP_075293429.1\|508851_510093_-	uracil permease	NA	NA	NA	NA
WP_075293430.1\|510194_510821_-	uracil phosphoribosyltransferase	NA	NA	NA	NA
WP_011609493.1\|511980_513330_-	NADP-specific glutamate dehydrogenase	NA	NA	NA	NA
WP_075293431.1\|513734_514142_+	hypothetical protein	NA	NA	NA	NA
WP_075293432.1\|514951_516742_-	beta-glucuronidase	B9U1V4	Vaccinia_virus	1.3e-136	44.2
WP_012341153.1\|516763_517792_-	sugar kinase	NA	NA	NA	NA
WP_075293433.1\|518292_519591_+	adenylosuccinate synthase	A0A285PX35	Cedratvirus	1.3e-66	34.9
WP_075293434.1\|519656_521009_-\|protease	metalloprotease PmbA	NA	NA	NA	NA

DBSCAN-SWA_3

1583805 : 1591076

Planktothrix_phage(16.67%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_075294159.1\|1583805_1585758_+	dipeptide/oligopeptide/nickel ABC transporter permease/ATP-binding protein	G9BWD6	Planktothrix_phage	1.8e-11	28.7
WP_012341601.1\|1585761_1586568_+	ABC transporter ATP-binding protein	G3M9Y6	Bacillus_virus	6.3e-19	32.3
WP_075294158.1\|1586648_1588235_+	FAD-binding protein	M1I0Y3	Acanthocystis_turfacea_Chlorella_virus	5.7e-08	23.7
WP_075319813.1\|1588390_1589527_-\|transposase	IS200/IS605 family element transposase accessory protein TnpB	A0A1B0VCD8	Salmonella_phage	5.2e-112	53.7
WP_075319814.1\|1589573_1589990_+\|transposase	IS200/IS605 family transposase	A0A1S5RHE3	Helicobacter_phage	1.5e-48	64.2
WP_075294045.1\|1590104_1591076_-	elongation factor P--(R)-beta-lysine ligase	A0A2K9L0E9	Tupanvirus	1.2e-05	19.7

DBSCAN-SWA_4

1788922 : 1837434

Haemophilus_phage(39.47%)

holin,head,tail,plate,transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_075294184.1\|1788922_1789723_-\|holin	phosphorylcholine transferase LicD	A0A1V0SD50	Indivirus	1.7e-08	31.0
WP_075294185.1\|1789724_1790423_-	NTP transferase domain-containing protein	NA	NA	NA	NA
WP_075294186.1\|1790419_1791352_-	DMT family transporter	NA	NA	NA	NA
WP_081376854.1\|1791338_1792142_-	phosphotransferase	NA	NA	NA	NA
WP_075294187.1\|1792746_1793751_+	type I glyceraldehyde-3-phosphate dehydrogenase	NA	NA	NA	NA
WP_011609618.1\|1793926_1794394_-	anaerobic ribonucleoside-triphosphate reductase-activating protein	H6WXC9	Vibrio_phage	8.0e-51	60.1
WP_075294188.1\|1794409_1796536_-	anaerobic ribonucleoside-triphosphate reductase	A0A2I7QNQ7	Vibrio_phage	2.6e-258	62.6
WP_075294189.1\|1796819_1798616_-	ABC transporter ATP-binding protein/permease	G3M9Y6	Bacillus_virus	1.4e-10	29.9
WP_075294190.1\|1798818_1800477_+	putative transporter	NA	NA	NA	NA
WP_012341368.1\|1800670_1800883_+	50S ribosomal protein L31	NA	NA	NA	NA
WP_081376598.1\|1800934_1801108_-\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_075294192.1\|1801796_1802594_-	transcriptional regulator	A0A0M4UKA3	Ralstonia_phage	8.6e-13	27.4
WP_075294193.1\|1802716_1802980_+	DNA-binding protein	NA	NA	NA	NA
WP_075294194.1\|1804949_1805831_+	AAA family ATPase	A0A0M3LP72	Mannheimia_phage	3.7e-134	85.0
WP_075294195.1\|1805838_1806027_+	hypothetical protein	F6MII8	Haemophilus_phage	1.3e-20	80.0
WP_075294196.1\|1806023_1806329_+	hypothetical protein	NA	NA	NA	NA
WP_075294197.1\|1807125_1807341_+	ANR family transcriptional regulator	NA	NA	NA	NA
WP_135026520.1\|1807325_1807568_+	hypothetical protein	NA	NA	NA	NA
WP_075294199.1\|1807705_1808164_+	regulatory protein GemA	NA	NA	NA	NA
WP_075294200.1\|1808257_1808446_-	ribbon-helix-helix protein, CopG family	Q19US2	Mannheimia_phage	2.8e-07	52.7
WP_075294201.1\|1809174_1809843_+	hypothetical protein	A0A0R6PJV6	Moraxella_phage	2.7e-20	45.3
WP_075294202.1\|1809853_1810060_+	hypothetical protein	NA	NA	NA	NA
WP_075294203.1\|1810184_1810610_+	mor transcription activator family protein	F6MIJ8	Haemophilus_phage	1.5e-48	66.4
WP_075294204.1\|1810699_1811242_+	N-acetylmuramoyl-L-alanine amidase	F6MIJ9	Haemophilus_phage	2.5e-72	67.2
WP_075294205.1\|1811248_1811479_+	DUF2644 domain-containing protein	F6MIK0	Haemophilus_phage	8.0e-12	52.7
WP_075294206.1\|1811475_1811733_+	DUF2681 domain-containing protein	NA	NA	NA	NA
WP_075294207.1\|1811656_1811866_+	lipoprotein	F6MIK2	Haemophilus_phage	1.6e-06	46.4
WP_075294208.1\|1811849_1812104_+	hypothetical protein	NA	NA	NA	NA
WP_075294209.1\|1812100_1812355_+	hypothetical protein	A0A0M3LP87	Mannheimia_phage	1.6e-08	45.0
WP_075294210.1\|1812357_1812867_+	DUF1804 family protein	F6MIK6	Haemophilus_phage	8.7e-67	72.2
WP_075294211.1\|1814662_1816282_+	DUF935 domain-containing protein	A0A0M3LRU4	Mannheimia_phage	4.4e-266	84.1
WP_081376597.1\|1817781_1818327_+	hypothetical protein	A0A0M3LPA7	Mannheimia_phage	1.1e-62	75.4
WP_075294213.1\|1818326_1819307_+\|head	head protein	B7SDP1	Haemophilus_phage	1.2e-133	73.8
WP_075294214.1\|1819385_1819808_+	DUF1320 domain-containing protein	A0A0M3LP98	Mannheimia_phage	6.5e-44	64.5
WP_075294215.1\|1819804_1820443_+	DUF1834 family protein	B7SDP5	Haemophilus_phage	5.0e-80	70.8
WP_075294216.1\|1820439_1820706_+	hypothetical protein	B7SDP6	Haemophilus_phage	6.0e-27	67.1
WP_075294217.1\|1820692_1820866_+	DUF2635 domain-containing protein	A0A0M3LQM9	Mannheimia_phage	3.7e-14	72.7
WP_075294218.1\|1820865_1822287_+\|tail	phage tail protein	B7SDP8	Haemophilus_phage	1.5e-196	74.8
WP_075294219.1\|1822298_1822673_+\|tail	phage tail protein	F6MIK8	Haemophilus_phage	3.3e-55	85.5
WP_087437316.1\|1822741_1823029_+	hypothetical protein	A0A0M3LSI2	Mannheimia_phage	3.5e-17	52.8
WP_075294221.1\|1823299_1825432_+	hypothetical protein	A0A0M3LPB6	Mannheimia_phage	9.8e-96	37.0
WP_075294222.1\|1825473_1826829_+	hypothetical protein	F6MIL2	Haemophilus_phage	1.4e-159	61.9
WP_075294228.1\|1826839_1827946_+\|tail	phage tail protein	F6MIL3	Haemophilus_phage	1.1e-159	72.3
WP_075294223.1\|1827942_1828602_+\|plate	phage baseplate assembly protein V	A0A0M3LPA3	Mannheimia_phage	1.3e-83	69.4
WP_075294224.1\|1828704_1829055_+	hypothetical protein	A0A0M3LQK5	Mannheimia_phage	9.9e-46	78.4
WP_075294225.1\|1829067_1830129_+\|plate	baseplate J/gp47 family protein	F6MIL6	Haemophilus_phage	1.1e-145	72.4
WP_075294226.1\|1830128_1830692_+	YmfQ family protein	A0A0M3LQE1	Mannheimia_phage	4.8e-34	41.9
WP_075294227.1\|1830694_1831234_+	hypothetical protein	M1TAS6	Escherichia_phage	2.1e-15	38.2
WP_157665525.1\|1831211_1832246_+	hypothetical protein	Q94MY0	Haemophilus_virus	2.5e-60	49.2
WP_012341722.1\|1832252_1832600_-	helix-turn-helix transcriptional regulator	A0A1S5NNJ5	Burkholderia_phage	1.3e-18	50.9
WP_012340329.1\|1832583_1832835_-	cytotoxic translational repressor of toxin-antitoxin stability system	A0A1S5NR91	Burkholderia_phage	1.2e-13	50.6
WP_075294466.1\|1832897_1833524_+	DUF4376 domain-containing protein	F6MIL9	Haemophilus_phage	1.8e-58	57.2
WP_011609624.1\|1834828_1835518_-	5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	NA	NA	NA	NA
WP_075294465.1\|1835712_1837434_-	single-stranded-DNA-specific exonuclease RecJ	A7KV88	Bacillus_phage	4.1e-68	30.5

Anti-CRISPR protein detection

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