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_CP013305	Vibrio cholerae strain CRC1106 chromosome 1, complete sequence	0 crisprs	DEDDh,DinG,csa3,cas3,WYL,csx1,RT	0	0	5	0
NZ_CP013306	Vibrio cholerae strain CRC1106 chromosome 2	0 crisprs	Cas9_archaeal,RT,PD-DExK,csa3,cas3	0	0	0	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

566792 : 574016

uncultured_Mediterranean_phage(33.33%)

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_000698379.1\|566792_567545_+	5'/3'-nucleotidase SurE	A0A1B1ITZ2	uncultured_Mediterranean_phage	8.0e-69	53.3
WP_000002982.1\|567537_568164_+	protein-L-isoaspartate(D-aspartate) O-methyltransferase	A0A1B1IU40	uncultured_Mediterranean_phage	2.0e-36	52.1
WP_000177568.1\|568163_569099_+	murein hydrolase activator NlpD	D7RWE0	Brochothrix_phage	7.8e-05	34.7
WP_000116737.1\|569172_570180_+	RNA polymerase sigma factor RpoS	F4YCU2	Synechococcus_phage	6.0e-35	34.2
WP_001894770.1\|570272_572861_-	DNA mismatch repair protein MutS	A0A1V0SC35	Catovirus	2.2e-33	23.0
WP_001279365.1\|573128_574016_-	cysteine synthase CysM	A0A1X9I5K7	Streptococcus_phage	4.1e-56	41.1

DBSCAN-SWA_2

805595 : 812788

Faustovirus(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_000775253.1\|805595_806810_+	IscS subfamily cysteine desulfurase	A0A0H3TPH2	Faustovirus	1.1e-32	30.5
WP_000331703.1\|806846_807230_+	Fe-S cluster assembly scaffold IscU	A0A218MKD1	uncultured_virus	5.4e-53	78.2
WP_000301571.1\|807290_807614_+	iron-sulfur cluster assembly protein IscA	A0A2H4N7N5	Lake_Baikal_phage	3.0e-25	50.5
WP_001105747.1\|807662_808178_+	co-chaperone HscB	NA	NA	NA	NA
WP_001196560.1\|808201_810052_+	Fe-S protein assembly chaperone HscA	A0A0N9QXN8	Chrysochromulina_ericina_virus	5.3e-106	41.1
WP_001124187.1\|810065_810404_+	ISC system 2Fe-2S type ferredoxin	NA	NA	NA	NA
WP_000872176.1\|810452_810647_+	Fe-S cluster assembly protein IscX	NA	NA	NA	NA
WP_000107237.1\|810866_812156_+	aminopeptidase PepB	Q6GYZ8	Mycoplasma_phage	1.7e-34	34.3
WP_001162850.1\|812359_812788_+	nucleoside-diphosphate kinase	D2E8E1	Anguillid_herpesvirus	1.0e-20	38.4

DBSCAN-SWA_3

1551161 : 1583771

Vibrio_phage(47.37%)

coat

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_149591715.1\|1551161_1553267_-	RTX toxin T1SS ABC transporter subunit RtxB	W8CYL7	Bacillus_phage	4.9e-39	27.1
WP_001906284.1\|1553693_1554041_+	hypothetical protein	NA	NA	NA	NA
WP_001881196.1\|1554066_1554528_+	RTX toxin-activating lysine-acyltransferase RtxC	NA	NA	NA	NA
WP_000517826.1\|1554551_1568189_+	MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin RtxA	B3Y8K3	Vibrio_virus	8.4e-07	100.0
WP_000593522.1\|1568646_1569021_-	cholera enterotoxin binding subunit CtxB	Q77DH7	Vibrio_virus	7.8e-65	100.0
WP_001881225.1\|1569017_1569794_-	cholera enterotoxin catalytic subunit CtxA	A0A142I6Y0	Vibrio_phage	1.3e-151	100.0
WP_000021616.1\|1569892_1571092_-	zonula occludens toxin ZOT	A0A142I6Z1	Vibrio_phage	5.3e-240	100.0
WP_000979342.1\|1571088_1571382_-	accessory cholera enterotoxin	A0A0F6YNQ7	Vibrio_phage	3.7e-46	100.0
WP_001268534.1\|1571378_1572566_-\|coat	minor coat protein pIII	A0A142I701	Vibrio_phage	1.4e-200	100.0
WP_000493022.1\|1572672_1572921_-	colonization factor	A0A0N7F140	Vibrio_phage	8.8e-33	100.0
WP_001911548.1\|1573056_1573416_-	hypothetical protein	A0A0N9HE73	Vibrio_phage	4.4e-65	100.0
WP_000743997.1\|1573417_1574497_-	replication initiation factor domain-containing protein	U5TQR3	Satellite_phage	2.2e-213	100.0
WP_000693566.1\|1574622_1574961_+	helix-turn-helix transcriptional regulator	U5TNA1	Satellite_phage	7.3e-54	100.0
WP_000053920.1\|1575472_1575697_-	RstC protein	U5TMI6	Satellite_phage	1.1e-34	100.0
WP_001911551.1\|1575790_1576141_-	hypothetical protein	U5TMH5	Satellite_phage	1.0e-63	100.0
WP_000743997.1\|1576142_1577222_-	replication initiation factor domain-containing protein	U5TQR3	Satellite_phage	2.2e-213	100.0
WP_000693566.1\|1577347_1577686_+	helix-turn-helix transcriptional regulator	U5TNA1	Satellite_phage	7.3e-54	100.0
WP_000170634.1\|1578175_1578760_-	DNA-binding protein	E3U9I9	Vibrio_phage	6.4e-114	100.0
WP_001161489.1\|1578752_1578920_-	hypothetical protein	E3U9J0	Vibrio_phage	2.3e-13	100.0
WP_001052672.1\|1578997_1579690_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_000512956.1\|1579819_1580089_-	hypothetical protein	NA	NA	NA	NA
WP_001881266.1\|1580108_1581677_-	replication protein	A7BJY2	Enterobacteria_phage	2.7e-58	32.3
WP_000005769.1\|1581853_1582405_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_001161489.1\|1583603_1583771_-	hypothetical protein	E3U9J0	Vibrio_phage	2.3e-13	100.0

DBSCAN-SWA_4

2322767 : 2405853

Vibrio_phage(83.67%)

tRNA,plate,capsid,terminase,head,tail,portal,integrase

attL 2339180:2339203|attR 2372290:2372313

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_000186559.1\|2322767_2323250_-\|tRNA	Cys-tRNA(Pro) deacylase	NA	NA	NA	NA
WP_000809002.1\|2323383_2325045_-	bifunctional UDP-sugar hydrolase/5'-nucleotidase	NA	NA	NA	NA
WP_000400335.1\|2325586_2326438_-	3-deoxy-8-phosphooctulonate synthase	E3T537	Cafeteria_roenbergensis_virus	2.6e-47	40.7
WP_000933144.1\|2326457_2327270_-	tetratricopeptide repeat protein	NA	NA	NA	NA
WP_000272895.1\|2327285_2327669_-	SirB2 family protein	NA	NA	NA	NA
WP_000117270.1\|2327668_2328529_-	peptide chain release factor N(5)-glutamine methyltransferase	NA	NA	NA	NA
WP_000647701.1\|2328532_2329621_-	peptide chain release factor 1	W8EDB3	Pseudomonas_phage	2.4e-05	46.4
WP_000054219.1\|2329650_2330910_-\|tRNA	glutamyl-tRNA reductase	NA	NA	NA	NA
WP_000993150.1\|2331068_2331686_+	lipoprotein localization protein LolB	NA	NA	NA	NA
WP_000581228.1\|2331682_2332555_+	4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase	NA	NA	NA	NA
WP_001113134.1\|2332585_2333530_+	ribose-phosphate pyrophosphokinase	A0A2K9L2G2	Tupanvirus	1.7e-44	38.0
WP_000081944.1\|2333698_2334289_+\|tRNA	aminoacyl-tRNA hydrolase	NA	NA	NA	NA
WP_000505884.1\|2334299_2335391_+	redox-regulated ATPase YchF	NA	NA	NA	NA
WP_000290380.1\|2337730_2338864_-	flagellin	NA	NA	NA	NA
2339180:2339203	attL	NA	NA	NA	NA
WP_000779002.1\|2339887_2341519_-	hypothetical protein	U3PB83	Vibrio_phage	0.0e+00	100.0
WP_000457681.1\|2341515_2341989_-	hypothetical protein	U3PDI0	Vibrio_phage	6.6e-77	100.0
WP_000267787.1\|2341976_2342870_-	hypothetical protein	U3PIM3	Vibrio_phage	2.8e-161	100.0
WP_071908294.1\|2342872_2343397_-\|tail	phage tail protein	A9ZT45	Vibrio_virus	4.1e-96	99.4
WP_000083759.1\|2343396_2345259_-\|tail	phage tail protein	Q8HA58	Vibrio_phage	0.0e+00	100.0
WP_000005870.1\|2345255_2345915_-	hypothetical protein	U3PB79	Vibrio_phage	8.2e-126	100.0
WP_000044509.1\|2345911_2347111_-\|plate	baseplate J/gp47 family protein	U3PDH5	Vibrio_phage	1.0e-222	100.0
WP_001113003.1\|2347107_2347440_-	DUF2590 family protein	U3PIM1	Vibrio_phage	1.7e-55	100.0
WP_000343647.1\|2347429_2349247_-\|tail	phage tail tape measure protein	U3PFL8	Vibrio_phage	0.0e+00	100.0
WP_000165786.1\|2349443_2349725_-	hypothetical protein	A9ZT39	Vibrio_virus	5.1e-45	100.0
WP_001881877.1\|2349721_2350024_-	hypothetical protein	U3PCH1	Vibrio_phage	1.5e-50	100.0
WP_000990572.1\|2349932_2350274_-	hypothetical protein	U3PB75	Vibrio_phage	1.1e-52	100.0
WP_000705022.1\|2350248_2350836_-	lysozyme	U3PDH1	Vibrio_phage	2.5e-110	100.0
WP_001077689.1\|2350822_2351050_-	hypothetical protein	U3PIL8	Vibrio_phage	2.1e-36	100.0
WP_000382491.1\|2351046_2351256_-	TraR/DksA family transcriptional regulator	U3PFL5	Vibrio_phage	2.0e-33	100.0
WP_000063627.1\|2351270_2351729_-	DUF2597 family protein	U3PCG7	Vibrio_phage	1.3e-82	100.0
WP_000312540.1\|2351728_2352838_-	DUF2586 family protein	U3PB71	Vibrio_phage	1.5e-209	100.0
WP_000461677.1\|2352839_2353499_-	phage virion morphogenesis protein	U3PDG7	Vibrio_phage	9.1e-117	100.0
WP_000122189.1\|2353485_2353974_-\|tail	phage tail protein	U3PIL4	Vibrio_phage	1.6e-89	100.0
WP_000493401.1\|2353970_2354432_-\|head	head completion/stabilization protein	U3PFL1	Vibrio_phage	1.5e-78	100.0
WP_000059165.1\|2354538_2355255_-\|terminase	terminase endonuclease subunit	U3PCG2	Vibrio_phage	1.3e-132	100.0
WP_000078361.1\|2355270_2356281_-\|capsid	phage major capsid protein, P2 family	U3PB67	Vibrio_phage	7.0e-193	100.0
WP_001127095.1\|2356317_2357217_-\|capsid	GPO family capsid scaffolding protein	A0A160DHM4	Vibrio_phage	4.0e-123	100.0
WP_000331803.1\|2357390_2359208_+\|terminase	terminase ATPase subunit family protein	U3PIL1	Vibrio_phage	0.0e+00	100.0
WP_001999948.1\|2359204_2360251_+\|portal	phage portal protein	U3PFK6	Vibrio_phage	5.7e-206	100.0
WP_000729650.1\|2360234_2360450_+	hypothetical protein	U3PCF7	Vibrio_phage	3.1e-34	100.0
WP_001263191.1\|2360520_2360772_+	ogr/Delta-like zinc finger family protein	U3PB63	Vibrio_phage	1.9e-43	100.0
WP_001292395.1\|2360772_2361018_-	hypothetical protein	U3PDF9	Vibrio_phage	1.5e-37	100.0
WP_001140408.1\|2361255_2361594_+	helix-turn-helix transcriptional regulator	U3PIK7	Vibrio_phage	2.8e-53	100.0
WP_000756239.1\|2361667_2362204_-	DUF262 domain-containing protein	U3PFK3	Vibrio_phage	4.1e-99	100.0
WP_001909657.1\|2362213_2364799_-	replication endonuclease	A0A166YHE2	Vibrio_phage	0.0e+00	99.9
WP_000613058.1\|2364795_2365380_-	hypothetical protein	U3PB60	Vibrio_phage	3.2e-105	100.0
WP_000629095.1\|2365376_2365487_-	hypothetical protein	NA	NA	NA	NA
WP_000099608.1\|2365483_2366101_-	DNA methyltransferase	U3PDF3	Vibrio_phage	1.2e-118	100.0
WP_001198814.1\|2366097_2366325_-	hypothetical protein	U3PIK2	Vibrio_phage	3.2e-37	100.0
WP_000997540.1\|2366574_2366985_-	hypothetical protein	U3PCE8	Vibrio_phage	1.8e-75	100.0
WP_001031152.1\|2366981_2367515_-	hypothetical protein	U3PB56	Vibrio_phage	3.9e-86	100.0
WP_001272765.1\|2367596_2368031_-	hypothetical protein	U3PDF0	Vibrio_phage	2.8e-74	100.0
WP_000253093.1\|2368043_2368583_-	phage regulatory CII family protein	U3PIJ8	Vibrio_phage	5.5e-96	100.0
WP_000959026.1\|2368693_2368906_-	hypothetical protein	U3PFJ1	Vibrio_phage	6.4e-32	100.0
WP_001881894.1\|2369051_2369699_+	phage repressor protein CI	A0A166YHA0	Vibrio_phage	1.1e-119	100.0
WP_000132153.1\|2369724_2370630_+	NAD-dependent DNA ligase	U3PB51	Vibrio_phage	1.3e-161	100.0
WP_000985033.1\|2370629_2371043_+	hypothetical protein	U3PDE6	Vibrio_phage	8.9e-70	100.0
WP_000116333.1\|2371042_2372080_+\|integrase	site-specific integrase	U3PIJ4	Vibrio_phage	1.5e-198	100.0
WP_000154827.1\|2372528_2373668_-	flagellin	NA	NA	NA	NA
2372290:2372313	attR	NA	NA	NA	NA
WP_000934642.1\|2374075_2375269_-	flagellar hook-associated protein FlgL	NA	NA	NA	NA
WP_000135483.1\|2375281_2377156_-	flagellar hook-associated protein FlgK	NA	NA	NA	NA
WP_000609516.1\|2377335_2378274_-	flagellar assembly peptidoglycan hydrolase FlgJ	S5M9Y4	Brevibacillus_phage	9.5e-11	31.9
WP_001225051.1\|2378284_2379370_-	flagellar basal body P-ring protein FlgI	NA	NA	NA	NA
WP_001911822.1\|2379460_2380237_-	flagellar basal body L-ring protein FlgH	NA	NA	NA	NA
WP_001182097.1\|2380260_2381049_-	flagellar basal-body rod protein FlgG	NA	NA	NA	NA
WP_000373284.1\|2381068_2381818_-	flagellar basal-body rod protein FlgF	NA	NA	NA	NA
WP_000122825.1\|2382000_2383305_-	flagellar hook protein FlgE	NA	NA	NA	NA
WP_000929365.1\|2383333_2384041_-	flagellar hook assembly protein FlgD	NA	NA	NA	NA
WP_000051920.1\|2384058_2384475_-	flagellar basal body rod protein FlgC	NA	NA	NA	NA
WP_001007981.1\|2384479_2384875_-	flagellar basal body rod protein FlgB	NA	NA	NA	NA
WP_000125387.1\|2385094_2385922_-	protein-glutamate O-methyltransferase	NA	NA	NA	NA
WP_000145786.1\|2385932_2386859_-	chemotaxis protein CheV	Q56AR1	Bacillus_thuringiensis_phage	1.4e-35	31.6
WP_001881906.1\|2386915_2387683_+	flagellar basal body P-ring formation protein FlgA	NA	NA	NA	NA
WP_000907265.1\|2387813_2388137_+	flagellar biosynthesis anti-sigma factor FlgM	NA	NA	NA	NA
WP_000729367.1\|2388240_2388666_+	flagellar protein FlgN	NA	NA	NA	NA
WP_001881911.1\|2388775_2389213_-	flagellar assembly lipoprotein FlgP	NA	NA	NA	NA
WP_000759070.1\|2389220_2389856_-	membrane protein	NA	NA	NA	NA
WP_000739493.1\|2390016_2391150_+	flagella assembly protein FlgT	NA	NA	NA	NA
WP_000523394.1\|2391279_2398533_-	non-ribosomal peptide synthetase	A0A2K9KZV5	Tupanvirus	2.9e-30	22.9
WP_000064348.1\|2398778_2399594_-	siderophore-interacting protein	NA	NA	NA	NA
WP_000279435.1\|2399897_2401961_-	TonB-dependent siderophore receptor	NA	NA	NA	NA
WP_001895039.1\|2402572_2403079_+	Fe3+-citrate ABC transporter substrate-binding protein	NA	NA	NA	NA
WP_000731531.1\|2403167_2404133_-	OmpA family protein	NA	NA	NA	NA
WP_000216841.1\|2404428_2405853_-\|tRNA	glutamate--tRNA ligase	NA	NA	NA	NA

DBSCAN-SWA_5

2460652 : 2467269

Staphylococcus_phage(66.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_000864130.1\|2460652_2461123_-	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	6.8e-34	48.7
WP_001122865.1\|2461387_2462497_-	bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	A0A2H4PQS2	Staphylococcus_phage	6.7e-64	39.8
WP_000493874.1\|2462537_2463191_-	riboflavin synthase	A0A2H4PQS5	Staphylococcus_phage	1.2e-31	38.2
WP_001131994.1\|2463195_2464299_-	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	A0A2H4PQS8	Staphylococcus_phage	1.3e-43	33.1
WP_000543544.1\|2464324_2464774_-	transcriptional regulator NrdR	NA	NA	NA	NA
WP_000366574.1\|2464873_2466124_-	glutamate-5-semialdehyde dehydrogenase	A0A1X9I5D4	Streptococcus_phage	5.0e-100	49.5
WP_000210573.1\|2466135_2467269_-	glutamate 5-kinase	A0A1X9I5D0	Streptococcus_phage	1.4e-64	40.4

Anti-CRISPR protein detection

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