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
CP027424	Staphylococcus cohnii strain FDAARGOS_334 plasmid unnamed5, complete sequence	0 crisprs	NA	0
CP027423	Staphylococcus cohnii strain FDAARGOS_334 plasmid unnamed4	0 crisprs	NA	0
CP027421	Staphylococcus cohnii strain FDAARGOS_334 plasmid unnamed3, complete sequence	0 crisprs	Cas14u_CAS-V	0
CP027420	Staphylococcus cohnii strain FDAARGOS_334 plasmid unnamed1, complete sequence	0 crisprs	WYL	0
CP027419	Staphylococcus cohnii strain FDAARGOS_334 plasmid unnamed2, complete sequence	0 crisprs	cas14j	4
CP027422	Staphylococcus cohnii strain FDAARGOS_334 chromosome, complete genome	0 crisprs	cas3,DEDDh,WYL,csa3,DinG	8

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

0 : 1583

Cyanophage(100.0%)

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
AVL76237.1\|122_1583_+	glucose-6-phosphate dehydrogenase	M4SIY3	Cyanophage	2.0e-71	35.9

DBSCAN-SWA_2

5616 : 7282

Lactobacillus_virus(50.0%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL76241.1\|5616_6759_-\|transposase	transposase	C1KFJ5	Lactobacillus_virus	4.3e-98	51.4
AVL76242.1\|6859_7282_+\|transposase	IS200/IS605 family transposase	A0A0P0IQC6	Lactobacillus_phage	1.7e-47	62.9

DBSCAN-SWA_3

10489 : 19031

Streptococcus_phage(25.0%)

protease

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL76246.1\|10489_11461_-	replication protein	A0A286QNA4	Streptococcus_phage	7.5e-19	47.6
AVL76247.1\|11877_12612_+	DUF536 domain-containing protein	NA	NA	NA	NA
AVL76248.1\|12712_13645_-	NADP-dependent oxidoreductase	A0A2L2DIY2	Acanthamoeba_polyphaga_mimivirus	4.9e-07	25.9
AVL76249.1\|13906_14548_+	3-hexulose-6-phosphate synthase	NA	NA	NA	NA
AVL76250.1\|14703_15222_+\|protease	protease	NA	NA	NA	NA
AVL76263.1\|15725_17741_+	daunorubicin resistance protein DrrC	A0A1B1IVR3	uncultured_Mediterranean_phage	1.0e-102	35.8
AVL76251.1\|17882_19031_-	glutathione-dependent formaldehyde dehydrogenase	E3SJ82	Synechococcus_phage	2.8e-12	24.4

DBSCAN-SWA_4

22902 : 27377

Mycobacterium_phage(25.0%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL76254.1\|22902_23514_-	transposon DNA-invertase	G8I4U3	Mycobacterium_phage	6.6e-13	29.7
AVL76255.1\|23651_24467_-	ATP-binding protein	A0A0M3LP72	Mannheimia_phage	3.0e-05	29.8
AVL76256.1\|25872_26466_-	HTH domain-containing protein	A0A0A7NPV4	Enterobacteria_phage	1.5e-41	51.1
AVL76257.1\|26702_27377_+\|transposase	IS6 family transposase	A0A0N9RU54	Staphylococcus_phage	1.1e-117	89.7

Anti-CRISPR protein detection

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

2. CP027422

Click the left colored region to show detailed information

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

180232 : 191994

Staphylococcus_phage(66.67%)

integrase

attL 174045:174062|attR 195631:195648

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
174045:174062	attL	NA	NA	NA	NA
AVL76504.1\|180232_180871_-	hypothetical protein	A0A2H4JFF8	uncultured_Caudovirales_phage	8.6e-64	60.8
AVL76505.1\|180830_181040_-	hypothetical protein	NA	NA	NA	NA
AVL76506.1\|181169_181511_-	pathogenicity island protein	NA	NA	NA	NA
AVL76507.1\|181798_183253_-	virulence-associated protein E	A0A1W6JQD6	Staphylococcus_phage	3.9e-213	70.5
AVL76508.1\|183268_184168_-	mobile element-associated protein	A0A1W6JQL5	Staphylococcus_phage	1.2e-82	53.9
AVL76509.1\|184229_184535_-	pathogenicity island protein	A0A1W6JQH0	Staphylococcus_phage	6.6e-14	51.9
AVL76510.1\|184536_184770_-	hypothetical protein	NA	NA	NA	NA
AVL76511.1\|184771_185059_-	hypothetical protein	NA	NA	NA	NA
AVL76512.1\|185246_185507_-	DUF771 domain-containing protein	NA	NA	NA	NA
AVL76513.1\|185523_186147_-	phage repressor protein	A0A1W6JPC3	Staphylococcus_phage	2.5e-55	53.4
AVL76514.1\|186143_186353_-	XRE family transcriptional regulator	A0A1W6JPB7	Staphylococcus_phage	2.9e-05	43.3
AVL76515.1\|186585_187389_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
AVL76516.1\|187398_188448_+\|integrase	site-specific integrase	U3PJ31	Staphylococcus_phage	6.6e-69	39.9
AVL76517.1\|188823_189669_-	YitT family protein	NA	NA	NA	NA
AVL76518.1\|190011_190956_-	DNA-binding protein WhiA	Q7AWZ3	Streptococcus_phage	5.4e-54	40.3
AVL76519.1\|191007_191994_-	hypothetical protein	A1IMD5	Streptococcus_phage	3.8e-50	41.5
195631:195648	attR	NA	NA	NA	NA

DBSCAN-SWA_2

227548 : 247941

uncultured_Caudovirales_phage(35.71%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL76550.1\|227548_228349_-	iron ABC transporter ATP-binding protein	Q9EMR9	Amsacta_moorei_entomopoxvirus	1.0e-13	29.4
AVL76551.1\|228345_229305_-	iron ABC transporter permease	A0A2H4J116	uncultured_Caudovirales_phage	1.9e-06	54.0
AVL76552.1\|229294_230263_-	iron ABC transporter permease	A0A2H4IY97	uncultured_Caudovirales_phage	2.2e-135	78.3
AVL76553.1\|230728_231697_-	class 1b ribonucleoside-diphosphate reductase subunit beta	A0A2H4J4P3	uncultured_Caudovirales_phage	1.8e-174	93.8
AVL76554.1\|231935_234041_-	class 1b ribonucleoside-diphosphate reductase subunit alpha	A0A2H4J2N6	uncultured_Caudovirales_phage	0.0e+00	90.6
AVL76555.1\|234003_234402_-	class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI	A0A2H4J545	uncultured_Caudovirales_phage	2.3e-51	73.5
AVL76556.1\|235113_236001_+	EamA/RhaT family transporter	NA	NA	NA	NA
AVL76557.1\|236014_236515_+	NADPH-dependent 7-cyano-7-deazaguanine reductase QueF	E7DN65	Pneumococcus_phage	1.2e-52	71.5
AVL76558.1\|236697_238212_+	peptide MFS transporter	A0A0P0IY73	Acinetobacter_phage	5.9e-71	36.4
AVL76559.1\|238472_239981_+	peptide MFS transporter	A0A0P0IY73	Acinetobacter_phage	8.0e-68	34.1
AVL76560.1\|240199_241141_+	diacylglycerol kinase family lipid kinase	A0A1V0SBJ0	Catovirus	9.6e-11	22.7
AVL76561.1\|241379_241928_-	5'(3')-deoxyribonucleotidase	A0A0A0PKY7	Bacillus_phage	2.9e-28	37.8
AVL76562.1\|242158_243214_-	histidinol-phosphate transaminase	A0A1X6WGT4	Pacmanvirus	5.1e-21	26.0
AVL76563.1\|243401_244916_-	glycine/betaine ABC transporter permease	NA	NA	NA	NA
AVL76564.1\|244912_245875_-	ABC transporter ATP-binding protein	G3M9Y6	Bacillus_virus	1.6e-24	32.1
AVL76565.1\|246162_247941_-	DNA helicase RecQ	A0A2K9L3P7	Tupanvirus	2.0e-78	36.7

DBSCAN-SWA_3

829934 : 836960

Staphylococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL77076.1\|829934_830249_+	ArsR family transcriptional regulator	A0A2H4PQT4	Staphylococcus_phage	7.3e-32	61.5
AVL77077.1\|830251_831541_+	arsenical efflux pump membrane protein ArsB	A0A2H4PQU3	Staphylococcus_phage	1.5e-184	80.0
AVL77078.1\|831558_831954_+	protein ArsC 2	A0A2H4PQT9	Staphylococcus_phage	2.6e-58	82.0
AVL77079.1\|832593_832962_+	transcriptional regulator	E4ZFI8	Streptococcus_phage	1.3e-56	86.9
AVL77080.1\|832954_835372_+	cadmium-translocating P-type ATPase	E4ZFI9	Streptococcus_phage	2.8e-248	63.0
AVL77081.1\|835476_836091_+	cadmium resistance protein CadD	NA	NA	NA	NA
AVL77082.1\|836519_836960_-	NUDIX domain-containing protein	D0R7J3	Paenibacillus_phage	4.6e-16	33.6

DBSCAN-SWA_4

1780558 : 1807997

Staphylococcus_phage(85.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL77923.1\|1780558_1781953_+	protoporphyrinogen oxidase	A0A0M3SGX2	Mollivirus	1.4e-05	33.3
AVL77924.1\|1782095_1782653_+	serine hydrolase family protein	NA	NA	NA	NA
AVL77925.1\|1784575_1785964_+	o-succinylbenzoate--CoA ligase	A0A2H4PQM9	Staphylococcus_phage	3.2e-164	59.3
AVL77926.1\|1785976_1786981_+	o-succinylbenzoate synthase	A0A2H4PQM0	Staphylococcus_phage	1.3e-93	54.0
AVL77927.1\|1786977_1787214_-	membrane protein insertion efficiency factor YidD	A0A2H4PQM5	Staphylococcus_phage	1.3e-30	75.3
AVL77928.1\|1787275_1787785_+	nucleoside triphosphatase YtkD	A0A2H4PQM4	Staphylococcus_phage	4.0e-48	58.5
AVL78652.1\|1787765_1788545_+	dipeptidyl aminopeptidase	A0A2H4PQM6	Staphylococcus_phage	6.5e-98	70.6
AVL77929.1\|1788571_1790161_-	phosphoenolpyruvate carboxykinase (ATP)	A0A2H4PQN1	Staphylococcus_phage	6.3e-257	80.3
AVL77930.1\|1790541_1791738_+	methionine adenosyltransferase	A0A2H4PQS6	Staphylococcus_phage	2.2e-193	85.6
AVL77931.1\|1791834_1792743_+	hypothetical protein	A0A2H4PQQ8	Staphylococcus_phage	7.4e-85	72.7
AVL77932.1\|1793193_1794030_+	aldo/keto reductase	A0A2H4PQR8	Staphylococcus_phage	2.7e-102	63.9
AVL77933.1\|1794108_1794465_-	CrcB family protein	NA	NA	NA	NA
AVL77934.1\|1794461_1794827_-	fluoride efflux transporter CrcB	A0A2H4PQR0	Staphylococcus_phage	5.3e-34	57.9
AVL77935.1\|1794887_1795193_-	hypothetical protein	NA	NA	NA	NA
AVL77936.1\|1795478_1796192_+	transaldolase	R9TM64	Synechococcus_phage	8.5e-20	36.5
AVL77937.1\|1796691_1797141_+	hypothetical protein	A0A2H4PQT8	Staphylococcus_phage	3.1e-20	47.5
AVL77938.1\|1797145_1797568_-	hypothetical protein	NA	NA	NA	NA
AVL77939.1\|1797578_1798058_-	sigma-70 family RNA polymerase sigma factor	NA	NA	NA	NA
AVL77940.1\|1798279_1798504_+	hypothetical protein	NA	NA	NA	NA
AVL77941.1\|1798668_1799523_+	autolysin	Q4ZCC7	Staphylococcus_virus	8.0e-41	43.3
AVL77942.1\|1799918_1800848_-	osmoprotectant ABC transporter substrate-binding protein	NA	NA	NA	NA
AVL77943.1\|1801009_1802485_+	pyridine nucleotide-disulfide oxidoreductase	A0A2H4PQX2	Staphylococcus_phage	8.5e-14	65.5
AVL77944.1\|1803171_1804215_+	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	A0A2H4PQS8	Staphylococcus_phage	4.8e-128	64.4
AVL77945.1\|1804221_1804854_+	riboflavin synthase	A0A2H4PQS5	Staphylococcus_phage	5.5e-71	63.8
AVL77946.1\|1804864_1806043_+	bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	A0A2H4PQS2	Staphylococcus_phage	3.9e-163	71.5
AVL77947.1\|1806054_1806513_+	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	1.9e-57	75.7
AVL77948.1\|1806995_1807997_-	proline dehydrogenase	A0A2H4PQT6	Staphylococcus_phage	1.4e-124	68.1

DBSCAN-SWA_5

1811009 : 1818673

Staphylococcus_phage(100.0%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL77952.1\|1811009_1811570_-	methyltransferase domain-containing protein	A0A2H4PQV0	Staphylococcus_phage	3.4e-64	63.2
AVL77953.1\|1811566_1812520_-	TIGR01212 family radical SAM protein	A0A2H4PQV5	Staphylococcus_phage	3.9e-68	85.4
AVL77954.1\|1812629_1813799_+	MFS transporter	A0A2H4PQR6	Staphylococcus_phage	2.6e-167	76.4
AVL77955.1\|1814248_1816663_+\|tRNA	leucine--tRNA ligase	A0A2H4PQS0	Staphylococcus_phage	0.0e+00	85.8
AVL77956.1\|1816684_1816996_+	rhodanese-like domain-containing protein	A0A2H4PQR9	Staphylococcus_phage	9.7e-37	73.8
AVL77957.1\|1817413_1818673_-	NAD(P)/FAD-dependent oxidoreductase	A0A2H4PQX1	Staphylococcus_phage	1.0e-39	72.6

DBSCAN-SWA_6

1941864 : 1951040

uncultured_Mediterranean_phage(50.0%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL78062.1\|1941864_1942866_+	Holliday junction branch migration DNA helicase RuvB	B3GAM6	uncultured_virus	7.5e-06	29.9
AVL78063.1\|1942868_1943894_+\|tRNA	tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA	NA	NA	NA	NA
AVL78064.1\|1943918_1945058_+\|tRNA	tRNA guanosine(34) transglycosylase Tgt	A0A1B1IVQ4	uncultured_Mediterranean_phage	1.2e-84	44.7
AVL78065.1\|1945075_1945336_+	preprotein translocase subunit YajC	A0A1B1IVR5	uncultured_Mediterranean_phage	4.3e-06	44.1
AVL78066.1\|1945661_1947938_+	protein translocase subunit SecDF	A0A1B1IVP7	uncultured_Mediterranean_phage	3.8e-29	34.5
AVL78067.1\|1948229_1950506_+	single-stranded-DNA-specific exonuclease RecJ	A7KV88	Bacillus_phage	3.2e-68	28.6
AVL78068.1\|1950521_1951040_+	adenine phosphoribosyltransferase	A0A1V0SKE5	Klosneuvirus	6.6e-30	46.9

DBSCAN-SWA_7

2075108 : 2087672

uncultured_Mediterranean_phage(25.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL78189.1\|2075108_2076023_-	aldo/keto reductase	A0A1V0SKP9	Klosneuvirus	1.5e-05	31.7
AVL78190.1\|2076212_2076755_+	NUDIX hydrolase	NA	NA	NA	NA
AVL78191.1\|2076859_2077306_+	transcriptional repressor	NA	NA	NA	NA
AVL78192.1\|2077342_2078230_+	site-specific tyrosine recombinase XerD	A0A0K2CP59	Brevibacillus_phage	4.3e-37	30.9
AVL78193.1\|2078321_2078828_-	DUF309 domain-containing protein	NA	NA	NA	NA
AVL78194.1\|2078919_2079654_+	segregation/condensation protein A	A0A1B1IVW1	uncultured_Mediterranean_phage	2.7e-08	25.2
AVL78195.1\|2079637_2080186_+	SMC-Scp complex subunit ScpB	A0A1B1IVT7	uncultured_Mediterranean_phage	3.6e-10	31.4
AVL78196.1\|2080178_2080916_+	rRNA pseudouridine synthase	NA	NA	NA	NA
AVL78197.1\|2081051_2081777_+	DNA-binding response regulator	W8CYM9	Bacillus_phage	1.2e-45	41.3
AVL78198.1\|2081760_2083533_+	two-component sensor histidine kinase	A0A1V0SGX0	Hokovirus	1.5e-20	25.6
AVL78199.1\|2083950_2084496_+	ECF transporter S component	NA	NA	NA	NA
AVL78200.1\|2084982_2085231_-	ferredoxin	A0A127AYY7	Bacillus_phage	2.2e-15	49.3
AVL78201.1\|2085340_2086306_+	hypothetical protein	NA	NA	NA	NA
AVL78202.1\|2086292_2087672_+	ATP-dependent DNA helicase RecQ	M1PGQ0	Moumouvirus	7.6e-57	33.7

DBSCAN-SWA_8

2512830 : 2521305

Synechococcus_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVL78582.1\|2512830_2513397_-	phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	4.7e-29	39.2
AVL78583.1\|2513399_2514428_-	phosphoribosylformylglycinamidine cyclo-ligase	Q58MH8	Prochlorococcus_phage	2.5e-65	42.9
AVL78584.1\|2514420_2515908_-	amidophosphoribosyltransferase	A0A0M3SGR2	Mollivirus	2.3e-43	30.9
AVL78585.1\|2515886_2518076_-	phosphoribosylformylglycinamidine synthase subunit PurL	A6N228	Microbacterium_phage	4.2e-134	38.3
AVL78586.1\|2518068_2518740_-	phosphoribosylformylglycinamidine synthase I	NA	NA	NA	NA
AVL78587.1\|2518739_2519000_-	phosphoribosylformylglycinamidine synthase subunit PurS	NA	NA	NA	NA
AVL78588.1\|2519001_2519703_-	phosphoribosylaminoimidazolesuccinocarboxamide synthase	G8EYA2	Synechococcus_phage	5.2e-46	41.2
AVL78589.1\|2519702_2520836_-	5-(carboxyamino)imidazole ribonucleotide synthase	NA	NA	NA	NA
AVL78590.1\|2520822_2521305_-	5-(carboxyamino)imidazole ribonucleotide mutase	A0A2P0VNU7	Tetraselmis_virus	7.5e-20	42.7

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. CP027419

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

2. CP027422

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection