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
NZ_CP054007	Staphylococcus hominis strain FDAARGOS_762 plasmid unnamed2, complete sequence	0 crisprs	NA	0
NZ_CP054006	Staphylococcus hominis strain FDAARGOS_762 chromosome, complete genome	0 crisprs	DEDDh,DinG,cas3,csa3,WYL	8
NZ_CP054009	Staphylococcus hominis strain FDAARGOS_762 plasmid unnamed4, complete sequence	0 crisprs	NA	0
NZ_CP054005	Staphylococcus hominis strain FDAARGOS_762 plasmid unnamed1, complete sequence	0 crisprs	csa3	0
NZ_CP054008	Staphylococcus hominis strain FDAARGOS_762 plasmid unnamed3	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

110351 : 116925

Staphylococcus_phage(14.29%)

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_002449571.1\|110351_111191_+	aldo/keto reductase	A0A2H4PQR8	Staphylococcus_phage	2.2e-59	43.2
WP_002449575.1\|111317_112301_+	glycosyltransferase family 2 protein	A8CG95	Salmonella_phage	1.0e-63	43.4
WP_002449079.1\|112346_112955_-	hypothetical protein	NA	NA	NA	NA
WP_002449094.1\|113063_113780_-	7-carboxy-7-deazaguanine synthase QueE	E7DN68	Pneumococcus_phage	2.5e-51	42.2
WP_002449084.1\|113779_114199_-	6-carboxytetrahydropterin synthase QueD	S4U060	uncultured_phage	1.8e-06	28.7
WP_002449071.1\|114195_114873_-	7-cyano-7-deazaguanine synthase QueC	A0A2H4J8Q7	uncultured_Caudovirales_phage	9.8e-66	56.1
WP_002449081.1\|115205_115799_+	aminodeoxychorismate/anthranilate synthase component II	A0A0P0IKJ1	Acinetobacter_phage	3.0e-34	39.1
WP_002449090.1\|115782_116925_+	anthranilate synthase component I family protein	A0A0B5J984	Pandoravirus	2.3e-22	39.1

DBSCAN-SWA_2

129581 : 142704

uncultured_Caudovirales_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002449088.1\|129581_130637_+	histidinol-phosphate transaminase	A0A0H3TLT9	Faustovirus	1.4e-23	24.7
WP_002449087.1\|130731_131268_+	5'-3'-deoxyribonucleotidase	A0A0A0PKY7	Bacillus_phage	3.4e-29	38.4
WP_002449080.1\|131330_132254_-	diacylglycerol kinase family lipid kinase	NA	NA	NA	NA
WP_002449073.1\|132382_133888_-	peptide MFS transporter	A0A0P0IY73	Acinetobacter_phage	1.7e-57	32.9
WP_002449091.1\|134171_134672_-	NADPH-dependent 7-cyano-7-deazaguanine reductase QueF	E7DN65	Pneumococcus_phage	2.2e-51	70.8
WP_002449096.1\|134682_135549_-	DMT family transporter	NA	NA	NA	NA
WP_002449085.1\|136286_136685_+	class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI	A0A2H4J545	uncultured_Caudovirales_phage	1.7e-54	75.8
WP_002449077.1\|136647_138753_+	class 1b ribonucleoside-diphosphate reductase subunit alpha	A0A2H4J2N6	uncultured_Caudovirales_phage	0.0e+00	92.2
WP_002449076.1\|138866_139835_+	class 1b ribonucleoside-diphosphate reductase subunit beta	A0A2H4J4P3	uncultured_Caudovirales_phage	6.3e-175	94.1
WP_002449086.1\|140019_140988_+	ABC transporter permease	A0A2H4IY97	uncultured_Caudovirales_phage	2.9e-148	86.0
WP_002449066.1\|140977_141937_+	iron chelate uptake ABC transporter family permease subunit	A0A2H4J116	uncultured_Caudovirales_phage	2.2e-10	72.0
WP_002449075.1\|141933_142704_+	ATP-binding cassette domain-containing protein	Q9EMR9	Amsacta_moorei_entomopoxvirus	7.6e-14	30.1

DBSCAN-SWA_3

339579 : 348049

Synechococcus_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002448044.1\|339579_340062_+	5-(carboxyamino)imidazole ribonucleotide mutase	A0A2P0VNU7	Tetraselmis_virus	3.6e-22	44.7
WP_002448136.1\|340048_341173_+	5-(carboxyamino)imidazole ribonucleotide synthase	NA	NA	NA	NA
WP_002448194.1\|341176_341881_+	phosphoribosylaminoimidazolesuccinocarboxamide synthase	A0A0E3FUQ7	Synechococcus_phage	3.6e-47	44.2
WP_002448160.1\|341880_342141_+	phosphoribosylformylglycinamidine synthase subunit PurS	NA	NA	NA	NA
WP_002448092.1\|342142_342814_+	phosphoribosylformylglycinamidine synthase subunit PurQ	NA	NA	NA	NA
WP_002448158.1\|342806_344996_+	phosphoribosylformylglycinamidine synthase subunit PurL	A6N228	Microbacterium_phage	3.1e-137	37.8
WP_002448145.1\|344974_346459_+	amidophosphoribosyltransferase	A0A0M3SGR2	Mollivirus	9.0e-48	32.6
WP_002448076.1\|346451_347480_+	phosphoribosylformylglycinamidine cyclo-ligase	Q58MH8	Prochlorococcus_phage	5.6e-65	43.6
WP_002448123.1\|347482_348049_+	phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	6.1e-29	41.4

DBSCAN-SWA_4

735260 : 747439

Bacillus_phage(25.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002449846.1\|735260_736640_-	ATP-dependent DNA helicase RecQ	M1PGQ0	Moumouvirus	2.4e-55	34.9
WP_002449747.1\|736620_737586_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_002449743.1\|737682_737931_+	ferredoxin	A0A127AYY7	Bacillus_phage	5.8e-16	49.3
WP_002449844.1\|738014_738560_-	ECF transporter S component	NA	NA	NA	NA
WP_002449735.1\|738997_740767_-	HAMP domain-containing protein	A0A1V0SGX0	Hokovirus	4.7e-19	26.8
WP_002449874.1\|740747_741473_-	response regulator transcription factor	W8CYM9	Bacillus_phage	8.3e-47	41.6
WP_002449899.1\|741680_742418_-	rRNA pseudouridine synthase	NA	NA	NA	NA
WP_002449749.1\|742419_742953_-	SMC-Scp complex subunit ScpB	A0A1B1IVT7	uncultured_Mediterranean_phage	4.3e-08	29.2
WP_002449902.1\|742945_743677_-	segregation/condensation protein A	A0A1B1IVW1	uncultured_Mediterranean_phage	2.8e-10	25.8
WP_002449814.1\|743775_744279_+	DUF309 domain-containing protein	NA	NA	NA	NA
WP_002449900.1\|744304_745192_-	site-specific tyrosine recombinase XerD	A0A0K2CP59	Brevibacillus_phage	2.7e-39	32.8
WP_002449777.1\|745359_745806_-	transcriptional repressor	NA	NA	NA	NA
WP_002449742.1\|745906_746449_-	NUDIX hydrolase	NA	NA	NA	NA
WP_002449875.1\|746530_747439_+	aldo/keto reductase	A0A1V0SKP9	Klosneuvirus	9.9e-05	32.5

DBSCAN-SWA_5

793506 : 801749

Staphylococcus_phage(16.67%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002449798.1\|793506_794283_-	metal ABC transporter ATP-binding protein	A0A2H4PQG7	Staphylococcus_phage	2.9e-21	30.0
WP_002449740.1\|794403_795294_-	deoxyribonuclease IV	A0A2H4UU70	Bodo_saltans_virus	1.6e-28	32.8
WP_002449896.1\|795303_796650_-	DEAD/DEAH box helicase	A0A1V0SBR7	Catovirus	4.2e-52	33.0
WP_002449766.1\|796674_797778_-	Nif3-like dinuclear metal center hexameric protein	A0A1S5V250	Saudi_moumouvirus	1.5e-07	29.0
WP_002449878.1\|797767_798457_-\|tRNA	tRNA (adenine(22)-N(1))-methyltransferase TrmK	NA	NA	NA	NA
WP_002449793.1\|798560_799667_-	RNA polymerase sigma factor RpoD	F4YCU2	Synechococcus_phage	1.1e-37	37.6
WP_002449887.1\|799940_801749_-	DNA primase	A0A0K1LMQ9	Caulobacter_phage	2.5e-55	37.1

DBSCAN-SWA_6

982884 : 1018790

Staphylococcus_phage(96.15%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_172848037.1\|982884_989985_-	DUF1542 domain-containing protein	A0A2H4PQU6	Staphylococcus_phage	2.6e-07	29.2
WP_002449646.1\|990231_990543_-	rhodanese-like domain-containing protein	A0A2H4PQR9	Staphylococcus_phage	9.7e-37	74.8
WP_002449629.1\|990561_992976_-\|tRNA	leucine--tRNA ligase	A0A2H4PQS0	Staphylococcus_phage	0.0e+00	88.6
WP_002449671.1\|993280_994465_-	MFS transporter	A0A2H4PQR6	Staphylococcus_phage	3.9e-179	81.6
WP_002449655.1\|994576_995536_+	TIGR01212 family radical SAM protein	A0A2H4PQV5	Staphylococcus_phage	5.6e-67	83.3
WP_002449652.1\|995532_996093_+	class I SAM-dependent methyltransferase	A0A2H4PQV0	Staphylococcus_phage	2.2e-71	71.4
WP_002449620.1\|996152_996554_-	MarR family transcriptional regulator	NA	NA	NA	NA
WP_002449637.1\|996873_997701_-	alpha/beta hydrolase	NA	NA	NA	NA
WP_002449663.1\|997909_998911_+	proline dehydrogenase	A0A2H4PQT6	Staphylococcus_phage	3.0e-127	67.6
WP_002449638.1\|998962_999421_-	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	1.2e-59	87.3
WP_002449675.1\|999433_1000618_-	3,4-dihydroxy-2-butanone-4-phosphate synthase	A0A2H4PQS2	Staphylococcus_phage	9.7e-178	77.2
WP_002449633.1\|1000629_1001262_-	riboflavin synthase	A0A2H4PQS5	Staphylococcus_phage	7.4e-84	72.9
WP_002449616.1\|1001268_1002312_-	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	A0A2H4PQS8	Staphylococcus_phage	3.4e-134	66.5
WP_002449656.1\|1002721_1004209_-	FAD/NAD(P)-binding protein	A0A2H4PQX2	Staphylococcus_phage	2.2e-17	80.7
WP_002449648.1\|1004506_1005355_-	glucosaminidase domain-containing protein	A0A1W6JQU5	Staphylococcus_phage	1.5e-39	43.0
WP_002449634.1\|1005601_1005826_-	hypothetical protein	NA	NA	NA	NA
WP_002449626.1\|1006073_1006520_+	sigma-70 family RNA polymerase sigma factor	A0A2H4PQT5	Staphylococcus_phage	3.4e-27	50.3
WP_002449640.1\|1006506_1006953_+	competence protein ComK	NA	NA	NA	NA
WP_002449665.1\|1006927_1007392_-	hypothetical protein	A0A2H4PQT8	Staphylococcus_phage	6.6e-13	37.3
WP_002449673.1\|1007590_1008304_-	transaldolase	M1PR54	Cyanophage	1.9e-19	35.5
WP_002449644.1\|1008549_1008858_+	hypothetical protein	NA	NA	NA	NA
WP_002449641.1\|1008897_1009263_+	fluoride efflux transporter CrcB	A0A2H4PQR0	Staphylococcus_phage	1.3e-32	60.2
WP_002449657.1\|1009259_1009613_+	CrcB family protein	NA	NA	NA	NA
WP_002449660.1\|1009673_1010507_-	aldo/keto reductase	A0A2H4PQR8	Staphylococcus_phage	1.8e-122	74.7
WP_002449668.1\|1010622_1011534_-	NERD domain-containing protein	A0A2H4PQQ8	Staphylococcus_phage	3.2e-96	77.4
WP_002449627.1\|1011632_1012829_-	methionine adenosyltransferase	A0A2H4PQS6	Staphylococcus_phage	1.3e-201	88.9
WP_002449643.1\|1013214_1014810_+	phosphoenolpyruvate carboxykinase (ATP)	A0A2H4PQN1	Staphylococcus_phage	1.7e-262	83.0
WP_039984211.1\|1014850_1015606_-	S9 family peptidase	A0A2H4PQM6	Staphylococcus_phage	1.1e-105	74.4
WP_002449666.1\|1015610_1016084_-	nucleoside triphosphatase YtkD	A0A2H4PQM4	Staphylococcus_phage	5.4e-47	55.1
WP_002449651.1\|1016151_1016397_+	membrane protein insertion efficiency factor YidD	A0A2H4PQM5	Staphylococcus_phage	5.7e-32	72.6
WP_002449662.1\|1016387_1017395_-	o-succinylbenzoate synthase	A0A2H4PQM0	Staphylococcus_phage	6.1e-96	52.1
WP_002449631.1\|1017395_1018790_-	o-succinylbenzoate--CoA ligase	A0A2H4PQM9	Staphylococcus_phage	6.3e-176	63.2

DBSCAN-SWA_7

1278667 : 1291889

Staphylococcus_phage(38.46%)

integrase

attL 1277987:1278011|attR 1291891:1291915

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
1277987:1278011	attL	NA	NA	NA	NA
WP_002448586.1\|1278667_1279933_-	Fic family protein	Q9AZ49	Lactococcus_phage	2.3e-44	30.8
WP_039984018.1\|1281387_1281648_-	hypothetical protein	NA	NA	NA	NA
WP_002448329.1\|1282605_1282971_-	hypothetical protein	A0A1W6JP87	Staphylococcus_phage	1.6e-35	55.1
WP_002448613.1\|1284062_1284404_-	hypothetical protein	A0A2H4JEH8	uncultured_Caudovirales_phage	1.4e-25	50.5
WP_002448499.1\|1284400_1284844_-	hypothetical protein	A0A2H4JBD6	uncultured_Caudovirales_phage	1.3e-37	55.9
WP_002448352.1\|1284854_1285523_-	hypothetical protein	Q4ZE82	Staphylococcus_phage	6.3e-25	30.8
WP_002448420.1\|1285812_1286598_-	ATP-binding protein	A0A2H4JCH7	uncultured_Caudovirales_phage	2.1e-80	56.4
WP_002448442.1\|1286609_1287716_-	DnaD domain protein	A0A0D4DCE1	Staphylococcus_phage	2.6e-52	63.5
WP_002448581.1\|1287708_1288032_-	helix-turn-helix domain-containing protein	A0A2I6PDA9	Staphylococcus_phage	4.5e-21	57.4
WP_002448498.1\|1288072_1288390_-	DUF1474 family protein	A0A2H4JB50	uncultured_Caudovirales_phage	1.6e-23	50.5
WP_002448426.1\|1288653_1289295_-	phage repressor protein	A0A2H4JB17	uncultured_Caudovirales_phage	2.6e-68	62.1
WP_002448320.1\|1289358_1289625_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_172848039.1\|1289664_1289901_-	helix-turn-helix transcriptional regulator	A0A1Q1PVY0	Staphylococcus_phage	7.9e-07	40.5
WP_002448549.1\|1290026_1290629_+	helix-turn-helix domain-containing protein	A0A141E1S0	Streptococcus_phage	4.7e-11	57.4
WP_002448511.1\|1290752_1291889_+\|integrase	site-specific integrase	A0A1S5S7K9	Streptococcus_phage	1.6e-73	41.5
1291891:1291915	attR	NA	NA	NA	NA

DBSCAN-SWA_8

1422954 : 1435413

uncultured_Caudovirales_phage(56.25%)

terminase,integrase

attL 1415753:1415768|attR 1436525:1436540

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
1415753:1415768	attL	NA	NA	NA	NA
WP_002448435.1\|1422954_1423527_-\|terminase	terminase small subunit	A0A2H4JBF3	uncultured_Caudovirales_phage	6.9e-97	93.7
WP_002454945.1\|1423537_1423867_-	transcriptional regulator	A0A2H4JEH8	uncultured_Caudovirales_phage	1.4e-46	88.1
WP_039984016.1\|1423863_1424301_-	pathogenicity island protein	A0A2H4JBD6	uncultured_Caudovirales_phage	5.9e-64	88.4
WP_002448371.1\|1424355_1424568_-	hypothetical protein	A0A2H4JHW4	uncultured_Caudovirales_phage	8.6e-29	98.6
WP_002448413.1\|1424567_1425158_-	hypothetical protein	A0A2H4JBG0	uncultured_Caudovirales_phage	2.5e-102	96.9
WP_002448487.1\|1425172_1425925_-	hypothetical protein	A0A2H4JD56	uncultured_Caudovirales_phage	5.5e-126	93.6
WP_002448465.1\|1425934_1426267_-	hypothetical protein	A0A2H4JHK4	uncultured_Caudovirales_phage	1.7e-47	86.4
WP_002448444.1\|1426683_1427268_-	hypothetical protein	NA	NA	NA	NA
WP_002448587.1\|1427264_1427909_-	hypothetical protein	Q4ZE67	Staphylococcus_phage	2.4e-74	63.6
WP_002448496.1\|1427910_1428432_-	hypothetical protein	NA	NA	NA	NA
WP_002448509.1\|1428738_1430448_-	DUF927 domain-containing protein	Q4ZE73	Staphylococcus_phage	1.1e-227	68.1
WP_002448617.1\|1430461_1431331_-	primase C-terminal domain-containing protein	A0A2H4JEH3	uncultured_Caudovirales_phage	7.3e-98	60.0
WP_002448519.1\|1431425_1431734_-	DUF1474 family protein	A0A2H4JB50	uncultured_Caudovirales_phage	1.1e-24	54.0
WP_002448390.1\|1431737_1431938_-	hypothetical protein	A0A1W6JPA6	Staphylococcus_phage	3.1e-12	53.8
WP_002448458.1\|1431952_1432135_-	hypothetical protein	NA	NA	NA	NA
WP_002448400.1\|1432153_1432426_-	helix-turn-helix domain-containing protein	Q4ZE77	Staphylococcus_phage	4.1e-31	70.0
WP_002448385.1\|1432429_1432639_-	helix-turn-helix transcriptional regulator	Q4ZE78	Staphylococcus_phage	7.7e-22	73.1
WP_002448621.1\|1432781_1433489_+	helix-turn-helix transcriptional regulator	Q4ZE79	Staphylococcus_phage	6.3e-15	33.9
WP_002448485.1\|1433569_1434178_+	hypothetical protein	NA	NA	NA	NA
WP_002448428.1\|1434198_1435413_+\|integrase	site-specific integrase	Q4ZE80	Staphylococcus_phage	5.8e-85	43.1
1436525:1436540	attR	NA	NA	NA	NA

Anti-CRISPR protein detection

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