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_CP042418	Leuconostoc citreum strain CBA3627 chromosome, complete genome	0 crisprs	csa3,cas3,DEDDh	0	0	6	0
NZ_CP042419	Leuconostoc citreum strain CBA3627 plasmid unnamed, complete sequence	0 crisprs	NA	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

33143 : 43185

Streptococcus_phage(33.33%)

tRNA

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_004908108.1\|33143_35105_-\|tRNA	threonine--tRNA ligase	A0A2K9L297	Tupanvirus	1.4e-101	33.3
WP_004900379.1\|35664_36384_-	aquaporin family protein	M1H9L8	Acanthocystis_turfacea_Chlorella_virus	2.4e-22	31.8
WP_133286229.1\|36635_37088_+	flavodoxin	NA	NA	NA	NA
WP_004900382.1\|37132_37855_-	YebC/PmpR family DNA-binding transcriptional regulator	NA	NA	NA	NA
WP_146992839.1\|37978_38467_-	phosphatidylglycerophosphatase A	A0A0A7DMW7	Lactobacillus_phage	3.7e-14	35.0
WP_004900387.1\|38475_39654_-	3-phosphoglycerate dehydrogenase	M1NSB9	Streptococcus_phage	2.8e-84	41.8
WP_004904228.1\|39650_40742_-	3-phosphoserine/phosphohydroxythreonine transaminase	M1Q1P2	Streptococcus_phage	6.4e-75	44.9
WP_085698856.1\|41388_43185_+	ABC transporter ATP-binding protein	W8CYL7	Bacillus_phage	2.1e-54	30.0

DBSCAN-SWA_2

531427 : 538711

Leuconostoc_phage(91.67%)

integrase

attL 529634:529649|attR 545006:545021

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
529634:529649	attL	NA	NA	NA	NA
WP_139988491.1\|531427_532549_-\|integrase	tyrosine-type recombinase/integrase	A0A097BYJ7	Leuconostoc_phage	1.2e-206	93.6
WP_004908203.1\|532668_532869_-	hypothetical protein	A0A097BYD9	Leuconostoc_phage	2.9e-26	78.8
WP_004908204.1\|532869_533274_-	hypothetical protein	A0A097BYD6	Leuconostoc_phage	3.9e-62	88.1
WP_146992911.1\|533477_533834_-	hypothetical protein	A0A097BYH9	Leuconostoc_phage	1.9e-12	37.6
WP_146992913.1\|534271_535675_-	DNA primase	A0A097BYJ2	Leuconostoc_phage	3.1e-239	92.5
WP_004908212.1\|535661_536432_-	DNA replication protein	I7A9C3	Enterococcus_phage	4.9e-13	30.0
WP_040176522.1\|536488_536671_-	hypothetical protein	A0A097BYL1	Leuconostoc_phage	9.7e-21	86.7
WP_012305011.1\|536673_536994_-	hypothetical protein	A0A097BYF1	Leuconostoc_phage	2.4e-46	97.0
WP_004908221.1\|536990_537269_-	hypothetical protein	NA	NA	NA	NA
WP_040176521.1\|537284_537551_-	hypothetical protein	A0A097BYJ6	Leuconostoc_phage	2.8e-32	75.6
WP_004908227.1\|537552_537714_-	hypothetical protein	A0A097BYK8	Leuconostoc_phage	1.2e-19	86.8
WP_004908230.1\|537820_538078_-	hypothetical protein	A0A097BYE6	Leuconostoc_phage	1.2e-29	79.8
WP_004908233.1\|538342_538711_+	helix-turn-helix transcriptional regulator	A0A097BYI9	Leuconostoc_phage	4.9e-19	48.1
545006:545021	attR	NA	NA	NA	NA

DBSCAN-SWA_3

817923 : 825813

Streptococcus_phage(66.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_012305425.1\|817923_818568_+	dTMP kinase	M1PSC7	Streptococcus_phage	4.0e-53	50.9
WP_004899218.1\|818574_818904_+	DUF970 domain-containing protein	NA	NA	NA	NA
WP_004899217.1\|818903_819839_+	DNA polymerase III subunit delta	M1NSC1	Streptococcus_phage	3.7e-07	25.5
WP_004899214.1\|819840_820716_+	16S rRNA (cytidine(1402)-2'-O)-methyltransferase	M1PLC5	Streptococcus_phage	2.1e-76	54.6
WP_004904406.1\|820726_821464_+	acyl-ACP thioesterase	NA	NA	NA	NA
WP_085699536.1\|821504_822497_+	UDP-glucose 4-epimerase GalE	A0A2K9L1R4	Tupanvirus	6.5e-50	36.0
WP_004904405.1\|822609_822816_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_085699540.1\|823532_824291_+	M15 family metallopeptidase	NA	NA	NA	NA
WP_004899199.1\|824360_825002_+	deoxynucleoside kinase	C1KFI3	Lactobacillus_virus	6.7e-48	44.8
WP_085699542.1\|825045_825813_+	pyrroline-5-carboxylate reductase	A0A1X9I6T5	Streptococcus_phage	4.7e-24	31.0

DBSCAN-SWA_4

1096154 : 1109341

Bacillus_phage(22.22%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_146992385.1\|1096154_1097432_+	insulinase family protein	A0A1X9I714	Streptococcus_phage	3.4e-43	30.1
WP_146992387.1\|1097428_1098700_+	insulinase family protein	A0A2K9L1M6	Tupanvirus	1.9e-17	30.5
WP_004904929.1\|1098714_1099587_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_012305368.1\|1099597_1100179_+	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	NA	NA	NA	NA
WP_146992389.1\|1100309_1101455_+	recombinase RecA	A0A0S2MVG1	Bacillus_phage	2.4e-117	65.4
WP_048801499.1\|1101566_1102256_+	response regulator transcription factor	Q56AR1	Bacillus_thuringiensis_phage	2.8e-07	34.8
WP_146992392.1\|1102439_1103351_+	phosphate ABC transporter substrate-binding protein PstS family protein	H6WG65	Cyanophage	3.3e-08	25.5
WP_099045062.1\|1103464_1104778_+	GHKL domain-containing protein	W8CYF6	Bacillus_phage	7.0e-28	34.5
WP_012305365.1\|1104875_1105757_+	phosphate ABC transporter substrate-binding protein PstS family protein	H6WG65	Cyanophage	7.6e-10	28.1
WP_004901956.1\|1105846_1106770_+	phosphate ABC transporter permease subunit PstC	NA	NA	NA	NA
WP_004901954.1\|1106769_1107654_+	phosphate ABC transporter permease PstA	NA	NA	NA	NA
WP_004901951.1\|1107734_1108574_+	phosphate ABC transporter ATP-binding protein	F2Y302	Organic_Lake_phycodnavirus	3.8e-11	30.4
WP_004901948.1\|1108570_1109341_+	phosphate ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	2.5e-17	28.9

DBSCAN-SWA_5

1262182 : 1327157

Lactobacillus_phage(33.33%)

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

attL 1286392:1286407|attR 1336634:1336649

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_133424630.1\|1262182_1262632_+\|tRNA	D-tyrosyl-tRNA(Tyr) deacylase	NA	NA	NA	NA
WP_012305301.1\|1262661_1263273_-	glycerol-3-phosphate 1-O-acyltransferase PlsY	NA	NA	NA	NA
WP_004907843.1\|1263476_1265540_+	DNA topoisomerase IV subunit B	G3M9Z3	Bacillus_virus	4.0e-126	43.1
WP_146992508.1\|1265663_1268102_+	DNA topoisomerase IV subunit A	A0A172JHV7	Bacillus_phage	7.3e-87	29.5
WP_146992510.1\|1268150_1269056_+	manganese-dependent inorganic pyrophosphatase	NA	NA	NA	NA
WP_002815032.1\|1269193_1269343_+	50S ribosomal protein L33	NA	NA	NA	NA
WP_004904725.1\|1269344_1269614_+	30S ribosomal protein S14	NA	NA	NA	NA
WP_004900921.1\|1269950_1270427_+	ribosome maturation factor RimP	NA	NA	NA	NA
WP_004900919.1\|1270498_1271590_+	transcription termination/antitermination protein NusA	NA	NA	NA	NA
WP_012305300.1\|1271645_1271942_+	YlxR family protein	NA	NA	NA	NA
WP_004907836.1\|1271931_1272252_+	50S ribosomal protein L7ae	NA	NA	NA	NA
WP_139988262.1\|1272252_1274775_+	translation initiation factor IF-2	A0A2H4UTS4	Bodo_saltans_virus	8.5e-22	23.7
WP_004900914.1\|1274820_1275174_+	30S ribosome-binding factor RbfA	NA	NA	NA	NA
WP_146992512.1\|1275268_1276447_+	aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme	NA	NA	NA	NA
WP_004900910.1\|1276462_1276978_+	hypothetical protein	NA	NA	NA	NA
WP_146992515.1\|1276964_1277873_+\|tRNA	tRNA pseudouridine(55) synthase TruB	NA	NA	NA	NA
WP_099044557.1\|1277869_1278820_+	riboflavin biosynthesis protein RibF	A0A1V0SD03	Indivirus	1.4e-06	28.5
WP_004900905.1\|1278947_1279976_+	heat-inducible transcription repressor HrcA	NA	NA	NA	NA
WP_004900903.1\|1279993_1280563_+	nucleotide exchange factor GrpE	NA	NA	NA	NA
WP_004904719.1\|1280648_1282493_+	molecular chaperone DnaK	G8DDB7	Micromonas_pusilla_virus	1.4e-135	47.6
WP_004900900.1\|1282585_1283473_+	DnaJ domain-containing protein	A0A0P0YNN4	Yellowstone_lake_phycodnavirus	1.2e-18	29.9
WP_004900898.1\|1283522_1284110_-	peptide deformylase	A0A2I7S809	Vibrio_phage	1.6e-11	37.3
WP_004904718.1\|1284165_1284438_+	hypothetical protein	NA	NA	NA	NA
WP_004904717.1\|1284434_1285223_+	inositol monophosphatase family protein	NA	NA	NA	NA
WP_004900891.1\|1285287_1287126_+	translational GTPase TypA	E4ZFJ7	Streptococcus_phage	1.9e-23	29.5
1286392:1286407	attL	NA	NA	NA	NA
WP_085699756.1\|1287424_1288603_-\|integrase	site-specific integrase	Q4ZCC1	Staphylococcus_virus	3.1e-06	21.9
WP_146992517.1\|1289051_1289501_-	hypothetical protein	A0A1B0Y4P2	Lactobacillus_phage	7.3e-09	43.2
WP_146992518.1\|1289570_1290272_-	hypothetical protein	E3W8I2	Leuconostoc_phage	1.9e-32	77.7
WP_146992520.1\|1290321_1290741_-	ImmA/IrrE family metallo-endopeptidase	E3W8B8	Leuconostoc_phage	2.7e-42	62.5
WP_146992523.1\|1290737_1291088_-	helix-turn-helix transcriptional regulator	E3W8B9	Leuconostoc_phage	4.3e-25	53.8
WP_146992525.1\|1291340_1291544_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_146992527.1\|1291554_1292346_+	phage repressor protein/antirepressor Ant	A0A0A7DN31	Lactobacillus_phage	2.9e-69	60.4
WP_040177065.1\|1292458_1292671_-	hypothetical protein	NA	NA	NA	NA
WP_004900864.1\|1292773_1293043_+	hypothetical protein	NA	NA	NA	NA
WP_040177063.1\|1293120_1293318_+	hypothetical protein	NA	NA	NA	NA
WP_040177061.1\|1293310_1293508_+	helix-turn-helix transcriptional regulator	S5MA03	Brevibacillus_phage	5.6e-06	45.2
WP_040177059.1\|1293497_1293680_+	hypothetical protein	NA	NA	NA	NA
WP_052437264.1\|1293683_1294484_+	DNA replication protein	D7RWG1	Brochothrix_phage	8.5e-77	64.5
WP_040177058.1\|1294487_1294754_+	hypothetical protein	NA	NA	NA	NA
WP_052437263.1\|1294831_1295743_+	DUF1351 domain-containing protein	V5UTB6	Oenococcus_phage	4.1e-19	29.9
WP_040177057.1\|1295739_1296363_+	ERF family protein	A0A1P8BKZ7	Lactococcus_phage	1.0e-13	40.3
WP_040177056.1\|1296349_1296799_+	single-stranded DNA-binding protein	A0A097BYB0	Leuconostoc_phage	1.7e-53	73.8
WP_040177054.1\|1296810_1297494_+	hypothetical protein	A0A097BYG8	Leuconostoc_phage	4.6e-79	66.4
WP_004903903.1\|1297502_1297907_+	hypothetical protein	A0A0P0IJF8	Lactobacillus_phage	3.9e-22	45.0
WP_004903898.1\|1298333_1298744_+	DUF722 domain-containing protein	A0A097BYG4	Leuconostoc_phage	1.2e-10	33.6
WP_146992529.1\|1299457_1299649_+	hypothetical protein	NA	NA	NA	NA
WP_146992531.1\|1299632_1300031_+	DUF2335 domain-containing protein	NA	NA	NA	NA
WP_004907787.1\|1300339_1300792_+	cupin domain-containing protein	Q2I8C5	Bacillus_phage	4.9e-29	45.5
WP_146992533.1\|1301190_1301724_+	HNH endonuclease	A8YQN7	Lactobacillus_phage	1.0e-38	46.3
WP_004907778.1\|1301723_1302038_+	hypothetical protein	NA	NA	NA	NA
WP_139988227.1\|1302290_1302857_+\|terminase	phage terminase small subunit P27 family	B8R648	Lactobacillus_phage	2.9e-15	31.3
WP_139988226.1\|1302843_1304724_+\|terminase	terminase large subunit	A8YQI8	Lactobacillus_phage	9.5e-236	63.3
WP_036060984.1\|1304720_1304912_+	hypothetical protein	NA	NA	NA	NA
WP_146992535.1\|1304916_1306068_+\|portal	phage portal protein	Q6J1Y4	Lactobacillus_phage	5.1e-99	50.9
WP_139988224.1\|1306064_1306754_+\|protease	Clp protease ClpP	A8YQJ1	Lactobacillus_phage	3.8e-57	51.8
WP_139988223.1\|1306764_1307928_+\|capsid	phage major capsid protein	Q6J1Y2	Lactobacillus_phage	5.7e-138	65.0
WP_012305284.1\|1307938_1308265_+\|head,tail	phage gp6-like head-tail connector protein	Q6J1Y1	Lactobacillus_phage	1.1e-22	54.3
WP_139988222.1\|1308257_1308629_+\|head	phage head closure protein	NA	NA	NA	NA
WP_139988221.1\|1308618_1309035_+	HK97 gp10 family phage protein	A8YQJ5	Lactobacillus_phage	1.4e-22	42.7
WP_139988220.1\|1309031_1309406_+	DUF806 family protein	A0A2P0ZLF4	Lactobacillus_phage	8.7e-16	38.9
WP_085699938.1\|1309409_1310060_+\|tail	phage tail protein	Q6J1X7	Lactobacillus_phage	1.9e-21	35.0
WP_139988219.1\|1310160_1310589_+	molecular chaperone	NA	NA	NA	NA
WP_085699940.1\|1310588_1310798_+	hypothetical protein	NA	NA	NA	NA
WP_146992538.1\|1310798_1316612_+\|tail	phage tail tape measure protein	Q8LTK2	Lactococcus_phage	7.9e-156	42.4
WP_139988217.1\|1316674_1319032_+\|tail	phage tail protein	Q38353	Lactococcus_phage	6.3e-27	23.1
WP_146992540.1\|1319082_1324665_+	hypothetical protein	A0A059PAB7	Leuconostoc_phage	2.2e-46	60.5
WP_146992543.1\|1324661_1324871_+	hypothetical protein	NA	NA	NA	NA
WP_139988214.1\|1324933_1325167_+	hypothetical protein	A0A097BYE3	Leuconostoc_phage	5.6e-13	48.6
WP_139988213.1\|1325303_1325765_+	hypothetical protein	NA	NA	NA	NA
WP_139988212.1\|1325764_1326187_+	hypothetical protein	A0A097BYC6	Leuconostoc_phage	9.8e-40	66.7
WP_146992545.1\|1326197_1327157_+	N-acetylmuramoyl-L-alanine amidase	A0A097BY89	Leuconostoc_phage	3.6e-138	74.6
1336634:1336649	attR	NA	NA	NA	NA

DBSCAN-SWA_6

1614891 : 1622487

Staphylococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_146992779.1\|1614891_1616196_-	NADPH-dependent oxidoreductase	A0A2P0ZL82	Lactobacillus_phage	1.0e-50	52.6
WP_085699018.1\|1616185_1616791_-	NAD(P)H-dependent oxidoreductase	A0A2P0ZL77	Lactobacillus_phage	4.3e-49	51.0
WP_085699016.1\|1616882_1617809_-	FAD:protein FMN transferase	NA	NA	NA	NA
WP_085699294.1\|1617887_1619084_-	ATP-binding protein	NA	NA	NA	NA
WP_085699014.1\|1619170_1619644_-	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	7.1e-31	46.8
WP_004905688.1\|1619667_1620870_-	bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	A0A2H4PQS2	Staphylococcus_phage	8.0e-87	42.9
WP_085699012.1\|1620859_1621459_-	riboflavin synthase	A0A2H4PQS5	Staphylococcus_phage	6.9e-23	35.4
WP_085699010.1\|1621443_1622487_-	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	A0A1V0SE20	Indivirus	1.4e-34	32.3

Anti-CRISPR protein detection

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