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
CP014060	Achromobacter xylosoxidans strain FDAARGOS_147, complete genome	0 crisprs	DinG,csa3,DEDDh,PD-DExK,WYL	0	0	6	0
CP014059	Achromobacter xylosoxidans strain FDAARGOS_147 plasmid, 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

1215868 : 1223878

uncultured_Mediterranean_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
AMG35477.2\|1215868_1216558_-	protein-L-isoaspartate(D-aspartate) O-methyltransferase	A0A1B1IU40	uncultured_Mediterranean_phage	9.4e-32	45.2
AMG35478.1\|1216677_1217436_-	5'/3'-nucleotidase SurE	A0A1B1ITZ2	uncultured_Mediterranean_phage	2.6e-67	51.6
AUZ17994.1\|1217626_1218265_+	glycerol-3-phosphate acyltransferase	NA	NA	NA	NA
AMG35479.1\|1218343_1219375_-\|tRNA	tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD	A0A0R6PI74	Moraxella_phage	2.4e-92	51.7
AMG35480.1\|1219483_1220776_+	NCS2 family permease	A0A0R6PHV4	Moraxella_phage	1.2e-64	36.3
AMG35481.1\|1220933_1221290_-	glyoxalase/bleomycin resistance/extradiol dioxygenase family protein	NA	NA	NA	NA
AMG35482.1\|1221659_1222682_+	LLM class flavin-dependent oxidoreductase	NA	NA	NA	NA
AMG35483.1\|1222882_1223257_+	thioredoxin	V9SJ74	Achromobacter_phage	5.5e-10	26.8
AMG35484.1\|1223290_1223878_-	DUF1949 domain-containing protein	A0A1X9I5T8	Streptococcus_phage	1.2e-19	39.6

DBSCAN-SWA_2

1973669 : 1996281

Pseudomonas_phage(40.91%)

tail,head

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AMG36099.1\|1973669_1974179_-	hypothetical protein	I6NSS1	Burkholderia_phage	1.3e-43	57.4
AMG36100.1\|1974181_1974625_-	hypothetical protein	A0A0A1IVG1	Pseudomonas_phage	2.0e-11	35.0
AMG36101.1\|1974722_1975172_-\|tail	phage tail protein	Q9ZXK5	Pseudomonas_virus	1.0e-26	48.6
AMG36102.2\|1975171_1976485_-	hypothetical protein	A0A2H4JF09	uncultured_Caudovirales_phage	3.8e-05	30.0
AMG36104.1\|1976484_1977150_-	DUF2612 domain-containing protein	D4N460	Pseudomonas_phage	1.6e-15	31.8
AMG36105.1\|1977149_1978601_-	hypothetical protein	A0A0N9SH53	Pseudomonas_phage	2.2e-75	36.0
AMG36106.1\|1978622_1978991_-	hypothetical protein	A0A218MAM6	Escherichia_phage	1.5e-12	36.2
AMG36107.1\|1978990_1979689_-	hypothetical protein	A0A2H4J8H6	uncultured_Caudovirales_phage	2.1e-10	29.7
AMG36108.1\|1979685_1980603_-	hypothetical protein	E5AGC0	Erwinia_phage	3.6e-39	32.2
AMG36109.1\|1980589_1980922_-	hypothetical protein	A0A0N9SG14	Pseudomonas_phage	2.1e-13	42.5
AMG36110.1\|1980926_1981547_-	hypothetical protein	I3PGV3	Xanthomonas_phage	1.7e-08	28.2
AMG36111.1\|1981560_1984023_-\|tail	tail tape measure protein	A0A0P0ZCJ4	Stx2-converting_phage	5.9e-20	28.3
AUZ18037.1\|1984019_1984247_-	hypothetical protein	NA	NA	NA	NA
AMG36112.1\|1984165_1984675_-	hypothetical protein	NA	NA	NA	NA
AMG36113.1\|1984674_1985103_-	DUF3277 domain-containing protein	A0A0N7GFC4	Pseudomonas_phage	8.7e-20	38.2
AMG36114.1\|1985118_1986477_-	DUF3383 domain-containing protein	A0A0N9SJA3	Pseudomonas_phage	3.3e-81	40.0
AMG36115.1\|1986543_1987002_-	hypothetical protein	NA	NA	NA	NA
AMG36116.1\|1987129_1987543_-	hypothetical protein	NA	NA	NA	NA
AMG36117.1\|1987547_1988000_-	hypothetical protein	A0A2K9V3I1	Faecalibacterium_phage	2.7e-11	32.8
AMG36118.1\|1987989_1988364_-	DUF4054 domain-containing protein	NA	NA	NA	NA
AMG36119.1\|1988366_1988753_-	hypothetical protein	NA	NA	NA	NA
AMG36120.1\|1988752_1989712_-	DUF2184 domain-containing protein	A0A0N9SG07	Pseudomonas_phage	2.0e-56	38.0
AMG36121.1\|1989779_1990232_-	hypothetical protein	NA	NA	NA	NA
AMG36122.1\|1990231_1991314_-	DUF2213 domain-containing protein	E5AGA6	Erwinia_phage	6.2e-54	39.6
AMG36123.2\|1991324_1992014_-\|head	phage head morphogenesis protein	I3PGT9	Xanthomonas_phage	5.9e-34	40.8
AMG36124.1\|1992105_1993386_-	DUF1073 domain-containing protein	A0A2H4PGN2	Escherichia_phage	5.6e-30	29.3
AMG36125.2\|1993385_1994909_-	hypothetical protein	A0A291LBL3	Klebsiella_phage	3.3e-114	46.8
AMG36126.1\|1994919_1995393_-	DUF2280 domain-containing protein	A0A125RNL6	Pseudomonas_phage	4.8e-35	56.6
AUZ18038.1\|1995930_1996281_-	hypothetical protein	A0A1B0VRJ1	Pseudomonas_phage	5.3e-15	44.1

DBSCAN-SWA_3

2129832 : 2147258

uncultured_Caudovirales_phage(17.65%)

tail,terminase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AMG40204.2\|2129832_2133663_-	hypothetical protein	I7HDJ4	Xanthomonas_virus	8.9e-55	27.2
AMG36243.1\|2133704_2134091_-	hypothetical protein	NA	NA	NA	NA
AMG36244.1\|2134092_2134569_-	DUF1833 domain-containing protein	I7GYA2	Xanthomonas_virus	3.8e-08	26.5
AMG36245.1\|2134570_2134915_-	hypothetical protein	NA	NA	NA	NA
AMG36246.1\|2134915_2137585_-\|tail	phage tail tape measure protein	A0A1V0E821	Vibrio_phage	3.7e-108	36.8
AMG36247.1\|2137609_2137900_-	hypothetical protein	A0A2H4JBP7	uncultured_Caudovirales_phage	1.9e-10	35.5
AMG36248.1\|2137917_2138247_-	hypothetical protein	A0A0M7QCN0	Escherichia_phage	7.7e-08	35.5
AMG40205.2\|2138259_2138778_-\|tail	phage tail protein	A0A2H4J6K6	uncultured_Caudovirales_phage	8.9e-27	39.9
AMG36249.1\|2138960_2139383_-	hypothetical protein	I6PDJ8	Cronobacter_phage	2.9e-07	29.2
AMG36250.1\|2139379_2139778_-	hypothetical protein	A0A088FBW9	Salmonella_phage	3.3e-21	42.4
AMG36251.1\|2139774_2140170_-	hypothetical protein	A0A2D2W284	Stenotrophomonas_phage	5.4e-08	36.7
AMG36252.1\|2140172_2140655_-	hypothetical protein	A0A2H4JE38	uncultured_Caudovirales_phage	6.8e-13	36.5
AMG36253.1\|2141074_2142043_-	hypothetical protein	R9TJ64	Synechococcus_phage	2.0e-125	73.2
AMG36254.1\|2142069_2142672_-	hypothetical protein	R9TF81	Synechococcus_phage	9.4e-28	46.5
AMG36255.1\|2142794_2143037_-	hypothetical protein	A0A0H5AUE5	Pseudomonas_phage	1.5e-16	54.5
AMG40206.1\|2143042_2144095_-	hypothetical protein	A0A0H5BBX3	Pseudomonas_phage	2.7e-94	50.6
AMG36256.1\|2144123_2145542_-	DUF4055 domain-containing protein	R9TF43	Synechococcus_phage	6.5e-96	41.1
AMG36257.1\|2145544_2146822_-\|terminase	terminase	A0A1B1P9C9	Acinetobacter_phage	1.7e-148	64.0
AMG36258.1\|2146808_2147258_-\|terminase	terminase	C7U0W1	Enterobacteria_phage	3.6e-40	63.1

DBSCAN-SWA_4

2270610 : 2284697

Burkholderia_phage(40.0%)

tail,integrase

attL 2264704:2264720|attR 2288557:2288573

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
2264704:2264720	attL	NA	NA	NA	NA
AMG36366.1\|2270610_2271141_-	hypothetical protein	A0A2H4JFP9	uncultured_Caudovirales_phage	8.2e-44	58.0
AMG36367.1\|2271130_2271592_-	hypothetical protein	A0A0U5LBV3	unidentified_phage	3.5e-14	38.0
AMG36368.1\|2271777_2272800_+\|integrase	site-specific integrase	A0A2H4JE37	uncultured_Caudovirales_phage	4.8e-24	32.2
AMG36369.1\|2272803_2273157_-\|tail	phage tail protein	NA	NA	NA	NA
AUZ18053.1\|2273929_2274916_-	hypothetical protein	A0A0A8J8U5	Ralstonia_phage	4.8e-29	35.2
AMG36370.1\|2274929_2275595_-	DUF2612 domain-containing protein	A9YX13	Burkholderia_phage	1.2e-73	61.6
AMG36371.1\|2275596_2276778_-	hypothetical protein	A9YX12	Burkholderia_phage	4.0e-131	64.1
AMG36372.1\|2276774_2277128_-	hypothetical protein	A9YX11	Burkholderia_phage	1.8e-34	65.8
AMG36373.1\|2277136_2277880_-	hypothetical protein	A9YX06	Burkholderia_phage	9.6e-83	62.2
AMG40216.1\|2277928_2278939_-	hypothetical protein	A9YX04	Burkholderia_phage	6.7e-79	52.4
AMG36374.1\|2278958_2279258_-	hypothetical protein	A0A2H4J495	uncultured_Caudovirales_phage	2.8e-17	46.0
AMG36375.2\|2279267_2279858_-	hypothetical protein	A0A0M3ULD5	Salmonella_phage	1.5e-17	32.6
AMG36376.1\|2279859_2281533_-\|tail	phage tail protein	NA	NA	NA	NA
AMG36377.1\|2281525_2281714_-	hypothetical protein	NA	NA	NA	NA
AMG36378.1\|2281710_2282160_-	hypothetical protein	A0A0N7IRF3	Acinetobacter_phage	3.8e-18	37.1
AMG36379.1\|2282163_2282604_-	DUF3277 domain-containing protein	A0A2H4J619	uncultured_Caudovirales_phage	5.2e-36	53.5
AMG36380.1\|2282617_2284093_-	DUF3383 domain-containing protein	A0A0P0I492	Acinetobacter_phage	1.7e-110	47.9
AMG36381.1\|2284103_2284697_-	hypothetical protein	A9YX29	Burkholderia_phage	1.5e-49	48.7
2288557:2288573	attR	NA	NA	NA	NA

DBSCAN-SWA_5

4840412 : 4857916

Burkholderia_virus(33.33%)

tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AMG38446.2\|4840412_4841771_+	DUF1254 domain-containing protein	M1H738	Paramecium_bursaria_Chlorella_virus	2.3e-42	28.8
AMG38447.2\|4841853_4842555_-	phage repressor protein	NA	NA	NA	NA
AMG38448.2\|4842827_4843418_+	hypothetical protein	NA	NA	NA	NA
AMG38449.1\|4843569_4844037_+	hypothetical protein	NA	NA	NA	NA
AMG38450.1\|4844042_4844516_+\|tail	phage tail protein	A4JX08	Burkholderia_virus	6.9e-26	44.4
AMG38451.1\|4844515_4844806_+	DUF4035 domain-containing protein	S4TND7	Salmonella_phage	7.0e-13	48.8
AUZ18169.1\|4844863_4846147_+\|tail	phage tail tape measure protein	K7PM62	Enterobacteria_phage	1.8e-15	27.6
AMG40338.1\|4846149_4846488_+\|tail	phage tail protein	Q6UAW6	Klebsiella_phage	5.8e-27	50.0
AUZ18170.1\|4846493_4849136_+	hypothetical protein	A0A1B1IX43	uncultured_Mediterranean_phage	7.8e-18	42.1
AMG38456.1\|4849138_4849867_+\|tail	phage minor tail protein L	A4JX13	Burkholderia_virus	3.9e-68	57.0
AMG38457.1\|4849869_4850649_+	hydrolase Nlp/P60	Q3HQU3	Burkholderia_phage	6.6e-66	48.1
AMG38458.1\|4850645_4851251_+\|tail	tail assembly protein	C7BGD3	Burkholderia_phage	6.5e-53	57.9
AMG40339.1\|4851376_4854880_+	host specificity protein J	A4JX16	Burkholderia_virus	9.3e-261	45.2
AMG38459.1\|4855237_4855450_+	hypothetical protein	NA	NA	NA	NA
AMG38460.1\|4855446_4856043_+\|tail	tail assembly protein	Q6JIL3	Burkholderia_virus	2.1e-51	53.3
AMG38461.1\|4856163_4857093_+	LysR family transcriptional regulator	NA	NA	NA	NA
AMG40340.2\|4857097_4857916_-	SDR family NAD(P)-dependent oxidoreductase	W8CYX9	Bacillus_phage	6.4e-11	50.7

DBSCAN-SWA_6

6713823 : 6790151

Burkholderia_virus(14.71%)

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

attL 6742690:6742710|attR 6793626:6793646

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AMG39934.1\|6713823_6716685_-\|tRNA	isoleucine--tRNA ligase	A0A1V0SJ93	Klosneuvirus	1.7e-74	25.9
AMG39935.1\|6716674_6717640_-	bifunctional riboflavin kinase/FAD synthetase	NA	NA	NA	NA
AMG39936.1\|6717703_6718369_+	phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	2.8e-25	36.2
AUZ18270.1\|6719382_6720777_+	rRNA methyltransferase	NA	NA	NA	NA
AMG39937.1\|6720799_6721195_-	hypothetical protein	NA	NA	NA	NA
AMG39938.1\|6721517_6722726_+	acyl-CoA desaturase	NA	NA	NA	NA
AMG39939.1\|6722722_6725014_+	DNA helicase II	A7KV33	Bacillus_phage	6.6e-106	35.7
AMG39940.1\|6725019_6725325_+	chorismate mutase	NA	NA	NA	NA
AUZ18229.1\|6725442_6726702_-	cytochrome-c peroxidase	NA	NA	NA	NA
AMG39941.2\|6726873_6729456_-	TonB-dependent receptor	NA	NA	NA	NA
AMG39942.1\|6729514_6731965_-	TonB-dependent receptor	NA	NA	NA	NA
AMG39943.2\|6732090_6734661_-	TonB-dependent receptor	NA	NA	NA	NA
AMG39944.1\|6735009_6735942_-	DUF4880 domain-containing protein	NA	NA	NA	NA
AMG39945.1\|6735938_6736427_-	RNA polymerase sigma factor	NA	NA	NA	NA
AMG39946.2\|6736552_6738487_-	ABC transporter	A0A2K9L0W2	Tupanvirus	1.3e-70	32.5
AMG39947.1\|6738483_6739380_-	50S ribosomal protein L3 N(5)-glutamine methyltransferase	NA	NA	NA	NA
AMG39948.1\|6739390_6740530_-	succinyl-diaminopimelate desuccinylase	NA	NA	NA	NA
AMG39949.1\|6740530_6741352_-	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase	NA	NA	NA	NA
AMG39950.2\|6741380_6742595_-	succinyldiaminopimelate transaminase	NA	NA	NA	NA
6742690:6742710	attL	NA	NA	NA	NA
AMG39951.1\|6742850_6743834_+\|integrase	site-specific integrase	A0A0A0YR56	Pseudomonas_phage	1.0e-55	43.8
AMG39952.1\|6744347_6744602_-	hypothetical protein	NA	NA	NA	NA
AMG39953.1\|6744602_6744899_-	ASCH domain-containing protein	A4PE68	Ralstonia_virus	1.1e-26	62.9
AMG39954.1\|6744891_6745464_-	hypothetical protein	NA	NA	NA	NA
AMG39955.1\|6745460_6746390_-	hypothetical protein	A0A291L9X3	Bordetella_phage	4.0e-17	37.3
AMG39956.1\|6746955_6747369_+	hypothetical protein	NA	NA	NA	NA
AMG39957.1\|6747365_6747590_-	hypothetical protein	A0A1B0VN94	Pseudomonas_phage	2.2e-14	60.7
AMG39958.2\|6747589_6747931_-	hypothetical protein	A0A248SL53	Klebsiella_phage	3.8e-18	42.7
AMG39959.1\|6748008_6748833_-	DNA methyltransferase	Q5QF26	Pseudomonas_virus	1.6e-94	64.0
AMG39960.1\|6748829_6749825_-	hypothetical protein	A1YZR3	Burkholderia_virus	9.3e-57	41.4
AUZ18271.1\|6750994_6751687_-	hypothetical protein	NA	NA	NA	NA
AMG39962.2\|6753607_6753988_+	hypothetical protein	NA	NA	NA	NA
AUZ18230.1\|6756293_6757532_-	ATPase	NA	NA	NA	NA
AMG39964.1\|6757659_6758748_-	phage repressor protein	L7TH81	Pseudomonas_virus	6.7e-08	36.6
AMG39965.2\|6758885_6759086_+	hypothetical protein	NA	NA	NA	NA
AMG39966.1\|6759270_6759663_-	hypothetical protein	NA	NA	NA	NA
AMG39967.1\|6759864_6760392_+	hypothetical protein	B7SYH6	Stenotrophomonas_phage	3.0e-22	35.9
AMG39968.1\|6760475_6760691_+	hypothetical protein	NA	NA	NA	NA
AMG39969.1\|6760683_6760968_+	hypothetical protein	NA	NA	NA	NA
AMG39970.2\|6760964_6761441_+	DUF1364 domain-containing protein	Q8W6N7	Burkholderia_virus	1.4e-13	43.2
AUZ18272.1\|6761437_6762379_+	hypothetical protein	A0A1W6JNY0	Morganella_phage	2.4e-14	44.6
AMG39971.2\|6762260_6763100_+	DNA replication protein DnaC	A0A067ZJ24	Vibrio_phage	6.9e-45	39.8
AMG39972.2\|6763096_6763537_+	VRR-NUC domain-containing protein	A0A1J0GWD9	Alteromonas_phage	1.3e-15	41.0
AMG39973.2\|6763686_6764112_+	hypothetical protein	NA	NA	NA	NA
AUZ18231.1\|6764747_6766472_-	OLD family endonuclease	NA	NA	NA	NA
AMG39975.1\|6766916_6767702_+	hypothetical protein	A0A1B0Z000	Pseudomonas_phage	2.5e-33	39.3
AMG39976.1\|6767698_6768196_+	DNA packaging Nu1	NA	NA	NA	NA
AUZ18273.1\|6768273_6770268_+\|terminase	terminase	R9TMM4	Vibrio_phage	2.0e-114	37.0
AMG39977.1\|6770314_6770521_+	hypothetical protein	A0A2H4EUL1	Aeromonas_phage	1.0e-05	41.2
AUZ18232.1\|6770517_6772017_+\|portal	phage portal protein	A0A2H4JFL5	uncultured_Caudovirales_phage	1.7e-126	51.0
AMG39978.2\|6771934_6773173_+\|protease	Clp protease ClpP	S5M7Q8	Escherichia_phage	2.4e-38	38.7
AMG39979.1\|6773200_6773551_+\|head	head decoration protein	A0A2H4JF15	uncultured_Caudovirales_phage	2.3e-18	47.8
AMG39980.1\|6773632_6774637_+\|capsid	major capsid protein	A0A2H4J890	uncultured_Caudovirales_phage	6.3e-69	42.8
AMG39981.1\|6774642_6774945_+	hypothetical protein	NA	NA	NA	NA
AMG39982.1\|6774941_6775364_+	hypothetical protein	NA	NA	NA	NA
AMG39983.1\|6775626_6776562_+	hypothetical protein	G8CLB2	Synechococcus_phage	1.3e-60	40.6
AUZ18233.1\|6776853_6777429_+	hypothetical protein	NA	NA	NA	NA
AMG39986.1\|6777462_6780435_+\|tail	phage tail tape measure protein	A0A2H4J9A1	uncultured_Caudovirales_phage	7.0e-92	32.2
AMG39987.1\|6780434_6780776_+\|tail	phage tail protein	Q6UAW6	Klebsiella_phage	2.2e-29	52.7
AMG39988.1\|6782304_6782748_+	hypothetical protein	NA	NA	NA	NA
AMG39989.1\|6782756_6783485_+\|tail	phage minor tail protein L	Q6JIL5	Burkholderia_virus	3.4e-64	54.5
AMG39990.1\|6783487_6784261_+	hydrolase Nlp/P60	Q3HQU3	Burkholderia_phage	6.5e-66	49.8
AMG39991.1\|6784264_6784858_+\|tail	tail assembly protein	Q6JIL3	Burkholderia_virus	8.0e-56	58.7
AMG39992.2\|6784854_6788034_+	host specificity protein J	A4JX16	Burkholderia_virus	7.2e-260	45.4
AUZ18234.1\|6788030_6788327_+	hypothetical protein	NA	NA	NA	NA
AUZ18235.1\|6788326_6789055_+	hypothetical protein	A0A0B5A5A1	Achromobacter_phage	7.0e-62	47.1
AMG39993.1\|6789156_6789600_+	hypothetical protein	A0A0U5LBV3	unidentified_phage	5.1e-15	42.2
AMG39994.1\|6789602_6790151_+	hypothetical protein	A0A0H5BBZ5	Pseudomonas_phage	3.7e-31	54.1
6793626:6793646	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