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_CP045782	Klebsiella pneumoniae strain LEMB18 chromosome, complete genome	0 crisprs	cas3,DEDDh,DinG,csa3,WYL	0	0	6	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

16677 : 84596

Enterobacteria_phage(51.43%)

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

attL 43860:43877|attR 79333:79350

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_102001278.1\|16677_17784_-\|tRNA	tRNA 2-thiouridine(34) synthase MnmA	NA	NA	NA	NA
WP_004150802.1\|17840_18299_-	NUDIX hydrolase	NA	NA	NA	NA
WP_004150801.1\|18315_18966_-	23S rRNA pseudouridine(2457) synthase RluE	NA	NA	NA	NA
WP_004150800.1\|19206_20457_+	NADP-dependent isocitrate dehydrogenase	Q77Z09	Phage_21	1.1e-19	92.6
WP_065518563.1\|20729_21443_-	metalloregulator ArsR/SmtB family transcription factor	NA	NA	NA	NA
WP_004150798.1\|21439_21832_-	amino acid-binding protein	NA	NA	NA	NA
WP_040235838.1\|21824_22148_-	antibiotic biosynthesis monooxygenase	NA	NA	NA	NA
WP_004140530.1\|22584_22812_-	DUF1272 domain-containing protein	NA	NA	NA	NA
WP_004140529.1\|22924_24118_-	glutathione-dependent formaldehyde dehydrogenase	NA	NA	NA	NA
WP_004148025.1\|24185_24521_-	hypothetical protein	NA	NA	NA	NA
WP_004150795.1\|24740_24926_+	general stress protein	NA	NA	NA	NA
WP_004148027.1\|25016_25511_+	ferritin-like domain-containing protein	NA	NA	NA	NA
WP_004140514.1\|25537_26044_+	ferritin-like domain-containing protein	NA	NA	NA	NA
WP_004140512.1\|26060_26948_+	manganese catalase family protein	NA	NA	NA	NA
WP_004140511.1\|27003_28410_+	cytochrome ubiquinol oxidase subunit I	NA	NA	NA	NA
WP_004140509.1\|28406_29417_+	cytochrome d ubiquinol oxidase subunit II	NA	NA	NA	NA
WP_004140506.1\|29532_29730_-	hypothetical protein	NA	NA	NA	NA
WP_004150791.1\|30296_30929_+	DNA-binding protein	NA	NA	NA	NA
WP_153244925.1\|30907_31096_-	hypothetical protein	NA	NA	NA	NA
WP_004150790.1\|31545_32232_+	EAL domain-containing protein	NA	NA	NA	NA
WP_004140497.1\|32542_34051_-	UbiD family decarboxylase	NA	NA	NA	NA
WP_004150788.1\|34171_35062_+	LysR family transcriptional regulator	NA	NA	NA	NA
WP_029602490.1\|35068_36853_-	sensor domain-containing diguanylate cyclase	A0A127AWB9	Bacillus_phage	2.6e-17	38.5
WP_004140494.1\|36926_38135_-	HD domain-containing protein	NA	NA	NA	NA
WP_004892909.1\|38437_39481_+	type II asparaginase	NA	NA	NA	NA
WP_004148038.1\|40142_41057_+	kdo(2)-lipid IV(A) palmitoleoyltransferase	A0A1W6JP29	Morganella_phage	1.1e-72	50.4
WP_004150783.1\|41146_41785_+	leucine efflux protein LeuE	NA	NA	NA	NA
WP_004140489.1\|41915_42179_+	DUF2534 family protein	NA	NA	NA	NA
WP_004140488.1\|42238_42364_-	hypothetical protein	NA	NA	NA	NA
WP_004213093.1\|42481_42556_-	protein YoaJ	NA	NA	NA	NA
WP_004150782.1\|42555_42657_-	YoaK family small membrane protein	NA	NA	NA	NA
WP_004176549.1\|42714_43728_-	sensor domain-containing diguanylate cyclase	A0A127AWB9	Bacillus_phage	1.9e-12	29.0
43860:43877	attL	NA	NA	NA	NA
WP_004213094.1\|43993_44977_-\|integrase	tyrosine-type recombinase/integrase	Q83VS6	Escherichia_phage	2.4e-150	79.8
WP_004213095.1\|45092_45392_-	helix-turn-helix transcriptional regulator	Q1JS61	Enterobacteria_phage	6.5e-38	77.8
WP_004131514.1\|45512_45791_+	hypothetical protein	Q1JS60	Enterobacteria_phage	5.3e-42	88.8
WP_004131515.1\|45811_46030_+	hypothetical protein	A0A0M5M1I3	Salmonella_phage	4.7e-06	49.1
WP_032432798.1\|46045_46423_+	hypothetical protein	NA	NA	NA	NA
WP_004213097.1\|46438_46711_+	hypothetical protein	NA	NA	NA	NA
WP_004213098.1\|46779_47004_+	hypothetical protein	NA	NA	NA	NA
WP_032444258.1\|47000_47567_+	3'-5' exoribonuclease	D4HTX2	Vibrio_phage	1.6e-13	33.2
WP_102001270.1\|47799_48756_+	Dam family site-specific DNA-(adenine-N6)-methyltransferase	A0A0M4QWR0	Salmonella_phage	1.0e-84	52.9
WP_102001269.1\|48773_51401_+	replication endonuclease	A0A0M4RTM8	Salmonella_phage	2.5e-189	50.0
WP_032442256.1\|51397_51907_+	hypothetical protein	NA	NA	NA	NA
WP_032442255.1\|52121_53087_-	DUF2806 domain-containing protein	NA	NA	NA	NA
WP_102001268.1\|53522_54584_-\|portal	phage portal protein	A0A0A7NPT9	Enterobacteria_phage	6.3e-144	68.1
WP_023287464.1\|54577_56305_-	helix-turn-helix domain-containing protein	A0A0A7NV54	Enterobacteria_phage	1.8e-233	68.3
WP_004215891.1\|56461_57301_+\|capsid	GPO family capsid scaffolding protein	A0A0A7NRY7	Enterobacteria_phage	1.9e-95	66.3
WP_004213107.1\|57310_58345_+\|capsid	phage major capsid protein, P2 family	A0A0M3ULA3	Salmonella_phage	6.2e-96	50.0
WP_102001267.1\|58394_59252_+\|terminase	terminase	A0A0A7NPX9	Enterobacteria_phage	5.7e-71	58.6
WP_004213109.1\|59364_59880_+\|head	head completion/stabilization protein	A0A0A7NPU2	Enterobacteria_phage	4.1e-40	49.4
WP_004131559.1\|59879_60080_+\|tail	tail protein	A0A0A7NV57	Enterobacteria_phage	1.6e-16	63.1
WP_004215823.1\|60070_60355_+	hypothetical protein	NA	NA	NA	NA
WP_004213111.1\|60351_60897_+	lysozyme	Q1I0Z1	Pasteurella_virus	1.3e-31	44.1
WP_004213112.1\|60908_61238_+	DUF2570 domain-containing protein	NA	NA	NA	NA
WP_023287467.1\|61419_61887_+\|tail	phage tail protein	A0A0A7NPU6	Enterobacteria_phage	5.4e-47	59.5
WP_102001266.1\|61883_62519_+	phage virion morphogenesis protein	A0A0A7NV60	Enterobacteria_phage	2.3e-56	51.9
WP_102001265.1\|62515_63103_+\|plate	phage baseplate assembly protein V	A0A0A7NRZ3	Enterobacteria_phage	4.1e-60	60.0
WP_004215831.1\|63099_63450_+	GPW/gp25 family protein	A0A0A7NQ90	Enterobacteria_phage	2.1e-27	55.7
WP_004213117.1\|63451_64375_+\|plate	baseplate assembly protein J	A0A0A7NPY5	Enterobacteria_phage	9.9e-53	43.9
WP_102001264.1\|64364_67391_+\|tail	phage tail protein I	D5LGZ2	Escherichia_phage	6.4e-24	40.7
WP_009486478.1\|67387_67600_+	hypothetical protein	NA	NA	NA	NA
WP_082225713.1\|67599_68697_+\|tail	phage tail protein	G4KKN6	Yersinia_phage	1.8e-08	74.4
WP_082225714.1\|68775_69615_-	hypothetical protein	NA	NA	NA	NA
WP_102001262.1\|69616_71860_-	AAA family ATPase	Q7Y4B3	Escherichia_virus	1.0e-10	24.9
WP_153676837.1\|71969_72461_-\|tail	phage tail protein	A0A0A7NV65	Enterobacteria_phage	4.9e-51	58.8
WP_102001261.1\|72476_75452_-\|tail	phage tail tape measure protein	A0A0A7NRZ9	Enterobacteria_phage	3.7e-218	46.3
WP_071993210.1\|75438_75576_-\|tail	GpE family phage tail protein	A0A0A7NQ96	Enterobacteria_phage	5.8e-10	65.9
WP_082225718.1\|75596_75914_-\|tail	phage tail protein	B9A7B2	Serratia_phage	4.6e-18	55.9
WP_023287479.1\|75960_76476_-\|tail	phage major tail tube protein	A0A0A7NPV8	Enterobacteria_phage	3.7e-57	61.2
WP_082225719.1\|76475_77648_-\|tail	phage tail sheath family protein	A0A0A7NV69	Enterobacteria_phage	1.6e-156	69.7
WP_075648433.1\|77802_78942_+	phage late control D family protein	B9A7A9	Serratia_phage	7.2e-146	70.7
WP_004213128.1\|78985_79237_+	ogr/Delta-like zinc finger family protein	A0A2I8TV89	Erwinia_phage	3.4e-08	49.2
WP_004179368.1\|79502_79742_+	DUF333 domain-containing protein	NA	NA	NA	NA
79333:79350	attR	NA	NA	NA	NA
WP_004150779.1\|79731_80088_-	DUF488 domain-containing protein	NA	NA	NA	NA
WP_004176547.1\|80074_80584_-	DUF523 domain-containing protein	NA	NA	NA	NA
WP_004140471.1\|80729_81422_+	CTP synthase	NA	NA	NA	NA
WP_153676838.1\|81453_82638_-	CynX/NimT family MFS transporter	NA	NA	NA	NA
WP_102001277.1\|82739_83549_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_002901080.1\|83532_83979_-	DUF441 domain-containing protein	NA	NA	NA	NA
WP_004892876.1\|84095_84596_-\|tRNA	YbaK/prolyl-tRNA synthetase associated domain-containing protein	NA	NA	NA	NA

DBSCAN-SWA_2

197552 : 212439

Salmonella_phage(40.0%)

integrase

attL 198336:198348|attR 204872:204884

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_004140269.1\|197552_198362_-	peptide ABC transporter ATP-binding protein SapF	A0A2H4PQG7	Staphylococcus_phage	2.1e-14	28.9
198336:198348	attL	NA	NA	NA	NA
WP_004140266.1\|198363_199356_-	peptide ABC transporter ATP-binding protein SapD	G9BWD6	Planktothrix_phage	3.0e-07	27.2
WP_004151901.1\|199355_200246_-	peptide ABC transporter permease SapC	NA	NA	NA	NA
WP_094354552.1\|200422_201610_+\|integrase	site-specific integrase	K7PGY1	Enterobacteria_phage	3.2e-120	52.2
WP_004892750.1\|201830_202070_-	DUF4060 family protein	M9P0E0	Enterobacteria_phage	8.0e-23	70.1
WP_032445491.1\|202077_202386_-	hypothetical protein	I6PD68	Cronobacter_phage	7.1e-24	55.9
WP_153676840.1\|202382_202994_-	DUF550 domain-containing protein	S4TSR6	Salmonella_phage	4.1e-39	76.3
WP_032445496.1\|202986_203331_-	hypothetical protein	NA	NA	NA	NA
WP_023286270.1\|203365_204454_-	recombinase RecT	H6WRX0	Salmonella_phage	3.7e-107	56.2
WP_153676841.1\|204466_207505_-	exodeoxyribonuclease	H6WRX1	Salmonella_phage	2.6e-291	57.2
204872:204884	attR	NA	NA	NA	NA
WP_153676842.1\|207642_207798_-	hypothetical protein	K7PGY4	Enterobacteria_phage	2.6e-14	74.0
WP_020804303.1\|207806_207998_-	YebW family protein	NA	NA	NA	NA
WP_022631176.1\|208104_208203_-	hypothetical protein	NA	NA	NA	NA
WP_153591391.1\|208291_208522_+	hypothetical protein	NA	NA	NA	NA
WP_049124969.1\|208780_209203_-	transcriptional regulator	A0A0H5BBV1	Pseudomonas_phage	3.2e-06	53.5
WP_023301223.1\|209305_209536_+	helix-turn-helix domain-containing protein	H6WRX5	Salmonella_phage	4.0e-11	42.7
WP_023320776.1\|209538_210075_+	bacteriophage regulatory protein CII	M9NZI6	Enterobacteria_phage	2.4e-59	68.3
WP_153676843.1\|210085_210349_+	hypothetical protein	NA	NA	NA	NA
WP_004215886.1\|210426_211347_+	hypothetical protein	K7PGZ0	Enterobacteria_phage	1.7e-92	61.3
WP_004215885.1\|211343_212087_+	replication protein P	A0A0M3ULE2	Salmonella_phage	3.1e-65	55.2
WP_153676844.1\|212079_212439_+	DUF977 family protein	H6WRX9	Salmonella_phage	4.7e-11	43.0

DBSCAN-SWA_3

218099 : 245861

Klebsiella_phage(20.0%)

holin,terminase,tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_004184503.1\|218099_218333_+	DinI-like family protein	K7PM44	Enterobacteria_phage	2.9e-25	68.8
WP_153676849.1\|218442_218664_+	hypothetical protein	NA	NA	NA	NA
WP_153676850.1\|218744_219344_+	DUF1367 family protein	K7PKS6	Enterobacteria_phage	1.7e-90	79.9
WP_032418472.1\|219552_219849_+	DUF1364 domain-containing protein	A0A0U2KD41	Escherichia_phage	4.6e-36	71.9
WP_023282412.1\|219845_220202_+	RusA family crossover junction endodeoxyribonuclease	K7P6W0	Enterobacteria_phage	1.5e-41	64.1
WP_023282413.1\|220317_221139_+	antitermination protein	K7PKS8	Enterobacteria_phage	4.0e-98	67.1
WP_001294159.1\|221832_222219_+	membrane protein	A0A192Y8P2	Salmonella_phage	1.6e-57	90.6
WP_071603196.1\|222205_222487_+\|holin	phage holin family protein	K7PKN9	Enterobacterial_phage	2.4e-18	47.3
WP_023282414.1\|222486_223116_+	glycoside hydrolase family 19 protein	F1C591	Cronobacter_phage	9.3e-87	74.4
WP_153676851.1\|223118_223394_+	hypothetical protein	G8C7W1	Escherichia_phage	3.8e-08	40.4
WP_016831932.1\|223577_223778_+	hypothetical protein	A0A1L6Z528	Klebsiella_phage	5.9e-19	73.3
WP_016831934.1\|224518_224740_+	hypothetical protein	NA	NA	NA	NA
WP_016831935.1\|225024_225270_+	DUF2560 family protein	A0A286N2R1	Klebsiella_phage	6.7e-33	95.1
WP_135715651.1\|225618_226614_+\|terminase	terminase small subunit	Q5QF76	Pseudomonas_virus	1.1e-38	45.5
WP_016946682.1\|226597_227911_+\|terminase	terminase	A0A0S2SYF1	Pseudomonas_phage	2.2e-183	73.6
WP_153676852.1\|227912_229313_+	DUF4055 domain-containing protein	A0A1B0VMH0	Pseudomonas_phage	1.9e-127	53.7
WP_153676853.1\|229296_230409_+	hypothetical protein	I6PD76	Cronobacter_phage	5.3e-109	55.2
WP_016946679.1\|230493_231279_+	hypothetical protein	A0A1B0VMG1	Pseudomonas_phage	1.0e-66	63.9
WP_102962071.1\|231289_232243_+	Ig domain-containing protein	A0A1B0VMF8	Pseudomonas_phage	6.5e-132	74.4
WP_023300922.1\|232564_232960_+	hypothetical protein	A0A0S2SYB7	Pseudomonas_phage	3.3e-13	43.3
WP_004190649.1\|232961_233216_+	hypothetical protein	J9Q7U0	Salmonella_phage	8.0e-21	52.4
WP_072032792.1\|233225_233459_+	hypothetical protein	A0A2H4J0Y9	uncultured_Caudovirales_phage	3.8e-09	45.6
WP_004217344.1\|233445_233829_+	hypothetical protein	A0A0S2SYG4	Pseudomonas_phage	7.1e-21	45.2
WP_047694613.1\|233830_234382_+	hypothetical protein	G8C7Q1	Escherichia_phage	3.9e-28	39.3
WP_004190640.1\|234378_234771_+	electron transfer flavoprotein subunit beta	NA	NA	NA	NA
WP_087783577.1\|234794_235967_+	Ig domain-containing protein	A0A0D4DBN5	Acinetobacter_phage	9.4e-24	27.0
WP_004190637.1\|236020_236503_+	hypothetical protein	NA	NA	NA	NA
WP_016831940.1\|236640_236847_+	hypothetical protein	NA	NA	NA	NA
WP_004217333.1\|236923_237280_+	hypothetical protein	A0A1V0E5P9	Salmonella_phage	1.1e-44	75.0
WP_077255553.1\|237276_237759_+	zinc ribbon domain-containing protein	I6PDJ9	Cronobacter_phage	1.1e-18	43.6
WP_153676854.1\|237832_240730_+\|tail	phage tail protein	A0A2H4J107	uncultured_Caudovirales_phage	2.3e-103	32.7
WP_015958316.1\|240813_241149_+	hypothetical protein	NA	NA	NA	NA
WP_047694619.1\|241463_241937_+	hypothetical protein	A0A286S298	Klebsiella_phage	1.9e-60	68.6
WP_032433045.1\|241923_242406_+	DUF1833 domain-containing protein	A0A286S2B1	Klebsiella_phage	4.3e-84	97.5
WP_017880229.1\|242415_242796_+	hypothetical protein	A0A286S2A6	Klebsiella_phage	4.6e-73	100.0
WP_153676855.1\|242792_245861_+	kinase	A0A286S259	Klebsiella_phage	0.0e+00	98.0

DBSCAN-SWA_4

526389 : 537276

Escherichia_phage(87.5%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_060589161.1\|526389_527010_-	aldolase	A0A077SK32	Escherichia_phage	2.3e-114	99.5
WP_004224682.1\|527002_528268_-	four-carbon acid sugar kinase family protein	A0A077SLJ7	Escherichia_phage	7.8e-234	99.8
WP_002903955.1\|528279_529182_-	NAD(P)-dependent oxidoreductase	A0A077SLF7	Escherichia_phage	2.6e-159	99.7
WP_002210513.1\|529442_530204_+	DeoR/GlpR transcriptional regulator	A0A077SK06	Escherichia_phage	1.9e-134	100.0
WP_004176269.1\|530224_531085_-	class A broad-spectrum beta-lactamase SHV-11	A0A077SL40	Escherichia_phage	2.2e-155	99.3
WP_004176262.1\|531382_531643_+	hypothetical protein	A0A077SK33	Escherichia_phage	5.4e-41	98.8
WP_001620097.1\|531729_532818_+	AAA family ATPase	A0A077SLJ9	Escherichia_phage	8.0e-211	100.0
WP_004176258.1\|532848_534114_-	MFS transporter	NA	NA	NA	NA
WP_004190234.1\|534168_537276_-	beta-galactosidase	L0N6M2	Herpes_simplex_virus	0.0e+00	59.5

DBSCAN-SWA_5

1494782 : 1501687

Bacillus_phage(33.33%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_064278091.1\|1494782_1496261_+	two-component system sensor histidine kinase BaeS	W8CYF6	Bacillus_phage	1.4e-29	28.3
WP_004175198.1\|1496257_1496980_+	two-component system response regulator BaeR	W8CYM9	Bacillus_phage	8.3e-31	33.2
WP_004144192.1\|1497298_1498660_+\|tRNA	tRNA 5-hydroxyuridine modification protein YegQ	Q6DW11	Phage_TP	1.8e-207	94.8
WP_002912636.1\|1498905_1499799_+	lipid kinase YegS	A0A1V0SBJ0	Catovirus	6.1e-15	29.8
WP_004180550.1\|1500039_1500813_-	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	3.9e-26	36.7
WP_004175147.1\|1500823_1501687_-	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	5.7e-10	27.5

DBSCAN-SWA_6

4990931 : 5000394

Dickeya_phage(16.67%)

tRNA,protease

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002896440.1\|4990931_4992047_+	macrolide transporter subunit MacA	A0A140XAI1	Dickeya_phage	1.3e-06	52.7
WP_102000964.1\|4992043_4993984_+	macrolide ABC transporter ATP-binding protein/permease MacB	G9BWD6	Planktothrix_phage	5.0e-38	41.0
WP_002896516.1\|4994060_4994282_-	cold shock-like protein CspD	A0A2H4N7Y6	Lake_Baikal_phage	1.3e-16	61.2
WP_002896520.1\|4994607_4994925_+\|protease	ATP-dependent Clp protease adapter ClpS	A0A1B1IT64	uncultured_Mediterranean_phage	2.0e-13	45.7
WP_002896522.1\|4994955_4997235_+\|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	A0A223W0B1	Agrobacterium_phage	1.6e-165	42.0
WP_001040187.1\|4997354_4997573_-	translation initiation factor IF-1	NA	NA	NA	NA
WP_002898014.1\|4997926_4998628_-\|tRNA	leucyl/phenylalanyl-tRNA--protein transferase	NA	NA	NA	NA
WP_004191145.1\|4998672_5000394_-	cysteine/glutathione ABC transporter ATP-binding protein/permease CydC	A0A2R8FG22	Brazilian_cedratvirus	1.2e-14	34.3

Anti-CRISPR protein detection

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