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_CP006738	Klebsiella pneumoniae HK787 chromosome, complete genome	1 crisprs	RT,csa3,cas3,DEDDh,DinG,WYL	0	1	6	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP006738_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP006738_1

3962695-3962790

Orphan

Consensus_repeat	Method
TGGCACTTTGTTGGCATTCTGTTGGCACAA	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_CP006738_1

>merge|NZ_CP006738|1|3962695-3962790|CRISPRCasFinder
TGGCACTTTGTTGGCATTCTGTTGGCACAACCTCGCCGGTACGCAGCGTGGTTACTGGGTTTGCGTTGGCACTTTGTTGGCATTCTGTTGGCACAA

>NZ_CP006738|1|1|3962695-3962790|CRISPRCasFinder
TGGCACTTTGTTGGCATTCTGTTGGCACAA	CCTCGCCGGTACGCAGCGTGGTTACTGGGTTTGCGT
TGGCACTTTGTTGGCATTCTGTTGGCACAA

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP006738.1\|WP_039108792.1\|3965097_3965445_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP006738.1\|WP_075209545.1\|3960864_3962280_-\|AAA-family-ATPase	unknown	unknown	gnl\|CDD\|274672
NZ_CP006738.1\|WP_004884186.1\|3960341_3960566_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|377645
NZ_CP006738.1\|WP_039108790.1\|3963408_3963630_-\|bacteriophage-CII-family-protein	unknown	unknown	gnl\|CDD\|336083
NZ_CP006738.1\|WP_004884208.1\|3959871_3960345_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|349904
NZ_CP006738.1\|WP_004191589.1\|3963669_3963888_-\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|238045
NZ_CP006738.1\|WP_039108779.1\|3957396_3957717_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|223880
NZ_CP006738.1\|WP_039108801.1\|3967064_3967811_+\|phage-recombination-protein-Bet	unknown	unknown	gnl\|CDD\|273871
NZ_CP006738.1\|WP_074423018.1\|3966362_3966488_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP006738.1\|WP_039108794.1\|3965651_3965864_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP006738.1\|WP_039108787.1\|3960562_3960865_-\|MarR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|378956
NZ_CP006738.1\|WP_052253486.1\|3958130_3958802_-\|DUF551-domain-containing-protein	unknown	unknown	gnl\|CDD\|367946
NZ_CP006738.1\|WP_004884201.1\|3959611_3959875_-\|DUF4752-family-protein	unknown	unknown	gnl\|CDD\|339554
NZ_CP006738.1\|WP_004151298.1\|3963176_3963323_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP006738.1\|WP_029602865.1\|3958798_3959092_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP006738.1\|WP_039108777.1\|3956574_3957042_-\|recombination-protein-NinB	unknown	unknown	gnl\|CDD\|368607
NZ_CP006738.1\|WP_039108796.1\|3966480_3966675_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP006738.1\|WP_004191591.1\|3963996_3964656_+\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|224885
NZ_CP006738.1\|WP_039108784.1\|3959091_3959619_-\|ead/Ea22-like-family-protein	unknown	unknown	unknown
NZ_CP006738.1\|WP_039108798.1\|3966763_3967048_+\|host-nuclease-inhibitor-GamL	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NZ_CP006738.1\|WP_004884186.1\|3960341_3960566_-\|hypothetical-protein	gnl\|CDD\|377645	pfam06289, FlbD, Flagellar protein (FlbD). This family consists of several bacterial FlbD flagellar proteins. The exact function of this family is unknown.	0.00569857
NZ_CP006738.1\|WP_039108790.1\|3963408_3963630_-\|bacteriophage-CII-family-protein	gnl\|CDD\|336083	pfam05269, Phage_CII, Bacteriophage CII protein. This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages.	6.54889e-09
NZ_CP006738.1\|WP_004884208.1\|3959871_3960345_-\|hypothetical-protein	gnl\|CDD\|349904	cd05653, M20_ArgE_LysK, M20 Peptidase acetylornithine deacetylase/acetyl-lysine deacetylase. Peptidase M20 family, acetylornithine deacetylase (ArgE)/acetyl-lysine deacetylase (LysK) subfamily. Proteins in this subfamily are mainly archaeal with related bacterial species and are deacetylases with specificity for both N-acetyl-ornithine and N-acetyl-lysine found within a lysine biosynthesis operon. ArgE catalyzes the conversion of N-acetylornithine to ornithine, while LysK, a homolog of ArgE, has deacetylating activities for both N-acetyllysine and N-acetylornithine at almost equal efficiency. These results suggest that LysK which may share an ancestor with ArgE functions not only for lysine biosynthesis, but also for arginine biosynthesis in species such as Thermus thermophilus. The substrate specificity of ArgE is quite broad in that several alpha-N-acyl-L-amino acids can be hydrolyzed, including alpha-N-acetylmethionine and alpha-N-formylmethionine. ArgE shares significant sequence homology and biochemical features, and possibly a common origin, with glutamate carboxypeptidase (CPG2) and succinyl-diaminopimelate desuccinylase (DapE), and aminoacylase I (ACY1), having all metal ligand binding residues conserved.	0.00202962
NZ_CP006738.1\|WP_004191589.1\|3963669_3963888_-\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|238045	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.	3.00798e-11
NZ_CP006738.1\|WP_039108779.1\|3957396_3957717_-\|hypothetical-protein	gnl\|CDD\|223880	COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane].	7.68553e-05
NZ_CP006738.1\|WP_039108801.1\|3967064_3967811_+\|phage-recombination-protein-Bet	gnl\|CDD\|273871	TIGR01913, Uncharacterized_protein_UU154, phage recombination protein Bet. This model represents the phage recombination protein Bet from a number of phage, including phage lambda. All members of this family are found in phage genomes or in putative prophage regions of bacterial genomes. [Mobile and extrachromosomal element functions, Prophage functions].	2.05022e-39
NZ_CP006738.1\|WP_039108787.1\|3960562_3960865_-\|MarR-family-transcriptional-regulator	gnl\|CDD\|378956	pfam12802, MarR_2, MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.	0.00137373
NZ_CP006738.1\|WP_052253486.1\|3958130_3958802_-\|DUF551-domain-containing-protein	gnl\|CDD\|367946	pfam04448, DUF551, Protein of unknown function (DUF551). This family represents the carboxy terminus of a protein of unknown function, found in dsDNA viruses with no RNA stage, including bacteriophages lambda and P22, and also in some Escherichia coli prophages.	9.52141e-10
NZ_CP006738.1\|WP_004884201.1\|3959611_3959875_-\|DUF4752-family-protein	gnl\|CDD\|339554	pfam15944, DUF4752, Domain of unknown function (DUF4752). This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 90 and 105 amino acids in length. There is a conserved GLA sequence motif.	6.40183e-41
NZ_CP006738.1\|WP_039108777.1\|3956574_3957042_-\|recombination-protein-NinB	gnl\|CDD\|368607	pfam05772, NinB, NinB protein. The ninR region of phage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage lambda. NinB binds to single-stranded DNA.	2.29258e-48
NZ_CP006738.1\|WP_004191591.1\|3963996_3964656_+\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|224885	COG1974, LexA, SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms].	1.60132e-32
NZ_CP006738.1\|WP_075209545.1\|3960864_3962280_-\|AAA-family-ATPase	gnl\|CDD\|274672	TIGR03600, phage_DnaB, phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model. [Mobile and extrachromosomal element functions, Prophage functions].	4.97498e-157

>NZ_CP006738.1|WP_075209545.1|3960864_3962280_-|AAA-family-ATPase
MTPPHSIEAEQSVLGGLLLDDDNSERTQKVLSILKPESFYARQHQVIFAEMRQMYRDHKPVDLLTLFDALDSKGLTETVGGFAYLAEMSKNTPSAANIVAYAMRVRETAMERYGIEKTTKAIELLYARNGMTAEQKFDAIQGLFTEITEHVKTGRRTGLRTFYDAVTDWSAEFDERLKPDGRSRGLSTGIRSLDELLGVKRIVRGSLFVIGARPKMGKTTLYTQMGVNCATVENEPALMFSLEMPEGQMVEKITAQKGRISPNLFYPDMTKDDYGYHGDWNSDLKKATGVMGALIDTNNLLIDDTPGISLAHVMAESRRIKRERGKVGMILVDYLTLMTADKAERNDLAYGLITKGLKTLAKELDCVVVLLTQLNRELEKRTNKRPLPSDSRDTGQIEQDCDYWLAIYREGAYDENANQSDTELLLRLNRHGETGVVYCEQRHGAIYDCDQEAASQRRREKEEKPTKRGGF
>NZ_CP006738.1|WP_039108787.1|3960562_3960865_-|MarR-family-transcriptional-regulator
MKKNSGKQVVLNYVSQHPGCTFQDIRRGTGLDSSVVNSSLWQMHRDGQVKREGECRSYRYTLIDTTAVTESDPSVQYRQRPGGVNPMTNLFNQCLAGVRK
>NZ_CP006738.1|WP_004884186.1|3960341_3960566_-|hypothetical-protein
MKFIKLSQRGTVERQGKYGWEPETVYEPVFVAAEHIVSMYFAGLTILKMTSGERIDVKETPEEIIAMLTEGASK
>NZ_CP006738.1|WP_004884208.1|3959871_3960345_-|hypothetical-protein
MTITLQAVNELIASLESAGELSIREQKFLKLAKEFRICSASLDAAIKTGNMLADQNAQLAAENVALKNAFGPGDSVLNFLTIALRHTTYDRIDLDDVTLAFKMSLPETPTTARIVAEAEARGVEKAIAHLEKKFSNIGVQIMNLQWLADSLREGADK
>NZ_CP006738.1|WP_004884201.1|3959611_3959875_-|DUF4752-family-protein
MNIATYLNTGLAILGWAYIMVKTGQWVTKNALRQWDKRRKESRRQKAVNEFYDAFELNSLEPGSTVRLATKGDLTIMMFRSEGKSND
>NZ_CP006738.1|WP_039108784.1|3959091_3959619_-|ead/Ea22-like-family-protein
MTDITELALRLKLEAHRAVSNFNPKMNIKTRDLMALVEALESEKRICATWRKTAKSTGEKLEKAQTINAAAEKLVRCKGRYHSEQNYRSLAALFGVTTPDLPPLEHENVHYADAAEMEIAALRQRIAELESRTVKLPDLRQIVSGDRYVWSDGVYNYSQDVKVALAAAGIKVEVE
>NZ_CP006738.1|WP_029602865.1|3958798_3959092_-|hypothetical-protein
MWRGTDRTRSQMILTEYRYDPKAKDSKSVYLVRHNSRIHQTVLEQHLTIERDSFGRFIPTIELKDFPEGLSDRESMLKLADWLHRLGVAIEDNWSQP
>NZ_CP006738.1|WP_052253486.1|3958130_3958802_-|DUF551-domain-containing-protein
MTKSTITRERIQRIIRAINSEAYDEEEIREWLSSDEIMELSRMALAAMDGEPDCNERNLFCSTDTARMRKVISVSAGTGDAPLYRRAQPALVIPDEMTAEQAYEIGYYYGDPVNVFARGANWMRQHIIDSTLAAAQHDTPALNSVQSVVTVPGKWIPVSERMPEVGVKVLCFPAEDEPIHAVFNGQLWLQDVSWSGSEEPIDNVIPVTVTHWMPLPAGPQEVR
>NZ_CP006738.1|WP_039108779.1|3957396_3957717_-|hypothetical-protein
MKKTLLLVCAVLVSNVALAIEKKEEIVPVRISCPAPVMPVKAQALRIEGSVDYAAWVNDKGDVYSVDITGDEVFFREAEVAIKKCKFMLGHPGVYRDTIKFSLVKP
>NZ_CP006738.1|WP_039108777.1|3956574_3957042_-|recombination-protein-NinB
MKQQFCLINDNVKRNVVNFIQSLPVDHRSPLIIEAREESRTDKQNRLMWPLLKDLSDQVIWHGEKLEPAEWKDLITVLVSQMQNPEREQKSAPGINGGRVYFGVRTSQSSKRYMVEVIEAIYWFGTEHNVKFSEKSSSRIAWAHEWRASHAQSAR
>NZ_CP006738.1|WP_004151298.1|3963176_3963323_-|hypothetical-protein
MPKSNRFYQAQTHKNVTRDRFIRSVNPVVGMKMRAILEELKRKEEGRE
>NZ_CP006738.1|WP_039108790.1|3963408_3963630_-|bacteriophage-CII-family-protein
MESSMTRNKVEARRIESWLHSQIAELGTTNIAKVAGVNKSTVSRWRESLLPNMSLLLAILISNRTGEKGDFEA
>NZ_CP006738.1|WP_004191589.1|3963669_3963888_-|helix-turn-helix-transcriptional-regulator
MNNLSKIRRRAGLTQRQIATELNLTAGAICHYENGKRDLSIEQCRKIVAALNKYGACVSIDDVFPPSKASAA
>NZ_CP006738.1|WP_004191591.1|3963996_3964656_+|helix-turn-helix-domain-containing-protein
MSMKWYDLAKSLMKTKGINQEELAEHLGITKGAVSHWLNARREPSLEDIAKILRFLGKNNFSVGAGGMIIDENIKGDVEYVGPYKRGNEYPVLSSVQAGSWREAIEPYSIKDVDLWLESNAHIQGEAFWLLVEGDSMTSPVGLSIPEGTYVLFDTGREPVNGSLVIAKLSESNEATFKKLIIDGGQKYLKGLNPQWPLVPINGNCRIIGVAVETKLRLV
>NZ_CP006738.1|WP_039108792.1|3965097_3965445_+|hypothetical-protein
MSHEFRDAVKVDGAEASIEEKQLYQVQIAVKSLIDFVVTSFEQLGIEKLHELVDPSLDELHEIILKLDNKAKELGALDLQQVLLTAQILIRDIKDKNPDMCAIGSRTLKRATIFK
>NZ_CP006738.1|WP_039108794.1|3965651_3965864_-|hypothetical-protein
MSNEDEFFAEMHPQIAQIIGIAVMQLLVEKREPSREALIEMIQVLWQEDQVDLAVELALDVLMQRKEWGQ
>NZ_CP006738.1|WP_074423018.1|3966362_3966488_+|hypothetical-protein
MLGCRMSKQGIRSLIYCLLICGVIWSAVVIKILHATGVFNG
>NZ_CP006738.1|WP_039108796.1|3966480_3966675_+|hypothetical-protein
MANSIPNSGRAVMMRNRRTGAAWLVSFDYRDGSYLHEPQGNLRHIRRPYASRSIEPNLVPAGTH
>NZ_CP006738.1|WP_039108798.1|3966763_3967048_+|host-nuclease-inhibitor-GamL
MNAYRAYDVIEERKWAEQTLSEEKEKWIDDRAQEIIDALPKEPSGLFRFSVPMDKSPYEGLRSDAAGEAYNDLISAVAYAQAEYDWDHRTGCPF
>NZ_CP006738.1|WP_039108801.1|3967064_3967811_+|phage-recombination-protein-Bet
MSTALSTMAGKLASRLGMDAGTDLMNTLKNTAFKGGNVTDEQFTALLIVANQYGLNPWTKEIYAFPDKGGIVPVVGVDGWARIINEHPQFDGMEFAYDKEEGACTCKIYRKDRTHPTIVTEYMGECKRNTQPWQSHPTRMLRHKTLIQCARLAFGFAGIFDQDEAERVIEGSATEVHVGHESDGRRPELIAKGESAARLGTVKYQEFWVALSAEEKQVIGAVEKRRMYDMSLAVDNAEPVDAAAPEDK

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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	Identity
NZ_CP006738_1	1.1\|3962725\|36\|NZ_CP006738\|CRISPRCasFinder	3962725-3962760	36	MK448233	Klebsiella phage ST11-VIM1phi8.1, complete genome	8447-8482	1.0
NZ_CP006738_1	1.1\|3962725\|36\|NZ_CP006738\|CRISPRCasFinder	3962725-3962760	36	MK448235	Klebsiella phage ST512-KPC3phi13.1, complete genome	8447-8482	1.0
NZ_CP006738_1	1.1\|3962725\|36\|NZ_CP006738\|CRISPRCasFinder	3962725-3962760	36	MK448231	Klebsiella phage ST101-KPC2phi6.1, complete genome	11383-11418	1.0

1. spacer 1.1|3962725|36|NZ_CP006738|CRISPRCasFinder matches to MK448233 (Klebsiella phage ST11-VIM1phi8.1, complete genome) position: , mismatch: 0, identity: 1.0

cctcgccggtacgcagcgtggttactgggtttgcgt	CRISPR spacer
cctcgccggtacgcagcgtggttactgggtttgcgt	Protospacer
************************************

2. spacer 1.1|3962725|36|NZ_CP006738|CRISPRCasFinder matches to MK448235 (Klebsiella phage ST512-KPC3phi13.1, complete genome) position: , mismatch: 0, identity: 1.0

cctcgccggtacgcagcgtggttactgggtttgcgt	CRISPR spacer
cctcgccggtacgcagcgtggttactgggtttgcgt	Protospacer
************************************

3. spacer 1.1|3962725|36|NZ_CP006738|CRISPRCasFinder matches to MK448231 (Klebsiella phage ST101-KPC2phi6.1, complete genome) position: , mismatch: 0, identity: 1.0

cctcgccggtacgcagcgtggttactgggtttgcgt	CRISPR spacer
cctcgccggtacgcagcgtggttactgggtttgcgt	Protospacer
************************************

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1327254 : 1341976

Morganella_phage(50.0%)

tail,integrase

attL 1327007:1327027|attR 1347071:1347091

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
1327007:1327027	attL	NA	NA	NA	NA
WP_032424540.1\|1327254_1328508_+\|integrase	site-specific integrase	A0A1W6JPG6	Morganella_phage	7.2e-147	60.4
WP_004213158.1\|1328603_1329611_+	hypothetical protein	NA	NA	NA	NA
WP_004213159.1\|1329741_1329960_+	AlpA family phage regulatory protein	NA	NA	NA	NA
WP_004213160.1\|1329959_1330394_+	hypothetical protein	A0A1W6JPH9	Morganella_phage	2.4e-25	55.3
WP_004213161.1\|1330407_1331010_+	hypothetical protein	A0A1W6JPH8	Morganella_phage	1.2e-54	57.8
WP_004213162.1\|1331009_1331189_+	DUF4222 domain-containing protein	NA	NA	NA	NA
WP_023302683.1\|1331185_1332151_+	ash family protein	A0A291AWU3	Escherichia_phage	3.9e-07	44.3
WP_004213165.1\|1332147_1332651_+	hypothetical protein	NA	NA	NA	NA
WP_004213166.1\|1332647_1332857_+	hypothetical protein	NA	NA	NA	NA
WP_004213167.1\|1332853_1333480_+	hypothetical protein	A0A286S1S7	Klebsiella_phage	1.6e-25	37.8
WP_004213168.1\|1333489_1333840_+	hypothetical protein	A0A1B5FPL8	Escherichia_phage	3.4e-38	70.0
WP_004213169.1\|1333832_1336595_+	TOPRIM and DUF927 domain-containing protein	A0A1W6JPG0	Morganella_phage	2.8e-292	56.1
WP_032424539.1\|1336934_1337381_+	single-stranded DNA-binding protein	NA	NA	NA	NA
WP_004213171.1\|1337361_1337745_+	PerC family transcriptional regulator	NA	NA	NA	NA
WP_004213172.1\|1337749_1338223_+	hypothetical protein	NA	NA	NA	NA
WP_004213173.1\|1338406_1338577_+	hypothetical protein	NA	NA	NA	NA
WP_004213174.1\|1338576_1338903_+	hypothetical protein	NA	NA	NA	NA
WP_004213175.1\|1338910_1341976_+\|tail	phage tail length tape measure family protein	B1GS57	Salmonella_phage	2.0e-94	40.5
1347071:1347091	attR	NA	NA	NA	NA

DBSCAN-SWA_2

1683963 : 1690868

Planktothrix_phage(33.33%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_004180551.1\|1683963_1684827_+	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	5.7e-10	27.5
WP_004214747.1\|1684837_1685611_+	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	5.1e-26	36.7
WP_004151134.1\|1685851_1686748_-	lipid kinase YegS	A0A1V0SBJ0	Catovirus	6.1e-15	29.8
WP_004144192.1\|1686990_1688352_-\|tRNA	tRNA 5-hydroxyuridine modification protein YegQ	Q6DW11	Phage_TP	1.8e-207	94.8
WP_004201558.1\|1688670_1689393_-	two-component system response regulator BaeR	W8CYM9	Bacillus_phage	8.3e-31	33.2
WP_004214740.1\|1689389_1690868_-	two-component system sensor histidine kinase BaeS	W8CYF6	Bacillus_phage	1.4e-29	28.3

DBSCAN-SWA_3

2722872 : 2733759

Escherichia_phage(87.5%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_004209809.1\|2722872_2725980_+	beta-galactosidase	L0N6M2	Herpes_simplex_virus	0.0e+00	59.5
WP_004176258.1\|2726034_2727300_+	MFS transporter	NA	NA	NA	NA
WP_004209813.1\|2727330_2728419_-	AAA family ATPase	A0A077SLJ9	Escherichia_phage	1.0e-210	99.7
WP_004176262.1\|2728505_2728766_-	hypothetical protein	A0A077SK33	Escherichia_phage	5.4e-41	98.8
WP_001620095.1\|2729063_2729924_+	class A broad-spectrum beta-lactamase SHV-1	A0A077SL40	Escherichia_phage	4.4e-156	99.7
WP_004209817.1\|2729944_2730706_-	DeoR/GlpR transcriptional regulator	A0A077SK06	Escherichia_phage	5.5e-134	99.6
WP_002903955.1\|2730966_2731869_+	NAD(P)-dependent oxidoreductase	A0A077SLF7	Escherichia_phage	2.6e-159	99.7
WP_004183946.1\|2731880_2733146_+	four-carbon acid sugar kinase family protein	A0A077SLJ7	Escherichia_phage	6.6e-233	99.3
WP_002210516.1\|2733138_2733759_+	aldolase	A0A077SK32	Escherichia_phage	8.0e-115	100.0

DBSCAN-SWA_4

2768967 : 2849377

Klebsiella_phage(20.93%)

tail,portal,transposase,holin,capsid,protease,integrase,terminase,head

attL 2794583:2794599|attR 2827340:2827356

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_004209779.1\|2768967_2769780_+\|protease	serine protease	NA	NA	NA	NA
WP_002903685.1\|2769793_2769910_+	hypothetical protein	NA	NA	NA	NA
WP_002903683.1\|2769953_2770283_-	multidrug efflux SMR transporter subunit KpnF	NA	NA	NA	NA
WP_002903681.1\|2770269_2770632_-	multidrug efflux SMR transporter subunit KpnE	NA	NA	NA	NA
WP_002903679.1\|2771074_2772109_+	AI-2E family transporter	NA	NA	NA	NA
WP_002903677.1\|2772333_2773989_+	malonate decarboxylase subunit alpha	NA	NA	NA	NA
WP_004143107.1\|2773988_2774831_+	triphosphoribosyl-dephospho-CoA synthase	NA	NA	NA	NA
WP_002903639.1\|2774848_2775148_+	malonate decarboxylase acyl carrier protein	NA	NA	NA	NA
WP_004143105.1\|2775140_2775974_+	biotin-independent malonate decarboxylase subunit beta	NA	NA	NA	NA
WP_004209782.1\|2775973_2776774_+	biotin-independent malonate decarboxylase subunit gamma	NA	NA	NA	NA
WP_004209783.1\|2776910_2777870_+	AEC family transporter	A0A0U2C0Y4	Salmonella_phage	2.7e-53	90.3
WP_004209784.1\|2777873_2778491_+	malonate decarboxylase holo-ACP synthase	NA	NA	NA	NA
WP_004209787.1\|2778490_2779393_+	malonate decarboxylase subunit epsilon	NA	NA	NA	NA
WP_004148289.1\|2779382_2780309_-	LysR family transcriptional regulator	NA	NA	NA	NA
WP_022615525.1\|2780466_2782122_-	malate dehydrogenase (quinone)	NA	NA	NA	NA
WP_004209791.1\|2782386_2783307_-	N-acetylmuramic acid 6-phosphate etherase	NA	NA	NA	NA
WP_004179716.1\|2783470_2783827_-	hypothetical protein	NA	NA	NA	NA
WP_004183910.1\|2783982_2785599_+	two-component system sensor histidine kinase DcuS	NA	NA	NA	NA
WP_004176303.1\|2785595_2786315_+	two-component system response regulator DcuR	NA	NA	NA	NA
WP_004209794.1\|2786295_2787246_-	FAD:protein FMN transferase	NA	NA	NA	NA
WP_004209796.1\|2787313_2790091_-	flavocytochrome c	A0A2P0ZL82	Lactobacillus_phage	6.8e-65	31.0
WP_004148278.1\|2790733_2792245_+	anion permease	NA	NA	NA	NA
WP_004152246.1\|2792299_2793952_+	class I fumarate hydratase	NA	NA	NA	NA
WP_023302609.1\|2794114_2795731_+	mechanosensitive ion channel	NA	NA	NA	NA
2794583:2794599	attL	NA	NA	NA	NA
WP_004143067.1\|2796770_2797160_-	4-carboxymuconolactone decarboxylase	NA	NA	NA	NA
WP_004215412.1\|2797152_2797917_-	3-oxoadipate enol-lactonase	NA	NA	NA	NA
WP_020316475.1\|2797906_2799259_-	3-carboxy-cis,cis-muconate cycloisomerase	NA	NA	NA	NA
WP_004214878.1\|2799268_2800471_-	3-oxoadipyl-CoA thiolase	NA	NA	NA	NA
WP_004176317.1\|2800481_2801138_-	CoA transferase subunit B	NA	NA	NA	NA
WP_002903522.1\|2801148_2801835_-	3-oxoacid CoA-transferase subunit A	NA	NA	NA	NA
WP_004151560.1\|2802004_2802811_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_004143055.1\|2802807_2803371_-	DNA endonuclease SmrA	NA	NA	NA	NA
WP_004148273.1\|2803472_2804381_-	LysR family transcriptional regulator	NA	NA	NA	NA
WP_004214881.1\|2804547_2805858_+	M20 family metallo-hydrolase	NA	NA	NA	NA
WP_004176321.1\|2805857_2807303_+	amidohydrolase	NA	NA	NA	NA
WP_022615523.1\|2807422_2808541_+	AbgT family transporter	NA	NA	NA	NA
WP_004214887.1\|2808669_2809770_+\|integrase	site-specific integrase	A0A1W6JP34	Morganella_phage	8.3e-115	56.8
WP_004214894.1\|2810971_2811271_-	hypothetical protein	NA	NA	NA	NA
WP_022615522.1\|2811438_2812083_+	hypothetical protein	NA	NA	NA	NA
WP_022615521.1\|2812138_2812873_-	hypothetical protein	NA	NA	NA	NA
WP_039108567.1\|2812885_2815039_-	hypothetical protein	B5TAB2	Burkholderia_phage	4.8e-90	42.2
WP_016530179.1\|2815111_2818189_-	hypothetical protein	A0A286S259	Klebsiella_phage	0.0e+00	61.5
WP_022615519.1\|2818185_2818566_-	nitrite transporter	A0A286S2A6	Klebsiella_phage	1.6e-57	80.2
WP_004864228.1\|2818578_2819055_-	DUF1833 family protein	A0A286S2B1	Klebsiella_phage	4.8e-51	65.8
WP_004177132.1\|2819041_2819515_-	hypothetical protein	A0A286S298	Klebsiella_phage	1.4e-55	62.1
WP_039108569.1\|2819535_2822925_-\|tail	phage tail tape measure protein	A0A0P0ZCJ4	Stx2-converting_phage	0.0e+00	60.5
WP_016530182.1\|2822985_2823219_-	hypothetical protein	K7PH16	Enterobacteria_phage	1.9e-08	47.2
WP_016530183.1\|2823292_2823598_-	DUF4035 domain-containing protein	Q9MCS5	Enterobacteria_phage	4.7e-28	64.6
WP_016530184.1\|2823600_2824005_-\|tail	phage tail assembly chaperone	K7PKV6	Enterobacterial_phage	3.2e-32	57.4
WP_016530185.1\|2824035_2824740_-	immunoglobulin domain-containing protein	K7PHL2	Enterobacterial_phage	6.6e-81	67.4
WP_016530186.1\|2824796_2825144_-	DUF3168 domain-containing protein	K7PKL6	Enterobacterial_phage	2.8e-32	63.7
WP_016530187.1\|2825140_2825590_-	HK97 gp10 family phage protein	Q9MCS9	Enterobacteria_phage	7.4e-62	81.9
WP_016530188.1\|2825586_2825925_-\|head	phage head closure protein	A0A2H4JHK5	uncultured_Caudovirales_phage	7.8e-40	70.5
WP_016530189.1\|2825933_2826251_-\|head,tail	phage gp6-like head-tail connector protein	A0A1W6JNZ5	Morganella_phage	1.8e-22	51.0
WP_023284978.1\|2826328_2827567_-\|capsid	phage major capsid protein	Q8SBH8	Shigella_phage	1.8e-158	69.4
2827340:2827356	attR	NA	NA	NA	NA
WP_000999827.1\|2827576_2828176_-\|head,protease	HK97 family phage prohead protease	Q8SBH9	Shigella_phage	1.0e-90	82.5
WP_016530190.1\|2828168_2829395_-\|portal	phage portal protein	Q8SBI0	Shigella_phage	3.2e-208	85.3
WP_025108055.1\|2829542_2831294_-\|terminase	terminase large subunit	A0A1P8DTK0	Proteus_phage	4.0e-252	72.5
WP_016530193.1\|2831297_2831795_-\|terminase	phage terminase small subunit P27 family	A0A1W6JP17	Morganella_phage	5.7e-63	73.9
WP_023317581.1\|2831952_2832303_-	HNH endonuclease	A0A1B5FP94	Escherichia_phage	4.6e-51	81.6
WP_039108578.1\|2832404_2832806_-	DUF2513 domain-containing protein	NA	NA	NA	NA
WP_039108580.1\|2832881_2833127_-	DUF2560 family protein	A0A286N2R1	Klebsiella_phage	4.8e-31	91.4
WP_039108582.1\|2833446_2833638_-	hypothetical protein	A0A286SGR9	Klebsiella_phage	3.4e-24	94.6
WP_039108585.1\|2833588_2833864_-	hypothetical protein	NA	NA	NA	NA
WP_039108587.1\|2833860_2834208_-	hypothetical protein	A0A286N2Q7	Klebsiella_phage	2.0e-38	78.3
WP_039108588.1\|2834204_2834744_-	glycoside hydrolase family 108 protein	A0A286N2Q6	Klebsiella_phage	4.8e-100	97.2
WP_024176410.1\|2834740_2835040_-\|holin	phage holin family protein	A0A286N2Q5	Klebsiella_phage	4.5e-39	83.8
WP_125330507.1\|2835855_2836182_-	hypothetical protein	NA	NA	NA	NA
WP_004886669.1\|2836449_2837271_+	hypothetical protein	NA	NA	NA	NA
WP_004886665.1\|2837295_2837781_+	hypothetical protein	NA	NA	NA	NA
WP_004886660.1\|2837829_2838171_-	antitermination protein from phage origin	A0A0P0ZCW0	Stx2-converting_phage	2.5e-54	84.1
WP_039108593.1\|2838189_2839170_-	DUF968 domain-containing protein	A0A291AWV9	Escherichia_phage	1.1e-134	66.9
WP_000779146.1\|2839182_2839560_-	RusA family crossover junction endodeoxyribonuclease	A0A1C9IIA0	Salmonella_phage	2.3e-48	73.6
WP_039108595.1\|2839569_2840379_-	Dam family site-specific DNA-(adenine-N6)-methyltransferase	A0A1C9II58	Salmonella_phage	5.0e-109	68.5
WP_039108597.1\|2840375_2841314_-	helix-turn-helix domain-containing protein	U5P0A0	Shigella_phage	2.0e-101	74.2
WP_004184738.1\|2841303_2841483_-	DUF4222 domain-containing protein	S5M7S5	Escherichia_phage	1.6e-15	75.0
WP_039108602.1\|2841681_2842767_+\|transposase	IS481-like element ISKpn28 family transposase	A0A0M3LR35	Mannheimia_phage	1.4e-05	21.9
WP_004213338.1\|2842821_2843283_-	hypothetical protein	K7PJS5	Enterobacterial_phage	1.7e-69	88.2
WP_016530206.1\|2843308_2843506_-	Cro/Cl family transcriptional regulator	H9C161	Pectobacterium_phage	2.7e-16	66.1
WP_016530207.1\|2843598_2844258_+	helix-turn-helix domain-containing protein	H9C160	Pectobacterium_phage	7.3e-74	62.7
WP_004213349.1\|2845025_2845325_+	hypothetical protein	K7PJS4	Enterobacterial_phage	9.4e-13	46.7
WP_004213351.1\|2845324_2846110_+	hypothetical protein	C7BGF1	Burkholderia_phage	5.3e-63	52.9
WP_004213355.1\|2846237_2846582_+	hypothetical protein	NA	NA	NA	NA
WP_039108606.1\|2846574_2847237_+	morphogenetic protein	Q71T76	Escherichia_phage	2.2e-54	56.0
WP_039108608.1\|2847233_2847419_+	hypothetical protein	NA	NA	NA	NA
WP_016530209.1\|2847538_2847799_+	pyocin activator PrtN family protein	A0A1L5C290	Pseudoalteromonas_phage	1.5e-11	43.7
WP_002903398.1\|2848410_2848569_-	hypothetical protein	NA	NA	NA	NA
WP_004213367.1\|2848861_2849377_+	methylated-DNA--[protein]-cysteine S-methyltransferase	M1PFU9	Streptococcus_phage	2.0e-23	54.9

DBSCAN-SWA_5

3440071 : 3449535

Brazilian_cedratvirus(16.67%)

protease,tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_004209699.1\|3440071_3441793_+	cysteine/glutathione ABC transporter ATP-binding protein/permease CydC	A0A2R8FG22	Brazilian_cedratvirus	1.5e-14	34.3
WP_002898014.1\|3441837_3442539_+\|tRNA	leucyl/phenylalanyl-tRNA--protein transferase	NA	NA	NA	NA
WP_001040187.1\|3442892_3443111_+	translation initiation factor IF-1	NA	NA	NA	NA
WP_002896522.1\|3443231_3445511_-\|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	A0A223W0B1	Agrobacterium_phage	1.6e-165	42.0
WP_002896520.1\|3445541_3445859_-\|protease	ATP-dependent Clp protease adapter ClpS	A0A1B1IT64	uncultured_Mediterranean_phage	2.0e-13	45.7
WP_002896516.1\|3446184_3446406_+	cold shock-like protein CspD	A0A2H4N7Y6	Lake_Baikal_phage	1.3e-16	61.2
WP_023302553.1\|3446482_3448423_-	macrolide ABC transporter ATP-binding protein/permease MacB	G9BWD6	Planktothrix_phage	1.2e-36	40.1
WP_039108682.1\|3448419_3449535_-	macrolide transporter subunit MacA	A0A140XAI1	Dickeya_phage	1.3e-06	52.7

DBSCAN-SWA_6

3929703 : 3973017

Salmonella_phage(35.29%)

plate,terminase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_039108738.1\|3929703_3931866_-	hypothetical protein	B5TAB2	Burkholderia_phage	8.4e-87	42.1
WP_114502289.1\|3931933_3932119_-	hypothetical protein	NA	NA	NA	NA
WP_124044855.1\|3932118_3933024_-	hypothetical protein	A0A1I9SEW2	Klebsiella_phage	1.3e-49	59.4
WP_032428613.1\|3933023_3933800_-	DUF2612 domain-containing protein	A0A2H4J1A9	uncultured_Caudovirales_phage	8.8e-79	56.5
WP_039108741.1\|3933796_3934996_-\|plate	baseplate J/gp47 family protein	A0A0M4RD32	Salmonella_phage	1.1e-157	72.9
WP_004152573.1\|3934995_3935349_-	hypothetical protein	A0A2H4J629	uncultured_Caudovirales_phage	2.3e-50	80.3
WP_039108743.1\|3935350_3936004_-	hypothetical protein	A0A0M5M1K7	Salmonella_phage	1.0e-72	57.5
WP_000506882.1\|3936091_3936409_+	DUF4236 domain-containing protein	NA	NA	NA	NA
WP_000734772.1\|3936439_3936772_-	hypothetical protein	A0A0M4RTY3	Salmonella_phage	3.4e-19	64.5
WP_039108746.1\|3936768_3937836_-	hypothetical protein	A0A0M4QX01	Salmonella_phage	4.4e-137	68.5
WP_074188356.1\|3937838_3938066_-	hypothetical protein	A0A2H4J495	uncultured_Caudovirales_phage	9.6e-18	52.0
WP_025269945.1\|3938141_3938717_-	hypothetical protein	A0A0M3ULD5	Salmonella_phage	5.0e-63	66.0
WP_039108751.1\|3938716_3940633_-	bacteriophage protein	A0A0M4REK7	Salmonella_phage	3.6e-198	58.1
WP_016244729.1\|3940622_3940775_-	hypothetical protein	A0A2H4J1A2	uncultured_Caudovirales_phage	1.4e-17	84.0
WP_039108753.1\|3940816_3941236_-	hypothetical protein	A0A2H4J2V6	uncultured_Caudovirales_phage	7.4e-40	65.2
WP_039108755.1\|3941239_3941680_-	DUF3277 family protein	A0A0M5M1K6	Salmonella_phage	2.1e-61	78.8
WP_025269950.1\|3941690_3942842_-	DUF3383 family protein	A0A0M4RD26	Salmonella_phage	2.1e-177	81.5
WP_064144275.1\|3942843_3943395_-	hypothetical protein	A0A2H4J1A0	uncultured_Caudovirales_phage	1.5e-40	44.9
WP_039108757.1\|3943387_3943792_-	hypothetical protein	A0A2H4J1A4	uncultured_Caudovirales_phage	3.7e-44	72.3
WP_025269952.1\|3943791_3944298_-	hypothetical protein	NA	NA	NA	NA
WP_039108758.1\|3944294_3944714_-	DUF4054 domain-containing protein	A0A0M5M3S2	Salmonella_phage	9.7e-40	60.7
WP_000725700.1\|3944682_3944964_-	hypothetical protein	NA	NA	NA	NA
WP_038435199.1\|3945003_3945945_-	DUF2184 domain-containing protein	A0A2H4J191	uncultured_Caudovirales_phage	1.3e-137	77.4
WP_032428595.1\|3945956_3946451_-	hypothetical protein	A0A2H4JHM9	uncultured_Caudovirales_phage	9.3e-50	62.7
WP_039108761.1\|3946454_3947657_-	DUF2213 domain-containing protein	A0A0M4R5A6	Salmonella_phage	7.7e-106	54.4
WP_025714257.1\|3947708_3948257_-	hypothetical protein	A0A0M4REK0	Salmonella_phage	1.0e-49	56.9
WP_039108763.1\|3948312_3949764_-	DUF1073 domain-containing protein	A0A0M4S6U1	Salmonella_phage	7.2e-191	68.4
WP_021312714.1\|3950001_3951402_-\|terminase	PBSX family phage terminase large subunit	A0A077KAW0	Edwardsiella_phage	9.4e-188	69.2
WP_020804051.1\|3951352_3951841_-	hypothetical protein	NA	NA	NA	NA
WP_001064347.1\|3952176_3952695_-	Rha family transcriptional regulator	Q38450	Enterobacteria_phage	2.9e-94	100.0
WP_039108769.1\|3952979_3953369_-	hypothetical protein	A0A192Y6H8	Salmonella_phage	4.5e-23	47.5
WP_039108771.1\|3953365_3953869_-	lysozyme	A0A1V0E5Q7	Salmonella_phage	6.5e-75	78.4
WP_004146347.1\|3953871_3954186_-	hypothetical protein	H6WRZ3	Salmonella_phage	6.3e-44	86.1
WP_004884209.1\|3955161_3955662_-	phage antitermination Q family protein	G8C7V7	Escherichia_phage	3.3e-87	91.5
WP_060613575.1\|3955658_3955799_-	YlcG family protein	NA	NA	NA	NA
WP_039108774.1\|3955795_3956431_-	recombination protein NinG	M9NYX8	Enterobacteria_phage	2.0e-81	77.9
WP_004196828.1\|3956423_3956594_-	hypothetical protein	G8C7V4	Escherichia_phage	3.3e-15	73.2
WP_039108777.1\|3956574_3957042_-	recombination protein NinB	Q8VNP6	Enterobacteria_phage	2.2e-32	46.2
WP_039108779.1\|3957396_3957717_-	hypothetical protein	NA	NA	NA	NA
WP_052253486.1\|3958130_3958802_-	DUF551 domain-containing protein	A5LH60	Enterobacteria_phage	2.5e-05	30.0
WP_029602865.1\|3958798_3959092_-	hypothetical protein	Q6UAT9	Klebsiella_phage	2.7e-44	86.6
WP_039108784.1\|3959091_3959619_-	ead/Ea22-like family protein	A0A2H4FRZ0	Salmonella_phage	4.8e-28	55.8
WP_004884201.1\|3959611_3959875_-	DUF4752 family protein	T1S9K2	Salmonella_phage	6.3e-29	74.4
WP_004884208.1\|3959871_3960345_-	hypothetical protein	R9TME7	Aeromonas_phage	9.4e-07	32.1
WP_004884186.1\|3960341_3960566_-	hypothetical protein	H9C169	Pectobacterium_phage	4.4e-15	53.4
WP_039108787.1\|3960562_3960865_-	MarR family transcriptional regulator	NA	NA	NA	NA
WP_075209545.1\|3960864_3962280_-	AAA family ATPase	Q9MCT4	Escherichia_phage	4.6e-182	66.5
WP_073545955.1\|3962284_3963136_-	DNA replication protein	F1C5C3	Cronobacter_phage	6.9e-85	56.3
WP_004151298.1\|3963176_3963323_-	hypothetical protein	NA	NA	NA	NA
WP_039108790.1\|3963408_3963630_-	bacteriophage CII family protein	NA	NA	NA	NA
WP_004191589.1\|3963669_3963888_-	helix-turn-helix transcriptional regulator	A0A1P8DTF8	Proteus_phage	1.4e-13	50.7
WP_004191591.1\|3963996_3964656_+	helix-turn-helix domain-containing protein	K7P7K3	Enterobacteria_phage	8.3e-70	62.4
WP_039108792.1\|3965097_3965445_+	hypothetical protein	NA	NA	NA	NA
WP_039108794.1\|3965651_3965864_-	hypothetical protein	A0A192Y6Q5	Salmonella_phage	4.3e-20	73.1
WP_074423018.1\|3966362_3966488_+	hypothetical protein	NA	NA	NA	NA
WP_039108796.1\|3966480_3966675_+	hypothetical protein	NA	NA	NA	NA
WP_039108798.1\|3966763_3967048_+	host nuclease inhibitor GamL	G8C7T1	Escherichia_phage	6.6e-40	80.9
WP_039108801.1\|3967064_3967811_+	phage recombination protein Bet	A0A1I9LJN0	Stx_converting_phage	5.3e-65	67.7
WP_039108803.1\|3967807_3968431_+	YqaJ viral recombinase family protein	A0A0S2SY31	Pseudomonas_phage	3.1e-58	59.7
WP_039108983.1\|3968459_3968987_+	phage N-6-adenine-methyltransferase	Q9ZWX6	Enterobacteria_phage	3.8e-57	61.6
WP_039108805.1\|3968983_3969754_+	hypothetical protein	D5LH17	Escherichia_phage	5.5e-65	52.0
WP_023304908.1\|3969750_3969969_+	hypothetical protein	A0A1I9LJM7	Stx_converting_phage	1.6e-09	47.2
WP_039108808.1\|3969970_3970186_+	TraR/DksA family transcriptional regulator	A0A0K2FI84	Escherichia_phage	9.1e-10	59.6
WP_071844011.1\|3970343_3970679_+	excisionase family DNA-binding protein	NA	NA	NA	NA
WP_004143017.1\|3972150_3973017_+	bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD	A0A249XZQ2	Enterococcus_phage	1.3e-30	34.8

Anti-CRISPR protein detection

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