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
LR134176	Legionella pneumophila strain NCTC12179 genome assembly, chromosome: 1	1 crisprs	DEDDh,DinG,cas3,PD-DExK,WYL,csa3,cas4,cas2,cas1,cas9	0	3	7	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: LR134176_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR134176_2

2976556-2978186

TypeII

Consensus_repeat	Method
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CRISPRCasFinder
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CRT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	PILER-CR

22 spacers

cas4,cas2,cas1,cas9

The CRISPR arrays of LR134176_2

>merge|LR134176|2|2976556-2978186|CRISPRCasFinder,CRT,PILER-CR
ATTTCATTAGTTAAATTTTTAGATGGGGGATTTTTGGTTGGCTATTAATATATTAGTCATATCTAATAAAGTGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGGTATCGGCCACAGAGGTTTGGGAATTGAGGCTAAGTGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGCCTGAGATTAATTACGTATTCGACAATATTACAGGATGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGAATTAAACCTAGCAGAATAGGATTATTATATAAAAAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTGCCATGTCTGGTGCGGGGCATTTGACTAGTTTTGTGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGGGCATTGATATGGCCTAAAAGGATTAGCATGTCTGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGCACACCAACAGAATCAAAGCTATGTTCTAAGTGGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGATTTAGTTTTTCCTCTAGTTTCCTCTTCTACTAAGTCGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGACACTATTAGCTATGACTAATACACTAATTTCGAAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGCTTTATGATATAGGTATAGTGGGAAATATCGGTAGAAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGAATTGGCCCAATTGATTATGGATGGACAGTCCCAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTGCATTTATGGTATTAATTCACCTTTTACTTACCGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTTAAATAATTTTGTCGAGCAGCGGAACACAATTTTGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTCCAAATTTGTTTTTTGTTATTTTTGTCGAATTTAGAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGAACAATACAAGACTTTTTTACCCAATTTACAGACAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTTATACAACTATCTATTAAGTCAATCATAACTAGTGGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTCACCGTGTACTGGGGTAGACTGCCTTAGATGTAAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGAACTACGACAATGAAGGAGTGCCGCGAGTGACAAACGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGATTATTTGTGACATAATGGGCCGGATGTATTACTAGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGCATACTGCTCGCCAAGTTGCCAGACCCAAGCTTTTGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGCCTAAATGACTTTGATCTAACGTAACATCTATGGTGGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGGTTAAAGTACAAAAAATTCTAGATCGTTGGTATCCCCGTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG

>LR134176|2|2|2976556-2978186|CRISPRCasFinder
ATTTCATTAGTTAAATTTTTAGATGGGGGATTTTTGG	TTGGCTATTAATATATTAGTCATATCTAATAAAGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GTATCGGCCACAGAGGTTTGGGAATTGAGGCTAAGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CCTGAGATTAATTACGTATTCGACAATATTACAGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AATTAAACCTAGCAGAATAGGATTATTATATAAAAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGCCATGTCTGGTGCGGGGCATTTGACTAGTTTTGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GGCATTGATATGGCCTAAAAGGATTAGCATGTCT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CACACCAACAGAATCAAAGCTATGTTCTAAGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATTTAGTTTTTCCTCTAGTTTCCTCTTCTACTAAGTC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ACACTATTAGCTATGACTAATACACTAATTTCGAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CTTTATGATATAGGTATAGTGGGAAATATCGGTAGAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AATTGGCCCAATTGATTATGGATGGACAGTCCCA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGCATTTATGGTATTAATTCACCTTTTACTTACC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAATAATTTTGTCGAGCAGCGGAACACAATTTT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TCCAAATTTGTTTTTTGTTATTTTTGTCGAATTTAGA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AACAATACAAGACTTTTTTACCCAATTTACAGACA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTATACAACTATCTATTAAGTCAATCATAACTAGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TCACCGTGTACTGGGGTAGACTGCCTTAGATGTAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AACTACGACAATGAAGGAGTGCCGCGAGTGACAAAC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATTATTTGTGACATAATGGGCCGGATGTATTACTA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CATACTGCTCGCCAAGTTGCCAGACCCAAGCTTTT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CCTAAATGACTTTGATCTAACGTAACATCTATGGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAAGTACAAAAAATTCTAGATCGTTGGTATCCCC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG

>LR134176|2|1|2976556-2978186|CRT
ATTTCATTAGTTAAATTTTTAGATGGGGGATTTTTGG	TTGGCTATTAATATATTAGTCATATCTAATAAAGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GTATCGGCCACAGAGGTTTGGGAATTGAGGCTAAGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CCTGAGATTAATTACGTATTCGACAATATTACAGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AATTAAACCTAGCAGAATAGGATTATTATATAAAAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGCCATGTCTGGTGCGGGGCATTTGACTAGTTTTGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GGCATTGATATGGCCTAAAAGGATTAGCATGTCT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CACACCAACAGAATCAAAGCTATGTTCTAAGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATTTAGTTTTTCCTCTAGTTTCCTCTTCTACTAAGTC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ACACTATTAGCTATGACTAATACACTAATTTCGAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CTTTATGATATAGGTATAGTGGGAAATATCGGTAGAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AATTGGCCCAATTGATTATGGATGGACAGTCCCA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGCATTTATGGTATTAATTCACCTTTTACTTACC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAATAATTTTGTCGAGCAGCGGAACACAATTTT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TCCAAATTTGTTTTTTGTTATTTTTGTCGAATTTAGA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AACAATACAAGACTTTTTTACCCAATTTACAGACA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTATACAACTATCTATTAAGTCAATCATAACTAGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TCACCGTGTACTGGGGTAGACTGCCTTAGATGTAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AACTACGACAATGAAGGAGTGCCGCGAGTGACAAAC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATTATTTGTGACATAATGGGCCGGATGTATTACTA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CATACTGCTCGCCAAGTTGCCAGACCCAAGCTTTT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CCTAAATGACTTTGATCTAACGTAACATCTATGGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAAGTACAAAAAATTCTAGATCGTTGGTATCCCC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG

>LR134176|2|1|2976628-2978186|PILER-CR
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GTATCGGCCACAGAGGTTTGGGAATTGAGGCTAAGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CCTGAGATTAATTACGTATTCGACAATATTACAGGAT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AATTAAACCTAGCAGAATAGGATTATTATATAAAAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGCCATGTCTGGTGCGGGGCATTTGACTAGTTTTGT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	GGCATTGATATGGCCTAAAAGGATTAGCATGTCT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CACACCAACAGAATCAAAGCTATGTTCTAAGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATTTAGTTTTTCCTCTAGTTTCCTCTTCTACTAAGTC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ACACTATTAGCTATGACTAATACACTAATTTCGAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CTTTATGATATAGGTATAGTGGGAAATATCGGTAGAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AATTGGCCCAATTGATTATGGATGGACAGTCCCA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TGCATTTATGGTATTAATTCACCTTTTACTTACC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAATAATTTTGTCGAGCAGCGGAACACAATTTT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TCCAAATTTGTTTTTTGTTATTTTTGTCGAATTTAGA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AACAATACAAGACTTTTTTACCCAATTTACAGACA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTATACAACTATCTATTAAGTCAATCATAACTAGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TCACCGTGTACTGGGGTAGACTGCCTTAGATGTAA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	AACTACGACAATGAAGGAGTGCCGCGAGTGACAAAC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	ATTATTTGTGACATAATGGGCCGGATGTATTACTA
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CATACTGCTCGCCAAGTTGCCAGACCCAAGCTTTT
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	CCTAAATGACTTTGATCTAACGTAACATCTATGGTG
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG	TTAAAGTACAAAAAATTCTAGATCGTTGGTATCCCC
GTTTCAGTGGTTGGATTTTTAGATGAGGGATTATTGG

Protein	Signature genes	Signature genes Name	Protein_function
LR134176.1\|VEB32170.1\|2976042_2976222_-\|Uncharacterised-protein	unknown	unknown	unknown
LR134176.1\|VEB32164.1\|2968573_2969761_-\|EcoKI-restriction-modification-system-protein-HsdS	unknown	unknown	gnl\|CDD\|341198
LR134176.1\|VEB32166.1\|2971345_2971948_-\|EcoKI-restriction-modification-system-protein-HsdS	unknown	unknown	gnl\|CDD\|341131
LR134176.1\|VEB32173.1\|2978975_2979275_-\|CRISPR-associated-endoribonuclease-Cas2	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	gnl\|CDD\|187856
LR134176.1\|VEB32179.1\|2986238_2986670_+\|Uncharacterised-protein	unknown	unknown	unknown
LR134176.1\|VEB32174.1\|2979281_2979689_-\|CRISPR-associated-endonuclease-Cas1	cas1	cd09634_cas1_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|187766
LR134176.1\|VEB32167.1\|2972069_2972681_+\|FRG-domain	unknown	unknown	gnl\|CDD\|214898
LR134176.1\|VEB32169.1\|2974921_2975398_+\|Uncharacterised-protein	unknown	unknown	unknown
LR134176.1\|VEB32162.1\|2965674_2967582_-\|ATP-dependent-DNA-helicase	unknown	unknown	gnl\|CDD\|225420
LR134176.1\|VEB32175.1\|2979809_2980826_+\|transposase-IS630-family	unknown	unknown	gnl\|CDD\|315923
LR134176.1\|VEB32176.1\|2980814_2981372_-\|CRISPR-associated-endonuclease-Cas1	cas1	pfam01867_cas1_CAS-I:CAS-II:CAS-III	gnl\|CDD\|376633
LR134176.1\|VEB32180.1\|2986659_2987610_+\|Nucleotidyl-transferase-of-uncharacterised-function-(DUF1814)	unknown	unknown	gnl\|CDD\|378065
LR134176.1\|VEB32177.1\|2981368_2985487_-\|CRISPR-associated-protein-Cas9/Csx12,-subtype-II-B/NMENI	cas9	cd09704_cas9_CAS-II-B	gnl\|CDD\|187835
LR134176.1\|VEB32181.1\|2987841_2988594_-\|transposase-TnpA-or-TnpA2	unknown	unknown	gnl\|CDD\|376574
LR134176.1\|VEB32165.1\|2969750_2971352_-\|putative-type-I-restriction-enzyme-M-protein	unknown	unknown	gnl\|CDD\|223363
LR134176.1\|VEB32168.1\|2973214_2974240_+\|Protein-of-uncharacterised-function-(DUF3800)	unknown	unknown	unknown
LR134176.1\|VEB32161.1\|2962408_2965678_-\|putative-type-I-restriction-enzyme-R-protein	unknown	unknown	gnl\|CDD\|273028
LR134176.1\|VEB32163.1\|2967581_2968577_-\|Uncharacterised-protein	unknown	unknown	unknown
LR134176.1\|VEB32178.1\|2985658_2985877_-\|phage-transcriptional-regulator-AlpA	unknown	unknown	gnl\|CDD\|225848
LR134176.1\|VEB32172.1\|2978401_2978995_-\|CRISPR-associated-protein-Cas4	cas4	cd09637_cas4_CAS-I:CAS-II:CAS-V	gnl\|CDD\|273040

Protein	Function_ID	Function_description	E-value
LR134176.1\|VEB32164.1\|2968573_2969761_-\|EcoKI-restriction-modification-system-protein-HsdS	gnl\|CDD\|341198	cd17517, RMtype1_S_EcoKI_StySPI-TRD2-CR2_like, Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR),similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) TRD2-CR2, and other TRD-CR's. Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3' and Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 both recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2.It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.	1.93294e-40
LR134176.1\|VEB32166.1\|2971345_2971948_-\|EcoKI-restriction-modification-system-protein-HsdS	gnl\|CDD\|341131	cd16961, RMtype1_S_TRD-CR_like, Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR) and similar domains. The restriction-modification (RM) system S subunit generally consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily represents a single TRD-CR unit; in addition to type I TRD-CR units, it includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P, as well as TRD-CR-like sequence-recognition domains of the M subunit of putative type I DNA methyltransferase such as M2.CinURNWORF2828P and M.Mae7806ORF3969P.	3.91906e-16
LR134176.1\|VEB32173.1\|2978975_2979275_-\|CRISPR-associated-endoribonuclease-Cas2	gnl\|CDD\|187856	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.	1.31074e-05
LR134176.1\|VEB32174.1\|2979281_2979689_-\|CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|187766	cd09634, Cas1_I-II-III, CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain.	8.05693e-39
LR134176.1\|VEB32167.1\|2972069_2972681_+\|FRG-domain	gnl\|CDD\|214898	smart00901, FRG, This domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised.	5.06874e-06
LR134176.1\|VEB32178.1\|2985658_2985877_-\|phage-transcriptional-regulator-AlpA	gnl\|CDD\|225848	COG3311, AlpA, Predicted transcriptional regulator [Transcription].	2.21188e-05
LR134176.1\|VEB32162.1\|2965674_2967582_-\|ATP-dependent-DNA-helicase	gnl\|CDD\|225420	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription].	3.70458e-53
LR134176.1\|VEB32176.1\|2980814_2981372_-\|CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|376633	pfam01867, Cas_Cas1, CRISPR associated protein Cas1. Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. This family of proteins corresponds to Cas1, a CRISPR-associated protein. Cas1 may be involved in linking DNA segments to CRISPR.	5.99956e-29
LR134176.1\|VEB32180.1\|2986659_2987610_+\|Nucleotidyl-transferase-of-uncharacterised-function-(DUF1814)	gnl\|CDD\|378065	pfam08843, AbiEii, Nucleotidyl transferase AbiEii toxin, Type IV TA system. This family was recently identified as belonging to the nucleotidyltransferase superfamily. AbiEii is the cognate toxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338.	2.1749e-20
LR134176.1\|VEB32177.1\|2981368_2985487_-\|CRISPR-associated-protein-Cas9/Csx12,-subtype-II-B/NMENI	gnl\|CDD\|187835	cd09704, Csx12, CRISPR/Cas system-associated protein Cas9. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Very large protein containing McrA/HNH-nuclease related domain and a RuvC-like nuclease domain; signature gene for type II.	0
LR134176.1\|VEB32181.1\|2987841_2988594_-\|transposase-TnpA-or-TnpA2	gnl\|CDD\|376574	pfam01610, DDE_Tnp_ISL3, Transposase. Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204, IS1001, IS1096 and IS1165.	3.51909e-68
LR134176.1\|VEB32165.1\|2969750_2971352_-\|putative-type-I-restriction-enzyme-M-protein	gnl\|CDD\|223363	COG0286, HsdM, Type I restriction-modification system methyltransferase subunit [Defense mechanisms].	3.53882e-127
LR134176.1\|VEB32161.1\|2962408_2965678_-\|putative-type-I-restriction-enzyme-R-protein	gnl\|CDD\|273028	TIGR00348, R_protein, type I site-specific deoxyribonuclease, HsdR family. This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity. [DNA metabolism, Restriction/modification].	1.08068e-132
LR134176.1\|VEB32175.1\|2979809_2980826_+\|transposase-IS630-family	gnl\|CDD\|315923	pfam13358, DDE_3, DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.	2.53111e-35
LR134176.1\|VEB32172.1\|2978401_2978995_-\|CRISPR-associated-protein-Cas4	gnl\|CDD\|273040	TIGR00372, conserved_hypothetical_protein, CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.	4.12817e-15

>LR134176.1|VEB32170.1|2976042_2976222_-|Uncharacterised-protein
MKYILLLLFNISYAPNHPVVTTSLEFSTQQACKDAGKQVQELTRTRNGSAVPDFICLKK
>LR134176.1|VEB32169.1|2974921_2975398_+|Uncharacterised-protein
MQSVGLFDMNVYPDEIFKFRILIKVTKSEYVNDLLNGNLYMNSFYYFREIEEKTARGDELEGVDAGYRAEDITLRISDGKGTFLPIKELVGRSNFHNNHVINSNLFSISGFSLEDFPIGQSNLFLDQKFREFGDKSVIIYDVPRFISMIERGFEKIKE
>LR134176.1|VEB32168.1|2973214_2974240_+|Protein-of-uncharacterised-function-(DUF3800)
MFFYIDESGNTGSNIFDPKQPIIYYGLLISPKSLNICNQITLMREKLNVNQLHARALGERLELVVEDLLKTIDELNLKFKLFTINKSDHVMIQFFDQVFDDNINPAVPFHWYNSPFRYKLLFAIAFYLFDEELRKLAWNSWTNKNDKISTEYFIRTCKKLRDRLHKLPLDKSKRFIIFSILKWAMANYQLIPFQLGKKAAYHINIVCFRAVIDGISSYIQDMGIEPSEIIVDQQSTYNVPQQEALELYRELKHYTFPNYPGIPEIDLRFTPKINLTFSSSRNNNGLELCDILLWVCKRKIEGKLPHSLEKLVDHPSFKWEYDISLHAIYTRFLEPEVKRRK
>LR134176.1|VEB32167.1|2972069_2972681_+|FRG-domain
MAASIRTIISTLEQLSLEGYVFRGHEDFRYQLTPSAFREHSIAQMKIDFNIHPTILDGWFNSKEIKKTIASWYSSNSVHLQHPAIYLLKEWCLYIMRYNHSLHLFVKNNPNNVSEQDAASFLLRDAEYWRQETTFKHMFERYLPTIINRHSLKDGVLIQRANPYEDLAAVDETLPQHYGIPTAALDWSYNFHVAIHFALGNES
>LR134176.1|VEB32166.1|2971345_2971948_-|EcoKI-restriction-modification-system-protein-HsdS
MDLINISTISAGYSFRGKILELKNSGIYCVQMKDINETYNVNWSTVIETILPSRQSQVLLQSGDILFAARGQRNYAALIDAELKERLAIAAPQFFVIRLNVPDVLPEYIAWFLNQTIAQRYFLSNAEGSTTPSIRRQVLEATPIILPTLEQQRTIIELAKTISKEKQLAHKIIANGELLMQTLLNEISQTQLNEEEVPSC
>LR134176.1|VEB32165.1|2969750_2971352_-|putative-type-I-restriction-enzyme-M-protein
MLNSNALNTISINANPVNQDTINKALMAACDTFRGTISADTYKDFILTMLFLKYISDVWQDHFEEYQKQYGDEPELIHEMMKNERFVIPEITLKNEDGSVRDHFQATFKNLWERRHEPGNGERIDLCLHAIEEANGTKLRDNAKSVFQDISFNTDKLGEEKQKNTILRHLLEDFAKPELNLRPSRVAGLDIIGNAYEYLIKHFAASGGQKAGEFYTPPEVSSLIATLLDPQPGDSICDPACGSGSLLMKCGRIIRENHHQKNYALFGQEAIGSTWSLAKMNMFLHGEDNHKIEWGDTIRNPKLLDSKGHLMLFDIVTANPPFSLDKWGHEEAENDHFGRFRRGIPPKTKGDYAFILHMIETLKPKTGRMGVVVPHGVLFRGSSEGKIRQKLIEENLLDTVIGLPEKLFYGTGIPAAILIFKKQKSDNKVLFIDASKEFKSGKNQNQLSQANIEKIIETYKQRQSIDRYSYLAGLDEIKGNNYNLNIPRYVDTFEEEEEIDLLAVRAERLLLKKELAELELQMEIYLRELGYGA
>LR134176.1|VEB32164.1|2968573_2969761_-|EcoKI-restriction-modification-system-protein-HsdS
MVPKEWTLETLGSITAESAFGPRFSSDLYDDNGTVGTIRTTDLDEEGNINYSTIPYAYLPKSFESHYLREHDLLITRSGSCGIPCLFENQTKPIIAGAFLIRFRLNNKAEPRFIHALLKSEKLQNKIQSMTAGGVQKNLSGTNLKKLEFFLPPLSEQKKIAQILSTWDKAITTTEKLLANSEQQKKALMQQLLTGKKRFLSFCDEWKQIRLKSVLKEEKARNRDNSIQQVLSITNHSGFVLPEEQFSKRIASDNISNYKIVRNGQFGYNPSRLNVGSFARLDKLNIGVLSPMYIVFSVKSDSLDSDYFLCWMQSNEAKQRVSNNTQGSVRDSVGFDALCRLPFKLPPMIEQKKIASMIAVANQEIEKIKQKLVYFRQEKKALMQQLLTGKRRVKL
>LR134176.1|VEB32163.1|2967581_2968577_-|Uncharacterised-protein
MTTENQSIPYLFEFDSFDEIYMQIKNESALWHAPAKKHWQIQFEEYHQYLDADFLKEFQLHFFSRIWELTLISYISQQLGKNDGLIKNKVKNKRYPDFCFKIDNQKFYLEAHAPSSGLSIELNASFEDIAGKARNVPIASYKERLCSSIREKGDILYYGKDGKSAYKDQIGVDSGFVIAVSMAKIPFFNQPIDYYVDLSCILGLSPRKIPILRDKDGNHFIGSIYHDKELSFQKSGTASPITTNYFSDDTYGHISAILISHSSWSFFPDADQYGIPLHWEKCRNDYILVHNPFAKIPLPSEYLSVYREITSREVLSLQQSNKFSLSNQESA
>LR134176.1|VEB32162.1|2965674_2967582_-|ATP-dependent-DNA-helicase
MQWTIQQIFDELIQLDEHQRIEAKRASEIGHSIMQTICAFANEPGLGGGWLLLGIAEPDSEHNTFWVSGIENIDKLLGELQNNCRTQFEHPVRIECKHEKIDGKSVIGVFVYELEPNAKPCRFIGKPDKHNKRKTGVWRRGANGDYECTEKELEPILMAKAGISYEQIILPDTTLDDLDENAIALYRKLRAKVRPNAEELQADDLGLLRALRVVKKHGGEYIPNIAGLLLFGKTLSLRGLLPAVRVDYVRVAGTEWVEDPNQRFQYSLDLREPLLTLIPKLENVILDDMPRYFRLEEGQLQRSDQPFLPQKVIREAIVNAVMHRDYHVHQPTMVVRYSNRLEIRNAGYSLKSLDEYDDTGSELRNPILSHVLYDLDFAETKGTGFRTMQRLLNDAGLTKPILLSNRQSNYFKATFLLHQLMNEEQLLWLKQFRDLNLSSDEAKALVLIREVGAIDNGALRAITDLDTLAASKVLGRLWQQYHLIEKGGSGRNTYYKPTHLLMSYHPSEHQNSDELNRNDSNLMANSSDLNRNGSDLDANSSHLPDALREEIDRLTPKSRQIKPIILKLCLNHSYSADQMATILNRNASALKTKQLVPMCEEGLITYTHPEVRNHPNQAYAITEKGRQWLKNKGLS
>LR134176.1|VEB32161.1|2962408_2965678_-|putative-type-I-restriction-enzyme-R-protein
MTQLPRFQEEYSAKIPALVVLNNLGWTFLSPEQALTLRENKPSEVVLKTALYDVLRKRRFIYAGKEYPLSDKSIDGIVAEISTPALNEGLTKANEQIYNHILYGITVTEFIGGKKINPTIPLIDWHNIQNNSFLFTEEYSVLGAGGVTRYPDIVCFVNGLPLVVIEAKRPNGKKGPTIEEGISQHLRNQRLSEIPQLFAYSQLLLSINGVDGLYGTQGTDAKFWATWRDEDIGANQFNQIKNLSLSTQQIDGFFNHRRATDRVWFEKLISQGPLAVTGQDKLLISLLSPQRLLDMTRYFMLFDKKAGKIVARYQQFFGIQRLIERINTPSSDGGREGGVIWHTTGSGKSLTMVFLSRALILHDSLKQCRIVVVTDRVDLEGQLSNTFHSGGEFSGKKEFSNAKVTSGRRLAEKISKGTERVIFSLIQKFNTAAKLPQCKNLSRDIVVLVDEGHRSQGGENYIRMKQALPNAAFIAFTGTPLLKEDKTTNKFGSIIHAYTMQRAVEDKMVTPLLYEERRPELMVNDRAIDSWFERITEELSDKQRADLKKKYAKKGEIYRSENRIELIALDIAHHFVKNIDEGLKGQIACDDRPSAIHYKKYLDEIGFFESAVVMSPPDTREGNTEVDESKIPELTKWWKDNVGNQDEREYTRQVIERFANDEDLKIIIVVDKLLTGFDEPRNTVLYIDKQLKEHNLIQAIARVNRLHEKKKFGLLIDYRGILKELDTTIAKYQDLASRTQQGYDITDLDGLYHQMSSEYKRLPLLYDALWKIFKEVKNKGDFEQLRQVLIPKIQEVDGDLVDTNLKVREDFYDALSEFANCLKVALQSDSFFDDKSITDAQRTHYKETLKQFTSLRQIAKLDAGEIIIYDKYADLVKKLMDKHVVGVQIKEPEGVYEVGKMGRQERPEEWNEEKTRNETDIIKTRIAKMIEQDLRDDPYAQETFSELLKIAIKEADELFEHPLKQYLLFQEFEHDVLNRKLKEIPADFSDNHHAQAYYGVFKLQLPVSFATLTEQEQKKWIDLAFTLDDLINVSIAEHSLNQQNTEADIRKKLLPIIFKACKDLGFGMEHAKNIIEQIIQIVRVGLISI
>LR134176.1|VEB32172.1|2978401_2978995_-|CRISPR-associated-protein-Cas4
MDTSSYKLPVNMIRQYCFCPRIVYYHMVIGLKVAYPGWVQYGEEYQHKQQILDKRRTLSKFKPISEQAILRQNTMLEHPSYPFYGICDGIIEDELEIIPIELKSFASKISLGQKMQLTAYGMLSELIFEKSCTRGYIITGEKAKAKLIKIDEKSKFKVLEIYAKIKKIFDTETLPYSTANGLQCIQCEFLNHCNDRF
>LR134176.1|VEB32173.1|2978975_2979275_-|CRISPR-associated-endoribonuclease-Cas2
MQTRLYKEYIVSYDIRDNSIRRTIYERLKDIGLTPVQKSVFWGYLNEPEKRYLTNVLKKELAKQDTAFITPCKLTQEYEVNLINLELDELRKPDGHIIV
>LR134176.1|VEB32174.1|2979281_2979689_-|CRISPR-associated-endonuclease-Cas1
MVNKDITNSMLNYAYSILSSWVWQAITNAGLELYAGILHTSKPGKPSLVLDLMEEFRPWCADRIIFKLRARAQKQNELTPALKKALIDEMANLYAKPLPYHKRRISLESIIQRQVYHLSAVFSGEGKYKGYLFKW
>LR134176.1|VEB32175.1|2979809_2980826_+|transposase-IS630-family
MKRLYLTPEEKDYLEREHALKENGKERDRIKAILLRSEGWTVSQISQALRLHQSTIIRHVQEYQEGKLKNTSGGSTGQLSEEQTQELIAHLEANLYHHNHQIILYVQERYGVTYTIPGMHKWLHRNGFSYKKPKGIPHKADAQLQKEFVAKYQQLKEELGGKEPILFMDSVHPTQATKLAYGWIRTGKVRHVGTTASRTRLNIIGAIQLGHIAEAITSQYDTINAESITAFMDKIRTQYADKTVHLILDMAPYHRSSLVAEHASRLNIKLHFLPPYSPNLNPIERLWRVMNEQVRNNRCFKGAKDFKEAISGFFTDTLPYIGSLLNERINDNFQFLKT
>LR134176.1|VEB32176.1|2980814_2981372_-|CRISPR-associated-endonuclease-Cas1
MKHLTLSEQGSSCKLQGERILVFNKDHMVFEGTLNRLKTISIAKQGVTLTSNLLVACAMRGIQIFILDYSGKAVCSLQGGLHRTAKVRENQFKYIYTKEASNMAARFILAKIKNQSAVLKYFAKAKNRPENEKIILHTASQKIAGIVSNITETNWIKLQDWRFTLLGFEGSAAKIYPRNFKMLSF
>LR134176.1|VEB32177.1|2981368_2985487_-|CRISPR-associated-protein-Cas9/Csx12,-subtype-II-B/NMENI
MESSQLLSPIGIDLGGKFTGVCLSHLESFAELPNHANTKYSVILMDHNNFQLSQAQRRITRHRVRNKKRNQFVKRVALQLFQHMLSRELNVKEEIALCHYLNNRGYTYVDTDLDEYLKDETTINLLKELLPPESEHNFIDWLLQKMQSSKFREILGSRVEEKKDDKELKNAVKNIKNFITGFEKNSVEGHRHRKVYFENIKSDITNDNQLDGIKKKIPSVCLSNLLGHLSNLQWKNLHRYLAKNPKQFDEQTFGNEFLRMLKNFKHLKGSQESLAVRDLIQQLEQSKDYISILEKTPPEITIPPYEARTNTGMEKDQSLLLNPEKLNNLYPKWRNLIPGIIDAHPFLEKNLEHTKLRDRKRIISPSKQDEKRDAYILQRYLDLNKKIDKFKIKKQLSFLGQGKQLPANLIETHKEMETHFSSSLVSALIQIASAYNKEREDAAQGVWFDNAFSLCELSNINPPRKQKILPLLVGAILSEDFINNKDKWAKFKSFWNTHKIGRTLLKYKCKEIEEARKNSGNAFKIDYEEALNHPEHSNNKALTKIIQTIPDIIQAIQSHLGHNDSQALIYNNPFSLSQLYTILETKRDGFHKNCVAVTCENYWRSQKTEIDPEISYASRLPADSVRPFDGVLARMMQRLAYEIAMAKWEQIKHIPDNSRLLIPIYLEQNRFEFEESFKKIKGISRDKTLEQAIEKQNIRWEEKFQRIINASMNVCPYKGTSIGRQGEIDHIYPRSLSKKHFGTIFNSEANLIYCSSQGNREKKEEHYLLEHLSPIYLKHQFGTDNVSDIKNFISQNVANIKKYISFHLLTPEQQKAARHALFLDYDDEAFKTVTKFLMSQQKARVNGTQKFLGKQIMEFLSTLADSKQLQLEFSIKQINAEEVHNHRELLSKQEPKLAKSQQQSFPSHAIDATLTMGIGLKEFPQFSQELDNSWFINHLMPDEVHLNPVQSKEKYNKPNISSTPLFKDSLYAERFIPVWVKGETFAIGFSEKDLFEIKPSNKEKLFTLLKTYSTKNPGESLQELQAISKAKWLYFPINKTLALEFLHHYFHKETVTPDDTTVCHFINSLRYYTKKESITVKILKESMPVLSVIFESSKKNVLGTFKHTIALPATKDWERLFNHPNFLALKANPNPNPKEFNEFIKKYFLSENNPNSDIPNNGHTIKPQKHKTVRKVFSLPVIPGNAGTMMRIRRKDNKGQPLYQLQTIDDTPSMGIQVNEGKLVKQEVLMDAYKTRNLSTIDGINNSERKAYAAFDNWLTLPVSTFKPEIIKLEMKPHSKTRRYIRITQSLADFIKTIDEALMIKPSDSIDDPLNMPNEIVCKNKLFGNELKPRDGKMKIVSTGKTVTYEFESDSTPQWIQKLYVTQLKKHP
>LR134176.1|VEB32178.1|2985658_2985877_-|phage-transcriptional-regulator-AlpA
MTKLPEIGFLRANQIIGDKNANPPIPALIPVGKSTWWAGVKSGRFPKPIKFGSRITVWRVEDIREFIEKASL
>LR134176.1|VEB32179.1|2986238_2986670_+|Uncharacterised-protein
MTRKYYKNSLKFRVLDRIEQASGNVVLRKDIEDMASPRQISRCFADLVEMGKLVKIGYGIYAKAYRSEYLNKPVIKGGFSQICKEALTKLGVEWIPGSAEQAYNSGLSTQVPVRTIVQLKSRFRGHLKYGNRQLVVEKGINAR
>LR134176.1|VEB32180.1|2986659_2987610_+|Nucleotidyl-transferase-of-uncharacterised-function-(DUF1814)
MLGKPLLELITTTGEILELEDLVIEKDYYVAQVINALSKVENDYFRLVFCGGTCLAKAHKVIYRMSEDIDFKIQIKEIDEHLSKTRLLKELKIFRSLIQSKLTHLDLSIGNSVVRNEGQYSRIELDYPSVFPFNSRLRPHILLEFTLSNIRLATSSLPIKTLIEETLENIILFAPCFTHCISVNETAIEKWAGLTRRVVAIERNYHPDDETLIRHVYDLNAIKQASKIDENFFTLAKTIVSNDAKQFKNQHPEYADNPSEEIKQSLSLLKNKLIWKARYQEFIETMVYDNINTIDYETAIANIEHISTKIMGFLSE
>LR134176.1|VEB32181.1|2987841_2988594_-|transposase-TnpA-or-TnpA2
MLNTPCPKVLGLDERFFSRKHGFATTLCDLKKHKVFDIVKGRREVDLNHYLNSLKGKDRVQVVCMDLSSTYRSLVKKHFPNAQIVADRFHVIRLVQHQCMMTYRELSSSIKNNRGLLALLRTKPDKLTPHKKIKRDSFLAENPAIEAIYHFQQQLHELLMNKTLTKVRCRKIIPLFLKMIQDLKQSPFKSLVALGKTLDSWKEEIACMWRFSKSNGITEGFHRKMKLIQRRAYGFRNFENYRLRVRVLCA

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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	Mismatch	Identity
LR134176_2	2.12\|2977390\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2977390-2977423	34	NZ_CP009595	Bacillus cereus strain 3a plasmid pBFC_3, complete sequence	81518-81551	7	0.794
LR134176_2	2.12\|2977390\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2977390-2977423	34	NZ_CP009606	Bacillus cereus strain S2-8 plasmid pBFR_2, complete sequence	260231-260264	7	0.794
LR134176_2	2.12\|2977390\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2977390-2977423	34	NZ_CP053994	Bacillus cereus strain FDAARGOS_780 plasmid unnamed1, complete sequence	21524-21557	7	0.794
LR134176_2	2.12\|2977390\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2977390-2977423	34	NZ_CP053992	Bacillus cereus strain FDAARGOS_781 plasmid unnamed2, complete sequence	4540-4573	7	0.794
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP025426	Enterococcus faecium strain SC4 plasmid p1, complete sequence	121102-121135	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	LT603679	Enterococcus faecium isolate Ef_DMG1500501 genome assembly, plasmid: 2	99521-99554	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP013995	Enterococcus faecium strain 6E6 plasmid unnamed1, complete sequence	148224-148257	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP027498	Enterococcus faecium strain AUSMDU00004167 plasmid unnamed1, complete sequence	98098-98131	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP027507	Enterococcus faecium strain AUSMDU00004055 plasmid unnamed1, complete sequence	74167-74200	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_LR135358	Enterococcus faecium isolate E7948 plasmid 2	122653-122686	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP050649	Enterococcus faecium strain BIOPOP-3 ALE plasmid pBIOPOP-3_ALE	132166-132199	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP050651	Enterococcus faecium strain BIOPOP-3 WT plasmid pBIOPOP-3_WT	2168-2201	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP040741	Enterococcus faecium strain VRE1 plasmid pVRE1-1, complete sequence	105589-105622	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_AP022342	Enterococcus faecium strain KUHS13 plasmid pKO1, complete sequence	141052-141085	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP019993	Enterococcus faecium isolate 2014-VREF-268 plasmid p268-1, complete sequence	160751-160784	9	0.735
LR134176_2	2.6\|2976958\|34\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2976958-2976991	34	NZ_CP042840	Enterococcus sp. DA9 plasmid unnamed4	124236-124269	9	0.735
LR134176_2	2.7\|2977029\|33\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2977029-2977061	33	AP014014	Uncultured Mediterranean phage uvMED isolate uvMED-GF-C103A-MedDCM-OCT-S38-C6, * SEQUENCING IN PROGRESS *	41663-41695	9	0.727
LR134176_2	2.7\|2977029\|33\|LR134176\|CRISPRCasFinder,CRT,PILER-CR	2977029-2977061	33	MN694426	Marine virus AFVG_250M547, complete genome	11807-11839	10	0.697

1. spacer 2.12|2977390|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP009595 (Bacillus cereus strain 3a plasmid pBFC_3, complete sequence) position: , mismatch: 7, identity: 0.794

tgcatt-tatggtattaattcaccttttacttacc	CRISPR spacer
-atattcttcggcattaattcaccttttacgtacc	Protospacer
 ..*** * .**.***************** ****

2. spacer 2.12|2977390|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP009606 (Bacillus cereus strain S2-8 plasmid pBFR_2, complete sequence) position: , mismatch: 7, identity: 0.794

tgcatt-tatggtattaattcaccttttacttacc	CRISPR spacer
-atattcttcggcattaattcaccttttacgtacc	Protospacer
 ..*** * .**.***************** ****

3. spacer 2.12|2977390|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP053994 (Bacillus cereus strain FDAARGOS_780 plasmid unnamed1, complete sequence) position: , mismatch: 7, identity: 0.794

tgcatt-tatggtattaattcaccttttacttacc	CRISPR spacer
-atattcttcggcattaattcaccttttacgtacc	Protospacer
 ..*** * .**.***************** ****

4. spacer 2.12|2977390|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP053992 (Bacillus cereus strain FDAARGOS_781 plasmid unnamed2, complete sequence) position: , mismatch: 7, identity: 0.794

tgcatt-tatggtattaattcaccttttacttacc	CRISPR spacer
-atattcttcggcattaattcaccttttacgtacc	Protospacer
 ..*** * .**.***************** ****

5. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP025426 (Enterococcus faecium strain SC4 plasmid p1, complete sequence) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

6. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to LT603679 (Enterococcus faecium isolate Ef_DMG1500501 genome assembly, plasmid: 2) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

7. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP013995 (Enterococcus faecium strain 6E6 plasmid unnamed1, complete sequence) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

8. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP027498 (Enterococcus faecium strain AUSMDU00004167 plasmid unnamed1, complete sequence) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

9. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP027507 (Enterococcus faecium strain AUSMDU00004055 plasmid unnamed1, complete sequence) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

10. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_LR135358 (Enterococcus faecium isolate E7948 plasmid 2) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

11. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP050649 (Enterococcus faecium strain BIOPOP-3 ALE plasmid pBIOPOP-3_ALE) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

12. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP050651 (Enterococcus faecium strain BIOPOP-3 WT plasmid pBIOPOP-3_WT) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

13. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP040741 (Enterococcus faecium strain VRE1 plasmid pVRE1-1, complete sequence) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

14. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_AP022342 (Enterococcus faecium strain KUHS13 plasmid pKO1, complete sequence) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

15. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP019993 (Enterococcus faecium isolate 2014-VREF-268 plasmid p268-1, complete sequence) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

16. spacer 2.6|2976958|34|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP042840 (Enterococcus sp. DA9 plasmid unnamed4) position: , mismatch: 9, identity: 0.735

ggcattgatatggcctaaaaggattagcatgtct	CRISPR spacer
tccattgatatggccaaaaagtattatcgggcca	Protospacer
  ************* ***** **** *. *.*

17. spacer 2.7|2977029|33|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to AP014014 (Uncultured Mediterranean phage uvMED isolate uvMED-GF-C103A-MedDCM-OCT-S38-C6, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 9, identity: 0.727

cacaccaacagaatcaaagctatgttctaagtg	CRISPR spacer
tgtaccaacagcatcaaagctatcttctgaact	Protospacer
...******** *********** ****.*..

18. spacer 2.7|2977029|33|LR134176|CRISPRCasFinder,CRT,PILER-CR matches to MN694426 (Marine virus AFVG_250M547, complete genome) position: , mismatch: 10, identity: 0.697

cacaccaacagaatcaaagctatgttctaagtg	CRISPR spacer
aaaactaacagaatcaaagttatgttcatttct	Protospacer
 * **.*************.*******    .

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

107639 : 202257

Escherichia_phage(21.05%)

integrase,transposase,tRNA

attL 114659:114675|attR 172428:172444

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
VEB29477.1\|107639_107870_-\|tRNA	valyl-tRNA synthetase	A0A1V0SK04	Klosneuvirus	2.9e-06	42.2
VEB29478.1\|107881_108793_-\|tRNA	valyl-tRNA synthetase	A0A1V0S951	Catovirus	4.7e-79	49.8
VEB29479.1\|109048_112096_-	hydrophobic/amphiphilic exporter-1 (mainly G-bacteria), HAE1 family	S5VTK5	Leptospira_phage	6.6e-61	22.6
VEB29480.1\|112212_113475_-	acriflavin resistance protein	NA	NA	NA	NA
VEB29481.1\|113715_114120_+	Uncharacterised protein	NA	NA	NA	NA
VEB29482.1\|114185_114623_+	Uncharacterised protein	NA	NA	NA	NA
114659:114675	attL	NA	NA	NA	NA
VEB29483.1\|114747_115059_+	putative periplasmic or secreted lipoprotein	NA	NA	NA	NA
VEB29484.1\|115086_116340_+	glycine hydroxymethyltransferase	A0A219Y950	Aeromonas_phage	2.8e-98	51.7
VEB29485.1\|116342_116810_+	ATP cone and Zn ribbon domains protein	NA	NA	NA	NA
VEB29486.1\|116867_117311_+	N utilization substance protein B	NA	NA	NA	NA
VEB29487.1\|117303_118260_+	thiamine monophosphate kinase (AIR synthase)	NA	NA	NA	NA
VEB29488.1\|118349_118832_+	phosphatidylglycerophosphatase A	NA	NA	NA	NA
VEB29489.1\|118831_119323_+	transmembrane permease	NA	NA	NA	NA
VEB29490.1\|119298_119883_+	transmembrane permease	NA	NA	NA	NA
VEB29491.1\|119874_120612_-	Uncharacterised protein	NA	NA	NA	NA
VEB29492.1\|120621_121260_-	opacity protein-like surface antigen	NA	NA	NA	NA
VEB29493.1\|121449_122874_+	Uncharacterised protein	NA	NA	NA	NA
VEB29494.1\|122925_124536_-	NAD synthase (glutamine-hydrolysing)	A0A2L0UZF5	Agrobacterium_phage	7.4e-88	36.3
VEB29495.1\|124818_128085_+	DNA helicase, SNF2/RAD54 family domain protein	M1GYP4	Paramecium_bursaria_Chlorella_virus	1.2e-36	27.6
VEB29496.1\|128239_128674_+	putative signal peptide protein	NA	NA	NA	NA
VEB29497.1\|128851_130234_+	Replicative DNA helicase	O80281	Escherichia_phage	2.9e-141	58.1
VEB29498.1\|130235_131309_+	alanine racemase	NA	NA	NA	NA
VEB29499.1\|131381_131831_+	Surface antigen	NA	NA	NA	NA
VEB29500.1\|132137_132572_+	putative manganese-dependent inorganic pyrophosphatase	NA	NA	NA	NA
VEB29501.1\|132614_133868_+	Uncharacterised protein	NA	NA	NA	NA
VEB29502.1\|133979_134252_+	glutamate synthetase	NA	NA	NA	NA
VEB29503.1\|134271_135822_+	diguanylate cyclase	A0A127AWB9	Bacillus_phage	8.3e-20	35.3
VEB29504.1\|135973_136963_+	lipoic acid synthetase	NA	NA	NA	NA
VEB29505.1\|137116_137398_-	endonuclease	NA	NA	NA	NA
VEB29506.1\|138106_139615_-	IraAB	NA	NA	NA	NA
VEB29507.1\|139653_140472_-	small-molecule methyltransferase IraA	NA	NA	NA	NA
VEB29508.1\|140634_140877_-	Uncharacterised protein	NA	NA	NA	NA
VEB29509.1\|140905_141103_-\|transposase	transposase	NA	NA	NA	NA
VEB29510.1\|141245_142103_-\|transposase	transposase	NA	NA	NA	NA
VEB29511.1\|142572_143595_+	N-acetylneuraminic acid synthetase	A0A1B1IVE2	uncultured_Mediterranean_phage	2.1e-35	38.5
VEB29512.1\|143594_144728_+	polysialic acid biosynthesis	NA	NA	NA	NA
VEB29513.1\|144717_145326_+	acetyltransferase	NA	NA	NA	NA
VEB29514.1\|145336_146839_+	pyridoxal phosphate-dependent enzyme	NA	NA	NA	NA
VEB29515.1\|146928_147492_+	dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC	I7HJC4	Enterobacteria_phage	1.1e-51	57.5
VEB29516.1\|147492_148377_+	dTDP-6-deoxy-L-mannose dehydrogenase RmlD	I7HXC9	Enterobacteria_phage	1.1e-32	34.5
VEB29517.1\|148336_149416_+	dTDP-D-glucose 4,6-dehydratase	I7HTA3	Enterobacteria_phage	1.7e-83	48.2
VEB29518.1\|149454_150954_+	glucose-6-phosphate isomerase	NA	NA	NA	NA
VEB29519.1\|151108_151984_+	glucose-1-phosphate thymidylyltransferase	A0A291LA53	Escherichia_phage	2.1e-92	58.0
VEB29520.1\|152004_152961_+	NAD dependent epimerase/dehydratase, UDP-glucose-4-epimerase	NA	NA	NA	NA
VEB29521.1\|152944_153949_+	UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase	NA	NA	NA	NA
VEB29522.1\|154280_154463_+\|transposase	transposase ORF-A, IS-type	NA	NA	NA	NA
VEB29523.1\|154652_154967_+\|integrase	integrase catalytic subunit	NA	NA	NA	NA
VEB29524.1\|155024_156182_+\|integrase	integrase catalytic subunit	K4I413	Acidithiobacillus_phage	3.3e-114	53.2
VEB29525.1\|156201_156957_+	IstB domain protein ATP-binding protein	NA	NA	NA	NA
VEB29526.1\|157187_158219_+	N-acetylneuraminic acid synthetase	NA	NA	NA	NA
VEB29527.1\|158215_158983_+	putative glycosyltransferase	NA	NA	NA	NA
VEB29528.1\|158983_159988_+	Oxidoreductase family, NAD-binding Rossmann fold	NA	NA	NA	NA
VEB29529.1\|160000_161311_+	putative aminotransferase class-III	NA	NA	NA	NA
VEB29530.1\|161345_162125_+	hydrolase	NA	NA	NA	NA
VEB29531.1\|162117_162954_+	acetyoacetyl CoA reductase	NA	NA	NA	NA
VEB29532.1\|162967_163804_+	lipopolysaccharide transport system permease	NA	NA	NA	NA
VEB29533.1\|163820_165650_+	ABC transporter of LPS O-antigen	A0A2H4PQG7	Staphylococcus_phage	6.6e-08	27.3
VEB29534.1\|165639_167556_+	Uncharacterised protein	NA	NA	NA	NA
VEB29535.1\|167576_169535_+	Uncharacterised protein	NA	NA	NA	NA
VEB29536.1\|169704_170112_-\|transposase	putative IS5376 transposase	A0A2L1IVA1	Escherichia_phage	1.5e-21	50.6
VEB29537.1\|170160_170538_-\|transposase	putative IS5376 transposase	A0A2L1IVA1	Escherichia_phage	2.6e-20	48.0
VEB29538.1\|171645_172839_-	Uncharacterised protein	NA	NA	NA	NA
172428:172444	attR	NA	NA	NA	NA
VEB29539.1\|173425_173647_-\|transposase	transposase	NA	NA	NA	NA
VEB29540.1\|173665_174274_-	Transposase	NA	NA	NA	NA
VEB29541.1\|174397_175846_-	Uncharacterised protein	NA	NA	NA	NA
VEB29542.1\|175940_176147_+	Uncharacterised protein	NA	NA	NA	NA
VEB29543.1\|176109_176967_+\|transposase	transposase	NA	NA	NA	NA
VEB29544.1\|177054_177306_+\|transposase	transposase	NA	NA	NA	NA
VEB29545.1\|177314_177494_+	Uncharacterised protein	NA	NA	NA	NA
VEB29546.1\|177586_178321_+	N-acylneuraminate cytidylyltransferase	NA	NA	NA	NA
VEB29547.1\|178340_179426_+	N-acetylneuraminic acid synthetase	NA	NA	NA	NA
VEB29548.1\|179461_181810_+	Uncharacterised protein	NA	NA	NA	NA
VEB29549.1\|182050_183073_+	Transposase domain (DUF772)	NA	NA	NA	NA
VEB29550.1\|183313_183622_+	Uncharacterised protein	NA	NA	NA	NA
VEB29551.1\|183624_184539_-	alginate O-acetyltransferase AlgI	A0A125RNP0	Pseudomonas_phage	1.2e-50	41.0
VEB29552.1\|184535_185702_-	Uncharacterised protein	NA	NA	NA	NA
VEB29553.1\|185919_186165_-	cell cycle protein MesJ	NA	NA	NA	NA
VEB29554.1\|186202_187216_-	cell cycle protein MesJ	NA	NA	NA	NA
VEB29555.1\|187208_187556_-	acetyl-CoA carboxylase carboxyl transferase subunit alpha	NA	NA	NA	NA
VEB29556.1\|187527_187773_-	acetyl-CoA carboxylase carboxyl transferase subunit alpha	NA	NA	NA	NA
VEB29557.1\|187846_188161_-	acetyl-CoA carboxylase carboxyl transferase subunit alpha	NA	NA	NA	NA
VEB29558.1\|188242_188980_+	phosphopantetheine-protein transferase	NA	NA	NA	NA
VEB29559.1\|188983_189976_+	biotin-[acetylCoA carboxylase] holoenzyme synthetase and biotin operon repressor	NA	NA	NA	NA
VEB29560.1\|190071_190266_-	global regulator (carbon storage regulator)	A0A2I7RT00	Vibrio_phage	3.0e-12	70.6
VEB29561.1\|190456_190906_-\|transposase	transposase	NA	NA	NA	NA
VEB29562.1\|190902_191550_-\|transposase	transposase	NA	NA	NA	NA
VEB29563.1\|192042_193446_+	FOG: Transposase	NA	NA	NA	NA
VEB29564.1\|193681_194539_+\|transposase	transposase	NA	NA	NA	NA
VEB29565.1\|194626_194878_+\|transposase	transposase	NA	NA	NA	NA
VEB29566.1\|194886_195015_+	Uncharacterised protein	NA	NA	NA	NA
VEB29567.1\|195033_195378_+	Uncharacterised protein	NA	NA	NA	NA
VEB29568.1\|195386_196430_-\|transposase	transposase IS630 family	NA	NA	NA	NA
VEB29569.1\|196608_197316_-	hydroxyacylglutathione hydrolase	NA	NA	NA	NA
VEB29570.1\|197547_198567_+	glycosyltransferase	NA	NA	NA	NA
VEB29571.1\|198560_199469_+	glycosyl transferase family protein	NA	NA	NA	NA
VEB29572.1\|199559_200822_+	Transposase domain (DUF772)	NA	NA	NA	NA
VEB29573.1\|200821_201160_+	Uncharacterised protein	NA	NA	NA	NA
VEB29574.1\|201213_202257_+\|transposase	transposase IS630 family	NA	NA	NA	NA

DBSCAN-SWA_2

247689 : 254528

Acinetobacter_phage(42.86%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VEB29619.1\|247689_248466_-	indole-3-glycerol phosphate synthase	A0A0P0IR83	Acinetobacter_phage	1.9e-57	48.2
VEB29620.1\|248458_249493_-	anthranilate phosphoribosyltransferase	A0A0N7IRD9	Acinetobacter_phage	2.1e-75	47.6
VEB29621.1\|249470_250049_-	anthranilate synthase component II	A0A0P0IKJ1	Acinetobacter_phage	3.5e-56	53.2
VEB29622.1\|250082_250808_-	ABC-type transport system protein involved in lipoprotein release, ATPase compnent	G9BWD6	Planktothrix_phage	3.1e-17	28.3
VEB29623.1\|250804_251314_-	lipopolysaccharide export system protein LptA	NA	NA	NA	NA
VEB29624.1\|251294_251864_-	Uncharacterized protein YrbK clustered with lipopolysaccharide transporters	NA	NA	NA	NA
VEB29625.1\|251860_252388_-	hydrolase	A0A140XBD6	Dickeya_phage	1.4e-27	47.7
VEB29626.1\|252401_253364_-	polysialic acid capsule expression protein	A0A2P0VNK5	Tetraselmis_virus	4.2e-38	34.1
VEB29627.1\|253730_254528_+	putative ABC transport system ATP-binding protein	G9BWD6	Planktothrix_phage	1.7e-21	33.8

DBSCAN-SWA_3

348298 : 416100

Escherichia_phage(26.67%)

integrase,transposase,tRNA

attL 355487:355501|attR 423805:423819

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VEB29730.1\|348298_351094_+\|tRNA	isoleucyl-tRNA synthetase	K7YVP8	Megavirus	5.2e-89	27.9
VEB29731.1\|351090_351555_+	signal peptidase II	NA	NA	NA	NA
VEB29732.1\|351852_352416_-	eda 2-dehydro-3-deoxy-phosphogluconate aldolase	NA	NA	NA	NA
VEB29733.1\|352591_354781_-	Dot/Icm system substrate protein LidA	NA	NA	NA	NA
VEB29734.1\|355025_358151_-	membrane protein	NA	NA	NA	NA
355487:355501	attL	NA	NA	NA	NA
VEB29735.1\|358412_359300_+	GTP-binding protein Era	NA	NA	NA	NA
VEB29736.1\|359289_359979_+	DNA repair protein RecO (recombination protein O)	NA	NA	NA	NA
VEB29737.1\|360233_360980_+	pyridoxal phosphate biosynthetic protein PdxJ	NA	NA	NA	NA
VEB29738.1\|360966_362784_+	2-oxoglutarate ferredoxin oxidoreductase subunit alpha	NA	NA	NA	NA
VEB29739.1\|362767_363736_+	2-oxoglutarate ferredoxin oxidoreductase beta subunit	NA	NA	NA	NA
VEB29740.1\|364122_364797_-	carrier/transport protein	A0A2H4JFM9	uncultured_Caudovirales_phage	4.0e-27	44.5
VEB29741.1\|365015_365822_+	nitrilase	NA	NA	NA	NA
VEB29742.1\|365833_367276_+	TldD protein	NA	NA	NA	NA
VEB29743.1\|367321_368200_+	phosphoesterase	NA	NA	NA	NA
VEB29744.1\|368226_369894_+	long-chain fatty-acid-CoA ligase	A0A1V0SBX8	Catovirus	9.5e-46	27.2
VEB29745.1\|369872_372038_-	transcription-repair coupling factor	NA	NA	NA	NA
VEB29746.1\|372579_373335_-	transcription-repair coupling factor	NA	NA	NA	NA
VEB29747.1\|373411_374674_-	transmembrane protein	NA	NA	NA	NA
VEB29748.1\|374677_375856_-	Uncharacterised protein	NA	NA	NA	NA
VEB29749.1\|375852_376752_-	Uncharacterised protein	NA	NA	NA	NA
VEB29750.1\|376973_377684_+	DNA ligase	A0A1Y0SVC9	Pseudomonas_phage	9.6e-48	45.2
VEB29751.1\|377739_378996_+	DNA ligase	A0A289ZTZ3	Serratia_phage	5.1e-92	43.1
VEB29752.1\|379097_380207_+	extracellular solute-binding protein	NA	NA	NA	NA
VEB29753.1\|380194_381280_+	extracellular solute-binding protein	NA	NA	NA	NA
VEB29754.1\|381276_382254_+	peptide ABC transporter, permease protein	NA	NA	NA	NA
VEB29755.1\|382277_383624_+	peptide ABC transporter permease	NA	NA	NA	NA
VEB29756.1\|383698_387145_+	DNA polymerase III subunit alpha	A0A2L1IZ23	Streptomyces_phage	6.3e-185	36.0
VEB29757.1\|387230_388472_-	Dot/Icm secretion system substrate	NA	NA	NA	NA
VEB29758.1\|388801_389686_+	4-hydroxybenzoate octaprenyltransferase	NA	NA	NA	NA
VEB29759.1\|389646_391092_+	LphB	NA	NA	NA	NA
VEB29760.1\|391247_391571_+	nucleoside-diphosphate sugar epimerase	NA	NA	NA	NA
VEB29761.1\|391654_393124_+	nucleoside-diphosphate sugar epimerase	L7Y3T9	Megavirus	3.1e-24	29.1
VEB29762.1\|393269_393821_-	Uncharacterised protein	NA	NA	NA	NA
VEB29763.1\|394226_395921_-	Uncharacterised protein	NA	NA	NA	NA
VEB29764.1\|396387_397128_+	Uncharacterised protein	NA	NA	NA	NA
VEB29765.1\|397230_398694_-	amino acid permease	NA	NA	NA	NA
VEB29766.1\|399074_400220_+	ecto-ATP diphosphohydrolase I	NA	NA	NA	NA
VEB29767.1\|400726_401485_+	proline hydroxylase	NA	NA	NA	NA
VEB29768.1\|401556_402624_+	Uncharacterised protein	NA	NA	NA	NA
VEB29769.1\|403106_403775_+	Uncharacterised ACR, COG2135	S5VY94	Leptospira_phage	5.7e-10	24.7
VEB29770.1\|403909_404416_+	SOS response transcriptional regulator	A0A1W6JNS2	Morganella_phage	2.3e-27	47.2
VEB29771.1\|404417_405680_+	UmuC	I6RSM4	Salmonella_phage	4.2e-94	46.0
VEB29772.1\|406012_406117_+\|transposase	transposase (resolvase, DNA invertase)	NA	NA	NA	NA
VEB29773.1\|406190_406439_+\|transposase	transposase (resolvase, DNA invertase)	A0A0F7LA37	Escherichia_phage	1.5e-19	59.7
VEB29774.1\|406632_407427_-\|transposase	transposase/IS protein	A0A2L1IVB6	Escherichia_phage	9.3e-76	54.3
VEB29775.1\|407423_408470_-\|transposase	putative IS5376 transposase	A0A2L1IVA1	Escherichia_phage	9.4e-84	47.4
VEB29776.1\|408568_409006_+	Uncharacterised protein	NA	NA	NA	NA
VEB29777.1\|410628_411567_-	Uncharacterized protein conserved in bacteria	NA	NA	NA	NA
VEB29778.1\|411634_412141_-	antirestriction protein	A0A0H4TJV8	Mycobacterium_phage	3.4e-15	33.3
VEB29779.1\|412206_412629_-	single-strand DNA-binding protein	A0A077SK05	Escherichia_phage	1.6e-18	42.2
VEB29780.1\|412728_412923_-	Uncharacterised protein	NA	NA	NA	NA
VEB29781.1\|413264_414290_-	Uncharacterised protein	NA	NA	NA	NA
VEB29782.1\|414401_415301_-\|integrase	integrase	NA	NA	NA	NA
VEB29783.1\|415293_416100_-\|integrase	putative integrase	NA	NA	NA	NA
423805:423819	attR	NA	NA	NA	NA

DBSCAN-SWA_4

615678 : 621616

Staphylococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VEB29974.1\|615678_616752_+	riboflavin biosynthesis protein	A0A2H4PQS8	Staphylococcus_phage	2.3e-29	27.5
VEB29975.1\|616736_617351_+	riboflavin synthase subunit alpha	A0A2I2L4R9	Orpheovirus	6.0e-22	38.4
VEB29976.1\|617347_618556_+	Riboflavin biosynthesis protein	A0A2H4PQS2	Staphylococcus_phage	3.1e-99	48.7
VEB29977.1\|618563_619031_+	riboflavin synthase subunit beta	A0A2H4PQS3	Staphylococcus_phage	9.2e-23	49.1
VEB29978.1\|619156_620704_+	CTP synthase	A0A1J0FA14	Only_Syngen_Nebraska_virus	2.0e-143	52.4
VEB29979.1\|620791_621616_+	2-dehydro-3-deoxyphosphooctonate aldolase	E3T537	Cafeteria_roenbergensis_virus	3.0e-53	43.9

DBSCAN-SWA_5

1528357 : 1538478

Bacillus_phage(14.29%)

protease

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VEB30818.1\|1528357_1530046_-\|protease	AprE, Subtilisin-like serine protease	A0A1B0T6A2	Bacillus_phage	8.0e-16	30.4
VEB30819.1\|1530177_1531185_-	transcriptional regulator OruR, AraC family	NA	NA	NA	NA
VEB30820.1\|1531308_1532634_-	adenosylhomocysteinase	S4VPF6	Pandoravirus	1.1e-47	31.2
VEB30821.1\|1532652_1533801_-	S-adenosylmethionine synthetase	A0A2H4PQS6	Staphylococcus_phage	1.3e-126	58.5
VEB30822.1\|1534009_1535122_-	carbamoyl phosphate synthase, small subunit	R4TGJ8	Halovirus	2.3e-51	35.4
VEB30823.1\|1535216_1536356_-	heat shock protein DnaJ, chaperone protein	A0A1V0SBY2	Catovirus	1.6e-23	26.9
VEB30824.1\|1536544_1537780_-	molecular chaperone DnaK	A0A2K9L0M7	Tupanvirus	1.2e-77	44.1
VEB30825.1\|1537770_1538478_-	molecular chaperone DnaK	A0A1S5V0Y8	Saudi_moumouvirus	1.4e-54	56.4

DBSCAN-SWA_6

1632037 : 1657837

Mycobacterium_phage(20.0%)

integrase,transposase

attL 1624930:1624944|attR 1653190:1653204

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
1624930:1624944	attL	NA	NA	NA	NA
VEB30935.1\|1632037_1632841_+\|integrase	putative integrase	NA	NA	NA	NA
VEB30936.1\|1632833_1633733_+\|integrase	putative integrase	NA	NA	NA	NA
VEB30937.1\|1633848_1634538_+	Uncharacterised protein	NA	NA	NA	NA
VEB30938.1\|1635125_1635311_+	Uncharacterised protein	NA	NA	NA	NA
VEB30939.1\|1635373_1635880_+	antirestriction protein	U5P3Z5	Mycobacterium_phage	1.1e-18	35.4
VEB30940.1\|1635955_1636345_+	Virulence protein STM3117	NA	NA	NA	NA
VEB30941.1\|1636371_1636590_+	Uncharacterised protein	NA	NA	NA	NA
VEB30942.1\|1636582_1636882_+	Uncharacterised protein	NA	NA	NA	NA
VEB30943.1\|1637214_1638465_+\|transposase	transposase, IS4 family TnpA	Q9JMP3	Wolbachia_phage	7.9e-45	31.3
VEB30944.1\|1638819_1639848_+	Uncharacterised protein	NA	NA	NA	NA
VEB30945.1\|1640054_1640294_-	Uncharacterised protein	NA	NA	NA	NA
VEB30946.1\|1640527_1640737_+	Cold shock protein	A0A1X9IGI9	Lactococcus_phage	6.3e-16	63.9
VEB30947.1\|1640976_1642383_+	ATP dependent RNA helicase DbpA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	2.4e-58	34.3
VEB30948.1\|1642539_1643451_+	Co/Zn/Cd cation transporter	NA	NA	NA	NA
VEB30949.1\|1644333_1645452_+	Uncharacterised protein	NA	NA	NA	NA
VEB30950.1\|1645795_1646548_-	Dot/Icm T4SS effector	NA	NA	NA	NA
VEB30951.1\|1646986_1648828_+	Uncharacterised protein	NA	NA	NA	NA
VEB30952.1\|1649369_1649765_+	Ankyrin repeat protein	NA	NA	NA	NA
VEB30953.1\|1649733_1650750_-\|transposase	transposase IS630 family	NA	NA	NA	NA
VEB30954.1\|1650791_1652213_+	Ankyrin repeat protein	NA	NA	NA	NA
VEB30955.1\|1652686_1653745_+	Uncharacterised protein	NA	NA	NA	NA
1653190:1653204	attR	NA	NA	NA	NA
VEB30956.1\|1654006_1654951_+	LysR family transporter transcriptional regulator	NA	NA	NA	NA
VEB30957.1\|1655049_1656801_-	Ankyrin repeat protein	NA	NA	NA	NA
VEB30958.1\|1657054_1657366_+\|transposase	ISSod6 transposase	A0A0N9SHJ4	Paenibacillus_phage	9.8e-13	38.3
VEB30959.1\|1657522_1657837_+\|transposase	transposase, ISSod6	NA	NA	NA	NA

DBSCAN-SWA_7

2021687 : 2055803

Acinetobacter_phage(28.57%)