CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Target MGE spacer number	Prophage number
NZ_CP041157	Leisingera aquaemixtae strain R2C4 plasmid unnamed2, complete sequence	0 crisprs	NA	0	10
NZ_CP041163	Leisingera aquaemixtae strain R2C4 plasmid unnamed5	0 crisprs	NA	0	0
NZ_CP041160	Leisingera aquaemixtae strain R2C4 plasmid unnamed9	0 crisprs	NA	0	0
NZ_CP041159	Leisingera aquaemixtae strain R2C4 chromosome, complete genome	0 crisprs	WYL,cas3,DEDDh,csa3	0	2
NZ_CP041155	Leisingera aquaemixtae strain R2C4 plasmid unnamed8	0 crisprs	NA	0	0
NZ_CP041162	Leisingera aquaemixtae strain R2C4 plasmid unnamed6	0 crisprs	NA	0	0
NZ_CP041164	Leisingera aquaemixtae strain R2C4 plasmid unnamed3, complete sequence	1 crisprs	NA	2	0
NZ_CP041161	Leisingera aquaemixtae strain R2C4 plasmid unnamed7	0 crisprs	NA	0	0
NZ_CP041156	Leisingera aquaemixtae strain R2C4 plasmid unnamed1, complete sequence	0 crisprs	NA	0	0
NZ_CP041158	Leisingera aquaemixtae strain R2C4 plasmid unnamed4, complete sequence	0 crisprs	NA	0	0

Results visualization

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CRISPR-Cas detection and classification

Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

0 : 4470

Erysipelothrix_phage(100.0%)

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_167510214.1\|714_1545_-	hypothetical protein	NA	NA	NA	NA
WP_167510215.1\|1541_2243_-	hypothetical protein	NA	NA	NA	NA
WP_141889179.1\|2654_3050_-	hypothetical protein	NA	NA	NA	NA
WP_167510221.1\|3018_4470_-	mercury(II) reductase	A0A2K5B2C5	Erysipelothrix_phage	3.4e-39	25.9

DBSCAN-SWA_2

9344 : 14158

Streptococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889189.1\|9344_11531_+	heavy metal translocating P-type ATPase	E4ZFI9	Streptococcus_phage	6.3e-122	42.4
WP_141889190.1\|11594_12104_+	L,D-transpeptidase family protein	NA	NA	NA	NA
WP_141889191.1\|12326_12782_-	DUF411 domain-containing protein	NA	NA	NA	NA
WP_141889192.1\|12784_14158_-	peptidoglycan DD-metalloendopeptidase family protein	G9BW84	Planktothrix_phage	8.2e-19	43.9

DBSCAN-SWA_3

22053 : 25277

Planktothrix_phage(50.0%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889201.1\|22053_22824_+	ATP-binding cassette domain-containing protein	G9BWD6	Planktothrix_phage	2.2e-21	33.3
WP_141889202.1\|22823_23567_+	phosphonate ABC transporter, permease protein PhnE	NA	NA	NA	NA
WP_141889203.1\|24248_25277_-\|transposase	IS110 family transposase	A0A1S7J231	Thermus_phage	1.8e-18	28.8

DBSCAN-SWA_4

41391 : 49872

Stx2-converting_phage(40.0%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889223.1\|41391_43659_-	heavy metal translocating P-type ATPase	E4ZFI9	Streptococcus_phage	8.5e-130	42.7
WP_141889224.1\|43696_44855_+\|transposase	IS3 family transposase	S5WIU1	Leptospira_phage	1.6e-47	42.9
WP_141889225.1\|45450_45774_-	H-NS histone family protein	NA	NA	NA	NA
WP_141889226.1\|45965_46352_+	metallopeptidase family protein	NA	NA	NA	NA
WP_141889227.1\|46524_47208_+	UPF0149 family protein	NA	NA	NA	NA
WP_167510219.1\|47435_47837_+\|transposase	transposase	A0A1B0YZU7	Pseudomonas_phage	7.4e-05	49.0
WP_141889229.1\|47833_48181_+	IS66 family insertion sequence element accessory protein TnpB	A0A0P0ZDM8	Stx2-converting_phage	3.0e-26	56.2
WP_141889295.1\|48243_49872_+\|transposase	IS66 family transposase	A0A0P0ZBS5	Stx2-converting_phage	1.1e-99	45.0

DBSCAN-SWA_5

54095 : 54992

Enterobacteria_phage(100.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889231.1\|54095_54992_-	ATP-binding protein	U5N3V8	Enterobacteria_phage	7.4e-53	49.4

DBSCAN-SWA_6

58772 : 61949

Rhizobium_phage(100.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889237.1\|58772_61949_-	hypothetical protein	L7TKC0	Rhizobium_phage	4.6e-33	47.4

DBSCAN-SWA_7

79243 : 80269

Rhodobacter_phage(100.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889254.1\|79243_80269_-	RepB family plasmid replication initiator protein	A0A0K1Y6J9	Rhodobacter_phage	3.5e-67	39.8

DBSCAN-SWA_8

85246 : 87137

Leptospira_phage(50.0%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889259.1\|85246_86405_+\|transposase	IS3 family transposase	S5WIU1	Leptospira_phage	2.4e-48	43.3
WP_141889260.1\|86777_87137_-	helix-turn-helix domain-containing protein	Q8W6G2	Sinorhizobium_phage	8.4e-16	42.9

DBSCAN-SWA_9

92994 : 98616

Vibrio_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889299.1\|92994_94320_+	DUF4942 domain-containing protein	M4M9L8	Vibrio_phage	2.9e-13	29.9
WP_141889266.1\|96001_96451_+	DUF3768 domain-containing protein	NA	NA	NA	NA
WP_141889267.1\|96756_98616_+	ParB N-terminal domain-containing protein	G8DH78	Emiliania_huxleyi_virus	2.7e-81	35.8

DBSCAN-SWA_10

105778 : 110085

Bacillus_phage(33.33%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141889280.1\|105778_106165_+	thermonuclease family protein	A0A1P8CWK6	Bacillus_phage	1.3e-06	38.7
WP_141889300.1\|106244_106562_+	H-NS histone family protein	NA	NA	NA	NA
WP_141889203.1\|106871_107900_-\|transposase	IS110 family transposase	A0A1S7J231	Thermus_phage	1.8e-18	28.8
WP_141889281.1\|108427_108811_-	hypothetical protein	NA	NA	NA	NA
WP_141889282.1\|108906_110085_-	hypothetical protein	A0A1D8KM27	Synechococcus_phage	7.5e-05	34.5

Anti-CRISPR protein detection

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

2. NZ_CP041164

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP041164_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP041164_1

4465-4652

Orphan

Consensus_repeat	Method
CCGGGCTGTCCCCGCGGGGACAGC	PILER-CR

2 spacers

The CRISPR arrays of NZ_CP041164_1

>merge|NZ_CP041164|1|4465-4652|PILER-CR
GCTGTCCCCGCGGGGACAGGTGGCGCCCGCGGCCCTGAAACGCATGAAAATCAGCGGGCCTTGGCGCCTGCGCGCCGGTTTGTCCCCGCGGGGACAGCAGCGCGAAATGCCATCGAAATCCCCTGATCAGACCCTGCCCCGCGGGCTGCGGCGGGCCATGCCGCCCGGGCTGTCCCCGCGGGGACAGC

>NZ_CP041164|1|1|4465-4652|PILER-CR
GCTGTCCCCGCGGGGACAGGTGGC	GCCCGCGGCCCTGAAACGCATGAAAATCAGCGGGCCTTGGCGCCTGCGCGCCGG
TTTGTCCCCGCGGGGACAGCAGCG	CGAAATGCCATCGAAATCCCCTGATCAGACCCTGCCCCGCGGGCTGCGGCGGGCCATGCCGCCCGG
GCTGTCCCCGCGGGGACAGC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP041164.1\|WP_141892206.1\|8524_9799_+\|Vi-polysaccharide-biosynthesis-UDP-N-acetylglucosamine-C-6-dehydrogenase-TviB	unknown	unknown	gnl\|CDD\|185104
NZ_CP041164.1\|WP_058284692.1\|5879_7184_-\|AAA-family-ATPase	unknown	unknown	gnl\|CDD\|274585
NZ_CP041164.1\|WP_141892266.1\|11961_15945_-\|PEP-utilizing-protein	unknown	unknown	gnl\|CDD\|235751
NZ_CP041164.1\|WP_141892203.1\|3119_4160_+\|OmpA-family-protein	unknown	unknown	gnl\|CDD\|143586
NZ_CP041164.1\|WP_141892208.1\|10310_11222_-\|SIS-domain-containing-protein	unknown	unknown	gnl\|CDD\|224651
NZ_CP041164.1\|WP_141892211.1\|16229_17126_+\|PhnD/SsuA/transferrin-family-substrate-binding-protein	unknown	unknown	gnl\|CDD\|270292
NZ_CP041164.1\|WP_141892265.1\|1411_2917_-\|caspase-family-protein	unknown	unknown	gnl\|CDD\|334197
NZ_CP041164.1\|WP_141892209.1\|11271_11574_-\|type-II-toxin-antitoxin-system-RelE/ParE-family-toxin	unknown	unknown	gnl\|CDD\|226194
NZ_CP041164.1\|WP_141892205.1\|7736_8420_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|273037
NZ_CP041164.1\|WP_141892210.1\|11566_11803_-\|type-II-toxin-antitoxin-system-ParD-family-antitoxin	unknown	unknown	gnl\|CDD\|226136
NZ_CP041164.1\|WP_141892204.1\|4755_5883_-\|ParB-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|319262
NZ_CP041164.1\|WP_141892207.1\|9863_10301_+\|GFA-family-protein	unknown	unknown	gnl\|CDD\|226314

Protein	Function_ID	Function_description	E-value
NZ_CP041164.1\|WP_141892206.1\|8524_9799_+\|Vi-polysaccharide-biosynthesis-UDP-N-acetylglucosamine-C-6-dehydrogenase-TviB	gnl\|CDD\|185104	PRK15182, PRK15182, Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB.	0
NZ_CP041164.1\|WP_058284692.1\|5879_7184_-\|AAA-family-ATPase	gnl\|CDD\|274585	TIGR03453, partition_RepA, plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error. [Mobile and extrachromosomal element functions, Plasmid functions].	1.11375e-59
NZ_CP041164.1\|WP_141892266.1\|11961_15945_-\|PEP-utilizing-protein	gnl\|CDD\|235751	PRK06241, PRK06241, phosphoenolpyruvate synthase; Validated.	1.83344e-37
NZ_CP041164.1\|WP_141892203.1\|3119_4160_+\|OmpA-family-protein	gnl\|CDD\|143586	cd07185, OmpA_C-like, Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA. OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane.	2.37901e-38
NZ_CP041164.1\|WP_141892208.1\|10310_11222_-\|SIS-domain-containing-protein	gnl\|CDD\|224651	COG1737, RpiR, Transcriptional regulators [Transcription].	2.06129e-38
NZ_CP041164.1\|WP_141892211.1\|16229_17126_+\|PhnD/SsuA/transferrin-family-substrate-binding-protein	gnl\|CDD\|270292	cd13574, PBP2_PnhD_4, Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold. This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.	1.85354e-85
NZ_CP041164.1\|WP_141892265.1\|1411_2917_-\|caspase-family-protein	gnl\|CDD\|334197	pfam00656, Peptidase_C14, Caspase domain.	1.47033e-46
NZ_CP041164.1\|WP_141892209.1\|11271_11574_-\|type-II-toxin-antitoxin-system-RelE/ParE-family-toxin	gnl\|CDD\|226194	COG3668, ParE, Plasmid stabilization system protein [General function prediction only].	3.43146e-18
NZ_CP041164.1\|WP_141892205.1\|7736_8420_+\|hypothetical-protein	gnl\|CDD\|273037	TIGR00362, DnaA, chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006). [DNA metabolism, DNA replication, recombination, and repair].	2.40398e-05
NZ_CP041164.1\|WP_141892210.1\|11566_11803_-\|type-II-toxin-antitoxin-system-ParD-family-antitoxin	gnl\|CDD\|226136	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription].	3.48285e-16
NZ_CP041164.1\|WP_141892204.1\|4755_5883_-\|ParB-N-terminal-domain-containing-protein	gnl\|CDD\|319262	cd16405, RepB_like_N, plasmid segregation replication protein B like protein, N-terminal domain. RepB, found on plasmids and secondary chromosomes, works along with repA in directing plasmid segregation, and has been shown in Rhizobium etli to require the parS centromere-like sequence for full transcriptional repression of the repABC operon, inducing plasmid incompatibility. RepA is a Walker-type ATPase that complexes with RepB to form DNA-protein complexes in the presence of ATP/ADP. RepC is an initiator protein for the plasmid. repA and repB are homologous to the parA and ParB genes of the parABS partitioning system found on primary chromosomes.	3.426e-10
NZ_CP041164.1\|WP_141892207.1\|9863_10301_+\|GFA-family-protein	gnl\|CDD\|226314	COG3791, COG3791, Uncharacterized conserved protein [Function unknown].	7.8161e-27

>NZ_CP041164.1|WP_141892203.1|3119_4160_+|OmpA-family-protein
MLRLTLSILTVFLLILRPALASGPFEHGWQLNAESSAIRFISIKKGSIAESSRFAAFSGSISEQGDAEIRIALDSVDTSIDLRNVRMRFLFFETFTYPEATITARIGPDQIADLSAVQRKQIELPVTLSLHGIEAQLMVPVAVTLLGNDRVAVATVQPVILKLEDFALNPGREKLEEAAGVTITPVGLVSLDLMFDRTAPGTASVPAGTVTAGAAAALEASGDFSREACTGRFEILSQGRSVNFAPSTARLDASSRDFLDSLSDIIRRCPGMIVEVGGHTDSQGKSAWNMQLSEKRAAAVNSYLLTTGIPAERLVAVGYGETTPLVPNNTAQNRAKNRRIEFKVLN
>NZ_CP041164.1|WP_141892265.1|1411_2917_-|caspase-family-protein
MWIRLAVLAAAVLGLARAAWAEERLALVIGNSAYGSVQPLDNPGRDARLMAETLERLGFDVTLAVDAPQLEMKRAIARFGRKLRGAGQDATGLFYYAGHGVQSFGSNYLLPVDVALSDAADLDLMAVEAQSVLRQMASARNRTNIVILDACRNNPFKAVADLNESGLAEMKAPTGTFLAYATAPGEVALDGEGENSPFTEALAREIVVPGAPVEQVFKQVRRAVLEQSGGGQTPWDTSSLVSDFTFAAAEPEAVMSAAEIEEAQIWRSVKASRDTMQIMLFLRGYGSGKYADEARALLASLMEEELHGGTGAAVAAAPAAPAEPAPAPAAADAETAMFQAAQGDGSKAAYEAYLMAYPEGRFVEMAAAEVAALAAGAGQDPQAGTEAPPAAAEDAPAAVALVETGPITFASPLDTDAAAISGLTLAEAVTRSPSFPPVDGLPESYWKDQSCSSCHQWTRERLCTQGNTYLSLNMQRSLGKQHPFGGALKQALKSWAAGGCQ
>NZ_CP041164.1|WP_141892204.1|4755_5883_-|ParB-N-terminal-domain-containing-protein
MSKRRVFDIDFPTEPNTPSEPKSVPAETAVQKPDQRMRKPSESRRGPMATAISENADALRTRAEAEMKIRAENDRLAHEFVRLKKLGLVVDRIPIGRIGMQKLVRDRKEGRDPELDELKASIKSIGLSNPIRVEENEDGTYELIQGYRRMRAYLELLSETGDDIYSHIPAGLVAKGDSLQSLYRRMVDENLVRRDISFAEMAQLALRYAEDTGTGAETIEDAVNDLYASAGRQKRIYIRHFAQVLKAVGDVLKHPEAIPRALGLDLKKRLEADAMNAQVLRDALARVKPQNEEAELEVLRSFAEGKRKNAPRTPAAPRAGVAKTTLRCTVPAGTVRCQARDGKIEMAMERDFSEIDRHKLEDAIAAFFAALEDPS
>NZ_CP041164.1|WP_058284692.1|5879_7184_-|AAA-family-ATPase
MFTHEDLSKMQAQSLKMQSWIRQQTFSPEMEKTLRRFSSWEVAELIFRVNQSTLRGRLATDPSLPQGHVEEDGRQRWYSLEEINELRRRIKINRKSLLPKRPAGKRALRVAISNFKGGAGKSTVALHFAHAAALDGYRVLCVDFDPQATLSHSMGLSDVTEDYTVWGIMARDLVRETERMNAVSQGAESGTALPQRQLPDAITGMGLQDLRVSDFVKPTSWPTIDIIPSCANAAFVEFASAQYRHLNPEWSFFAAVSRYLDQLPAEDYDLMIFDCPPAIGYQSMNAVFAADMLYIPSGPGYWEYDSTTSFIGQLSEALEDLSAFNGVVPAGTFALPKVFQDVRFLLTRYESGNDLHRAMRSAFMKVFEGRMTEHPIEMTRAVEQSGRFLSSIYEIDYREMTRETWRRARASFDQAYDEFKAYALEAWENLEDEA
>NZ_CP041164.1|WP_141892205.1|7736_8420_+|hypothetical-protein
MLAKRPAGRNASALKYDILTAMGAYALGQGKGAQKLVLRFMTLMTARYNWQRDELAVGQREIARLWDVDERTVKREMAKLRGMGWLVVKRQGARGRVTEYGIDLERLLADTEERWGAVGPDFEHRMQGADEPAPNVVPLRPGAVPPAPDVSDGSEWSLAKAVLHAEDPANYASWVQGLERAGRAGGRLVLKAPSRFHANYVMSHLMPRLLAACRDVDGEVSAIVVEA
>NZ_CP041164.1|WP_141892206.1|8524_9799_+|Vi-polysaccharide-biosynthesis-UDP-N-acetylglucosamine-C-6-dehydrogenase-TviB
MNGAQDRICIIGLGYVGLPLAAAFGQHREVIGFDIDPGRIAELRRGEDRTRELEPQDLAAAEFLKFTSDPAEIAECSIYIVTVPTPVDASHRPDLRPLLAASAIVGGVLKAGDLVIYESTVYPGATEEDCVPVLEARSGLKFNADFFAGYSPERINPGDKQRRLKDVVKVTSGSTPEVAERVDALYREVVAAGTHKAASIRVAEAAKVIENSQRDINIALVNELAKIFNKMGIDTQAVLEAAGTKWNFLPFRPGLVGGHCIGVDPYYLTHKAEQLGYHPEILLAGRRLNDGMGAYVAGEMVKAMLKRGLPVAGARVLVMGLTFKENCPDLRNTRVIDVVRELQQYGAVVDVHDPHADPQEAQEEYGISLMAEPGQGAYAGIVLAVAHSEFRDMGAAAIRALGSEGALVYDLKYVLAPEEADLRL
>NZ_CP041164.1|WP_141892207.1|9863_10301_+|GFA-family-protein
MMSDVLEGRCLCGAVKIRVEGSHDPRAGACHCRMCQRWSGGLFLCFEADAEAVTVEGPVSRYQSSAFAERAFCSTCGSHLWMRDVDEDGAPYDLMPGLFDAALAWPLRSEIYADRAMASVRLEGDHKRATRDEWEAQNPFIDGDV
>NZ_CP041164.1|WP_141892208.1|10310_11222_-|SIS-domain-containing-protein
MDPHLDPRKTARLIQHLEDQMEQLPPKLKAAAKYVIDNPGDFGLDTVRTSAQRTGISANGFVRLAQHLGYDTFEAFRAPFRAALTTAHEADLGQDWLERMAGAGPAGALQAAAARNQLNITSRSLRLMTAERTQAIVGTLTTARRSYVTATRSSYALAYYFHYVGRMALPSLDLVPRHMGAALDDLLDIGPEDCLIAITFAPYSAGTIQALRLAGERGASVILISDSEVIAPGIRTDHVLAVAANSLHPFGAIGGAMAVLECLLTHLIDAGGEDARRRIEAYDALRQDSGAYWSGPKLPRVGG
>NZ_CP041164.1|WP_141892209.1|11271_11574_-|type-II-toxin-antitoxin-system-RelE/ParE-family-toxin
MAEPRWRIRPAACADLAAIWRYGRDTWGAAQADAYADSLFALFDLLADFPEMARERTEFTPPVRIHPSGAHLVIYRLEQSRPEILRILHARRDLMAFLSE
>NZ_CP041164.1|WP_141892210.1|11566_11803_-|type-II-toxin-antitoxin-system-ParD-family-antitoxin
MATMNVSLPDQMKDWVEEQARTGTYANSSDYVRDLIRRDQARTAAIAELQTAIDAGLASGPAEPLTAEDFKAAMRRNG
>NZ_CP041164.1|WP_141892266.1|11961_15945_-|PEP-utilizing-protein
MQITVLTALFSAVPVAALAIPSPELVIGSVSSLSQVLAVGIAMISGLGAVVAAKLGFTPKPGGSPRRYPVKLISVLVLAAIALAAGNYWQYSSHAQQELARLQATLTRPAQFDGTTIKDAALKETSFTKQEDHPLAMSTADAAAALEDGSTLFYDIRETGENAMGTLPGATHIRFPDFVQSQPVKPGQKVVLFCHNGNRSSETCAKLAAMGIDCSFIAGGIEKWIVEGRAFSDKDVKTLSDLRAIPDYPGKDVLLSTDDFTNLLTTEDLQIVDTRYPGDFESGHLPGAVNIPIRKMTTAELMDRIAELDPGKPTIAACYDRRSCFMSQVLGLELSQQGIDFRGRYTLPWEYFVAPKPKPHVQAWLADQQTGLWDKAISALAAALLWVHERSHILLGLLALSIVTRILVLPVALKSERDQIITNETADEMKALKAKLAHDPVRKARAVQAFYKDKGLTPMKNLTALLFLPVMMLGVSAAQEASASLQTPFLWMADLGAPDPLFILPVLFCALAAVYLLWAVAKTPRQKLLWMVLGMPSLFAMVFSLTAAANAYLCFSLTLLLVQRAYVTGMHRKLAEALSLRAHKRRLAKLPRGVIPMGYTEELEHAGNKALRLSILRNAGLPVPGGVIVRSDAIHDYREMTDAKKDAFAARVFALAGGKPVAVRSSASNEDGHDQSFAGVFESVLDVTADTMRAALDEVVTSFSSERAASYSGEGDSTDQGNIVVQEMVQAEYAGVLFTQDPMAPGMCMIEWVEGCGEDLVSGRVTPTSLRFGRYTGLPAAEDQDQTLDMAPLLALGRQIEETFGCPQDVEWAYANGQFQIVQSRDITTLSLGTEQEQTRLAEWRDLLDRYAAADPDQTILEQDEMSEVLPRPTPLSFSLMSELWAPGGSVDLACRELGVPYGLPEGRDGHLVNLFGKTYVDVALKQGMTLKLTAAKAKQLRKQAHPMITRFRGEVMPELKNKLAIWQAVDYAALPQDKLLEAISTLKDMFIREVYLEAEKINILAGFTMGEAGTAAAGDPALRAHLMHAELPNAPSSLLASCTGRDAQARATQLMGHRSIFDYELSSPRYREAPALLESLLSNTVEPIGSVPVPANLPDELDDTIGIAIAYQDLKEQAKHEALRVVAELRRALLALGQISGLGDLVFSLTFDEVLSGNWTAPARLRELAEARAAKEELRKKSAPTAVSLTLRDCELLSLGAQAQAGDGTMGGTCVAGSGSATARVFWMEDDSCIDPAAFADFQDGDILVCRMVNPAWLPYVQRSGAVLSEVGGWLSHMAIVAREKDVLMLVACKGLDSLSHGEQVTVSEDGSIQPLEEKGLKAASA
>NZ_CP041164.1|WP_141892211.1|16229_17126_+|PhnD/SsuA/transferrin-family-substrate-binding-protein
MKLFEWTIGIIKLFLRPLRAAAPAAVLSACLAAFVPAPGQAGIELVFGTYAADKPTATVKKYQPFLSFLAGRMSEELGEPVSIRLKVAKEYGEGIRQLASGEVDFARFGPASYVHVMKENPGIRIVAMESKNGRKRFKGVIVVHKDSSVQAMEDLAGLSFAFGDELSTIGRYLAQEYLLNAGISSADLYEFAYLGRHDLVGEAVGAGRYSAGALKESTYKKLVAKGVPIRVLASFDNVTKPWLASSQMPENVLEAMRKVMLSSENEEIVRRISKNGFLLGADQDYDIIRRAMERSLAF

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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
NZ_CP041164_1	1.1\|4489\|54\|NZ_CP041164\|PILER-CR	4489-4542	54	NZ_CP041164	Leisingera aquaemixtae strain R2C4 plasmid unnamed3, complete sequence	4485-4538	0	1.0
NZ_CP041164_1	1.2\|4567\|66\|NZ_CP041164\|PILER-CR	4567-4632	66	NZ_CP041164	Leisingera aquaemixtae strain R2C4 plasmid unnamed3, complete sequence	4563-4628	6	0.909

1. spacer 1.1|4489|54|NZ_CP041164|PILER-CR matches to NZ_CP041164 (Leisingera aquaemixtae strain R2C4 plasmid unnamed3, complete sequence) position: , mismatch: 0, identity: 1.0

tggcgcccgcggccctgaaacgcatgaaaatcagcgggccttggcgcctgcgcg	CRISPR spacer
tggcgcccgcggccctgaaacgcatgaaaatcagcgggccttggcgcctgcgcg	Protospacer
******************************************************

2. spacer 1.2|4567|66|NZ_CP041164|PILER-CR matches to NZ_CP041164 (Leisingera aquaemixtae strain R2C4 plasmid unnamed3, complete sequence) position: , mismatch: 6, identity: 0.909

agcgcgaaatgccatcgaaatcccctgatcagaccctgccccgcgggctgcggcgggcca	CRISPR spacer
agcgcgaaatgccatcgaaatcccctgatcagaccctgccccgcgggctgcggcgggcca	Protospacer
************************************************************

Prophage detection

Region	Region Position	Protein_number	Hit_taxonomy	Key_proteins	Att_site	Prophage annotation

Anti-CRISPR protein detection

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

3. NZ_CP041159

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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

1569539 : 1605930

Paracoccus_phage(27.27%)

protease,tRNA,tail,capsid,head

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_141890413.1\|1569539_1570604_-\|tRNA	tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA	NA	NA	NA	NA
WP_141890414.1\|1570664_1574141_-	DUF3971 domain-containing protein	NA	NA	NA	NA
WP_141890415.1\|1574191_1574653_+	redoxin domain-containing protein	NA	NA	NA	NA
WP_141890416.1\|1574927_1575770_+	DUF455 family protein	NA	NA	NA	NA
WP_141890417.1\|1575859_1576396_+	hypothetical protein	NA	NA	NA	NA
WP_058287013.1\|1576620_1577952_+	peptidoglycan DD-metalloendopeptidase family protein	A8ATH6	Listeria_phage	3.0e-18	45.0
WP_141890418.1\|1577941_1578481_+	polymer-forming cytoskeletal protein	NA	NA	NA	NA
WP_141890419.1\|1578735_1580106_+	calcium-binding protein	NA	NA	NA	NA
WP_141892075.1\|1580159_1581122_-	DUF3179 domain-containing protein	NA	NA	NA	NA
WP_058287016.1\|1581275_1581824_-	peptidylprolyl isomerase	A0A1B1IVS0	uncultured_Mediterranean_phage	2.3e-41	60.6
WP_058287017.1\|1581816_1582323_-	peptidylprolyl isomerase	A0A1B1IVS0	uncultured_Mediterranean_phage	2.1e-41	55.0
WP_141890420.1\|1582463_1583654_+	phosphoglycerate kinase	NA	NA	NA	NA
WP_141890421.1\|1583721_1585356_-	DNA alkylation response protein	NA	NA	NA	NA
WP_058287020.1\|1585587_1585887_+	septum formation initiator precursor	NA	NA	NA	NA
WP_141890422.1\|1586241_1587255_+	pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha	NA	NA	NA	NA
WP_141890423.1\|1587271_1588642_+	pyruvate dehydrogenase complex E1 component subunit beta	NA	NA	NA	NA
WP_058287023.1\|1588650_1588911_+	hypothetical protein	NA	NA	NA	NA
WP_141890424.1\|1588912_1590235_+	pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase	NA	NA	NA	NA
WP_141890425.1\|1590634_1592110_+	hypothetical protein	NA	NA	NA	NA
WP_141890426.1\|1592394_1593459_-	pyridoxal-phosphate dependent enzyme	A0A1X9I5F1	Streptococcus_phage	4.8e-67	45.5
WP_058287027.1\|1593760_1594573_-	serine O-acetyltransferase	NA	NA	NA	NA
WP_141890427.1\|1594727_1595036_-	hypothetical protein	NA	NA	NA	NA
WP_141890428.1\|1595032_1598947_-	host specificity protein	A0A0B5A7K5	Paracoccus_phage	3.6e-237	40.3
WP_058287030.1\|1598946_1599486_-	peptidase	A0A1V0DYB6	Dinoroseobacter_phage	8.4e-28	39.7
WP_141890429.1\|1599482_1600370_-	DUF2163 domain-containing protein	A0A0K0PVK1	Roseobacter_phage	4.9e-57	38.7
WP_141890430.1\|1600366_1600999_-	TIGR02217 family protein	A0A0B5A2K3	Paracoccus_phage	1.6e-57	52.4
WP_141890431.1\|1601016_1601676_-\|tail	phage tail tape measure protein	D6PFD6	uncultured_phage	5.1e-11	33.0
WP_141890432.1\|1601668_1601884_-\|tail	phage tail assembly chaperone	NA	NA	NA	NA
WP_141890433.1\|1601880_1602201_-	gene transfer agent family protein	NA	NA	NA	NA
WP_141890434.1\|1602204_1602618_-\|tail	phage major tail protein, TP901-1 family	NA	NA	NA	NA
WP_141890435.1\|1602664_1603072_-	DUF3168 domain-containing protein	NA	NA	NA	NA
WP_141890436.1\|1603068_1603401_-\|head,tail	head-tail adaptor protein	NA	NA	NA	NA
WP_141890437.1\|1603397_1603997_-	hypothetical protein	NA	NA	NA	NA
WP_141890438.1\|1604179_1605361_-\|capsid	phage major capsid protein	A0A2D1GNH4	Pseudomonas_phage	3.4e-66	38.5
WP_141890439.1\|1605357_1605930_-\|head,protease	HK97 family phage prohead protease	A0A0U2BX10	Paracoccus_phage	1.9e-33	50.9

DBSCAN-SWA_2

3184786 : 3191701

Thermoanaerobacterium_phage(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_058287535.1\|3184786_3185353_+	helix-turn-helix transcriptional regulator	I3VYZ1	Thermoanaerobacterium_phage	2.1e-05	43.3
WP_008554505.1\|3185627_3185834_+	cold-shock protein	A0A1W6JNX5	Morganella_phage	1.6e-11	58.9
WP_141891564.1\|3185898_3186300_-	VOC family protein	NA	NA	NA	NA
WP_141891565.1\|3186463_3187651_+	glycine C-acetyltransferase	D2TEZ5	Emiliania_huxleyi_virus	4.4e-37	29.6
WP_141892123.1\|3187665_3188694_+	L-threonine 3-dehydrogenase	R9TPW0	Vibrio_phage	4.5e-14	66.7
WP_141891566.1\|3188772_3189501_-	serine/threonine protein phosphatase	A0A1V0EF12	Caulobacter_phage	6.2e-34	38.6
WP_141891567.1\|3189655_3190054_+	hypothetical protein	NA	NA	NA	NA
WP_141891568.1\|3190105_3191701_-	phosphoglycerate dehydrogenase	A0A2R8FDS8	Brazilian_cedratvirus	1.2e-45	38.3

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NZ_CP041157

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CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

2. NZ_CP041164

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CRISPR-Cas detection and classification

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Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

3. NZ_CP041159

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CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection