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_CP010872	Confluentimicrobium sp. EMB200-NS6 strain EMBL200_NS6 plasmid pNS6003, complete sequence	0 crisprs	csa3	0	0
NZ_CP010870	Confluentimicrobium sp. EMB200-NS6 strain EMBL200_NS6 plasmid pNS6001, complete sequence	0 crisprs	NA	0	1
NZ_CP010871	Confluentimicrobium sp. EMB200-NS6 strain EMBL200_NS6 plasmid pNS6002, complete sequence	0 crisprs	NA	0	1
NZ_CP010869	Confluentimicrobium sp. EMB200-NS6 strain EMBL200_NS6 chromosome, complete genome	1 crisprs	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,WYL	5	2

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

51438 : 100996

Enterobacteria_phage(27.27%)

transposase,integrase

attL 48016:48031|attR 62219:62234

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
48016:48031	attL	NA	NA	NA	NA
WP_139211443.1\|51438_52425_-\|integrase	tyrosine-type recombinase/integrase	NA	NA	NA	NA
WP_054540542.1\|52704_53595_+	DUF1403 family protein	NA	NA	NA	NA
WP_054540543.1\|53597_54197_+	SMC-Scp complex subunit ScpB	NA	NA	NA	NA
WP_082386774.1\|54180_55215_-	TniQ family protein	NA	NA	NA	NA
WP_054540544.1\|55211_56093_-	TniB family NTP-binding protein	NA	NA	NA	NA
WP_054540545.1\|56094_57729_-\|transposase	Mu transposase C-terminal domain-containing protein	NA	NA	NA	NA
WP_009574212.1\|59088_59916_-	universal stress protein	NA	NA	NA	NA
WP_009574213.1\|60170_60410_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_054540548.1\|60545_63269_+	cation-transporting P-type ATPase	M1IAU8	Acanthocystis_turfacea_Chlorella_virus	4.5e-61	26.8
62219:62234	attR	NA	NA	NA	NA
WP_040402893.1\|66701_66971_-	TniQ family protein	NA	NA	NA	NA
WP_009573528.1\|66967_67834_-	TniB family NTP-binding protein	NA	NA	NA	NA
WP_157445667.1\|68158_69793_+\|transposase	Mu transposase C-terminal domain-containing protein	NA	NA	NA	NA
WP_054540550.1\|69794_70673_+	TniB family NTP-binding protein	NA	NA	NA	NA
WP_054540551.1\|70669_71455_+	TniQ family protein	NA	NA	NA	NA
WP_082386777.1\|71994_72597_-	histidine phosphatase family protein	NA	NA	NA	NA
WP_054540554.1\|72620_73208_-	recombinase family protein	A0A0A7NPV4	Enterobacteria_phage	8.6e-26	38.5
WP_054540555.1\|73371_76254_+\|transposase	Tn3 family transposase	A0A1B0V7H9	Salmonella_phage	4.8e-186	38.3
WP_054540556.1\|77205_77769_+	recombinase family protein	A0A0A7NPV4	Enterobacteria_phage	7.1e-46	55.3
WP_054540557.1\|79408_80383_+	AAA family ATPase	Q6QIE1	Burkholderia_phage	2.8e-05	26.2
WP_054540558.1\|80379_81087_+	UPF0149 family protein	NA	NA	NA	NA
WP_157445671.1\|81256_81862_-	TetR family transcriptional regulator	NA	NA	NA	NA
WP_054540616.1\|82079_83756_+	electron transfer flavoprotein-ubiquinone oxidoreductase	NA	NA	NA	NA
WP_054540560.1\|83848_84970_+	thiolase family protein	NA	NA	NA	NA
WP_054540561.1\|84972_87270_+	3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein	NA	NA	NA	NA
WP_054540562.1\|87294_89058_+	acyl-CoA dehydrogenase C-terminal domain-containing protein	NA	NA	NA	NA
WP_054540563.1\|89086_90703_+	long-chain-fatty-acid--CoA ligase	A0A2H4PQM9	Staphylococcus_phage	4.3e-27	25.5
WP_173585989.1\|90748_91222_+	MaoC family dehydratase	NA	NA	NA	NA
WP_054540564.1\|91427_92186_-	ATP-binding protein	A0A059NT77	Lactococcus_phage	5.1e-31	34.1
WP_054540566.1\|92738_93974_+\|transposase	IS21 family transposase	A0A2L1IVA1	Escherichia_phage	7.8e-45	35.8
WP_054540567.1\|93970_94813_+	ATP-binding protein	U5N3V8	Enterobacteria_phage	3.3e-55	50.9
WP_054540568.1\|95011_95236_-	hypothetical protein	NA	NA	NA	NA
WP_082386779.1\|95701_96910_-	PQQ-binding-like beta-propeller repeat protein	NA	NA	NA	NA
WP_054540570.1\|97337_97904_-	recombinase family protein	A0A219Y912	Aeromonas_phage	2.3e-36	47.0
WP_054540571.1\|98044_100996_+\|transposase	Tn3 family transposase	A0A1B0V7H9	Salmonella_phage	1.5e-195	39.4

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_CP010869

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP010869_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP010869_1

578322-578899

TypeI-E

Consensus_repeat	Method
CCGTTCCCCGCCCACGCGGGGATCAACCG	PILER-CR
CCGTTCCCCGCCCACGCGGGGATCAACCG	CRISPRCasFinder
CCGTTCCCCGCCCACGCGGGGATCAACCG	CRT

9 spacers

cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,cas3

The CRISPR arrays of NZ_CP010869_1

>merge|NZ_CP010869|1|578322-578899|PILER-CR,CRISPRCasFinder,CRT
CCGTTCCCCGCCCACGCGGGGATCAACCGAAATTCCGACCCATGAGGTATTCGCCCTGATCCCGTTCCCCGCCCACGCGGGGATCAACCGAAGGGTTACCTGATCGGCTCGAACAGTCAGATCCGTTCCCCGCCCACGCGGGGATCAACCGCTGCAAGAGAGCGACACCACGACAAGCGGTGACCGTTCCCCGCCCACGCGGGGATCAACCGTCGATATAGCCCGTCACGCCCGTTGCGGCATTCCGTTCCCCGCCCACGCGGGGATCAACCGCAGCTGGCTATACTGCGCGAGACGGATCCGGTCCGTTCCCCGCCCACGCGGGGATCAACCGCGCTCGCTGCGGCAGACAAGTTCGCAAAGCGGCCGTTCCCCGCCCACGCGGGGATCAACCGGTGACGTAGTTGCGGGTGTTTTTGCGGCGCTGCCGTTCCCCGCCCACGCGGGGATCAACCGCAAATCGAAGCCAAGGGTGCCGCCGACCCGGTCCGTTCCCCGCCCACGCGGGGATCAACCGGATTTCAACCCGCTGGATGACTGGTACGGCTTCCGTTCCCCGCCCACGCGGGGATCAACCG

>NZ_CP010869|1|1|578322-578899|PILER-CR
CCGTTCCCCGCCCACGCGGGGATCAACCG	AAATTCCGACCCATGAGGTATTCGCCCTGATC
CCGTTCCCCGCCCACGCGGGGATCAACCG	AAGGGTTACCTGATCGGCTCGAACAGTCAGAT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CTGCAAGAGAGCGACACCACGACAAGCGGTGA
CCGTTCCCCGCCCACGCGGGGATCAACCG	TCGATATAGCCCGTCACGCCCGTTGCGGCATT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CAGCTGGCTATACTGCGCGAGACGGATCCGGT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CGCTCGCTGCGGCAGACAAGTTCGCAAAGCGG
CCGTTCCCCGCCCACGCGGGGATCAACCG	GTGACGTAGTTGCGGGTGTTTTTGCGGCGCTG
CCGTTCCCCGCCCACGCGGGGATCAACCG	CAAATCGAAGCCAAGGGTGCCGCCGACCCGGT
CCGTTCCCCGCCCACGCGGGGATCAACCG	GATTTCAACCCGCTGGATGACTGGTACGGCTT
CCGTTCCCCGCCCACGCGGGGATCAACCG

>NZ_CP010869|1|1|578322-578899|CRISPRCasFinder
CCGTTCCCCGCCCACGCGGGGATCAACCG	AAATTCCGACCCATGAGGTATTCGCCCTGATC
CCGTTCCCCGCCCACGCGGGGATCAACCG	AAGGGTTACCTGATCGGCTCGAACAGTCAGAT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CTGCAAGAGAGCGACACCACGACAAGCGGTGA
CCGTTCCCCGCCCACGCGGGGATCAACCG	TCGATATAGCCCGTCACGCCCGTTGCGGCATT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CAGCTGGCTATACTGCGCGAGACGGATCCGGT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CGCTCGCTGCGGCAGACAAGTTCGCAAAGCGG
CCGTTCCCCGCCCACGCGGGGATCAACCG	GTGACGTAGTTGCGGGTGTTTTTGCGGCGCTG
CCGTTCCCCGCCCACGCGGGGATCAACCG	CAAATCGAAGCCAAGGGTGCCGCCGACCCGGT
CCGTTCCCCGCCCACGCGGGGATCAACCG	GATTTCAACCCGCTGGATGACTGGTACGGCTT
CCGTTCCCCGCCCACGCGGGGATCAACCG

>NZ_CP010869|1|1|578322-578899|CRT
CCGTTCCCCGCCCACGCGGGGATCAACCG	AAATTCCGACCCATGAGGTATTCGCCCTGATC
CCGTTCCCCGCCCACGCGGGGATCAACCG	AAGGGTTACCTGATCGGCTCGAACAGTCAGAT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CTGCAAGAGAGCGACACCACGACAAGCGGTGA
CCGTTCCCCGCCCACGCGGGGATCAACCG	TCGATATAGCCCGTCACGCCCGTTGCGGCATT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CAGCTGGCTATACTGCGCGAGACGGATCCGGT
CCGTTCCCCGCCCACGCGGGGATCAACCG	CGCTCGCTGCGGCAGACAAGTTCGCAAAGCGG
CCGTTCCCCGCCCACGCGGGGATCAACCG	GTGACGTAGTTGCGGGTGTTTTTGCGGCGCTG
CCGTTCCCCGCCCACGCGGGGATCAACCG	CAAATCGAAGCCAAGGGTGCCGCCGACCCGGT
CCGTTCCCCGCCCACGCGGGGATCAACCG	GATTTCAACCCGCTGGATGACTGGTACGGCTT
CCGTTCCCCGCCCACGCGGGGATCAACCG

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP010869.1\|WP_162231803.1\|569797_572251_+\|CRISPR-associated-helicase-Cas3'	cas3	cd09639_cas3_CAS-I	gnl\|CDD\|182031
NZ_CP010869.1\|WP_037204931.1\|584450_585365_-\|branched-chain-amino-acid-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|119324
NZ_CP010869.1\|WP_037204911.1\|576368_577040_+\|type-I-E-CRISPR-associated-protein-Cas6/Cse3/CasE	cas6e	cd09727_cas6e_CAS-I-E	gnl\|CDD\|215025
NZ_CP010869.1\|WP_054537934.1\|574598_575657_+\|type-I-E-CRISPR-associated-protein-Cas7/Cse4/CasC	cas7	pfam09344_cas7_CAS-I-E	gnl\|CDD\|378153
NZ_CP010869.1\|WP_054537933.1\|574098_574602_+\|type-I-E-CRISPR-associated-protein-Cse2/CasB	cse2gr11	cd09731_cse2gr11_CAS-I-E	gnl\|CDD\|187862
NZ_CP010869.1\|WP_054537940.1\|580032_581337_-\|FAD-binding-oxidoreductase	unknown	unknown	gnl\|CDD\|223737
NZ_CP010869.1\|WP_157445497.1\|579036_579342_+\|transposase	unknown	unknown	gnl\|CDD\|372671
NZ_CP010869.1\|WP_054537942.1\|582704_583463_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|223488
NZ_CP010869.1\|WP_054537937.1\|577963_578248_+\|type-I-E-CRISPR-associated-endoribonuclease-Cas2	cas2	pfam09707_cas2_CAS-I-E	gnl\|CDD\|236930
NZ_CP010869.1\|WP_054537935.1\|575649_576372_+\|type-I-E-CRISPR-associated-protein-Cas5/CasD	cas5	cd09645_cas5_CAS-I-E	gnl\|CDD\|187776
NZ_CP010869.1\|WP_054537939.1\|579537_580002_-\|L-2-amino-thiazoline-4-carboxylic-acid-hydrolase	unknown	unknown	gnl\|CDD\|372958
NZ_CP010869.1\|WP_054537936.1\|577041_577983_+\|type-I-E-CRISPR-associated-endonuclease-Cas1	cas1	cd09719_cas1_CAS-I-E	gnl\|CDD\|274693
NZ_CP010869.1\|WP_054537932.1\|572590_574102_+\|type-I-E-CRISPR-associated-protein-Cse1/CasA	cas8e	cd09729_cas8e_CAS-I-E	gnl\|CDD\|187860
NZ_CP010869.1\|WP_054537941.1\|581991_582708_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|223487
NZ_CP010869.1\|WP_054537945.1\|586665_587175_-\|L-2-amino-thiazoline-4-carboxylic-acid-hydrolase	unknown	unknown	gnl\|CDD\|372958
NZ_CP010869.1\|WP_081940079.1\|581453_581927_+\|Lrp/AsnC-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224439
NZ_CP010869.1\|WP_082386498.1\|569360_569783_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP010869.1\|WP_054537944.1\|585430_586543_-\|penicillin-binding-protein-activator	unknown	unknown	gnl\|CDD\|380572
NZ_CP010869.1\|WP_054537930.1\|568127_568988_+\|extensin-family-protein	unknown	unknown	gnl\|CDD\|369129
NZ_CP010869.1\|WP_054537943.1\|583459_584458_-\|branched-chain-amino-acid-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|119323

Protein	Function_ID	Function_description	E-value
NZ_CP010869.1\|WP_162231803.1\|569797_572251_+\|CRISPR-associated-helicase-Cas3'	gnl\|CDD\|182031	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3.	1.48422e-102
NZ_CP010869.1\|WP_037204931.1\|584450_585365_-\|branched-chain-amino-acid-ABC-transporter-permease	gnl\|CDD\|119324	cd06582, TM_PBP1_LivH_like, Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. E. coli LivH forms a heterodimer with another TM, LivM, to generate the transmembrane pore. LivM is not included in this subgroup. The LIV-1/LS transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBPs, LivJ (LIV-BP) or LivK (LS-BP). In addition to transporting branched-chain AAs including leucine, isoleucine and valine, the E. coli LIV-1/LS transporter is involved in the uptake of the aromatic AA, phenylalanine.	2.26043e-70
NZ_CP010869.1\|WP_037204911.1\|576368_577040_+\|type-I-E-CRISPR-associated-protein-Cas6/Cse3/CasE	gnl\|CDD\|215025	smart01101, CRISPR_assoc, This domain forms an anti-parallel beta strand structure with flanking alpha helical regions.	3.62737e-43
NZ_CP010869.1\|WP_054537933.1\|574098_574602_+\|type-I-E-CRISPR-associated-protein-Cse2/CasB	gnl\|CDD\|187862	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2. 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; Small alpha-helical protein; also known as Cse2/CasB/YgcK family; specific gene for I-E subtype;.	3.94167e-13
NZ_CP010869.1\|WP_054537940.1\|580032_581337_-\|FAD-binding-oxidoreductase	gnl\|CDD\|223737	COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism].	2.61871e-54
NZ_CP010869.1\|WP_157445497.1\|579036_579342_+\|transposase	gnl\|CDD\|372671	pfam13683, rve_3, Integrase core domain.	6.10081e-07
NZ_CP010869.1\|WP_054537942.1\|582704_583463_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|223488	COG0411, LivG, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism].	7.20589e-120
NZ_CP010869.1\|WP_054537937.1\|577963_578248_+\|type-I-E-CRISPR-associated-endoribonuclease-Cas2	gnl\|CDD\|236930	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional.	1.39116e-50
NZ_CP010869.1\|WP_054537935.1\|575649_576372_+\|type-I-E-CRISPR-associated-protein-Cas5/CasD	gnl\|CDD\|187776	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5. 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; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex.	2.87235e-33
NZ_CP010869.1\|WP_054537939.1\|579537_580002_-\|L-2-amino-thiazoline-4-carboxylic-acid-hydrolase	gnl\|CDD\|372958	pfam14196, ATC_hydrolase, L-2-amino-thiazoline-4-carboxylic acid hydrolase. This family of enzymes catalyzes the conversion of L-2-amino-delta2-thiazoline-4-carboxylic acid (L-ATC) to N-carbamoyl-L-cysteine. It cleaves the carbon-sulphur bond in the ring structure of L-ATC to produce N-carbamoyl-L-cysteine.	8.6859e-40
NZ_CP010869.1\|WP_054537936.1\|577041_577983_+\|type-I-E-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|274693	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the ECOLI subtype of CRISPR/Cas system.	7.08998e-132
NZ_CP010869.1\|WP_054537932.1\|572590_574102_+\|type-I-E-CRISPR-associated-protein-Cse1/CasA	gnl\|CDD\|187860	cd09729, Cse1_I-E, CRISPR/Cas system-associated protein Cse1. 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; Large proteins, some contain Zn-finger domain; subunit of the Cascade complex; signature gene for I-E subtype; also known as Cse1/CasA/YgcL family.	6.56979e-99
NZ_CP010869.1\|WP_054537941.1\|581991_582708_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|223487	COG0410, LivF, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism].	2.96123e-104
NZ_CP010869.1\|WP_054537945.1\|586665_587175_-\|L-2-amino-thiazoline-4-carboxylic-acid-hydrolase	gnl\|CDD\|372958	pfam14196, ATC_hydrolase, L-2-amino-thiazoline-4-carboxylic acid hydrolase. This family of enzymes catalyzes the conversion of L-2-amino-delta2-thiazoline-4-carboxylic acid (L-ATC) to N-carbamoyl-L-cysteine. It cleaves the carbon-sulphur bond in the ring structure of L-ATC to produce N-carbamoyl-L-cysteine.	1.58078e-12
NZ_CP010869.1\|WP_081940079.1\|581453_581927_+\|Lrp/AsnC-family-transcriptional-regulator	gnl\|CDD\|224439	COG1522, Lrp, Transcriptional regulators [Transcription].	1.68654e-36
NZ_CP010869.1\|WP_054537934.1\|574598_575657_+\|type-I-E-CRISPR-associated-protein-Cas7/Cse4/CasC	gnl\|CDD\|378153	pfam09344, Cas_CT1975, CT1975-like protein. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is represented by CT1975 of Chlorobium tepidum.	9.98276e-107
NZ_CP010869.1\|WP_054537944.1\|585430_586543_-\|penicillin-binding-protein-activator	gnl\|CDD\|380572	cd06349, PBP1_ABC_HAAT-like, type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally.	4.94392e-138
NZ_CP010869.1\|WP_054537930.1\|568127_568988_+\|extensin-family-protein	gnl\|CDD\|369129	pfam06904, Extensin-like_C, Extensin-like protein C-terminus. This family represents the C-terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress. Note that many family members of this family are hypothetical.	1.87248e-59
NZ_CP010869.1\|WP_054537943.1\|583459_584458_-\|branched-chain-amino-acid-ABC-transporter-permease	gnl\|CDD\|119323	cd06581, TM_PBP1_LivM_like, Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. E. coli LivM forms a heterodimer with another TM, LivH, to generate the transmembrane pore. LivH is not included in this subgroup. The LIV-1/LS transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBPs, LivJ (LIV-BP) or LivK (LS-BP). In addition to transporting branched-chain AAs including leucine, isoleucine and valine, the E. coli LIV-1/LS transporter is involved in the uptake of the aromatic AA, phenylalanine.	2.46744e-81

>NZ_CP010869.1|WP_054537937.1|577963_578248_+|type-I-E-CRISPR-associated-endoribonuclease-Cas2
MMVIVVSRAPPRLRGRLAAWLLEIRAGVFVGDYSARTRGRIWDQVLGGLEDGDAVMVWRAPNDQGFDFATAGQNRRMPEDFDGLKLVKFLPRSG
>NZ_CP010869.1|WP_054537936.1|577041_577983_+|type-I-E-CRISPR-associated-endonuclease-Cas1
MTGMPGLPPPRPIPLRDRAQLVFVERARLDVRDGAFCAVNADGTVTQLPVGGLAGLMLEPGARISHAAVALAARTGTLITWVGEGGVRLYSAGQPGGARSDKLLWQASLALNDAARLRIVRRMYQIRFGEAAPERRSIDQLRGIEGVRVRESYALLARKYGVKWSRRKYDPKDWEAGDTPNRCLSAATACLHGLTEAAVLAAGYAPAIGFLHTGKPLSFVYDIADLWKLQTVVPEAFRIAGEAAKGRLDMAPDRAVRLACRDAFRRSGLLSKIIPQIEIVLAAGDLPKPVPAPDMLGPAFEDEEDGGDDGHRG
>NZ_CP010869.1|WP_037204911.1|576368_577040_+|type-I-E-CRISPR-associated-protein-Cas6/Cse3/CasE
MIYLSRVRLSRDPQVAALDALLDPAQGGARADAHHRLIWSLFAGDPTAERDFLWRAEGEGAFIVQSVCPPQTSPLFEPPEIREHAPDLRPGDRLSYLLRANATRDLRGEKRNRVDIVMHRLHGLPKADRNARRLDLAAEAASEWMAGQGARAGFEALRTQVQHYQTLTLPGHRGKRRGEPRFGILDLTGEIAVTDPKAFLAKLAQGFGRAKGFGCGLMLIRRA
>NZ_CP010869.1|WP_054537935.1|575649_576372_+|type-I-E-CRISPR-associated-protein-Cas5/CasD
MREYLIFQLVAAIGAMGEFGGHDRRGTLSLPGRSAVIGTLGAALGRRRDQPFADLEQLDIAVASFGRSAPLRDYHTVQTVPSAAVKAPQSRPEALREAAGSDKLNTTLTSRDYRCDCVFGVAVSGGDLPGLARALQRPAFQVYLGRKSCPLSAPFDPRIVAADNPARALTQLRLPPWIGARQMIEIVADEGTDLDAPARQQTRHDRAIDRGLWHFGKGRYSVAHPEVNAAMVQDPGEGAP
>NZ_CP010869.1|WP_054537934.1|574598_575657_+|type-I-E-CRISPR-associated-protein-Cas7/Cse4/CasC
MTTFVQFHLLTTYPLSNPNRDDQGRPKQALIGGSPRLRISSQSLKRAVRDSSYFAQDLAGNIGTRTQRLATVLAEELTQQGVTEAEAKRIAIEIGTVFSKLEKGSTKATTLAFVSPDEWALARALAAKAVAGEDFPKDKELKQAMLRRADGAVDIAMFGRMLADSPAYNREAAVQLAHAFTTHRAQVQDDWFSAVDDLKTRDEDAGAGHLGENGFGSGIYYLYACVNVDLLVENLAGDKALAAKGIDALARALATATPKGKQNSHAHHPRAGYIRVERGPAQPRDLSGAFHKAVAPDLGGSIDALTDMADKIDRAYGISFETRMMDVPKGHGTLAEIAAFAAETASGLCADA
>NZ_CP010869.1|WP_054537933.1|574098_574602_+|type-I-E-CRISPR-associated-protein-Cse2/CasB
MSKHEKTKRPGQIILGWWTRELGSRKTGEQKALSARLRRGDDVTVLCHKPVHQLAQALGLRDGTRIARLARVLAHVREDAKASLPRRLGVGDPPALSPLRFERLVQSSDEDVETAIRRALPTVRHSVNVAHLGAAILFWNDRTRTNWCFDYYRAVAPWDNQPEDVSQ
>NZ_CP010869.1|WP_054537932.1|572590_574102_+|type-I-E-CRISPR-associated-protein-Cse1/CasA
MPLNLISDSWIPVRLKDGSRRTIAPHQMTDPEIAAPDWPRADLNLACYELLIGMVFMATPPEDDFSWEGGRSDPVRLQERLAEYASAFSLLGDGPKFLQDLEDLPGAPSGPDLLFIDSAGGNTAKNNADLMVHRDRYAALDLPLAAMALYAFQQFAPSGGAGNRTSMRGGGPLVTLADPGTGLWDLVWANVPCGRPANPGDLPWMRPTRTSEADQSVGAGQAHPVEAFFGMPRRLRLVAEPDRVTGVVQRPYGTNYGLWRHPLSPYYRPKEGAELLPRHPATGRLPWRNWIGILLSDPKQESGLRLRAACIEGFYERYGRQAKRMIAAGWAMDNMKPKDFLWEELPLLTFDAAAQRQAESMIGAAETVASALRRALTALVAEGSARDAEYEQFWSATEGDFLDALAVLSAPDFDAADISQKFLGALGRQALAQFDALALPGLYWKKFPNIEDKKKKATGVLKIVEERTTLMALVYGRSKQGKSLWAGLDVVPPERTTQREVMT
>NZ_CP010869.1|WP_162231803.1|569797_572251_+|CRISPR-associated-helicase-Cas3'
MALLDWPGKSAPEDGTEHPALYHMIDVGAVAECLVARLDIPAGRKAFYSLAAALHDLGKISDSFRDMLRDGKPQTEGRHWEVTELWLQDFDDDLATLAVNSHARKALYAAIAGHHGCPPKKEDFYRMRVAAGPGAPGDARDCLRQFIALWPEARFEMPLQEIVAQSWWLPGLIATADWIGSNPAFFPPVAAGPDARAYLDLARDKAAQAVRRAGLDIPQVSSCSIIPQTWSLRPMQRSVCDVDLPDHPILALIEDETGSGKTEAALILAQRMMRAGKGQGLYFALPTMATANAMFDRVADLVGGLFDAPPSVALAHGRATLSHRFREVIRTEPDPVLPSCTTWLADDRRRALLANVGVGTIDQALLSGLPVRHAMLRHYALSQKILIVDEVHEMGDPYMAGQLCQLLRLHRRMGGSAILMTATLPVAFREMLCEAFGVSPPTSRAYPALSIAGHSQVTGLTTVSRRGPVAVKRVPDVASVLDLLDRAVTDGAAALWVRNAVDDAIQAATALRERGIEADLLHARFALADRMRHEAQALATFGKGRGDRPGRVLVATQVVESSLDLDFDVMVSDLAPIPALVQRAGRLWRHMDRRPQNTRPRPSPVLHVLSPDPDQVADDLWLRQVLDRGAFTYPLDLQWRAARAIFSAGSIDAPGGLRDLIEAGLTDGELPQVLDQAERDRVGKSYAQSDLAEQNLIDLASPYRRIKGFSDEADFPTRLGREQRALVLARITDKGLLPLEGEVWSAETRQYAEVSAAAYKLDRLPLPDQMTPEVSAVKEGWPDWMQTRLVVCPLGEAGAICEGLSYDRERGLVFGSS
>NZ_CP010869.1|WP_082386498.1|569360_569783_+|hypothetical-protein
MTFSKAANLLRVADMATSRYDRIRLQDVTDEFGCEHRTAQRMVHAFEAVFPQVNVTGHQRLVKGVSLALPRRPVRQFLVLGMNGNRWPHSPGSDPFFTEAEIALIRQKTGLQLNGRRGKLARGLELFRRQPPAAPAGPDR
>NZ_CP010869.1|WP_054537930.1|568127_568988_+|extensin-family-protein
MRRGAALVAMLLALLAGEAAPAAPDHSPLPRPRPVLMPRLLPVFAPPVDAVRPRLRPAARTAARSAPVRMSGAASASLAGMRSLWPRLRPSGLVRPAAAAVRAPAAPVATSSAGAVCGDRGIIGVRLAPIEGRLAGCGIDRPVRITSVDGVMLNRPATMDCETAKALKSWVKKGVKPHVKRLGGGVAKLEVASGYACRTRNNQPGAKVSEHGRGKAVDISAITLANGATLNVQSGWGKGAEGALLTRMHKSACGPFGTVLGPESDHFHKDHFHLDTADHRSGPYCR
>NZ_CP010869.1|WP_157445497.1|579036_579342_+|transposase
MIFVSDVWAKARTKALERENRELKQANEILRKGETILRNLGHARIVIAARAADNNTERPHSSLEYQTTADFARTLTIAIARLAAQGEAPRVGPLLNRRQSE
>NZ_CP010869.1|WP_054537939.1|579537_580002_-|L-2-amino-thiazoline-4-carboxylic-acid-hydrolase
MQNLPILERRRIEAMILKHVLDVITERSGRAEAEMVIGETCSRSAIEQGQALASDLGHTPDLSDFATILPNWTKEDALEMEVLVTEPDRMEFNVTRCRYAEMYREMGLGDIGHLLSCNRDGDFCVGYNPQIELTRTQTLMKGASHCDFRYKMAK
>NZ_CP010869.1|WP_054537940.1|580032_581337_-|FAD-binding-oxidoreductase
MQNAAPFPPSIWADTSPARTPNTPLVGTVETDSVIIGGGFSGLSAALHLAKVGRDVTVLEGHAVGWGASGRNNGQVIPTLTAAEPDMWVARFGETGRKFAELIGASAAMLFDKIREEGIEAEAEQTGWFQPAHSPGRTKLSQNRVDAWRRFGLEVEYLDHTATTAMLGTDHWFGGMLAPSGGHINPLALARGIAGAVERHGGKIYEQTRVDSYAHTGTEWLVKTPKGMIKARALILATNAYTGELAPRLARQLAHSVIPVHSWQMSTEPLSDIVRATLLPGRQAVSDTRGDLRFFRYDARNRLITGGAIVGGGDVHARIARKVADNLADSFPQLAPPKMTHVWSGYLAMNWDHFPRVHQLGPNGWTWIGCNGRGVALGNALGREIARAVDGEDVRGLALPVTEPHPFPFHAIARRVAPLYMTWLQRNDRKEPKI
>NZ_CP010869.1|WP_081940079.1|581453_581927_+|Lrp/AsnC-family-transcriptional-regulator
MSDMSFDEIDQRILDILQVNSDLPIAEVADRIGLSPTPIWRRIKRMETAGLIRARVALVDQKVANVPMTIFIGVTAPRHAMEWFKQFRALIEDIPEVVEAYRLTGATDYIMKVVVPDIATYDVVYQRMIEEVEFSTVNSSISMEELKFTTAVPTKYL
>NZ_CP010869.1|WP_054537941.1|581991_582708_-|ABC-transporter-ATP-binding-protein
MSNILEIKKLSLKIGIQDILHDISVTVPQQGIVSVLGANGVGKTSLMRCISGIYHPTGGQILLEGEDISKLKSHQIVDRGIMQAPEGRQIFSNMSVLENLIIGGGPLGRQELDHVLALFPRLEERLKQQAGSMSGGEQQMLCIGRALMRKPKVLLLDEPSLGLAPRLVGFICDLVSKIRSEGYAVLLVEQNVKAALRISDMAAVIEHGKIVIEGDAKALSNDPRVAEAYLGGHVHESA
>NZ_CP010869.1|WP_054537942.1|582704_583463_-|ABC-transporter-ATP-binding-protein
MTAILELDGLTRAFGGLKAVDNVTTRVDHGELFGLIGPNGAGKTTLFNLISGFTPPSSGEVRFKGEKITGLSAHQIAHKGMSRTFQNLRVFPNMTVFDNISVGALGMLGVGPFSSLFGRSSHAKEISERSWEMLEKVGLADHADDLAANLSYGKRKYLEIARALAMKPDLLILDEPAAGMNDSETTELARFITGLNKEGLTIMLVEHDMGLVMGICERLVVLASGRKIADDVPAVVRQDPGVLAAYLGGDEE
>NZ_CP010869.1|WP_054537943.1|583459_584458_-|branched-chain-amino-acid-ABC-transporter-permease
MSKSRLIKTGLVLAAFAVVPAVLVGFDKGYYYQIATLAAIFMLLAASLHLVTGVAGLLQLGHAAFYGVGAYVAAILGADHGVGFTVGLPLAGLSAAAIAFLVALPTMRLMSIYFAVATLAIGQMLYLVFLNWVDLTNGPNGVMLFSGINLFGIEIESDLGIYYVVAAVVAVSILVLNRLSHSYYGNALRSLREDDQCASAMGINVTVMKIQAFVISSFFAGIAGALWAYTTGYISPNDFHFSQSILILTMVVVGGLGSLPGVLIGALLLILLPEALRSVGDIRNIIVGLVMFGSILFLPKGLFGEVSALNFARRLLGANWSNDEGQKGIGWK
>NZ_CP010869.1|WP_037204931.1|584450_585365_-|branched-chain-amino-acid-ABC-transporter-permease
MLDPYILQQLAIGLSLGMIYALMAIGFTLIFGVLNVVNFAHGEIYTIGAFAGLMVISVFGPPLLVVLFIALATGALAGFGLERLAFRPFRRFSDEASLKSRAMREATLMSSLAMSIIAREAMEMIFGSQFQSVDLAYLINKPIGIGPITIVNGDLIIFGITVVMLGGLQWLLKKSPVGLSIRAVSNNALGAKYCGINTDRTIIITFVIGSAMGALAGILVGLYYGAIFPSMGFTPGIKAFVAMVMGGLSSIPGAVISAIILGLSESLSTSFMSSVWSDMVAYAFLLLTLIFFPQGLFGARRERV
>NZ_CP010869.1|WP_054537944.1|585430_586543_-|penicillin-binding-protein-activator
MKLTRRTAIAIAVTAALTPAAAFAEETVKIGYQLPLTGNTAQYGQDFKDAAEIALTKFNASGALPVPVEIIYEDSRSDAKEGVTIARKFVDDDGIVGVLGDFTSTVSMAAAQVYKKAGMAQLSQTASHPDFAKISKWQFRNITTQDQEGSVNAQWMLDQGIKKVAVIAEQTDWGQSVVKGFVEPFEAAGGEIVYTEFFNRGLADFRPIITKLENNTPDAVYTGFFYEDGGQFLKQMKQLDAGIPVYSTSAAYNDKLIELAGDASEGLFLTATFLPTRMDANVQEFVGEWSKTHDAAPGQFPAQAYDAVNIMLSAVVKAYPEITRESLRDALAETTDFPGVTGNTSFDENGEPLKELTKASVSNGMFVEVQ
>NZ_CP010869.1|WP_054537945.1|586665_587175_-|L-2-amino-thiazoline-4-carboxylic-acid-hydrolase
MTDAPATPEITLEQLSGAYAMRAKFYMHMFDVLREEYGPDKTIELMSKATFRLGVEMGEKLKAHGPANIEALTEQFLNGIPCRDHLFSPELLKCDAEGMEIQFHRCPLKDNWEAAGREGDELEMLCRAAGAIDAGLFGAAGFTFKGETWKPGKTGCCRLIVEPGLAAAD

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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_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP046574	Rhodococcus sp. WAY2 plasmid pRWAY02, complete sequence	8699-8730	5	0.844
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP046575	Rhodococcus sp. WAY2 plasmid pRWAY03, complete sequence	18555-18586	5	0.844
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NC_012520	Rhodococcus opacus B4 plasmid pROB01, complete sequence	319244-319275	6	0.812
NZ_CP010869_1	1.4\|578534\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578534-578565	32	NZ_CP012748	Paraburkholderia caribensis MBA4 plasmid unnamed, complete sequence	723933-723964	7	0.781
NZ_CP010869_1	1.4\|578534\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578534-578565	32	NC_010625	Paraburkholderia phymatum STM815 plasmid pBPHY01, complete sequence	452345-452376	7	0.781
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP013631	Rhizobium sp. N324 plasmid pRspN324a, complete sequence	12807-12838	8	0.75
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP021915	Sagittula sp. P11 plasmid unnamed2, complete sequence	81709-81740	8	0.75
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP010856	Marinovum algicola DG 898 plasmid pMaD1, complete sequence	88457-88488	8	0.75
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP045373	Sulfitobacter sp. THAF37 plasmid pTHAF37_a, complete sequence	66853-66884	8	0.75
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP018081	Sulfitobacter sp. AM1-D1 plasmid unnamed5, complete sequence	183254-183285	8	0.75
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP031947	Ruegeria sp. AD91A plasmid unnamed1, complete sequence	396154-396185	8	0.75
NZ_CP010869_1	1.9\|578839\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578839-578870	32	NZ_CP040096	Pantoea sp. SO10 plasmid unnamed1, complete sequence	541152-541183	8	0.75
NZ_CP010869_1	1.9\|578839\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578839-578870	32	NZ_CP016453	Sphingobium sp. RAC03 plasmid pBSY17_1, complete sequence	1247-1278	8	0.75
NZ_CP010869_1	1.5\|578595\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578595-578626	32	NZ_CP051543	Paracoccus sanguinis strain OM2164 plasmid pPspOM122, complete sequence	105469-105500	9	0.719
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP015236	Rhodococcus fascians D188 plasmid pFiD188, complete sequence	73122-73153	9	0.719
NZ_CP010869_1	1.2\|578412\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578412-578443	32	NZ_CP017783	Rhodobacter sp. LPB0142 plasmid pEJ02, complete sequence	1975-2006	10	0.688
NZ_CP010869_1	1.2\|578412\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578412-578443	32	NZ_CP017784	Rhodobacter sp. LPB0142 plasmid pEJ03, complete sequence	3047-3078	10	0.688
NZ_CP010869_1	1.2\|578412\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578412-578443	32	NZ_CP028921	Gemmobacter sp. HYN0069 plasmid unnamed3, complete sequence	17181-17212	10	0.688
NZ_CP010869_1	1.4\|578534\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578534-578565	32	MT723933	Streptomyces phage Keanu, complete genome	5646-5677	10	0.688
NZ_CP010869_1	1.8\|578778\|32\|NZ_CP010869\|PILER-CR,CRISPRCasFinder,CRT	578778-578809	32	NZ_CP017076	Novosphingobium resinovorum strain SA1 plasmid pSA1, complete sequence	1211804-1211835	10	0.688

1. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP046574 (Rhodococcus sp. WAY2 plasmid pRWAY02, complete sequence) position: , mismatch: 5, identity: 0.844

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
caattcgaagccaagggtgccgccgaggtggc	Protospacer
*** **********************  .**.

2. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP046575 (Rhodococcus sp. WAY2 plasmid pRWAY03, complete sequence) position: , mismatch: 5, identity: 0.844

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
caattcgaagccaagggtgccgccgaggtggc	Protospacer
*** **********************  .**.

3. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NC_012520 (Rhodococcus opacus B4 plasmid pROB01, complete sequence) position: , mismatch: 6, identity: 0.812

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
caattcgaagccgagggtgccgccgaggtggc	Protospacer
*** ********.*************  .**.

4. spacer 1.4|578534|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP012748 (Paraburkholderia caribensis MBA4 plasmid unnamed, complete sequence) position: , mismatch: 7, identity: 0.781

tcgatatagcccgtcacgcccgttgcggcatt	CRISPR spacer
ccgatatcgctcgtcacgcccgttgccgtttc	Protospacer
.****** **.*************** *. *.

5. spacer 1.4|578534|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NC_010625 (Paraburkholderia phymatum STM815 plasmid pBPHY01, complete sequence) position: , mismatch: 7, identity: 0.781

tcgatatagcccgtcacgcccgttgcggcatt	CRISPR spacer
ccgatatcgctcgtcacgcccgttgccgtttc	Protospacer
.****** **.*************** *. *.

6. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP013631 (Rhizobium sp. N324 plasmid pRspN324a, complete sequence) position: , mismatch: 8, identity: 0.75

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
gacgtcgaagcgaaggatgccgccgacgagat	Protospacer
 * .******* ****.**********  *.*

7. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP021915 (Sagittula sp. P11 plasmid unnamed2, complete sequence) position: , mismatch: 8, identity: 0.75

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
aagatcgaggccaaggctgccgccgaagccgc	Protospacer
 *.*****.******* *********  * *.

8. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP010856 (Marinovum algicola DG 898 plasmid pMaD1, complete sequence) position: , mismatch: 8, identity: 0.75

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
aagatcgaggccaaggctgccgccgaagccgc	Protospacer
 *.*****.******* *********  * *.

9. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP045373 (Sulfitobacter sp. THAF37 plasmid pTHAF37_a, complete sequence) position: , mismatch: 8, identity: 0.75

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
aagatcgaggccaaggctgccgccgaagccgc	Protospacer
 *.*****.******* *********  * *.

10. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP018081 (Sulfitobacter sp. AM1-D1 plasmid unnamed5, complete sequence) position: , mismatch: 8, identity: 0.75

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
aagatcgaggccaaggctgccgccgaagccgc	Protospacer
 *.*****.******* *********  * *.

11. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP031947 (Ruegeria sp. AD91A plasmid unnamed1, complete sequence) position: , mismatch: 8, identity: 0.75

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
aagatcgaagccaaggaggccgccgaagctga	Protospacer
 *.*************. ********  * *

12. spacer 1.9|578839|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP040096 (Pantoea sp. SO10 plasmid unnamed1, complete sequence) position: , mismatch: 8, identity: 0.75

gatttcaacccgctggatgactggtacggctt	CRISPR spacer
gatttcaactcgctggattactggctggatct	Protospacer
*********.******** *****.  *...*

13. spacer 1.9|578839|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP016453 (Sphingobium sp. RAC03 plasmid pBSY17_1, complete sequence) position: , mismatch: 8, identity: 0.75

gatttcaacccgctggatgactggt---acggctt	CRISPR spacer
actttcaacctgctgggtgactggtcgaaggg---	Protospacer
. ********.*****.********   * **

14. spacer 1.5|578595|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP051543 (Paracoccus sanguinis strain OM2164 plasmid pPspOM122, complete sequence) position: , mismatch: 9, identity: 0.719

cagctggctatactgcgcgagacggatccggt	CRISPR spacer
gcgctggccatgctgcgcgagacggccgccgc	Protospacer
  ******.**.************* . * *.

15. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP015236 (Rhodococcus fascians D188 plasmid pFiD188, complete sequence) position: , mismatch: 9, identity: 0.719

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
gcggtcttcgccaatggtgccgccggcccggt	Protospacer
  ..**   ***** **********.******

16. spacer 1.2|578412|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP017783 (Rhodobacter sp. LPB0142 plasmid pEJ02, complete sequence) position: , mismatch: 10, identity: 0.688

aagggttacctgatcggctcgaacagtcagat	CRISPR spacer
cgcttctgcctgatcgtctcgaacaggcagac	Protospacer
 .   .*.******** ********* ****.

17. spacer 1.2|578412|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP017784 (Rhodobacter sp. LPB0142 plasmid pEJ03, complete sequence) position: , mismatch: 10, identity: 0.688

aagggttacctgatcggctcgaacagtcagat	CRISPR spacer
cgcttctgcctgatcgtctcgaacaggcagac	Protospacer
 .   .*.******** ********* ****.

18. spacer 1.2|578412|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP028921 (Gemmobacter sp. HYN0069 plasmid unnamed3, complete sequence) position: , mismatch: 10, identity: 0.688

aagggttacctgatcggctcgaacagtcagat	CRISPR spacer
cgcttctgcctgatcgtctcgaacaggcagac	Protospacer
 .   .*.******** ********* ****.

19. spacer 1.4|578534|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to MT723933 (Streptomyces phage Keanu, complete genome) position: , mismatch: 10, identity: 0.688

tcgatatagcccgtcacgcccgttgcggcatt	CRISPR spacer
gggcagcagcccgtcacccccggtgcggcacc	Protospacer
  *  ..********** **** *******..

20. spacer 1.8|578778|32|NZ_CP010869|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP017076 (Novosphingobium resinovorum strain SA1 plasmid pSA1, complete sequence) position: , mismatch: 10, identity: 0.688

caaatcgaagccaagggtgccgccgacccggt	CRISPR spacer
gcgatcgaagccgatggtgccgccgacagcaa	Protospacer
  .*********.* ************   .

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

665319 : 708518

Streptococcus_phage(16.67%)

holin,protease,tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_054538006.1\|665319_665658_+\|tRNA	tRNA-binding protein	NA	NA	NA	NA
WP_054538007.1\|665657_666614_+	D-glycerate dehydrogenase	M1NSB9	Streptococcus_phage	6.5e-15	28.2
WP_054538008.1\|666678_666879_+	CsbD family protein	NA	NA	NA	NA
WP_054538009.1\|666897_667488_-	thymidine kinase	C4MZJ3	Enterobacteria_phage	2.7e-51	52.2
WP_037205204.1\|667853_668315_+	hypothetical protein	NA	NA	NA	NA
WP_082386505.1\|668348_669617_-	DEAD/DEAH box helicase	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	3.4e-51	32.8
WP_054538011.1\|669865_673093_-	carbamoyl-phosphate synthase large subunit	NA	NA	NA	NA
WP_157445503.1\|673165_674431_-	DUF2029 domain-containing protein	NA	NA	NA	NA
WP_157445504.1\|674606_675278_+\|protease	CPBP family intramembrane metalloprotease	NA	NA	NA	NA
WP_054538014.1\|675281_676511_-	class I SAM-dependent methyltransferase	A0A2I2L5L3	Orpheovirus	9.2e-46	36.3
WP_054538015.1\|676815_678591_+\|tRNA	aspartate--tRNA ligase	NA	NA	NA	NA
WP_054538016.1\|678689_680069_+	DUF1800 domain-containing protein	NA	NA	NA	NA
WP_054538017.1\|680071_681313_+	DUF1501 domain-containing protein	NA	NA	NA	NA
WP_054538018.1\|681390_682116_+	GNAT family N-acetyltransferase	NA	NA	NA	NA
WP_054538019.1\|682125_682845_-	response regulator	NA	NA	NA	NA
WP_054538020.1\|682988_683393_+	methylmalonyl-CoA epimerase	NA	NA	NA	NA
WP_054538021.1\|683392_683686_+	DUF1467 family protein	NA	NA	NA	NA
WP_054538022.1\|683600_684341_-	EI24 domain-containing protein	NA	NA	NA	NA
WP_054538023.1\|684337_684916_-	nitroreductase	NA	NA	NA	NA
WP_173585951.1\|685045_685348_+	DUF167 domain-containing protein	NA	NA	NA	NA
WP_054538024.1\|685351_685591_-	hypothetical protein	NA	NA	NA	NA
WP_054538025.1\|685754_686444_+\|protease	M48 family metalloprotease	NA	NA	NA	NA
WP_054538026.1\|686525_686783_+	hypothetical protein	NA	NA	NA	NA
WP_054538027.1\|686786_687041_+	hypothetical protein	NA	NA	NA	NA
WP_054538028.1\|687143_687578_+	DsrE family protein	NA	NA	NA	NA
WP_037205149.1\|687608_687746_-	entericidin A/B family lipoprotein	NA	NA	NA	NA
WP_081940086.1\|687806_687944_-	entericidin A/B family lipoprotein	NA	NA	NA	NA
WP_054538029.1\|688082_688643_+	PhnA domain-containing protein	NA	NA	NA	NA
WP_054538030.1\|688639_689011_-	hypothetical protein	NA	NA	NA	NA
WP_054538031.1\|689188_689680_+	cytochrome b/b6 domain-containing protein	NA	NA	NA	NA
WP_052071250.1\|689691_689967_-	hypothetical protein	NA	NA	NA	NA
WP_054538032.1\|690041_690620_-	DUF4334 domain-containing protein	NA	NA	NA	NA
WP_054538033.1\|690663_691410_-	ethanolamine ammonia-lyase subunit EutC	NA	NA	NA	NA
WP_054538034.1\|691406_692804_-	ethanolamine ammonia-lyase subunit EutB	NA	NA	NA	NA
WP_054538035.1\|692842_694063_-	ABC transporter permease	NA	NA	NA	NA
WP_054538036.1\|694059_694983_-	ABC transporter permease	NA	NA	NA	NA
WP_054538037.1\|694986_696081_-	ABC transporter ATP-binding protein	Q6GZ03	Mycoplasma_phage	2.0e-23	57.3
WP_054540305.1\|696193_697336_-	extracellular solute-binding protein	NA	NA	NA	NA
WP_054538038.1\|697604_699092_+	PLP-dependent aminotransferase family protein	NA	NA	NA	NA
WP_054538039.1\|699076_699826_-	SDR family oxidoreductase	NA	NA	NA	NA
WP_157445505.1\|699990_701313_+	aminotransferase class III-fold pyridoxal phosphate-dependent enzyme	NA	NA	NA	NA
WP_054538040.1\|701337_702996_-\|holin	choline dehydrogenase	A0A1V0SI18	Klosneuvirus	4.8e-58	30.9
WP_054538041.1\|703041_704499_-	betaine-aldehyde dehydrogenase	NA	NA	NA	NA
WP_054538042.1\|704532_706041_-\|holin	choline-sulfatase	NA	NA	NA	NA
WP_052071423.1\|706037_706625_-	transcriptional regulator BetI	NA	NA	NA	NA
WP_054538043.1\|706703_707621_+\|holin	choline ABC transporter substrate-binding protein	NA	NA	NA	NA
WP_054538044.1\|707684_708518_+\|holin	choline ABC transporter permease subunit	NA	NA	NA	NA

DBSCAN-SWA_2

1655616 : 1668521

Paracoccus_phage(33.33%)

portal,tail,protease,capsid,head

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_054538738.1\|1655616_1656792_+\|portal	phage portal protein	W8ECU7	Geobacillus_phage	1.4e-59	37.1
WP_037205302.1\|1656788_1657031_+	hypothetical protein	NA	NA	NA	NA
WP_054540375.1\|1657060_1657636_+\|head,protease	HK97 family phage prohead protease	A0A0U2BX10	Paracoccus_phage	8.1e-37	52.3
WP_054538739.1\|1657639_1658824_+\|capsid	phage major capsid protein	B0VK33	Azospirillum_phage	3.4e-66	43.5
WP_054538740.1\|1658976_1659576_+	hypothetical protein	NA	NA	NA	NA
WP_037205310.1\|1659572_1659914_+\|head,tail	head-tail adaptor protein	NA	NA	NA	NA
WP_037205312.1\|1659910_1660321_+	DUF3168 domain-containing protein	NA	NA	NA	NA
WP_037205485.1\|1660342_1660756_+\|tail	phage major tail protein, TP901-1 family	NA	NA	NA	NA
WP_037205315.1\|1660755_1661088_+	gene transfer agent family protein	NA	NA	NA	NA
WP_037205317.1\|1661074_1661269_+\|tail	phage tail assembly chaperone	NA	NA	NA	NA
WP_037205320.1\|1661272_1661935_+\|tail	phage tail tape measure protein	A0A1W6JP49	Morganella_phage	1.4e-11	30.0
WP_054538741.1\|1661944_1662577_+	DUF2460 domain-containing protein	A0A0B5A2K3	Paracoccus_phage	1.9e-55	48.6
WP_054538742.1\|1662576_1663464_+	DUF2163 domain-containing protein	A0A0B5A5B8	Paracoccus_phage	2.1e-60	41.4
WP_054538743.1\|1663460_1663907_+	C40 family peptidase	F4YXU4	Roseobacter_phage	5.3e-28	48.5
WP_054538744.1\|1663906_1667821_+\|tail	glycoside hydrolase/phage tail family protein	F4YXU5	Roseobacter_phage	2.2e-234	38.8
WP_054538745.1\|1667813_1668521_+	DUF2793 domain-containing protein	A0A0K1LM54	Rhodobacter_phage	4.6e-18	43.2

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_CP010871

Click the left colored region to show detailed information

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

124399 : 154644

uncultured_Mediterranean_phage(14.29%)

integrase,transposase,holin

attL 128409:128424|attR 135116:135131

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_054540713.1\|124399_126034_+\|integrase,transposase	DDE-type integrase/transposase/recombinase	NA	NA	NA	NA
WP_054540714.1\|126050_126917_+	TniB family NTP-binding protein	NA	NA	NA	NA
WP_082386792.1\|126913_127924_+	TniQ family protein	NA	NA	NA	NA
WP_054540751.1\|127939_128551_-	SMC-Scp complex subunit ScpB	A0A1B1IVT7	uncultured_Mediterranean_phage	3.5e-14	28.7
128409:128424	attL	NA	NA	NA	NA
WP_054540715.1\|128598_129483_-	DUF1403 family protein	NA	NA	NA	NA
WP_054540555.1\|129697_132580_-\|transposase	Tn3 family transposase	A0A1B0V7H9	Salmonella_phage	4.8e-186	38.3
WP_054540554.1\|132743_133331_+	recombinase family protein	A0A0A7NPV4	Enterobacteria_phage	8.6e-26	38.5
WP_173586000.1\|133418_134453_+\|integrase	tyrosine-type recombinase/integrase	NA	NA	NA	NA
WP_054540717.1\|134540_135821_-	replication protein C	L7TKN6	Rhizobium_phage	8.7e-15	26.7
135116:135131	attR	NA	NA	NA	NA
WP_054540718.1\|136046_137066_-	ParB N-terminal domain-containing protein	NA	NA	NA	NA
WP_173585998.1\|137062_138418_-	AAA family ATPase	A0A240F4U1	Ochrobactrum_phage	5.8e-17	26.3
WP_054540720.1\|138848_139289_+	DUF2383 domain-containing protein	NA	NA	NA	NA
WP_054540721.1\|139327_140152_+	manganese catalase family protein	NA	NA	NA	NA
WP_054540722.1\|140581_141436_+	SDR family oxidoreductase	A0A2N9QUX2	Trichoplusia_ni_ascovirus	2.3e-59	45.9
WP_054540723.1\|141704_142274_-	hypothetical protein	NA	NA	NA	NA
WP_054540724.1\|142679_142877_+	hypothetical protein	NA	NA	NA	NA
WP_054540725.1\|142975_143479_-	superoxide dismutase family protein	Q461V7	Trichoplusia_ni_single_nucleopolyhedrovirus	1.7e-06	28.6
WP_082386793.1\|143620_144316_+	trehalose-phosphatase	NA	NA	NA	NA
WP_054540726.1\|144349_144670_+	trehalose-6-phosphate synthase	NA	NA	NA	NA
WP_054540727.1\|144978_145473_-	hypothetical protein	NA	NA	NA	NA
WP_054540728.1\|145644_146598_-	YihY/virulence factor BrkB family protein	NA	NA	NA	NA
WP_054540729.1\|146900_147482_+	hypothetical protein	NA	NA	NA	NA
WP_054540730.1\|147481_147910_+\|holin	phage holin family protein	NA	NA	NA	NA
WP_054540731.1\|147902_149003_+	DUF3618 domain-containing protein	NA	NA	NA	NA
WP_054540732.1\|149341_149680_+	hypothetical protein	NA	NA	NA	NA
WP_054540733.1\|150132_151821_+	hypothetical protein	NA	NA	NA	NA
WP_054540734.1\|151893_152478_-	exopolysaccharide biosynthesis protein	NA	NA	NA	NA
WP_054540735.1\|152803_153145_+	type II toxin-antitoxin system RelE/ParE family toxin	NA	NA	NA	NA
WP_054540736.1\|153141_153435_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_054540737.1\|153508_154330_-\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_054540738.1\|154326_154644_-\|transposase	transposase	NA	NA	NA	NA

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NZ_CP010870

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

2. NZ_CP010869

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

3. NZ_CP010871

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection