CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Prophage number
NZ_CP016458	Blastomonas sp. RAC04 plasmid pBSY18_2, complete sequence	0 crisprs	NA	0
NZ_CP016462	Blastomonas sp. RAC04 plasmid pBSY18_1, complete sequence	0 crisprs	NA	10
NZ_CP016461	Blastomonas sp. RAC04 plasmid pBSY18_4, complete sequence	0 crisprs	RT,cas4	1
NZ_CP016459	Blastomonas sp. RAC04 plasmid pBSY18_3, complete sequence	0 crisprs	NA	0
NZ_CP016460	Blastomonas sp. RAC04 chromosome, complete genome	1 crisprs	DinG,RT,csa3,cas3,DEDDh	4

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 : 28062

Emiliania_huxleyi_virus(50.0%)

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_150126433.1\|1169_1703_-	cation transporter	NA	NA	NA	NA
WP_069052084.1\|1807_2185_-	hypothetical protein	NA	NA	NA	NA
WP_069052085.1\|2243_5471_-	CusA/CzcA family heavy metal efflux RND transporter	NA	NA	NA	NA
WP_069052086.1\|5475_6663_-	efflux RND transporter periplasmic adaptor subunit	NA	NA	NA	NA
WP_054135016.1\|6666_7980_-	TolC family protein	NA	NA	NA	NA
WP_082382295.1\|8605_8776_-	MerR family DNA-binding transcriptional regulator	NA	NA	NA	NA
WP_069052215.1\|8859_9486_+	cation transporter	NA	NA	NA	NA
WP_083231705.1\|9665_10289_+	DUF3703 domain-containing protein	NA	NA	NA	NA
WP_082382514.1\|10578_10986_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_054136697.1\|11195_11825_+	cation transporter	NA	NA	NA	NA
WP_150126406.1\|12111_12336_+	hypothetical protein	NA	NA	NA	NA
WP_069052087.1\|12352_13090_-	glutaredoxin	NA	NA	NA	NA
WP_069052088.1\|13163_13571_+	MerR family transcriptional regulator	NA	NA	NA	NA
WP_150126407.1\|13617_13875_+	hypothetical protein	NA	NA	NA	NA
WP_069052090.1\|13871_14309_+	periplasmic heavy metal sensor	NA	NA	NA	NA
WP_069052091.1\|14305_14878_+	sigma-70 family RNA polymerase sigma factor	NA	NA	NA	NA
WP_083231689.1\|14884_16747_+	copper resistance system multicopper oxidase	NA	NA	NA	NA
WP_069052092.1\|16743_17862_+	copper resistance protein B	NA	NA	NA	NA
WP_069052093.1\|17878_18268_+	copper homeostasis periplasmic binding protein CopC	NA	NA	NA	NA
WP_069052094.1\|18269_19199_+	copper homeostasis membrane protein CopD	NA	NA	NA	NA
WP_069052095.1\|19230_19758_+	nuclear transport factor 2 family protein	NA	NA	NA	NA
WP_083231707.1\|20247_24408_-	strawberry notch family protein	V5LQJ6	Emiliania_huxleyi_virus	1.1e-21	23.4
WP_069052097.1\|24630_24897_-	WGR domain-containing protein	NA	NA	NA	NA
WP_054136698.1\|25610_26690_+	replication initiation protein	NA	NA	NA	NA
WP_054136652.1\|26859_28062_+	AAA family ATPase	A0A1I9KF58	Aeromonas_phage	7.6e-45	34.4

DBSCAN-SWA_2

32251 : 33790

Stx2-converting_phage(100.0%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_069052102.1\|32251_33790_+\|transposase	IS66 family transposase	A0A0P0ZEB3	Stx2-converting_phage	6.2e-100	39.8

DBSCAN-SWA_3

42320 : 42911

Geobacillus_virus(100.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_083231709.1\|42320_42911_+	lytic transglycosylase domain-containing protein	A0A0H3V0Q1	Geobacillus_virus	5.4e-28	55.2

DBSCAN-SWA_4

70476 : 123434

Leptospira_phage(42.86%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_171900311.1\|70476_71028_+\|transposase	transposase family protein	S5WIU1	Leptospira_phage	1.3e-15	46.1
WP_171900312.1\|71154_71565_+	MarR family transcriptional regulator	NA	NA	NA	NA
WP_069052134.1\|72086_74408_-	TonB-dependent receptor	NA	NA	NA	NA
WP_083231712.1\|74772_77697_-	TonB-dependent receptor	NA	NA	NA	NA
WP_150126428.1\|80895_81856_-\|transposase	IS630 family transposase	S5VXX4	Leptospira_phage	1.1e-06	23.3
WP_069052136.1\|82287_83727_-	efflux transporter outer membrane subunit	NA	NA	NA	NA
WP_069052137.1\|83719_86944_-	multidrug efflux RND transporter permease subunit	S5VTK5	Leptospira_phage	5.3e-53	22.2
WP_069052138.1\|86957_88085_-	efflux RND transporter periplasmic adaptor subunit	NA	NA	NA	NA
WP_069052139.1\|88275_88914_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_150126415.1\|88959_89325_+\|transposase	transposase	NA	NA	NA	NA
WP_069052141.1\|90065_91664_-	ubiquinone biosynthesis protein	G8DDN0	Micromonas_pusilla_virus	2.5e-27	27.1
WP_069052220.1\|91660_92302_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA
WP_069052142.1\|92507_93488_-	MCE family protein	NA	NA	NA	NA
WP_069052144.1\|93730_93934_+	hypothetical protein	NA	NA	NA	NA
WP_069052145.1\|96089_96416_-	2Fe-2S iron-sulfur cluster binding domain-containing protein	NA	NA	NA	NA
WP_150126417.1\|96445_97723_-	cytochrome P450	NA	NA	NA	NA
WP_069052146.1\|97877_98663_+	FadR family transcriptional regulator	NA	NA	NA	NA
WP_083231698.1\|98675_99701_+	nitronate monooxygenase	NA	NA	NA	NA
WP_069052147.1\|99717_100893_+	transporter	NA	NA	NA	NA
WP_069052148.1\|100889_101366_+	OB-fold domain-containing protein	NA	NA	NA	NA
WP_069052149.1\|101362_102586_+	acyl-CoA dehydrogenase family protein	NA	NA	NA	NA
WP_069052150.1\|102585_103677_+	acyl-CoA/acyl-ACP dehydrogenase	NA	NA	NA	NA
WP_069052151.1\|103701_105315_+	acyl-CoA synthetase	A0A2H4PQU7	Staphylococcus_phage	1.0e-12	27.2
WP_069052152.1\|105311_106919_+	NAD(P)/FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_069052153.1\|106915_107896_+	alpha/beta hydrolase	NA	NA	NA	NA
WP_069052154.1\|108008_108794_+	NUDIX hydrolase	NA	NA	NA	NA
WP_150126430.1\|111092_112538_-	DHA2 family efflux MFS transporter permease subunit	NA	NA	NA	NA
WP_069052156.1\|112628_113774_-	EmrA/EmrK family multidrug efflux transporter periplasmic adaptor subunit	NA	NA	NA	NA
WP_069052157.1\|113770_115213_-	efflux transporter outer membrane subunit	NA	NA	NA	NA
WP_069052158.1\|115202_115616_-	hotdog fold thioesterase	NA	NA	NA	NA
WP_069052159.1\|115612_116497_-	alpha/beta hydrolase	NA	NA	NA	NA
WP_069052222.1\|116570_117020_+	MarR family transcriptional regulator	NA	NA	NA	NA
WP_069052160.1\|117433_118450_+\|transposase	IS110 family transposase	NA	NA	NA	NA
WP_069052161.1\|119395_119704_+	MerR family DNA-binding protein	NA	NA	NA	NA
WP_054136179.1\|119712_120036_-	YnfA family protein	A0A2H4JF35	uncultured_Caudovirales_phage	8.9e-25	48.6
WP_069052223.1\|120159_121059_-	multidrug DMT transporter permease	NA	NA	NA	NA
WP_069052162.1\|121382_122648_+\|transposase	IS1182 family transposase	NA	NA	NA	NA
WP_150126418.1\|122668_123434_+\|transposase	IS5 family transposase	A0A0N9SHJ4	Paenibacillus_phage	6.1e-24	46.8

DBSCAN-SWA_5

128569 : 130171

Hepacivirus(100.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_069052224.1\|128569_130171_+	acyl--CoA ligase	Q75ZG1	Hepacivirus	1.6e-26	24.4

DBSCAN-SWA_6

154650 : 157065

Ochrobactrum_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_069052183.1\|154650_155961_-	chromate efflux transporter	A0A219VHC2	Ochrobactrum_phage	3.9e-26	62.8
WP_069052184.1\|156729_157065_-	single-stranded DNA-binding protein	A0A0S2SY36	Pseudomonas_phage	3.9e-07	31.8

DBSCAN-SWA_7

160491 : 164140

Rhizobium_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_069052191.1\|160491_160863_-	DUF3768 domain-containing protein	L7TKV8	Rhizobium_phage	1.7e-08	33.6
WP_069052192.1\|160922_162596_-	ATP-binding protein	NA	NA	NA	NA
WP_069052193.1\|162826_163279_-	type II toxin-antitoxin system VapC family toxin	NA	NA	NA	NA
WP_069052194.1\|163278_163548_-	type II toxin-antitoxin system Phd/YefM family antitoxin	NA	NA	NA	NA
WP_069052195.1\|163648_164140_-	hypothetical protein	A0A1X9SH15	Bradyrhizobium_phage	3.3e-15	35.1

DBSCAN-SWA_8

169054 : 175152

Caulobacter_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_058456856.1\|169054_170005_-	DUF1738 domain-containing protein	A0A1V0EEV1	Caulobacter_phage	5.9e-69	46.4
WP_083231702.1\|170088_172194_-	ParB/RepB/Spo0J family partition protein	G8DH78	Emiliania_huxleyi_virus	5.8e-32	35.5
WP_083231703.1\|172549_173350_-	DUF3703 domain-containing protein	NA	NA	NA	NA
WP_069052228.1\|173346_173973_-	cation transporter	NA	NA	NA	NA
WP_069052203.1\|174056_174461_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_069052204.1\|174460_174811_+	DUF3147 family protein	NA	NA	NA	NA
WP_150126425.1\|174807_175152_+	YnfA family protein	A0A2H4JF35	uncultured_Caudovirales_phage	2.1e-24	58.3

DBSCAN-SWA_9

179194 : 180430

Leptospira_phage(100.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_069052210.1\|179194_180430_+	efflux RND transporter periplasmic adaptor subunit	S5VL44	Leptospira_phage	2.4e-06	29.0

DBSCAN-SWA_10

184222 : 185146

Bacillus_virus(100.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_069052213.1\|184222_185146_-	NAD(P)/FAD-dependent oxidoreductase	G3MA85	Bacillus_virus	2.7e-18	28.6

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_CP016460

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Crispr_ID: NZ_CP016460_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP016460_1

3673748-3673845

Orphan

Consensus_repeat	Method
GGCTCGGGTCACGGTCGCAGCGC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_CP016460_1

>merge|NZ_CP016460|1|3673748-3673845|CRISPRCasFinder
GGCTCGGGTCACGGTCGCAGCGCCAGGCACGGTCGCGCTCCGCCTGCTCCCGATCAAAGCGGGGGCACTCCCGTCGGCTCGGGTCGCGGTCGCAGCGC

>NZ_CP016460|1|1|3673748-3673845|CRISPRCasFinder
GGCTCGGGTCACGGTCGCAGCGC	CAGGCACGGTCGCGCTCCGCCTGCTCCCGATCAAAGCGGGGGCACTCCCGTC
GGCTCGGGTCGCGGTCGCAGCGC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP016460.1\|WP_069051407.1\|3670068_3670836_-\|type-I-methionyl-aminopeptidase	unknown	unknown	gnl\|CDD\|235576
NZ_CP016460.1\|WP_069051417.1\|3682033_3682936_+\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|187572
NZ_CP016460.1\|WP_069051412.1\|3676001_3676979_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226651
NZ_CP016460.1\|WP_069051414.1\|3677999_3678725_+\|SDR-family-oxidoreductase	unknown	unknown	gnl\|CDD\|226674
NZ_CP016460.1\|WP_069051410.1\|3674203_3675091_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176109
NZ_CP016460.1\|WP_069051416.1\|3681076_3681940_-\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|375319
NZ_CP016460.1\|WP_150126399.1\|3665652_3665799_+\|DUF4177-domain-containing-protein	unknown	unknown	unknown
NZ_CP016460.1\|WP_150126400.1\|3683154_3684420_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|273327
NZ_CP016460.1\|WP_069052020.1\|3668733_3669681_-\|CPBP-family-intramembrane-metalloprotease	unknown	unknown	gnl\|CDD\|376806
NZ_CP016460.1\|WP_069052019.1\|3667640_3668645_-\|alpha/beta-hydrolase	unknown	unknown	gnl\|CDD\|369561
NZ_CP016460.1\|WP_069051411.1\|3675212_3675854_+\|NAD(P)H-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|376808
NZ_CP016460.1\|WP_054133727.1\|3680093_3680996_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176163
NZ_CP016460.1\|WP_054133787.1\|3670837_3671047_-\|ParD-like-family-protein	unknown	unknown	gnl\|CDD\|314732
NZ_CP016460.1\|WP_069052021.1\|3671414_3672089_+\|response-regulator-transcription-factor	unknown	unknown	gnl\|CDD\|223816
NZ_CP016460.1\|WP_069051413.1\|3676986_3677856_-\|AraC-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|377694
NZ_CP016460.1\|WP_069051405.1\|3664849_3665260_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP016460.1\|WP_069051408.1\|3672085_3673441_+\|HAMP-domain-containing-histidine-kinase	unknown	unknown	gnl\|CDD\|223715
NZ_CP016460.1\|WP_117352102.1\|3665841_3666744_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176114
NZ_CP016460.1\|WP_069051415.1\|3678877_3679993_-\|aldo/keto-reductase	unknown	unknown	gnl\|CDD\|381306
NZ_CP016460.1\|WP_054133784.1\|3666967_3667381_+\|RidA-family-protein	unknown	unknown	gnl\|CDD\|100004

Protein	Function_ID	Function_description	E-value
NZ_CP016460.1\|WP_069051407.1\|3670068_3670836_-\|type-I-methionyl-aminopeptidase	gnl\|CDD\|235576	PRK05716, PRK05716, methionine aminopeptidase; Validated.	7.88228e-131
NZ_CP016460.1\|WP_069051412.1\|3676001_3676979_+\|hypothetical-protein	gnl\|CDD\|226651	COG4188, COG4188, Predicted dienelactone hydrolase [General function prediction only].	1.23552e-33
NZ_CP016460.1\|WP_069051410.1\|3674203_3675091_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|176109	cd08417, PBP2_Nitroaromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	6.4179e-48
NZ_CP016460.1\|WP_069051416.1\|3681076_3681940_-\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|375319	pfam17765, MLTR_LBD, MmyB-like transcription regulator ligand binding domain. This domain is found in a family of actinobacterial transcription factors. The structure shows it has a PAS domain like fold and it is bound to Myristic acid.	2.05548e-48
NZ_CP016460.1\|WP_069051414.1\|3677999_3678725_+\|SDR-family-oxidoreductase	gnl\|CDD\|226674	COG4221, COG4221, Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only].	6.82167e-96
NZ_CP016460.1\|WP_150126400.1\|3683154_3684420_-\|MFS-transporter	gnl\|CDD\|273327	TIGR00895, transport_protein, benzoate transport. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids].	1.84607e-87
NZ_CP016460.1\|WP_069052020.1\|3668733_3669681_-\|CPBP-family-intramembrane-metalloprotease	gnl\|CDD\|376806	pfam02517, Abi, CAAX protease self-immunity. Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide being removed by one of the CAAX prenyl proteases). The family contains the CAAX prenyl protease. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding. While they are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin. Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity.	1.26967e-09
NZ_CP016460.1\|WP_069052019.1\|3667640_3668645_-\|alpha/beta-hydrolase	gnl\|CDD\|369561	pfam07859, Abhydrolase_3, alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes.	1.63319e-49
NZ_CP016460.1\|WP_069051411.1\|3675212_3675854_+\|NAD(P)H-dependent-oxidoreductase	gnl\|CDD\|376808	pfam02525, Flavodoxin_2, Flavodoxin-like fold. This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.	3.67918e-36
NZ_CP016460.1\|WP_054133727.1\|3680093_3680996_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176163	cd08474, PBP2_CrgA_like_5, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	1.23488e-87
NZ_CP016460.1\|WP_054133787.1\|3670837_3671047_-\|ParD-like-family-protein	gnl\|CDD\|314732	pfam11903, ParD_like, ParD-like antitoxin of type II bacterial toxin-antitoxin system. ParD-like antitoxin is a family of archaeal and bacterial proteins of a type II bacterial toxin-antitoxin system. Many of the cognate toxins for these molecules fall into family ParE-like_toxin, pfam15781. Gene-pairs are expressed from the same operon, the toxin of the pair being expressed first, eg, for UniProtKB:Q3AQ93 and UniProtKB:Q3AQ94.	1.80124e-22
NZ_CP016460.1\|WP_069052021.1\|3671414_3672089_+\|response-regulator-transcription-factor	gnl\|CDD\|223816	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription].	1.3334e-66
NZ_CP016460.1\|WP_069051413.1\|3676986_3677856_-\|AraC-family-transcriptional-regulator	gnl\|CDD\|377694	pfam06719, AraC_N, AraC-type transcriptional regulator N-terminus. This family represents the N-terminus of bacterial ARAC-type transcriptional regulators. In E. coli, these regulate the L-arabinose operon through sensing the presence of arabinose, and when the sugar is present, transmitting this information from the arabinose-binding domains to the protein's DNA-binding domains. This family might represent the N-terminal arm of the protein, which binds to the C-terminal DNA binding domains to hold them in a state where the protein prefers to loop and remain non-activating. All family members contain the pfam00165 domain.	1.59794e-63
NZ_CP016460.1\|WP_069051417.1\|3682033_3682936_+\|SDR-family-oxidoreductase	gnl\|CDD\|187572	cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup contains atypical SDRs of unknown function. Members of this subgroup have a glycine-rich NAD(P)-binding motif consensus that matches the extended SDRs, TGXXGXXG, but lacks the characteristic active site residues of the SDRs. This subgroup has basic residues (HXXXR) in place of the active site motif YXXXK, these may have a catalytic role. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.	2.18003e-117
NZ_CP016460.1\|WP_069051408.1\|3672085_3673441_+\|HAMP-domain-containing-histidine-kinase	gnl\|CDD\|223715	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms].	2.94901e-48
NZ_CP016460.1\|WP_117352102.1\|3665841_3666744_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|176114	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	1.9971e-76
NZ_CP016460.1\|WP_069051415.1\|3678877_3679993_-\|aldo/keto-reductase	gnl\|CDD\|381306	cd19080, AKR_AKR9A_9B, AKR9A and AKR9B families of aldo-keto reductase (AKR). The AKR9A family includes Aspergillus nidulans sterigmatocystin biosynthesis dehydrogenase StcV, Aspergillus flavus norsolorinic acid reductase (NOR), and Phanerochaete chrysosporium aryl-alcohol dehydrogenase [NADP(+)] (AAD), are founding members of aldo-keto reductase family 9 member A1-3 (AKR9A1-3), respectively. StcV may be involved in the dehydration of 5'-hydroxyaverantin to form averufin. NOR is involved in aflatoxin biosynthesis. AAD (EC1.1.1.91) is involved in lignin degradation and reduces aromatic benzaldehydes to their respective alcohols in the presence of NADP(H). The AKR9B family includes Saccharomyces cerevisiae aryl-alcohol dehydrogenases AAD14p, AAD3p, AAD4p, and AAD10p, which are founding members of aldo-keto reductase family 9 member B1-4 (AKR9B1-4), respectively.	1.02838e-132
NZ_CP016460.1\|WP_054133784.1\|3666967_3667381_+\|RidA-family-protein	gnl\|CDD\|100004	cd00448, YjgF_YER057c_UK114_family, YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.	3.4121e-20

>NZ_CP016460.1|WP_069051408.1|3672085_3673441_+|HAMP-domain-containing-histidine-kinase
MTRPSSLRRPLIIYPLAVNFAILTISFAIIIAIAIRFDSGGPYTDEQIIPVIARAIERDENGQLTVEMTPELAQLRAETPQLWFLAEDDTGRSVSFGPVPRHYDSLIGRLSDLSFAQLRDRNPPYKLAAVVRRQTTDIGVLTILGHGALSDLNLTVILASNVIVLPIFVVLALTSLLVTPWIVRRSLAGVHRIAREAEAIDAHARGRSLSEDEVPREVAPLVSAFNAALRRLDEDHERQRRFLGLAAHELRTPVAVLRSKVESSENSETRSLAGDIQRLATLAEQLLDLQRMENDERCDRIDIAALIRNTVADLAPLMIASGKTVAVEVAANQPVLGDPAAIERVVMNLVQNAAQHGGQHIIVRVRDVGFEVEDDGPGIPPDERERIFEPFYRLRPSAAGSGLGLSLVKEVIARHDGRVDILDAPGGGAIVRVELRGRHSGQDTPEAKGRA
>NZ_CP016460.1|WP_069052021.1|3671414_3672089_+|response-regulator-transcription-factor
MRILLIEDEPRLAESVCAVLRKERFVVDHVDRLSTAKEASQMAGFDLALLDRKLPDGEGLSLVPALRARNPGIRIIVLSACGEIADRVAGLDEGADDYLVKPFAMDEMLARIRAVRRRPAELEGAEIRAGSVVFDLANEEVEVKGGRLDLPRRELRVLAALMKRRGRTVLRETLEQAVFGFDDEVQSNTLDSHISRLRKKLTKSGAEVEIHAIRGVGYLLREAA
>NZ_CP016460.1|WP_054133787.1|3670837_3671047_-|ParD-like-family-protein
MGIVKIDDALHEEVRRASAVMCRSINAQAEFWMKIGRLAEANPALSFNDIISRELASVQVSELDERAAA
>NZ_CP016460.1|WP_069051407.1|3670068_3670836_-|type-I-methionyl-aminopeptidase
MVKTPDELALMRISGRLLASVFEMLDGLDLTGMSTLEVNDLVERYITVDLASRPASKGQYGFAFVLNCSLNDVVCHGVPDANEIIRDGDIINLDITLEKNGYIADSSKTWVVGNASGAARRLVRIANEAMWAGIRQVRPGASLGDIGFAIERHAKRNRCSVVRDYCGHGIGREMHEEPQVLNFGRPDSGLRLREGMVFTIEPMINAGRRQVVTDSDGWTVRTSDGRLSAQFEHTVAVTADGVEVLTLREGEAALM
>NZ_CP016460.1|WP_069052020.1|3668733_3669681_-|CPBP-family-intramembrane-metalloprotease
MSGRGESWLTRPDKAVEASGVPEGVEYHRIYAGEGRRLIRGVAAIVLLLAGLIIFAQACLAMAAAIDTHILGRTGFTPVQFAAGAISLALLIPYSMLLQRWLYGVPARSLHSVAGCFRFGVFGRALLVFGPLVLVAMSVGPMVPDDRIPWSKGDLVAFFVIGMTLIPLAAAGEEYGVRGLMFRVIGSWTRRSLPGAILGIALTTVLFSLFHGTLDPYILGSYLVLFGAMATITWRTGGLEVAVVLHAVYNVSALVLATTLHLDVGGDLGSRGEIVGTPANLVPSAALAIITAGIWWTTRKSGPACTPEISSEQSE
>NZ_CP016460.1|WP_069052019.1|3667640_3668645_-|alpha/beta-hydrolase
MSKSRNAAEQPGVKVGERIIPVPASISPEAQERLRAAVGPDGTPLNALYAMPSANDPEAWRRMKHAADSHYAAAIRDRGQSGAVEVETTQIGCATVHIATPSEEAFDNCVYLDLHGGAFVFGSGEACRESARSQAIAHGMCCYGIDYRTPPDHPFPAALDDCLAVYESAVARYGAQKVVIGGRSAGGNLALATVLRAHDEGKAMPAGLVLLSPEIDLTESGDSFNVNSTVDVVLPNPLMPANLLYAHGADLAHPYLSPLFAEFFDGFPTTFIQSGTRDLFLSNAVRLHRSLRRSGISADLHVFEAMPHGGFGGTPEDAELLDEVVRFVRHSLRR
>NZ_CP016460.1|WP_054133784.1|3666967_3667381_+|RidA-family-protein
MTRPLVRLNPPALWDATGNHHSQGTLIETGRLAIFSGQIAAQKGTDHVPASLREQTDIVCRNLRLCLESIGASPSDIVSLRAYIVDWTPDKAAEVFEPLVAFLGDTMPAMTGIGVNALFSPELRIEIEMVARVPDQS
>NZ_CP016460.1|WP_117352102.1|3665841_3666744_-|LysR-family-transcriptional-regulator
MTARSLNEIVIFMAVADAGSFARGGRTMGLTGSAASKAVARLEARLGVRLLHRNSRAVSLTSEGERFRESGRAILEAMDEAEASIAVPDGKPRGLLRLSVPDAFGRRVIMPLVSEYLERWPDVRIDIDFSDRPVDLVEEGFDLAIRIGGESAPDGIVSRVVAEYPVWICAAPSYLERRGHPPHVEALSGHDCILFRSRTRTQEWFDHPGGEHADKVLAHGRLRMNSAEAIRMAALSGLGIALLPAFLVDDDLSAGHLVRLFPELGVQTVRILCLYPSRRLVDPRVRTFIDNVSAALTRVT
>NZ_CP016460.1|WP_150126399.1|3665652_3665799_+|DUF4177-domain-containing-protein
MQWEYKLVTETLNADQLNEFGADGWELVMVVSPAHYVFHYFFKRELRD
>NZ_CP016460.1|WP_069051405.1|3664849_3665260_-|hypothetical-protein
MKRSPKSRLGETLSGCLVAVLIGLGTVALTNADAIVASGDGTWGITRSVLAVHVVLVALPFIAISILPNAGRAAWLTAGILTAIVWSLPSLDQLVRKGEGGANIGLGIFMLISPLFILGGALAARAAARRRGRASG
>NZ_CP016460.1|WP_069051410.1|3674203_3675091_-|LysR-family-transcriptional-regulator
MNLRSVDMNLLVLLDVLLEEHHVGRAAERVGLSQPAMSAALQRCRHLFRDQLLERSRGTMRPTPKADSLRQPLKELLAAATTIIAPPVVPIDELKATLRLTMADLSALLVLEPLLADLALSAPGIDIVLQPWTGAAHARRALKDGSTDIAVSVFETGDDDLFCAPVTEEAYVVAMRDDHPAAHGFTLEKWMSFPHIVVSGRGDARTSLDSQLAARGLRRRIGVVVPTFGMVIPLLRCTPMIAMAPEKLVSRTPGLSVFRPPVAVPNISLSLAWHRRRESDPALRHVADRLAAHLY
>NZ_CP016460.1|WP_069051411.1|3675212_3675854_+|NAD(P)H-dependent-oxidoreductase
MHEDDEQTVTQILLFHPNIERSTANAALARAAAGLRHVEIADMAALYPAGIEMERDSEREAARLLRADRIVLQFPMQWYSTPALMKQWQDIVLTRMAYIYGDTEGAGLAGKPLMVAATMGAEESTYRPEGRNRFTVAELLAPLQASANRFAMDWRDPFLVFDADGLPADDLAEAGRAYGRALSRLAKAAFGAWPYGSSSDCHENGHAARASRA
>NZ_CP016460.1|WP_069051412.1|3676001_3676979_+|hypothetical-protein
MNNLIGLARLIPTPEATLAASFSPVSLAMPGRPQPLQLRVTAPVQGDALPIVLLSHGHGPSLYIPSKDGYGPIANFLAERGFVVIQPTHANSKVGGLPRDMSGAPLFWRERTEEMTAILDGLGAIETALPFLKGRLDHERIGAVGHSLGGHTVALLLGMRVTIEGAEIDLRELRIKAGVLLASPGAGGDNLSENGKSYGPAFSPDFAHLATRTLVVFGDMDVSPHLTVRGADWHADPYHLGPGADALLTIAGGRHGLGGIAGYDAKETDDEDPDRLELTCRMVWAYLRSALIEGDQAWNDASAAFAGPAGALGRLDRKAREAVSG
>NZ_CP016460.1|WP_069051413.1|3676986_3677856_-|AraC-family-transcriptional-regulator
MSDTPDLARIIARNTPQEGVFQTLVPGLSLIRADDPGMPMPTVYEPSLCIIAQGAKTVSLGAQTLHYDDAHCLVAGVDLALIGQVTAASPDHPYLCCKIDIDQTVLADLITADGNALPPGNPPPLAVHPIGPELLDASTRLLRLLDRPHSIPVLAPLVQREILYHLLIGPQGAMLRHAASGDCHLGQVSRAIGWIRHHSHEQLRIRDVAGAARMSISSLHHHFKRITGLTPLQFQKQLRLQAARQMMIAEGINAGSAGFAVGYDSPSQFSREYRRLFGAPPRADISGLN
>NZ_CP016460.1|WP_069051414.1|3677999_3678725_+|SDR-family-oxidoreductase
MAQLHNRTILITGASSGIGEATARELAQAGANLFLGARRTDRLAALSRELGDRIGWCALDVTDATSFDGFVDAAEERFGRVDALVNNAGVMPLSPLASVKRDEWKRMIDVNINGVLNGIASVLPRFTAQRDGHVVNVASIGAHMVLPTAAVYCGTKHAVRAITEGLRLEHDDIRATLISPGVVATELGHDISDPALAADLSEWRKKSLTPDAIARVVRFALEQPTGVDINEIIVRPTAAGM
>NZ_CP016460.1|WP_069051415.1|3678877_3679993_-|aldo/keto-reductase
MNLDTYRPLGHSGLLVSPLALGTMTFGTPRWGLDEAGSRAVMDSYTELGGNFIDTADVYAGGRSEEMVGAFIAERSIRNRTVISTKSGFATGRGYHAGGNGARHILASVDASLRRLGTDFIDLYWVHIWDGLTPADELLRTMTALVASGKIRYWGISNSPAWYVAQVATLAKMLGSAGPIGLQYFYSLVERGAESEHLPLARAAGMGLVPWSPLAYGLLTGKYDREVVEASPKREGGVPNTRAAEDTARLESDKRLDGDNPFGDTLFTERNWKIVDVVRDVAAKMDQTPARVALAWVVGTPGVASTLMGVSRPGQVTDNVLALALDLPAAHRAALDAVSGGDQAFLYTLFTPETRNQIVFGGADIQRDWLG
>NZ_CP016460.1|WP_054133727.1|3680093_3680996_+|LysR-family-transcriptional-regulator
MDRDRWSGLAIFAEIVDAGSFARAAERLGLSASALSHAMRSLETKLGVRLLDRTTRSLAPTLAGEALLASLRPAIASVTRALDDLDNARDTPAGRIRVSAHRVAAVYAILPRLTDFARNFPDIAVELVVDDGFVDIVAERFDCGVRHAQALQGDMISVRLGDPVPLVYVASPAYLDGQAAPTSPSDLDDHRCLCYRYTSSGVVHRWGFERDGRSFERTIRGDFTTNDIDVLRDAAVSGLGIACLPLPHAALQLAAGTLVEVLSGWAPTLPPNHLYYPSRRQATAAFRVFVDAMRADPADG
>NZ_CP016460.1|WP_069051416.1|3681076_3681940_-|helix-turn-helix-domain-containing-protein
MAIERTDEGSLGAYLKARRRRLNPAALGFSASRRRTPGLRREEVAQRANISATWYTWLEQGRGGAPSANVLDRVASALLLTEAEREHVFLMALGRLPDVRYKPAEGVTPRLQRVLDAMETTPAILRTMTWDVVAWNAAAAAVLTDYAALPPDRRNILRLIFLDAEARAAQVEWDDVARFVVAVFRAEVARAGATELAAPLVAELSRSSPEFAMMWETHDVRSHGDGVKMLRHPILGLVPLEYSAFAVDGRPDLSMITYHPTCPEDAAAISALVRTRTTSSEPGPWDE
>NZ_CP016460.1|WP_069051417.1|3682033_3682936_+|SDR-family-oxidoreductase
MRVFVTGATGFVGSAIVAELLGVGHQVVGLARSDKSAKALEAAGVEVRLGSLEDLSGLTEAASASDAVIHTAFGHDFTRFAESSAVDRHAIAALGEALSGSSRPLLATAGVAFLAPGRTAVESDTPPVDPGYPRQSEAAIAALAARGVRASLVRLPPSVHGPGDRGFVPMLADIARQKGVSAYIGEGNNRWTGVHRSDAARVYRLALEHCATERAYHAVAEASIPFRAIAEKVAAGLGLPIRSISADEAADHFGWFAPFAAMDTPASSERTRAVLGWQPDQVGLLTDLSSPGYFDGETTG
>NZ_CP016460.1|WP_150126400.1|3683154_3684420_-|MFS-transporter
MGRLQIAAIVLCVLLNALDGFDVLAISFASPGIAAEWGIDRAALGLVLSMELIGMAAGSIVLGSVADRIGRRPTTLICLVIMALGMAAATFAGTVEELSAYRLFTGLGIGGMLACTNAMVAEFANARARSLAVAIMAAGYPMGAILGGSFASQLLVDGDWRDVFTFGAVITAVFLPVTFLLLPESIGFLVHKRPAGALARVNAILSRMGHDQVDALPDPDPAAPKAGYRQMFAPGLAKTTVFLTLAYFCHIMTFYFILKWVPKIVVDMGYAASAAGGVLVWANVGGLIGALLLSALSWRFPIRNLVIGAMLLSFVTVTIFGQGQSDIAMLAAVAAAAGFCTNAGVVGLYALIAQAFPTPVRASGTGFVIGFGRGGAAVGPILAGFLFSIDLGLASVGLAMACGSLLAAAMLLWLPKPAPVR

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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

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

556141 : 616134

Acinetobacter_phage(18.75%)

integrase,portal,protease,head,tail,tRNA,holin

attL 586707:586725|attR 625644:625662

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_069049694.1\|556141_556819_+\|protease	rhomboid family intramembrane serine protease	NA	NA	NA	NA
WP_054133250.1\|556851_557076_-	DUF4170 domain-containing protein	NA	NA	NA	NA
WP_150126196.1\|557218_557587_-	hypothetical protein	NA	NA	NA	NA
WP_069049695.1\|557583_558066_-\|holin	phage holin family protein	NA	NA	NA	NA
WP_069049696.1\|558098_558689_-	hypothetical protein	NA	NA	NA	NA
WP_069049697.1\|558903_560178_+	phosphopyruvate hydratase	A0A1X9I5Z8	Streptococcus_phage	6.8e-145	60.7
WP_054133170.1\|560261_560573_+	septum formation initiator family protein	NA	NA	NA	NA
WP_069051676.1\|560823_561846_+	pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha	NA	NA	NA	NA
WP_069049698.1\|561845_563222_+	pyruvate dehydrogenase complex E1 component subunit beta	NA	NA	NA	NA
WP_069049699.1\|563256_564165_-	pilus assembly protein	NA	NA	NA	NA
WP_069049700.1\|564161_564758_-	pilus assembly protein	NA	NA	NA	NA
WP_083231294.1\|564757_566716_-	Tad domain-containing protein	NA	NA	NA	NA
WP_150126197.1\|566842_567505_+	hypothetical protein	NA	NA	NA	NA
WP_069049702.1\|567557_568007_+	hypothetical protein	NA	NA	NA	NA
WP_054133163.1\|568007_569378_-\|tRNA	methylenetetrahydrofolate--tRNA-(uracil(54)- C(5))-methyltransferase (FADH(2)-oxidizing) TrmFO	NA	NA	NA	NA
WP_069049703.1\|569488_570160_+	lysoplasmalogenase	NA	NA	NA	NA
WP_054133161.1\|570191_570419_+	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	NA	NA	NA	NA
WP_069049704.1\|570420_570807_+	type II toxin-antitoxin system death-on-curing family toxin	NA	NA	NA	NA
WP_069049705.1\|570810_573513_-	DNA gyrase subunit A	A0A172JHV7	Bacillus_phage	2.0e-85	28.5
WP_069049706.1\|573653_574349_-	SDR family NAD(P)-dependent oxidoreductase	Q56AQ6	Bacillus_thuringiensis_phage	1.5e-32	39.6
WP_069051678.1\|574345_575104_-	YaaA family protein	NA	NA	NA	NA
WP_069049707.1\|575356_576667_+	hypothetical protein	NA	NA	NA	NA
WP_054133156.1\|576742_577210_-	Lrp/AsnC family transcriptional regulator	NA	NA	NA	NA
WP_069049708.1\|577504_579445_+	HAMP domain-containing histidine kinase	NA	NA	NA	NA
WP_069049709.1\|579526_580516_+	WalW protein	NA	NA	NA	NA
WP_171900287.1\|580865_581345_+	endonuclease	NA	NA	NA	NA
WP_069051679.1\|582094_583192_+	cobalamin-independent methionine synthase II family protein	NA	NA	NA	NA
WP_069049711.1\|583330_586147_-	CHAT domain-containing protein	NA	NA	NA	NA
WP_054133150.1\|586317_587040_-	transcriptional repressor LexA	Q38089	Lactococcus_phage	2.4e-06	37.4
586707:586725	attL	NA	NA	NA	NA
WP_069049712.1\|587129_588332_-	molybdopterin molybdotransferase MoeA	NA	NA	NA	NA
WP_069049713.1\|588331_588802_-	cyclic pyranopterin monophosphate synthase MoaC	NA	NA	NA	NA
WP_069049714.1\|588801_589596_-	indole-3-glycerol phosphate synthase TrpC	A0A0P0IR83	Acinetobacter_phage	5.3e-55	50.4
WP_069049715.1\|589592_590594_-	anthranilate phosphoribosyltransferase	A0A0N7IRD9	Acinetobacter_phage	4.7e-40	33.4
WP_069049716.1\|590590_591211_-	aminodeoxychorismate/anthranilate synthase component II	A0A0P0IKJ1	Acinetobacter_phage	1.2e-49	52.1
WP_069049717.1\|591207_592731_-	chorismate-binding protein	NA	NA	NA	NA
WP_069049718.1\|592730_594674_-	peptidylprolyl isomerase	NA	NA	NA	NA
WP_083231295.1\|594862_595609_+	triose-phosphate isomerase	NA	NA	NA	NA
WP_054133142.1\|595734_596202_+	preprotein translocase subunit SecG	NA	NA	NA	NA
WP_054133141.1\|596303_597941_+	CTP synthase	A0A1J0FA14	Only_Syngen_Nebraska_virus	3.3e-152	50.6
WP_054133140.1\|598228_598912_+	Crp/Fnr family transcriptional regulator	NA	NA	NA	NA
WP_054133139.1\|599365_599851_-	Hsp20 family protein	M4QDX9	Cyanophage	4.0e-21	37.3
WP_069049719.1\|600410_601649_+	lipoprotein-releasing ABC transporter permease subunit	NA	NA	NA	NA
WP_054133137.1\|601641_602316_+	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	4.4e-34	37.7
WP_054133136.1\|602312_602789_+	glutathione peroxidase	NA	NA	NA	NA
WP_040370991.1\|602935_603274_+	hypothetical protein	NA	NA	NA	NA
WP_069049720.1\|603319_606805_+	DNA polymerase III subunit alpha	A0A1B1PA77	Streptomyces_phage	2.0e-178	38.1
WP_069049721.1\|606862_608485_+	long-chain fatty acid--CoA ligase	A0A2H4PQU7	Staphylococcus_phage	1.8e-20	23.8
WP_069049722.1\|608503_609283_-	SDR family oxidoreductase	NA	NA	NA	NA
WP_069051681.1\|609435_610299_-	methyltransferase domain-containing protein	NA	NA	NA	NA
WP_069049723.1\|610340_611090_+	ComF family protein	NA	NA	NA	NA
WP_054133131.1\|611165_611423_+	glutaredoxin 3	V9QKN6	Rhizobium_phage	9.5e-14	51.9
WP_069049724.1\|611430_612258_+	carbon-nitrogen hydrolase family protein	NA	NA	NA	NA
WP_069049725.1\|612254_612764_+	DUF1178 family protein	NA	NA	NA	NA
WP_069049726.1\|612937_614014_-\|integrase	tyrosine-type recombinase/integrase	A0A291AUF0	Sinorhizobium_phage	3.8e-48	38.8
WP_069049727.1\|614010_614193_-	hypothetical protein	NA	NA	NA	NA
WP_069049728.1\|614189_614453_-\|head,tail	phage gp6-like head-tail connector protein	NA	NA	NA	NA
WP_069049729.1\|614449_615598_-\|portal	phage portal protein	Q6JIM9	Burkholderia_virus	2.9e-46	35.5
WP_069049730.1\|615588_616134_-\|head,protease	HK97 family phage prohead protease	A0A2K9VGN9	Pontimonas_phage	2.0e-29	50.3
625644:625662	attR	NA	NA	NA	NA

DBSCAN-SWA_2

1064209 : 1073246

Pelagibacter_phage(16.67%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_082382284.1\|1064209_1065199_-	curlin	M1ICK2	Pelagibacter_phage	5.1e-47	45.1
WP_171900183.1\|1065201_1065609_-	hypothetical protein	NA	NA	NA	NA
WP_083231337.1\|1066544_1067636_+	lytic murein transglycosylase	NA	NA	NA	NA
WP_069050009.1\|1067662_1068778_+	septal ring lytic transglycosylase RlpA family protein	F5B3X9	Synechococcus_phage	1.7e-14	44.7
WP_054134917.1\|1068832_1069978_+	D-alanyl-D-alanine carboxypeptidase	B6DZZ7	Stx2-converting_phage	8.8e-51	39.1
WP_069050010.1\|1069982_1070615_+	dTMP kinase	Q2Z0N0	Pseudomonas_phage	1.1e-21	37.0
WP_083231338.1\|1070619_1071630_+	hypothetical protein	A0A1U9WR94	Streptococcus_virus	4.5e-06	28.9
WP_069050011.1\|1071683_1073246_+\|tRNA	methionine--tRNA ligase	A0A1V0SHR2	Klosneuvirus	1.7e-92	36.7

DBSCAN-SWA_3

2511384 : 2556403

Clostridium_phage(25.0%)

integrase,transposase

attL 2554960:2554974|attR 2564674:2564688

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_054135860.1\|2511384_2512527_+\|integrase	site-specific integrase	A0A077KET4	Ralstonia_phage	5.3e-72	41.0
WP_150126279.1\|2512722_2512947_+	excisionase family DNA-binding protein	NA	NA	NA	NA
WP_171900229.1\|2512933_2513557_+	crossover junction endodeoxyribonuclease RuvC	A0A2H4P7J7	Pseudomonas_phage	1.0e-13	34.6
WP_171900152.1\|2514030_2514642_-	hypothetical protein	NA	NA	NA	NA
WP_054135857.1\|2514616_2515798_-	ImmA/IrrE family metallo-endopeptidase	A0A0A7RTT7	Clostridium_phage	8.1e-07	22.7
WP_054135856.1\|2515794_2517171_-	7-cyano-7-deazaguanine synthase	NA	NA	NA	NA
WP_150126281.1\|2517170_2517740_-	hypothetical protein	NA	NA	NA	NA
WP_054135855.1\|2518038_2518497_-	response regulator	NA	NA	NA	NA
WP_150126282.1\|2518965_2519808_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_054135854.1\|2520247_2520901_-	Crp/Fnr family transcriptional regulator	NA	NA	NA	NA
WP_069050842.1\|2520978_2521890_-	SDR family oxidoreductase	NA	NA	NA	NA
WP_054135852.1\|2521948_2523454_-	NAD(P)/FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_054135884.1\|2523793_2524426_-\|integrase	tyrosine-type recombinase/integrase	A0A0A8WF93	Clostridium_phage	5.1e-08	29.1
WP_150126283.1\|2524697_2524934_+	hypothetical protein	NA	NA	NA	NA
WP_054135851.1\|2525086_2526097_+	rod shape-determining protein	NA	NA	NA	NA
WP_054135883.1\|2526251_2526632_+\|transposase	transposase	NA	NA	NA	NA
WP_054135850.1\|2526628_2526970_+	IS66 family insertion sequence element accessory protein TnpB	A0A0P0ZBY2	Stx2-converting_phage	1.1e-28	55.3
WP_054135849.1\|2527031_2528675_+\|transposase	IS66 family transposase	A0A0P0ZEB3	Stx2-converting_phage	1.7e-108	44.3
WP_150126284.1\|2528886_2529285_-	hypothetical protein	NA	NA	NA	NA
WP_069050843.1\|2529484_2530159_-	hypothetical protein	NA	NA	NA	NA
WP_054135847.1\|2530937_2531348_-	nucleoside diphosphate kinase regulator	NA	NA	NA	NA
WP_054135846.1\|2531613_2532273_-	HPP family protein	NA	NA	NA	NA
WP_082382406.1\|2533647_2534046_+	hydroxyisourate hydrolase	NA	NA	NA	NA
WP_082382405.1\|2534048_2534522_+	heme-binding protein	NA	NA	NA	NA
WP_069050844.1\|2534569_2535520_+	DMT family transporter	NA	NA	NA	NA
WP_054135843.1\|2535597_2536023_-	Rrf2 family transcriptional regulator	NA	NA	NA	NA
WP_054135842.1\|2536106_2536586_+	group III truncated hemoglobin	NA	NA	NA	NA
WP_054135841.1\|2536582_2536888_+	DUF1971 domain-containing protein	NA	NA	NA	NA
WP_069050845.1\|2536880_2537345_+	hypothetical protein	NA	NA	NA	NA
WP_054135839.1\|2537409_2537886_+	hypothetical protein	NA	NA	NA	NA
WP_082382402.1\|2538066_2538792_+	oxidase	NA	NA	NA	NA
WP_156318285.1\|2539097_2539262_+	hypothetical protein	A0A240F763	uncultured_virus	8.8e-05	56.5
WP_054136563.1\|2539528_2540371_-	hypothetical protein	NA	NA	NA	NA
WP_150126285.1\|2540397_2541156_-	hypothetical protein	NA	NA	NA	NA
WP_054135998.1\|2541608_2542388_-	NYN domain-containing protein	NA	NA	NA	NA
WP_069050846.1\|2543335_2544961_+	Kef family K(+) transporter	NA	NA	NA	NA
WP_150126286.1\|2545042_2545366_+	hypothetical protein	NA	NA	NA	NA
WP_069050848.1\|2545550_2546570_+\|transposase	IS110 family transposase	NA	NA	NA	NA
WP_069050849.1\|2547251_2548610_-	HAMP domain-containing histidine kinase	NA	NA	NA	NA
WP_054135463.1\|2548606_2549284_-	response regulator transcription factor	W8CYM9	Bacillus_phage	2.4e-27	32.4
WP_069051906.1\|2549507_2550383_+	NTP transferase domain-containing protein	NA	NA	NA	NA
WP_069050850.1\|2550427_2551087_+	HAD-IB family phosphatase	NA	NA	NA	NA
WP_082382359.1\|2551154_2552321_+	hypothetical protein	NA	NA	NA	NA
WP_171900230.1\|2552416_2553637_+	oligosaccharide flippase family protein	NA	NA	NA	NA
WP_054135468.1\|2553620_2554412_+	FkbM family methyltransferase	NA	NA	NA	NA
WP_171900231.1\|2554808_2555612_-	hypothetical protein	NA	NA	NA	NA
2554960:2554974	attL	NA	NA	NA	NA
WP_054135470.1\|2555608_2556403_-\|integrase	site-specific integrase	NA	NA	NA	NA
WP_054135470.1\|2555608_2556403_-\|integrase	site-specific integrase	NA	NA	NA	NA
2564674:2564688	attR	NA	NA	NA	NA

DBSCAN-SWA_4

3547902 : 3560443

Rhodococcus_phage(11.11%)

capsid,portal,protease,head,tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_069051328.1\|3547902_3548643_-	7-carboxy-7-deazaguanine synthase QueE	A0A2P1JXY9	Rhodococcus_phage	2.1e-21	33.5
WP_069051329.1\|3548757_3549597_-	hypothetical protein	NA	NA	NA	NA
WP_069051330.1\|3549909_3550296_+	hypothetical protein	NA	NA	NA	NA
WP_082382491.1\|3550352_3550886_+	MmcB family DNA repair protein	B2ZY91	Ralstonia_phage	8.1e-07	43.5
WP_069051331.1\|3551006_3551528_+	hypothetical protein	NA	NA	NA	NA
WP_069051332.1\|3551524_3552853_+	DNA-packaging protein	A0A1V0DY66	Dinoroseobacter_phage	3.4e-78	41.9
WP_069051333.1\|3552854_3553991_+\|portal	phage portal protein	W8ECU7	Geobacillus_phage	1.0e-51	34.3
WP_054136508.1\|3553990_3554299_+	hypothetical protein	K4I011	Acidithiobacillus_phage	2.6e-05	34.8
WP_054136507.1\|3554295_3554682_+\|head,protease	HK97 family phage prohead protease	A0A1W6JQG3	Corynebacterium_phage	3.2e-13	37.5
WP_069052008.1\|3554808_3555993_+\|capsid	phage major capsid protein	Q3HQT0	Burkholderia_phage	3.9e-70	40.7
WP_069051334.1\|3556130_3557303_+	hypothetical protein	A0A2I7RDR8	Vibrio_phage	5.9e-18	40.1
WP_171900269.1\|3557289_3557448_+	hypothetical protein	NA	NA	NA	NA
WP_054136505.1\|3557497_3557779_+	hypothetical protein	NA	NA	NA	NA
WP_054136504.1\|3557778_3558321_+\|head,tail	phage head-tail connector protein	NA	NA	NA	NA
WP_150126319.1\|3558317_3558542_+	hypothetical protein	NA	NA	NA	NA
WP_054136503.1\|3558538_3558931_+	DUF3168 domain-containing protein	NA	NA	NA	NA
WP_054136502.1\|3558947_3559355_+\|tail	phage tail protein	NA	NA	NA	NA
WP_069051335.1\|3559351_3559672_+	gene transfer agent family protein	NA	NA	NA	NA
WP_054136500.1\|3559668_3559887_+\|tail	phage tail assembly chaperone	NA	NA	NA	NA
WP_069051336.1\|3559879_3560443_+\|tail	tail tape measure protein	D6PEW0	uncultured_phage	2.0e-08	32.5

Anti-CRISPR protein detection

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

3. NZ_CP016461

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

0 : 36450

Bordetella_phage(20.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_150126402.1\|1760_2480_+	hypothetical protein	NA	NA	NA	NA
WP_083231681.1\|2511_3528_+	DUF4238 domain-containing protein	NA	NA	NA	NA
WP_083231682.1\|3973_5251_-	RNA-directed DNA polymerase	NA	NA	NA	NA
WP_069052058.1\|5445_6672_-	hypothetical protein	NA	NA	NA	NA
WP_069052059.1\|7289_8156_-	hypothetical protein	NA	NA	NA	NA
WP_150126403.1\|8143_8596_-	hypothetical protein	NA	NA	NA	NA
WP_069052060.1\|8601_11616_-	hypothetical protein	NA	NA	NA	NA
WP_171900309.1\|11949_12528_-	OmpA family protein	NA	NA	NA	NA
WP_069052062.1\|12860_13781_-	hypothetical protein	NA	NA	NA	NA
WP_150126404.1\|14389_15178_+	hypothetical protein	NA	NA	NA	NA
WP_069052064.1\|15183_15429_+	hypothetical protein	NA	NA	NA	NA
WP_171900306.1\|15485_17186_+	DUF2326 domain-containing protein	NA	NA	NA	NA
WP_069052066.1\|17523_18897_-	hypothetical protein	NA	NA	NA	NA
WP_171900307.1\|18893_21980_-	DEAD/DEAH box helicase	NA	NA	NA	NA
WP_083231686.1\|21996_22806_-	hypothetical protein	NA	NA	NA	NA
WP_069052068.1\|23318_24029_-	hypothetical protein	NA	NA	NA	NA
WP_069052069.1\|24038_26975_-	Ti-type conjugative transfer relaxase TraA	A0A291LA07	Bordetella_phage	3.3e-09	27.3
WP_069052070.1\|27149_27473_+	conjugal transfer protein TraD	NA	NA	NA	NA
WP_171900308.1\|27474_27711_+	conjugal transfer protein TraD	NA	NA	NA	NA
WP_069052072.1\|27729_27924_+	hypothetical protein	NA	NA	NA	NA
WP_069052073.1\|27930_28359_-	MucR family transcriptional regulator	NA	NA	NA	NA
WP_069052074.1\|28382_29306_-	HEPN domain-containing protein	NA	NA	NA	NA
WP_083231684.1\|29360_29609_-	sigma-70 region 4 domain-containing protein	NA	NA	NA	NA
WP_069052075.1\|29605_30514_-	DUF1738 domain-containing protein	A0A1V0EEV1	Caulobacter_phage	1.6e-50	39.8
WP_069052082.1\|30924_31128_+	AlpA family transcriptional regulator	A0A2H4J8C8	uncultured_Caudovirales_phage	1.4e-07	49.0
WP_069052076.1\|31683_34557_+	ATP-dependent helicase	A7KV33	Bacillus_phage	6.5e-34	27.1
WP_083231687.1\|34656_36450_+	site-specific DNA-methyltransferase	A0A222ZMD5	Mycobacterium_phage	2.1e-38	30.1

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_CP016462

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_CP016460

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_CP016461

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