CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
NC_011526	Coxiella burnetii CbuK_Q154 plasmid pQpRS_K_Q154, complete sequence	0 crisprs	NA	0	0	0	0
NC_011528	Coxiella burnetii CbuK_Q154, complete sequence	1 crisprs	cas3,DEDDh,cas8f,cas5f,cas6f	0	1	2	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_011528_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011528_1

565903-565984

Orphan

Consensus_repeat	Method
TCTTTCAGCTAAGCTTCGCCCTTCGG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_011528_1

>merge|NC_011528|1|565903-565984|CRISPRCasFinder
TCTTTCAGCTAAGCTTCGCCCTTCGGCGAGCCTTTTTCAAAACCTTTTTATTCGACTCTTTCAGCTAAGCTTCGTCCTTCGG

>NC_011528|1|1|565903-565984|CRISPRCasFinder
TCTTTCAGCTAAGCTTCGCCCTTCGG	CGAGCCTTTTTCAAAACCTTTTTATTCGAC
TCTTTCAGCTAAGCTTCGTCCTTCGG

Protein	Signature genes	Signature genes Name	Protein_function
NC_011528.1\|WP_005772880.1\|561498_562854_-\|Do-family-serine-endopeptidase	unknown	unknown	gnl\|CDD\|273938
NC_011528.1\|WP_005769000.1\|573008_574961_-\|acetoacetate--CoA-ligase	unknown	unknown	gnl\|CDD\|235134
NC_011528.1\|WP_005769023.1\|556102_557122_-\|IS110-like-element-IS1111A-family-transposase	unknown	unknown	gnl\|CDD\|226077
NC_011528.1\|WP_005768989.1\|579507_580149_+\|hypothetical-protein	unknown	unknown	unknown
NC_011528.1\|WP_005768315.1\|555833_556106_+\|hypothetical-protein	unknown	unknown	unknown
NC_011528.1\|WP_012570687.1\|567538_568165_+\|transcriptional-regulator	unknown	unknown	gnl\|CDD\|238045
NC_011528.1\|WP_005769011.1\|566332_566764_-\|Rpn-family-recombination-promoting-nuclease/putative-transposase	unknown	unknown	gnl\|CDD\|368098
NC_011528.1\|WP_005769012.1\|564787_565555_+\|outer-membrane-protein-assembly-factor-BamD	unknown	unknown	gnl\|CDD\|274513
NC_011528.1\|WP_005769002.1\|568185_568776_+\|hypothetical-protein	unknown	unknown	unknown
NC_011528.1\|WP_005768992.1\|578069_578510_+\|hypothetical-protein	unknown	unknown	unknown
NC_011528.1\|WP_005769009.1\|566845_567220_-\|response-regulator	unknown	unknown	gnl\|CDD\|381099
NC_011528.1\|WP_005769019.1\|560452_561499_-\|efflux-RND-transporter-periplasmic-adaptor-subunit	unknown	unknown	gnl\|CDD\|273776
NC_011528.1\|WP_005768993.1\|577217_578000_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176114
NC_011528.1\|WP_005769029.1\|553800_554820_-\|IS110-like-element-IS1111A-family-transposase	unknown	unknown	gnl\|CDD\|226077
NC_011528.1\|WP_012570686.1\|563693_564677_-\|23S-rRNA-pseudouridine(1911/1915/1917)-synthase-RluD	unknown	unknown	gnl\|CDD\|183020
NC_011528.1\|WP_010957785.1\|567435_567546_+\|hypothetical-protein	unknown	unknown	unknown
NC_011528.1\|WP_005769017.1\|563014_563722_-\|peptidoglycan-editing-factor-PgeF	unknown	unknown	gnl\|CDD\|182677
NC_011528.1\|WP_005769021.1\|557336_560405_-\|efflux-RND-transporter-permease-subunit	unknown	unknown	gnl\|CDD\|223911
NC_011528.1\|WP_005769027.1\|555171_555717_-\|DUF962-domain-containing-protein	unknown	unknown	gnl\|CDD\|226914
NC_011528.1\|WP_012570688.1\|575196_575652_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|225382

Protein	Function_ID	Function_description	E-value
NC_011528.1\|WP_005772880.1\|561498_562854_-\|Do-family-serine-endopeptidase	gnl\|CDD\|273938	TIGR02037, Probable_periplasmic_serine_protease_do/HhoA-like, periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides].	1.87707e-156
NC_011528.1\|WP_005769000.1\|573008_574961_-\|acetoacetate--CoA-ligase	gnl\|CDD\|235134	PRK03584, PRK03584, acetoacetate--CoA ligase.	0
NC_011528.1\|WP_005769023.1\|556102_557122_-\|IS110-like-element-IS1111A-family-transposase	gnl\|CDD\|226077	COG3547, COG3547, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	3.98804e-36
NC_011528.1\|WP_012570687.1\|567538_568165_+\|transcriptional-regulator	gnl\|CDD\|238045	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.	0.00233391
NC_011528.1\|WP_005769011.1\|566332_566764_-\|Rpn-family-recombination-promoting-nuclease/putative-transposase	gnl\|CDD\|368098	pfam04754, Transposase_31, Putative transposase, YhgA-like. This family of putative transposases includes the YhgA sequence from Escherichia coli and several prokaryotic homologs.	1.74956e-45
NC_011528.1\|WP_005769012.1\|564787_565555_+\|outer-membrane-protein-assembly-factor-BamD	gnl\|CDD\|274513	TIGR03302, OM_YfiO, outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795). [Protein fate, Protein and peptide secretion and trafficking].	1.06407e-91
NC_011528.1\|WP_005769009.1\|566845_567220_-\|response-regulator	gnl\|CDD\|381099	cd17546, REC_hyHK_CKI1_RcsC-like, phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators similar to Arabidopsis thaliana CKI1 and Escherichia coli RcsC. This family is composed of hybrid sensor histidine kinases/response regulators that are sensor histidine kinases (HKs) fused with a REC domain, similar to the sensor histidine kinase CKI1 from Arabidopsis thaliana, which is involved in multi-step phosphorelay (MSP) signaling that mediates responses to a variety of important stimuli in plants. MSP involves a signal being transferred from HKs via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. The CKI1 REC domain specifically interacts with the downstream signaling protein AHP2, AHP3 and AHP5. The plant MSP system has evolved from the prokaryotic two-component system (TCS), which allows organisms to sense and respond to changes in environmental conditions. This family also includes bacterial hybrid sensor HKs such as Escherichia coli RcsC, which is a component of the Rcs signalling pathway that controls a variety of physiological functions like capsule synthesis, cell division, and motility. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.	1.21636e-34
NC_011528.1\|WP_005769019.1\|560452_561499_-\|efflux-RND-transporter-periplasmic-adaptor-subunit	gnl\|CDD\|273776	TIGR01730, COG0845:_Membrane-fusion_protein, RND family efflux transporter, MFP subunit. This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed functions imply outward transport. These functions include nodulation, acriflavin resistance, heavy metal efflux, and multidrug resistance proteins. Most members of this family are found in Gram-negative bacteria. The proposed function of MFP proteins is to bring the inner and outer membranes together and enable transport to the outside of the outer membrane. Note, however, that a few members of this family are found in Gram-positive bacteria, where there is no outer membrane. [Transport and binding proteins, Unknown substrate].	6.30797e-72
NC_011528.1\|WP_005768993.1\|577217_578000_+\|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.	1.44189e-58
NC_011528.1\|WP_005769029.1\|553800_554820_-\|IS110-like-element-IS1111A-family-transposase	gnl\|CDD\|226077	COG3547, COG3547, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	1.54711e-36
NC_011528.1\|WP_012570686.1\|563693_564677_-\|23S-rRNA-pseudouridine(1911/1915/1917)-synthase-RluD	gnl\|CDD\|183020	PRK11180, rluD, 23S rRNA pseudouridine(1911/1915/1917) synthase RluD.	2.6959e-141
NC_011528.1\|WP_005769017.1\|563014_563722_-\|peptidoglycan-editing-factor-PgeF	gnl\|CDD\|182677	PRK10723, PRK10723, polyphenol oxidase.	3.34087e-105
NC_011528.1\|WP_005769021.1\|557336_560405_-\|efflux-RND-transporter-permease-subunit	gnl\|CDD\|223911	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms].	0
NC_011528.1\|WP_005769027.1\|555171_555717_-\|DUF962-domain-containing-protein	gnl\|CDD\|226914	COG4539, COG4539, Predicted membrane protein [Function unknown].	2.07081e-11
NC_011528.1\|WP_012570688.1\|575196_575652_-\|hypothetical-protein	gnl\|CDD\|225382	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair].	0.000133671

>NC_011528.1|WP_005769012.1|564787_565555_+|outer-membrane-protein-assembly-factor-BamD
MKKILFLATLLLILSGCVRKDVDPYQAYRGKTSAELFTSGERALAKKDYSEAVKNFEALDAIYPFGPHAEQAQLDIIYAYYKNNDTSSAIAAADRYIRLYPRGRNVDYAYYMRGVIGFDLGLSWLQKLARVSPVSRDVSTLQQSFTSFATLAEVFPHSRYTPDALTRMRYIRNLMAQREIMIAEFYMKRRAYVAAANRGSYVVQHFQGSPQVAKALAIMVQAYRALGLPKMADASNHLLQTNYPHTLEARKLRKA
>NC_011528.1|WP_012570686.1|563693_564677_-|23S-rRNA-pseudouridine(1911/1915/1917)-synthase-RluD
MSGPMCASRIELKKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHGATLQFSHPVDQRPMACHAPLPADMAHLLECLEDDYSQLARS
>NC_011528.1|WP_005769017.1|563014_563722_-|peptidoglycan-editing-factor-PgeF
MIIPNWPAPKRIKAVTTTRSDGNLALHVGDDAAQVQQNRLRLTENLQLPSPPVWLNQVHGSGVISLPLHYNAPPTADAAYCRQPNRVCAVLTADCLPVLITDKNGQEIAAVHAGWRGLAAGVLDQALTFFQADPRDLLIWLGPAIGPKAFEVGNEVRQAFLDRQRDYETAFVAHNGRWLANLYQLATINLNQLGVSHIYGGKFCTYQDKIHFYSYRREKGHTGRMATLVWIETET
>NC_011528.1|WP_005772880.1|561498_562854_-|Do-family-serine-endopeptidase
MKKLSKIILSSIFAGLPLLLPVSSYAHLPSAVEGKTIPSLAPMLNKTTPSVVNIAVEKLIPQTPNPLQPEMDQNTAPTKVLGVGSGVIIDAKKGYIVTNAHVVKDQKIMVVTLKDGRRYRAKVIGKDEGFDLAVIQIHANHLTALPIGNSDQLKVGDFVVAVGSPFGLTQTVTSGVISALNRQEPRIDNFQSFIQTDAPINPGNSGGALIDLEGKLIGINTAIVTPSAGNIGIGFAIPSDMVKSVAEQLIKYGKVERGMLGVTAQNITPELADALNLKHNKGALVTKVVAESPAAKAGVEVQDIIESVNGIRIHSSAQLHNMLGLVRPGTKIELTVLRDHKVLPIKTEVADPKKVLLQRELPFLGGMRMQKFNDLEPDGTILQGVLVTGVDDSSDGALGGLEPGDIIISANGQLTPTVDELMKIAEGKPKELLLKVARGAGQLFLVIQQSQ
>NC_011528.1|WP_005769019.1|560452_561499_-|efflux-RND-transporter-periplasmic-adaptor-subunit
MKKRTKIIITLGVVGCFIAAGLIFSHKKAQETPNRPPLLVKESPVEVADLPIIATATGTLVANNQTNISPKVAGYVTKIAFSPGDFVTAGSVLIQLDNQKQKNDLAAAKADVELSELQYQRDALALKKGLILQTTVYSDKVSLDKDKALAQTDQTALQDMTLRAPFSGYLGAKQFSLGDYVTPGQKLVTLVDQQKLKVVYDLPNHFAPQLQIGQPVTVTADFLPGQRFNGKVNYVAPYVNSDSQTIETQALLNNKNGALKPGQFVTVSQTLETLKKAILIPENSLFANMNGHYVFKVKNGKAISTPVKVGERLYGKVQIIDGLKPGNHIITTGQDQIYKSGAKVKVVH
>NC_011528.1|WP_005769021.1|557336_560405_-|efflux-RND-transporter-permease-subunit
MNISEICIKRPVLALVLSLVLVVVGIMGFNDLNTRFFPKFEQNVINISTAYPGASAKLVESSITTPLEEGISGVQGIDTIISQSFQGESDLKLTLDYGVNVYEVANQIRDKVEQARVQLPTNINAPVVQVGWGNMELMDVGFTAPNENPKAIRDYLERNVIDQIEQIPGIADVEVAGANQYAMRIWLDPQKMAARGLSVNDVQMAIQNSNVELPAGEIKGSSINYPITAETKLNTADQFNNIIVKNDNGQVIRIKDIGQAQLGDDSADQSIVTLDGQPGVLLSINNATDANPLDAAKNVNHFLNQIRPHLPNGMKIVPSFDIYAYMHGSIHEVYISIGIAILCVILVIFLFLGRLRTVAIPIATIPVCLIASFGAMYLLGFSINVITLLALVLSIGLVVDDAIVMLENIYRHIENGEKPLIAAIKGSKEITFPVIAMTITLAAVYAPIGLMQNQAANIFRSFAFTLAGAVLISGFVALTLSPMMCSRFLKAQGGEPKGYSRIIETIYERMAQGYQKILAAILNKRILVVFAAVLIAVGGFFLAKNIPMAFVPQEDMGFVIAAVSTSSGSSINTINRGLEQVASIFKQAPAVASVVTVADTNAKAFDSVFAMLKPFKDRKQSASQVADVINQKIKQIPGLNAAAFAPSFGGSMQHQLEFYLMGDTYSDLYAVSQKLINQLGNYPGLRVIQSNMRFDSQQYNMTVNRDIAGQLQVNIKDIDNTMAALYGGSKISTFDANGKTYNVYLQAQENDLHSLASINKFYVNNAQNKLIPLSNLISIKPILSQVVLPHYNRLRAAQMSAQLAPGYNLGTVVNYLQTELPQLLPANVKYAFTGQAHDLLTSNNSIGLIFLLAMVFIYLVLAAQFESFIDPFIILLAVPLSIVGAMASLKLIGGTLNIYTDIGLVTLIGLLSKHGILITQFANRLQKEGLAMREALLKAASIRLRPILMTTAAMVFGALPLLFSSGGSAQSRHQIGIVIIGGLIFGTFFSLVVVPVAYSYAYKFKLFLKRFKTTDEMSLSGK
>NC_011528.1|WP_005769023.1|556102_557122_-|IS110-like-element-IS1111A-family-transposase
MKDIKILGVDIAKDVFQLCGIDEWGKVIYTRRVKRAQYVSTVASLKVGCVVMEACGGANHWYRTFMGMGISTQLISPQHVKPYVKSNKNDRNDAQAIAEAASRASMRFVRGKTVEQQDVQALLKIRDRLVKSRTALINEIRGLLQEYGLTMARGAKRFYEELPLILASEAVGLTPRMKRVLNCLYTELLNRDEAIGDYEEELKAVAKANEDCQRVQSIPGVGYLTALSVYASVGDIHQFHRSRQLSAFIGLVPRQHSRGNKEVLLGISKRGNLMLRTLLIHGARALLRHVKNKTDKKSLWLKALIERRGMNRACVALANKNARIIWALLTRQETYRCGA
>NC_011528.1|WP_005768315.1|555833_556106_+|hypothetical-protein
MDPPLLSTISFDEKKAVAFVYPASRFKLATIGALMNYARLMLIGLSASQSPRMNQLNQPQVLPYFHQPSLFRTRLVCLLLLILFFTHGGV
>NC_011528.1|WP_005769027.1|555171_555717_-|DUF962-domain-containing-protein
MESLAKRLTEYRLYHTHRMNKILHYIGIPLIVLALLIALSWISLSVAVRWHISFAWIAVIALLIYYYFLDIKLALLMTVIMILVTLLCTWIAFPVPTAGSLILFLVLLIGGGALLFIGHTFETSKVDFSTYMKSIFIGPLYVVAELLLALNLGKQFGLQEHQPPTPPTPKPPPTSKTPPSL
>NC_011528.1|WP_005769029.1|553800_554820_-|IS110-like-element-IS1111A-family-transposase
MKDIKILGVDIAKDVFQLCGIDEWGKVIYTRRVKRAQYVSTVASLKVGCVVMEACGGANHWYRTFMGMGISTQLISPQHVKPYVKSNKNDRNDAQAIAEAASRASMRFVRGKTVEQQDVQALLKIRDRLVKSRTALINEIRGLLQEYGLTMARGAKRFYEELPLILASEAVGLTPRMKRVLNCLYTELLNRDEAIGDYEEELKAVAKANEDCQRVQSIPGVGYLTALSVYASVGDIHQFHRSRQLSAFIGLVPRQHSRGNKEVLLGISKRGNVMLRTLLIHGARALLRHVKNKTDKKSLWLKALIERRGMNRACVALANKNARIIWALLTRQETYRCGA
>NC_011528.1|WP_005769011.1|566332_566764_-|Rpn-family-recombination-promoting-nuclease/putative-transposase
MKKIHNPHDYYFRTAMSDTRVAKEFFEYHLPNNILKAADLNSLQLQKSSFIDEHLKASMADVLYSVKLNRRPGYFYIIVEHQRNPDKLMPYRLLRYILRIIDHHLKKKDYLPLPIVVPLVFYNGKKRYPFQRIFLLYLAKKSH
>NC_011528.1|WP_005769009.1|566845_567220_-|response-regulator
MITKKPIKKPLILLVEDNPFIQKIHVQLLKKLNCEVTLAIDGQSALALYSDKFDLIFLDINLSDMNGMEICKAIRQRTSSTSIIALTSESSKNKPRYFSTGINDFIKKPTTQAALKRVLNYWIQ
>NC_011528.1|WP_010957785.1|567435_567546_+|hypothetical-protein
MRFFLHLLKSGGDGYEAFEGRTLGQSKAGASGARND
>NC_011528.1|WP_012570687.1|567538_568165_+|transcriptional-regulator
MTKLSRREFAKKSGIANTTLQHWEDGEKHTLPEKSVRRFIKALLNLGVHCSYDWLMHGKGPAPQYAGHVIFQEETTDLPTHGARQKNEDEEIKEELTLFLSRNKNTVHLVVSDDAMEPRFVQGEVVAGVRVYGKEIEKLIGLDCIVLVQGGDLLLRTILKGDVEGYYHLGYTNPKTTASKPFLYNIELVNAAPVILARRNSHLYKSPK
>NC_011528.1|WP_005769002.1|568185_568776_+|hypothetical-protein
MDKGYHKTVGGIGGHILRRFIHLSMLIIPFLYYSYAKSRFNLFGLSYKSLLLVIIGLMLLFEIVRLKRGWLLWGQREREGKNFSSLAWTIVSLCLVLLLAPGKQYAIPIIWSCAIVDPLLGELRRTQLSRTWIVFIGIVVVMLIWGLASWWFKLDWLLVLLMGPLVVILEWPNFRWLDDNALVQLVPLLVILILYG
>NC_011528.1|WP_005769000.1|573008_574961_-|acetoacetate--CoA-ligase
MEASKPLWEPSSETRLQSQMSHFISDINKRFSLKIEGYPALYQWSLDQPALFWKAVWDFCGISASQAPTNVLVRGKRMEESQWFLGAKLNFAENLLRHRNQNVALIFTSETGFSRSITYAELYTEVAALAGFLRQCHVVPGDRVVGVLSNQIETVIAMLATASVGAIWSACSPDFGLEGLVDRFGQIKPKVLFAVDSHTYKGKTYHHLDKIRQLQQQLTSLTHTIIVPNHQKNIAINELKNASLYPDCLRATSLPFYFEALPFDHPVYILYSSGTTGKPKCMVHSAGGTLLQHLKELILHTDLRPSQRIFFYTTCSWMMWNWLMSSLAVGATVVLYDGAPFYPTPTALFDLIDKVGISIFGVGAKILESAEKFDLVPKKTHNLLSLKTILTTGSPLLPKSFDYVYNNVKSDIQLSSISGGSDIISCFALGNSLLPVYRGELQCIGLGMDVKIFNDDGDSVIEEKGELVCKSPFPSMPIYFWNDPEGKKYHQAYFDKYPNTWAHGDYAKTTKRGTLIIYGRSDTTLNPGGIRIGTAEIYQQVEKIKEILDCLVTSQQWKGDERIILFVVLQKETTLTDPLRKKIQTTIRQNLSPHHVPNKIIAVPDLPRTKSGKIVELAVKKIINGESVNNLTALENPKILEYFQNLKELG
>NC_011528.1|WP_012570688.1|575196_575652_-|hypothetical-protein
MPPCGIITHMFSNLSKKIFFLAAFLPLTYCLAQTSNGSTTSSNSQTIPFTFVNKLDRTIYFRANVNRDVAPSLGQVRPNSSYTFSLHKITSTIHPNGYEPVYIQGVDDGNSAYFSISIDRSKLEVHGQLAAKMNRCPRKCLGYKTPQELFI
>NC_011528.1|WP_005768993.1|577217_578000_+|LysR-family-transcriptional-regulator
MSHTIRLLEESLRTPLFVRDTRNIRLTEEGELLFSQCKRLKEELDAARNLVAGFNSSPSGTLRMSCNPYFAETHLFDLLQTYTQRFPKVKVELLVEERMPNMEREKIDIVFGINWPAPSDVVAKTIDKTRYVLCASPKYLNKFGIPKTVKALEQHRYIPHLGRSPENVIMNLKNKVTLNLTPQLKLNNAHLIKKCALNGLGIIQLHDYMVKEELANGSLVEVLKDHFQAEIPIYIYYQKHRFVQPKVRQFINLVNVHFSG
>NC_011528.1|WP_005768992.1|578069_578510_+|hypothetical-protein
MHKEKSRSFHYLVRGLLAVLAPLGFASGGTVVCNQTYAICTSASCVPIPGNTVKALCDCKVENGASLGNTSCAYRKPKLIAYALKQIISTYSFTETKINRVMTCSAGTPWANCLNAKCIVDRNAPSKAVCTCQIVASGSYVTYGGN
>NC_011528.1|WP_005768989.1|579507_580149_+|hypothetical-protein
MKIEALRKLAGKEEIDYPFILSALKEYARPRDKISGWLKSGELIRIKKGLYVFGKSVALQPYSKEVLANLVYGPSAISLTYALSYYGLIPERVDVVTSVTNNRIKSFSTSIGEFKYYYLHPKKYAVGIVLNSVSKEQSFLIGSPEKALCDQIHIIDKDYPLSSIKDMEKYLLGNLRMDAPLLFKFKLKNLKEIINVYNDPRLDLLYDIIKARK

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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
NC_011528_1	1.1\|565929\|30\|NC_011528\|CRISPRCasFinder	565929-565958	30	CP016198	Bacillus thuringiensis serovar coreanensis strain ST7 plasmid pST7-4, complete sequence	38385-38414	6	0.8
NC_011528_1	1.1\|565929\|30\|NC_011528\|CRISPRCasFinder	565929-565958	30	NC_006821	Bacillus thuringiensis sv darmstadiensis INTA 14-4 plasmid pBMBt1, complete sequence	224-253	6	0.8
NC_011528_1	1.1\|565929\|30\|NC_011528\|CRISPRCasFinder	565929-565958	30	NC_006821	Bacillus thuringiensis sv darmstadiensis INTA 14-4 plasmid pBMBt1, complete sequence	258-287	6	0.8
NC_011528_1	1.1\|565929\|30\|NC_011528\|CRISPRCasFinder	565929-565958	30	NC_029024	Bacillus phage 250, complete genome	8905-8934	7	0.767
NC_011528_1	1.1\|565929\|30\|NC_011528\|CRISPRCasFinder	565929-565958	30	NZ_CP053953	Bacillus cereus strain FDAARGOS_798 plasmid unnamed2, complete sequence	164485-164514	7	0.767
NC_011528_1	1.1\|565929\|30\|NC_011528\|CRISPRCasFinder	565929-565958	30	NZ_CP053950	Bacillus cereus strain FDAARGOS_799 plasmid unnamed2, complete sequence	58732-58761	7	0.767
NC_011528_1	1.1\|565929\|30\|NC_011528\|CRISPRCasFinder	565929-565958	30	CP008938	Candidatus Caedibacter acanthamoebae plasmid Plasmid_00002, complete sequence	52114-52143	9	0.7

1. spacer 1.1|565929|30|NC_011528|CRISPRCasFinder matches to CP016198 (Bacillus thuringiensis serovar coreanensis strain ST7 plasmid pST7-4, complete sequence) position: , mismatch: 6, identity: 0.8

cgagcctttttcaaaacctttttattcgac	CRISPR spacer
aatgcctttttcaatacctttttgttcggc	Protospacer
 . *********** ********.****.*

2. spacer 1.1|565929|30|NC_011528|CRISPRCasFinder matches to NC_006821 (Bacillus thuringiensis sv darmstadiensis INTA 14-4 plasmid pBMBt1, complete sequence) position: , mismatch: 6, identity: 0.8

cgagcctttttcaaaacctttttattcgac	CRISPR spacer
taatcctttttcaaaacctttttagttgag	Protospacer
..* ******************** *.**

3. spacer 1.1|565929|30|NC_011528|CRISPRCasFinder matches to NC_006821 (Bacillus thuringiensis sv darmstadiensis INTA 14-4 plasmid pBMBt1, complete sequence) position: , mismatch: 6, identity: 0.8

cgagcctttttcaaaacctttttattcgac	CRISPR spacer
gaaccctttttcaaaacctttttagttgag	Protospacer
 .* ******************** *.**

4. spacer 1.1|565929|30|NC_011528|CRISPRCasFinder matches to NC_029024 (Bacillus phage 250, complete genome) position: , mismatch: 7, identity: 0.767

cgagcctttttcaaaacctttttattcgac	CRISPR spacer
ttagcttttttcaaatcctttttattctgt	Protospacer
. ***.********* *********** ..

5. spacer 1.1|565929|30|NC_011528|CRISPRCasFinder matches to NZ_CP053953 (Bacillus cereus strain FDAARGOS_798 plasmid unnamed2, complete sequence) position: , mismatch: 7, identity: 0.767

cgagcctttttcaaaacctttttattcgac	CRISPR spacer
aatgcctttttcaatacctttttgttctgc	Protospacer
 . *********** ********.*** .*

6. spacer 1.1|565929|30|NC_011528|CRISPRCasFinder matches to NZ_CP053950 (Bacillus cereus strain FDAARGOS_799 plasmid unnamed2, complete sequence) position: , mismatch: 7, identity: 0.767

cgagcctttttcaaaacctttttattcgac	CRISPR spacer
aatgcctttttcaatacctttttgttctgc	Protospacer
 . *********** ********.*** .*

7. spacer 1.1|565929|30|NC_011528|CRISPRCasFinder matches to CP008938 (Candidatus Caedibacter acanthamoebae plasmid Plasmid_00002, complete sequence) position: , mismatch: 9, identity: 0.7

cgagcctttttcaaaacctttttattcgac	CRISPR spacer
acgacctttttctaaacctttttgttccca	Protospacer
  ..******** **********.***

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

436797 : 445723

uncultured_Mediterranean_phage(25.0%)

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_005771456.1\|436797_438117_+	polynucleotide adenylyltransferase PcnB	G3MAR3	Bacillus_virus	4.3e-25	35.0
WP_005771454.1\|438113_438674_+	2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase	S4VNV0	Pandoravirus	4.5e-16	39.2
WP_005771452.1\|438670_439150_+	pantetheine-phosphate adenylyltransferase	A0A1B1IVQ3	uncultured_Mediterranean_phage	3.1e-26	42.6
WP_005771450.1\|439164_439410_+	YfhL family 4Fe-4S dicluster ferredoxin	A0A1B1IWY9	uncultured_Mediterranean_phage	3.3e-16	51.1
WP_005771448.1\|439423_439636_-	50S ribosomal protein L33	NA	NA	NA	NA
WP_005771445.1\|439646_439886_-	50S ribosomal protein L28	NA	NA	NA	NA
WP_005771440.1\|439979_440654_-	DNA repair protein RadC	A0A1B2LRS6	Wolbachia_phage	2.4e-16	26.7
WP_010957483.1\|440929_441415_+	dUTP diphosphatase	Q2NP83	Xanthomonas_phage	2.5e-47	58.0
WP_005771434.1\|441392_442808_+	phosphomannomutase/phosphoglucomutase	A0A127AWJ1	Bacillus_phage	1.5e-52	29.9
WP_010957485.1\|444268_444916_-	orotate phosphoribosyltransferase	NA	NA	NA	NA
WP_005771423.1\|444943_445723_+	exodeoxyribonuclease III	E3T4M6	Cafeteria_roenbergensis_virus	1.6e-32	32.9

DBSCAN-SWA_2

1712944 : 1770762

Streptococcus_phage(23.08%)

tRNA,holin,transposase,protease

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_005771127.1\|1712944_1713964_-\|transposase	IS110 family transposase	M1NSC9	Streptococcus_phage	1.1e-09	25.9
WP_005772077.1\|1714182_1714902_+	hypothetical protein	NA	NA	NA	NA
WP_005772078.1\|1714936_1715731_-	thymidylate synthase	A6M9A2	Geobacillus_virus	1.7e-109	65.9
WP_005772079.1\|1715727_1716102_-	hypothetical protein	NA	NA	NA	NA
WP_005772080.1\|1716103_1716889_-	prolipoprotein diacylglyceryl transferase	NA	NA	NA	NA
WP_040953710.1\|1716943_1719217_-	phosphoenolpyruvate--protein phosphotransferase	A0A1V0SGR7	Hokovirus	9.1e-15	28.6
WP_005772082.1\|1719224_1719734_-	RNA pyrophosphohydrolase	NA	NA	NA	NA
WP_010958296.1\|1720111_1720213_+	hypothetical protein	NA	NA	NA	NA
WP_005772083.1\|1720234_1723060_+	ribonucleoside-diphosphate reductase subunit alpha	A0A2H4P767	Pseudomonas_phage	2.3e-177	43.6
WP_005772084.1\|1723109_1724315_+	ribonucleotide-diphosphate reductase subunit beta	A0A060BQZ3	Podovirus	7.9e-34	29.5
WP_005768315.1\|1725510_1725783_-	hypothetical protein	NA	NA	NA	NA
WP_005771875.1\|1725981_1727127_+\|transposase	ISAs1-like element ISCbu1 family transposase	NA	NA	NA	NA
WP_005772086.1\|1727236_1728940_+	Dot/Icm T4SS effector CoxCC11	NA	NA	NA	NA
WP_005772089.1\|1729326_1729602_+	FmdB family transcriptional regulator	NA	NA	NA	NA
WP_005772090.1\|1729598_1730228_+	DUF502 domain-containing protein	A0A2I7S9X1	Vibrio_phage	2.2e-11	25.4
WP_010958300.1\|1730396_1730489_+	hypothetical protein	NA	NA	NA	NA
WP_010958301.1\|1730537_1730663_+	hypothetical protein	NA	NA	NA	NA
WP_010958302.1\|1730745_1731534_+	hypothetical protein	NA	NA	NA	NA
WP_193333244.1\|1731530_1733057_-	hypothetical protein	NA	NA	NA	NA
WP_012570887.1\|1734171_1736004_+\|tRNA	aspartate--tRNA ligase	NA	NA	NA	NA
WP_005772098.1\|1736019_1736754_+	Dot/Icm type IV secretion system effector transcriptional regulator CvpC	NA	NA	NA	NA
WP_005772101.1\|1736869_1737388_+	crossover junction endodeoxyribonuclease RuvC	NA	NA	NA	NA
WP_005772102.1\|1737384_1737987_+	Holliday junction branch migration protein RuvA	NA	NA	NA	NA
WP_005772105.1\|1739840_1740896_+	Holliday junction branch migration DNA helicase RuvB	B3GAM6	uncultured_virus	1.0e-05	27.4
WP_005768315.1\|1740981_1741254_+	hypothetical protein	NA	NA	NA	NA
WP_005772106.1\|1741250_1742270_-\|transposase	IS110-like element IS1111A family transposase	M1NSC9	Streptococcus_phage	1.8e-10	26.4
WP_005772107.1\|1742457_1743693_+	MFS transporter	NA	NA	NA	NA
WP_005772108.1\|1743768_1744482_+	protein TolQ	NA	NA	NA	NA
WP_005772109.1\|1744459_1744903_+	protein TolR	NA	NA	NA	NA
WP_005768315.1\|1744939_1745212_+	hypothetical protein	NA	NA	NA	NA
WP_005771045.1\|1745208_1746228_-\|transposase	IS110-like element IS1111A family transposase	M1NSC9	Streptococcus_phage	3.0e-10	26.4
WP_005772110.1\|1746419_1748822_+	CBU_1576 family Dot/Icm T4SS effector	NA	NA	NA	NA
WP_005772111.1\|1748787_1749732_-	L,D-transpeptidase family protein	NA	NA	NA	NA
WP_005772112.1\|1749734_1750571_-	YihY family inner membrane protein	NA	NA	NA	NA
WP_005772113.1\|1750681_1751275_+	NAD(P)H:quinone oxidoreductase	NA	NA	NA	NA
WP_005772114.1\|1751271_1752369_+	cell division protein ZapE	NA	NA	NA	NA
WP_010958312.1\|1752779_1752902_+	hypothetical protein	NA	NA	NA	NA
WP_005772117.1\|1752942_1753323_-	monovalent cation/H(+) antiporter subunit G	NA	NA	NA	NA
WP_005772118.1\|1753315_1753618_-	sodium:proton antiporter	NA	NA	NA	NA
WP_005772119.1\|1753614_1753962_-	Na+/H+ antiporter subunit E	NA	NA	NA	NA
WP_005772120.1\|1753958_1755458_-	hypothetical protein	NA	NA	NA	NA
WP_005772121.1\|1755454_1755826_-	NADH-quinone oxidoreductase subunit K	NA	NA	NA	NA
WP_005772122.1\|1755822_1756230_-	Na+/H+ antiporter subunit B	NA	NA	NA	NA
WP_005772123.1\|1756226_1758533_-	putative monovalent cation/H+ antiporter subunit A	NA	NA	NA	NA
WP_005772124.1\|1758653_1758962_-\|holin	bacteriophage holin	NA	NA	NA	NA
WP_005772126.1\|1759050_1760304_+	sodium:proton antiporter	A0A2H4J178	uncultured_Caudovirales_phage	6.7e-36	39.0
WP_005768315.1\|1760432_1760705_+	hypothetical protein	NA	NA	NA	NA
WP_005772127.1\|1761932_1762157_+	30S ribosomal protein S21	NA	NA	NA	NA
WP_005772128.1\|1762184_1762634_+	CBU_1594 family Dot/Icm type IV secretion system effector	A0A2I7SAL1	Vibrio_phage	1.8e-07	31.6
WP_005772129.1\|1762731_1764393_+	DNA primase	A0A1S5RG58	Helicobacter_phage	4.1e-41	29.2
WP_005772130.1\|1764512_1766609_+	RNA polymerase sigma factor RpoD	A0A2I7SAT0	Vibrio_phage	1.1e-35	35.0
WP_010958323.1\|1766775_1766886_-	lipoprotein	NA	NA	NA	NA
WP_143433568.1\|1767884_1768019_+	hypothetical protein	NA	NA	NA	NA
WP_012570890.1\|1770276_1770762_+\|protease	ATP-dependent zinc protease	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