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
NZ_CP018005	Coxiella burnetii strain RSA439 chromosome, complete genome	1 crisprs	cas7f,cas3,DEDDh,cas8f	0	1	2	0
NZ_CP018006	Coxiella burnetii strain RSA439 plasmid pQpH1, complete sequence	0 crisprs	NA	0	0	0	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP018005_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP018005_1

676284-676365

Orphan

Consensus_repeat	Method
TTTTTGTTCGAGTCTTTCAGCTAAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_CP018005_1

>merge|NZ_CP018005|1|676284-676365|CRISPRCasFinder
TTTTTGTTCGAGTCTTTCAGCTAAGCTTCGTCCTTCGGCGAGGCCTTTTTCAAAGCCCTTTTTTTCGAGTCTTTCAGCTAAG

>NZ_CP018005|1|1|676284-676365|CRISPRCasFinder
TTTTTGTTCGAGTCTTTCAGCTAAG	CTTCGTCCTTCGGCGAGGCCTTTTTCAAAGCC
CTTTTTTTCGAGTCTTTCAGCTAAG

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP018005.1\|WP_010957776.1\|664057_665032_-\|KpsF/GutQ-family-sugar-phosphate-isomerase	unknown	unknown	gnl\|CDD\|182814
NZ_CP018005.1\|WP_010957778.1\|667449_667632_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP018005.1\|WP_005769002.1\|678522_679113_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP018005.1\|WP_012220489.1\|675180_675948_+\|outer-membrane-protein-assembly-factor-BamD	unknown	unknown	gnl\|CDD\|274513
NZ_CP018005.1\|WP_010957788.1\|685593_685725_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP018005.1\|WP_010957791.1\|688624_689890_+\|ATP-binding-protein	unknown	unknown	gnl\|CDD\|379306
NZ_CP018005.1\|WP_010957784.1\|677182_677557_-\|response-regulator	unknown	unknown	gnl\|CDD\|381099
NZ_CP018005.1\|WP_010957782.1\|674086_675070_-\|23S-rRNA-pseudouridine(1911/1915/1917)-synthase-RluD	unknown	unknown	gnl\|CDD\|183020
NZ_CP018005.1\|WP_010957790.1\|687771_688458_+\|GMP-synthase	unknown	unknown	gnl\|CDD\|181323
NZ_CP018005.1\|WP_010957777.1\|666477_667419_+\|alpha/beta-hydrolase	unknown	unknown	gnl\|CDD\|378924
NZ_CP018005.1\|WP_010957781.1\|673407_674046_-\|peptidoglycan-editing-factor-PgeF	unknown	unknown	gnl\|CDD\|182677
NZ_CP018005.1\|WP_010957786.1\|677875_678502_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|238045
NZ_CP018005.1\|WP_010957780.1\|670845_671892_-\|efflux-RND-transporter-periplasmic-adaptor-subunit	unknown	unknown	gnl\|CDD\|273776
NZ_CP018005.1\|WP_010957785.1\|677772_677883_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP018005.1\|WP_010957779.1\|667729_670798_-\|efflux-RND-transporter-permease-subunit	unknown	unknown	gnl\|CDD\|223911
NZ_CP018005.1\|WP_005769011.1\|676669_677101_-\|Rpn-family-recombination-promoting-nuclease/putative-transposase	unknown	unknown	gnl\|CDD\|368098
NZ_CP018005.1\|WP_040948120.1\|686136_687672_+\|MFS-transporter	unknown	unknown	gnl\|CDD\|129794
NZ_CP018005.1\|WP_005771755.1\|665182_666487_+\|UDP-N-acetylglucosamine-1-carboxyvinyltransferase	unknown	unknown	gnl\|CDD\|236486
NZ_CP018005.1\|WP_005772880.1\|671891_673247_-\|Do-family-serine-endopeptidase	unknown	unknown	gnl\|CDD\|273938
NZ_CP018005.1\|WP_040948119.1\|683343_685296_-\|acetoacetate--CoA-ligase	unknown	unknown	gnl\|CDD\|235134

Protein	Function_ID	Function_description	E-value
NZ_CP018005.1\|WP_010957776.1\|664057_665032_-\|KpsF/GutQ-family-sugar-phosphate-isomerase	gnl\|CDD\|182814	PRK10892, PRK10892, arabinose-5-phosphate isomerase KdsD.	1.38298e-151
NZ_CP018005.1\|WP_012220489.1\|675180_675948_+\|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].	5.87353e-92
NZ_CP018005.1\|WP_010957791.1\|688624_689890_+\|ATP-binding-protein	gnl\|CDD\|379306	pfam13635, DUF4143, Domain of unknown function (DUF4143). This domain is almost always found C-terminal to an ATPase core family.	4.00098e-54
NZ_CP018005.1\|WP_010957784.1\|677182_677557_-\|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.	2.67703e-36
NZ_CP018005.1\|WP_010957782.1\|674086_675070_-\|23S-rRNA-pseudouridine(1911/1915/1917)-synthase-RluD	gnl\|CDD\|183020	PRK11180, rluD, 23S rRNA pseudouridine(1911/1915/1917) synthase RluD.	3.7604e-142
NZ_CP018005.1\|WP_010957790.1\|687771_688458_+\|GMP-synthase	gnl\|CDD\|181323	PRK08250, PRK08250, glutamine amidotransferase; Provisional.	2.12126e-89
NZ_CP018005.1\|WP_010957777.1\|666477_667419_+\|alpha/beta-hydrolase	gnl\|CDD\|378924	pfam12697, Abhydrolase_6, Alpha/beta hydrolase family. This family contains alpha/beta hydrolase enzymes of diverse specificity.	6.77286e-05
NZ_CP018005.1\|WP_010957781.1\|673407_674046_-\|peptidoglycan-editing-factor-PgeF	gnl\|CDD\|182677	PRK10723, PRK10723, polyphenol oxidase.	2.28366e-92
NZ_CP018005.1\|WP_010957786.1\|677875_678502_+\|helix-turn-helix-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.	0.00197757
NZ_CP018005.1\|WP_010957780.1\|670845_671892_-\|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].	8.45082e-73
NZ_CP018005.1\|WP_040948119.1\|683343_685296_-\|acetoacetate--CoA-ligase	gnl\|CDD\|235134	PRK03584, PRK03584, acetoacetate--CoA ligase.	0
NZ_CP018005.1\|WP_010957779.1\|667729_670798_-\|efflux-RND-transporter-permease-subunit	gnl\|CDD\|223911	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms].	0
NZ_CP018005.1\|WP_005769011.1\|676669_677101_-\|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
NZ_CP018005.1\|WP_040948120.1\|686136_687672_+\|MFS-transporter	gnl\|CDD\|129794	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Other].	4.41872e-42
NZ_CP018005.1\|WP_005771755.1\|665182_666487_+\|UDP-N-acetylglucosamine-1-carboxyvinyltransferase	gnl\|CDD\|236486	PRK09369, PRK09369, UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated.	0
NZ_CP018005.1\|WP_005772880.1\|671891_673247_-\|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

>NZ_CP018005.1|WP_012220489.1|675180_675948_+|outer-membrane-protein-assembly-factor-BamD
MKKILFLATLLLILSGCVRKDVDPYQAYRGKTSAELFTSGERALAKKDYSEAVKNFEALDAIYPFGPHAEQAQLDIIYAYYKNNDTSSAIAAADRYIRLYPRGRNVDYAYYMRGVISFDLGLSWLQKLARVSPVSRDVSTLQQSFTSFATLAEVFPHSRYTPDALTRMRYIRNLMAQREIMIAEFYMKRRAYVAAANRGSYVVQHFQGSPQVAKALAIMVQAYRALGLPKMADASNHLLQTNYPHTLEARKLRKA
>NZ_CP018005.1|WP_010957782.1|674086_675070_-|23S-rRNA-pseudouridine(1911/1915/1917)-synthase-RluD
MSGPMCASRIELKKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQFSHPVDQRPMACHAPLPADMAHLLECLEDDYSQLARS
>NZ_CP018005.1|WP_010957781.1|673407_674046_-|peptidoglycan-editing-factor-PgeF
MALHVGDDAAQVQQNRLRLTENLQLPSPPVWLNQVHGSGVISLPLHYNAPPTADAAYCRQPNRVCAVLTADCLPVLITDKNGQEIAAVHAGWRGLAAGVLDQALTFFQADPRDLLIWLGPAIGPKAFEVGNEVRQAFLDRQRDYETAFVAHNGRWLANLYQLATINLNQLGVSHIYGGKFCTYQDKIHFYFYRREKGHTGRMATLVWIETET
>NZ_CP018005.1|WP_005772880.1|671891_673247_-|Do-family-serine-endopeptidase
MKKLSKIILSSIFAGLPLLLPVSSYAHLPSAVEGKTIPSLAPMLNKTTPSVVNIAVEKLIPQTPNPLQPEMDQNTAPTKVLGVGSGVIIDAKKGYIVTNAHVVKDQKIMVVTLKDGRRYRAKVIGKDEGFDLAVIQIHANHLTALPIGNSDQLKVGDFVVAVGSPFGLTQTVTSGVISALNRQEPRIDNFQSFIQTDAPINPGNSGGALIDLEGKLIGINTAIVTPSAGNIGIGFAIPSDMVKSVAEQLIKYGKVERGMLGVTAQNITPELADALNLKHNKGALVTKVVAESPAAKAGVEVQDIIESVNGIRIHSSAQLHNMLGLVRPGTKIELTVLRDHKVLPIKTEVADPKKVLLQRELPFLGGMRMQKFNDLEPDGTILQGVLVTGVDDSSDGALGGLEPGDIIISANGQLTPTVDELMKIAEGKPKELLLKVARGAGQLFLVIQQSQ
>NZ_CP018005.1|WP_010957780.1|670845_671892_-|efflux-RND-transporter-periplasmic-adaptor-subunit
MKKRTKIIITLGVVGCFIAAGLIFSHKKAQATPNRPPLLVKESPVEVADLPIIATATGTLVANNQTNISPKVAGYVTKIAFSPGDFVTAGSVLIQLDNQKQKNDLAAAKADVELSELQYQRDALALKKGLILQTTVYSDKVSLDKDKALAQTDQTALQDMTLRAPFSGYLGAKQFSLGDYVTPGQKLVTLVDQQKLKVVYDLPNHFAPQLQIGQPVTVTADFLPGQRFNGKVNYVAPYVNSDSQTIETQALLNNKNGALKPGQFVTVSQTLETLKKAILIPENSLFANMNGHYVFKVKNGKAISTPVKVGERLYGKVQIIDGLKPGDHIITTGQDQIYKSGAKVKVVH
>NZ_CP018005.1|WP_010957779.1|667729_670798_-|efflux-RND-transporter-permease-subunit
MNISEICIKRPVLALVLSLVLVVVGIMGFNDLNTRFFPKFEQNVINISTAYPSASAKLVESSITTPLEEGISGVQGIDTIISQSFQGESDIKLTLDYGVNVYEVANQIRDKVEQARVQLPTNINAPVVQVGWGNMELMDVGFTAPNENPKAIRDYLERNVIDQIEQIPGIADVEVAGANQYAMRIWLDPQKMAARGLSVNDVQMAIQNSNVELPAGEIKGSSINYPITAETKLNTADQFNNIIVKNDNGQVIRIKDIGQAQLDDDSADQSIVTLDGQPGVLLSINNATDANPLDAAKNVNHFLNQIRPHLPNGMKIVPSFDISAYMHGSIHEVYISIGIAILCVILVIFLFLGRLRTVAIPIATIPVCLIASFGAMYLLGFSINVITLLALVLSIGLVVDDAIVMLENIYRHIENGEKPLIAAIKGSKEITFPVIAMTITLAAVYAPIGLMQNQAANIFRSFAFTLAGAVLISGFVALSLSPMMCSRFLKAQGGEPKGYSRIIETIYERMAQGYQKILAAILNKRILVVFAAVLIAVGGFFLAKNIPMAFVPQEDMGFVIAAVSTSSGSSINTINRGLEQVASIFKQAPAVASVVTVADTNAKAFDSVFAMLKPFKDRKQSASQVADVINQKIKQIPGLNAAAFAPSFGGSMQHQLEFYLMGDTYSDLYAVSQKLINQLGNYPGLRVIQSNMRFDSQQYNMTVNRDIAGQLQANIKDIDNTMAALYGGSKISTFDANGKTYNVYLQAQENDLHSLASINKFYVNNAQNKLIPLSNLISIKPILSQVVLPHYNHLRAAQMSAQLAPGYNLGTVVNYLQTELPQLLPANVKYAFTGQAHDLLTSNNSMGLIFLLAMVFIYLVLAAQFESFIDPFIILLAVPLSIVGAMASLKLIGGTLNIYTDIGLVTLIGLVSKHGILITQFANRLQKEGLAMREALLKAASIRLRPILMTTAAMVFGALPLLFSSGGSAQSRHQIGIVIIGGLIFGTFFSLVVVPVAYSYAYKFKLFLKRFKTTDEMSLSGK
>NZ_CP018005.1|WP_010957778.1|667449_667632_+|hypothetical-protein
MNLIPAKAPRRQPGAIESVGFQQVARMSEAKYGKTMMSSIVPVFRFAHTGYVPLALFLAF
>NZ_CP018005.1|WP_010957777.1|666477_667419_+|alpha/beta-hydrolase
MVVNLMSRTVKVGIVLLAAFFLLLFIFLLIGHLLDKEAERVVNQLYGRNEKGIIKGMEPIQHVHSHLSALIIIHGYLGSPDIFRDLADNKKINAKVDVYVPLLPYEGRNLETVSKYNNKLTSDYLKTYINKLSPHYKHVVILAYSYGGALLINLARENQLPKNSQIILYAPAVFVKGNGFRLNVLLRTYSLWRKYCNYAAIGCEFPGKNIADETATVYIENMKSLRYIATPAVKEIFKLDDNNRAFFKKMCPSFSVIIAKDDSLISYEQLNEACRENHCCKIYTYPSGNHLLHVGKFKEDFTHLITKLINQKI
>NZ_CP018005.1|WP_005771755.1|665182_666487_+|UDP-N-acetylglucosamine-1-carboxyvinyltransferase
MDKLIIVGGVPLNGSIRISGAKNAVLPILAATLLIEEPVILSNIPHLNDVTTMIELLGRMGAQITIDERMSIEVDCSQIQNVHASYELVKTMRASILVLGPLLSRFGKAEVSLPGGCAIGSRPVDVHIDGMRALGADIELVDGFIHATVEGRLKGAELNLGKITVTGTENLIMAATLAEGQTIIHNAACEPEVQDLANFLNKMGARISGAGTDTIVIDGVDRLSGGSYSILPDRIEAGTYLVAAAMTRGHVRIRDVFPKTLGAVLEKLHEAGARVKIGENWVDLDMQGRRAKAVDIVTAPYPEMPTDMQAQFMALNVVAEGQAVITETVFENRFMHVHELQRMGADIKLQGSKALIRGKEKLTGAPVMATDLRASAGLVLAGLMARGNTIVDRIYHIDRGYECIEEKLAQLGAEIRRVSSHVYAARYAAQKRWL
>NZ_CP018005.1|WP_010957776.1|664057_665032_-|KpsF/GutQ-family-sugar-phosphate-isomerase
MSNNENFYTLGKAVIATELRAIQSLHARIDEKFVTACNTLFNCKGRVVVLGVGKSGHIAKKIAATLASTGTPSFYVHPSEASHGDMGMVTPQDVALAISYSGETPEIINLLPTLKRLGVALIALTGKMQSTLARIADTVIDVSVEQEACPLGLAPTSSTTATLVMGDALAIALLEARGFTADDFARIHPGGSLGRRLLLHIADLMHPKDKMPIVKPDCLLDEALVEITKKSLGMTTVVSDSGQLLGVFTDGDLRRTLDKGYDIHRTPIEKVMTKNSITVPPKLLAAEALKMMQQNKITSLVVVDTDASPVGVIHMHDLLRAGVS
>NZ_CP018005.1|WP_005769011.1|676669_677101_-|Rpn-family-recombination-promoting-nuclease/putative-transposase
MKKIHNPHDYYFRTAMSDTRVAKEFFEYHLPNNILKAADLNSLQLQKSSFIDEHLKASMADVLYSVKLNRRPGYFYIIVEHQRNPDKLMPYRLLRYILRIIDHHLKKKDYLPLPIVVPLVFYNGKKRYPFQRIFLLYLAKKSH
>NZ_CP018005.1|WP_010957784.1|677182_677557_-|response-regulator
MITKKPIKKPLILLVEDNPFIQKIHVQLLKKLNCEVTLAIDGQSALALYSDKFDLIFLDINLSDMNGMEVCKAIRQRTSSTPIIALTSESSKNKPRYFSTGINDFIKKPTTQAALKRVLNYWIQ
>NZ_CP018005.1|WP_010957785.1|677772_677883_+|hypothetical-protein
MRFFLHLLKSGGDGYEAFEGRTLGQSKAGASGARND
>NZ_CP018005.1|WP_010957786.1|677875_678502_+|helix-turn-helix-transcriptional-regulator
MTKLSRREFAKKSGIANTTLQHWEDGEKHTLPEKSVRRFIKALLNLGVHCSYDWLMHGKGPAPQYAGHVIFQEETTDLPTHGARQKNEDEEIKEELTLFLSRNKNTVHLVVSDDAMEPRFVQGEVVAGVRVYGKEIEKLIGLDCIVLVQGGDLLLRTILKGDVEGYYHLGYTNPKTTASKPFLYNIELVNAAPVIWARRNSHLYKSPK
>NZ_CP018005.1|WP_005769002.1|678522_679113_+|hypothetical-protein
MDKGYHKTVGGIGGHILRRFIHLSMLIIPFLYYSYAKSRFNLFGLSYKSLLLVIIGLMLLFEIVRLKRGWLLWGQREREGKNFSSLAWTIVSLCLVLLLAPGKQYAIPIIWSCAIVDPLLGELRRTQLSRTWIVFIGIVVVMLIWGLASWWFKLDWLLVLLMGPLVVILEWPNFRWLDDNALVQLVPLLVILILYG
>NZ_CP018005.1|WP_040948119.1|683343_685296_-|acetoacetate--CoA-ligase
MEASKPLWEPSSETRLQSQMSHFISDINKRFSLKIEGYPALYQWSIDQPALFWKAVWDFCGISASQAPTNVLVRGKRMEESQWFLGAKLNFAENLLRHRNQNVALIFTSETGFSRSITYAELYTEVAALAGFLRQCHVVPGDRVVGVLSNQIETVIAMLATASVGAIWSACSPDFGLEGLVDRFGQIKPKVLFAVDSHTYKGKTYHHLDKIRQLQQQLTSLTHTIIVPNHQKNIAINELKNASLYPDCLRATSLPFYFEELPFDHPVYILYSSGTTGKPKCMVHSAGGTLLQHLKELILHTDLRPSQRIFFYTTCSWMMWNWLMSSLAVGATVVLYDGAPFYPTPTALFDLIDKVGISIFGVGAKILESAEKFDLVPKKTHNLLSLKTILTTGSPLLPKSFDYVYNNVKSDIQLSSISGGSDIISCFALGNSLLPVYRGELQCIGLGMDVKIFNDDGDSVIEEKGELVCKSPFPSMPIYFWNDPEGKKYHQAYFDKYPNTWAHGDYAKTTKRGTLIIYGRSDTTLNPGGIRIGTAEIYQQVEKIKEILDCLVTSQQWKGDERIILFVVLQKETTLTDPLRKKIQTTIRQNLSPHHVPNKIIAVPDLPRTKSGKIVELAVKKIINGESVNNLTALENPKILEYFQNLKELG
>NZ_CP018005.1|WP_010957788.1|685593_685725_+|hypothetical-protein
MLLVDQALLQQAILLGWTSELPIIVKMNDLPKEKQPHSADPDF
>NZ_CP018005.1|WP_040948120.1|686136_687672_+|MFS-transporter
MFSYFLAKGSFNHVYKERYSESYYHAIAEKDKIFKITLVISAFLSMIFLDQTAVGVTLASIQKELVLSASTIAWIMNAYMITLSAFLLLFARLSDSIGIKNLFCAGILIFLLASLGCAVSNSGAGLIINRGLQGIGASMEYATYLLIFNNQVPANKRGKVLGKSAAFAAVFLALAPLIGGFFSNVISWRYLFWLNVPICLVCFYFAISACNKDSHPVNHAFLDKLGLLIYLFAMTGLIFFLMEGPTLGWTNPAILISLISSLLFFTLFVYHEKRQRQPLIEMALFKNKEFFASVLILFGNYACITTMAFWALWIEQVLGYSPLMTGVALLPAGVPFGIIIDGSHTGFKTSMDALNLTTKPFVFSHSGVYCLAPHVRNVRDEQIKSVAATGGVIGVNGLGILLGDVNASIGKYVDHIDYITKLVGAQHVAIGLDNLYFANQFSEFMSQQGITHPQAYASKVNNATLWRCLQPENVIEVVEMLLQRGYSENEIKGILGGNILRIMGYFSSCSN
>NZ_CP018005.1|WP_010957790.1|687771_688458_+|GMP-synthase
MKIHYIMHAPFEKLSAIEVWATQKSYDLSGTHVYKGEKLPRALNFDCLILMGGPQSPFKTDKYPYLLDEIQFVKKALAGNKKILGICLGAQLIAEALGAKTLHSPYKEIGIYPIQTLPEATDDPFFSKLPKSFDVMHWHNDMPGIPKDVVLLAKGEGCPHQAFRYGDRVYGFQFHMELTLSVIEEMIEKYRGDLEPGKFVRTKEEMLHSNYNEVNAKMFTFLDYLEGV
>NZ_CP018005.1|WP_010957791.1|688624_689890_+|ATP-binding-protein
MAIMQFNCILVEISMYLSRTLEPIIQKASRQFPVVMVTGARQVGKTTFLRHLAGKKRNYVTLDDPTLLALAKEEPKLFLERFKPPVLIDEIQYAPELLPHIKINVDNNRIAGQYWLTGSQPFHLMRGVSESLAGRVGILNLLGLSQWEIQKLPNFDLPFLPGDKSIGKKLTKMEPASLEAVYKRIWYGSFPAIALNVNADKDLFFSSYVQTYLQRDVRDLAQVGNESSFLRFLKVTAARTGQLLNLADIARDTDISPNTAKHWLSILQTSGIIYLLEPYHNNLNKRLIKTPKLYYIDTGLCSYLTRWSDYKTLEAGAMSGAILETFVVMEILKSYWHNGLQAPLYFYRDKDKKEIDLLIVKNQKIYPIEIKKTASPKREILKDFKVLDSFKENVSHGAVVCLVDTLIPLDRYVDAVPITLI

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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_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NZ_CP036488	Rahnella aquatilis strain MEM40 plasmid pMEM40-1, complete sequence	30343-30374	8	0.75
NZ_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NZ_CP032297	Rahnella aquatilis strain ZF7 plasmid pRAZF7, complete sequence	532636-532667	8	0.75
NZ_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NC_017060	Rahnella aquatilis HX2 plasmid PRA1, complete sequence	112646-112677	8	0.75
NZ_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NC_015062	Rahnella sp. Y9602 plasmid pRAHAQ01, complete sequence	115816-115847	8	0.75
NZ_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NZ_CP034838	Rahnella aquatilis strain KM12 plasmid pKM12v1, complete sequence	116094-116125	8	0.75
NZ_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NZ_CP034839	Rahnella aquatilis strain KM25 plasmid pKM12v2, complete sequence	116094-116125	8	0.75
NZ_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NZ_CP034837	Rahnella aquatilis strain KM05 plasmid pKM05, complete sequence	94007-94038	8	0.75
NZ_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NC_012811	Methylorubrum extorquens AM1 megaplasmid, complete sequence	1120014-1120045	9	0.719
NZ_CP018005_1	1.1\|676309\|32\|NZ_CP018005\|CRISPRCasFinder	676309-676340	32	NZ_CP040452	Halomonas sp. PA16-9 plasmid p_unnamed1, complete sequence	1684755-1684786	10	0.688

1. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NZ_CP036488 (Rahnella aquatilis strain MEM40 plasmid pMEM40-1, complete sequence) position: , mismatch: 8, identity: 0.75

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
cactgtgcttcggtgaggcctttttcaggggc	Protospacer
* ..** ******.*************..* *

2. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NZ_CP032297 (Rahnella aquatilis strain ZF7 plasmid pRAZF7, complete sequence) position: , mismatch: 8, identity: 0.75

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
cactgtgcttcggtgaggcctttttcaggggc	Protospacer
* ..** ******.*************..* *

3. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NC_017060 (Rahnella aquatilis HX2 plasmid PRA1, complete sequence) position: , mismatch: 8, identity: 0.75

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
cactgtgcttcggtgaggcctttttcaggggc	Protospacer
* ..** ******.*************..* *

4. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NC_015062 (Rahnella sp. Y9602 plasmid pRAHAQ01, complete sequence) position: , mismatch: 8, identity: 0.75

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
cactgtgcttcggtgaggcctttttcaggggc	Protospacer
* ..** ******.*************..* *

5. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NZ_CP034838 (Rahnella aquatilis strain KM12 plasmid pKM12v1, complete sequence) position: , mismatch: 8, identity: 0.75

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
cactgtgcttcggtgaggcctttttcaggggc	Protospacer
* ..** ******.*************..* *

6. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NZ_CP034839 (Rahnella aquatilis strain KM25 plasmid pKM12v2, complete sequence) position: , mismatch: 8, identity: 0.75

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
cactgtgcttcggtgaggcctttttcaggggc	Protospacer
* ..** ******.*************..* *

7. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NZ_CP034837 (Rahnella aquatilis strain KM05 plasmid pKM05, complete sequence) position: , mismatch: 8, identity: 0.75

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
cactgtgcttcggtgaggcctttttcaggggc	Protospacer
* ..** ******.*************..* *

8. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NC_012811 (Methylorubrum extorquens AM1 megaplasmid, complete sequence) position: , mismatch: 9, identity: 0.719

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
atcccggctacggcgaggcctttttccaaggg	Protospacer
 *.*   ** **************** ***

9. spacer 1.1|676309|32|NZ_CP018005|CRISPRCasFinder matches to NZ_CP040452 (Halomonas sp. PA16-9 plasmid p_unnamed1, complete sequence) position: , mismatch: 10, identity: 0.688

cttcgtccttcggcgaggcctttttcaaagcc	CRISPR spacer
tctcgtccatcggcgatgcctttttgttgagc	Protospacer
..****** ******* ********   .. *

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

255670 : 264702

uncultured_Mediterranean_phage(28.57%)

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\|255670_256990_+	polynucleotide adenylyltransferase PcnB	G3MAR3	Bacillus_virus	4.3e-25	35.0
WP_005771454.1\|256986_257547_+	2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase	S4VNV0	Pandoravirus	4.5e-16	39.2
WP_005771452.1\|257543_258023_+	pantetheine-phosphate adenylyltransferase	A0A1B1IVQ3	uncultured_Mediterranean_phage	3.1e-26	42.6
WP_005771450.1\|258037_258283_+	YfhL family 4Fe-4S dicluster ferredoxin	A0A1B1IWY9	uncultured_Mediterranean_phage	3.3e-16	51.1
WP_005771448.1\|258296_258509_-	50S ribosomal protein L33	NA	NA	NA	NA
WP_005771445.1\|258519_258759_-	50S ribosomal protein L28	NA	NA	NA	NA
WP_010957482.1\|259536_259893_-	hypothetical protein	NA	NA	NA	NA
WP_010957483.1\|259906_260392_+	dUTP diphosphatase	Q2NP83	Xanthomonas_phage	2.5e-47	58.0
WP_005771434.1\|260369_261785_+	phosphomannomutase/phosphoglucomutase	A0A127AWJ1	Bacillus_phage	1.5e-52	29.9
WP_010957484.1\|261781_263251_-	sel1 repeat family protein	NA	NA	NA	NA
WP_010957485.1\|263247_263895_-	orotate phosphoribosyltransferase	NA	NA	NA	NA
WP_010957486.1\|263922_264702_+	exodeoxyribonuclease III	E3T4M6	Cafeteria_roenbergensis_virus	1.3e-32	32.9

DBSCAN-SWA_2

605785 : 660282

Tupanvirus(13.33%)

protease,transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_010957722.1\|605785_606931_+\|transposase	ISAs1 family transposase	NA	NA	NA	NA
WP_010957723.1\|607022_608009_+	CBU_0665 family Dot/Icm T4SS effector	NA	NA	NA	NA
WP_005771873.1\|608022_609147_-	succinyl-diaminopimelate desuccinylase	NA	NA	NA	NA
WP_010957724.1\|609152_609968_-	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase	NA	NA	NA	NA
WP_005771871.1\|609964_610144_-	hypothetical protein	NA	NA	NA	NA
WP_010957725.1\|610143_610317_+	hypothetical protein	NA	NA	NA	NA
WP_010957726.1\|610567_611830_+	DEAD/DEAH box helicase	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	2.0e-51	32.1
WP_005771868.1\|612253_613687_+	mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase	A0A1V0SH58	Hokovirus	1.1e-63	31.9
WP_010957727.1\|613672_615289_-	hypothetical protein	NA	NA	NA	NA
WP_010957728.1\|615281_615827_-	HAD family hydrolase	NA	NA	NA	NA
WP_010957729.1\|615820_616411_-	SIS domain-containing protein	NA	NA	NA	NA
WP_010957730.1\|616414_617158_-	transaldolase	A0A0E3FJJ0	Synechococcus_phage	3.6e-13	31.7
WP_005771860.1\|617337_618351_+	SDR family oxidoreductase	A0A0F7LC08	uncultured_marine_virus	5.2e-31	32.8
WP_010957731.1\|618347_619385_+	NAD-dependent epimerase/dehydratase family protein	Q58M85	Prochlorococcus_phage	3.7e-56	40.0
WP_010957746.1\|621187_622747_+	sulfotransferase	NA	NA	NA	NA
WP_010957747.1\|622782_624540_-	bifunctional sulfate adenylyltransferase/adenylylsulfate kinase	A0A2K9L4R9	Tupanvirus	1.2e-118	40.5
WP_010957748.1\|624521_625355_-	3'(2'),5'-bisphosphate nucleotidase CysQ	NA	NA	NA	NA
WP_010957749.1\|625491_626241_+	SDR family oxidoreductase	A0A0N9R355	Chrysochromulina_ericina_virus	5.3e-12	27.5
WP_010957750.1\|626250_627114_+	ABC transporter permease	NA	NA	NA	NA
WP_005771814.1\|627123_627900_+	ABC transporter ATP-binding protein	W6JKT0	Anomala_cuprea_entomopoxvirus	5.6e-09	24.8
WP_010957751.1\|628611_628941_-	hypothetical protein	NA	NA	NA	NA
WP_010957752.1\|628957_629668_-	hypothetical protein	NA	NA	NA	NA
WP_010957753.1\|629781_630072_-	AI-2E family transporter	NA	NA	NA	NA
WP_040948109.1\|630118_630520_+\|transposase	transposase	NA	NA	NA	NA
WP_005771808.1\|631801_631945_-	hypothetical protein	NA	NA	NA	NA
WP_032075117.1\|632004_632460_-	hypothetical protein	NA	NA	NA	NA
WP_010957754.1\|632936_633572_-	response regulator	NA	NA	NA	NA
WP_010957755.1\|633630_634881_-	MFS transporter	NA	NA	NA	NA
WP_010957756.1\|634930_635341_-	DUF3775 domain-containing protein	NA	NA	NA	NA
WP_010957757.1\|635513_636506_+\|transposase	IS30 family transposase	W5R8L2	Staphylococcus_phage	3.7e-37	34.7
WP_010957758.1\|636564_637485_-	NAD(P)/FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_080692293.1\|637632_637953_+	hypothetical protein	NA	NA	NA	NA
WP_080512964.1\|637888_638569_+	hypothetical protein	NA	NA	NA	NA
WP_052341912.1\|638546_639302_+	hypothetical protein	NA	NA	NA	NA
WP_010957759.1\|639536_639821_+	membrane protein	NA	NA	NA	NA
WP_010957760.1\|639817_640243_+	hypothetical protein	NA	NA	NA	NA
WP_005771798.1\|640298_641180_-	agmatinase	NA	NA	NA	NA
WP_010957761.1\|641179_642241_-	deoxyhypusine synthase	NA	NA	NA	NA
WP_010957762.1\|642264_643467_-	type III PLP-dependent enzyme	A0A2K9L4I2	Tupanvirus	1.2e-26	28.4
WP_010957757.1\|643712_644705_-\|transposase	IS30 family transposase	W5R8L2	Staphylococcus_phage	3.7e-37	34.7
WP_124224292.1\|644817_645015_-	serine hydrolase	NA	NA	NA	NA
WP_080713024.1\|644906_645758_-	serine hydrolase	NA	NA	NA	NA
WP_017252738.1\|645729_645960_-	hypothetical protein	NA	NA	NA	NA
WP_005772900.1\|646212_647346_+	MlaE family lipid ABC transporter permease subunit	NA	NA	NA	NA
WP_010957764.1\|647342_648152_+	ATP-binding cassette domain-containing protein	G9BWD6	Planktothrix_phage	3.1e-26	35.7
WP_005771786.1\|648135_649062_+	MCE family protein	NA	NA	NA	NA
WP_005771783.1\|649064_649664_+	hypothetical protein	NA	NA	NA	NA
WP_010957765.1\|649660_650131_-	hypothetical protein	NA	NA	NA	NA
WP_010957766.1\|651218_651443_-	hypothetical protein	NA	NA	NA	NA
WP_005772902.1\|651424_652273_+	nucleoside phosphorylase	NA	NA	NA	NA
WP_010957767.1\|652293_652947_-	hypothetical protein	NA	NA	NA	NA
WP_010957768.1\|653235_654564_+	trigger factor	NA	NA	NA	NA
WP_010957769.1\|654573_655161_+	ATP-dependent Clp endopeptidase proteolytic subunit ClpP	A0A223W000	Agrobacterium_phage	1.1e-49	52.3
WP_005771771.1\|655215_656484_+\|protease	ATP-dependent Clp protease ATP-binding subunit ClpX	G3M9Z9	Bacillus_virus	2.1e-133	54.9
WP_010957770.1\|656497_658951_+	endopeptidase La	A0A0R6PGP8	Moraxella_phage	2.1e-211	49.9
WP_010957771.1\|658959_660282_+\|protease	metalloprotease PmbA	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