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_017248	Brucella melitensis NI chromosome I, complete sequence	1 crisprs	csa3,WYL,DEDDh	0	1	3	0
NC_017283	Brucella melitensis NI chromosome II, complete sequence	0 crisprs	csa3,cas3,DEDDh	0	0	0	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_017248_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_017248_1

656148-656230

Orphan

Consensus_repeat	Method
ATCCCGAAAAGTGCGAAGCGGTTTTCGG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_017248_1

>merge|NC_017248|1|656148-656230|CRISPRCasFinder
ATCCCGAAAAGTGCGAAGCGGTTTTCGGATAAGATGCGCGCAAGGAAAGATCTGTATCCCGAAAAGTGCGAAGCGGTGTTCGG

>NC_017248|1|1|656148-656230|CRISPRCasFinder
ATCCCGAAAAGTGCGAAGCGGTTTTCGG	ATAAGATGCGCGCAAGGAAAGATCTGT
ATCCCGAAAAGTGCGAAGCGGTGTTCGG

Protein	Signature genes	Signature genes Name	Protein_function
NC_017248.1\|WP_004686526.1\|654686_655568_+\|4-hydroxy-tetrahydrodipicolinate-synthase	unknown	unknown	gnl\|CDD\|235107
NC_017248.1\|WP_002963797.1\|660847_661426_+\|orotate-phosphoribosyltransferase	unknown	unknown	gnl\|CDD\|273579
NC_017248.1\|WP_002971501.1\|665702_666542_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|380379
NC_017248.1\|WP_004683363.1\|646097_647024_-\|site-specific-integrase	unknown	unknown	gnl\|CDD\|271177
NC_017248.1\|WP_002963787.1\|651173_651356_+\|hypothetical-protein	unknown	unknown	unknown
NC_017248.1\|WP_004686530.1\|644601_645735_-\|pyridoxal-phosphate-dependent-aminotransferase	unknown	unknown	gnl\|CDD\|181255
NC_017248.1\|WP_004683386.1\|656973_657549_-\|NYN-domain-containing-protein	unknown	unknown	gnl\|CDD\|350235
NC_017248.1\|WP_002966733.1\|666591_667167_+\|DUF2062-domain-containing-protein	unknown	unknown	gnl\|CDD\|225757
NC_017248.1\|WP_004683357.1\|643514_644165_+\|hypothetical-protein	unknown	unknown	unknown
NC_017248.1\|WP_002963795.1\|657945_658347_+\|DNA-directed-RNA-polymerase-subunit-omega	unknown	unknown	gnl\|CDD\|234744
NC_017248.1\|WP_002963791.1\|655658_656135_+\|SsrA-binding-protein-SmpB	unknown	unknown	gnl\|CDD\|235455
NC_017248.1\|WP_006136160.1\|644209_644584_-\|DUF423-domain-containing-protein	unknown	unknown	gnl\|CDD\|225238
NC_017248.1\|WP_004685525.1\|658587_660840_+\|bifunctional-(p)ppGpp-synthetase/guanosine-3',5'-bis(diphosphate)-3'-pyrophosphohydrolase	unknown	unknown	gnl\|CDD\|223394
NC_017248.1\|WP_002963786.1\|650476_651118_+\|hypothetical-protein	unknown	unknown	unknown
NC_017248.1\|WP_002963792.1\|656271_656943_-\|uracil-DNA-glycosylase	unknown	unknown	gnl\|CDD\|381681
NC_017248.1\|WP_004683395.1\|664239_665451_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|341031
NC_017248.1\|WP_005969508.1\|651434_652091_+\|endonuclease	unknown	unknown	gnl\|CDD\|237082
NC_017248.1\|WP_004686525.1\|661585_662341_+\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|236494
NC_017248.1\|WP_004686524.1\|662721_664056_+\|oxygen-independent-coproporphyrinogen-III-oxidase	unknown	unknown	gnl\|CDD\|237356
NC_017248.1\|WP_004685524.1\|652153_654211_-\|lytic-transglycosylase-domain-containing-protein	unknown	unknown	gnl\|CDD\|381604

Protein	Function_ID	Function_description	E-value
NC_017248.1\|WP_004686526.1\|654686_655568_+\|4-hydroxy-tetrahydrodipicolinate-synthase	gnl\|CDD\|235107	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional.	7.73311e-177
NC_017248.1\|WP_004683363.1\|646097_647024_-\|site-specific-integrase	gnl\|CDD\|271177	cd00796, INT_Rci_Hp1_C, Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain. Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.	1.39039e-42
NC_017248.1\|WP_005969508.1\|651434_652091_+\|endonuclease	gnl\|CDD\|237082	PRK12373, PRK12373, NADH-quinone oxidoreductase subunit E.	1.44499e-28
NC_017248.1\|WP_004686530.1\|644601_645735_-\|pyridoxal-phosphate-dependent-aminotransferase	gnl\|CDD\|181255	PRK08153, PRK08153, pyridoxal phosphate-dependent aminotransferase.	0
NC_017248.1\|WP_004683386.1\|656973_657549_-\|NYN-domain-containing-protein	gnl\|CDD\|350235	cd10911, PIN_LabA, PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins. This subfamily contains Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. This subfamily belongs to the LabA-like domain family which includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Also included in the LabA-like domain family are human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB , which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.	1.30427e-60
NC_017248.1\|WP_002966733.1\|666591_667167_+\|DUF2062-domain-containing-protein	gnl\|CDD\|225757	COG3216, COG3216, Uncharacterized protein conserved in bacteria [Function unknown].	5.43979e-83
NC_017248.1\|WP_002963795.1\|657945_658347_+\|DNA-directed-RNA-polymerase-subunit-omega	gnl\|CDD\|234744	PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega; Reviewed.	1.70484e-25
NC_017248.1\|WP_002963791.1\|655658_656135_+\|SsrA-binding-protein-SmpB	gnl\|CDD\|235455	PRK05422, smpB, SsrA-binding protein SmpB.	1.57135e-88
NC_017248.1\|WP_006136160.1\|644209_644584_-\|DUF423-domain-containing-protein	gnl\|CDD\|225238	COG2363, COG2363, Uncharacterized small membrane protein [Function unknown].	6.855e-30
NC_017248.1\|WP_004685525.1\|658587_660840_+\|bifunctional-(p)ppGpp-synthetase/guanosine-3',5'-bis(diphosphate)-3'-pyrophosphohydrolase	gnl\|CDD\|223394	COG0317, SpoT, Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription].	0
NC_017248.1\|WP_002971501.1\|665702_666542_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|380379	cd06124, cupin_NimR-like_N, AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain. This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.	5.72308e-33
NC_017248.1\|WP_002963792.1\|656271_656943_-\|uracil-DNA-glycosylase	gnl\|CDD\|381681	cd10031, UDG-F5_TTUDGB_like, Uracil DNA glycosylase family 5, includes Thermotoga maritima TTUDGB and similar proteins. Uracil DNA glycosylase family 5 includes Thermus thermophilus HB8 TTUDGB (also called UDGb) which is not only a UDG acting on double-stranded uracil-containing DNA, but also a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA (except for the C/I base pair), as well as a xanthine DNA glycosylase acting on both, double-stranded and single-stranded xanthine-containing DNA. TTUDGB also excises thymine from G:T mismatched DNA, and removes analogs of uracil from DNA, including 5-hydroxymethyluracil (hmU) and 5-fluorouracil (fU). This subfamily also contains Bradyrhizobium diazoefficiens family 5 homolog Blr5068 (UdgB) which has been found to efficiently excise uracil from ssDNA and dsDNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Similar to family 4 UDGs, members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other.	7.75632e-104
NC_017248.1\|WP_004683395.1\|664239_665451_-\|MFS-transporter	gnl\|CDD\|341031	cd17478, MFS_FsR, Fosmidomycin resistance protein of the Major Facilitator Superfamily of transporters. Fosmidomycin resistance protein (FsR) confers resistance against fosmidomycin. It shows sequence similarity with the bacterial drug-export proteins that mediate resistance to tetracycline and chloramphenicol. This FsR family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement.	8.97193e-108
NC_017248.1\|WP_002963797.1\|660847_661426_+\|orotate-phosphoribosyltransferase	gnl\|CDD\|273579	TIGR01367, Orotate_phosphoribosyltransferase, orotate phosphoribosyltransferase, Thermus family. This model represents a distinct clade of orotate phosphoribosyltransferases. Members include the experimentally determined example from Thermus aquaticus and additional examples from Caulobacter crescentus, Helicobacter pylori, Mesorhizobium loti, and related species. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis].	2.00708e-76
NC_017248.1\|WP_004686525.1\|661585_662341_+\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|236494	PRK09391, fixK, transcriptional regulator FixK; Provisional.	1.10991e-50
NC_017248.1\|WP_004686524.1\|662721_664056_+\|oxygen-independent-coproporphyrinogen-III-oxidase	gnl\|CDD\|237356	PRK13347, PRK13347, coproporphyrinogen III oxidase; Provisional.	0
NC_017248.1\|WP_004685524.1\|652153_654211_-\|lytic-transglycosylase-domain-containing-protein	gnl\|CDD\|381604	cd13401, Slt70-like, 70kDa soluble lytic transglycosylase (Slt70) and similar proteins. Catalytic domain of the 70kda soluble lytic transglycosylase (LT)-like proteins, which also have an N-terminal U-shaped U-domain and a linker L-domain. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda.	2.23686e-60

>NC_017248.1|WP_002963791.1|655658_656135_+|SsrA-binding-protein-SmpB
MNKPKNSPARKMIAENRKARFNFEILDTLEAGLVLTGTEVKSLRANQANIAESYASFEDGEFWLINSYIPEYTQGNRFNHEPRRLRKLLVSRREMSRLFNSVSREGMTVVPLKLYFNDRGRAKLELALARGKKTHDKRETEKKRDWNREKARLLRDRG
>NC_017248.1|WP_004686526.1|654686_655568_+|4-hydroxy-tetrahydrodipicolinate-synthase
MLKGSITALVTPFDREGAFDEKAFRAFVNWQIEEGTKGLVPVGTTGETPTLSHDEHKRVIEVCIEVAAGRVPVIAGAGSNNTVEAIELAQHAEKAGADAVLVVTPYYNKPNQRGLYEHFSRVARSISIPLVIYNVPGRSIIDMTPETMGALVRDCKNIVGVKDATGKIERVSEQRAICGKEFIQLSGEDATALGFNAHGGVGCISVTSNIAPRLCAEFQEACQAGNFAKALELQDRLMPLHKALFLEPNPSGPKYALSRLGRIENVLRSPMVTIEAATAEKIDHAMKHAVLIN
>NC_017248.1|WP_004685524.1|652153_654211_-|lytic-transglycosylase-domain-containing-protein
MVSLAQSSLPPEIPTPLARPFAPTATHQSPISLVTPRPRPIAPDPMATSAVSRTDNPAVIGGTLKNGLDALSAKNVASAIASRNNLPRGSLDRQILTWAIATSGMDGVPSTEIAAAASELSGWPGMATLRRNSERALFKENPSSATIIATFGSTRPQTTEGMIALARAYVATGNSTKAHQLLSPWWTRKRLSSDDEQKILKEFSAILTREDHQRRLLHSLYNGHLQSARLLAGPAQAQSLYNAYAAVAQKSPNAASAIAAVDRSWQANPVYQFLKIRYLRRAERYNEAAELLLKAPRKASVLVDPDAWWVERRILSRELLDLGKPQLAYRLAAAHAAETPTMAAEAEFHAGWYALRALNQPKLAAPHFAKITQISARPISASRAYYWLGRAAEAGSGGDARAYYRRSAHFGTTFYGQLAAAKLNEKAPELAYPKPTEAERVRFASRPAVQAIKRLEQVGYGNKAAALYTQLSQELDSVGELALLAVMAERNDNHYMALRVGKTAAMRGLDVGALSHPLGAIPASANIKGSGKALAYAIARQESEFNVSAVSKAGARGLLQLMPATAKTVATRNGMSFSAQKLTADAAYNATLGAHFLGEQLDRFNGSYVLTFAGYNAGPRRASEWVEKYGDPRGKSVEQVVDWIERIPYSETRNYVQRVMENYEVYKTRLTGRADIKTDLVYGRR
>NC_017248.1|WP_005969508.1|651434_652091_+|endonuclease
MPLLIVQLAILIAVAFVVGCFLGRILRRRKSAGSDHERTIVAAALSTPPLAEKPEPVPPAEPVRADSDPLKRKAGLEKARIEPVEGSADSDVAAAPVLKKVPAETPDDAGRPQWREAPRRGKADELTAIEGIGKAIEAVLHELGIFHYDQIAQWTREEAIWIERRIGFPGRVEREGWIAQAAKLAEPPAKSTTKRGAKTKKAANNVRSGTRRAKKQAG
>NC_017248.1|WP_002963787.1|651173_651356_+|hypothetical-protein
MTVFPIRPFLCYDYSAKGLKCLAKYYAESLMLYLVETFWPVLVLAILIGAATGWLTAGER
>NC_017248.1|WP_002963786.1|650476_651118_+|hypothetical-protein
MKKWFWPCLTWTACLTALALWFGADRVETDIAEQTAKALEPYVWAGFYVDGRDVVLKGMAPDPDMQRAAHAALEHVWAIRDITDLTTVLQLASPYRFKIGRNAQGLVLSGFIPNNESRDQVMTAAGEVAPDIFIDDEMAVARGNQPEFMERVLFAIDLAKKLPEAEIEIVDEKLSIRGTVSDEAIYDEIEALKAAQLPYGLKLAVLDVKKSVQ
>NC_017248.1|WP_004683363.1|646097_647024_-|site-specific-integrase
MIIVGETKIDTGDKYAPIIDYNLNYISGKNPKHRLVEHYSVAELTAKYINILWDDGPHKYNVRSFLGEIDEILKGARFSGFDQEMLDSIIGTLRERGNSNATINRKMAALSKLLRKAHKMGDIFNLPEFIRQKERVGRIRFLEQEEEKRLFAAIKSRCEDSYRLSVFLVDTGCRLGEAIGLTWNDIQEQRVTFWVTKSNRSRTVPLTRRARKASHIPRERLKGPFSMLNQVRFRQIWNEAKAEVGLGADDQIVPHILRHTCASRLVRGGIDIRRVQMWLGHQTLQMTMRYAHLATHDLDSCVKVLEIH
>NC_017248.1|WP_004686530.1|644601_645735_-|pyridoxal-phosphate-dependent-aminotransferase
MAQPRLTPLVESLPSTVPFIGPETLELQRGKPFEARIGANENSFGPAPSVIEAMRNEATEVWKYGDPENYALRHAIAAHHGLKAEHIMPGAGVDALLGLIVRQYVQQGDKVINSLGGYPTFNYHVAGYGGQLVTVPYRDDKPDLDALIDAAAREKPALLYIANPDNPMGTWHGGADIQSFIERLPETTLLILDEAYCETAPASAFPPFETDRPNVLRMRTFSKAYGLAGIRCGYAVGNPVAIKTFDKVRDHFAVSRMAQAAAIAALKDQAYLHEVVGKICAGRDRIAAIAEANGLHAVASATNFVAIDCGRGKDFAQAVLNGLISRDIFVRKPGTPVLDRCIRVSVGVKEQLDQFEAAFPEALEEARKICAANAENT
>NC_017248.1|WP_006136160.1|644209_644584_-|DUF423-domain-containing-protein
MPSINGQPSSVLFGTLAGLCGALGIASYAGAAHMGESHLGTIAPLLLAHAPALLFLSLISPVSRVVRIGGAILVVGLALFCGDLFMRDMTGDRLFPFAAPTGGSLMILGWLCLGCSGWFSANAK
>NC_017248.1|WP_004683357.1|643514_644165_+|hypothetical-protein
MSIRTITAMAGTAFIMGAAAIAFSSPASALTMKECSTKYQAAKDAGTLGNMKWNDFRKAQCGDDAASAPAAAPAAAPATKKAAKAAAPASNDGAKSLTMKQCSAKYQAAKDASTDNGMKWNDFRKAECGPGADPVALSTDGDSEPAAPSVAAPKGVKFPTAVSAKYSKESAGKARMHTCLDQYHALKDANALGGLKWVQKGGGYYSLCNARLKGNS
>NC_017248.1|WP_002963792.1|656271_656943_-|uracil-DNA-glycosylase
MISEPSPNCSICPRLHAFLQEWRQKEPAWHNAPVPPFLPGSDEDVRLLIVGLAPGLRGANRTGRPFTGDYAGELLYSTLCEFGFATGKFEARPDDSLRLLDACIVNAVRCVPPENKPVGSEINNCRQFLTPMLTRFPNLDAVVTLGTIAHQSTVRALGVPVSRHPFGHGKATDIGPLRIFSSYHCSRYNTNTGVLTDAMFRDVFKNVRAYLSEKAAGSARLSV
>NC_017248.1|WP_004683386.1|656973_657549_-|NYN-domain-containing-protein
MFDSREKIALFIDGANLYAASKTLGFDIDYRKLLKAFQKRGYLLRAYYYTALVEDQEYSSIRPLIDWLDYNGYKVVTKAAREFTDSTGRRKVKGNMDIELTVDAMQLTDTVDHFVIFSGYGDFRSLVEALQRKGRKVSVVSTLTTQPAMISDELRRQADHFIDLVSLKAEIGRDPSERAPRRQEEDFDESY
>NC_017248.1|WP_002963795.1|657945_658347_+|DNA-directed-RNA-polymerase-subunit-omega
MARVTVEDCVDKVENRFELVLLAGHRARQISQGAPITVDRDNDKNPVVALREIADETLSPDDLKEDLIHSLQKHVEVDEPEAAPAQIANAAEEIAEGIAEAGEEDVVTFDRMSEEELLAGIEGLVAPEKNDGF
>NC_017248.1|WP_004685525.1|658587_660840_+|bifunctional-(p)ppGpp-synthetase/guanosine-3',5'-bis(diphosphate)-3'-pyrophosphohydrolase
MMRQYELVERVQRYKPDVNEALLNKAYVYAMQKHGSQKRASGDPYFSHPLEVAAILTDMHLDEATIAIALLHDTIEDTTATRQEIDQLFGPEIGKLVEGLTKLKKLDLVSKKAVQAENLRKLLLAISEDVRVLLVKLADRLHNMRTLGVMREDKRLRIAEETMDIYAPLAGRMGMQDMREELEELAFRYINPDAWRAVTDRLAELLEKNRGLLQKIETDLSEIFEKNGIKASVKSRQKKPWSVFRKMESKGLSFEQLSDIFGFRVMVDTVQDCYRALGLIHTTWSMVPGRFKDYISTPKQNDYRSIHTTIIGPSRQRIELQIRTREMDEIAEFGVAAHSIYKDRGSANNPHKISTETNAYAWLRQTIEQLSEGDNPEEFLEHTKLELFQDQVFCFTPKGRLIALPRGATPIDFAYAVHTDIGDSCVGAKVNGRIMPLMTELKNGDEVDIIRSKAQVPPAAWESLVATGKARAAIRRATRSAVRKQYSGLGMRILERAFERAGKPFSKDILKPGLPRLARKDVEDVLAAVGRGELPSTDVVKAVYPDYQDTRVTTQNNPAKAGEKGWFNIQNAAGMIFKVPEGGEGAAAKVDPAATTPKPGKRALPIRGTNPDLPVRFAPEGAVPGDRIVGILQPGAGITIYPIQSPALTAYDDQPERWIDVRWDIDDQMSERFPARISVSAINSPGSLAEIAQIAAANDANIHNLSMVRTAPDFTEMIIDVEVWDLKHLNRIISQLKESASVSSAKRVNG
>NC_017248.1|WP_002963797.1|660847_661426_+|orotate-phosphoribosyltransferase
MNTDDVLAVFREAGAILEGHFILTSGLRSPVFLQKARVFMHADKTEKLCKALAEKIRAADLGPIDYVVGPAIGGLIPSYETSRHLGVPSVWVERENGVFRLRRFDVPKGARVVIVEDIVTTGLSIRETIDCMKDLGIEVVAAACIVDRSAGKADVGTRLISLAEYEVPAYPADKLPPELAAIPAVKPGSRNI
>NC_017248.1|WP_004686525.1|661585_662341_+|helix-turn-helix-domain-containing-protein
MVVVPFALDQNQKLAARTPCNVCEDCCVRSMAVCSALDDGDLAALEAIMTSKKLDTNEMLVEEGEPKLRVYSLTSGMLRIYTSLPDGRRQIAGFLFPGDFLGLADDEVYSLSAEAVVPSALCAFSAKEMERLMERFPKLKERLYQMTRLALRTARDNQLVLGRLAPVEKLASFLLVLSARAEKRGEKPNPVHLLMNRTDIADYLGLTIETVSRSFTKLKTQGLIQLRDANTVEILSRRSLAVVAGLDPDNL
>NC_017248.1|WP_004686524.1|662721_664056_+|oxygen-independent-coproporphyrinogen-III-oxidase
MHDDAIRRYAALAVPRYTSYPTAADFVPVGMDTTRRWLRQIGPEESVSLYIHVPYCSQICHYCGCNAKMAIREDVIENFVNALLGEIRTVSASLTARPRVAHLHWGGGTPSILNAGQFQTVLAAIRTAFDFDLSMEHAIELDPRTVTPLLAKTLAEMGVNRASLGVQDVDSRVQMAIGRVQPIETVAEATRLLREVGINRINFDLIYGLPLQTVETLRETCERVVTLSPDRVACYGYAHLPQRRANQRLIDENTLPDADERFRQARIVTDSFIGFGYQPVGIDHFALPDDDLAIAAREGTLNRNFQGYTNDRCGTLIGFGPSSISQFPGGYAQNISDVGQYRKRVEAGELATVRGYTLRDADRIRSAIISALMCNFCVDLNAVAPGMEFSDEFALLRPLVADGLVAVEGRTIRATENGKSLIRLVAAAFDEFRRDSVHGFSFAV
>NC_017248.1|WP_004683395.1|664239_665451_-|MFS-transporter
MSVSAAQQPSNSSADNTVLTIILATSLGHFLNDMMQSLLPAIYPMLKENYSLSFWQIGLLTFTFQMTASILQPLVGIYTDRKPMPYSLTFGMGCTLIGLVFLATAHHYSFLLLGAACVGFGSSVFHPEAARVARLASGGRHGFAQSLFQVGGNFGSSIGPLLAAFIVLPFGQISVSWFSVAALIGMFVLWYVGNWYNRYRLANANKPKPDKTLPLPRNRVIASVAVLALLVFTKYIYMASLTSYYTFYTISHFGVSVQTSQLLLFLFLGAVAAGTIIGGPIGDKIGARKVIWASILGVLPFTLALPYANLEMTAVLTIIIGLILASAFPAIIVFAQELLPGRVGMLSGLFFGFAFGMAGIAAAVLGIVADQKGIEFVYRICSYLPFLGLLTIFLPKLERRRKA
>NC_017248.1|WP_002971501.1|665702_666542_+|helix-turn-helix-transcriptional-regulator
MPENEDLQRFHEHRIAMLESMTGPAIALPTRYPDGYFVPRHSHSRAQLLCASQGVVLVTTDAGRWMIPSDHAMWIPAGVEHSVAILGDVFMRSIYISVDAISGVPNYLHVVGLTDLMRCLIIDATSHDSIPAPESRDGLVIELILRDLHTLPEYPLGLPFPSDPRLQKLCRDFVKKPSSRATIDEWADRMAMSRRSFTRHFQRETGVSLSVWRQQACLFAAVPRLSEGEPVTSVALDLGYDSVSAFTTMFRRMLGVPPKFYQPRLDVAPFERSDKAAFG
>NC_017248.1|WP_002966733.1|666591_667167_+|DUF2062-domain-containing-protein
MLFQRRYPPTRWERLRLYLWPRRSFSRSFRYGGKRILRITASPHAVAAGLAVGVFSAFTPFFGFHLIIAIVLAYFLAGNVAAAALGTTLANPLTLPFIWGSTFELGRFIMSGSVDSVPPVHLGHALETMRFEEVWTPLLKPMLFGSTILGAAFAVLVYFVTRYAVSVFRRRRLERLAEKHRLHRQRELQKA

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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_017248_1	1.1\|656176\|27\|NC_017248\|CRISPRCasFinder	656176-656202	27	NZ_CP013986	Klebsiella variicola strain LMG 23571 plasmid unnamed, complete sequence	45587-45613	5	0.815

1. spacer 1.1|656176|27|NC_017248|CRISPRCasFinder matches to NZ_CP013986 (Klebsiella variicola strain LMG 23571 plasmid unnamed, complete sequence) position: , mismatch: 5, identity: 0.815

ataagatgcgcgcaaggaaagatctgt	CRISPR spacer
aacagatgctctcaaggaaagatctga	Protospacer
*  ****** * **************

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

534962 : 608850

Paracoccus_phage(15.79%)

transposase,holin,tail,portal

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_077281772.1\|534962_535313_+\|transposase	transposase	NA	NA	NA	NA
WP_002963675.1\|536740_537520_-	LPS biosynthesis N-formyltransferase WbkC	E3SNR5	Prochlorococcus_phage	3.3e-09	31.4
WP_002963676.1\|537546_538401_-	hypothetical protein	NA	NA	NA	NA
WP_004686562.1\|538397_539156_-	ABC transporter ATP-binding protein	NA	NA	NA	NA
WP_004683211.1\|539152_539935_-	ABC transporter permease	NA	NA	NA	NA
WP_002963679.1\|539949_541053_-	DegT/DnrJ/EryC1/StrS aminotransferase family protein	A0A2K9L470	Tupanvirus	3.5e-44	31.9
WP_002963680.1\|541060_542149_-	GDP-mannose 4,6-dehydratase	M1IBC3	Acanthocystis_turfacea_Chlorella_virus	3.4e-137	68.4
WP_002963682.1\|545408_546527_+	glycosyltransferase family 4 protein	NA	NA	NA	NA
WP_077281774.1\|547284_547437_-	hypothetical protein	NA	NA	NA	NA
WP_005975609.1\|547479_548034_-\|transposase	IS3 family transposase	Q8W6R2	Burkholderia_virus	3.0e-12	33.9
WP_148262946.1\|548197_548960_+\|transposase	IS5 family transposase	A0A0N9SHJ4	Paenibacillus_phage	2.8e-21	40.0
WP_002975117.1\|548857_549175_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_004685492.1\|549785_551141_+	phosphomannomutase	NA	NA	NA	NA
WP_002963689.1\|551211_552636_+	mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase	A0A1V0SH58	Hokovirus	9.0e-53	30.8
WP_002963690.1\|552668_553841_+	AGE family epimerase/isomerase	NA	NA	NA	NA
WP_002969456.1\|553923_555033_+	glycosyltransferase family 4 protein	NA	NA	NA	NA
WP_002969455.1\|558359_559322_+	substrate-binding domain-containing protein	NA	NA	NA	NA
WP_004683241.1\|559379_560432_+	sugar phosphate isomerase/epimerase	NA	NA	NA	NA
WP_004683244.1\|560439_561612_+	Gfo/Idh/MocA family oxidoreductase	NA	NA	NA	NA
WP_002966715.1\|561653_562961_-	xylose isomerase	NA	NA	NA	NA
WP_004683247.1\|563007_564459_-	xylulokinase	NA	NA	NA	NA
WP_004685498.1\|564491_565523_-	LacI family DNA-binding transcriptional regulator	NA	NA	NA	NA
WP_004686553.1\|565785_566229_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_004683253.1\|566210_566780_-	AraC family transcriptional regulator	NA	NA	NA	NA
WP_004686552.1\|567318_568782_-	betaine-aldehyde dehydrogenase	NA	NA	NA	NA
WP_004686551.1\|568933_570616_-\|holin	choline dehydrogenase	A0A1V0S9M4	Catovirus	6.0e-40	30.6
WP_004683258.1\|570618_571215_-	transcriptional regulator BetI	NA	NA	NA	NA
WP_002963705.1\|571405_572428_+	asparaginase	NA	NA	NA	NA
WP_002967489.1\|572472_572943_+	GreA/GreB family elongation factor	NA	NA	NA	NA
WP_004686549.1\|572939_573329_-	type II toxin-antitoxin system death-on-curing family toxin	A0A1B3AYM0	Gordonia_phage	7.7e-07	43.1
WP_004683261.1\|573325_573556_-	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	NA	NA	NA	NA
WP_002963709.1\|573616_574609_-	magnesium transporter CorA family protein	NA	NA	NA	NA
WP_004683264.1\|574764_575442_+	FadR family transcriptional regulator	NA	NA	NA	NA
WP_004686548.1\|575438_576737_+	CynX/NimT family MFS transporter	NA	NA	NA	NA
WP_002963712.1\|576793_577156_-	hypothetical protein	NA	NA	NA	NA
WP_002963713.1\|577491_579003_+	DUF853 domain-containing protein	A0A248XCZ8	Klebsiella_phage	1.4e-83	44.3
WP_002963714.1\|579200_579917_-	L,D-transpeptidase	NA	NA	NA	NA
WP_006139491.1\|579975_580218_+	hypothetical protein	NA	NA	NA	NA
WP_004683270.1\|581094_581694_+	superoxide dismutase	Q56AR7	Bacillus_thuringiensis_phage	6.2e-40	43.1
WP_002963717.1\|581865_582201_-	hypothetical protein	NA	NA	NA	NA
WP_002967492.1\|582318_584427_-	S9 family peptidase	NA	NA	NA	NA
WP_002963720.1\|584999_585428_+	MucR family transcriptional regulator	A0A1P8VVG0	Erythrobacter_phage	1.0e-20	47.6
WP_006136191.1\|585635_585947_-	hypothetical protein	NA	NA	NA	NA
WP_004686544.1\|586128_586584_+	hypothetical protein	NA	NA	NA	NA
WP_005969604.1\|586580_587354_+	hypothetical protein	NA	NA	NA	NA
WP_002967494.1\|587466_588804_+	amidase	NA	NA	NA	NA
WP_002963725.1\|588844_589270_-	SufE family protein	NA	NA	NA	NA
WP_004683280.1\|589349_589814_-	hypothetical protein	NA	NA	NA	NA
WP_004686543.1\|590104_591934_+	HAMP domain-containing histidine kinase	W8CYF6	Bacillus_phage	1.2e-22	28.9
WP_002971535.1\|591908_592877_+	peptidoglycan-binding protein	NA	NA	NA	NA
WP_002963729.1\|592890_593238_+	DUF1491 family protein	NA	NA	NA	NA
WP_006136186.1\|593248_594307_-	hypothetical protein	NA	NA	NA	NA
WP_004683287.1\|594504_595047_-	hypothetical protein	NA	NA	NA	NA
WP_002963732.1\|595039_595651_-	DUF1214 domain-containing protein	NA	NA	NA	NA
WP_006136183.1\|595657_597832_-	penicillin-binding protein 1A	NA	NA	NA	NA
WP_014490024.1\|598171_598684_+	hypothetical protein	NA	NA	NA	NA
WP_005969588.1\|598622_599882_+	DNA-packaging protein	A0A1V0DY66	Dinoroseobacter_phage	1.3e-71	40.6
WP_002963736.1\|599913_601107_+\|portal	phage portal protein	W8ECU7	Geobacillus_phage	7.0e-67	40.0
WP_002967499.1\|601103_601481_+	hypothetical protein	NA	NA	NA	NA
WP_002963743.1\|601531_601945_+\|tail	phage major tail protein, TP901-1 family	NA	NA	NA	NA
WP_004683300.1\|601941_602283_+	gene transfer agent family protein	NA	NA	NA	NA
WP_004683301.1\|602326_602497_+\|tail	phage tail assembly chaperone	NA	NA	NA	NA
WP_002970984.1\|602501_603047_+\|tail	phage tail tape measure protein	A0A0S2SYD9	Pseudomonas_phage	2.8e-07	46.4
WP_002963747.1\|603049_603682_+	TIGR02217 family protein	A0A0B5A2K3	Paracoccus_phage	2.9e-48	47.6
WP_004683305.1\|603678_604554_+	DUF2163 domain-containing protein	A0A0K1Y6Z2	Rhodobacter_phage	4.5e-47	38.9
WP_004683307.1\|604550_604985_+	C40 family peptidase	NA	NA	NA	NA
WP_014490027.1\|604988_606176_+	hypothetical protein	A0A0B5A7K5	Paracoccus_phage	6.4e-36	34.8
WP_006136163.1\|606192_608850_+\|tail	glycoside hydrolase/phage tail family protein	A0A0B5A7K5	Paracoccus_phage	2.7e-143	35.4

DBSCAN-SWA_2

872198 : 884110

uncultured_Mediterranean_phage(90.0%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_004683698.1\|872198_873050_+	segregation/condensation protein A	A0A1B1IVW1	uncultured_Mediterranean_phage	4.4e-31	33.5
WP_002964011.1\|873042_873768_+	SMC-Scp complex subunit ScpB	A0A1B1IVT7	uncultured_Mediterranean_phage	1.5e-43	45.7
WP_002964012.1\|873913_874132_+	twin-arginine translocase TatA/TatE family subunit	A0A1B1IVR9	uncultured_Mediterranean_phage	1.5e-07	65.1
WP_006094283.1\|874242_874809_+	twin-arginine translocase subunit TatB	NA	NA	NA	NA
WP_002964014.1\|874805_875630_+	twin-arginine translocase subunit TatC	A0A1B1IVR7	uncultured_Mediterranean_phage	9.8e-44	41.1
WP_004683702.1\|875706_876990_+\|tRNA	serine--tRNA ligase	A0A1B1IVT2	uncultured_Mediterranean_phage	2.6e-104	47.2
WP_004683703.1\|877138_877906_+	5'/3'-nucleotidase SurE	A0A1B1ITZ2	uncultured_Mediterranean_phage	1.0e-39	40.2
WP_004683704.1\|877902_878571_+	protein-L-isoaspartate(D-aspartate) O-methyltransferase	A0A1B1IU40	uncultured_Mediterranean_phage	6.6e-14	38.5
WP_002964018.1\|878715_878901_+	hypothetical protein	NA	NA	NA	NA
WP_002964019.1\|878949_880248_+	peptidoglycan DD-metalloendopeptidase family protein	Q8SBN9	Clostridium_phage	1.0e-18	41.1
WP_002964020.1\|880296_881163_-	ATP-binding protein	NA	NA	NA	NA
WP_002964021.1\|881322_881664_+	preprotein translocase subunit YajC	A0A1B1IVR5	uncultured_Mediterranean_phage	9.1e-12	40.2
WP_014490079.1\|881782_884110_+	protein translocase subunit SecDF	A0A1B1IVP7	uncultured_Mediterranean_phage	6.2e-51	43.5

DBSCAN-SWA_3

953130 : 963020

Brucella_phage(42.86%)

integrase

attL 953013:953053|attR 967995:968035

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
953013:953053	attL	NA	NA	NA	NA
WP_004686457.1\|953130_954156_-\|integrase	site-specific integrase	A0A141GEZ3	Brucella_phage	5.6e-49	36.7
WP_004683737.1\|954142_954346_-	hypothetical protein	NA	NA	NA	NA
WP_005968947.1\|954348_954564_-	hypothetical protein	NA	NA	NA	NA
WP_002964088.1\|954560_954764_-	hypothetical protein	NA	NA	NA	NA
WP_005968944.1\|954813_955518_+	hypothetical protein	A0A076GD06	Sinorhizobium_phage	4.5e-05	46.8
WP_002964091.1\|955514_955745_+	hypothetical protein	NA	NA	NA	NA
WP_002964092.1\|955741_956017_+	hypothetical protein	NA	NA	NA	NA
WP_002966806.1\|956039_956516_+	hypothetical protein	NA	NA	NA	NA
WP_004683739.1\|956861_957572_+	porin family protein	O11861	Bartonella_henselae_phage	5.1e-41	36.8
WP_002964095.1\|957919_958090_-	DUF1508 domain-containing protein	A0A2P1N580	Mycobacterium_phage	3.1e-05	45.1
WP_004683740.1\|958437_958752_-	BrnA antitoxin family protein	K4NZP3	Burkholderia_phage	2.0e-05	42.1
WP_002966807.1\|958751_958997_-	BrnT family toxin	NA	NA	NA	NA
WP_006135935.1\|960464_961157_+	hypothetical protein	A0A141GEY5	Brucella_phage	4.4e-106	97.5
WP_006135932.1\|961568_963020_+	hypothetical protein	A0A141GEY6	Brucella_phage	1.1e-135	56.9
967995:968035	attR	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