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_LT963351	Brucella melitensis isolate 1 chromosome 2	0 crisprs	DEDDh,csa3,cas3	0	0	0	0
NZ_LT963350	Brucella melitensis isolate 1 chromosome 1	1 crisprs	WYL,csa3,DEDDh	0	1	3	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NZ_LT963350_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_LT963350_1

1346882-1346964

Orphan

Consensus_repeat	Method
CCGAACACCGCTTCGCACTTTTCGGGAT	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_LT963350_1

>merge|NZ_LT963350|1|1346882-1346964|CRISPRCasFinder
CCGAACACCGCTTCGCACTTTTCGGGATACAGATCTTTCCTTGCGCGCATCTTATCCGAAAACCGCTTCGCACTTTTCGGGAT

>NZ_LT963350|1|1|1346882-1346964|CRISPRCasFinder
CCGAACACCGCTTCGCACTTTTCGGGAT	ACAGATCTTTCCTTGCGCGCATCTTAT
CCGAAAACCGCTTCGCACTTTTCGGGAT

Protein	Signature genes	Signature genes Name	Protein_function
NZ_LT963350.1\|WP_004683363.1\|1356084_1357011_+\|site-specific-integrase	unknown	unknown	gnl\|CDD\|271177
NZ_LT963350.1\|WP_002963797.1\|1341685_1342264_-\|orotate-phosphoribosyltransferase	unknown	unknown	gnl\|CDD\|273579
NZ_LT963350.1\|WP_002971501.1\|1336569_1337409_-\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|380379
NZ_LT963350.1\|WP_004683386.1\|1345562_1346138_+\|NYN-domain-containing-protein	unknown	unknown	gnl\|CDD\|350235
NZ_LT963350.1\|WP_101433142.1\|1351993_1352635_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT963350.1\|WP_004686526.1\|1347543_1348425_-\|4-hydroxy-tetrahydrodipicolinate-synthase	unknown	unknown	gnl\|CDD\|235107
NZ_LT963350.1\|WP_002963792.1\|1346168_1346840_+\|uracil-DNA-glycosylase	unknown	unknown	gnl\|CDD\|381681
NZ_LT963350.1\|WP_002963791.1\|1346976_1347453_-\|SsrA-binding-protein-SmpB	unknown	unknown	gnl\|CDD\|235455
NZ_LT963350.1\|WP_004686530.1\|1357373_1358507_+\|pyridoxal-phosphate-dependent-aminotransferase	unknown	unknown	gnl\|CDD\|181255
NZ_LT963350.1\|WP_004685524.1\|1348900_1350958_+\|lytic-transglycosylase-domain-containing-protein	unknown	unknown	gnl\|CDD\|381604
NZ_LT963350.1\|WP_004685525.1\|1342271_1344524_-\|bifunctional-(p)ppGpp-synthetase/guanosine-3',5'-bis(diphosphate)-3'-pyrophosphohydrolase	unknown	unknown	gnl\|CDD\|223394
NZ_LT963350.1\|WP_006136158.1\|1352778_1353867_-\|porin	unknown	unknown	gnl\|CDD\|308243
NZ_LT963350.1\|WP_004683395.1\|1337660_1338872_+\|MFS-transporter	unknown	unknown	gnl\|CDD\|341031
NZ_LT963350.1\|WP_004686525.1\|1340770_1341526_-\|helix-turn-helix-domain-containing-protein	unknown	unknown	gnl\|CDD\|236494
NZ_LT963350.1\|WP_002963795.1\|1344764_1345166_-\|DNA-directed-RNA-polymerase-subunit-omega	unknown	unknown	gnl\|CDD\|234744
NZ_LT963350.1\|WP_005969508.1\|1351020_1351677_-\|endonuclease	unknown	unknown	gnl\|CDD\|237082
NZ_LT963350.1\|WP_002966733.1\|1335944_1336520_-\|DUF2062-domain-containing-protein	unknown	unknown	gnl\|CDD\|225757
NZ_LT963350.1\|WP_002963787.1\|1351755_1351938_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT963350.1\|WP_004686524.1\|1339055_1340390_-\|oxygen-independent-coproporphyrinogen-III-oxidase	unknown	unknown	gnl\|CDD\|237356
NZ_LT963350.1\|WP_002970988.1\|1354706_1355810_+\|porin	unknown	unknown	gnl\|CDD\|308243

Protein	Function_ID	Function_description	E-value
NZ_LT963350.1\|WP_002963797.1\|1341685_1342264_-\|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
NZ_LT963350.1\|WP_002971501.1\|1336569_1337409_-\|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
NZ_LT963350.1\|WP_004683386.1\|1345562_1346138_+\|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
NZ_LT963350.1\|WP_004686526.1\|1347543_1348425_-\|4-hydroxy-tetrahydrodipicolinate-synthase	gnl\|CDD\|235107	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional.	7.73311e-177
NZ_LT963350.1\|WP_002963792.1\|1346168_1346840_+\|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
NZ_LT963350.1\|WP_002963791.1\|1346976_1347453_-\|SsrA-binding-protein-SmpB	gnl\|CDD\|235455	PRK05422, smpB, SsrA-binding protein SmpB.	1.57135e-88
NZ_LT963350.1\|WP_004686530.1\|1357373_1358507_+\|pyridoxal-phosphate-dependent-aminotransferase	gnl\|CDD\|181255	PRK08153, PRK08153, pyridoxal phosphate-dependent aminotransferase.	0
NZ_LT963350.1\|WP_004685524.1\|1348900_1350958_+\|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
NZ_LT963350.1\|WP_004685525.1\|1342271_1344524_-\|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
NZ_LT963350.1\|WP_006136158.1\|1352778_1353867_-\|porin	gnl\|CDD\|308243	pfam02530, Porin_2, Porin subfamily. This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to pfam00267. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria.	2.63888e-115
NZ_LT963350.1\|WP_004683395.1\|1337660_1338872_+\|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
NZ_LT963350.1\|WP_004686525.1\|1340770_1341526_-\|helix-turn-helix-domain-containing-protein	gnl\|CDD\|236494	PRK09391, fixK, transcriptional regulator FixK; Provisional.	1.10991e-50
NZ_LT963350.1\|WP_002963795.1\|1344764_1345166_-\|DNA-directed-RNA-polymerase-subunit-omega	gnl\|CDD\|234744	PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega; Reviewed.	1.70484e-25
NZ_LT963350.1\|WP_005969508.1\|1351020_1351677_-\|endonuclease	gnl\|CDD\|237082	PRK12373, PRK12373, NADH-quinone oxidoreductase subunit E.	1.44499e-28
NZ_LT963350.1\|WP_002966733.1\|1335944_1336520_-\|DUF2062-domain-containing-protein	gnl\|CDD\|225757	COG3216, COG3216, Uncharacterized protein conserved in bacteria [Function unknown].	5.43979e-83
NZ_LT963350.1\|WP_004683363.1\|1356084_1357011_+\|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
NZ_LT963350.1\|WP_004686524.1\|1339055_1340390_-\|oxygen-independent-coproporphyrinogen-III-oxidase	gnl\|CDD\|237356	PRK13347, PRK13347, coproporphyrinogen III oxidase; Provisional.	0
NZ_LT963350.1\|WP_002970988.1\|1354706_1355810_+\|porin	gnl\|CDD\|308243	pfam02530, Porin_2, Porin subfamily. This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to pfam00267. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria.	7.06318e-105

>NZ_LT963350.1|WP_002963792.1|1346168_1346840_+|uracil-DNA-glycosylase
MISEPSPNCSICPRLHAFLQEWRQKEPAWHNAPVPPFLPGSDEDVRLLIVGLAPGLRGANRTGRPFTGDYAGELLYSTLCEFGFATGKFEARPDDSLRLLDACIVNAVRCVPPENKPVGSEINNCRQFLTPMLTRFPNLDAVVTLGTIAHQSTVRALGVPVSRHPFGHGKATDIGPLRIFSSYHCSRYNTNTGVLTDAMFRDVFKNVRAYLSEKAAGSARLSV
>NZ_LT963350.1|WP_004683386.1|1345562_1346138_+|NYN-domain-containing-protein
MFDSREKIALFIDGANLYAASKTLGFDIDYRKLLKAFQKRGYLLRAYYYTALVEDQEYSSIRPLIDWLDYNGYKVVTKAAREFTDSTGRRKVKGNMDIELTVDAMQLTDTVDHFVIFSGYGDFRSLVEALQRKGRKVSVVSTLTTQPAMISDELRRQADHFIDLVSLKAEIGRDPSERAPRRQEEDFDESY
>NZ_LT963350.1|WP_002963795.1|1344764_1345166_-|DNA-directed-RNA-polymerase-subunit-omega
MARVTVEDCVDKVENRFELVLLAGHRARQISQGAPITVDRDNDKNPVVALREIADETLSPDDLKEDLIHSLQKHVEVDEPEAAPAQIANAAEEIAEGIAEAGEEDVVTFDRMSEEELLAGIEGLVAPEKNDGF
>NZ_LT963350.1|WP_004685525.1|1342271_1344524_-|bifunctional-(p)ppGpp-synthetase/guanosine-3',5'-bis(diphosphate)-3'-pyrophosphohydrolase
MMRQYELVERVQRYKPDVNEALLNKAYVYAMQKHGSQKRASGDPYFSHPLEVAAILTDMHLDEATIAIALLHDTIEDTTATRQEIDQLFGPEIGKLVEGLTKLKKLDLVSKKAVQAENLRKLLLAISEDVRVLLVKLADRLHNMRTLGVMREDKRLRIAEETMDIYAPLAGRMGMQDMREELEELAFRYINPDAWRAVTDRLAELLEKNRGLLQKIETDLSEIFEKNGIKASVKSRQKKPWSVFRKMESKGLSFEQLSDIFGFRVMVDTVQDCYRALGLIHTTWSMVPGRFKDYISTPKQNDYRSIHTTIIGPSRQRIELQIRTREMDEIAEFGVAAHSIYKDRGSANNPHKISTETNAYAWLRQTIEQLSEGDNPEEFLEHTKLELFQDQVFCFTPKGRLIALPRGATPIDFAYAVHTDIGDSCVGAKVNGRIMPLMTELKNGDEVDIIRSKAQVPPAAWESLVATGKARAAIRRATRSAVRKQYSGLGMRILERAFERAGKPFSKDILKPGLPRLARKDVEDVLAAVGRGELPSTDVVKAVYPDYQDTRVTTQNNPAKAGEKGWFNIQNAAGMIFKVPEGGEGAAAKVDPAATTPKPGKRALPIRGTNPDLPVRFAPEGAVPGDRIVGILQPGAGITIYPIQSPALTAYDDQPERWIDVRWDIDDQMSERFPARISVSAINSPGSLAEIAQIAAANDANIHNLSMVRTAPDFTEMIIDVEVWDLKHLNRIISQLKESASVSSAKRVNG
>NZ_LT963350.1|WP_002963797.1|1341685_1342264_-|orotate-phosphoribosyltransferase
MNTDDVLAVFREAGAILEGHFILTSGLRSPVFLQKARVFMHADKTEKLCKALAEKIRAADLGPIDYVVGPAIGGLIPSYETSRHLGVPSVWVERENGVFRLRRFDVPKGARVVIVEDIVTTGLSIRETIDCMKDLGIEVVAAACIVDRSAGKADVGTRLISLAEYEVPAYPADKLPPELAAIPAVKPGSRNI
>NZ_LT963350.1|WP_004686525.1|1340770_1341526_-|helix-turn-helix-domain-containing-protein
MVVVPFALDQNQKLAARTPCNVCEDCCVRSMAVCSALDDGDLAALEAIMTSKKLDTNEMLVEEGEPKLRVYSLTSGMLRIYTSLPDGRRQIAGFLFPGDFLGLADDEVYSLSAEAVVPSALCAFSAKEMERLMERFPKLKERLYQMTRLALRTARDNQLVLGRLAPVEKLASFLLVLSARAEKRGEKPNPVHLLMNRTDIADYLGLTIETVSRSFTKLKTQGLIQLRDANTVEILSRRSLAVVAGLDPDNL
>NZ_LT963350.1|WP_004686524.1|1339055_1340390_-|oxygen-independent-coproporphyrinogen-III-oxidase
MHDDAIRRYAALAVPRYTSYPTAADFVPVGMDTTRRWLRQIGPEESVSLYIHVPYCSQICHYCGCNAKMAIREDVIENFVNALLGEIRTVSASLTARPRVAHLHWGGGTPSILNAGQFQTVLAAIRTAFDFDLSMEHAIELDPRTVTPLLAKTLAEMGVNRASLGVQDVDSRVQMAIGRVQPIETVAEATRLLREVGINRINFDLIYGLPLQTVETLRETCERVVTLSPDRVACYGYAHLPQRRANQRLIDENTLPDADERFRQARIVTDSFIGFGYQPVGIDHFALPDDDLAIAAREGTLNRNFQGYTNDRCGTLIGFGPSSISQFPGGYAQNISDVGQYRKRVEAGELATVRGYTLRDADRIRSAIISALMCNFCVDLNAVAPGMEFSDEFALLRPLVADGLVAVEGRTIRATENGKSLIRLVAAAFDEFRRDSVHGFSFAV
>NZ_LT963350.1|WP_004683395.1|1337660_1338872_+|MFS-transporter
MSVSAAQQPSNSSADNTVLTIILATSLGHFLNDMMQSLLPAIYPMLKENYSLSFWQIGLLTFTFQMTASILQPLVGIYTDRKPMPYSLTFGMGCTLIGLVFLATAHHYSFLLLGAACVGFGSSVFHPEAARVARLASGGRHGFAQSLFQVGGNFGSSIGPLLAAFIVLPFGQISVSWFSVAALIGMFVLWYVGNWYNRYRLANANKPKPDKTLPLPRNRVIASVAVLALLVFTKYIYMASLTSYYTFYTISHFGVSVQTSQLLLFLFLGAVAAGTIIGGPIGDKIGARKVIWASILGVLPFTLALPYANLEMTAVLTIIIGLILASAFPAIIVFAQELLPGRVGMLSGLFFGFAFGMAGIAAAVLGIVADQKGIEFVYRICSYLPFLGLLTIFLPKLERRRKA
>NZ_LT963350.1|WP_002971501.1|1336569_1337409_-|helix-turn-helix-transcriptional-regulator
MPENEDLQRFHEHRIAMLESMTGPAIALPTRYPDGYFVPRHSHSRAQLLCASQGVVLVTTDAGRWMIPSDHAMWIPAGVEHSVAILGDVFMRSIYISVDAISGVPNYLHVVGLTDLMRCLIIDATSHDSIPAPESRDGLVIELILRDLHTLPEYPLGLPFPSDPRLQKLCRDFVKKPSSRATIDEWADRMAMSRRSFTRHFQRETGVSLSVWRQQACLFAAVPRLSEGEPVTSVALDLGYDSVSAFTTMFRRMLGVPPKFYQPRLDVAPFERSDKAAFG
>NZ_LT963350.1|WP_002966733.1|1335944_1336520_-|DUF2062-domain-containing-protein
MLFQRRYPPTRWERLRLYLWPRRSFSRSFRYGGKRILRITASPHAVAAGLAVGVFSAFTPFFGFHLIIAIVLAYFLAGNVAAAALGTTLANPLTLPFIWGSTFELGRFIMSGSVDSVPPVHLGHALETMRFEEVWTPLLKPMLFGSTILGAAFAVLVYFVTRYAVSVFRRRRLERLAEKHRLHRQRELQKA
>NZ_LT963350.1|WP_002963791.1|1346976_1347453_-|SsrA-binding-protein-SmpB
MNKPKNSPARKMIAENRKARFNFEILDTLEAGLVLTGTEVKSLRANQANIAESYASFEDGEFWLINSYIPEYTQGNRFNHEPRRLRKLLVSRREMSRLFNSVSREGMTVVPLKLYFNDRGRAKLELALARGKKTHDKRETEKKRDWNREKARLLRDRG
>NZ_LT963350.1|WP_004686526.1|1347543_1348425_-|4-hydroxy-tetrahydrodipicolinate-synthase
MLKGSITALVTPFDREGAFDEKAFRAFVNWQIEEGTKGLVPVGTTGETPTLSHDEHKRVIEVCIEVAAGRVPVIAGAGSNNTVEAIELAQHAEKAGADAVLVVTPYYNKPNQRGLYEHFSRVARSISIPLVIYNVPGRSIIDMTPETMGALVRDCKNIVGVKDATGKIERVSEQRAICGKEFIQLSGEDATALGFNAHGGVGCISVTSNIAPRLCAEFQEACQAGNFAKALELQDRLMPLHKALFLEPNPSGPKYALSRLGRIENVLRSPMVTIEAATAEKIDHAMKHAVLIN
>NZ_LT963350.1|WP_004685524.1|1348900_1350958_+|lytic-transglycosylase-domain-containing-protein
MVSLAQSSLPPEIPTPLARPFAPTATHQSPISLVTPRPRPIAPDPMATSAVSRTDNPAVIGGTLKNGLDALSAKNVASAIASRNNLPRGSLDRQILTWAIATSGMDGVPSTEIAAAASELSGWPGMATLRRNSERALFKENPSSATIIATFGSTRPQTTEGMIALARAYVATGNSTKAHQLLSPWWTRKRLSSDDEQKILKEFSAILTREDHQRRLLHSLYNGHLQSARLLAGPAQAQSLYNAYAAVAQKSPNAASAIAAVDRSWQANPVYQFLKIRYLRRAERYNEAAELLLKAPRKASVLVDPDAWWVERRILSRELLDLGKPQLAYRLAAAHAAETPTMAAEAEFHAGWYALRALNQPKLAAPHFAKITQISARPISASRAYYWLGRAAEAGSGGDARAYYRRSAHFGTTFYGQLAAAKLNEKAPELAYPKPTEAERVRFASRPAVQAIKRLEQVGYGNKAAALYTQLSQELDSVGELALLAVMAERNDNHYMALRVGKTAAMRGLDVGALSHPLGAIPASANIKGSGKALAYAIARQESEFNVSAVSKAGARGLLQLMPATAKTVATRNGMSFSAQKLTADAAYNATLGAHFLGEQLDRFNGSYVLTFAGYNAGPRRASEWVEKYGDPRGKSVEQVVDWIERIPYSETRNYVQRVMENYEVYKTRLTGRADIKTDLVYGRR
>NZ_LT963350.1|WP_005969508.1|1351020_1351677_-|endonuclease
MPLLIVQLAILIAVAFVVGCFLGRILRRRKSAGSDHERTIVAAALSTPPLAEKPEPVPPAEPVRADSDPLKRKAGLEKARIEPVEGSADSDVAAAPVLKKVPAETPDDAGRPQWREAPRRGKADELTAIEGIGKAIEAVLHELGIFHYDQIAQWTREEAIWIERRIGFPGRVEREGWIAQAAKLAEPPAKSTTKRGAKTKKAANNVRSGTRRAKKQAG
>NZ_LT963350.1|WP_002963787.1|1351755_1351938_-|hypothetical-protein
MTVFPIRPFLCYDYSAKGLKCLAKYYAESLMLYLVETFWPVLVLAILIGAATGWLTAGER
>NZ_LT963350.1|WP_101433142.1|1351993_1352635_-|hypothetical-protein
MKKWFWPCLTWTACLTALALWFGADRVETDIAEQTAKALEPYVWAGFYVDGRDVVLKGMAPDPDMQRAAHAALEHVWAIRDITDLTTVLQLASPYRFKIGRNAQGLVLSGFIPNNESRDQVMTAAGEVAPDIFIDNEMAVARGNQPEFMERVLFAIDLAKKLPEAEIEIVDEKLSIRGTVSDEAIYDEIEALKAAQLPYGLKLAVLDVKKSVQ
>NZ_LT963350.1|WP_006136158.1|1352778_1353867_-|porin
MNIKSLLLGSAAALVAASGAQAADAIVAPESEAVEYVRVCDAYGAGYFYIPGTETCLRVHGYVRYDVKGGDDVYSGTDRNGWDKGARFALRVSTGSETELGTLKTFTELRFNYAANNSGVDGKYGNETSSGTVMEFAYIQLGGLRVGIDESEFHTFTGYLGDVINDDVISAGSYRTGKIAYTFTGGNGFSAVIALEQGGDNDGGYTGTTNYHIDGYMPDVVGGLKYAGGWGSIAGVVAYDSVIEEWAAKVRGDVNITDQFSVWLQGAYSSAATPDQNYGQWGGDWAVWGGLKYQATQKAAFNLQAAHDDWGKTAVTANVAYELVPGFTVTPEVSYTKFGGEWKNTVAEDNAWGGIVRFQRSF
>NZ_LT963350.1|WP_002970988.1|1354706_1355810_+|porin
MNIKSLLLGSAAALVAASGAQAADAIVAPEPEAVEYVRVCDAYGAGYFYIPGTETCLRVHGYVRYDVKGGDDVYSGTDRNGWDKGARFALMFNTNSETELGTLGTYTQLRFNYTSNNSRHDGQYGDFSDDRDVADGGVSTGTDLQFAYITLGGFKVGIDESEFHTFTGYLGDVINDDVVAAGSYRTGKIAYTFTGGNGFSAVIALEQGGEDVDNDYTIDGYMPHVVGGLKYAGGWGSIAGVVAYDSVIEEWATKVRGDVNITDRFSVWLQGAYSSAATPNQNYGQWGGDWAVWGGAKFIAPEKATFNLQAAHDDWGKTAVTANVAYQLVPGFTITPEVSYTKFGGEWKDTVAEDNAWGGIVRFQRSF
>NZ_LT963350.1|WP_004683363.1|1356084_1357011_+|site-specific-integrase
MIIVGETKIDTGDKYAPIIDYNLNYISGKNPKHRLVEHYSVAELTAKYINILWDDGPHKYNVRSFLGEIDEILKGARFSGFDQEMLDSIIGTLRERGNSNATINRKMAALSKLLRKAHKMGDIFNLPEFIRQKERVGRIRFLEQEEEKRLFAAIKSRCEDSYRLSVFLVDTGCRLGEAIGLTWNDIQEQRVTFWVTKSNRSRTVPLTRRARKASHIPRERLKGPFSMLNQVRFRQIWNEAKAEVGLGADDQIVPHILRHTCASRLVRGGIDIRRVQMWLGHQTLQMTMRYAHLATHDLDSCVKVLEIH
>NZ_LT963350.1|WP_004686530.1|1357373_1358507_+|pyridoxal-phosphate-dependent-aminotransferase
MAQPRLTPLVESLPSTVPFIGPETLELQRGKPFEARIGANENSFGPAPSVIEAMRNEATEVWKYGDPENYALRHAIAAHHGLKAEHIMPGAGVDALLGLIVRQYVQQGDKVINSLGGYPTFNYHVAGYGGQLVTVPYRDDKPDLDALIDAAAREKPALLYIANPDNPMGTWHGGADIQSFIERLPETTLLILDEAYCETAPASAFPPFETDRPNVLRMRTFSKAYGLAGIRCGYAVGNPVAIKTFDKVRDHFAVSRMAQAAAIAALKDQAYLHEVVGKICAGRDRIAAIAEANGLHAVASATNFVAIDCGRGKDFAQAVLNGLISRDIFVRKPGTPVLDRCIRVSVGVKEQLDQFEAAFPEALEEARKICAANAENT

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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_LT963350_1	1.1\|1346910\|27\|NZ_LT963350\|CRISPRCasFinder	1346910-1346936	27	NZ_CP013986	Klebsiella variicola strain LMG 23571 plasmid unnamed, complete sequence	45587-45613	5	0.815

1. spacer 1.1|1346910|27|NZ_LT963350|CRISPRCasFinder matches to NZ_CP013986 (Klebsiella variicola strain LMG 23571 plasmid unnamed, complete sequence) position: , mismatch: 5, identity: 0.815

acagatctttccttgcgcgcatcttat	CRISPR spacer
tcagatctttccttgagagcatctgtt	Protospacer
 ************** * ******  *

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1040430 : 1048769

Brucella_phage(33.33%)

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_006135932.1\|1040430_1041882_-	hypothetical protein	A0A141GEY6	Brucella_phage	1.1e-135	56.9
WP_029077469.1\|1042293_1042986_-	hypothetical protein	A0A141GEY5	Brucella_phage	1.3e-105	97.0
WP_002966807.1\|1044585_1044831_+	BrnT family toxin	NA	NA	NA	NA
WP_004683740.1\|1044830_1045145_+	BrnA antitoxin family protein	K4NZP3	Burkholderia_phage	2.0e-05	42.1
WP_002964095.1\|1045492_1045663_+	DUF1508 domain-containing protein	A0A2P1N580	Mycobacterium_phage	3.1e-05	45.1
WP_004683739.1\|1046010_1046721_-	porin family protein	O11861	Bartonella_henselae_phage	5.1e-41	36.8
WP_002966806.1\|1047066_1047543_-	hypothetical protein	NA	NA	NA	NA
WP_002964092.1\|1047565_1047841_-	hypothetical protein	NA	NA	NA	NA
WP_002964091.1\|1047837_1048068_-	hypothetical protein	NA	NA	NA	NA
WP_005968944.1\|1048064_1048769_-	hypothetical protein	A0A076GD06	Sinorhizobium_phage	4.5e-05	46.8

DBSCAN-SWA_2

1119476 : 1131388

uncultured_Mediterranean_phage(90.0%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_014490079.1\|1119476_1121804_-	protein translocase subunit SecDF	A0A1B1IVP7	uncultured_Mediterranean_phage	6.2e-51	43.5
WP_002964021.1\|1121922_1122264_-	preprotein translocase subunit YajC	A0A1B1IVR5	uncultured_Mediterranean_phage	9.1e-12	40.2
WP_002964020.1\|1122423_1123290_+	ATP-binding protein	NA	NA	NA	NA
WP_002964019.1\|1123338_1124637_-	peptidoglycan DD-metalloendopeptidase family protein	Q8SBN9	Clostridium_phage	1.0e-18	41.1
WP_002964018.1\|1124685_1124871_-	hypothetical protein	NA	NA	NA	NA
WP_004683704.1\|1125015_1125684_-	protein-L-isoaspartate(D-aspartate) O-methyltransferase	A0A1B1IU40	uncultured_Mediterranean_phage	6.6e-14	38.5
WP_004683703.1\|1125680_1126448_-	5'/3'-nucleotidase SurE	A0A1B1ITZ2	uncultured_Mediterranean_phage	1.0e-39	40.2
WP_004683702.1\|1126596_1127880_-\|tRNA	serine--tRNA ligase	A0A1B1IVT2	uncultured_Mediterranean_phage	2.6e-104	47.2
WP_002964014.1\|1127956_1128781_-	twin-arginine translocase subunit TatC	A0A1B1IVR7	uncultured_Mediterranean_phage	9.8e-44	41.1
WP_006094283.1\|1128777_1129344_-	twin-arginine translocase subunit TatB	NA	NA	NA	NA
WP_002964012.1\|1129454_1129673_-	twin-arginine translocase TatA/TatE family subunit	A0A1B1IVR9	uncultured_Mediterranean_phage	1.5e-07	65.1
WP_002964011.1\|1129818_1130544_-	SMC-Scp complex subunit ScpB	A0A1B1IVT7	uncultured_Mediterranean_phage	1.5e-43	45.7
WP_004683698.1\|1130536_1131388_-	segregation/condensation protein A	A0A1B1IVW1	uncultured_Mediterranean_phage	4.4e-31	33.5

DBSCAN-SWA_3

1356084 : 1403198

Mesorhizobium_phage(12.5%)

tail,integrase,portal,protease

attL 1346889:1346903|attR 1360326:1360340

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
1346889:1346903	attL	NA	NA	NA	NA
WP_004683363.1\|1356084_1357011_+\|integrase	site-specific integrase	A0A076YL28	Mesorhizobium_phage	5.9e-29	31.6
WP_004686530.1\|1357373_1358507_+	pyridoxal phosphate-dependent aminotransferase	A0A1X7QHI1	Faustovirus	2.4e-16	24.2
WP_006136160.1\|1358524_1358899_+	DUF423 domain-containing protein	NA	NA	NA	NA
WP_004683357.1\|1358943_1359594_-	hypothetical protein	NA	NA	NA	NA
WP_004683355.1\|1360248_1361019_+	YitT family protein	NA	NA	NA	NA
1360326:1360340	attR	NA	NA	NA	NA
WP_004683353.1\|1361078_1361336_-	sel1 repeat family protein	NA	NA	NA	NA
WP_004686532.1\|1361605_1361845_+	hypothetical protein	NA	NA	NA	NA
WP_002963776.1\|1361841_1362189_+	DUF2147 domain-containing protein	NA	NA	NA	NA
WP_004683348.1\|1362247_1362958_-	glutathione S-transferase N-terminal domain-containing protein	NA	NA	NA	NA
WP_002971518.1\|1363152_1363320_+	hypothetical protein	NA	NA	NA	NA
WP_004683346.1\|1363316_1363484_+	hypothetical protein	NA	NA	NA	NA
WP_004683344.1\|1363524_1365027_+	AMP nucleosidase	NA	NA	NA	NA
WP_006136161.1\|1365079_1366156_+	endonuclease/exonuclease/phosphatase family protein	NA	NA	NA	NA
WP_004683340.1\|1366271_1367963_-	electron transfer flavoprotein-ubiquinone oxidoreductase	NA	NA	NA	NA
WP_002963769.1\|1368351_1369224_+	uracil-DNA glycosylase	NA	NA	NA	NA
WP_005969556.1\|1369385_1370642_+	MFS transporter	NA	NA	NA	NA
WP_002963767.1\|1370646_1371606_-	DMT family transporter	NA	NA	NA	NA
WP_004685516.1\|1371831_1374483_+	aminopeptidase N	NA	NA	NA	NA
WP_002963765.1\|1374873_1377225_+	PAS-domain containing protein	A0A1V0SGX0	Hokovirus	6.3e-27	34.8
WP_002966727.1\|1377495_1379607_+	O-antigen ligase family protein	NA	NA	NA	NA
WP_004685514.1\|1379651_1382603_-	bifunctional [glutamine synthetase] adenylyltransferase/[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase	NA	NA	NA	NA
WP_005969562.1\|1382725_1384132_-	HAMP domain-containing histidine kinase	NA	NA	NA	NA
WP_004683323.1\|1384128_1384836_-	response regulator transcription factor	NA	NA	NA	NA
WP_004683321.1\|1384929_1386471_-\|protease	DegQ family serine endoprotease	A0A1B1IT49	uncultured_Mediterranean_phage	1.7e-28	29.8
WP_004683319.1\|1386612_1387089_-	cytochrome c-type biogenesis protein CcmH	NA	NA	NA	NA
WP_002963758.1\|1387085_1389077_-	heme lyase CcmF/NrfE family subunit	NA	NA	NA	NA
WP_002963757.1\|1389096_1389594_-	cytochrome c maturation protein CcmE	NA	NA	NA	NA
WP_004686536.1\|1389590_1390730_-	c-type cytochrome biogenesis protein CcmI	NA	NA	NA	NA
WP_002971524.1\|1390830_1391283_-	hypothetical protein	NA	NA	NA	NA
WP_002969444.1\|1391376_1392687_-	hypothetical protein	NA	NA	NA	NA
WP_002963753.1\|1392761_1393451_-	response regulator transcription factor	NA	NA	NA	NA
WP_002971526.1\|1393529_1393826_-	hypothetical protein	NA	NA	NA	NA
WP_002969445.1\|1393987_1394194_-	hypothetical protein	NA	NA	NA	NA
WP_004683307.1\|1398126_1398561_-	C40 family peptidase	NA	NA	NA	NA
WP_004683305.1\|1398557_1399433_-	DUF2163 domain-containing protein	A0A0K1Y6Z2	Rhodobacter_phage	4.5e-47	38.9
WP_002963747.1\|1399429_1400062_-	TIGR02217 family protein	A0A0B5A2K3	Paracoccus_phage	2.9e-48	47.6
WP_002970984.1\|1400064_1400610_-\|tail	phage tail tape measure protein	A0A0S2SYD9	Pseudomonas_phage	2.8e-07	46.4
WP_004683301.1\|1400614_1400785_-\|tail	phage tail assembly chaperone	NA	NA	NA	NA
WP_004683300.1\|1400828_1401170_-	gene transfer agent family protein	NA	NA	NA	NA
WP_002963743.1\|1401166_1401580_-\|tail	phage major tail protein, TP901-1 family	NA	NA	NA	NA
WP_002967499.1\|1401630_1402008_-	hypothetical protein	NA	NA	NA	NA
WP_002963736.1\|1402004_1403198_-\|portal	phage portal protein	W8ECU7	Geobacillus_phage	7.0e-67	40.0

Anti-CRISPR protein detection

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