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_018644	Alpha proteobacterium HIMB59, complete sequence	1 crisprs	DEDDh,cas3	0	3	3	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_018644_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018644_1

284800-285215

Orphan

Consensus_repeat	Method
AANGCTGCAAANAANAAAGC	CRT

7 spacers

The CRISPR arrays of NC_018644_1

>merge|NC_018644|1|284800-285215|CRT
ATGGCTGTAAAAAAGAAAAAAGCTGCCAAGAAGAAAGCAGCTCCTAAGAAAAAGACTGCTAGAAAAGCAGCAACTAAGAAAAAAGCTGTAAAGAAAAAAGCAGCACCTAAGAAAGCTGCAAAAAAGAAAGCAGCACCTAAGAAGAAAAAAGCCACTAAGAAAAAAGCTGCAAAGAGAAAAGCTGTAAAGAGAAAAGCAGCTAAGAAAAAAGCAGCACCTAAGAAAGCTGCAAAGAAAAAAGCGGCTCCTAAGAAGAAGAAGGCTGCACCTAAGAGAAAGGCTGCAAAGAAAAAAGCGGCTCCTAAGAAGAAGGCTGCACCTAAAAAGAAAAAGGCAGCTCCTAAGAAGAAGAAGGCAGCTCCAAAAAAAGCGGCTAAAAGAAAAGCAGCACCTAAGAAGGCTGCAAAAAGAAAAGC

>NC_018644|1|1|284800-285215|CRT
ATGGCTGTAAAAAAGAAAAA	AGCTGCCAAGAAGAAAGCAGCTCCTAAGAAAAAGACTGCTAGA
AAAGCAGCAACTAAGAAAAA	AGCTGTAAAGAAAAAAGCAGCACCTAAG
AAAGCTGCAAAAAAGAAAGC	AGCACCTAAGAAGAAAAAAGCCACTAAGAAA
AAAGCTGCAAAGAGAAAAGC	TGTAAAGAGAAAAGCAGCTAAGAAAAAAGCAGCACCTAAG
AAAGCTGCAAAGAAAAAAGC	GGCTCCTAAGAAGAAGAAGGCTGCACCTAAGAGA
AAGGCTGCAAAGAAAAAAGC	GGCTCCTAAGAAGAAGGCTGCACCTAAAAAGAAAAAGGCAGCTCCTAAGAAGAAG
AAGGCAGCTCCAAAAAAAGC	GGCTAAAAGAAAAGCAGCACCTAAG
AAGGCTGCAAAAAGAAAAGC

Protein	Signature genes	Signature genes Name	Protein_function
NC_018644.1\|WP_014954352.1\|290459_291299_-\|ABC-transporter-permease-subunit	unknown	unknown	gnl\|CDD\|223836
NC_018644.1\|WP_014954348.1\|287358_287811_+\|cytochrome-c-maturation-CcmE-like-protein	unknown	unknown	gnl\|CDD\|376989
NC_018644.1\|WP_014954339.1\|280292_280643_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|370551
NC_018644.1\|WP_014954345.1\|285294_285894_+\|heme-ABC-exporter-ATP-binding-protein-CcmA	unknown	unknown	gnl\|CDD\|237421
NC_018644.1\|WP_014954342.1\|281695_282130_-\|TerB-family-tellurite-resistance-protein	unknown	unknown	gnl\|CDD\|377455
NC_018644.1\|WP_041485377.1\|278457_279369_-\|homocysteine-S-methyltransferase-family-protein	unknown	unknown	gnl\|CDD\|376828
NC_018644.1\|WP_014954347.1\|286549_287257_+\|heme-exporter-protein-CcmC	unknown	unknown	gnl\|CDD\|273492
NC_018644.1\|WP_014954337.1\|279496_279985_+\|RecX-family-protein	unknown	unknown	gnl\|CDD\|234646
NC_018644.1\|WP_014954338.1\|279986_280247_-\|50S-ribosomal-protein-L32	unknown	unknown	gnl\|CDD\|223410
NC_018644.1\|WP_014954334.1\|277576_278050_+\|GcrA-cell-cycle-regulator	unknown	unknown	gnl\|CDD\|254404
NC_018644.1\|WP_014954353.1\|291299_292166_-\|ABC-transporter-permease-subunit	unknown	unknown	gnl\|CDD\|226670
NC_018644.1\|WP_014954335.1\|278068_278461_+\|hypothetical-protein	unknown	unknown	unknown
NC_018644.1\|WP_014954340.1\|280644_281367_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|224248
NC_018644.1\|WP_014954349.1\|287811_289644_+\|heme-lyase-CcmF/NrfE-family-subunit	unknown	unknown	gnl\|CDD\|224061
NC_018644.1\|WP_014954346.1\|285890_286550_+\|CcmB-protein	unknown	unknown	gnl\|CDD\|281385
NC_018644.1\|WP_014954343.1\|282119_284666_-\|helicase	unknown	unknown	gnl\|CDD\|350192
NC_018644.1\|WP_041485247.1\|292158_293265_-\|FAD-binding-oxidoreductase	unknown	unknown	gnl\|CDD\|223737
NC_018644.1\|WP_014954351.1\|290097_290457_+\|cytochrome-c-biogenesis-protein	unknown	unknown	gnl\|CDD\|319866
NC_018644.1\|WP_014954350.1\|289640_290123_+\|redoxin-domain-containing-protein	unknown	unknown	gnl\|CDD\|239308
NC_018644.1\|WP_014954341.1\|281366_281699_-\|ferredoxin-family-protein	unknown	unknown	gnl\|CDD\|378771

Protein	Function_ID	Function_description	E-value
NC_018644.1\|WP_014954352.1\|290459_291299_-\|ABC-transporter-permease-subunit	gnl\|CDD\|223836	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism].	1.78457e-37
NC_018644.1\|WP_014954348.1\|287358_287811_+\|cytochrome-c-maturation-CcmE-like-protein	gnl\|CDD\|376989	pfam03100, CcmE, CcmE. CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.	7.72313e-41
NC_018644.1\|WP_014954339.1\|280292_280643_+\|hypothetical-protein	gnl\|CDD\|370551	pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.	1.90319e-07
NC_018644.1\|WP_014954345.1\|285294_285894_+\|heme-ABC-exporter-ATP-binding-protein-CcmA	gnl\|CDD\|237421	PRK13539, PRK13539, cytochrome c biogenesis protein CcmA; Provisional.	2.20201e-41
NC_018644.1\|WP_014954342.1\|281695_282130_-\|TerB-family-tellurite-resistance-protein	gnl\|CDD\|377455	pfam05099, TerB, Tellurite resistance protein TerB. This family contains the TerB tellurite resistance proteins from a a number of bacteria.	3.366e-20
NC_018644.1\|WP_041485377.1\|278457_279369_-\|homocysteine-S-methyltransferase-family-protein	gnl\|CDD\|376828	pfam02574, S-methyl_trans, Homocysteine S-methyltransferase. This is a family of related homocysteine S-methyltransferases enzymes: 5-methyltetrahydrofolate--homocysteine S-methyltransferases also known EC:2.1.1.13; Betaine--homocysteine S-methyltransferase (vitamin B12 dependent), EC:2.1.1.5; and Homocysteine S-methyltransferase, EC:2.1.1.10,.	4.54702e-44
NC_018644.1\|WP_014954347.1\|286549_287257_+\|heme-exporter-protein-CcmC	gnl\|CDD\|273492	TIGR01191, Heme_exporter_protein_C, heme exporter protein CcmC. This model describes the cyt c biogenesis protein encoded by ccmC in bacteria. It must be noted an arabidopsis, a tritcum and a piscum plant proteins were recognizable in the clade. Quite likely they are of organellar origin. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes, ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in the heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c. [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Other].	5.41691e-57
NC_018644.1\|WP_014954337.1\|279496_279985_+\|RecX-family-protein	gnl\|CDD\|234646	PRK00117, recX, recombination regulator RecX; Reviewed.	3.56049e-09
NC_018644.1\|WP_014954338.1\|279986_280247_-\|50S-ribosomal-protein-L32	gnl\|CDD\|223410	COG0333, RpmF, Ribosomal protein L32 [Translation, ribosomal structure and biogenesis].	3.85319e-18
NC_018644.1\|WP_014954334.1\|277576_278050_+\|GcrA-cell-cycle-regulator	gnl\|CDD\|254404	pfam07750, GcrA, GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.	1.44375e-32
NC_018644.1\|WP_014954353.1\|291299_292166_-\|ABC-transporter-permease-subunit	gnl\|CDD\|226670	COG4215, ArtQ, ABC-type arginine transport system, permease component [Amino acid transport and metabolism].	1.52961e-39
NC_018644.1\|WP_014954340.1\|280644_281367_-\|hypothetical-protein	gnl\|CDD\|224248	COG1329, COG1329, Transcriptional regulators, similar to M. xanthus CarD [Transcription].	8.44223e-45
NC_018644.1\|WP_014954349.1\|287811_289644_+\|heme-lyase-CcmF/NrfE-family-subunit	gnl\|CDD\|224061	COG1138, CcmF, Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones].	2.10282e-123
NC_018644.1\|WP_014954346.1\|285890_286550_+\|CcmB-protein	gnl\|CDD\|281385	pfam03379, CcmB, CcmB protein. CcmB is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor. CcmB is required for the export of haem to the periplasm.	7.25192e-09
NC_018644.1\|WP_014954343.1\|282119_284666_-\|helicase	gnl\|CDD\|350192	cd18805, SF2_C_suv3, C-terminal helicase domain of ATP-dependent RNA helicase. The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.	6.31403e-34
NC_018644.1\|WP_041485247.1\|292158_293265_-\|FAD-binding-oxidoreductase	gnl\|CDD\|223737	COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism].	8.86771e-28
NC_018644.1\|WP_014954351.1\|290097_290457_+\|cytochrome-c-biogenesis-protein	gnl\|CDD\|319866	cd16378, CcmH_N, N-terminal domain of cytochrome c-type biogenesis protein CcmH and related proteins. Cytochrome c-type biogenesis protein CcmH is a membrane-anchored thiol-oxidoreductase that is essential in the maturation of c-type cytochromes. CcmH consists of an N-terminal catalytic domain with the active site CXXC motif and a C-terminal domain of unknown function which is predicted to contain TPR-like repeats. Other members of this family include NrfF, CycL, and Ccl2.	3.97417e-18
NC_018644.1\|WP_014954350.1\|289640_290123_+\|redoxin-domain-containing-protein	gnl\|CDD\|239308	cd03010, TlpA_like_DsbE, TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif. Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. The reductase activity of DsbE in the oxidizing environment of the periplasm is crucial in the maturation of cytochrome c.	1.52155e-38
NC_018644.1\|WP_014954341.1\|281366_281699_-\|ferredoxin-family-protein	gnl\|CDD\|378771	pfam11953, DUF3470, Domain of unknown function (DUF3470). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 50 amino acids in length. This domain is found associated with pfam00037. This domain has a single completely conserved residue N that may be functionally important.	1.7791e-15

>NC_018644.1|WP_014954343.1|282119_284666_-|helicase
MSQVEIILGPTNTGKTFYAFEQMFSYQSGVFGFPLRLLARENYDKACNLYPINQIALITGEEKIIPKDAKYFFCTVESMPEDFFEFVCVDEIQLAADYERGHIFTQRILYARGEQKTIFLGSTTMEEIIKELIPDVEIKFKNRFSELNFIGHKKIQNIKPRSAIIAFNLIGLYEIAEQIRSLKGGVALVAGALSPKTRNSQVKLYEDGEVDYIVATDAIGMGLNLNINQVYFSGLEKFDGKYTRPLSDMEVAQIAGRAGRYTKSGYFGSTLGAKFTNMEIVENVLAHRFEPVRKIFWRNHLLSFKSTYELTQSLKKQPTNQRLILKKDAEDQKFLFSILNNKKISSLLNSPESLQQLWDVCRIPDYQSISEEKHTSLLIEIFTELKNHNWLLTDLFLKKNIERLQDYSGSIDDLIYTLNETRIWLYITNQKQWIPNNSWVEQVKNIEDKLSEEIHQSLMQKFVDKNKSEVVQNLNISEKNISVSNHTYVMIKDEKIGVITGFKIFFDEKFNDILNNNYKKIIKEQISQNMTINVENFLSAPDESLILKPDFDDQGQFTNLYIAWGEANIGIVSKGNEILKPKISAIYDDNLINIEQADQILKKIETWFQNTFLQKVDLSILLGKYNSTPEERSFIFKLIENQYNFHQLNILDEFKQIEESKRKEIHSLNFRLGKNVIFNSELIRPELMKLKFYLWNIFYSENNNVDFYIPKDGNATLNAQSTLNLDLIKFLGFIFQNKLLIRIDIFNEFEKQLFKRENRGPFSLPMDLSNLLGIKKEKLIEILNERSYLVQEIEENDLLISKKITSNKKPTSKKSNKLAEKKNKKEKKSTPKKLFNNPFDQLKDIDAK
>NC_018644.1|WP_014954342.1|281695_282130_-|TerB-family-tellurite-resistance-protein
MLNKFFQSFHEPKNSDENTFQSDLYNLIYEIIIADHEISPEEIDLSAELVEFYFQIPKDQNKQEFLKLADKQHFNTDLSQFTQRLKVSLSYEQRMDIILICWQVLMVDGIEDQLETSTVRTLSTLLGLEDKDFILIRNRVKDSL
>NC_018644.1|WP_014954341.1|281366_281699_-|ferredoxin-family-protein
MTYLVNDKCIKCKYMDCVEVCPVDCFYEGENMLVINPDECIDCGVCEPECPIEAIIPDNLDDGTKWLDVNEKYSQIWPNIKSKKESPADAKEYEGVENKFEKYFSEKGAE
>NC_018644.1|WP_014954340.1|280644_281367_-|hypothetical-protein
MPAKKKATTKKTTKKKIVKTKAVKKAAVKKTTTKKKTVTKKVAKVAKKTAKKVVKKTAKKVVKKIVTPKAPKIKKIVAPQEFKAGENIVYPTHGVGRILTIEKFQYDLVEEQLYVIQFFQDKLTIRVPFAKAKLIGLRNITSKPSMTRTLSILKQKPKIKKAMWSRRAQEYDQKINSGDIKQLSEVVRDLFRKDDQTEQSYSERQMFQVAFERYTREFAISSDLKFEEASSKILEILNKR
>NC_018644.1|WP_014954339.1|280292_280643_+|hypothetical-protein
MYKSATMSEENIDLGHKRTCPHCSVKYYDFYQDELDCPECGKTIEAVNIMKPKRGRKAGVTVATTSTKTVKENDELKDLIDETDDSAVPSDEDDNDNLAEDISLDISKDKSDDETA
>NC_018644.1|WP_014954338.1|279986_280247_-|50S-ribosomal-protein-L32
MAVPKRKTTPSKRNMRRSHHRAGTQSFAEDKKSGELRRPHHIDLSTGMYRGKQILVKKPKKEEVAESSAPVNAEEAAKTIEAPASK
>NC_018644.1|WP_014954337.1|279496_279985_+|RecX-family-protein
MKKEASEYLFNEAVKYLGKYPATRKKIKEYLQKKIKNKKTYARAIFLEGVDKEEMIERIVGRLDELKIINEDQFLESMFHYYQQSLFSIRKIKNKLFQKGFDSKIIDEFIDQKFYENPELEIEILKQYIVKKKLANLDESDLKKKLYQQSFSENSIFRVIKE
>NC_018644.1|WP_041485377.1|278457_279369_-|homocysteine-S-methyltransferase-family-protein
MNIEFNNQKPLILDGGMGQTLIKYGMIPQGTLWSATALLDSSLHQMVIDAHQDFMRAGAKVITTNNFTVRKLRFSENNILDKFDEALHTAGLLAKKANQQNIVFKDVLIAGSIPTRNQTYMAKFELSVEEIFNEFQCSGEILNDYVDIFYLDVLSSLEEIKLALKALKKFQKKFLIGVHIKKNSFMEDGNCITQLKDLIDQYDILGLVVACTDQSTVLSVIKKIHNLQVPFGFKVNAFANIPDGWKIKPGNPTESLGVNKSFNSESFISFAEKCRLEGASILGGCCEVLPNHIKALADFYRKN
>NC_018644.1|WP_014954335.1|278068_278461_+|hypothetical-protein
MLRIIGKLLVLILSFFAIFLGVCAVLGIQIYFPFNIAEGKEIPYHRMQSIRVAVFITFTFYGTLYLINSIKEVYPIHFLKVFMISFGITSFLFSYQAQEGIKEIVLAIFYLCCGLVFHLISKPEIKKYFT
>NC_018644.1|WP_014954334.1|277576_278050_+|GcrA-cell-cycle-regulator
MSWNTQKVEDLKKLWNEGVATSRIGEQLGFTKNAVIGKAFRLGLERRQNSRKKTTPTQQLSSTTMYRETSVSPSTQTTVKREVTRRREKFSFKKSIVGTGSFKSCQWPIGDPLEEGFHYCGGQNIPTKPYCIEHYKKAYNVDEKYLDRLLDFLHEKN
>NC_018644.1|WP_014954345.1|285294_285894_+|heme-ABC-exporter-ATP-binding-protein-CcmA
MIEISNLSFARGNFLIFKDVSFAVNSGEILILRGPNGKGKTTLLSNIIQLLDPFSGEVKYQGIKVDSYIASQCFLYLGENHFAYDQLSLNQNIDYWLSIHNVTFNKTIIDQSIRYLFGELNLNKKFYQLSFGQKKKLQLLLLMLVNKPIWILDDPFNGLDNDTIIKITTLLSKKVENKGTIIIASHQNLTIPHRTYELT
>NC_018644.1|WP_014954346.1|285890_286550_+|CcmB-protein
MINNFFKLLANEFSLMIKGSIFTFVLFCLLMIASSIFSLALRHISFDIEIPLAFLWIMIFFISLIKVEKVYASDFSEAKLQQYILSPFALEIIIFVKNIMIYLNLLILFFIFSPIILVILNINLSYLFSINILLALSLLSIVFISSMTSSITISRNNKLSITSVLTLPLFVPILIFSMAISDVIDIDINKLYIFFLAYFLLNLAFSPLLTSFALKKLSV
>NC_018644.1|WP_014954347.1|286549_287257_+|heme-exporter-protein-CcmC
MFAITPQMMSSFLNSISKYIILLAITLCAIAGLLIFLLENDYYQGISFKIMFIHVPAAWLSLMIFFSMGISSIIGLIFKSPTSFTISRSLSPIGLIMSIVVLITGSIWGNLTWGTYWVWDARLTSMLILAFIYLGHLFLLYSFEHFQKADFAASILAIIGMVNLPIVKFSVDWWTTLHQGSSVFKVGGPSMTTDYLITLMVSFFGILLLSLYWFTNIFYIIIENRRIERAKLLND
>NC_018644.1|WP_014954348.1|287358_287811_+|cytochrome-c-maturation-CcmE-like-protein
MQIIKLNRQIKKRLIFLFIIFFCFAFSIFLISYTLKDQIAYFVSPTELKKMDIASDKYLRVGGLVKANTLKFENEKWNFEVEDEDGGSIKVEFSKSLPGLVEEDKGIIVEGYMSQNSIFLAEIVLAKHDENYMPQSAIDKMKNEGIWRGN
>NC_018644.1|WP_014954349.1|287811_289644_+|heme-lyase-CcmF/NrfE-family-subunit
MISLFGNLSFYLTLFFILIFYLGWGKKIFLKDQVLVNLIYLGGITPFIFLVIGFTVSDFSILNVIQNSYIDDPLFFKITSAWGSHEGSILLWIFLINFFGFTFLKSNNNFQIHKQIIFISSLFILYLLLSSNPFVYVENSSEIVGLGLNPILQHFLFVIHPPTLFLGYIGLIIPFVLASHILVTKDFSQNLFKQMLFWAKISWFFLTFGIVLGSYWAYSELGWGGWWFWDPVENISLIPWLLNTALIHSLQVSIKNDQLKLWSLNLALYSFIAAVFGTFLVRSNLIVSVHSFATDPLRGLFLIVIIGYLFLVTIKLNIKSALHFNQDTFSLISKESFLLLNNIFFIASALTVFIGTIYPLFSELFFESSVSIGAPYYNFAFNILMAPIILLMAFAPQVSWNKNENKNNKVWITIVLAGAISIICFFYFTNIYFAIACFIASPIMIQSLIVIFKSFNKDLRFYSQWLAHLSIAIFIIAAVYTEQFDQEENFVFEKNGSSQLLMSNKSDVYLKNIKDTSYTNYQEILVELSIVNGDDEYILSPSKNIYQPSGQITNEVSTVNKWLHQYYATISSIESDRVAINLVYKPMINLLWISAIMLVFSIFLSIIKRR
>NC_018644.1|WP_014954350.1|289640_290123_+|redoxin-domain-containing-protein
MRKSLIIPILGLVILGISAFIFLNKNEGTGNKDIALPSSLFNTADFYDMKTLNQKELDDVYIVNFFASWCKPCLAEHPLLMELQSKGMQIIGINFRDDEDNFTQWINEHGNPFFHIIRDDGSIAYEMGLIGVPETFFIEKSKIQKKVQGPLFYEDIEKYL
>NC_018644.1|WP_014954351.1|290097_290457_+|cytochrome-c-biogenesis-protein
MKILKSIYKLFFIFCFVLFTNISLANVNQLSEYYKTIRCLVCEGQSIQESDTEFAINLKEQIQKKYESGMDLKQINQELITIYGEEISFSPTNDHFILWGLPLLLLLIIIFLVRNKYKK
>NC_018644.1|WP_014954352.1|290459_291299_-|ABC-transporter-permease-subunit
MSCYQTVLDYGLRSVGYGERLLPKADITLCEQFVLIGSGMIWNIYFAFLALLFGFLFSTVLALGKNSSHMIFNKPSRIFIFIFRGSPLFIQFFFAYDLFIILPKLGFDIELGFMTVTVETRWLTKAWLGALIVLFFNTSAYAAEIFYGALRAVPSKDIEAADSFGFSGVKKFRRIIWPTMLRLAWPSYTNEAIFLFHATTLVFFTGFPAWQQRGDAIYYASYFADKTFNPFVPYPIVGLYFIIFTLFIIAVFSVINKRLNKHLLPNERSKLKIRLNLIR
>NC_018644.1|WP_014954353.1|291299_292166_-|ABC-transporter-permease-subunit
MFEYCADPKSLEGLVWLSCYVTTPKHMSFYGSFLVVMCLLSLAAPLAMLFGFIGAIASRSSQGLIRFLGKGYLAMIRGIPDIVFFLFIPIALDQAFEYLRHKILCPEVIEPIRQGNDFVVCTAAKLPLSAASEWVHDLYGFSLALLAFGFVFGAFTGNVLFGAMAAVPKSQLETGEAFGFSPKQVFRRILIPQMWIYALPGLSNLWMILIKATPLLFLLGIEDIVYWARELGGIKTGVYDYPHPDWRAWYFGVLMIFYLLLTYVSQIVLDRLSNKLSTGQATLAGKTI
>NC_018644.1|WP_041485247.1|292158_293265_-|FAD-binding-oxidoreductase
MITDIIIVGGGIVGASFAYHAHINKIKNISVITDAFPGDARQATSNTWGWVNGYANNDEEYALLRLASLNYWPNLIDSINDTSFTSKGAFFWDLDETEIFQTIEQHQNWGHSVSIKQESEIKKVLPSLFNQPRNAGYGKNDLAVEATEISKKLFEKSHANFLNKKVTILIFEQNQVKGIQVGEEKIYADEVILATGLGTSEILKSIDINFSMRTSLGLLAYTNPLPPLLNHPITGDDFHARQDSQGRLVIGGRFDDDAAKEINLDKAAEKLVEEMASRLNYKGDITLAHFTVGKRPLPIDGRPKIGRLKNSIGEIIKGVYIAVMHSGVTNAPIAGKLGIEEIISGKQDRMLNTFSPQMNRNNQENSDV

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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_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NC_028765	Staphylococcus phage phiIPLA-RODI, complete genome	131004-131031	5	0.821
NC_018644_1	1.3\|284931\|31\|NC_018644\|CRT	284931-284961	31	LT960610	Bacillus phage SBSphiC genome assembly, complete genome: monopartite	63399-63429	5	0.839
NC_018644_1	1.7\|285171\|25\|NC_018644\|CRT	285171-285195	25	NZ_CP020458	Lactobacillus amylolyticus strain L6 plasmid pL6-1, complete sequence	31264-31288	5	0.8
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_LR135246	Enterococcus faecium isolate E6988 plasmid 4	53881-53908	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_CP041258	Enterococcus faecium strain 515 plasmid p27, complete sequence	68278-68305	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_LR135222	Enterococcus faecium isolate E7040 plasmid 4	41171-41198	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_LR134108	Enterococcus faecium isolate E6043 plasmid 4	34669-34696	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_LR135289	Enterococcus faecium isolate E7199 plasmid 3	20341-20368	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_LR135238	Enterococcus faecium isolate E7067 plasmid 4	12260-12287	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_CP014534	Enterococcus faecium strain E745 plasmid pl5, complete sequence	31379-31406	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_LR135193	Enterococcus faecium isolate E4438 plasmid 3	13770-13797	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	LR135186	Enterococcus faecium isolate E4413 genome assembly, plasmid: 2	12354-12381	6	0.786
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_CP011829	Enterococcus faecium strain UW8175 plasmid unnamed1, complete sequence	46315-46342	7	0.75
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_CP032307	Enterococcus faecium strain HY07 plasmid unnamed2, complete sequence	51327-51354	7	0.75
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	MN693005	Marine virus AFVG_117M50, complete genome	50962-50989	7	0.75
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_CP040704	Enterococcus faecium strain HOU503 plasmid p1, complete sequence	81372-81399	7	0.75
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_CP035137	Enterococcus faecium strain SRCM103341 plasmid unnamed1, complete sequence	192942-192969	7	0.75
NC_018644_1	1.2\|284883\|28\|NC_018644\|CRT	284883-284910	28	NZ_CP035221	Enterococcus faecium strain SRCM103470 plasmid unnamed1	100183-100210	7	0.75
NC_018644_1	1.3\|284931\|31\|NC_018644\|CRT	284931-284961	31	MN693245	Marine virus AFVG_25M69, complete genome	34410-34440	8	0.742
NC_018644_1	1.3\|284931\|31\|NC_018644\|CRT	284931-284961	31	NZ_LN907828	Erwinia gerundensis isolate E_g_EM595 plasmid pEM01, complete sequence	387418-387448	8	0.742

1. spacer 1.2|284883|28|NC_018644|CRT matches to NC_028765 (Staphylococcus phage phiIPLA-RODI, complete genome) position: , mismatch: 5, identity: 0.821

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
agtagagaagaaaaaagaagcacctaag	Protospacer
**. * .********** **********

2. spacer 1.3|284931|31|NC_018644|CRT matches to LT960610 (Bacillus phage SBSphiC genome assembly, complete genome: monopartite) position: , mismatch: 5, identity: 0.839

agcacctaagaagaaaaaagccactaagaaa	CRISPR spacer
agcacctaagaagaaaaaagccaagaaatga	Protospacer
***********************  **. .*

3. spacer 1.7|285171|25|NC_018644|CRT matches to NZ_CP020458 (Lactobacillus amylolyticus strain L6 plasmid pL6-1, complete sequence) position: , mismatch: 5, identity: 0.8

ggctaaaagaaaagcagcacctaag	CRISPR spacer
tattagaagaaaagcagcacctaat	Protospacer
 ..**.******************

4. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_LR135246 (Enterococcus faecium isolate E6988 plasmid 4) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

5. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_CP041258 (Enterococcus faecium strain 515 plasmid p27, complete sequence) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

6. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_LR135222 (Enterococcus faecium isolate E7040 plasmid 4) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

7. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_LR134108 (Enterococcus faecium isolate E6043 plasmid 4) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

8. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_LR135289 (Enterococcus faecium isolate E7199 plasmid 3) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

9. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_LR135238 (Enterococcus faecium isolate E7067 plasmid 4) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

10. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_CP014534 (Enterococcus faecium strain E745 plasmid pl5, complete sequence) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

11. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_LR135193 (Enterococcus faecium isolate E4438 plasmid 3) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

12. spacer 1.2|284883|28|NC_018644|CRT matches to LR135186 (Enterococcus faecium isolate E4413 genome assembly, plasmid: 2) position: , mismatch: 6, identity: 0.786

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
aggattaaagaaaaaaccagcacctact	Protospacer
**   *********** *********

13. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_CP011829 (Enterococcus faecium strain UW8175 plasmid unnamed1, complete sequence) position: , mismatch: 7, identity: 0.75

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
gggattaaagaaaaaaccagcacctact	Protospacer
.*   *********** *********

14. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_CP032307 (Enterococcus faecium strain HY07 plasmid unnamed2, complete sequence) position: , mismatch: 7, identity: 0.75

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
gggattaaagaaaaaaccagcacctact	Protospacer
.*   *********** *********

15. spacer 1.2|284883|28|NC_018644|CRT matches to MN693005 (Marine virus AFVG_117M50, complete genome) position: , mismatch: 7, identity: 0.75

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
cgctgtaaagaaaaaagaagcaggagaa	Protospacer
 **************** ****   .*.

16. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_CP040704 (Enterococcus faecium strain HOU503 plasmid p1, complete sequence) position: , mismatch: 7, identity: 0.75

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
gggattaaagaaaaaaccagcacctact	Protospacer
.*   *********** *********

17. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_CP035137 (Enterococcus faecium strain SRCM103341 plasmid unnamed1, complete sequence) position: , mismatch: 7, identity: 0.75

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
gggattaaagaaaaaaccagcacctact	Protospacer
.*   *********** *********

18. spacer 1.2|284883|28|NC_018644|CRT matches to NZ_CP035221 (Enterococcus faecium strain SRCM103470 plasmid unnamed1) position: , mismatch: 7, identity: 0.75

agctgtaaagaaaaaagcagcacctaag	CRISPR spacer
gggattaaagaaaaaaccagcacctact	Protospacer
.*   *********** *********

19. spacer 1.3|284931|31|NC_018644|CRT matches to MN693245 (Marine virus AFVG_25M69, complete genome) position: , mismatch: 8, identity: 0.742

agcacctaagaagaaaaaagccactaagaaa	CRISPR spacer
aaggaaaaagaagaaaaaaactactaagaaa	Protospacer
*. .   ************.*.*********

20. spacer 1.3|284931|31|NC_018644|CRT matches to NZ_LN907828 (Erwinia gerundensis isolate E_g_EM595 plasmid pEM01, complete sequence) position: , mismatch: 8, identity: 0.742

agcacctaagaagaaaaaagccactaagaaa	CRISPR spacer
tgagcctaagaaaaaagaagccactaacagc	Protospacer
 * .********.***.********** *.

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

446101 : 461468

uncultured_virus(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_014954526.1\|446101_448570_+	DNA topoisomerase (ATP-hydrolyzing) subunit B	G3M9Z3	Bacillus_virus	3.9e-104	39.6
WP_014954527.1\|448571_449822_+	HAMP domain-containing histidine kinase	NA	NA	NA	NA
WP_014954528.1\|449809_450367_+	ActR/PrrA/RegA family redox response regulator transcription factor	NA	NA	NA	NA
WP_014954529.1\|450399_453078_+	DNA polymerase I	A0A218MKQ4	uncultured_virus	3.5e-66	29.7
WP_014954530.1\|453089_453653_-	DUF924 domain-containing protein	E3T4R4	Cafeteria_roenbergensis_virus	6.5e-15	34.2
WP_014954531.1\|453652_453892_-	glutaredoxin	A0A0A0V276	uncultured_virus	8.6e-17	57.4
WP_014954532.1\|453892_454882_-	ribonucleoside-diphosphate reductase	A0A1I9KN73	Myxoma_virus	8.1e-85	48.9
WP_014954533.1\|454915_457654_-	ribonucleoside-diphosphate reductase subunit alpha	D5K687	Spodoptera_litura_multicapsid_nucleopolyhedrovirus	8.1e-236	52.0
WP_014954534.1\|458004_458955_+	adenosine kinase	NA	NA	NA	NA
WP_014954535.1\|459012_460293_+	adenosylhomocysteinase	S4W1G4	Pandoravirus	8.3e-50	32.4
WP_014954536.1\|460295_461468_+	methionine adenosyltransferase	A0A2H4PQS6	Staphylococcus_phage	2.0e-95	49.7

DBSCAN-SWA_2

985284 : 997892

uncultured_Mediterranean_phage(80.0%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_014955100.1\|985284_985611_-	iron-sulfur cluster assembly accessory protein	A0A218MM00	uncultured_virus	3.8e-15	37.5
WP_014955101.1\|985611_986715_+	dNTP triphosphohydrolase	NA	NA	NA	NA
WP_014955102.1\|986707_988360_+\|tRNA	arginine--tRNA ligase	NA	NA	NA	NA
WP_014955103.1\|988496_989504_+	glycoside hydrolase family 3 protein	A0A1B1IVS3	uncultured_Mediterranean_phage	1.3e-18	40.6
WP_014955104.1\|989493_990228_+	segregation/condensation protein A	A0A1B1IVW1	uncultured_Mediterranean_phage	9.4e-22	31.1
WP_014955105.1\|990220_990874_+	SMC-Scp complex subunit ScpB	A0A1B1IVT7	uncultured_Mediterranean_phage	7.5e-39	38.3
WP_014955106.1\|990863_991910_+	ABC transporter ATP-binding protein	Q6GZ03	Mycoplasma_phage	4.6e-14	29.1
WP_014955107.1\|991938_992133_+	twin-arginine translocase TatA/TatE family subunit	A0A1B1IVR9	uncultured_Mediterranean_phage	1.3e-07	58.0
WP_014955108.1\|992132_992426_+	twin-arginine translocase subunit TatB	NA	NA	NA	NA
WP_014955109.1\|992422_993196_+	twin-arginine translocase subunit TatC	A0A1B1IVR7	uncultured_Mediterranean_phage	7.5e-46	44.3
WP_014955110.1\|993195_994458_+\|tRNA	serine--tRNA ligase	A0A1B1IVT2	uncultured_Mediterranean_phage	4.4e-104	61.0
WP_014955111.1\|994444_995206_-	DUF815 domain-containing protein	NA	NA	NA	NA
WP_014955112.1\|995275_995539_+	preprotein translocase subunit YajC	A0A1B1IVR5	uncultured_Mediterranean_phage	1.5e-14	48.2
WP_014955113.1\|995565_997023_+	protein translocase subunit SecD	NA	NA	NA	NA
WP_014955114.1\|997019_997892_+	protein translocase subunit SecF	A0A1B1IVP7	uncultured_Mediterranean_phage	7.4e-34	39.3

DBSCAN-SWA_3

1290778 : 1297296

Staphylococcus_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_014955411.1\|1290778_1291207_-	6,7-dimethyl-8-ribityllumazine synthase	A0A2I2L4Y7	Orpheovirus	4.8e-10	39.5
WP_157721010.1\|1291203_1292226_-	3,4-dihydroxy-2-butanone-4-phosphate synthase	A0A2H4PQS2	Staphylococcus_phage	2.4e-47	37.9
WP_014955413.1\|1292284_1292869_-	riboflavin synthase	A0A2H4PQS5	Staphylococcus_phage	4.8e-21	31.4
WP_014955414.1\|1292861_1293851_-	diaminohydroxyphosphoribosylaminopyrimidine deaminase	A0A1V0SE20	Indivirus	2.2e-21	29.6
WP_014955415.1\|1293852_1294308_-	transcriptional repressor NrdR	NA	NA	NA	NA
WP_014955416.1\|1294313_1295594_-	serine hydroxymethyltransferase	A0A240F3L3	Aeromonas_phage	4.2e-102	52.1
WP_050990672.1\|1295590_1296013_-	ribose 5-phosphate isomerase B	NA	NA	NA	NA
WP_014955418.1\|1296008_1296641_-	DNA replication and repair protein RecO	NA	NA	NA	NA
WP_014955419.1\|1296648_1297296_-	double-stranded RNA-binding protein,RNase3-like protein	A0A2P0VNZ5	Tetraselmis_virus	7.0e-05	27.5

Anti-CRISPR protein detection

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