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_CP053015	Sphingomonas sp. CSW-10 chromosome, complete genome	1 crisprs	csa3,DEDDh,cas3,DinG	0	1	4	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP053015_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP053015_1

2369635-2369722

Orphan

Consensus_repeat	Method
CGGCGAAGAAGGCCAAGGCTGACGAGGC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_CP053015_1

>merge|NZ_CP053015|1|2369635-2369722|CRISPRCasFinder
AGGCCAAGAAGGCTCCGGCGAAGAAGGCCAAGGCTGACGAGGCTGCCGCAGAAGACAAGCCGGCGAAGAAGCCGGCGGCCAAGAAGGC

>NZ_CP053015|1|1|2369635-2369722|CRISPRCasFinder
AGGCCAAGAAGGCTCCGGCGAAGAAGGC	CAAGGCTGACGAGGCTGCCGCAGAAGACAAGC
CGGCGAAGAAGCCGGCGGCCAAGAAGGC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP053015.1\|WP_169946756.1\|2370785_2372057_+\|ATP-dependent-Clp-protease-ATP-binding-subunit-ClpX	unknown	unknown	gnl\|CDD\|235422
NZ_CP053015.1\|WP_169948275.1\|2379538_2379976_+\|M67-family-metallopeptidase	unknown	unknown	gnl\|CDD\|163701
NZ_CP053015.1\|WP_169946765.1\|2377611_2378517_-\|RNA-polymerase-sigma-factor-RpoH	unknown	unknown	gnl\|CDD\|235838
NZ_CP053015.1\|WP_169946767.1\|2378565_2379522_-\|RluA-family-pseudouridine-synthase	unknown	unknown	gnl\|CDD\|161659
NZ_CP053015.1\|WP_169946758.1\|2372391_2375646_+\|TonB-dependent-receptor	unknown	unknown	gnl\|CDD\|379297
NZ_CP053015.1\|WP_169946740.1\|2361098_2362268_-\|DUF3089-domain-containing-protein	unknown	unknown	gnl\|CDD\|378625
NZ_CP053015.1\|WP_169946742.1\|2362378_2364118_+\|DUF4153-domain-containing-protein	unknown	unknown	gnl\|CDD\|372672
NZ_CP053015.1\|WP_169946748.1\|2366155_2367622_+\|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatB	unknown	unknown	gnl\|CDD\|235489
NZ_CP053015.1\|WP_169946754.1\|2369959_2370598_+\|ATP-dependent-Clp-endopeptidase-proteolytic-subunit-ClpP	unknown	unknown	gnl\|CDD\|178955
NZ_CP053015.1\|WP_169946761.1\|2375776_2376454_-\|monofunctional-biosynthetic-peptidoglycan-transglycosylase	unknown	unknown	gnl\|CDD\|234603
NZ_CP053015.1\|WP_169946750.1\|2367628_2367814_-\|hypothetical-protein	unknown	unknown	unknown
NZ_CP053015.1\|WP_169946736.1\|2359272_2360268_-\|aspartate-carbamoyltransferase-catalytic-subunit	unknown	unknown	gnl\|CDD\|234849
NZ_CP053015.1\|WP_169946763.1\|2376469_2377342_-\|AraC-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|378964
NZ_CP053015.1\|WP_169946738.1\|2360319_2360616_-\|DUF1294-domain-containing-protein	unknown	unknown	gnl\|CDD\|377743
NZ_CP053015.1\|WP_169946746.1\|2364669_2366154_+\|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatA	unknown	unknown	gnl\|CDD\|234572
NZ_CP053015.1\|WP_169946734.1\|2358049_2359276_-\|amidohydrolase-family-protein	unknown	unknown	gnl\|CDD\|236479
NZ_CP053015.1\|WP_169948272.1\|2360612_2361077_-\|Holliday-junction-resolvase-RuvX	unknown	unknown	gnl\|CDD\|335420
NZ_CP053015.1\|WP_169946769.1\|2380064_2380703_+\|histidine-phosphotransferase	unknown	unknown	gnl\|CDD\|227675
NZ_CP053015.1\|WP_169946744.1\|2364233_2364536_+\|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatC	unknown	unknown	gnl\|CDD\|178810
NZ_CP053015.1\|WP_169946771.1\|2380779_2383227_+\|chemotaxis-protein-CheW	unknown	unknown	gnl\|CDD\|223716

Protein	Function_ID	Function_description	E-value
NZ_CP053015.1\|WP_169946756.1\|2370785_2372057_+\|ATP-dependent-Clp-protease-ATP-binding-subunit-ClpX	gnl\|CDD\|235422	PRK05342, clpX, ATP-dependent Clp protease ATP-binding subunit ClpX.	0
NZ_CP053015.1\|WP_169948275.1\|2379538_2379976_+\|M67-family-metallopeptidase	gnl\|CDD\|163701	cd08070, MPN_like, Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.	7.19998e-28
NZ_CP053015.1\|WP_169946765.1\|2377611_2378517_-\|RNA-polymerase-sigma-factor-RpoH	gnl\|CDD\|235838	PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed.	1.87219e-177
NZ_CP053015.1\|WP_169946758.1\|2372391_2375646_+\|TonB-dependent-receptor	gnl\|CDD\|379297	pfam13620, CarboxypepD_reg, Carboxypeptidase regulatory-like domain.	1.23638e-16
NZ_CP053015.1\|WP_169946740.1\|2361098_2362268_-\|DUF3089-domain-containing-protein	gnl\|CDD\|378625	pfam11288, DUF3089, Protein of unknown function (DUF3089). This family of proteins has no known function but appears to have an alpha/beta hydrolase domain and so is likely to be enzymatic.	3.44855e-75
NZ_CP053015.1\|WP_169946742.1\|2362378_2364118_+\|DUF4153-domain-containing-protein	gnl\|CDD\|372672	pfam13687, DUF4153, Domain of unknown function (DUF4153). Members of this family are annotated as putative inner membrane proteins.	5.57818e-18
NZ_CP053015.1\|WP_169946748.1\|2366155_2367622_+\|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatB	gnl\|CDD\|235489	PRK05477, gatB, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB.	0
NZ_CP053015.1\|WP_169946754.1\|2369959_2370598_+\|ATP-dependent-Clp-endopeptidase-proteolytic-subunit-ClpP	gnl\|CDD\|178955	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed.	1.5884e-143
NZ_CP053015.1\|WP_169946761.1\|2375776_2376454_-\|monofunctional-biosynthetic-peptidoglycan-transglycosylase	gnl\|CDD\|234603	PRK00056, mtgA, monofunctional biosynthetic peptidoglycan transglycosylase; Provisional.	1.2979e-82
NZ_CP053015.1\|WP_169946767.1\|2378565_2379522_-\|RluA-family-pseudouridine-synthase	gnl\|CDD\|161659	TIGR00005, Ribosomal_large_subunit_pseudouridine_synthase_D, pseudouridine synthase, RluA family. In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP\|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification].	8.46657e-109
NZ_CP053015.1\|WP_169946736.1\|2359272_2360268_-\|aspartate-carbamoyltransferase-catalytic-subunit	gnl\|CDD\|234849	PRK00856, pyrB, aspartate carbamoyltransferase catalytic subunit.	1.58799e-178
NZ_CP053015.1\|WP_169946763.1\|2376469_2377342_-\|AraC-family-transcriptional-regulator	gnl\|CDD\|378964	pfam12833, HTH_18, Helix-turn-helix domain.	1.40627e-07
NZ_CP053015.1\|WP_169946738.1\|2360319_2360616_-\|DUF1294-domain-containing-protein	gnl\|CDD\|377743	pfam06961, DUF1294, Protein of unknown function (DUF1294). This family includes a number of hypothetical bacterial and archaeal proteins of unknown function.	2.50003e-19
NZ_CP053015.1\|WP_169946746.1\|2364669_2366154_+\|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatA	gnl\|CDD\|234572	PRK00012, gatA, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA.	0
NZ_CP053015.1\|WP_169946734.1\|2358049_2359276_-\|amidohydrolase-family-protein	gnl\|CDD\|236479	PRK09357, pyrC, dihydroorotase; Validated.	7.20991e-121
NZ_CP053015.1\|WP_169948272.1\|2360612_2361077_-\|Holliday-junction-resolvase-RuvX	gnl\|CDD\|335420	pfam03652, RuvX, Holliday junction resolvase. This family of nucleases resolves the Holliday junction intermediates in genetic recombination.	3.90082e-50
NZ_CP053015.1\|WP_169946769.1\|2380064_2380703_+\|histidine-phosphotransferase	gnl\|CDD\|227675	COG5385, COG5385, Uncharacterized protein conserved in bacteria [Function unknown].	4.55579e-22
NZ_CP053015.1\|WP_169946744.1\|2364233_2364536_+\|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatC	gnl\|CDD\|178810	PRK00034, gatC, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC.	4.10919e-38
NZ_CP053015.1\|WP_169946771.1\|2380779_2383227_+\|chemotaxis-protein-CheW	gnl\|CDD\|223716	COG0643, CheA, Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms].	4.36294e-106

>NZ_CP053015.1|WP_169946750.1|2367628_2367814_-|hypothetical-protein
MATSPRPDTINPQSPDETPATPSPVEQPVPTGPDATPPESLPDGGDTVYPGRGPQELPAAP
>NZ_CP053015.1|WP_169946748.1|2366155_2367622_+|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatB
MSNYRIKGETGEWEVVIGLEVHAQITTQAKLFSGAATAFGAEPNTQVSLVDAAMPGMLPVPNRECIRQAVRTGLAIEAEINQWSRFDRKNYFYADLPQGYQISQLYHPLVGEGSLTIEADEKAGIPEAKRIGIERIHVEQDAGKLMHDQHPSMSFVDLNRSGVALMEIVSRPDMRSPAEAGAYVRKLRSILRYVGSCDGNMEEGSMRADVNVSVRKPGEEFGTRTETKNVNSVRFVMAAIEYEAKRQIELIESGGTVVQETRLFDPDKGVTRSMRSKEDAHDYRYFPDPDLLPLVLDDAFVAECRASLPELPDAKRARYEGAGISAYAAGVLTAEVEAARWFDALLDTGAKPVAAANWVTSELFGALNRLGREISDSPVSPTQAAELLALVDDGTLSGSLAKQVFEKMLETGDTAGVIVERDGLRQTSDTGAIEAAVDEVLAANADKVEQYRAGKEALFGFFVGQTMKAMGGKANPKMVNEVIRAKLG
>NZ_CP053015.1|WP_169946746.1|2364669_2366154_+|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatA
MTNLTDLGIAAIRDGVRDGSFSAVEVATAFNAAVDGADALNAFIVKTPEHALAAAKAADDARAKGETLGAMAGVPIGMKDLFATQGVQTTAASHMLEGFVPQYESTVSAKLWAAGAGMLGKLNLDQFAMGSSNETSYFGNVISPWRRNNGDTAPLAPGGSSGGSSAAIAARLCPAATGTDTGGSIRQPAAFTGISGIKPTYGRCSRWGIVAFASSLDQAGPMARDVRDCAIMLEAMAGFDPKDATSLDMAVPQWEAGLNADLKGKRVGIPKEYRVDGIDADIARVWDDGIKWLKDAGAEIVDISLPHTKYALPTYYIIAPAEASSNLARYDGVRYGLRDLPQGAGLQDMYAATRAAGFGPEVKRRIMIGTYVLSAGFYDAYYTQAQKVRALIARDFEQAWNSCDVILTPTAPSAAFGLGDKTADPLSMYLNDVFAVPASLAGLPAMSVPGGLDAQGLPLGLQIIGRAFDEQGVLNAGLAIEQRSGFNARADKWW
>NZ_CP053015.1|WP_169946744.1|2364233_2364536_+|Asp-tRNA(Asn)/Glu-tRNA(Gln)-amidotransferase-subunit-GatC
MSVDNATVTKIAKLARIAVSDAEVEALVPELNNILGWVEQLGEVDVTGVEPMTAVIPNTLRLRDDVVNADPLTGGNVRDKVLANAPEPQHGFFGVPKVIE
>NZ_CP053015.1|WP_169946742.1|2362378_2364118_+|DUF4153-domain-containing-protein
MAEGSSQRIDVRDIPWAARPWIMAMVGTAAGWIFWWAVTSADQSGQDMALSRGWSVTATFVAVAAISFIMTVELRRLHWATGFALFWGAIIAFVGWSSLGYNRGFELVSLSFLASIFAVLLAAPLFQTARDEGGWRFPPLAVQMHAWTDAVIGATGMVFVGISFALFALIAGLFDLIGIEFFSNLLKEGWFGLMLAGSAFGAAVGILRERDALVGTMQRLVRIILSVLAPVLAFALVLFLLSLPVTGLAGLWDGWVSAAVLTLLAAAGCFILLNAAIGPKDGDEVGDGEAKPVQPVLLWSALVLALVVLPLALLAVSALWLRIGQYGWTPERIWGLLSALIALAYGIAGWWAVIRQRLGFSSLLRILETRLALAVCGLALLLSLPIVDFGAISARDQLSRLQSGAVKPADFDWAAMAFDFGPAGRAALERLARTGPADQRELAGEALKAEDRYRLANAQRNAPDSATIRQAMVIRPAGRAVPDAAVRVIRQMGLCGAGTCLVQWIDDERFVLVSGREEGEYPLVVLFTSAEDGAQWSSNYLNSGASQLTGDLEAVRIEARPVSRRQVYVNGQPVGDEFE
>NZ_CP053015.1|WP_169946740.1|2361098_2362268_-|DUF3089-domain-containing-protein
MVRKFLYLVAFVIALVIVLAVAYRLNPGPFMRAAMVPTEEFREPQPLRQGYAENAMWIARAGMTGDNPTLWMPRAIDTATRDPAEGPVANPPRVPVEPERGNAAIFFIHPTSYLKRDHWNAPLDDAEANWRALLFVRGMASTMAGAGDVWVPRYQQAAMGAFLTEDTDTANRALNVAYGDVSAAFDQFLADVGPDRPIILAGHSQGALHLTRLLRDKVAGRPIASRIVAAYVVGWPVSVRHDLPRMGLPACEGQESTNCVLGWQTFAEPADPSLILEVYDNSIGFDGQSRRDSAMLCVNPISGTANGTAPRSANLGTVKADDGFADGTLFPGATGARCDGGRGFLLIGEGPEVGPFVLPGNNYHVFDYPLFWANVRADARRRLAAFQAR
>NZ_CP053015.1|WP_169948272.1|2360612_2361077_-|Holliday-junction-resolvase-RuvX
MLTEDVAAFSAALPEGGRLIGLDVGTKTIGTALCDAGWSFATPADLVRRTKYSADLASLTAQVQREHVVGLIVGLPLNLDGSDSPRTQSVRAFARNIRSLGLPILLWDERWSTAAVERAMIAADMSRAKRAERVDNAAAAYILQGALDALVRQA
>NZ_CP053015.1|WP_169946738.1|2360319_2360616_-|DUF1294-domain-containing-protein
MSRTEIAFYWLLFASFTGFALMVWDKHQAKTGGWRVAESTLIFWAVVGGANGVFAAQQILRHKTTKQPISSILTTLVVIEIPLCLTLYFYASQLLPRP
>NZ_CP053015.1|WP_169946736.1|2359272_2360268_-|aspartate-carbamoyltransferase-catalytic-subunit
MTSPPPAPFSRYPAGSAAFPHPHLLGLAGLQPWEISFLLDEAERWVDLGRSGAVKKADVLHGLTVINAFFENSTRTLLSFEIAGKRLGADVVNMHVAQSSVKKGETLIDTAMTLNAMRADALVIRHMSSGAVALIADKVDCPVLNAGDGWHEHPTQGLLDALTIRRRKGRLDGLIVAICGDIRHSRVARSNMIGLATMGAQVRVAGPATLVPQEVELLGAQRFTRIEDALDGADVVMMLRLQNERMDGTFIPSAREFHALFGLTATRLALAKPDALVMHPGPMNRGVEIDSAIADDPERSAITEQVEMGVAVRMACLDVLTRKARGAEGWA
>NZ_CP053015.1|WP_169946734.1|2358049_2359276_-|amidohydrolase-family-protein
MSMMLIINARLVRSDADVSQSGTLLVENGRIAAINPDAASLDVETFDARGQLLAPGIIDLGVFATDRRAFHFGGITRAALMPDGPPVLDNPGLIERAAKGGKPDLWVHPLAAATRGLDGRELAEVGLMQRAGARAVATGRHRIADAGVMARLLSYASALGLTTIVHSEDEGLTRNAVATEGEMALRLGLPAAPALAEAMAIARDLTLVEQTGAPVHFRQVTTARGFDLIRSAKAAGLPVSCGITPAHLLLSEVALGEWRTFSRLSPPLRHERDRQAALQALSDGTIDVLASGHDPRGPEDKRLPFADAAPGMAGAETLLASGLGFVRDGLISLQRLFELLSAAPARLLGVSAGKLELGLEADMILIDSEVPWQVDARRMPGLAGNTPFDGLPVQGRVTAVWKGGNRVA
>NZ_CP053015.1|WP_169946754.1|2369959_2370598_+|ATP-dependent-Clp-endopeptidase-proteolytic-subunit-ClpP
MHDPFDTITNALVPIVIEQSNRGERSFDIFSRLLRERIVFVTGEVEDNMASLIVAQLLFLESENPTKDIYMYINSPGGVVTAGMAIHDTMQYIRPRVGTVCIGQAASMGSFLLAAGEPGMRVALSNARVMIHQPSGGARGMASDIEIQAREILRIRKRMNELYVKYTGQPLEKVEKAMDRDTFLEAEEAKEFGLVDLVFEKRPTGTDAVAGA
>NZ_CP053015.1|WP_169946756.1|2370785_2372057_+|ATP-dependent-Clp-protease-ATP-binding-subunit-ClpX
MTKLSGSDSKSTLYCSFCGKSQHEVRKLIAGPTVFICDECVELCNDIIREEAKGAAAPRKGGGVPSPREICDVLDDYVIGQFAAKRVLSVAVHNHYKRLNHSGKGDDVELAKSNILLVGPTGCGKTLLAQTLARTFDVPFTMADATTLTEAGYVGEDVENIILKLLQAADYNVEKAQRGIVYIDEIDKISRKAENPSITRDVSGEGVQQALLKMMEGTVASVPPQGGRKHPQQEFLQVDTTNILFICGGAFAGLEKIIGDRMQGKSIGFGAHVAGPEERRTGEVLRNVEPEDLLKFGLIPEFVGRLPVIATLEDLDESALVKILSEPKNALVKQYRKLFELEEVGLTFTDDALVAIARKAIQRKTGARGLRSIVEAILLDTMFDLPQLDGVSEVVIDKDVVAGSKEPIRVFAEAARAGAGDAA
>NZ_CP053015.1|WP_169946758.1|2372391_2375646_+|TonB-dependent-receptor
MSMRIYLAASVAGLSLATAMASPAAAQETTAAVRGTVEAEGAPVTGATVVITHGPSGTTVRTTTGSDGSFSANGLRIGGPFTVTVDASGYETSTITDLNLTAGQAFRLPIVLQASNDIIVTAANLGGALETSTGPITALGRTEIEGAASINRDIRDLARRDPLVTMDLSNSRTIEIAGNNGRLNRFSVDGVQFSDDFGLNNGGLPTSRGPVPFDAIEQFSVKTAPYDVAEGDFQGGAINVVLRSGGNRFRGSGFFTYTDDSLTGDSTRGRAVSLDFDSKQYGGHISGPIVRDRLFFALTYERTEESDPFDNGVGAGFSNQVPGITQAQIDQVSAIAQSVYGYDTLGQIQNATETDEKIVAKLDWNVTDDHRASLTYIRNVGTQQFQQNTFTTAPFALGLFSNGYELSEEVNSGVFQLNSTWSDDLSSELRVSYRDYNRDQTPFGGRGFGQFEVCLDPTSINAGTNTAISCGGSRLFFGPDVSRQSNDLNTENLSVDFTARYEAGDHSFKFMVGYTNVSVFNLFLQRSLGDFYFDSVADLQARNANRLRLGGAVPSLDPNDAAASFGTQNWTIGLQDDWQVNDTLQVTLGVRYDLFNNDAYPPLNPNFVGRYGFSNRETFSGKGVFQPRFGFNWQASDALIVRGGVGIFAGGTPDVFVSNSFSNTGLLTNSIDINRTNCAASNTCAGLNGVTGRTIPGEVGNFLATNVGSLALAPTNAIDPDLDVARKLKASLQADYEADLGALGDGWLFGAQILYDENLRGYTWTDIRSVPGGTLPDGRVRYRALPGVTGTNQDLLMTNSFRGRGIFGSLRVAKEFDFGLSFDASYTRSDVQDEGALTSATAGSLYSNNAFADANFAAYGRSIYEIRDQWKFSVDFRRELFGDNETRISLFGEYRSGRPYSITALDNSSGRLATWGTIGNGGRVLAYIPTLNDPRVSFDTAASEAAFNTLVTQLGLDRFRGSVVPKNSQTSPDFFKIDLHLSQELPVPVLGGAKIRLFADIENVLNLIDSDWGALRQVGFPYTAALARVACLTAATPTGTAGTVSTSTATNCAQYRYSNVLAPNEVLVTRQSLYGIRVGVRFEF
>NZ_CP053015.1|WP_169946761.1|2375776_2376454_-|monofunctional-biosynthetic-peptidoglycan-transglycosylase
MIKALRFLLQSILWFVGLSLLWVLAYAVIPPPTTLTMMLDDRGATREWMTLAEMDPDMARAAIAAEDGNFCRHNGFEIEAIREAMRRNAEGGRMRGGSTISQQTAKNAFLWQGSGVASRALRKIPEAWFTFLIETIWGKRRIMEVYLNIAETGIGTYGANAGAQRYFGHDASRLSREEAARIAAVLPLPKKRGAVAPRGFTRRYGNSIIARMRIVEGSGLDSCLR
>NZ_CP053015.1|WP_169946763.1|2376469_2377342_-|AraC-family-transcriptional-regulator
MRPAPSLEGLVSGYHVYCAGPPGSPVWQELFFPGWSNIRLTLEDGGWHCAPVGEPMRPVPEIALFGPASRGVHSRSTGGLMVGAGITPLGWHRLFRVPAHVLTDCIVPLSPHIAHVPEGLIERARHDPSPQAIQQLFDEWLTSCLRPASPVAPSIAGLFSRLTHSDDSELADLQTVLDLSASQLRRLARNHFGLPPKLLLRRTRFLKSISSIISMPDTNWSGVIDQRYFDYAHFVRDCQEFLGMAPSKFLALDRPMTRLSMMKRAEQLGAPLQGLHRPDPDLLPLQPAGN
>NZ_CP053015.1|WP_169946765.1|2377611_2378517_-|RNA-polymerase-sigma-factor-RpoH
MAEGSNVPATMPTLGGEAGLNRYLSEIRKFPMLTPEQEYMLAKRYQQHQDSDAAAQLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPDRGFRLATYAMWWIRASIQEFILRSWSLVKLGTTAAQKKLFFNLRRMKNNLAAFEDGDLSPEHVAKIATDLGVTEEEVVSMNRRMSMGGDASLNVPMREDGEGQWQDLLQDDTVLQDERVADAQERDHRHALLAEAMERLNDRERDILTRRRLTDEPETLEELSQTYNVSRERVRQIEVRAFEKLQKAMLAIAGERKLLPAN
>NZ_CP053015.1|WP_169946767.1|2378565_2379522_-|RluA-family-pseudouridine-synthase
MERGFTILPVEIDASQVGERFDRAIANRVPDLSRERVQALLAEGRIAVTGAHDVPRASARVGSPMLLSITLPPPVTPEAGPEAMDLVIAWEDEHLVVVDKPAGMVVHPANGNPDGTLVNGLLHHCAGQLSGIGGVARPGIVHRIDKDTSGLIVVAKTDKAHEGLARQFFDHSIERVYQAIVNGHPAPPAGTVDAPLARSTNDRKKIAVVNDGRGKRAVTHFRTLERLSGAALVECRLETGRTHQVRVHMTHIGHALLGDPVYGRAQSRHAGTLRSVGFARQALHAARLGFIHPVTGATVLCDSPLPTDMQQLFTRLSV
>NZ_CP053015.1|WP_169948275.1|2379538_2379976_+|M67-family-metallopeptidase
MAVRISRAVLEAIISDASTTPTVERCGLLLGSADHVTAWLSVANVHPEPDQHFELDPATLIAVERAARQGHGPGVAGHYHSHPKGSAVPSLADAEAAAPDGRLWLMTAQGECRLWRSVAAMPLANDGTGALWLSRFVEEEIDVTD
>NZ_CP053015.1|WP_169946769.1|2380064_2380703_+|histidine-phosphotransferase
MADDAIDFASMMVSRLCHDLLSPVGSFGNGLELLADEQDAEMQKRCIELLESSARVAINRLKYFRIAFGSAGGYGDAIAAADIREALLGLVPEGRAVELNWIGGESGVPKSAARLLLLFGMVTVDALVRGGRIDMAIESRGETLELAVRGSGDRLVIDTASEAHFAGGTEPLAPKTVPIELARRIARERGGDIMMSRPSPTELVVGAIIKAE
>NZ_CP053015.1|WP_169946771.1|2380779_2383227_+|chemotaxis-protein-CheW
MDDLLKEFVGETLDMMDAVAGDLVAWEADPADRSGLDGIFRTVHTVKGSSSFFDLPRITAIAHATEELLDVLRSRKGAPTRASVAVVLVAFDKIREIAVHLSASGGEPLGDDSRLIAALLADVRSADRQSVVSASGEAQLGHAKGSAPALEELPQAWRTVRVPLALLDELMIGVSDLVLSRNEVAAQLRARGEDMEAFAAFGRMSQLLGSVRAMVSTMRMVPLRHLYAPLPRLVRQLAGELDKQVQLSLEGGDVEIDRELVEVLRDPIIHMLRNAVDHGVEGETHRQYAGKPAAGHIRVCARQAGNRILISISDDGKGLPIEAIVASAIRAGHVTPDDVAAMDEAGKADLVFLPGLSTAATISGISGRGVGMDVVRANIERLGGVIRIDSRSGHGVTLTLDVPMTLTVISALAVDAGNQSFAIPRSAIDEVMLLSSDAVQQHDQPATAGLVRVRERMLPMLRLESILGVGDDGADEEGDRALIICRHGNAAAFALDVPDVRDHEELVIKPLPPVLLSIGMYSGLSLPDSGKPMLVLDIDEIARRHIGTVPASIKPDRKDAVVPAEKRGRSWLTYRAETGGPWRAVPMDHVERLYDVPANHVHASGGGLVAQVDDRLIAVAGDRLPEAALAHYRMIRLNDGCRVAMLPVWQIGDTVELKAELPPADLNAGLSGLTLMDGDLVELVDSYVLLARYGNLPGRRDVPCSPDRPEPVEHNRELWIVDPAGSEWTTSFLVPTLVAAGYRLAIVTERNQVTTERSPVILLSPKGPADPLTLETGEAVHHLSAYDREGLLSIIGGGPAPSAPIPVVRDEGAAA

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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_CP053015_1	1.1\|2369663\|32\|NZ_CP053015\|CRISPRCasFinder	2369663-2369694	32	NZ_LR594691	Variovorax sp. WDL1 plasmid 3	316742-316773	5	0.844
NZ_CP053015_1	1.1\|2369663\|32\|NZ_CP053015\|CRISPRCasFinder	2369663-2369694	32	NZ_LR594691	Variovorax sp. WDL1 plasmid 3	316838-316869	5	0.844
NZ_CP053015_1	1.1\|2369663\|32\|NZ_CP053015\|CRISPRCasFinder	2369663-2369694	32	NC_017073	Selenomonas ruminantium subsp. lactilytica TAM6421 plasmid pSRC3, complete sequence	30832-30863	7	0.781
NZ_CP053015_1	1.1\|2369663\|32\|NZ_CP053015\|CRISPRCasFinder	2369663-2369694	32	NC_047975	Microbacterium phage Squash, complete genome	22252-22283	8	0.75
NZ_CP053015_1	1.1\|2369663\|32\|NZ_CP053015\|CRISPRCasFinder	2369663-2369694	32	NC_019555	Agrobacterium tumefaciens strain F64/95 plasmid pAoF64/95, complete sequence	130296-130327	9	0.719

1. spacer 1.1|2369663|32|NZ_CP053015|CRISPRCasFinder matches to NZ_LR594691 (Variovorax sp. WDL1 plasmid 3) position: , mismatch: 5, identity: 0.844

---caaggctgacgaggctgccgcagaagacaagc	CRISPR spacer
ccccaaggc---cgaggctgcagccgaagacaagc	Protospacer
   ******   ********* ** **********

2. spacer 1.1|2369663|32|NZ_CP053015|CRISPRCasFinder matches to NZ_LR594691 (Variovorax sp. WDL1 plasmid 3) position: , mismatch: 5, identity: 0.844

---caaggctgacgaggctgccgcagaagacaagc	CRISPR spacer
ccccaaggc---cgaggctgcagccgaagacaagc	Protospacer
   ******   ********* ** **********

3. spacer 1.1|2369663|32|NZ_CP053015|CRISPRCasFinder matches to NC_017073 (Selenomonas ruminantium subsp. lactilytica TAM6421 plasmid pSRC3, complete sequence) position: , mismatch: 7, identity: 0.781

caaggctgacgaggctgccgcagaagacaagc--	CRISPR spacer
caaggctgacgatgcttccgcag--tgcaggctt	Protospacer
************ *** ******   .**.**

4. spacer 1.1|2369663|32|NZ_CP053015|CRISPRCasFinder matches to NC_047975 (Microbacterium phage Squash, complete genome) position: , mismatch: 8, identity: 0.75

caaggctgacgaggctgccgcagaagacaagc	CRISPR spacer
cggggccgacgaggatgccgcagaagcatggc	Protospacer
*..***.******* ***********   .**

5. spacer 1.1|2369663|32|NZ_CP053015|CRISPRCasFinder matches to NC_019555 (Agrobacterium tumefaciens strain F64/95 plasmid pAoF64/95, complete sequence) position: , mismatch: 9, identity: 0.719

caaggctgacgaggctgccgcagaagacaagc	CRISPR spacer
ggggcgaggcgaagctgccgcagaaggcaagc	Protospacer
 ..*   *.***.*************.*****

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

987581 : 1003723

uncultured_Mediterranean_phage(37.5%)

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_169944289.1\|987581_989132_+	hypothetical protein	A0A1B1IRS4	uncultured_Mediterranean_phage	1.8e-70	36.0
WP_169944291.1\|989142_989382_+	hypothetical protein	NA	NA	NA	NA
WP_169944293.1\|989390_990062_+	hypothetical protein	NA	NA	NA	NA
WP_169944295.1\|990089_991730_+	hypothetical protein	A0A221SAN2	Ralstonia_phage	7.1e-86	35.1
WP_169944297.1\|991719_992016_+	hypothetical protein	NA	NA	NA	NA
WP_169944299.1\|992008_992929_+	hypothetical protein	D6PEG5	uncultured_phage	7.9e-10	26.5
WP_169944301.1\|993178_994087_+	hypothetical protein	A0A221SAM2	Ralstonia_phage	1.7e-44	38.8
WP_169944303.1\|994177_994615_+	hypothetical protein	A0A221SAL8	Ralstonia_phage	4.6e-08	33.6
WP_169944305.1\|994730_995342_+	hypothetical protein	A0A1B1IRI7	uncultured_Mediterranean_phage	2.0e-17	31.7
WP_169944307.1\|995338_997549_+	hypothetical protein	A0A1B1ITR4	uncultured_Mediterranean_phage	4.8e-45	28.5
WP_169944309.1\|997548_997989_+	hypothetical protein	NA	NA	NA	NA
WP_169944311.1\|997988_998498_+	hypothetical protein	NA	NA	NA	NA
WP_169944313.1\|998501_1000466_+	hypothetical protein	NA	NA	NA	NA
WP_169944315.1\|1000462_1003723_+	hypothetical protein	A0A0F7L8F5	uncultured_marine_virus	8.6e-59	37.5

DBSCAN-SWA_2

1603427 : 1656764

Mycoplasma_phage(11.11%)

protease,head,capsid,tail,tRNA,portal

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_169945499.1\|1603427_1603982_-\|protease	TIGR02281 family clan AA aspartic protease	NA	NA	NA	NA
WP_169945501.1\|1604022_1605003_-	hypothetical protein	NA	NA	NA	NA
WP_169945503.1\|1605065_1605788_-	folate-binding protein YgfZ	NA	NA	NA	NA
WP_169948095.1\|1605920_1606955_+	dihydroorotase	NA	NA	NA	NA
WP_169945505.1\|1607030_1608626_+\|tRNA	lysine--tRNA ligase	NA	NA	NA	NA
WP_169945507.1\|1608632_1609670_-	fatty acid desaturase family protein	NA	NA	NA	NA
WP_169945509.1\|1609792_1611388_+	toll/interleukin-1 receptor domain-containing protein	NA	NA	NA	NA
WP_169945511.1\|1611416_1611956_+	hypothetical protein	NA	NA	NA	NA
WP_169945513.1\|1612005_1613388_+	DUF4071 domain-containing protein	NA	NA	NA	NA
WP_169945515.1\|1613415_1614087_-	Crp/Fnr family transcriptional regulator	NA	NA	NA	NA
WP_169945517.1\|1614162_1616025_-	DUF885 domain-containing protein	NA	NA	NA	NA
WP_169945519.1\|1616093_1617365_-	amidohydrolase family protein	NA	NA	NA	NA
WP_169945521.1\|1617524_1618799_-	RcnB family protein	NA	NA	NA	NA
WP_169945523.1\|1618936_1619869_-	N-acetyl-gamma-glutamyl-phosphate reductase	NA	NA	NA	NA
WP_169945525.1\|1619865_1620249_-	SH3 domain-containing protein	NA	NA	NA	NA
WP_169948097.1\|1620193_1620505_-	MarR family transcriptional regulator	NA	NA	NA	NA
WP_169945527.1\|1620639_1622034_-	leucyl aminopeptidase family protein	Q6GYZ8	Mycoplasma_phage	3.1e-26	32.1
WP_169945529.1\|1622083_1623625_-	NAD(P)/FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_169948099.1\|1623819_1624944_+	DUF47 family protein	NA	NA	NA	NA
WP_169945531.1\|1624962_1625976_+	inorganic phosphate transporter	NA	NA	NA	NA
WP_169945533.1\|1625995_1626373_-	hypothetical protein	NA	NA	NA	NA
WP_169945535.1\|1626401_1627334_-	D-alanyl-D-alanine carboxypeptidase family protein	NA	NA	NA	NA
WP_169945537.1\|1627397_1628192_-	hypothetical protein	NA	NA	NA	NA
WP_169948101.1\|1628334_1628688_-	hypothetical protein	NA	NA	NA	NA
WP_169945539.1\|1629182_1629911_+	GGDEF domain-containing protein	A0A127AWB9	Bacillus_phage	1.9e-14	36.8
WP_169945541.1\|1629907_1630270_-	hypothetical protein	NA	NA	NA	NA
WP_169945543.1\|1630266_1630908_-	hypothetical protein	NA	NA	NA	NA
WP_169945545.1\|1630988_1631498_-	hypothetical protein	NA	NA	NA	NA
WP_169945547.1\|1631751_1632498_+	sterol desaturase family protein	NA	NA	NA	NA
WP_169945549.1\|1632421_1632883_+	DUF2141 domain-containing protein	NA	NA	NA	NA
WP_169945551.1\|1632870_1633161_-	hypothetical protein	NA	NA	NA	NA
WP_169948103.1\|1633333_1634872_+	NAD(P)/FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_169948105.1\|1634938_1635796_-	enoyl-CoA hydratase/isomerase family protein	NA	NA	NA	NA
WP_169945553.1\|1635798_1637031_-	cytochrome P450	NA	NA	NA	NA
WP_169945555.1\|1637042_1638404_-	NAD(P)-binding domain-containing protein	NA	NA	NA	NA
WP_169945557.1\|1638598_1639006_+	BLUF domain-containing protein	NA	NA	NA	NA
WP_169948107.1\|1639270_1641112_+	phosphomethylpyrimidine synthase ThiC	NA	NA	NA	NA
WP_169945559.1\|1641104_1641629_+	DUF3429 domain-containing protein	NA	NA	NA	NA
WP_169945561.1\|1642185_1642836_-	hypothetical protein	NA	NA	NA	NA
WP_169945563.1\|1642987_1644193_-	methionine adenosyltransferase	A0A2H4PQS6	Staphylococcus_phage	2.1e-95	48.9
WP_169945565.1\|1644254_1645904_-	apolipoprotein N-acyltransferase	NA	NA	NA	NA
WP_169945567.1\|1645973_1646390_+	VOC family protein	NA	NA	NA	NA
WP_169945569.1\|1646487_1647129_-	DedA family protein	NA	NA	NA	NA
WP_169945571.1\|1647446_1648028_+	hypothetical protein	NA	NA	NA	NA
WP_169948109.1\|1648137_1649400_+	DNA-packaging protein	A0A1V0DY66	Dinoroseobacter_phage	4.3e-67	36.7
WP_169945573.1\|1649725_1650889_+\|portal	phage portal protein	W8ECU7	Geobacillus_phage	1.1e-48	35.2
WP_169945575.1\|1650885_1651197_+	hypothetical protein	K4I011	Acidithiobacillus_phage	7.5e-13	52.8
WP_169945577.1\|1651193_1651622_+\|head,protease	HK97 family phage prohead protease	A0A0U2BX10	Paracoccus_phage	4.8e-18	43.5
WP_169945579.1\|1651749_1652895_+\|capsid	phage major capsid protein	Q8W627	Enterobacteria_phage	3.6e-76	44.9
WP_169945581.1\|1652993_1654442_+\|tail	tail fiber domain-containing protein	M1PRW7	Synechococcus_phage	4.9e-14	40.8
WP_169945583.1\|1654645_1654927_+	hypothetical protein	NA	NA	NA	NA
WP_169945585.1\|1654926_1655472_+	hypothetical protein	NA	NA	NA	NA
WP_169945587.1\|1655468_1655735_+	hypothetical protein	NA	NA	NA	NA
WP_169945589.1\|1655724_1656132_+	hypothetical protein	NA	NA	NA	NA
WP_169948111.1\|1656356_1656764_+\|tail	phage tail protein	NA	NA	NA	NA

DBSCAN-SWA_3

2103538 : 2114809

uncultured_Mediterranean_phage(25.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_169946334.1\|2103538_2104615_-	NTP transferase domain-containing protein	A0A1V0SH58	Hokovirus	2.1e-17	27.1
WP_169946336.1\|2104639_2105434_-	class I mannose-6-phosphate isomerase	NA	NA	NA	NA
WP_169946338.1\|2105542_2106838_-	UDP-N-acetyl-D-mannosamine dehydrogenase	M1H3J6	Paramecium_bursaria_Chlorella_virus	2.7e-24	25.6
WP_169946340.1\|2106821_2107961_-	UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)	A0A1V0SAG5	Catovirus	3.0e-19	27.7
WP_169946342.1\|2108151_2109126_+	NAD-dependent epimerase/dehydratase family protein	A0A218MN53	uncultured_virus	5.4e-126	63.1
WP_169948218.1\|2109214_2110123_+	NAD-dependent epimerase/dehydratase family protein	M1HTL0	Acanthocystis_turfacea_Chlorella_virus	5.2e-54	40.3
WP_169946343.1\|2110246_2111257_+	SDR family NAD(P)-dependent oxidoreductase	M4QPK0	Synechococcus_phage	2.5e-25	31.5
WP_169946345.1\|2112459_2113170_+	acylneuraminate cytidylyltransferase family protein	A0A1B1IVD3	uncultured_Mediterranean_phage	5.3e-06	36.4
WP_169946348.1\|2113169_2113808_+	NeuD/PglB/VioB family sugar acetyltransferase	NA	NA	NA	NA
WP_169946350.1\|2113804_2114809_+	N-acetylneuraminate synthase	A0A1B1IVE2	uncultured_Mediterranean_phage	7.5e-30	34.1

DBSCAN-SWA_4

2129472 : 2138628

Enterobacteria_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_169946383.1\|2129472_2130603_+	NAD-dependent epimerase/dehydratase family protein	A0A2K9L4U8	Tupanvirus	3.8e-30	31.0
WP_169946385.1\|2130599_2131667_+	dTDP-glucose 4,6-dehydratase	I7HTA3	Enterobacteria_phage	2.9e-88	49.5
WP_169946387.1\|2131663_2132557_+	dTDP-4-dehydrorhamnose reductase	A0A291LA50	Escherichia_phage	3.1e-27	35.2
WP_169946389.1\|2132588_2133467_+	glucose-1-phosphate thymidylyltransferase RfbA	I7I009	Enterobacteria_phage	2.0e-95	58.2
WP_169946392.1\|2133468_2134020_+	dTDP-4-dehydrorhamnose 3,5-epimerase	I7HJC4	Enterobacteria_phage	1.6e-45	50.8
WP_169946394.1\|2134148_2135534_+	O-antigen ligase family protein	NA	NA	NA	NA
WP_169946396.1\|2135600_2136320_+	polysaccharide export protein	NA	NA	NA	NA
WP_169946398.1\|2136384_2138628_+	polysaccharide biosynthesis tyrosine autokinase	A0A1X9I5D6	Streptococcus_phage	1.2e-14	30.3

Anti-CRISPR protein detection

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