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
LR134089	Staphylococcus saprophyticus subsp. saprophyticus strain NCTC7666 genome assembly, chromosome: 1	1 crisprs	csa3,WYL,DEDDh,cas3,DinG	1	0	8	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: LR134089_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR134089_2

292631-292741

Orphan

Consensus_repeat	Method
TCGTAACATTAATTACCAAGTGAAATTAAGGAATACAAAA	CRISPRCasFinder

1 spacers

The CRISPR arrays of LR134089_2

>merge|LR134089|2|292631-292741|CRISPRCasFinder
TCGTAACATTAATTACCAAGTGAAATTAAGGAATACAAAAAAATCTTTTGCATAAGAATCACTAAGGAAAATCGTAACATTAATTACCAAGTGAAATTAATGAATACAAAA

>LR134089|2|1|292631-292741|CRISPRCasFinder
TCGTAACATTAATTACCAAGTGAAATTAAGGAATACAAAA	AAATCTTTTGCATAAGAATCACTAAGGAAAA
TCGTAACATTAATTACCAAGTGAAATTAATGAATACAAAA

Protein	Signature genes	Signature genes Name	Protein_function
LR134089.1\|VDZ21585.1\|289424_290180_+\|metal-dependent-membrane-protease	unknown	unknown	gnl\|CDD\|376806
LR134089.1\|VDZ21592.1\|297822_298377_-\|transcriptional-regulator	unknown	unknown	gnl\|CDD\|224228
LR134089.1\|VDZ21581.1\|285286_286096_-\|Uncharacterised-protein	unknown	unknown	gnl\|CDD\|379298
LR134089.1\|VDZ21586.1\|290521_291340_+\|ABC-transporter-periplasmic-protein	unknown	unknown	gnl\|CDD\|224381
LR134089.1\|VDZ21594.1\|299198_299405_+\|Uncharacterised-protein	unknown	unknown	unknown
LR134089.1\|VDZ21588.1\|292782_294072_-\|O-acetylhomoserine-sulfhydrylase	unknown	unknown	gnl\|CDD\|225428
LR134089.1\|VDZ21589.1\|294289_295195_+\|cysteine-synthase	unknown	unknown	gnl\|CDD\|107204
LR134089.1\|VDZ21591.1\|296434_297685_-\|MFS-type-transporter	unknown	unknown	gnl\|CDD\|340882
LR134089.1\|VDZ21587.1\|291383_292316_+\|lactate-dehydrogenase	unknown	unknown	gnl\|CDD\|133426
LR134089.1\|VDZ21579.1\|283315_284674_+\|PTS-system-sugar-specific-permease-component-family-protein	unknown	unknown	gnl\|CDD\|236502
LR134089.1\|VDZ21584.1\|288293_289211_-\|2-dehydropantoate-2-reductase	unknown	unknown	gnl\|CDD\|183829
LR134089.1\|VDZ21593.1\|298550_299021_-\|putative-thioesterase	unknown	unknown	gnl\|CDD\|223894
LR134089.1\|VDZ21597.1\|300963_301653_-\|urease-accessory-protein-UreF	unknown	unknown	gnl\|CDD\|223900
LR134089.1\|VDZ21590.1\|295191_296340_+\|cystathionine-gamma-synthase	unknown	unknown	gnl\|CDD\|181076
LR134089.1\|VDZ21583.1\|287422_288199_+\|transcriptional-antiterminator	unknown	unknown	gnl\|CDD\|225117
LR134089.1\|VDZ21596.1\|300335_300950_-\|Urease-accessory-protein-UreG	unknown	unknown	gnl\|CDD\|349776
LR134089.1\|VDZ21580.1\|284757_285264_-\|Uncharacterized-protein-containing-double-stranded-beta-helix-domain	unknown	unknown	gnl\|CDD\|380348
LR134089.1\|VDZ21595.1\|299492_300335_-\|urease-accessory-protein-UreD	unknown	unknown	gnl\|CDD\|223899
LR134089.1\|VDZ21582.1\|286828_287404_+\|LysE-type-translocator-family-protein	unknown	unknown	gnl\|CDD\|224199
LR134089.1\|VDZ21578.1\|283007_283292_+\|PTS-system-transporter-subunit-IIB	unknown	unknown	gnl\|CDD\|99905

Protein	Function_ID	Function_description	E-value
LR134089.1\|VDZ21585.1\|289424_290180_+\|metal-dependent-membrane-protease	gnl\|CDD\|376806	pfam02517, Abi, CAAX protease self-immunity. Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide being removed by one of the CAAX prenyl proteases). The family contains the CAAX prenyl protease. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding. While they are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin. Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity.	4.95371e-10
LR134089.1\|VDZ21592.1\|297822_298377_-\|transcriptional-regulator	gnl\|CDD\|224228	COG1309, AcrR, Transcriptional regulator [Transcription].	6.36006e-12
LR134089.1\|VDZ21581.1\|285286_286096_-\|Uncharacterised-protein	gnl\|CDD\|379298	pfam13622, 4HBT_3, Thioesterase-like superfamily. This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily.	5.14755e-47
LR134089.1\|VDZ21586.1\|290521_291340_+\|ABC-transporter-periplasmic-protein	gnl\|CDD\|224381	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism].	6.23317e-97
LR134089.1\|VDZ21588.1\|292782_294072_-\|O-acetylhomoserine-sulfhydrylase	gnl\|CDD\|225428	COG2873, MET17, O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism].	0
LR134089.1\|VDZ21589.1\|294289_295195_+\|cysteine-synthase	gnl\|CDD\|107204	cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine.	2.16753e-109
LR134089.1\|VDZ21591.1\|296434_297685_-\|MFS-type-transporter	gnl\|CDD\|340882	cd17324, MFS_NepI_like, Purine ribonucleoside efflux pump NepI and similar transporters of the Major Facilitator Superfamily. This family is composed of purine efflux pumps such as Escherichia coli NepI and Bacillus subtilis PbuE, sugar efflux transporters such as Corynebacterium glutamicum arabinose efflux permease, multidrug resistance (MDR) transporters such as Streptomyces lividans chloramphenicol resistance protein (CmlR), and similar proteins. NepI and PbuE are involved in the efflux of purine ribonucleosides such as guanosine, adenosine and inosine, as well as purine bases like guanine, adenine, and hypoxanthine, and purine base analogs. They play a role in the maintenance of cellular purine base pools, as well as in protecting the cells and conferring resistance against toxic purine base analogs such as 6-mercaptopurine. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. The NepI-like 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.	1.1894e-20
LR134089.1\|VDZ21587.1\|291383_292316_+\|lactate-dehydrogenase	gnl\|CDD\|133426	cd05290, LDH_3, A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of some bacterial LDHs from firmicutes, gammaproteobacteria, and actinobacteria. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenase, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.	5.78908e-159
LR134089.1\|VDZ21579.1\|283315_284674_+\|PTS-system-sugar-specific-permease-component-family-protein	gnl\|CDD\|236502	PRK09410, ulaA, PTS system ascorbate-specific transporter subunit IIC; Reviewed.	0
LR134089.1\|VDZ21584.1\|288293_289211_-\|2-dehydropantoate-2-reductase	gnl\|CDD\|183829	PRK12921, PRK12921, oxidoreductase.	1.72629e-127
LR134089.1\|VDZ21593.1\|298550_299021_-\|putative-thioesterase	gnl\|CDD\|223894	COG0824, FcbC, Predicted thioesterase [General function prediction only].	2.74376e-25
LR134089.1\|VDZ21597.1\|300963_301653_-\|urease-accessory-protein-UreF	gnl\|CDD\|223900	COG0830, UreF, Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones].	5.42683e-92
LR134089.1\|VDZ21590.1\|295191_296340_+\|cystathionine-gamma-synthase	gnl\|CDD\|181076	PRK07671, PRK07671, bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase.	0
LR134089.1\|VDZ21583.1\|287422_288199_+\|transcriptional-antiterminator	gnl\|CDD\|225117	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription].	3.85878e-16
LR134089.1\|VDZ21596.1\|300335_300950_-\|Urease-accessory-protein-UreG	gnl\|CDD\|349776	cd05540, UreG, urease accessory protein UreG. UreG is one of the four accessory proteins of urease. Urease is an enzyme which catalyzes the decomposition of urea to form ammonia and carbon dioxide. Bacterial urease is a trimer of three subunits which are encoded by genes ureA, ureB, and ureC. Up to four accessory proteins (ureD, ureE, ureF, and ureG) are required for urease catalytical function. UreG may play an important role in nickel incorporation of the urease metallocenter. UreG is a member of the Fer4_NifH superfamily which contains an ATP-binding domain. Proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.	2.41468e-117
LR134089.1\|VDZ21580.1\|284757_285264_-\|Uncharacterized-protein-containing-double-stranded-beta-helix-domain	gnl\|CDD\|380348	cd02219, cupin_YjlB-like, Bacillus subtilis YjlB and related proteins, cupin domain. This family includes bacterial and fungal proteins homologous to YjlB, a Bacillus subtilis protein of unknown function with a cupin beta barrel fold. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two-domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.	1.77466e-76
LR134089.1\|VDZ21595.1\|299492_300335_-\|urease-accessory-protein-UreD	gnl\|CDD\|223899	COG0829, UreH, Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones].	1.83725e-86
LR134089.1\|VDZ21582.1\|286828_287404_+\|LysE-type-translocator-family-protein	gnl\|CDD\|224199	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism].	8.27153e-19
LR134089.1\|VDZ21578.1\|283007_283292_+\|PTS-system-transporter-subunit-IIB	gnl\|CDD\|99905	cd05563, PTS_IIB_ascorbate, PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a transmembrane channel IIC subunit. Subunits IIA, IIB, and IIC are encoded by the sgaA, sgaB, and sgaT genes of the E. coli sgaTBA operon. In some bacteria, the IIB (SgaB) domain is fused C-terminal to the IIA (SgaT) domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include ascorbate, chitobiose/lichenan, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.	1.80933e-30

>LR134089.1|VDZ21587.1|291383_292316_+|lactate-dehydrogenase
MSKLGIIGLGKVGTQVLTDVQQLNLFSEIILIDDRADVASGEALDHSHSQGLINTAHIKIRSGVYQDLTDADFIVIAASEATDKNNGDRTLLAQGNHDIIKGIMSQIAEVTQEAVVILISNPVDSMVYFANQIDYPAHKIIGTGTALETSRFKTIIADHYQIDPNNVEAFVIGEHGQHAIPVWSKVHIHGMELSEFEALSDRPAIDKSHISSIINEVSMDVFYQKGWTNAAISKVTSFLIQSIALDQRTITPLTSLSAEYGLEDGAFSLPTLIDKKGIVQRFAITLDKEEERQLKEAYEYIRQTIHTAQQ
>LR134089.1|VDZ21586.1|290521_291340_+|ABC-transporter-periplasmic-protein
MRKWFILGSLFVLTIILAACGKSNGEKEDKEITIAASPAPHGVVLEHAKEEMKKKGYDLKIKTVNDYKVPNKLLDKGDVDANAFQHTPYLKAEKKDHNYKIEEAGKVFTTPMGVYSKKYKDIKDIPKGSTIYVSNNPAEEGRFLSFFVDKGLIKIKKGVSIEDAKFDDIVENKKDLKFNNKQGAEFLPKTYNSKEGAAVIMNSNYAIDNGLTPHKDAIAIEGKSSPFANIVAVQEGHKNDKKFKELMKVLQSKEMKKFITDKYGQDVIPYEK
>LR134089.1|VDZ21585.1|289424_290180_+|metal-dependent-membrane-protease
MSFKNDHKYQWKDIQGRDFLLPFIYLIGNFCLSIVILTIMIGINETQGKNNANFNANFSGTPGILMEMIAFIIIFALWILFHRHSFRQSWKQGLQNIKQHWKLIVITFIVIIVFKEIYPYLVNAFAPEHWKFEETQNDKMVEEMFATPVSTILAFFSIVIIAPMTEEFLFRHLIIGELGKKLNFYVMSVISIIVFASLHVTEAKSPLEIVMYLAIAVGIVYVYMKSQRSLAVAIALHALNNLLAYIFMIIM
>LR134089.1|VDZ21584.1|288293_289211_-|2-dehydropantoate-2-reductase
MRILVLGAGGIGGYFGGRLAESGQNVTFLVRPKRKSFLERNGLAIHSEQGDYHFNPQLITKDDRVAPFDVILLSSKSYHLEQAMTDLKPFVDGHTAIIPLLNGVAHIPQLQSIFGRDKVMGGYCVIETTLDSMGEIIQTSPFDKLFFGELDGSKSERAQKIAQAFSETKAEFKLSTSIEQGMWHKYLMITVLSSITTLMHAPIGPIRDSDGGINFVRSLYNEVASIMRAHRAPLADDIVSQYMTSFDQLSYHFKTSMQRDMEKGLNIETDHLQGYLLNLADTYQIDAPLLKCVYQNHKVYKEMLK
>LR134089.1|VDZ21583.1|287422_288199_+|transcriptional-antiterminator
MNEFNFKNAIGITALEVKMDDFTYKKHSHQEYSIGVTLKGIQGYHLKGERKQSYQNGVMFFNPEENHDGMSNGVQGLEYIMLYIKPEQLLEATNQKHMVQFKEPIVYNNKIAQNILQLANSIFNGSDDVICYEHFQNLVDGLKIDTYYDEFNVDNVKLKLAKDIIKNNVSTSFKLDFICSELNLSKYQFIRFFKQQTGITPYQYYINYKAEVAKHIIEKSKDVYLAIAECAFVDLAHLNKVFKYRYGVTAYQYMSKLK
>LR134089.1|VDZ21582.1|286828_287404_+|LysE-type-translocator-family-protein
MNLLPFIMYTFLITMTPGPTNIDILNTIRNKGLKGGIQYTYGAITAFVFLLIISTVVNIFLSEKMPSFLLFMKLIGSIYMLYLIYTLFRKHSENKVENDIGTFYSGFALQFLNPKVVTFTMTVIPTFVLVNQPSTLMISIYVIMTSIIALISFSFWIFFGTLLKTFIQKHEMIVNITMALFLLYAAIIVWV
>LR134089.1|VDZ21581.1|285286_286096_-|Uncharacterised-protein
MSSKHNFDKATELTIQSSGVYRGQTSESYANMVGPFGGVIASTLLRAVLDHDERLGDPISLTINYAAPVANGDFKIVATPSRTNRSTQHWYIELTQNEQIIITGTAVTANRRDTWSSTELSFPDVPNPDQIEPTPLDSAPPWAQNYEIRMIKGAPLAIATTDYPDSITLQWIRDNPNRDLDFLSLAAICDAFFPRIYVRRKELVPIGTISLTIYFHADAETLLANGSRSVLGHTRALKFFNGYFDQTGEIWSQDHNLLATTSQIVYYKS
>LR134089.1|VDZ21580.1|284757_285264_-|Uncharacterized-protein-containing-double-stranded-beta-helix-domain
MKPMSDITVSTLCFIDDGTIPNNPTLPVLIYHHVLGSHEHLEKTITSNQWGNTWTGGVFSYHHYHSNAHETLLAIRGEANLLIGGRKGSTINVTAGDVLILPAGTGHKLLNASHDFIVMGAYPNGQSFDICTGDKNNRTQDIMNIENVPLPETDPLWGEQGPLLLHWH
>LR134089.1|VDZ21579.1|283315_284674_+|PTS-system-sugar-specific-permease-component-family-protein
MKPILDFIVDILSQPAILVALIAFIGLIMQKKSATDITSGTIKTILGFLVLSAGANVVTQSLEPFGKIFQHAFGVQGVVPNNEAIISIALEQYGTTAALIMVFGMIVNIIIARITNLKYIFLTGHHTFYMAAFLAILLSVGHITGTLTVVIGAIILGLIMAILPALAHPTMKKITGNNQVALGHFGTISYWAAGEVGKLFKGKSKSTEEINFPKGLSFLRESTISISLTMTLLYFVAALFAGPHYVHSEISNGQNFIVFSLIQGVTFAAGVFIILTGVRLILAEIVPAFKGISEKLVPNTKPALDCPIVFPYAQNAVLIGFFVSFIVGVIGMFVLFLFGGVVILPGVVAHFFLGATAGVFGNARGGIKGAVAGSALNGILITFLPLLFLPFLGDLGGAATTFSDTDFLVVGIVFGNVAKFLGLIGIIILVIVVAAFAIILQKRTDAKEVKEQ
>LR134089.1|VDZ21578.1|283007_283292_+|PTS-system-transporter-subunit-IIB
MKILVVCGHGLGSSFMVEMNAQEALKNLNAPSDIKVEHSDVMSASPDMADLFICGRDLEENTKNLGDVIVLDNILDKEELQNKLSEKLSELNLL
>LR134089.1|VDZ21588.1|292782_294072_-|O-acetylhomoserine-sulfhydrylase
MTQTPWHLDTLSIHGGQVVDDFSKARAVPIYQTSSYVFDNTEHARKLFALEEDGNIYTRIMNPTQNVFEERIAALEGGVGALATSSGQAAIHLALLNIVESGDEIVASSNLYGGTYNLLNITFKKLGIKVHFVDPSHPDNFKNAITDKTKAVYAETIGNPRIDVLDIEAVADIAHNHNIPLIVDNTFPTPYLLRPFEFGADIIVHSATKFIGGHGTSIGGVIVDSGKFNWDNGKFPGLVEPDESYHGISYTKDVGEAAYITKARVQLLRDLGSAVSPFNVHEFLIGLETLHLRLERHSENALRVAQYLEQHPKVTWVNYPGLENNAYHQLAQKYLPDGQGAILTFGIDGTVDDIAKFVDGLNLFSHLANVGDSKSLIIHPASTTHLQLSPEDQKASGVVPELVRLSVGTENINDIIADLDNGFKESLGN
>LR134089.1|VDZ21589.1|294289_295195_+|cysteine-synthase
MIAFDLIGNTPLVLLESFSNKDVQIYAKLEQYNPGGSVKDRLGKHLIETAIRENIIQKGDVVVEASAGNTGIGVAIAANHYGVSAVIFAPEGFSEEKISIIKALGAEVIRTDQTLGMAGAQKAARDYELQTGAYYLNQFESYRNPETYKSTIGKEITDKLKDIDYFVGGVGSGGTFAGVAEHLAASYRTESVIVEPEGSILSGGNAHSHDIEGIGSEKWPSFLPKALVSDIIKVSDDAAFQNVKLLARQEGLLVGSSSGAALQGALEIKKHINKGVIVTIFPDGSDRYMSKQILNYKETIK
>LR134089.1|VDZ21590.1|295191_296340_+|cystathionine-gamma-synthase
MNKKTQLIHGGQTTDPYTGAVTTPIYQTSTYMQDGIGDMRQGYEYSRSANPTRSALEGLIADLEQGESGFAFGSGMAAISAVIMLLDKGDHLLINSDVYGGTYRALTKVFNRFGIDAEFIDTTNIEVVEQYIKPETKMLYIETPSNPLLRVTDIKKSAEIAKKHHLISVVDNTFMTPYFQNPLTLGIDIVLHSATKYIGGHSDVVAGLVATSDAELAERLGFIQNSTGGVLGPQDSYLLIRGIKTLGLRMEQVQRNTLAIIDMLQQHSAVKQVFHPSISDHLNHDIHEAQSEGHTGVVAFEVADIESAKKVISESHYFTLAESLGAVESLISVPALMTHASIPKDIREKEGIADGLVRLSVGIEDTKDLVEDLEQSLNALDK
>LR134089.1|VDZ21591.1|296434_297685_-|MFS-type-transporter
MKFSKLVFPGIAMIATTYGLGRFSFGLFLPDITNDLSLSASQAGLISSLFYLAYCFTIVYSTLQTDTIGPKRMIILAGISVVIGLITIGVSSNAIILSIGVIFTGASTGLVSPPYGYTISLWINLQDQGKANTWINSGTSMGLMFTGITAMLVFLDWRHTYLIYALIALVVLFWNYIVIPKLQKDIKIHTGSLNIRDISASTRIVTASTLLGISTAPFWTFSKSFVQLTGNYSDIALSIFWILIGIFGVVGGISGSIIDKKGIHFAFNFGVIALACASVLLAFTPSIWLLPFVASSLFGLSYIFLTGVLLVWGIKLFVKNASLGIGIPFLLLAVGQVIGSSIAGIVIDILNYQYSFIIFGIIGLIPLLIYPKVEVTENKIPKGRYSKLQKTNSDILNDTYAQHQTSNSNNDEYNHI
>LR134089.1|VDZ21592.1|297822_298377_-|transcriptional-regulator
MSQKKQDILSVAERLFYEYGFKGVGLKQIIQEANVATMTLYNHFESKDNLVAQVLKQRETRYWHYLDSHVEQHPEKPFISAVTAHCQWLNDYSYKGDMFMRAIEDYADTDNEIESTARGHKERLLHYLEKLADDAGIENGYDLAVQYTLLLEGTTSMTALLGSKDATSHAITMAKLLLNEAHNQ
>LR134089.1|VDZ21593.1|298550_299021_-|putative-thioesterase
MTDEYIYKNTVQPSWIDNNNHMHDAQYYSIFSDAVVGFFESIDFSTDYRHSQDVTMFSIEAHISFLKELLLDESFYIKVHIYDYDAKRVHLFLTMYNSNDERNATYEAIMMGVGNETRRSMDFPKPIQEKIKHYFDQQNTFDVPKQLGHVIGIPKK
>LR134089.1|VDZ21594.1|299198_299405_+|Uncharacterised-protein
MVLVALILFIISIVFLIYSITLLMGKDGTMFSLFTKEEKALTKGQKLTIYLITIVLFVASLVWLLNLI
>LR134089.1|VDZ21595.1|299492_300335_-|urease-accessory-protein-UreD
MSNNKQAWTGQLDLSVFNNGKKSVARDVFFEKALKVMRPVYLNQSDIPTFYIVNVGGGYLDGDRYTMNFNIDSDAKVILTSQGATKIYKTLNDHVEQYQTFNIKNNGYAEYVGDPIIAFENAKFYQHNVFNLESTASLFYTDILTPGYSKSDKRFSYTYMHLLNEIYVDDALVTFDNMLLDPQKQNVDGLGYMEDYTHLGSCYFIHPSVNQKFIEQVYEEIKHFQHKYDCRFGITHLPTHGFSLRILSNKTQVIESIITAVQCYVVKQIFDRDVDFLRKY
>LR134089.1|VDZ21596.1|300335_300950_-|Urease-accessory-protein-UreG
MTDTIKIGVGGPVGAGKTQLIEKIVKRLAKDMSIGVITNDIYTKEDEKILVNSGVLPEDRIIGVETGGCPHTAIREDASMNFAAIDELKERNDDIELIFIESGGDNLAATFSPELVDFSIYIIDVAQGEKIPRKGGQGMIKSDFFVINKTDLAPYVGASLDRMAEDTKVFRGKRPFTFTNLKTDEGLDEVIQWIEQDVFLKGLA
>LR134089.1|VDZ21597.1|300963_301653_-|urease-accessory-protein-UreF
MIDHAHLRLFQFCDSQFPTGAFSHSFGLETYIQRDTVHDEESFQQWLVLFLNEQLTYADGLTMRLVYDALNENDTKAILKLDRILFVQNLPKETRQGSKQMGNRMVKLASELYDSDWINWYHDQMKDKKASLHPAICFTMLGHHLGVDIETIIDYYLYQNVSSLTQNAVRAIPLGQTAGQRIVHKMIPIMKETRDHIMTIPASQLGITAPGLEINQMEHENVNVRIFIS

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
LR134089_1	1.8\|163694\|34\|LR134089\|CRT	163694-163727	34	LR134089.1	158432-158465	2	0.941

1. spacer 1.8|163694|34|LR134089|CRT matches to position: 158432-158465, mismatch: 2, identity: 0.941

tgagtcattaagtgagagtgagtcactaagtgca	CRISPR spacer
tgagtcattaagtgcgagtgagtcattaagtgca	Protospacer
************** **********.********

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1036534 : 1070826

Staphylococcus_phage(96.15%)

tRNA

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
VDZ22325.1\|1036534_1038070_+	O-succinylbenzoic acid-CoA ligase	A0A2H4PQM9	Staphylococcus_phage	8.5e-166	61.1
VDZ22326.1\|1038089_1039094_+	O-succinylbenzoic acid synthetase	A0A2H4PQM0	Staphylococcus_phage	1.7e-90	49.7
VDZ22327.1\|1039083_1039335_-	Putative cytosolic protein	A0A2H4PQM5	Staphylococcus_phage	4.2e-30	81.1
VDZ22328.1\|1039394_1039871_+	low G+C gram positive nudix hydrolase YtkD	A0A2H4PQM4	Staphylococcus_phage	2.8e-43	53.5
VDZ22329.1\|1039854_1040646_+	peptidase	A0A2H4PQM6	Staphylococcus_phage	1.6e-99	71.4
VDZ22330.1\|1040741_1042331_-	phosphoenolpyruvate carboxykinase	A0A2H4PQN1	Staphylococcus_phage	4.2e-261	81.6
VDZ22331.1\|1042719_1043916_+	S-adenosylmethionine synthetase	A0A2H4PQS6	Staphylococcus_phage	7.5e-194	86.1
VDZ22332.1\|1044014_1044923_+	Predicted HD superfamily hydrolase	A0A2H4PQQ8	Staphylococcus_phage	4.3e-101	75.8
VDZ22333.1\|1045131_1045968_+	aldo keto reductase	A0A2H4PQR8	Staphylococcus_phage	2.5e-111	68.2
VDZ22334.1\|1046237_1046594_-	CrcB-like protein	NA	NA	NA	NA
VDZ22335.1\|1046590_1046956_-	camphor resistance protein CrcB	A0A2H4PQR0	Staphylococcus_phage	3.3e-36	62.8
VDZ22336.1\|1047166_1047472_-	membrane protein	NA	NA	NA	NA
VDZ22337.1\|1047756_1048470_+	Transaldolase	E3SKN5	Synechococcus_phage	5.0e-20	35.8
VDZ22338.1\|1048985_1049486_+	Uncharacterized protein conserved in bacteria	NA	NA	NA	NA
VDZ22339.1\|1049585_1050035_+	membrane protein	A0A2H4PQT8	Staphylococcus_phage	1.3e-21	47.5
VDZ22340.1\|1050042_1050468_-	comK family protein	NA	NA	NA	NA
VDZ22341.1\|1050481_1050952_-	DNA-binding protein	A0A2H4PQT5	Staphylococcus_phage	1.3e-24	44.4
VDZ22342.1\|1051172_1051397_+	putative staphylococcal protein	NA	NA	NA	NA
VDZ22343.1\|1051564_1052416_+	mannosyl-glycoprotein endo-beta-N-acetylglucosamidase	A0A0E3T9J6	Staphylococcus_phage	1.7e-38	43.3
VDZ22344.1\|1052638_1053565_-	glycine/betaine ABC transporter	NA	NA	NA	NA
VDZ22345.1\|1053739_1055206_+	pyridine nucleotide-disulfide oxidoreductase family protein	A0A2H4PQX2	Staphylococcus_phage	5.5e-13	58.6
VDZ22346.1\|1055746_1056790_+	riboflavin specific deaminase	A0A2H4PQS8	Staphylococcus_phage	2.3e-130	64.4
VDZ22347.1\|1056796_1057429_+	riboflavin synthase subunit alpha	A0A2H4PQS5	Staphylococcus_phage	5.0e-72	64.8
VDZ22348.1\|1057440_1058622_+	riboflavin biosynthesis protein	A0A2H4PQS2	Staphylococcus_phage	1.0e-163	71.0
VDZ22349.1\|1058635_1059094_+	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	1.5e-57	75.7
VDZ22350.1\|1059358_1060360_-	proline dehydrogenase	A0A2H4PQT6	Staphylococcus_phage	4.3e-126	68.5
VDZ22351.1\|1060593_1061451_+	lysophospholipase	NA	NA	NA	NA
VDZ22352.1\|1061686_1062643_+	L-lactate dehydrogenase	NA	NA	NA	NA
VDZ22353.1\|1062793_1063195_+	repressor of toxins	NA	NA	NA	NA
VDZ22354.1\|1063314_1063875_-	SAM-dependent methyltransferase, MraW methylase family	A0A2H4PQV0	Staphylococcus_phage	9.5e-67	63.8
VDZ22355.1\|1063871_1064825_-	Fe-S oxidoreductase	A0A2H4PQV5	Staphylococcus_phage	1.9e-67	84.0
VDZ22356.1\|1064934_1066104_+	major facilitator superfamily permease	A0A2H4PQR6	Staphylococcus_phage	2.2e-166	77.2
VDZ22357.1\|1066632_1069047_+\|tRNA	leucyl-tRNA synthetase	A0A2H4PQS0	Staphylococcus_phage	0.0e+00	85.3
VDZ22358.1\|1069065_1069377_+	rhodanese-like domain-containing protein	A0A2H4PQR9	Staphylococcus_phage	4.5e-34	68.9
VDZ22359.1\|1069572_1070826_-	flavoprotein	A0A2H4PQX1	Staphylococcus_phage	1.9e-38	77.2

DBSCAN-SWA_2

1192602 : 1201726

uncultured_Mediterranean_phage(50.0%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VDZ22468.1\|1192602_1193607_+	Holliday junction DNA helicase RuvB	B3GAM6	uncultured_virus	1.7e-05	29.9
VDZ22469.1\|1193609_1194635_+\|tRNA	S-adenosylmethionine:tRNA ribosyltransferase-isomerase	NA	NA	NA	NA
VDZ22470.1\|1194655_1195801_+\|tRNA	queuine tRNA-ribosyltransferase	A0A1B1IVQ4	uncultured_Mediterranean_phage	2.1e-84	44.5
VDZ22471.1\|1195816_1196077_+	preprotein translocase subunit	A0A1B1IVR5	uncultured_Mediterranean_phage	7.4e-06	44.1
VDZ22472.1\|1196457_1198734_+	bifunctional preprotein translocase subunit SecD/SecF	A0A1B1IVP7	uncultured_Mediterranean_phage	1.0e-29	34.2
VDZ22473.1\|1198915_1201195_+	single-strand DNA-specific exonuclease	A7KV88	Bacillus_phage	4.9e-69	29.4
VDZ22474.1\|1201207_1201726_+	Adenine phosphoribosyltransferase	A0A1V0SKE5	Klosneuvirus	6.6e-30	46.2

DBSCAN-SWA_3

1328030 : 1337993

uncultured_Mediterranean_phage(28.57%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VDZ22756.1\|1328030_1328918_+	site-specific recombinase	A0A0K2CP59	Brevibacillus_phage	5.1e-38	31.4
VDZ22759.1\|1328986_1329493_-	Putative cytosolic protein	NA	NA	NA	NA
VDZ22761.1\|1329584_1330319_+	segregation and condensation protein A	A0A1B1IVW1	uncultured_Mediterranean_phage	1.8e-09	23.6
VDZ22763.1\|1330302_1330851_+	transcriptional regulator	A0A1B1IVT7	uncultured_Mediterranean_phage	2.1e-10	31.4
VDZ22765.1\|1330843_1331581_+	ribosomal large subunit pseudouridine synthase B	NA	NA	NA	NA
VDZ22767.1\|1331707_1332433_+	respiratory response protein SrrA	W8CYM9	Bacillus_phage	1.1e-46	42.6
VDZ22769.1\|1332416_1334180_+	respiratory response protein SrrB	A0A1V0SGX0	Hokovirus	7.8e-22	24.0
VDZ22773.1\|1334602_1335148_+	riboflavin transporter	NA	NA	NA	NA
VDZ22775.1\|1335303_1335552_-	Ferredoxin	A0A127AYY7	Bacillus_phage	4.9e-15	48.0
VDZ22776.1\|1335661_1336621_+	Uncharacterised protein	NA	NA	NA	NA
VDZ22778.1\|1336613_1337993_+	ATP-dependent DNA helicase	M1PGQ0	Moumouvirus	2.4e-55	32.7

DBSCAN-SWA_4

1776935 : 1785410

Synechococcus_phage(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VDZ23629.1\|1776935_1777502_-	phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	2.2e-26	37.6
VDZ23631.1\|1777504_1778533_-	phosphoribosylaminoimidazole synthetase	Q58MH8	Prochlorococcus_phage	9.3e-68	44.5
VDZ23635.1\|1778525_1780013_-	amidophosphoribosyltransferase	A0A0M3SGR2	Mollivirus	3.8e-46	32.2
VDZ23637.1\|1779991_1782181_-	phosphoribosylformylglycinamidine synthase II	A6N228	Microbacterium_phage	1.2e-136	39.4
VDZ23639.1\|1782173_1782845_-	phosphoribosylformylglycinamidine synthase I	NA	NA	NA	NA
VDZ23641.1\|1782844_1783105_-	phosphoribosylformylglycinamidine synthase PurS component	NA	NA	NA	NA
VDZ23643.1\|1783107_1783809_-	phosphoribosylaminoimidazole-succinocarboxamide synthase	A0A1D7SE76	Cyanophage	6.8e-46	42.5
VDZ23645.1\|1783813_1784941_-	phosphoribosylaminoimidazole carboxylase ATPase subunit	NA	NA	NA	NA
VDZ23647.1\|1784927_1785410_-	phosphoribosylcarboxyaminoimidazole mutase	A0A2P0VNU7	Tetraselmis_virus	2.6e-20	44.0

DBSCAN-SWA_5

1967663 : 1974490

uncultured_Caudovirales_phage(33.33%)

transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VDZ24398.1\|1967663_1968083_-	alcohol dehydrogenase	A0A2L2DIY2	Acanthamoeba_polyphaga_mimivirus	4.5e-05	33.3
VDZ24400.1\|1968083_1968377_-	YolD-like protein	A0A2H4JEH6	uncultured_Caudovirales_phage	2.9e-14	81.0
VDZ24406.1\|1968386_1968578_-	Uncharacterised protein	U3PCX8	Staphylococcus_phage	2.9e-31	100.0
VDZ24416.1\|1968697_1968904_+	Uncharacterised protein	NA	NA	NA	NA
VDZ24423.1\|1968995_1969520_-	membrane protein	NA	NA	NA	NA
VDZ24431.1\|1970013_1970415_+	Uncharacterised protein	NA	NA	NA	NA
VDZ24439.1\|1970390_1970783_-\|transposase	transposase	A0A2H4JB14	uncultured_Caudovirales_phage	1.7e-14	42.9
VDZ24446.1\|1971612_1972077_-	tmRNA-binding protein SmpB	W5RAM5	Staphylococcus_phage	1.2e-75	92.9
VDZ24454.1\|1972099_1974490_-	exoribonuclease	Q0GXV6	Lactococcus_phage	2.4e-90	38.4

DBSCAN-SWA_6

1987312 : 1994483

Streptococcus_phage(33.33%)

protease

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VDZ24534.1\|1987312_1987897_-\|protease	ATP-dependent Clp protease proteolytic subunit	A0A223W000	Agrobacterium_phage	3.7e-53	55.8
VDZ24537.1\|1988601_1989099_+	surface lipoprotein-related protein	A0A1P8D5Q9	Corynebacterium_phage	4.9e-06	57.8
VDZ24546.1\|1989214_1990060_-	membrane protein	NA	NA	NA	NA
VDZ24553.1\|1990298_1991243_-	sporulation Regulator WhiA C terminal domain protein	Q7AWZ3	Streptococcus_phage	3.1e-54	40.6
VDZ24562.1\|1991281_1992280_-	2-phospho-L-lactate transferase-like protein	A1IMD5	Streptococcus_phage	1.0e-47	40.8
VDZ24567.1\|1992266_1993193_-	glmZ(sRNA)-inactivating NTPase	A0A0R8VB27	Thermobifida_phage	1.4e-09	37.0
VDZ24573.1\|1993538_1994483_-	thioredoxin reductase	G3MA85	Bacillus_virus	9.4e-83	49.5

DBSCAN-SWA_7

2029053 : 2047782

uncultured_Caudovirales_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VDZ24679.1\|2029053_2030022_-	cobalamin Fe3+-siderophores ABC transporter permease	A0A2H4IY97	uncultured_Caudovirales_phage	1.5e-136	78.6
VDZ24683.1\|2030435_2031404_-	ribonucleotide reductase of class Ib (aerobic), beta subunit	A0A2H4J4P3	uncultured_Caudovirales_phage	2.2e-175	94.1
VDZ24691.1\|2031525_2033631_-	ribonucleotide-diphosphate reductase subunit alpha	A0A2H4J2N6	uncultured_Caudovirales_phage	0.0e+00	90.2
VDZ24694.1\|2033593_2033992_-	ribonucleotide reductase stimulatory protein	A0A2H4J545	uncultured_Caudovirales_phage	2.5e-53	75.8
VDZ24697.1\|2034718_2035606_+	permease	NA	NA	NA	NA
VDZ24700.1\|2035619_2036120_+	NADPH dependent preQ0 reductase	E7DN65	Pneumococcus_phage	2.0e-52	72.3
VDZ24705.1\|2036302_2037817_+	di-tripeptide permease	A0A0P0IY73	Acinetobacter_phage	9.5e-69	35.8
VDZ24708.1\|2038186_2039692_+	di-tripepride permease	A0A0P0IY73	Acinetobacter_phage	1.1e-64	32.2
VDZ24711.1\|2040149_2041109_+	Transcription regulator (contains diacylglycerol kinase catalytic domain)	A0A1V0SBJ0	Catovirus	2.2e-10	24.4
VDZ24714.1\|2041278_2041827_-	5'-3'-deoxyribonucleotidase, putative	A0A0A0PKY7	Bacillus_phage	2.0e-29	39.0
VDZ24717.1\|2042004_2043060_-	histidinol-phosphate aminotransferase	A0A1X6WGT4	Pacmanvirus	2.3e-21	27.2
VDZ24720.1\|2043218_2044736_-	glycine/betaine ABC transporter periplasmic protein	NA	NA	NA	NA
VDZ24725.1\|2044732_2045695_-	glycine/betaine ABC transporter ATPase	G3M9Y6	Bacillus_virus	4.8e-26	32.5
VDZ24728.1\|2046003_2047782_-	ATP-dependent DNA helicase	M1PGQ0	Moumouvirus	5.9e-78	36.8

DBSCAN-SWA_8

2056083 : 2063632

Pandoravirus(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VDZ24752.1\|2056083_2057226_-	para-aminobenzoate synthase component	S4VNU7	Pandoravirus	5.4e-24	36.7
VDZ24755.1\|2057209_2057803_-	glutamine amidotransferase class-I protein	A0A0P0IKJ1	Acinetobacter_phage	3.2e-36	40.9
VDZ24758.1\|2058058_2058730_+	putative ExsB family protein	A0A2H4J8Q7	uncultured_Caudovirales_phage	1.2e-63	54.9
VDZ24761.1\|2058731_2059157_+	6-pyruvoyl tetrahydrobiopterin synthase	NA	NA	NA	NA
VDZ24766.1\|2059149_2059866_+	radical activating enzyme	A0A1U9WRB6	Streptococcus_virus	2.5e-51	43.4
VDZ24769.1\|2060106_2060700_+	Uncharacterised protein	NA	NA	NA	NA
VDZ24773.1\|2060768_2061020_+	transglycosylase associated family protein	NA	NA	NA	NA
VDZ24776.1\|2061237_2062299_-	glucosyl transferase	A0A192Y8W7	Salmonella_phage	1.1e-60	42.3
VDZ24779.1\|2062792_2063632_-	aldo keto reductase	A0A2H4PQR8	Staphylococcus_phage	4.9e-51	39.5

Anti-CRISPR protein detection

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