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
LS483443	Aggregatibacter segnis strain NCTC10977 genome assembly, chromosome: 1	2 crisprs	csm2gr11,csm3gr7,csm4gr5,csm5gr7,cas6,csx16,csx1,cas2,cas1,cas3,DEDDh,DinG,csa3	0	5	2	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: LS483443_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LS483443_1

276173-276708

TypeIII

Consensus_repeat	Method
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAAC	PILER-CR
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	CRISPRCasFinder
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	CRT

7 spacers

csx1,csx16,cas6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas2,cas1

The CRISPR arrays of LS483443_1

>merge|LS483443|1|276173-276708|PILER-CR,CRISPRCasFinder,CRT
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAACAAAGGATATTTGATGAATATAAGAGACTTGAATGGTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAACAGCGAATAAAATTCATCGCCATTATACTCGTGGTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAACCCAGACGGTTCTTGAAAAGCTTCACACGCAGGATGTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAACATTTGCCGCTCTTTTAAATTGACTTGCGTCTCGTGGTCGAAAGACCCCGCCCTGTTCTAAAGGGATTGAAAGTACAGCGCACCGTTTTTGTAAACACGGATGTCATATGTCGAAAGACCTCGCCCTGCTCCAAAGGGATTGAAACTCTGGGTGGTATTTGATTGCCATTCTTTTATATGTCGAAAGACACCGCCCTGTTCCAAAGGGATTGAAACTAAGCTACTTGTTCAGTAGTGATGTTTTAACACACAGTCGAAAGACCCCGCCCTGCTCCAAAGGGATTGAAAC

>LS483443|1|1|276173-276708|PILER-CR
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAAC	AAAGGATATTTGATGAATATAAGAGACTTGAATG
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAAC	AGCGAATAAAATTCATCGCCATTATACTCGTG
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAAC	CCAGACGGTTCTTGAAAAGCTTCACACGCAGGAT
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATTAAAAC	ATTTGCCGCTCTTTTAAATTGACTTGCGTCTCGTG
GTCGAAAGACCCCGCCCTGTTCTAAAGGGATTGAAAG	TACAGCGCACCGTTTTTGTAAACACGGATGTCATAT
GTCGAAAGACCTCGCCCTGCTCCAAAGGGATTGAAAC	TCTGGGTGGTATTTGATTGCCATTCTTTTATAT
GTCGAAAGACACCGCCCTGTTCCAAAGGGATTGAAAC	TAAGCTACTTGTTCAGTAGTGATGTTTTAACACACA
GTCGAAAGACCCCGCCCTGCTCCAAAGGGATTGAAAC

>LS483443|1|1|276173-276703|CRISPRCasFinder
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	AAAACAAAGGATATTTGATGAATATAAGAGACTTGAATG
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	AAAACAGCGAATAAAATTCATCGCCATTATACTCGTG
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	AAAACCCAGACGGTTCTTGAAAAGCTTCACACGCAGGAT
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	AAAACATTTGCCGCTCTTTTAAATTGACTTGCGTCTCGTG
GTCGAAAGACCCCGCCCTGTTCTAAAGGGATT	GAAAGTACAGCGCACCGTTTTTGTAAACACGGATGTCATAT
GTCGAAAGACCTCGCCCTGCTCCAAAGGGATT	GAAACTCTGGGTGGTATTTGATTGCCATTCTTTTATAT
GTCGAAAGACACCGCCCTGTTCCAAAGGGATT	GAAACTAAGCTACTTGTTCAGTAGTGATGTTTTAACACACA
GTCGAAAGACCCCGCCCTGCTCCAAAGGGATT

>LS483443|1|1|276173-276703|CRT
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	AAAACAAAGGATATTTGATGAATATAAGAGACTTGAATG
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	AAAACAGCGAATAAAATTCATCGCCATTATACTCGTG
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	AAAACCCAGACGGTTCTTGAAAAGCTTCACACGCAGGAT
GTCGAAAGACCCCGCCCTGTTCCAAAGGGATT	AAAACATTTGCCGCTCTTTTAAATTGACTTGCGTCTCGTG
GTCGAAAGACCCCGCCCTGTTCTAAAGGGATT	GAAAGTACAGCGCACCGTTTTTGTAAACACGGATGTCATAT
GTCGAAAGACCTCGCCCTGCTCCAAAGGGATT	GAAACTCTGGGTGGTATTTGATTGCCATTCTTTTATAT
GTCGAAAGACACCGCCCTGTTCCAAAGGGATT	GAAACTAAGCTACTTGTTCAGTAGTGATGTTTTAACACACA
GTCGAAAGACCCCGCCCTGCTCCAAAGGGATT

Protein	Signature genes	Signature genes Name	Protein_function
LS483443.1\|SQH63780.1\|272446_273589_+\|Domain-of-uncharacterised-function-(DUF1887)	csx1	pfam09002_csx1_CAS-III	gnl\|CDD\|312526
LS483443.1\|SQH63783.1\|277672_277798_+\|Uncharacterised-protein	unknown	unknown	unknown
LS483443.1\|SQH63777.1\|269538_271167_+\|RAMP-superfamily	csm5gr7	mkCas0182_csm5gr7_CAS-III-A	gnl\|CDD\|224251
LS483443.1\|SQH63791.1\|285238_286279_+\|Phosphoribosylformylglycinamidine-cyclo-ligase	unknown	unknown	gnl\|CDD\|235439
LS483443.1\|SQH63785.1\|278423_279278_+\|Uncharacterised-protein	unknown	unknown	unknown
LS483443.1\|SQH63787.1\|279586_280657_+\|CRISPR-associated-endonuclease-Cas1	cas1	cd09634_cas1_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|376633
LS483443.1\|SQH63790.1\|284553_285054_-\|Uncharacterised-protein	unknown	unknown	gnl\|CDD\|374773
LS483443.1\|SQH63772.1\|264441_265056_-\|ComE-operon-protein-1	unknown	unknown	gnl\|CDD\|378965
LS483443.1\|SQH63788.1\|280669_280957_+\|CRISPR-associated-endoribonuclease-Cas2	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	gnl\|CDD\|378256
LS483443.1\|SQH63774.1\|267495_267879_+\|CRISPR-type-III-A/MTUBE-associated-protein-Csm2	csm2gr11	cd09647_csm2gr11_CAS-III-A	gnl\|CDD\|367635
LS483443.1\|SQH63786.1\|279293_279578_+\|CRISPR-associated-protein-Cas2	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	gnl\|CDD\|187856
LS483443.1\|SQH63775.1\|267889_268594_+\|CRISPR-type-III-A/MTUBE-associated-RAMP-protein-Csm3	csm3gr7	cd09684_csm3gr7_CAS-III-A:CAS-III-D	gnl\|CDD\|187815
LS483443.1\|SQH63792.1\|286278_286917_+\|Phosphoribosylglycinamide-formyltransferase	unknown	unknown	gnl\|CDD\|235544
LS483443.1\|SQH63784.1\|277975_278335_+\|Uncharacterised-protein	unknown	unknown	unknown
LS483443.1\|SQH63779.1\|272147_272438_+\|putative-CRISPR-associated-protein,-VVA1548-family	csx16	cd09695_csx16_CAS-I:CAS-III	gnl\|CDD\|370601
LS483443.1\|SQH63781.1\|273588_274743_+\|CRISPR-associated-protein,-NE0113-family	csx1	pfam09623_csx1_CAS-III	gnl\|CDD\|187872
LS483443.1\|SQH63773.1\|265282_267487_+\|CRISPR-associated-protein-Cas10/Csm1,-subtype-III-A/MTUBE	cas10	cd09680_cas10_CAS-III	gnl\|CDD\|187811
LS483443.1\|SQH63778.1\|271163_272087_+\|Uncharacterized-conserved-protein-(DUF2276)	cas6	mkCas0066_cas6_CAS-I:CAS-III	gnl\|CDD\|187890
LS483443.1\|SQH63776.1\|268603_269542_+\|CRISPR-type-III-A/MTUBE-associated-RAMP-protein-Csm4	csm4gr5	mkCas0089_csm4gr5_CAS-III-A:CAS-III-D	gnl\|CDD\|273866
LS483443.1\|SQH63789.1\|281883_284454_+\|Heat-shock-protein-F84.1	unknown	unknown	gnl\|CDD\|274529

Protein	Cas_name	Cas_description	E-value	Identity	Coverage
LS483443.1\|SQH63780.1\|272446_273589_+\|Domain-of-uncharacterised-function-(DUF1887)	csx1	pfam09002_csx1_CAS-III	9.6e-128	420.7	11.1
LS483443.1\|SQH63777.1\|269538_271167_+\|RAMP-superfamily	csm5gr7	mkCas0182_csm5gr7_CAS-III-A	2.8e-18	60.8	19.3
LS483443.1\|SQH63787.1\|279586_280657_+\|CRISPR-associated-endonuclease-Cas1	cas1	cd09634_cas1_CAS-I:CAS-II:CAS-III:CAS-V	9.1e-76	249.6	0.0
LS483443.1\|SQH63788.1\|280669_280957_+\|CRISPR-associated-endoribonuclease-Cas2	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	5.6e-19	63.0	0.0
LS483443.1\|SQH63774.1\|267495_267879_+\|CRISPR-type-III-A/MTUBE-associated-protein-Csm2	csm2gr11	cd09647_csm2gr11_CAS-III-A	4.2e-17	57.6	1.4
LS483443.1\|SQH63773.1\|265282_267487_+\|CRISPR-associated-protein-Cas10/Csm1,-subtype-III-A/MTUBE	cas10	cd09680_cas10_CAS-III	7.5e-112	369.6	1.5
LS483443.1\|SQH63775.1\|267889_268594_+\|CRISPR-type-III-A/MTUBE-associated-RAMP-protein-Csm3	csm3gr7	cd09684_csm3gr7_CAS-III-A:CAS-III-D	3.4e-70	230.9	0.2
LS483443.1\|SQH63779.1\|272147_272438_+\|putative-CRISPR-associated-protein,-VVA1548-family	csx16	cd09695_csx16_CAS-I:CAS-III	8.1e-31	100.8	0.0
LS483443.1\|SQH63781.1\|273588_274743_+\|CRISPR-associated-protein,-NE0113-family	csx1	pfam09623_csx1_CAS-III	3.1e-83	273.6	0.0
LS483443.1\|SQH63786.1\|279293_279578_+\|CRISPR-associated-protein-Cas2	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	5.3e-17	56.7	0.1
LS483443.1\|SQH63778.1\|271163_272087_+\|Uncharacterized-conserved-protein-(DUF2276)	cas6	mkCas0066_cas6_CAS-I:CAS-III	4.7e-101	332.9	0.0
LS483443.1\|SQH63776.1\|268603_269542_+\|CRISPR-type-III-A/MTUBE-associated-RAMP-protein-Csm4	csm4gr5	mkCas0089_csm4gr5_CAS-III-A:CAS-III-D	8e-115	378.2	0.1

Protein	Function_ID	Function_description	E-value
LS483443.1\|SQH63780.1\|272446_273589_+\|Domain-of-uncharacterised-function-(DUF1887)	gnl\|CDD\|312526	pfam09002, DUF1887, Domain of unknown function (DUF1887). This domain is found in a set of hypothetical bacterial proteins.	2.77445e-134
LS483443.1\|SQH63789.1\|281883_284454_+\|Heat-shock-protein-F84.1	gnl\|CDD\|274529	TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. [Protein fate, Protein folding and stabilization].	0
LS483443.1\|SQH63777.1\|269538_271167_+\|RAMP-superfamily	gnl\|CDD\|224251	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms].	5.3179e-05
LS483443.1\|SQH63787.1\|279586_280657_+\|CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|376633	pfam01867, Cas_Cas1, CRISPR associated protein Cas1. Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. This family of proteins corresponds to Cas1, a CRISPR-associated protein. Cas1 may be involved in linking DNA segments to CRISPR.	1.64137e-92
LS483443.1\|SQH63790.1\|284553_285054_-\|Uncharacterised-protein	gnl\|CDD\|374773	pfam16747, Adhesin_E, Surface-adhesin protein E. Adhesin E plays a role in pathogenesis. It binds to host proteins including plasminogen, vitronectin and laminin.	2.628e-68
LS483443.1\|SQH63772.1\|264441_265056_-\|ComE-operon-protein-1	gnl\|CDD\|378965	pfam12836, HHH_3, Helix-hairpin-helix motif. The HhH domain is a short DNA-binding domain.	6.61763e-23
LS483443.1\|SQH63788.1\|280669_280957_+\|CRISPR-associated-endoribonuclease-Cas2	gnl\|CDD\|378256	pfam09827, CRISPR_Cas2, CRISPR associated protein Cas2. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages.	5.57358e-16
LS483443.1\|SQH63774.1\|267495_267879_+\|CRISPR-type-III-A/MTUBE-associated-protein-Csm2	gnl\|CDD\|367635	pfam03750, Csm2_III-A, Csm2 Type III-A. Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-associated) proteins. This entry represents Csm2 Type III-A, a family of Cas proteins also known as TM1810/Csm2.	1.65213e-15
LS483443.1\|SQH63773.1\|265282_267487_+\|CRISPR-associated-protein-Cas10/Csm1,-subtype-III-A/MTUBE	gnl\|CDD\|187811	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; signature gene for type III; also known as Csm1 family.	4.59627e-107
LS483443.1\|SQH63775.1\|267889_268594_+\|CRISPR-type-III-A/MTUBE-associated-RAMP-protein-Csm3	gnl\|CDD\|187815	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein.	1.19956e-74
LS483443.1\|SQH63792.1\|286278_286917_+\|Phosphoribosylglycinamide-formyltransferase	gnl\|CDD\|235544	PRK05647, purN, phosphoribosylglycinamide formyltransferase; Reviewed.	1.68351e-112
LS483443.1\|SQH63791.1\|285238_286279_+\|Phosphoribosylformylglycinamidine-cyclo-ligase	gnl\|CDD\|235439	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional.	0
LS483443.1\|SQH63779.1\|272147_272438_+\|putative-CRISPR-associated-protein,-VVA1548-family	gnl\|CDD\|370601	pfam09652, Cas_VVA1548, Putative CRISPR-associated protein (Cas_VVA1548). This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas (CRISPR-associated) genes.	9.7515e-42
LS483443.1\|SQH63781.1\|273588_274743_+\|CRISPR-associated-protein,-NE0113-family	gnl\|CDD\|187872	cd09741, Csx1_III-U, CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as NE0113 family.	4.26247e-94
LS483443.1\|SQH63786.1\|279293_279578_+\|CRISPR-associated-protein-Cas2	gnl\|CDD\|187856	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.	4.71647e-11
LS483443.1\|SQH63778.1\|271163_272087_+\|Uncharacterized-conserved-protein-(DUF2276)	gnl\|CDD\|187890	cd09760, Cas6_III, CRISPR/Cas system-associated RAMP superfamily protein Cas6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6 is an endoribonuclease that generates crRNAs, predicted subunit of Cascade complex.	3.5841e-08
LS483443.1\|SQH63776.1\|268603_269542_+\|CRISPR-type-III-A/MTUBE-associated-RAMP-protein-Csm4	gnl\|CDD\|273866	TIGR01903, Hypothetical_protein., CRISPR type III-A/MTUBE-associated RAMP protein Csm4. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm4, for CRISPR/cas Subtype Mtube, protein 4.	2.75795e-08

>LS483443.1|SQH63781.1|273588_274743_+|CRISPR-associated-protein,-NE0113-family
MKTYNKRILLSVTGKSPAVVTETLYALVTEKNFIPTEIQVITTIEGRNELLSALLGIEGKRKGALQEFIEDYGSQYGFDHIHFNEDCVHIIKDTNGEQLPDIRTPKENEQAANSIVQLVGKLCQDDETQLHVSIAGGRKTMGFFMGYALSLYGREQDSLSHVLVDEEFETLSNFYYRKPKEYRIVNDRNGKELDASQANIMLAEIPWVRLGLGVPEDLKQQAISYSDSVKNAQALLEAPSLTFLSPIEDCLVTFGSKTIKLAPRGYALFLSLVIAKKQGWNVGTGNREEARTIATYLNIYSQMKNDVEMENRLKGANNDLKNVLSESRTDINKKVMASFSLGKGAKSAYIPSSNRKTGNYELNIHLDNIDVSKIESDLKRLKLI
>LS483443.1|SQH63780.1|272446_273589_+|Domain-of-uncharacterised-function-(DUF1887)
MQKYDIHVCLVSDQAAPNLLPILDSEFKPQKAVFVVSTKDEIKEKANSLKLAFKQNDIDVDILELSNEFDFQSMETELFDLLSSYENENIALNVTGGTKLMAIAAQNVFSGVKPIFYINTNKEEIIFISKENDKHIPVQKLNTKTLINTYLSSYGVSVLKNKDDFNFYKLGVFTERFVRRQEDYKDIISKLNLLAFNASNSKLETNFTNYSNDLKLILEDLADEDLVRLNGDIVDFKNEQTRSFLNGNWLEYFTYKQANSIADVIDADWNVEVVNSKYEKNKVGVNNELDVIFMAKNKCHIIECKTINFENTENKDKLQSYLDKLNSLKGYGGSLTKVCLVSFYAIPQNIKRRAEKDNIEIIDDYRIKNLKERIQSWIKK
>LS483443.1|SQH63779.1|272147_272438_+|putative-CRISPR-associated-protein,-VVA1548-family
MTTWFISRHPGAIEWVKQQNIQINRFESHLDTSLVQANDVVIGTLPIHLAAEVCQKGAKFYFLSINVTPEQRGIELTCKQLTEQQCSIQPFRIEKL
>LS483443.1|SQH63778.1|271163_272087_+|Uncharacterized-conserved-protein-(DUF2276)
MIPNSFPIARYQFDFVVSEPILLPEYSGSTLRGAFGRALRKISCMTKQEDCKGCPLYRTCPYTNIFETPAPTEHELQKFSQVPNGYIIEPPAWGERLYAEGETLTFSLVLFGRLIEQLPLIAFAFKRAFEYNVGRGKANLLDIAKVESNLTTRQSILQNGNIIEHQKTIEIPTALDSVAQIKIDTPLRLQENGKPLRVNEITAERFFISLAKRLSLLSEFHSEPLNLDFGLLKNQIEQIQDNKHLKWQDWTRYSSRQDHKMKLGGVIGLWQFNNLSPELAKLLYIGQWLHCGKNATFGLGKYRITNL
>LS483443.1|SQH63777.1|269538_271167_+|RAMP-superfamily
MKPFIQIHNVYLTPLSPIHIGCGEDFEPTNYVIDNETLFNFEPSHLMLNERERTNLLNAVNKDILAIHNFFSSNKSKIIPLSQYFSAITKGFVSEYNKNIENPAHKEKNGNKVFNQLQIERTAYLPYQGLAFIPGSSFKGAFTTPVLSKRHIDNGGNPLIKREKKTSKTALSLISQKINEDYLYNINNLKSFDEVKENFAHNEFRSIKFSDFSPLNNVQTKIFYCLNFNRELKNGEKTFNTKIVQRRESILPGQYRAFSANLSILDDKVNKLLSLNEYLTINDSYYKKIFIEEMEDLVAKGFVSQNYLNGILNIINKAGFLIRLGKNGSDSKVLKGKNVAQIEIKPKKNQEVYYQDKATTYWLSADSKTQKNNLLPFGWALIEVDPTTENEALKTWCEAQPKSKFDRSEILAKREAQKAEQARLQAEAEAKRLAEQQAEKEKLALLDSLSDNQRLVEAKLVEWNSQERKPFTVSPIFSEAKKLLEDAQQWNKEDRHYLYEKLDPTKSNEGLQKYVDGLSGFSNLKAKSAVEFKKLRNKLVAE
>LS483443.1|SQH63776.1|268603_269542_+|CRISPR-type-III-A/MTUBE-associated-RAMP-protein-Csm4
MKLYRFTLTPQSAMGTPLVGDTLFGQLCWAVRNRFGEARLSELLKGYTTQRPFMVVSDAFPESFLPLPTLPSTFWETKTETDRKSLKKAQWVKITDTEKSAVKFWQECALQANFQFKKETQDQFHNTIDRQTNTTGDGQFAPYSTELTWFGAQQKFELYVVLDENRFSLEALQIVLQDVGNIGFGRDASIGLGKFRCENPQAFDFAQPNANCYLTLANCAPQGLGLNKEYCYYQITTRFGRHGDIQALSSNPFKKPIILAKPAAIFTPENYQPRLFLGNGLGNVSYAQPEAVHQSYAPVLNLFVDFEHKDHK
>LS483443.1|SQH63775.1|267889_268594_+|CRISPR-type-III-A/MTUBE-associated-RAMP-protein-Csm3
MKLNKIIEIKAKLVLQTGLHIGSGNSEMQIGGIDSQVVRNPITREPYIPGSSLKGKIRTLLEWLSGEVKNEPLSLGNIKDIHNKETVKDILRLFGFAGHSENNKELCVELKASRLSFWDCSLSKKWKNEYSEDGFIITETKSENTIDRITSVTTGGGVRQTERVPAGAEFDFKLMLRQFEGDKPELLDLVLKGLKLLELDSLGGSGSRGYGKVKFTELTVDGEARNLDDIKPFE
>LS483443.1|SQH63774.1|267495_267879_+|CRISPR-type-III-A/MTUBE-associated-protein-Csm2
MDLSKIKFPAEAGSGIFDSVAENAAKEIRDSKVNKKTQIRKFYDELIMWNERVQHSKISKEEKYIELEPFIKMLKAKVTYAKGRGHIDEKFQSIFNHCIDQIKDAKTLQHAKLFMEAVTGYSRELEK
>LS483443.1|SQH63773.1|265282_267487_+|CRISPR-associated-protein-Cas10/Csm1,-subtype-III-A/MTUBE
MSDHTISLAFSVLHHYLKLFAEKQEPHLPLPSFPSQFKQVDISPFLSQAEHLVLGKQPELKESNKLFSLFENINQENKKTQFSYDFQPLSPNTIFPKKEENNTALSTHWDKFVQAIAKIPKSHCDNPSLWLDHFDTAMQCFTCNLPSPYSDDISFYDFTKAVAAFVVALADQEINKEEPFLLIQGDFFGIQDFIFSGGSASNKGAAKILRGRSFQVSLFTELAALKVLNACQLPTTSQMMNAAGKFLIVAPNTKAVKEAIKQVQAELNQWFIKETYGLIGLGIAVQSAKYSDFEQNHYETLVKKLFENLEEQKLKRLDLTDTTQSVQEVEYPNGVCEMNSFFPSQKEEDCPTIDGKKVNYSVISEDQINIGKWLSKKDRIIITDNESKIHSDSDTKILKLPIFGFNVIFTEEEEETGKFGLHVHKIHRFWDFSLPKNTNSTIWNGYARRYINAYVPFDDEGKIVTFEDIQARDEGQKALMTLKGDVDNLGTIFQKGIQPANIAKMAALSRQMNQFFSLWLPAYCSEQSQNMYTVFAGGDDFFLIGPWYSTQKVAHAMQQAFAHYVAENPEIHFSVGMVMSKSNIPVPRLGDLAEEALEKAKGIDKGKTVSTAEGKNAVTIFNRSVKWADWKQLCGLEEEIHRLADTYKISTSYLYSLIRLCEQAANTENIESTMWRSRFYYKTVRYVLDKIKREEDRKDALKVLSETLGKNGIELYKINFSIPLFNYFYKKRNI
>LS483443.1|SQH63772.1|264441_265056_-|ComE-operon-protein-1
MKSLKSLLALAVAIAVSSTALAEESVLSEVKEGAKSAWQTVKEDSKVAGTKIKNGAVKVKETTKEKFGEAKDATKEKFSEAKDATKEKLTEAKEVTQEKVAEGKKAIKDKLRNDKPAQVEDKSTAKEKSAVENKAQMTQGKKVDVNTADVAALESLSGIGEAKAKAIIEYREKNGKFKNLSDLSKVPGIGDATLEKMKSHVRFN
>LS483443.1|SQH63783.1|277672_277798_+|Uncharacterised-protein
MEFILAFLDEWYKTQSIHRKNPSRFKEIKNISKINRTFSIF
>LS483443.1|SQH63784.1|277975_278335_+|Uncharacterised-protein
MLNLRMHHKATQVIFNPSYAESEINAIAAGFVEVRDERAYNGRYFIKNGKKWIHNLEALRKKLNTKYGRYIDDEELSSPAPEGFGYDIKTYYLYNSTSSTHNEFSTRFRTILEKVCIKH
>LS483443.1|SQH63785.1|278423_279278_+|Uncharacterised-protein
MFYITKHNYYKNIICKLDIDIPTIEKTGFFSSYKLDLFDLDLSYFAKNEREMLIISDHLFRNISNINKNVIFKQIKHKENNWVYKLSVPAYHADRHCPNLTKEFNNIRIPYSLEPSLCKEYRQFFIDNKDRYGNKAGLIEPKVFARKLKEKFNLSEELDELLENHILPEIRENSGVECVNITVEQLIDEINELIDIFKNFIKKEQISGLLSRRSWLSTKDDSELSETERESMQKVYEQKRRICARILAFHFQHFEKEGFNISENLLEMLGFQACPNCCKHIIPF
>LS483443.1|SQH63786.1|279293_279578_+|CRISPR-associated-protein-Cas2
MDTRRSRYLIAYDIADSHRLYQMHKHVEAYAIGGQKSFYECWLTEHEMIAFQQDVNALIDASDDRVFIFRIPNNIEPLLFGKATLQSNSPFLLV
>LS483443.1|SQH63787.1|279586_280657_+|CRISPR-associated-endonuclease-Cas1
MSSLYIDRKGTEIKLNGEALVCYENGERVGTIPLAPIERIYLKSYVTVQASLLAKLGEKGIGIIFLSGRKNTPTLFLAQPHNDATRRLNQYELAKNESFCLAFAKKLMQLKLVTQKNWLWQASNARADKKSQLAEKAGELDQLIGKINEQTTLASLRGIEGRAASVYFTALSLYLPPALRFQGRNRRPPRDPFNAGLSLTYTLIHSEAVLAAYGAGLDPYIGFYHALDFGRESLACDLIEPLRPLIDNWCLGLFRQNILREESFSTTQEGCFLGKAGRVEFYKSYESAVGNWRKMLTENSLDIVNLIKQADFISSPQRRESEWQTFSGINERQWQGLLGRYYFNQQTMLQDVIFQF
>LS483443.1|SQH63788.1|280669_280957_+|CRISPR-associated-endoribonuclease-Cas2
MQYLIGYDIADPKRLQRIHRRMTKYATPIQYSIFLFEGSEKLLTQCLTEVMQIFHKKEDDLRIYPLPHKCSQWRLGKASLPQGIIWTALPISLTL
>LS483443.1|SQH63789.1|281883_284454_+|Heat-shock-protein-F84.1
MNIEKFTTKFQQAIAEAQSLAIGKDNQFIEPVHLLSALLNQQDGSVAPILTASGVNVAALRNELNNELAKLPQVSGNGGDVQLSRQLLNLLNLCDKLAQQRQDKFISSELFLLAALEEKGAVSEILKKCGAKKDQILQAIDHIRGGQNVNDQNAEESRQALEKYTIDLTARAESGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGEVPEGLKNKRVLSLDMGALIAGAKYRGEFEERLKAVLKELAQEEGRVILFIDEIHTMVGAGKTDGAMDAGNLLKPSLARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVGEPSVEDTIAILRGLKERYEIHHHVQITDPAIVAAATLSHRYISDRQLPDKAIDLIDEAASSIRMEIDSKPQPLDRLDRRIIQLKLEQQALQKEDDDASRKRLEMLEKELSEKEREYAELEEVWKSEKAALSGTQHIKAELENARTQMEQARRAGDLSKMSELQYGKIPELEKQLAAAEGAEGKEMSLLRYRVTDEEIAEVLSRATGIPVSKMMEGEKEKLLRMEEELHKRVIGQNEAVDAVANAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKTLAKFLFDSEDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHHDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQGNQEESYDDMKTLVMSVVSQHFRPEFINRIDETVVFHPLNKDNIRAIAEIQLKRLINRMESRGYVLHFTDATLNFISEIGYDPIYGARPLKRAIQQEIENPLAQQILSGSLLPEKPISVDYVDGKIVAKQ
>LS483443.1|SQH63790.1|284553_285054_-|Uncharacterised-protein
MKKTFVFLTALLLAACSSSPSTKPALNSQVNAKAQGDVPLVPPKETKNGFLQLVPGIFYYVDTNSVWVDNKDKRLIHFDVVINLDKGLYVFKDHPTLYAKSMRQYKILNCESHYFTHVRSDFYADFWGDGIRTAPKRQSQHTIALQPQSSLYTLGQVMCANMYRRK
>LS483443.1|SQH63791.1|285238_286279_+|Phosphoribosylformylglycinamidine-cyclo-ligase
MSTQSLSYKDAGVDIHAGNELVERIKPEVKRTTRPEVMGGLGGFGALCAIPSKYKEPILVSGTDGVGTKLRLAIDLNRHDSIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDVAANVIKGIANGCEQSGCALVGGETAEMPGMYHEGDYDLAGFCVGVVEKSEIIDGSQVKVGDALIALASSGPHSNGYSLIRKVIDVAGVNPAEAQLEGSPLADHVLAPTKIYVKSILQLIKHVNVHAIAHLTGGGFWENIPRVLPNSVKAVINENSWQWPAVFDWLQQQGNITDYEMYRTFNCGVGMVIALPQEDVETALGLLQQAGENAWVVGDIQHLADENEPQVVIR
>LS483443.1|SQH63792.1|286278_286917_+|Phosphoribosylglycinamide-formyltransferase
MKKIVVLISGYGANLQAIIDACESRYIDGEVVGVFSNRADAFGLQRAKSAGIFHRTFLRSDYADNLAMDRHIADEIDNLGADLIVLAGYMKILTAEFTQRFAGKILNIHPSLLPKYPGLHTYQRAIEAGETEHGMTIHFVNEEVDGGAIVLQAKVPIFAEDDIADIEQRVKEQEIRFYPLAIKWFAEGRLRLIDNHAYLDGNRLPPQGYAID

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Crispr_ID: LS483443_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LS483443_2

281174-281707

TypeIII

Consensus_repeat	Method
CAGTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACTTCTC	PILER-CR
GTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACT	CRISPRCasFinder
GCCCTGNTCCAAAGGGATTNANACT	CRT
GTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACT	CRISPRCasFinder

7 spacers

cas2,cas1,csx1,csx16

The CRISPR arrays of LS483443_2

>merge|LS483443|2|281174-281707|PILER-CR,CRISPRCasFinder,CRT,CRISPRCasFinder
CAGTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACTACTCAAGCTTCTCGAGTCTAGCAGGTTCACCGTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACTTCTCCTTTAATTTCGCTTCGATTTCAGAAATCAGTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACTTGTAAAGTGCTAAATAAACCTTATCCATTATTGTGTCGAAAGACACCGCCCTGTTCGAAAGGGATTAAGACTTATCACCGCTTTGCCGGCTATCAAGCATTTGCAGTCGAAAGACACCGCCCTGTTCCAAAGGGATTGAAACGAATATGGGATATTGATATTAATTTCGTTCATTTGTCGAAAGCCCCGCCCTGCTCCAAAGGGATTGAAATGCGTTTAATGGGCGCTAAAATACGATTTAAACCTGTCGAAAGACCTCACCCTGCTCCAAAGGGATTGAAACTCTGGGTGGTATTTGATTGCCATTCTTTTATATGTCGAAAGACCCCGCCCTGCTCCAAAGGGATTCTCCAT

>LS483443|2|2|281174-281354|PILER-CR
CAGTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACTACTC	AAGCTTCTCGAGTCTAGCAGGTTCA
CCGTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACTTCTC	CTTTAATTTCGCTTCGATTTCAGAAAT
CAGTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACTT

>LS483443|2|2|281176-281497|CRISPRCasFinder
GTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACT	ACTCAAGCTTCTCGAGTCTAGCAGGTTCACC
GTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACT	TCTCCTTTAATTTCGCTTCGATTTCAGAAATCA
GTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACT	TGTAAAGTGCTAAATAAACCTTATCCATTATTGT
GTCGAAAGACACCGCCCTGTTCGAAAGGGATTAAGACT	TATCACCGCTTTGCCGGCTATCAAGCATTTGCA
GTCGAAAGACACCGCCCTGTTCCAAAGGGATTGAAACGAATATGGGATATTGATATTAATTTCGTTCATTTGTCGAAAGCCCCGCCCTGCTCCAAAGGGATTGAAATGCGTTTAATGGGCGCTAAAATACGATTTAAACCTGTCGAAAGACCTCACCCTGCTCCAAAGGGATTGAAACT	CTGGGTGGTATTTGATTGCCATTCTTTTATAT


>LS483443|2|2|281189-281707|CRT
GCCCTGTTCCAAAGGGATTAAGACT	ACTCAAGCTTCTCGAGTCTAGCAGGTTCACCGTCGAAAGACCTT
GCCCTGTTCCAAAGGGATTAAGACT	TCTCCTTTAATTTCGCTTCGATTTCAGAAATCAGTCGAAAGACCTT
GCCCTGTTCCAAAGGGATTAAGACT	TGTAAAGTGCTAAATAAACCTTATCCATTATTGTGTCGAAAGACACC
GCCCTGTTCGAAAGGGATTAAGACT	TATCACCGCTTTGCCGGCTATCAAGCATTTGCAGTCGAAAGACACC
GCCCTGTTCCAAAGGGATTGAAACG	AATATGGGATATTGATATTAATTTCGTTCATTTGTCGAAAGCCCC
GCCCTGCTCCAAAGGGATTGAAATG	CGTTTAATGGGCGCTAAAATACGATTTAAACCTGTCGAAAGACCTC
ACCCTGCTCCAAAGGGATTGAAACT	CTGGGTGGTATTTGATTGCCATTCTTTTATATGTCGAAAGACCCC
GCCCTGCTCCAAAGGGATTCTCCAT

>LS483443|2|3|281600-281707|CRISPRCasFinder
	ACTCAAGCTTCTCGAGTCTAGCAGGTTCACC
GTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACT	TCTCCTTTAATTTCGCTTCGATTTCAGAAATCA
GTCGAAAGACCTTGCCCTGTTCCAAAGGGATTAAGACT	TGTAAAGTGCTAAATAAACCTTATCCATTATTGT
GTCGAAAGACACCGCCCTGTTCGAAAGGGATTAAGACT	TATCACCGCTTTGCCGGCTATCAAGCATTTGCA
GTCGAAAGACACCGCCCTGTTCCAAAGGGATTGAAACGAATATGGGATATTGATATTAATTTCGTTCATTTGTCGAAAGCCCCGCCCTGCTCCAAAGGGATTGAAATGCGTTTAATGGGCGCTAAAATACGATTTAAACCTGTCGAAAGACCTCACCCTGCTCCAAAGGGATTGAAACT	CTGGGTGGTATTTGATTGCCATTCTTTTATAT
GTCGAAAGACCCCGCCCTGCTCCAAAGGGATTCTCCAT

Protein	Signature genes	Signature genes Name	Protein_function
LS483443.1\|SQH63780.1\|272446_273589_+\|Domain-of-uncharacterised-function-(DUF1887)	csx1	pfam09002_csx1_CAS-III	gnl\|CDD\|312526
LS483443.1\|SQH63783.1\|277672_277798_+\|Uncharacterised-protein	unknown	unknown	unknown
LS483443.1\|SQH63785.1\|278423_279278_+\|Uncharacterised-protein	unknown	unknown	unknown
LS483443.1\|SQH63782.1\|276221_276437_+\|Uncharacterised-protein	unknown	unknown	unknown
LS483443.1\|SQH63787.1\|279586_280657_+\|CRISPR-associated-endonuclease-Cas1	cas1	cd09634_cas1_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|376633
LS483443.1\|SQH63790.1\|284553_285054_-\|Uncharacterised-protein	unknown	unknown	gnl\|CDD\|374773
LS483443.1\|SQH63791.1\|285238_286279_+\|Phosphoribosylformylglycinamidine-cyclo-ligase	unknown	unknown	gnl\|CDD\|235439
LS483443.1\|SQH63789.1\|281883_284454_+\|Heat-shock-protein-F84.1	unknown	unknown	gnl\|CDD\|274529
LS483443.1\|SQH63797.1\|290881_292516_+\|CTP-synthase	unknown	unknown	gnl\|CDD\|235437
LS483443.1\|SQH63794.1\|288052_288610_+\|DNA-utilization-protein-GntX	unknown	unknown	gnl\|CDD\|183221
LS483443.1\|SQH63788.1\|280669_280957_+\|CRISPR-associated-endoribonuclease-Cas2	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	gnl\|CDD\|378256
LS483443.1\|SQH63792.1\|286278_286917_+\|Phosphoribosylglycinamide-formyltransferase	unknown	unknown	gnl\|CDD\|235544
LS483443.1\|SQH63784.1\|277975_278335_+\|Uncharacterised-protein	unknown	unknown	unknown
LS483443.1\|SQH63796.1\|289353_290652_-\|LIV-II	unknown	unknown	gnl\|CDD\|283235
LS483443.1\|SQH63779.1\|272147_272438_+\|putative-CRISPR-associated-protein,-VVA1548-family	csx16	cd09695_csx16_CAS-I:CAS-III	gnl\|CDD\|370601
LS483443.1\|SQH63781.1\|273588_274743_+\|CRISPR-associated-protein,-NE0113-family	csx1	pfam09623_csx1_CAS-III	gnl\|CDD\|187872
LS483443.1\|SQH63786.1\|279293_279578_+\|CRISPR-associated-protein-Cas2	cas2	pfam09827_cas2_CAS-I:CAS-II:CAS-III	gnl\|CDD\|187856
LS483443.1\|SQH63798.1\|292818_293481_+\|Thiamine-phosphate-synthase	unknown	unknown	gnl\|CDD\|179586
LS483443.1\|SQH63793.1\|286952_287768_-\|Putative-bifunctional-phosphatase/peptidyl-prolyl-cis-trans-isomerase	unknown	unknown	gnl\|CDD\|319819
LS483443.1\|SQH63795.1\|288719_289304_+\|Fe/S-biogenesis-protein-nfuA	unknown	unknown	gnl\|CDD\|183027

Protein	Function_ID	Function_description	E-value
LS483443.1\|SQH63780.1\|272446_273589_+\|Domain-of-uncharacterised-function-(DUF1887)	gnl\|CDD\|312526	pfam09002, DUF1887, Domain of unknown function (DUF1887). This domain is found in a set of hypothetical bacterial proteins.	2.77445e-134
LS483443.1\|SQH63791.1\|285238_286279_+\|Phosphoribosylformylglycinamidine-cyclo-ligase	gnl\|CDD\|235439	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional.	0
LS483443.1\|SQH63787.1\|279586_280657_+\|CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|376633	pfam01867, Cas_Cas1, CRISPR associated protein Cas1. Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. This family of proteins corresponds to Cas1, a CRISPR-associated protein. Cas1 may be involved in linking DNA segments to CRISPR.	1.64137e-92
LS483443.1\|SQH63790.1\|284553_285054_-\|Uncharacterised-protein	gnl\|CDD\|374773	pfam16747, Adhesin_E, Surface-adhesin protein E. Adhesin E plays a role in pathogenesis. It binds to host proteins including plasminogen, vitronectin and laminin.	2.628e-68
LS483443.1\|SQH63797.1\|290881_292516_+\|CTP-synthase	gnl\|CDD\|235437	PRK05380, pyrG, CTP synthetase; Validated.	0
LS483443.1\|SQH63789.1\|281883_284454_+\|Heat-shock-protein-F84.1	gnl\|CDD\|274529	TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. [Protein fate, Protein folding and stabilization].	0
LS483443.1\|SQH63794.1\|288052_288610_+\|DNA-utilization-protein-GntX	gnl\|CDD\|183221	PRK11595, PRK11595, DNA utilization protein GntX; Provisional.	3.57327e-67
LS483443.1\|SQH63788.1\|280669_280957_+\|CRISPR-associated-endoribonuclease-Cas2	gnl\|CDD\|378256	pfam09827, CRISPR_Cas2, CRISPR associated protein Cas2. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages.	5.57358e-16
LS483443.1\|SQH63792.1\|286278_286917_+\|Phosphoribosylglycinamide-formyltransferase	gnl\|CDD\|235544	PRK05647, purN, phosphoribosylglycinamide formyltransferase; Reviewed.	1.68351e-112
LS483443.1\|SQH63796.1\|289353_290652_-\|LIV-II	gnl\|CDD\|283235	pfam05525, Branch_AA_trans, Branched-chain amino acid transport protein. This family consists of several bacterial branched-chain amino acid transport proteins which are responsible for the transport of leucine, isoleucine and valine via proton motive force.	6.44252e-151
LS483443.1\|SQH63779.1\|272147_272438_+\|putative-CRISPR-associated-protein,-VVA1548-family	gnl\|CDD\|370601	pfam09652, Cas_VVA1548, Putative CRISPR-associated protein (Cas_VVA1548). This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas (CRISPR-associated) genes.	9.7515e-42
LS483443.1\|SQH63781.1\|273588_274743_+\|CRISPR-associated-protein,-NE0113-family	gnl\|CDD\|187872	cd09741, Csx1_III-U, CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as NE0113 family.	4.26247e-94
LS483443.1\|SQH63786.1\|279293_279578_+\|CRISPR-associated-protein-Cas2	gnl\|CDD\|187856	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.	4.71647e-11
LS483443.1\|SQH63798.1\|292818_293481_+\|Thiamine-phosphate-synthase	gnl\|CDD\|179586	PRK03512, PRK03512, thiamine phosphate synthase.	9.1729e-117
LS483443.1\|SQH63793.1\|286952_287768_-\|Putative-bifunctional-phosphatase/peptidyl-prolyl-cis-trans-isomerase	gnl\|CDD\|319819	cd07517, HAD_HPP, phosphatase, similar to Bacteroides thetaiotaomicron VPI-5482 BT4131 hexose phosphate phosphatase; belongs to the haloacid dehalogenase-like superfamily. Bacteroides thetaiotaomicron VPI-5482 BT4131 is a phosphatase with preference for hexose phosphates. In addition this family includes uncharacterized Bacillus subtilis YkrA, a putative phosphatase and uncharacterized Streptococcus pyogenes MGAS10394 a putative bifunctional phosphatase/peptidyl-prolyl cis-trans isomerase. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.	5.93381e-74
LS483443.1\|SQH63795.1\|288719_289304_+\|Fe/S-biogenesis-protein-nfuA	gnl\|CDD\|183027	PRK11190, PRK11190, iron-sulfur cluster biogenesis protein NfuA.	2.65754e-152

>LS483443.1|SQH63788.1|280669_280957_+|CRISPR-associated-endoribonuclease-Cas2
MQYLIGYDIADPKRLQRIHRRMTKYATPIQYSIFLFEGSEKLLTQCLTEVMQIFHKKEDDLRIYPLPHKCSQWRLGKASLPQGIIWTALPISLTL
>LS483443.1|SQH63787.1|279586_280657_+|CRISPR-associated-endonuclease-Cas1
MSSLYIDRKGTEIKLNGEALVCYENGERVGTIPLAPIERIYLKSYVTVQASLLAKLGEKGIGIIFLSGRKNTPTLFLAQPHNDATRRLNQYELAKNESFCLAFAKKLMQLKLVTQKNWLWQASNARADKKSQLAEKAGELDQLIGKINEQTTLASLRGIEGRAASVYFTALSLYLPPALRFQGRNRRPPRDPFNAGLSLTYTLIHSEAVLAAYGAGLDPYIGFYHALDFGRESLACDLIEPLRPLIDNWCLGLFRQNILREESFSTTQEGCFLGKAGRVEFYKSYESAVGNWRKMLTENSLDIVNLIKQADFISSPQRRESEWQTFSGINERQWQGLLGRYYFNQQTMLQDVIFQF
>LS483443.1|SQH63786.1|279293_279578_+|CRISPR-associated-protein-Cas2
MDTRRSRYLIAYDIADSHRLYQMHKHVEAYAIGGQKSFYECWLTEHEMIAFQQDVNALIDASDDRVFIFRIPNNIEPLLFGKATLQSNSPFLLV
>LS483443.1|SQH63785.1|278423_279278_+|Uncharacterised-protein
MFYITKHNYYKNIICKLDIDIPTIEKTGFFSSYKLDLFDLDLSYFAKNEREMLIISDHLFRNISNINKNVIFKQIKHKENNWVYKLSVPAYHADRHCPNLTKEFNNIRIPYSLEPSLCKEYRQFFIDNKDRYGNKAGLIEPKVFARKLKEKFNLSEELDELLENHILPEIRENSGVECVNITVEQLIDEINELIDIFKNFIKKEQISGLLSRRSWLSTKDDSELSETERESMQKVYEQKRRICARILAFHFQHFEKEGFNISENLLEMLGFQACPNCCKHIIPF
>LS483443.1|SQH63784.1|277975_278335_+|Uncharacterised-protein
MLNLRMHHKATQVIFNPSYAESEINAIAAGFVEVRDERAYNGRYFIKNGKKWIHNLEALRKKLNTKYGRYIDDEELSSPAPEGFGYDIKTYYLYNSTSSTHNEFSTRFRTILEKVCIKH
>LS483443.1|SQH63783.1|277672_277798_+|Uncharacterised-protein
MEFILAFLDEWYKTQSIHRKNPSRFKEIKNISKINRTFSIF
>LS483443.1|SQH63782.1|276221_276437_+|Uncharacterised-protein
MNIRDLNGRKTPPCSKGIKTANKIHRHYTRGRKTPPCSKGIKTQTVLEKLHTQDVERPRPVPKGLKHLPLF
>LS483443.1|SQH63781.1|273588_274743_+|CRISPR-associated-protein,-NE0113-family
MKTYNKRILLSVTGKSPAVVTETLYALVTEKNFIPTEIQVITTIEGRNELLSALLGIEGKRKGALQEFIEDYGSQYGFDHIHFNEDCVHIIKDTNGEQLPDIRTPKENEQAANSIVQLVGKLCQDDETQLHVSIAGGRKTMGFFMGYALSLYGREQDSLSHVLVDEEFETLSNFYYRKPKEYRIVNDRNGKELDASQANIMLAEIPWVRLGLGVPEDLKQQAISYSDSVKNAQALLEAPSLTFLSPIEDCLVTFGSKTIKLAPRGYALFLSLVIAKKQGWNVGTGNREEARTIATYLNIYSQMKNDVEMENRLKGANNDLKNVLSESRTDINKKVMASFSLGKGAKSAYIPSSNRKTGNYELNIHLDNIDVSKIESDLKRLKLI
>LS483443.1|SQH63780.1|272446_273589_+|Domain-of-uncharacterised-function-(DUF1887)
MQKYDIHVCLVSDQAAPNLLPILDSEFKPQKAVFVVSTKDEIKEKANSLKLAFKQNDIDVDILELSNEFDFQSMETELFDLLSSYENENIALNVTGGTKLMAIAAQNVFSGVKPIFYINTNKEEIIFISKENDKHIPVQKLNTKTLINTYLSSYGVSVLKNKDDFNFYKLGVFTERFVRRQEDYKDIISKLNLLAFNASNSKLETNFTNYSNDLKLILEDLADEDLVRLNGDIVDFKNEQTRSFLNGNWLEYFTYKQANSIADVIDADWNVEVVNSKYEKNKVGVNNELDVIFMAKNKCHIIECKTINFENTENKDKLQSYLDKLNSLKGYGGSLTKVCLVSFYAIPQNIKRRAEKDNIEIIDDYRIKNLKERIQSWIKK
>LS483443.1|SQH63779.1|272147_272438_+|putative-CRISPR-associated-protein,-VVA1548-family
MTTWFISRHPGAIEWVKQQNIQINRFESHLDTSLVQANDVVIGTLPIHLAAEVCQKGAKFYFLSINVTPEQRGIELTCKQLTEQQCSIQPFRIEKL
>LS483443.1|SQH63789.1|281883_284454_+|Heat-shock-protein-F84.1
MNIEKFTTKFQQAIAEAQSLAIGKDNQFIEPVHLLSALLNQQDGSVAPILTASGVNVAALRNELNNELAKLPQVSGNGGDVQLSRQLLNLLNLCDKLAQQRQDKFISSELFLLAALEEKGAVSEILKKCGAKKDQILQAIDHIRGGQNVNDQNAEESRQALEKYTIDLTARAESGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGEVPEGLKNKRVLSLDMGALIAGAKYRGEFEERLKAVLKELAQEEGRVILFIDEIHTMVGAGKTDGAMDAGNLLKPSLARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVGEPSVEDTIAILRGLKERYEIHHHVQITDPAIVAAATLSHRYISDRQLPDKAIDLIDEAASSIRMEIDSKPQPLDRLDRRIIQLKLEQQALQKEDDDASRKRLEMLEKELSEKEREYAELEEVWKSEKAALSGTQHIKAELENARTQMEQARRAGDLSKMSELQYGKIPELEKQLAAAEGAEGKEMSLLRYRVTDEEIAEVLSRATGIPVSKMMEGEKEKLLRMEEELHKRVIGQNEAVDAVANAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKTLAKFLFDSEDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHHDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQGNQEESYDDMKTLVMSVVSQHFRPEFINRIDETVVFHPLNKDNIRAIAEIQLKRLINRMESRGYVLHFTDATLNFISEIGYDPIYGARPLKRAIQQEIENPLAQQILSGSLLPEKPISVDYVDGKIVAKQ
>LS483443.1|SQH63790.1|284553_285054_-|Uncharacterised-protein
MKKTFVFLTALLLAACSSSPSTKPALNSQVNAKAQGDVPLVPPKETKNGFLQLVPGIFYYVDTNSVWVDNKDKRLIHFDVVINLDKGLYVFKDHPTLYAKSMRQYKILNCESHYFTHVRSDFYADFWGDGIRTAPKRQSQHTIALQPQSSLYTLGQVMCANMYRRK
>LS483443.1|SQH63791.1|285238_286279_+|Phosphoribosylformylglycinamidine-cyclo-ligase
MSTQSLSYKDAGVDIHAGNELVERIKPEVKRTTRPEVMGGLGGFGALCAIPSKYKEPILVSGTDGVGTKLRLAIDLNRHDSIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDVAANVIKGIANGCEQSGCALVGGETAEMPGMYHEGDYDLAGFCVGVVEKSEIIDGSQVKVGDALIALASSGPHSNGYSLIRKVIDVAGVNPAEAQLEGSPLADHVLAPTKIYVKSILQLIKHVNVHAIAHLTGGGFWENIPRVLPNSVKAVINENSWQWPAVFDWLQQQGNITDYEMYRTFNCGVGMVIALPQEDVETALGLLQQAGENAWVVGDIQHLADENEPQVVIR
>LS483443.1|SQH63792.1|286278_286917_+|Phosphoribosylglycinamide-formyltransferase
MKKIVVLISGYGANLQAIIDACESRYIDGEVVGVFSNRADAFGLQRAKSAGIFHRTFLRSDYADNLAMDRHIADEIDNLGADLIVLAGYMKILTAEFTQRFAGKILNIHPSLLPKYPGLHTYQRAIEAGETEHGMTIHFVNEEVDGGAIVLQAKVPIFAEDDIADIEQRVKEQEIRFYPLAIKWFAEGRLRLIDNHAYLDGNRLPPQGYAID
>LS483443.1|SQH63793.1|286952_287768_-|Putative-bifunctional-phosphatase/peptidyl-prolyl-cis-trans-isomerase
MSIPNYRDQIKVVFFDIDDTLFMKQRDFLPATVPVFMRKLKENGIIPAIATGRTRCAFPHKLNQVIEQEGIDLFVTMNGQMASYRGQVIEKHVIPTEKIRRLVHFFEQHNMPYAFVADHTVAVSERNSVVQFAMDPILKDYIVDKTFFETNDIGQVLPFYRAEHDELVQNSGVLDGLRVVRWHEDSVDLFDAEGSKARGIQAVVKHLGLQMDNVMAFGDQLNDLEMLSTVGVGVAMGNGNEKLKAIADHVAEPLDQDGIYRFLIKAGLINE
>LS483443.1|SQH63794.1|288052_288610_+|DNA-utilization-protein-GntX
MENALHCGNCLQQEPAWDRMVIIGRYNEPLSTLIHRFKFQKQFQLDRTLARLLYLAIREARRNHQLPLPEVILPVPLHHVRQWQRGYNQADLLAHQLSSWLKIPAKNDLIIRAKRTPTQRGLSAKDRRQNLKNAFQLSAKARDFPYRHVALIDDVITTGATLNEIAKLLRKANVTHIQVWGLART
>LS483443.1|SQH63795.1|288719_289304_+|Fe/S-biogenesis-protein-nfuA
MQQITISAEAQAHFRRLLDQQEEGTNIRIFVVNPGTPSAECGVSYCPPNSVEASDTEMKYDTFSAFVDDISLPFLEDAEIDYVTEELGAQLTLKAPNAKMRKVADDAPLIERVEYVIQTQINPQLASHGGKITLLEITDDGYAILQFGGGCNGCSMVDVTLKDGVEKQLISLFPDELKGAKDVTEHQRGEHSYY
>LS483443.1|SQH63796.1|289353_290652_-|LIV-II
MFSRKDIVVLGMMIFALFLGAGNIIFPPMEGYTAGQHWATAALGFVVTGVLMPFITLVIVSVLGRGEELTRDLPKWAEILFLATLYLVIGSTFAMPRITNVAYEMALVPLEIVSDTPANHLIFAVVFNIIAMLFMLKPNTIISSVGKFMTPALLVLLVVVTVTVFMSPLSDIAAPSKSYADSSALTTGLISGYQTMDVLAAIAFGGIVARALSAKNVTEPQKIMRYTISAGCISVVLLAALYFSLFYLGATSDQVAQGASNGGQIFSRYVNVLFGKEGSWIMSGIIFLASLTTLVGVTSACAYYFAKFSNRLPYAFWVVVFTIMTTIISENGLTKLLQVTIPALLLIYPVAIMLVVLQFVRAKLPRVKLTYNATIAVTVCFSLCDSLNNVGLLSDSVKQFLGNFPLYDNGLAWLIPALGVMFLTMLVGKRAK
>LS483443.1|SQH63797.1|290881_292516_+|CTP-synthase
MATNYIFVTGGVVSSLGKGIAAASLAAILEARGLNVTIMKLDPYINVDPGTMSPTQHGEVFVTQDGAETDLDLGHYERFIRTKMTKRNNFTTGKIYSEVLRKERRGDYLGATIQVIPHITNEIKARVIDGAAGHDVAIVEVGGTVGDIESLPFLEALRQLAVQVGRERTIFMHLTLVPYIPTAGEVKTKPTQHSVKELLSIGIQPDVLICRSDRMIPPNERAKIALFCNVPERAVVSLKDVSSIYQIPALLKSQGLDDFICNRFHLTCPEADLSEWEQVLYQQANPTGEVTIGMVGKYTELPDAYKSVNEALKHAGLKNRLSVNIKYIDSQDVETKGVDILKGLDGILVPGGFGYRGVEGKILTAKYARENNIPYLGICLGMQVALIEFARNVAGMTQANSSEFDRTCPQPVVGLITEWQNAEGNTEVRSDESDLGGTMRLGAQKCHLIEGSLARQLYGAETIEERHRHRYEVNNVLLPQIEKAGLKVTGLSADKKLVEIIEVPNHPWFVACQFHPEFTSTPRDGHPLFEGFVKAAKTNQKKSD
>LS483443.1|SQH63798.1|292818_293481_+|Thiamine-phosphate-synthase
MSEAVSHLSEIIPPKAPFAPTEFKLGLYVIVDSYEWIERLIHAGVKTLQIRIKDRSPEQAEEEIARCIALAKQHQVRLFVDDFWSLAIKYQAYGVHLGQEDLLTADLNAIQQAGLRLGVSTHNQEEVDLVLPLRPSYVALGHIFPTQTKDMPSAPQGITNLAAQVKNLGKMPTVAIGGISASHFPDILATGVGSIAVISAVTKAQDWQRAVKNLQQYFVE

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Click the colored protein region to show detailed information

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
LS483443_2	2.2\|281287\|27\|LS483443\|PILER-CR	281287-281313	27	NZ_CP031652	Pantoea agglomerans strain TH81 plasmid unnamed3, complete sequence	46146-46172	5	0.815
LS483443_2	2.2\|281287\|27\|LS483443\|PILER-CR	281287-281313	27	MN508623	UNVERIFIED: Enterobacter phage EC-F1, complete genome	75965-75991	6	0.778
LS483443_2	2.2\|281287\|27\|LS483443\|PILER-CR	281287-281313	27	MH823906	Citrobacter phage Maroon, complete genome	54529-54555	6	0.778
LS483443_2	2.2\|281287\|27\|LS483443\|PILER-CR	281287-281313	27	KU160494	Vibrio phage vB_VmeM-32, complete genome	100960-100986	6	0.778
LS483443_2	2.2\|281287\|27\|LS483443\|PILER-CR	281287-281313	27	NC_048646	Cronobacter phage vB_CsaM_leE, complete genome	56127-56153	6	0.778
LS483443_1	1.2\|276281\|32\|LS483443\|PILER-CR	276281-276312	32	NZ_CP027854	Plesiomonas shigelloides strain MS-17-188 plasmid pPS-MS-17-188-2, complete sequence	37326-37357	7	0.781
LS483443_2	2.5\|281354\|34\|LS483443\|CRISPRCasFinder	281354-281387	34	MG945179	UNVERIFIED: Microviridae sp. isolate 515-1801, complete genome	2153-2186	7	0.794
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	MT708547	Klebsiella phage Muenster, complete genome	229940-229971	8	0.75
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	NZ_KY352353	Bacillus thuringiensis serovar israelensis strain 1.24 plasmid pT0124-4, complete sequence	42878-42909	9	0.719
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	LC128536	Bacillus thuringiensis serovar israelensis plasmid pBTI-6 DNA, complete sequence, strain: HD522	31197-31228	9	0.719
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	NC_010076	Bacillus thuringiensis serovar israelensis plasmid pBtoxis, complete sequence	42879-42910	9	0.719
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	NC_018510	Bacillus thuringiensis HD-789 plasmid pBTHD789-3, complete sequence	119150-119181	9	0.719
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	NZ_CP053973	Bacillus thuringiensis strain FDAARGOS_796 plasmid unnamed4, complete sequence	72715-72746	9	0.719
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	NZ_CP013279	Bacillus thuringiensis serovar israelensis strain AM65-52 plasmid pAM65-52-4-128K, complete sequence	41810-41841	9	0.719
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	NZ_CP039725	Bacillus thuringiensis strain BT-59 plasmid p4, complete sequence	85776-85807	9	0.719
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	NZ_CP045026	Bacillus thuringiensis strain JW-1 plasmid p4, complete sequence	42877-42908	9	0.719
LS483443_2	2.4\|281283\|33\|LS483443\|CRISPRCasFinder	281283-281315	33	MN508623	UNVERIFIED: Enterobacter phage EC-F1, complete genome	75961-75993	10	0.697
LS483443_2	2.4\|281283\|33\|LS483443\|CRISPRCasFinder	281283-281315	33	MH823906	Citrobacter phage Maroon, complete genome	54527-54559	10	0.697
LS483443_2	2.4\|281283\|33\|LS483443\|CRISPRCasFinder	281283-281315	33	NC_048646	Cronobacter phage vB_CsaM_leE, complete genome	56125-56157	10	0.697
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	MG592456	Vibrio phage 1.081.O._10N.286.52.C2, partial genome	60094-60125	10	0.688
LS483443_2	2.14\|281638\|32\|LS483443\|CRISPRCasFinder	281638-281669	32	NZ_CP040853	Lactobacillus murinus strain V10 plasmid unnamed, complete sequence	101473-101504	11	0.656

1. spacer 2.2|281287|27|LS483443|PILER-CR matches to NZ_CP031652 (Pantoea agglomerans strain TH81 plasmid unnamed3, complete sequence) position: , mismatch: 5, identity: 0.815

ctttaatttcgcttcgatttcagaaat	CRISPR spacer
ctttaatttcgcttcgattttatcggt	Protospacer
********************.*  ..*

2. spacer 2.2|281287|27|LS483443|PILER-CR matches to MN508623 (UNVERIFIED: Enterobacter phage EC-F1, complete genome) position: , mismatch: 6, identity: 0.778

ctttaatttcgcttcgatttcagaaat	CRISPR spacer
atttaatttctcttcgatttcaaacca	Protospacer
 ********* ***********.*

3. spacer 2.2|281287|27|LS483443|PILER-CR matches to MH823906 (Citrobacter phage Maroon, complete genome) position: , mismatch: 6, identity: 0.778

ctttaatttcgcttcgatttcagaaat	CRISPR spacer
atttaatttctcttcgatttcaaacca	Protospacer
 ********* ***********.*

4. spacer 2.2|281287|27|LS483443|PILER-CR matches to KU160494 (Vibrio phage vB_VmeM-32, complete genome) position: , mismatch: 6, identity: 0.778

ctttaatttcgcttcgatttcagaaat	CRISPR spacer
gaataatttcgcttcgaattcacaaaa	Protospacer
   ************** **** ***

5. spacer 2.2|281287|27|LS483443|PILER-CR matches to NC_048646 (Cronobacter phage vB_CsaM_leE, complete genome) position: , mismatch: 6, identity: 0.778

ctttaatttcgcttcgatttcagaaat	CRISPR spacer
atttaatttctcttcgatttcaaacca	Protospacer
 ********* ***********.*

6. spacer 1.2|276281|32|LS483443|PILER-CR matches to NZ_CP027854 (Plesiomonas shigelloides strain MS-17-188 plasmid pPS-MS-17-188-2, complete sequence) position: , mismatch: 7, identity: 0.781

agcgaataaaattcatcgccattatactcgtg	CRISPR spacer
atctagtaaaattcatcgtcatcatactccta	Protospacer
* * *.************.***.****** *.

7. spacer 2.5|281354|34|LS483443|CRISPRCasFinder matches to MG945179 (UNVERIFIED: Microviridae sp. isolate 515-1801, complete genome) position: , mismatch: 7, identity: 0.794

tgtaaagtg---ctaaataaaccttatccattattgt	CRISPR spacer
---aaaatgtatctaaataaagattatccattattgg	Protospacer
   ***.**   *********  *************

8. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to MT708547 (Klebsiella phage Muenster, complete genome) position: , mismatch: 8, identity: 0.75

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctgatcttcatttgattgccatgcttttctat	Protospacer
***. .  .************* ***** ***

9. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to NZ_KY352353 (Bacillus thuringiensis serovar israelensis strain 1.24 plasmid pT0124-4, complete sequence) position: , mismatch: 9, identity: 0.719

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctaatactaatttgatttccatacttttatat	Protospacer
**..     ******** **** *********

10. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to LC128536 (Bacillus thuringiensis serovar israelensis plasmid pBTI-6 DNA, complete sequence, strain: HD522) position: , mismatch: 9, identity: 0.719

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctaatactaatttgatttccatacttttatat	Protospacer
**..     ******** **** *********

11. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to NC_010076 (Bacillus thuringiensis serovar israelensis plasmid pBtoxis, complete sequence) position: , mismatch: 9, identity: 0.719

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctaatactaatttgatttccatacttttatat	Protospacer
**..     ******** **** *********

12. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to NC_018510 (Bacillus thuringiensis HD-789 plasmid pBTHD789-3, complete sequence) position: , mismatch: 9, identity: 0.719

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctaatactaatttgatttccatacttttatat	Protospacer
**..     ******** **** *********

13. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to NZ_CP053973 (Bacillus thuringiensis strain FDAARGOS_796 plasmid unnamed4, complete sequence) position: , mismatch: 9, identity: 0.719

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctaatactaatttgatttccatacttttatat	Protospacer
**..     ******** **** *********

14. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to NZ_CP013279 (Bacillus thuringiensis serovar israelensis strain AM65-52 plasmid pAM65-52-4-128K, complete sequence) position: , mismatch: 9, identity: 0.719

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctaatactaatttgatttccatacttttatat	Protospacer
**..     ******** **** *********

15. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to NZ_CP039725 (Bacillus thuringiensis strain BT-59 plasmid p4, complete sequence) position: , mismatch: 9, identity: 0.719

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctaatactaatttgatttccatacttttatat	Protospacer
**..     ******** **** *********

16. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to NZ_CP045026 (Bacillus thuringiensis strain JW-1 plasmid p4, complete sequence) position: , mismatch: 9, identity: 0.719

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
ctaatactaatttgatttccatacttttatat	Protospacer
**..     ******** **** *********

17. spacer 2.4|281283|33|LS483443|CRISPRCasFinder matches to MN508623 (UNVERIFIED: Enterobacter phage EC-F1, complete genome) position: , mismatch: 10, identity: 0.697

tctcctttaatttcgcttcgatttcagaaatca	CRISPR spacer
gatcatttaatttctcttcgatttcaaaccatg	Protospacer
  ** ********* ***********.*   ..

18. spacer 2.4|281283|33|LS483443|CRISPRCasFinder matches to MH823906 (Citrobacter phage Maroon, complete genome) position: , mismatch: 10, identity: 0.697

tctcctttaatttcgcttcgatttcagaaatca	CRISPR spacer
gatcatttaatttctcttcgatttcaaaccatg	Protospacer
  ** ********* ***********.*   ..

19. spacer 2.4|281283|33|LS483443|CRISPRCasFinder matches to NC_048646 (Cronobacter phage vB_CsaM_leE, complete genome) position: , mismatch: 10, identity: 0.697

tctcctttaatttcgcttcgatttcagaaatca	CRISPR spacer
gatcatttaatttctcttcgatttcaaaccatg	Protospacer
  ** ********* ***********.*   ..

20. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to MG592456 (Vibrio phage 1.081.O._10N.286.52.C2, partial genome) position: , mismatch: 10, identity: 0.688

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
gcttgccatatttgatagccattctattatac	Protospacer
 .  *. .******** ******** *****.

21. spacer 2.14|281638|32|LS483443|CRISPRCasFinder matches to NZ_CP040853 (Lactobacillus murinus strain V10 plasmid unnamed, complete sequence) position: , mismatch: 11, identity: 0.656

ctgggtggtatttgattgccattcttttatat	CRISPR spacer
agatgttgtatttgatcgccattctttagctg	Protospacer
  . ** *********.********** ..

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

44570 : 67725

uncultured_Caudovirales_phage(46.15%)

integrase,head,capsid,tail,portal,protease,terminase

attL 53158:53177|attR 68082:68101

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
SQH63563.1\|44570_46586_+	DNA ligase	A0A289ZTZ3	Serratia_phage	7.7e-143	49.8
SQH63564.1\|46656_47235_-	Thymidine kinase	A0A076YPF1	Citrobacter_phage	5.2e-52	51.6
SQH63565.1\|47234_47468_-	Uncharacterised protein	NA	NA	NA	NA
SQH63566.1\|47538_48567_-	t(6)A37 threonylcarbamoyladenosine biosynthesis protein	A0A0R6PI74	Moraxella_phage	7.3e-113	59.1
SQH63567.1\|48791_49007_+	30S ribosomal protein S21	NA	NA	NA	NA
SQH63568.1\|49128_50889_+	DNA primase	A0A1S5RF71	Helicobacter_phage	1.1e-44	32.2
SQH63569.1\|50964_52830_+	Sigma-70	A0A2I7SAT0	Vibrio_phage	3.4e-36	36.3
53158:53177	attL	NA	NA	NA	NA
SQH63570.1\|53231_54428_+\|integrase	Prophage CP4-57 integrase	A0A1V0E8G8	Vibrio_phage	1.2e-79	39.7
SQH63571.1\|54592_55639_-	phage/plasmid primase, P4 family, C-terminal domain	Q7M2A8	Enterobacteria_phage	3.0e-66	42.6
SQH63572.1\|55650_56379_-	Uncharacterised protein	NA	NA	NA	NA
SQH63573.1\|56362_56806_-	Uncharacterised protein	NA	NA	NA	NA
SQH63574.1\|56805_57030_-	Uncharacterised protein	NA	NA	NA	NA
SQH63575.1\|57022_57373_-	Uncharacterised protein	NA	NA	NA	NA
SQH63576.1\|57359_57551_-	Uncharacterised protein	NA	NA	NA	NA
SQH63577.1\|57566_57749_-	Uncharacterised protein	NA	NA	NA	NA
SQH63578.1\|58539_58851_-	Uncharacterised protein	NA	NA	NA	NA
SQH63579.1\|58862_59066_-	Predicted transcriptional regulator	NA	NA	NA	NA
SQH63580.1\|59210_60167_-	Uncharacterised protein	NA	NA	NA	NA
SQH63581.1\|60311_60872_-	Uncharacterised protein	NA	NA	NA	NA
SQH63582.1\|60864_61137_-	Uncharacterised protein	NA	NA	NA	NA
SQH63583.1\|61418_63038_-\|terminase	Phage terminase-like protein, large subunit	A0A2H4JB64	uncultured_Caudovirales_phage	2.6e-242	72.8
SQH63584.1\|63094_63463_-\|terminase	Phage terminase, small subunit	A0A2H4JHS3	uncultured_Caudovirales_phage	3.0e-37	66.1
SQH63585.1\|64054_64369_-	uncharacterized phage protein (possible DNA packaging)	A0A2H4JD08	uncultured_Caudovirales_phage	2.7e-18	49.5
SQH63586.1\|64355_64700_-\|head,tail	Bacteriophage head-tail adaptor	NA	NA	NA	NA
SQH63587.1\|64683_65916_-\|portal	phage portal protein, HK97 family	A0A2H4JFJ9	uncultured_Caudovirales_phage	2.8e-143	62.5
SQH63588.1\|65917_66484_-\|head,protease	phage prohead protease, HK97 family	A0A2H4JB68	uncultured_Caudovirales_phage	1.1e-49	63.4
SQH63589.1\|66537_67725_-\|capsid	Predicted phage phi-C31 gp36 major capsid-like protein	A0A2H4JED2	uncultured_Caudovirales_phage	1.4e-131	63.3
68082:68101	attR	NA	NA	NA	NA

DBSCAN-SWA_2

1645779 : 1735063

Mannheimia_phage(22.22%)

integrase,head,tRNA,capsid,tail,portal,protease,terminase

attL 1676953:1676970|attR 1709395:1709412

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
SQH65046.1\|1645779_1646706_-\|protease	FtsH protease regulator HflK	NA	NA	NA	NA
SQH65047.1\|1652847_1653921_-	Undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase	NA	NA	NA	NA
SQH65048.1\|1654047_1655331_+	Glutamate-1-semialdehyde 2,1-aminomutase	NA	NA	NA	NA
SQH65049.1\|1655401_1657993_-	PII uridylyl-transferase	NA	NA	NA	NA
SQH65050.1\|1658059_1658863_-	Methionine aminopeptidase	NA	NA	NA	NA
SQH65051.1\|1658998_1659340_+	Iron-sulfur cluster insertion protein erpA	A0A2H4N7M3	Lake_Baikal_phage	2.9e-26	49.1
SQH65052.1\|1659296_1659704_+	Uncharacterised protein family (UPF0231)	NA	NA	NA	NA
SQH65053.1\|1659734_1662116_+	Murein polymerase	NA	NA	NA	NA
SQH65054.1\|1662247_1663939_-	D-lactate dehydrogenase	NA	NA	NA	NA
SQH65055.1\|1664236_1665832_+	L-lactate permease	NA	NA	NA	NA
SQH65056.1\|1665929_1666655_+	Lactate utilization protein A	NA	NA	NA	NA
SQH65057.1\|1666661_1668074_+	Lactate utilization protein B	NA	NA	NA	NA
SQH65058.1\|1668073_1668781_+	Lactate utilization protein C	NA	NA	NA	NA
SQH65059.1\|1668966_1670874_+	Ferrous iron uptake protein	NA	NA	NA	NA
SQH65060.1\|1670916_1671438_+	Pathogen-specific membrane antigen	NA	NA	NA	NA
SQH65061.1\|1671567_1672986_+	Predicted membrane protein	NA	NA	NA	NA
SQH65062.1\|1672988_1674314_+	Macrolide export ATP-binding/permease protein MacB	NA	NA	NA	NA
SQH65063.1\|1674300_1675440_+	outer membrane-specific lipoprotein transporter subunit LolE	NA	NA	NA	NA
SQH65064.1\|1675441_1676113_+	Lipoprotein-releasing system ATP-binding protein LolD	A0A1M7XV31	Cedratvirus	9.2e-16	31.4
SQH65065.1\|1676102_1676609_+	Thiol-disulfide oxidoreductase resA	NA	NA	NA	NA
SQH65066.1\|1676605_1676917_+	Cytochrome c553	NA	NA	NA	NA
1676953:1676970	attL	NA	NA	NA	NA
SQH65067.1\|1682851_1683055_-	lipoprotein	NA	NA	NA	NA
SQH65068.1\|1683138_1684071_-	Bifunctional protein BirA	NA	NA	NA	NA
SQH65069.1\|1684221_1685688_+	Inosine-5'-monophosphate dehydrogenase	A0A1V0SHK8	Klosneuvirus	1.2e-97	41.4
SQH65070.1\|1685894_1687271_+	Xanthine permease XanQ	H9YQ34	environmental_Halophage	7.9e-22	45.4
SQH65071.1\|1687426_1688782_+	Putative cryptic C4-dicarboxylate transporter DcuD	NA	NA	NA	NA
SQH65072.1\|1688891_1689761_+	Predicted permease, DMT superfamily	NA	NA	NA	NA
SQH65073.1\|1689931_1691491_+	GMP synthase [glutamine-hydrolyzing]	NA	NA	NA	NA
SQH65074.1\|1691693_1692893_+\|integrase	Putative prophage CPS-53 integrase	G9L697	Escherichia_phage	5.6e-133	58.2
SQH65075.1\|1692907_1693477_-	Uncharacterised protein	NA	NA	NA	NA
SQH65076.1\|1693476_1693809_-	Uncharacterised protein	NA	NA	NA	NA
SQH65077.1\|1693870_1694722_-	Uncharacterised protein	NA	NA	NA	NA
SQH65078.1\|1694762_1695101_-	Uncharacterised protein	NA	NA	NA	NA
SQH65079.1\|1695097_1698313_-	Domain of uncharacterised function (DUF1983)	A0A0M3LR06	Mannheimia_phage	1.3e-06	63.2
SQH65080.1\|1698352_1699018_-\|tail	Phage-related protein, tail component	A0A0M3LQC4	Mannheimia_phage	7.7e-31	44.3
SQH65081.1\|1698963_1699776_-	NlpC/P60 family	A0A0M3LP75	Mannheimia_phage	2.1e-62	47.8
SQH65082.1\|1699723_1700458_-\|tail	phage minor tail protein L	A0A0M3LPR8	Mannheimia_phage	1.2e-72	56.4
SQH65083.1\|1700457_1700745_-	Phage-related protein	A0A0P0ZBQ8	Stx2-converting_phage	2.9e-11	37.2
SQH65084.1\|1700799_1704126_-\|tail	Phage-related minor tail protein	A0A0E3GMH8	Enterobacteria_phage	1.2e-60	26.7
SQH65085.1\|1704189_1704387_-	Uncharacterised protein	NA	NA	NA	NA
SQH65086.1\|1704462_1704888_-	Uncharacterised protein	NA	NA	NA	NA
SQH65087.1\|1705070_1705265_+	Uncharacterised protein	NA	NA	NA	NA
SQH65088.1\|1705514_1705922_-	Uncharacterised protein	NA	NA	NA	NA
SQH65089.1\|1705982_1706636_-	Uncharacterised protein	NA	NA	NA	NA
SQH65090.1\|1706639_1706984_-	Protein of uncharacterised function (DUF3168)	NA	NA	NA	NA
SQH65091.1\|1706985_1707468_-	phage protein, HK97 gp10 family	A0A220NRP5	Escherichia_phage	8.9e-13	31.5
SQH65092.1\|1707460_1707784_-\|head,tail	Bacteriophage head-tail adaptor	A0A286S2A2	Klebsiella_phage	5.8e-16	46.3
SQH65093.1\|1707780_1708101_-\|head,tail	Phage gp6-like head-tail connector protein	A0A2H4J8C5	uncultured_Caudovirales_phage	2.2e-07	37.3
SQH65094.1\|1708150_1709377_-\|capsid	Predicted phage phi-C31 gp36 major capsid-like protein	Q8SBH8	Shigella_phage	3.9e-145	64.8
SQH65095.1\|1709442_1710045_-\|head,protease	phage prohead protease, HK97 family	Q8SBH9	Shigella_phage	5.8e-78	71.9
1709395:1709412	attR	NA	NA	NA	NA
SQH65096.1\|1710037_1711258_-\|portal	phage portal protein, HK97 family	A0A1W6JP33	Morganella_phage	1.2e-143	60.9
SQH65097.1\|1711254_1711407_-	Uncharacterised protein	NA	NA	NA	NA
SQH65098.1\|1711403_1713110_-\|terminase	Phage terminase-like protein, large subunit	Q8HAD6	Salmonella_phage	1.9e-243	71.4
SQH65099.1\|1713106_1713589_-\|terminase	Phage terminase, small subunit	Q8W632	Enterobacteria_phage	1.4e-29	44.9
SQH65100.1\|1714317_1714674_-	Protein of uncharacterised function (DUF2570)	NA	NA	NA	NA
SQH65101.1\|1714649_1715225_-	Phage-related lysozyme (muraminidase)	A0A0M3LPQ1	Mannheimia_phage	1.2e-35	43.0
SQH65102.1\|1715208_1715445_-	Uncharacterised protein	NA	NA	NA	NA
SQH65103.1\|1715595_1716102_-	Phage antitermination protein Q	K7PHU3	Enterobacteria_phage	3.2e-13	31.4
SQH65104.1\|1716094_1716457_-	Crossover junction endodeoxyribonuclease rusA	A0A0M3LPZ2	Mannheimia_phage	6.0e-30	49.2
SQH65105.1\|1716453_1716747_-	82 prophage-derived uncharacterized protein ybcO	A0A220NQY2	Salmonella_phage	7.8e-28	68.1
SQH65106.1\|1716816_1717452_-	Protein of uncharacterised function (DUF1367)	K7PKS6	Enterobacteria_phage	9.3e-18	26.9
SQH65107.1\|1717421_1717940_-	phage N-6-adenine-methyltransferase	D0UIL3	Aggregatibacter_phage	4.5e-79	82.4
SQH65108.1\|1717936_1718611_-	Replication protein P	D0UIL4	Aggregatibacter_phage	9.0e-120	93.8
SQH65109.1\|1718607_1719381_-	Uncharacterised protein	D0UIL5	Aggregatibacter_phage	3.8e-58	97.4
SQH65110.1\|1719380_1720145_-	KilA-N domain	Q8W644	Enterobacteria_phage	5.2e-31	38.7
SQH65111.1\|1720188_1720485_-	Protein of uncharacterised function (DUF3718)	Q7Y5W3	Haemophilus_phage	1.2e-47	99.0
SQH65112.1\|1720505_1720706_-	Uncharacterized protein conserved in bacteria, prophage-related	NA	NA	NA	NA
SQH65113.1\|1720826_1721519_+	Peptidase S24-like	Q7Y5W5	Haemophilus_phage	1.4e-83	90.9
SQH65114.1\|1721786_1722617_+	Uncharacterised protein	NA	NA	NA	NA
SQH65115.1\|1722609_1722978_+	Uncharacterised protein	NA	NA	NA	NA
SQH65116.1\|1723009_1723498_+	Uncharacterised protein	NA	NA	NA	NA
SQH65117.1\|1723857_1724382_-	Uncharacterised protein	Q7Y5W8	Haemophilus_phage	1.1e-59	69.4
SQH65118.1\|1724887_1725355_+	Uncharacterised protein	NA	NA	NA	NA
SQH65119.1\|1725517_1725727_+	Uncharacterised protein	NA	NA	NA	NA
SQH65120.1\|1725973_1726306_-	Uncharacterised protein	NA	NA	NA	NA
SQH65121.1\|1726659_1727028_+	Uncharacterised protein	Q776W5	Haemophilus_phage	5.9e-09	41.9
SQH65122.1\|1727020_1727308_+	Uncharacterised protein	NA	NA	NA	NA
SQH65123.1\|1727294_1727459_+	Uncharacterised protein	NA	NA	NA	NA
SQH65124.1\|1727461_1728379_+	Uncharacterised protein	A0A0M3LR66	Mannheimia_phage	5.8e-61	47.8
SQH65125.1\|1728391_1729273_+	phage recombination protein Bet	A0A2H4JAQ4	uncultured_Caudovirales_phage	5.2e-59	59.4
SQH65126.1\|1729269_1729929_+	putative phage-type endonuclease	A0A0M3LPU0	Mannheimia_phage	2.9e-83	74.4
SQH65127.1\|1730102_1730537_+	Predicted acetyltransferase	NA	NA	NA	NA
SQH65128.1\|1730734_1730947_+	Uncharacterised protein	NA	NA	NA	NA
SQH65129.1\|1730952_1731132_+	Predicted transcriptional regulator	A0A2H4J8C8	uncultured_Caudovirales_phage	5.6e-05	44.9
SQH65130.1\|1731825_1732779_+	Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha	NA	NA	NA	NA
SQH65131.1\|1732850_1733708_+	Pyridoxamine kinase	NA	NA	NA	NA
SQH65132.1\|1733752_1735063_+\|tRNA	tRNA(Ile)-lysidine synthase	NA	NA	NA	NA

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. LS483443

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection