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
CP034074	Salmonella enterica subsp. diarizonae strain 16-SA00356 chromosome, complete genome	1 crisprs	csa3,DEDDh,cas3,DinG,RT,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,WYL	0	6	2	0
CP034075	Salmonella enterica subsp. diarizonae strain 16-SA00356 plasmid pSE16-SA00356, complete sequence	0 crisprs	NA	0	0	0	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: CP034074_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

CP034074_2

4027090-4027789

TypeI-E

I-E

Consensus_repeat	Method
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CRISPRCasFinder
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CRT
CGGTTTATCCCCGCTGGCGCGGGGAACAC	PILER-CR

11 spacers

cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e

The CRISPR arrays of CP034074_2

>merge|CP034074|2|4027090-4027789|CRISPRCasFinder,CRT,PILER-CR
TAGCTTATCCCCGCTGACGCGGGGAACACGACCACAGTAACTTCAGCAGCCTGACCGGCAGCGGTTTATCCCCGCTGACGCGGGGAACACGCGTAGAAGCTGTTGACGTCAGCGAGCGCAAACGGTTTATCCCCGCTAGCGCGGGGAACACGTATTATAGCGGGTAATTGAGGAGAAAATCATCGGTTTATCCCCGCTGGCGCGGGGAACACCGTAACCTAAATCAATGCTCAAGGTCGTCCACCGGTTTATCCCCGCTGGCGCGGGGAACACGGATTATATGTCACAGACAACAATTACACTGGCGGTTTATCCCCGCTGGCGCGGGGAACACACCAATACCCAGAACAATACCTATCAACGCGCCGGTTTATCCCCGCTGGCGCGGGGAACACTAACGATGCGTCGTGGTGGTATCTCCAGACACCGGTTTATCCCCGCTGGCGCGGGGAACACTTTTCTGCATACATAGTCGCATTATTTGTAATCGGTTTATCCCCGCTGGCGCGGGGAACACTGCATCGCCCGTGGTGCTGCGGGTGTTTCTCCCGGTTTATCCCCGCTGGCGCGGGGAACACCATTTTTTATCTCCCACCAGACGCTGACCCCGCGGTTTATCCCCGCTGGCGCGGGGAACACCTTCTGTGCTAATGACGTTGCCACGTGGCGCGCGGTTTATCCCCGCTGGCGCGGGGAACAC

>CP034074|2|2|4027090-4027789|CRISPRCasFinder
TAGCTTATCCCCGCTGACGCGGGGAACAC	GACCACAGTAACTTCAGCAGCCTGACCGGCAG
CGGTTTATCCCCGCTGACGCGGGGAACAC	GCGTAGAAGCTGTTGACGTCAGCGAGCGCAAA
CGGTTTATCCCCGCTAGCGCGGGGAACAC	GTATTATAGCGGGTAATTGAGGAGAAAATCAT
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CGTAACCTAAATCAATGCTCAAGGTCGTCCAC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	GGATTATATGTCACAGACAACAATTACACTGG
CGGTTTATCCCCGCTGGCGCGGGGAACAC	ACCAATACCCAGAACAATACCTATCAACGCGC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TAACGATGCGTCGTGGTGGTATCTCCAGACAC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TTTTCTGCATACATAGTCGCATTATTTGTAAT
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TGCATCGCCCGTGGTGCTGCGGGTGTTTCTCC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CATTTTTTATCTCCCACCAGACGCTGACCCCG
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CTTCTGTGCTAATGACGTTGCCACGTGGCGCG
CGGTTTATCCCCGCTGGCGCGGGGAACAC

>CP034074|2|1|4027090-4027789|CRT
TAGCTTATCCCCGCTGACGCGGGGAACAC	GACCACAGTAACTTCAGCAGCCTGACCGGCAG
CGGTTTATCCCCGCTGACGCGGGGAACAC	GCGTAGAAGCTGTTGACGTCAGCGAGCGCAAA
CGGTTTATCCCCGCTAGCGCGGGGAACAC	GTATTATAGCGGGTAATTGAGGAGAAAATCAT
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CGTAACCTAAATCAATGCTCAAGGTCGTCCAC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	GGATTATATGTCACAGACAACAATTACACTGG
CGGTTTATCCCCGCTGGCGCGGGGAACAC	ACCAATACCCAGAACAATACCTATCAACGCGC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TAACGATGCGTCGTGGTGGTATCTCCAGACAC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TTTTCTGCATACATAGTCGCATTATTTGTAAT
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TGCATCGCCCGTGGTGCTGCGGGTGTTTCTCC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CATTTTTTATCTCCCACCAGACGCTGACCCCG
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CTTCTGTGCTAATGACGTTGCCACGTGGCGCG
CGGTTTATCCCCGCTGGCGCGGGGAACAC

>CP034074|2|1|4027151-4027789|PILER-CR
CGGTTTATCCCCGCTGACGCGGGGAACAC	GCGTAGAAGCTGTTGACGTCAGCGAGCGCAAA
CGGTTTATCCCCGCTAGCGCGGGGAACAC	GTATTATAGCGGGTAATTGAGGAGAAAATCAT
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CGTAACCTAAATCAATGCTCAAGGTCGTCCAC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	GGATTATATGTCACAGACAACAATTACACTGG
CGGTTTATCCCCGCTGGCGCGGGGAACAC	ACCAATACCCAGAACAATACCTATCAACGCGC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TAACGATGCGTCGTGGTGGTATCTCCAGACAC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TTTTCTGCATACATAGTCGCATTATTTGTAAT
CGGTTTATCCCCGCTGGCGCGGGGAACAC	TGCATCGCCCGTGGTGCTGCGGGTGTTTCTCC
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CATTTTTTATCTCCCACCAGACGCTGACCCCG
CGGTTTATCCCCGCTGGCGCGGGGAACAC	CTTCTGTGCTAATGACGTTGCCACGTGGCGCG
CGGTTTATCCCCGCTGGCGCGGGGAACAC

Protein	Signature genes	Signature genes Name	Protein_function
CP034074.1\|QAY25516.1\|4022828_4023434_-\|adenylyl-sulfate-kinase	unknown	unknown	gnl\|CDD\|179661
CP034074.1\|QAY25524.1\|4030484_4031540_-\|type-I-E-CRISPR-associated-protein-Cas7/Cse4/CasC	cas7	pfam09344_cas7_CAS-I-E	gnl\|CDD\|273843
CP034074.1\|QAY25518.1\|4024869_4025778_-\|sulfate-adenylyltransferase-subunit-2	unknown	unknown	gnl\|CDD\|235375
CP034074.1\|QAY25528.1\|4037789_4038524_-\|phosphoadenosine-phosphosulfate-reductase	unknown	unknown	gnl\|CDD\|234997
CP034074.1\|QAY25526.1\|4032086_4033643_-\|type-I-E-CRISPR-associated-protein-Cse1/CasA	cas8e	cd09669_cas8e_CAS-I-E	gnl\|CDD\|274192
CP034074.1\|QAY25527.1\|4036748_4037702_+\|type-III-secretion-system-effector-SopD	unknown	unknown	gnl\|CDD\|185277
CP034074.1\|QAY25513.1\|4021223_4021934_-\|2-C-methyl-D-erythritol-4-phosphate-cytidylyltransferase	unknown	unknown	gnl\|CDD\|234670
CP034074.1\|QAY25515.1\|4022454_4022811_-\|DUF3561-family-protein	unknown	unknown	gnl\|CDD\|371891
CP034074.1\|QAY25514.1\|4021952_4022264_-\|cell-division-protein-FtsB	unknown	unknown	gnl\|CDD\|179156
CP034074.1\|QAY25520.1\|4027885_4028179_-\|type-I-E-CRISPR-associated-endoribonuclease-Cas2	cas2	cd09648_cas2_CAS-I-E	gnl\|CDD\|236930
CP034074.1\|QAY25525.1\|4031553_4032090_-\|type-I-E-CRISPR-associated-protein-Cse2/CasB	cse2gr11	cd09731_cse2gr11_CAS-I-E	gnl\|CDD\|187862
CP034074.1\|QAY25517.1\|4023420_4024860_-\|sulfate-adenylyltransferase-subunit-CysN	unknown	unknown	gnl\|CDD\|235349
CP034074.1\|QAY25529.1\|4038632_4040345_-\|assimilatory-sulfite-reductase-(NADPH)-hemoprotein-subunit	unknown	unknown	gnl\|CDD\|237402
CP034074.1\|QAY25519.1\|4026028_4027075_+\|aminopeptidase	unknown	unknown	gnl\|CDD\|182299
CP034074.1\|QAY25523.1\|4029727_4030474_-\|type-I-E-CRISPR-associated-protein-Cas5/CasD	cas5	cd09645_cas5_CAS-I-E	gnl\|CDD\|187776
CP034074.1\|QAY25512.1\|4020744_4021224_-\|2-C-methyl-D-erythritol-2,4-cyclodiphosphate-synthase	unknown	unknown	gnl\|CDD\|178851
CP034074.1\|QAY25522.1\|4029095_4029746_-\|type-I-E-CRISPR-associated-protein-Cas6/Cse3/CasE	cas6e	cd09664_cas6e_CAS-I-E	gnl\|CDD\|273869
CP034074.1\|QAY25510.1\|4018956_4019718_-\|5'/3'-nucleotidase-SurE	unknown	unknown	gnl\|CDD\|234732
CP034074.1\|QAY25511.1\|4019698_4020748_-\|tRNA-pseudouridine(13)-synthase-TruD	unknown	unknown	gnl\|CDD\|234884
CP034074.1\|QAY25521.1\|4028178_4029099_-\|type-I-E-CRISPR-associated-endonuclease-Cas1	cas1	cd09719_cas1_CAS-I-E	gnl\|CDD\|274693

Protein	Function_ID	Function_description	E-value
CP034074.1\|QAY25516.1\|4022828_4023434_-\|adenylyl-sulfate-kinase	gnl\|CDD\|179661	PRK03846, PRK03846, adenylylsulfate kinase; Provisional.	3.23556e-146
CP034074.1\|QAY25524.1\|4030484_4031540_-\|type-I-E-CRISPR-associated-protein-Cas7/Cse4/CasC	gnl\|CDD\|273843	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI. 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. This family is represented by CT1975 of Chlorobium tepidum and is part of the Ecoli subtype of CRISPR/Cas locis. It is designated Cse4, for CRISPR/Cas Subtype Ecoli protein 4.	1.68093e-134
CP034074.1\|QAY25518.1\|4024869_4025778_-\|sulfate-adenylyltransferase-subunit-2	gnl\|CDD\|235375	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD.	0
CP034074.1\|QAY25528.1\|4037789_4038524_-\|phosphoadenosine-phosphosulfate-reductase	gnl\|CDD\|234997	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase.	2.98201e-136
CP034074.1\|QAY25526.1\|4032086_4033643_-\|type-I-E-CRISPR-associated-protein-Cse1/CasA	gnl\|CDD\|274192	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1. 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. This model family, represented by CT1972 from Chlorobium tepidum, is found in Ecoli subtype CRISPR/Cas regions of many bacteria, most of which are mesophiles, and not in Archaea. It is designated Cse1.	4.33685e-180
CP034074.1\|QAY25527.1\|4036748_4037702_+\|type-III-secretion-system-effector-SopD	gnl\|CDD\|185277	PRK15379, PRK15379, type III secretion system effector SopD.	0
CP034074.1\|QAY25513.1\|4021223_4021934_-\|2-C-methyl-D-erythritol-4-phosphate-cytidylyltransferase	gnl\|CDD\|234670	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase.	4.74538e-119
CP034074.1\|QAY25515.1\|4022454_4022811_-\|DUF3561-family-protein	gnl\|CDD\|371891	pfam12084, DUF3561, Protein of unknown function (DUF3561). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.	3.90492e-49
CP034074.1\|QAY25514.1\|4021952_4022264_-\|cell-division-protein-FtsB	gnl\|CDD\|179156	PRK00888, ftsB, cell division protein FtsB; Reviewed.	9.72909e-65
CP034074.1\|QAY25520.1\|4027885_4028179_-\|type-I-E-CRISPR-associated-endoribonuclease-Cas2	gnl\|CDD\|236930	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional.	2.76144e-63
CP034074.1\|QAY25525.1\|4031553_4032090_-\|type-I-E-CRISPR-associated-protein-Cse2/CasB	gnl\|CDD\|187862	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2. 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; Small alpha-helical protein; also known as Cse2/CasB/YgcK family; specific gene for I-E subtype;.	1.13405e-29
CP034074.1\|QAY25517.1\|4023420_4024860_-\|sulfate-adenylyltransferase-subunit-CysN	gnl\|CDD\|235349	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.	0
CP034074.1\|QAY25529.1\|4038632_4040345_-\|assimilatory-sulfite-reductase-(NADPH)-hemoprotein-subunit	gnl\|CDD\|237402	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit.	0
CP034074.1\|QAY25519.1\|4026028_4027075_+\|aminopeptidase	gnl\|CDD\|182299	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional.	0
CP034074.1\|QAY25523.1\|4029727_4030474_-\|type-I-E-CRISPR-associated-protein-Cas5/CasD	gnl\|CDD\|187776	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5. 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; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex.	2.56616e-48
CP034074.1\|QAY25512.1\|4020744_4021224_-\|2-C-methyl-D-erythritol-2,4-cyclodiphosphate-synthase	gnl\|CDD\|178851	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed.	7.17105e-104
CP034074.1\|QAY25522.1\|4029095_4029746_-\|type-I-E-CRISPR-associated-protein-Cas6/Cse3/CasE	gnl\|CDD\|273869	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI. 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. This model family, represented by CT1974 from Chlorobium tepidum, is found in the Ecoli subtype of CRISPR/Cas regions and is designated Cse3 (CRISPR/Cas Subtype Ecoli protein 3). The representative of this family from Thermus thermophilus HB8 (TTHB192) has been crystallized and found to have a structure consisting of two domains with opposing parallel beta-sheets known as a beta-sheet platform. This structure is similar to those found in the Sex-lethal protein and poly(A)-binding protein. This structure is consistent with an RNA-binding function.	7.81393e-75
CP034074.1\|QAY25510.1\|4018956_4019718_-\|5'/3'-nucleotidase-SurE	gnl\|CDD\|234732	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional.	9.82932e-146
CP034074.1\|QAY25511.1\|4019698_4020748_-\|tRNA-pseudouridine(13)-synthase-TruD	gnl\|CDD\|234884	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed.	0
CP034074.1\|QAY25521.1\|4028178_4029099_-\|type-I-E-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|274693	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the ECOLI subtype of CRISPR/Cas system.	1.30706e-158

>CP034074.1|QAY25519.1|4026028_4027075_+|aminopeptidase
MFSATRRFTVILALGVGFILPAQAASPGPGEIANTQARHIATFFPGRMTGSPAEMLSADYLRQQFTQMGYQSDIRTFNSRFIYTTKDNRKNWHNVTGSTVIAAHEGRVPQQIIIMAHLDTYAPQSDADVDANLGGLTLQGMDDNAAGLGVMLELAARLKDIPTHYGIRFIATSGEEEGKPGAENLLKRMSDAEKKNTLLVINFDNLIVGDKLYFNSGKNTPEAVRTLTRDRALAIARRYGIAASTNPGLNPSYPKGTGCCNDAEVFDKAGISVLSVEATNWNLGKKDGYQQRAKNASFPNGNSWHDVRLDNQQHIDKALPGRIERRSRDVVRIMLPLVKELAKTEKTS
>CP034074.1|QAY25518.1|4024869_4025778_-|sulfate-adenylyltransferase-subunit-2
MDQKRLTHLRQLEAESIHIIREVAAEFANPVMLYSIGKDSSVMLHLARKAFYPGTLPFPLLHVDTGWKFREMYAFRDRTANAYGCELLVHKNPEGVAMGINPFVHGSAKHTDIMKTEGLKQALNKYGFDAAFGGARRDEEKSRAKERIYSFRDRFHRWDPKNQRPELWRNYNGQINKGESIRVFPLSNWTEQDIWQYIWLENIDIVPLYLAAERPVLERDGMLMMVDDDRIDLQPGEVIKKRMVRFRTLGCWPLTGAVESHAQTLPEIIEEMLVSTTSERQGRMIDRDQAGSMELKKRQGYF
>CP034074.1|QAY25517.1|4023420_4024860_-|sulfate-adenylyltransferase-subunit-CysN
MNTILAQQIANEGGVEAWMIAQQHKSLLRFLTCGSVDDGKSTLIGRLLHDTRQIYEDQLSSLHNDSKRHGTQGEKLDLALLVDGLQAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQTRRHSFISTLLGIKHLVVAINKMDLVDYREETFARIREDYLTFAEQLPGDLDIRFVPLSALEGDNVAAQSANMRWYSGPTLLEVLETVDIQRAVDRQPMRFPVQYVNRPNLDFRGYAGTLASGSVKVGERIKVLPSGVESSVARIVTFDGDKEVAYAGEAITLVLNDDIDISRGDLLLAANETLAPARHAAIDVVWMAEQPLAPGQSYDVKLAGKKTRARIETIRYQIDINNLTQRDVESLPLNGIGLVEMTFDEPLALDIYQQNPVTGGLIFIDRLSNVTVGAGMVREPVERGVTPPVEYSAFELELNALVRRHFPHWDARDLLGDKHGAA
>CP034074.1|QAY25516.1|4022828_4023434_-|adenylyl-sulfate-kinase
MALHDENVVWHSHPVTVAAREQLHGHRGVVLWFTGLSGSGKSTVAGALEEALHHRGVSTYLLDGDNVRHGLCRDLGFSDADRQENIRRVGEVASLMADAGLIVLTAFISPHRAERQLVQERVGHDRFIEIYVDTPLAICEQRDPKGLYKKARAGELRNFTGIDAIYEAPESPQIHLNGEQLVTNLVSQLLDLLRRRDIIRS
>CP034074.1|QAY25515.1|4022454_4022811_-|DUF3561-family-protein
MPGMVKVTGFDMRNSHNITFTRSDAFIVDDDTTSSLPGAVVGFVSWLLALGIPFLLYGPNTLFFFLYTWPFFLALMPVSVIIGIALHLLVKGKILFSIMFTLLAVGALFGVLFIWLLG
>CP034074.1|QAY25514.1|4021952_4022264_-|cell-division-protein-FtsB
MGKLTLLLLALLVWLQYSLWFGKNGIHDYSRVNDDVVAQQATNAKLKARNDQLFAEIDDLNGGQEAIEERARNELSMTKPGETFYRLVPDASKRAATAGQTNR
>CP034074.1|QAY25513.1|4021223_4021934_-|2-C-methyl-D-erythritol-4-phosphate-cytidylyltransferase
MAATLLDVCAVVPAAGFGRRMQTECPKQYLSIGNKTILEHSVHALLAHPRVTRVVIAISPGDYRFAQLPLANHPQITVVDGGNERADSVLAGLQAVAEAQWVLVHDAARPCLHQDDLARLLAISENSRVGGILASPVRDTMKRGEPGKTAIAHTVERADLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPALVEGRADNIKVTRPEDLALAEFYLTRTIHQEII
>CP034074.1|QAY25512.1|4020744_4021224_-|2-C-methyl-D-erythritol-2,4-cyclodiphosphate-synthase
MRIGHGFDVHAFGGEGPITICGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLMKTAK
>CP034074.1|QAY25511.1|4019698_4020748_-|tRNA-pseudouridine(13)-synthase-TruD
MTEFDNLIWLHGKPQSSGLLKANPEDFVVIEDLGFTPDGEGEHILLRILKNGCNTRFVADALAKFLKIHVREVSFAGQKDKHAVTEQWLCARVPGKEMPDFSAFQLEGCKVLEYARHKRKLRLGALKGNAFTLVLREISDRRDVETRLQAIRDSGVPNYFGAQRFGIGGSNLQGALRWAQSDAPVRDRNKRSFWLSAARSALFNQIVHQRLKKPDFNQVVDGDALQLTGRGSWFVATSEELPELQRRVDEKELMITASLPGSGEWGTQREALAFEQDAIAQEMVLQSLLLREKVEASRRAMLLYPQQLSWNWWDDVTVELRFWLPAGSFATSVVRELINTMGDYAHIAE
>CP034074.1|QAY25510.1|4018956_4019718_-|5'/3'-nucleotidase-SurE
MRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDLIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQIKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKCDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW
>CP034074.1|QAY25520.1|4027885_4028179_-|type-I-E-CRISPR-associated-endoribonuclease-Cas2
MSMVVVVTENVPPRLRGRLAIWLLEIRAGVYVGDTSKRIREMIWQQITQLGGVGNVVMAWATNTESGFEFQTWGENRRIPVDLDGLRLVSFLPVENQ
>CP034074.1|QAY25521.1|4028178_4029099_-|type-I-E-CRISPR-associated-endonuclease-Cas1
MTFVPLNPIPLKDRTSMIFLQYGQIDVLDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVHLASTVGTLLVWVGEAGVRVYSSGQPGGARADKLLYQAKLALDDDLRLKVVRKMYELRFREPPPARRSIEQLRGIEGSRVRATYALLAKQYGVKWNGRNYDPKDWEKGDVVNRCISAATSCLYGISEAAVLAAGYAPAIGFIHSGKPLSFVYDIADIIKFESVVPKAFEIAARHPAEPDKEVRLACRDIFRSSKLTGKLIPLIEEVLAAGEIEPPQPAPDMLPPAIPEPESLGDSGHRGHG
>CP034074.1|QAY25522.1|4029095_4029746_-|type-I-E-CRISPR-associated-protein-Cas6/Cse3/CasE
MYLSRITLHTAQLVPSQLLHLVERGEYVMHQWLWELFPGGKERQFLYRREELQGAFRFFVLSQERPAESAIFDVQCRPFAPELSVGQILRFTLRANPTICKAGKRHDLLMEAKRQVKTQPDSRDIWTYQQQAALEWLSRQGEQNGFSLREASVDAYRQQQIRREKSRQMIQFSSVDYAGVLVVNNPVLFLQRLVQGYGKSRAFGCGMMLIKPGDSE
>CP034074.1|QAY25523.1|4029727_4030474_-|type-I-E-CRISPR-associated-protein-Cas5/CasD
MSQYLVFQLHGPMASWGVDAPGEVRHSHDLPSRSALLGLLAAALGIRRDEEERLSAFNRHYSFLLCASRNPRWARDYHTVQMPKEVRKARYFSRCEELQDPELLSALISRRDYYTDAWWMIAVSATPDAPYTLAQLQASLQHPVFPLYLGRKSHPLALPLAPQLLEGSAADVLREAYRQYQDKFNALKLTLPRLQNECWWEGEHEGLTANKILRRRDMPLSRQQWLFGERSVNQGQWLRKEDACISQE
>CP034074.1|QAY25524.1|4030484_4031540_-|type-I-E-CRISPR-associated-protein-Cas7/Cse4/CasC
MTTFIQLHLLTAYPAANLNRDDTGAPKTVVLGGATRLRISSQSLKRAWRTSELFEQALAGNIGIRSGRIAREAAQILIDSGIDAKKAVEYVEKIANCFGKIKADKKAKDPLTNADTEQLVHISPAEFEAVKALAHRLAEEKRPATEEEAALLRHDRMAVDIAMFGRMLANKPDFNVEAACQVAHAFGVSETIVEDDFFTAVDDLRAASDDAGAGHLGETGFGSALFYTYICIDKDLLVKNLNGNEELANKTLRAFTEAALKVSPTGKQNSFASRAYASWALAEKGTDQPRSLAAAFYEPINGTDQLNVAVKRITALRENMNAVYAQETAFKDFNVMNQQGSMKDMLDFICA
>CP034074.1|QAY25525.1|4031553_4032090_-|type-I-E-CRISPR-associated-protein-Cse2/CasB
MSIVKDDHNATLRQWHEELQEQRGARASLRRSVTVNDVCLSEGFRSLLMQTHTLWKIEGQEWRFTALALTAAVAAHIKSIDERQKFAAQLNNVMSELRFSRLCAVKTPDELLRQLRRAVKLLNGTVNLISLAEDIFHWCQENNELLNHHRRQQRPTEFIRIRWALEYYQAGDDDNEKD
>CP034074.1|QAY25526.1|4032086_4033643_-|type-I-E-CRISPR-associated-protein-Cse1/CasA
MKSFSLLTNCWLPVRFNDGSTGKLAPVDLADENVVDIAATRADLQGAAWQFLLGLLQCSIAPKNSARWEDIWLDGLTEEMLREALAPLEHAFQFGAETPSFMQDFEPLTGEKVSVASLLPETPGAQTTKFNKDHFVKRGVTERFCPHCAALALFSLQLNAPSGGKGYRTGLRGGGPMTTLIELQAYQSERQTPLWRKLWLNVMPQDAADLPLPVTCDASVFPWLAATRTSEQASAVTTPEQVNELQAYWGMPRRIRLDFTTTQPGACNICGADSDELLSVMTVKNYGVNYDGWRHPLTPYRLPVKEGSGFFSVKPQPGGLIWRDWLGLSQENHTEANKEYPALVVKVFNARRLRDVKAGLWGFGADFDNMKIRCWYEHHFPLLMTEGLIPDLRKAAQTAARLLSLLRSALKEAWFASAKDTRGDFSFIDIDFWNLTQGRFLNLIHDLENGHKPDERLTKWQRELWLFTRRYFDDHVFTSPYESSDLKRIMTARKKYFTTSAEKQSAKAAKAKKQEAAE
>CP034074.1|QAY25527.1|4036748_4037702_+|type-III-secretion-system-effector-SopD
MPVTLNFGNHQNYTLNETRLAHLLSADKEKATHMGNWDKVRDHFRSEKKDHALEVLYAIIHGRGPGEPGEMEVNVEDMSKIYAFKRLQHLACPAHQDLFKIEMDASQTQLLFMVGDTVISQSKIQDILNTSDNVVVESMSREERQLFLQICEVIGATITWHPELLQGSVSTLRKEVTGNAQIKEAVYGMMRPAEAPDHQLVEWQDSLTENEKSMLTCINAGNFEPTTQFCKIGYQEVEGEVAFSMMHPCISYLLHTYTPLVDFKGTNAGFLNELNQDYNGYHKNKMFIDVILERIYLAHEHSLHIGKNECSRNILLT
>CP034074.1|QAY25528.1|4037789_4038524_-|phosphoadenosine-phosphosulfate-reductase
MSQLDLNALNNLPKVDRILALAETNAELETLTAEERVAWALENLPGEYVLSSSFGIQAAVSLHLINQIRPEIPVILTDTGYLFPETYQFIDELTDKLKLNLKVYRAGESPAWQEARYGKLWEQGVEGIEKYNEINKVEPMNRALQELNAQTWFAGLRREQSGSRAHLSVLAIQRGIFKVLPIIDWDNRTVYQYLQKQGLKYHPLWEQGYLSVGDTHTTRKWEPGMAEEETRFFGLKRECGLHEG
>CP034074.1|QAY25529.1|4038632_4040345_-|assimilatory-sulfite-reductase-(NADPH)-hemoprotein-subunit
MSEKHPGPLVVEGKLSDAERMKLESNYLRGTIAEDLNDGLTGGFKGDNFLLIRFHGMYQQDDRDIRAERAEQKLEPRHAMLLRCRLPGGVITTAQWQAIDKFAADNTIYGSIRLTNRQTFQFHGILKKNVKPVHQMLHAVGLDALATANDMNRNVLCTSNPYESQLHAEAYEWAKKISEHLLPRTRAYAEIWLDQEKVATTDEEPILGQTYLPRKFKTTVVIPPQNDIDLHANDMNFVAIAENGKLVGFNLLVGGGLSIEHGNKKTYARTASEFGYLPLEHTLAVAEAVVTTQRDWGNRTDRKNAKTKYTLERVGLETFKAEVERRAGITFEPIRPYEFTGRGDRIGWVKGIDDKWHLTLFIENGRILDYPGRPLKTGLLEIAKIHQGEFRITANQNLIVASVPESQKAKIEKLARGHGLMNAVTPQRENSMACVSFPTCPLAMAEAERFLPSFIDKVEAMMAKHGVGDEHIVLRVTGCPNGCGRAMLAEIGLVGKAPGRYNLHLGGNRIGSRIPRMYKENITEPDILASLDELIGRWAKAREVGEGFGDFTVRAGIIRPVLDPARDFWE

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP034699	Salmonella enterica subsp. enterica serovar Karamoja strain RSE40 plasmid pRSE40, complete sequence	179828-179859	0	1.0
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP034710	Salmonella enterica subsp. enterica serovar Karamoja strain RSE21 plasmid pRSE21, complete sequence	65262-65293	0	1.0
CP034074_2	2.8\|4027546\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027546-4027577	32	KT630649	Salmonella phage SEN34, complete genome	21942-21973	0	1.0
CP034074_2	2.9\|4027607\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027607-4027638	32	KT630649	Salmonella phage SEN34, complete genome	5481-5512	0	1.0
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	AGRM01000007	Salmonella enterica subsp. houtenae str. ATCC BAA-1581 plasmid pSEHO0A2, complete sequence, whole genome shotgun sequence	8907-8938	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP029990	Salmonella enterica subsp. diarizonae serovar 48:i:z strain SA20121591 plasmid pSA20121591.1, complete sequence	7530-7561	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP030197	Salmonella enterica strain SA20051401 plasmid pSA20051401.1, complete sequence	87602-87633	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP030218	Salmonella enterica strain SA20075157 plasmid pSA20075157.1, complete sequence	20285-20316	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP030177	Salmonella enterica subsp. enterica serovar Milwaukee str. SA19950795 plasmid pIncFII.2, complete sequence	72336-72367	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP025255	Salmonella enterica subsp. enterica serovar Newport str. CDC 2010K-2159 plasmid pSNE1-2010K-2159, complete sequence	54912-54943	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	CP053415	Salmonella enterica strain 2011K-0868 plasmid unnamed, complete sequence	90385-90416	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	CP053327	Salmonella enterica subsp. salamae serovar 58:c:z6 strain 2013K-0366 plasmid unnamed, complete sequence	98707-98738	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP030289	Salmonella enterica subsp. enterica serovar Gaminara str. SA20063285 plasmid pIncI1.1, complete sequence	61911-61942	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP033339	Salmonella enterica subsp. enterica serovar Anatum strain CFSAN076215 plasmid pCFSAN076215, complete sequence	84558-84589	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP024167	Salmonella enterica subsp. enterica serovar Gaminara strain CFSAN070644 plasmid pCFSAN024441_02, complete sequence	31273-31304	4	0.875
CP034074_2	2.2\|4027180\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027180-4027211	32	NZ_CP022118	Salmonella enterica subsp. enterica serovar Macclesfield str. S-1643 plasmid unnamed1, complete sequence	35777-35808	4	0.875
CP034074_2	2.1\|4027119\|32\|CP034074\|CRISPRCasFinder,CRT	4027119-4027150	32	MH588547	Caulobacter phage CcrSC, complete genome	101522-101553	7	0.781
CP034074_2	2.1\|4027119\|32\|CP034074\|CRISPRCasFinder,CRT	4027119-4027150	32	NC_048047	Caulobacter phage CcrBL9, complete genome	102162-102193	7	0.781
CP034074_2	2.3\|4027241\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027241-4027272	32	NZ_CP034366	Pantoea sp. CCBC3-3-1 plasmid unnamed3, complete sequence	19524-19555	7	0.781
CP034074_2	2.1\|4027119\|32\|CP034074\|CRISPRCasFinder,CRT	4027119-4027150	32	NZ_CP049252	Rhizobium rhizoryzae strain DSM 29514 plasmid unnamed5, complete sequence	5757-5788	9	0.719
CP034074_2	2.1\|4027119\|32\|CP034074\|CRISPRCasFinder,CRT	4027119-4027150	32	HQ110084	Erwinia phage ENT90, complete genome	27362-27393	9	0.719
CP034074_2	2.6\|4027424\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027424-4027455	32	NZ_KX426231	Acinetobacter lwoffii strain EK30A plasmid pALWEK1.5, complete sequence	856-887	9	0.719
CP034074_2	2.6\|4027424\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027424-4027455	32	NZ_CP053911	Hymenobacter sp. BRD128 plasmid unnamed3, complete sequence	49870-49901	9	0.719
CP034074_2	2.8\|4027546\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027546-4027577	32	NC_012520	Rhodococcus opacus B4 plasmid pROB01, complete sequence	394514-394545	9	0.719
CP034074_2	2.8\|4027546\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027546-4027577	32	AP014335	Uncultured Mediterranean phage uvMED isolate uvMED-GF-U-MedDCM-OCT-S36-C6, * SEQUENCING IN PROGRESS *	23647-23678	9	0.719
CP034074_2	2.8\|4027546\|32\|CP034074\|CRISPRCasFinder,CRT,PILER-CR	4027546-4027577	32	LR214966	Mycoplasma fermentans strain NCTC10117 genome assembly, plasmid: 12	35654-35685	10	0.688

1. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP034699 (Salmonella enterica subsp. enterica serovar Karamoja strain RSE40 plasmid pRSE40, complete sequence) position: , mismatch: 0, identity: 1.0

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagcgagcgcaaa	Protospacer
********************************

2. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP034710 (Salmonella enterica subsp. enterica serovar Karamoja strain RSE21 plasmid pRSE21, complete sequence) position: , mismatch: 0, identity: 1.0

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagcgagcgcaaa	Protospacer
********************************

3. spacer 2.8|4027546|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to KT630649 (Salmonella phage SEN34, complete genome) position: , mismatch: 0, identity: 1.0

ttttctgcatacatagtcgcattatttgtaat	CRISPR spacer
ttttctgcatacatagtcgcattatttgtaat	Protospacer
********************************

4. spacer 2.9|4027607|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to KT630649 (Salmonella phage SEN34, complete genome) position: , mismatch: 0, identity: 1.0

tgcatcgcccgtggtgctgcgggtgtttctcc	CRISPR spacer
tgcatcgcccgtggtgctgcgggtgtttctcc	Protospacer
********************************

5. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to AGRM01000007 (Salmonella enterica subsp. houtenae str. ATCC BAA-1581 plasmid pSEHO0A2, complete sequence, whole genome shotgun sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

6. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP029990 (Salmonella enterica subsp. diarizonae serovar 48:i:z strain SA20121591 plasmid pSA20121591.1, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

7. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP030197 (Salmonella enterica strain SA20051401 plasmid pSA20051401.1, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

8. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP030218 (Salmonella enterica strain SA20075157 plasmid pSA20075157.1, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

9. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP030177 (Salmonella enterica subsp. enterica serovar Milwaukee str. SA19950795 plasmid pIncFII.2, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

10. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP025255 (Salmonella enterica subsp. enterica serovar Newport str. CDC 2010K-2159 plasmid pSNE1-2010K-2159, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

11. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to CP053415 (Salmonella enterica strain 2011K-0868 plasmid unnamed, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

12. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to CP053327 (Salmonella enterica subsp. salamae serovar 58:c:z6 strain 2013K-0366 plasmid unnamed, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

13. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP030289 (Salmonella enterica subsp. enterica serovar Gaminara str. SA20063285 plasmid pIncI1.1, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

14. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP033339 (Salmonella enterica subsp. enterica serovar Anatum strain CFSAN076215 plasmid pCFSAN076215, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

15. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP024167 (Salmonella enterica subsp. enterica serovar Gaminara strain CFSAN070644 plasmid pCFSAN024441_02, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagggcgta	Protospacer
*********************** ** **. *

16. spacer 2.2|4027180|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP022118 (Salmonella enterica subsp. enterica serovar Macclesfield str. S-1643 plasmid unnamed1, complete sequence) position: , mismatch: 4, identity: 0.875

gcgtagaagctgttgacgtcagcgagcgcaaa	CRISPR spacer
gcgtagaagctgttgacgtcagccagaacgaa	Protospacer
*********************** ** .*.**

17. spacer 2.1|4027119|32|CP034074|CRISPRCasFinder,CRT matches to MH588547 (Caulobacter phage CcrSC, complete genome) position: , mismatch: 7, identity: 0.781

gaccacagtaacttcagcagcctgaccggcag	CRISPR spacer
gcaggcagcatcttcagcagcctgaccggcgg	Protospacer
*   .***.* *******************.*

18. spacer 2.1|4027119|32|CP034074|CRISPRCasFinder,CRT matches to NC_048047 (Caulobacter phage CcrBL9, complete genome) position: , mismatch: 7, identity: 0.781

gaccacagtaacttcagcagcctgaccggcag	CRISPR spacer
gcgggcagcatcttcagcagcctgaccggcgg	Protospacer
*   .***.* *******************.*

19. spacer 2.3|4027241|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP034366 (Pantoea sp. CCBC3-3-1 plasmid unnamed3, complete sequence) position: , mismatch: 7, identity: 0.781

gtattatagcgggtaattgaggagaaaatcat	CRISPR spacer
gaacaaaagcgggcaattgaggagcaaatcaa	Protospacer
* *. * ******.********** ******

20. spacer 2.1|4027119|32|CP034074|CRISPRCasFinder,CRT matches to NZ_CP049252 (Rhizobium rhizoryzae strain DSM 29514 plasmid unnamed5, complete sequence) position: , mismatch: 9, identity: 0.719

gaccacagtaacttcagcagcctgaccggcag	CRISPR spacer
accttcgagaacttcagcatcctgaccgacag	Protospacer
. *. *.. ********** ********.***

21. spacer 2.1|4027119|32|CP034074|CRISPRCasFinder,CRT matches to HQ110084 (Erwinia phage ENT90, complete genome) position: , mismatch: 9, identity: 0.719

gaccacagtaacttcagcagcctgaccggcag	CRISPR spacer
aaaggaataaacttccgcagcctgaccgacag	Protospacer
.*  . *  ****** ************.***

22. spacer 2.6|4027424|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_KX426231 (Acinetobacter lwoffii strain EK30A plasmid pALWEK1.5, complete sequence) position: , mismatch: 9, identity: 0.719

accaatacccagaacaatacctatcaacgcgc	CRISPR spacer
cacaatacccagaacaatatctttcaattttg	Protospacer
  *****************.** ****. .

23. spacer 2.6|4027424|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP053911 (Hymenobacter sp. BRD128 plasmid unnamed3, complete sequence) position: , mismatch: 9, identity: 0.719

accaatacccagaacaatacctatcaacgcgc	CRISPR spacer
tccaatccccagaacattacctatggcaaccc	Protospacer
 ***** ********* ******* .  .* *

24. spacer 2.8|4027546|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to NC_012520 (Rhodococcus opacus B4 plasmid pROB01, complete sequence) position: , mismatch: 9, identity: 0.719

ttttctgcatacatagtcgcattatttgtaat	CRISPR spacer
atatgcagatacatagtcgcatagtttgtaaa	Protospacer
 * * .. ************** .*******

25. spacer 2.8|4027546|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to AP014335 (Uncultured Mediterranean phage uvMED isolate uvMED-GF-U-MedDCM-OCT-S36-C6, *** SEQUENCING IN PROGRESS ***) position: , mismatch: 9, identity: 0.719

ttttctgcatacatagtcgcattatttgtaat	CRISPR spacer
atcgatacatttatagtcgcattatttgtacc	Protospacer
 *.  *.*** .****************** .

26. spacer 2.8|4027546|32|CP034074|CRISPRCasFinder,CRT,PILER-CR matches to LR214966 (Mycoplasma fermentans strain NCTC10117 genome assembly, plasmid: 12) position: , mismatch: 10, identity: 0.688

ttttctgcatacatagtcgcattatttgtaat	CRISPR spacer
aaaattgcatacattgtcacattatttgactt	Protospacer
    .********* ***.*********   *

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

2737833 : 2826039

100

Escherichia_phage(70.77%)

terminase,tail,protease,lysis,holin,plate,integrase,transposase

attL 2769044:2769059|attR 2829771:2829786

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
QAY24400.1\|2737833_2738715_-\|protease	protease HtpX	NA	NA	NA	NA
QAY24401.1\|2738907_2740956_-	carboxy terminal-processing peptidase	A0A0R6PIZ1	Moraxella_phage	1.2e-87	33.7
QAY24402.1\|2740975_2741662_-	RNA chaperone ProQ	NA	NA	NA	NA
QAY24403.1\|2741759_2742257_-	GAF domain-containing protein	NA	NA	NA	NA
QAY24404.1\|2742385_2743669_+	paraquat-inducible protein A	NA	NA	NA	NA
QAY24405.1\|2743631_2746271_+	PqiB family protein	NA	NA	NA	NA
QAY24406.1\|2746348_2747788_+	16S rRNA (cytosine(1407)-C(5))-methyltransferase RsmF	NA	NA	NA	NA
QAY24407.1\|2747902_2748142_+	DUF1480 family protein	NA	NA	NA	NA
QAY24408.1\|2748252_2748444_+	DUF1482 family protein	NA	NA	NA	NA
QAY24409.1\|2748471_2749122_-	protein-serine/threonine phosphatase	A0A222YWF0	Escherichia_phage	1.4e-58	50.9
QAY24410.1\|2749792_2750515_-	type III secretion system guanine nucleotide exchange factor SopE2	NA	NA	NA	NA
QAY24411.1\|2751205_2751601_+	DUF1398 domain-containing protein	C6ZCX4	Enterobacteria_phage	7.8e-15	30.4
QAY24412.1\|2751926_2752427_+	hypothetical protein	NA	NA	NA	NA
QAY24413.1\|2752543_2753542_+	hypothetical protein	NA	NA	NA	NA
QAY26336.1\|2753689_2754412_-	chemotaxis protein	NA	NA	NA	NA
QAY24414.1\|2755415_2756030_+	long polar fimbrial protein LpfA	NA	NA	NA	NA
QAY24415.1\|2756218_2758702_+	fimbrial outer membrane usher protein StdB	NA	NA	NA	NA
QAY24416.1\|2758762_2759515_+	fimbrial chaperone protein StdC	NA	NA	NA	NA
QAY24417.1\|2760012_2760690_+	hypothetical protein	NA	NA	NA	NA
QAY24418.1\|2760816_2761326_+	CaiF/GrlA family transcriptional regulator	NA	NA	NA	NA
QAY26337.1\|2761312_2762119_+	transcriptional regulator	NA	NA	NA	NA
QAY26338.1\|2763486_2764299_+	cytolethal distending toxin subunit B family protein	A5LH53	Enterobacteria_phage	2.3e-61	47.6
QAY24419.1\|2764456_2764834_+	DUF1353 domain-containing protein	I1TQ41	Pseudomonas_phage	7.4e-15	38.2
QAY24420.1\|2765011_2765554_-	hypothetical protein	A0A0U2S643	Escherichia_phage	6.8e-70	65.4
QAY24421.1\|2765750_2766482_-	pertussis-like toxin subunit ArtA	A0A0U2KD26	Escherichia_phage	2.3e-60	52.0
QAY24422.1\|2766478_2766931_-	subtilase cytotoxin subunit B	NA	NA	NA	NA
QAY24423.1\|2767048_2767468_-	subtilase cytotoxin subunit B	NA	NA	NA	NA
QAY26339.1\|2768330_2768405_-	hypothetical protein	NA	NA	NA	NA
QAY24424.1\|2768546_2768903_-	lysozyme	M9P0E5	Enterobacteria_phage	9.1e-31	61.5
QAY26340.1\|2768883_2769090_-\|lysis	lysis protein	H9C183	Pectobacterium_phage	3.1e-07	46.4
2769044:2769059	attL	NA	NA	NA	NA
QAY24425.1\|2769240_2769480_+	hypothetical protein	NA	NA	NA	NA
QAY24426.1\|2769591_2770041_+	hypothetical protein	NA	NA	NA	NA
QAY24427.1\|2770500_2770965_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA
QAY26341.1\|2772023_2772587_-	DUF4376 domain-containing protein	A0A0U2QQK4	Escherichia_phage	1.8e-73	71.1
QAY24428.1\|2775540_2776086_-\|tail	tail fiber assembly protein	Q8W612	Enterobacteria_phage	2.4e-75	75.8
QAY24429.1\|2776088_2777642_-\|tail	phage tail protein	A0A0U2SAV1	Escherichia_phage	1.3e-227	79.0
QAY24430.1\|2777638_2778265_-	hypothetical protein	A0A0U2RK03	Escherichia_phage	4.4e-121	99.5
QAY24431.1\|2778248_2779475_-	hypothetical protein	A0A0U2RJZ0	Escherichia_phage	1.7e-225	98.8
QAY24432.1\|2779515_2780676_-	type I restriction endonuclease subunit R	A0A1S5SAB0	Streptococcus_phage	2.2e-33	30.3
QAY24433.1\|2780825_2781173_-	hypothetical protein	A0A0U2I1S2	Escherichia_phage	2.2e-61	97.4
QAY24434.1\|2781455_2782169_-\|plate	phage baseplate protein	A0A0U2JTX5	Escherichia_phage	4.1e-123	94.5
QAY24435.1\|2782168_2783176_-	hypothetical protein	A0A0U2QL72	Escherichia_phage	1.2e-181	91.0
QAY24436.1\|2783175_2783442_-	hypothetical protein	A0A0U2JGJ3	Escherichia_phage	2.8e-45	98.9
QAY24437.1\|2783438_2784107_-	hypothetical protein	A0A0U2JGI7	Escherichia_phage	4.0e-120	97.3
QAY24438.1\|2784110_2786186_-	lytic transglycosylase domain-containing protein	A0A0U2QV45	Escherichia_phage	1.9e-128	43.2
QAY24439.1\|2786250_2786868_-	hypothetical protein	A0A0U2S634	Escherichia_phage	3.6e-83	75.5
QAY26342.1\|2786864_2787296_-	hypothetical protein	A0A0U2S616	Escherichia_phage	3.3e-75	100.0
QAY24440.1\|2787319_2788657_-	hypothetical protein	A0A0U2KD19	Escherichia_phage	4.4e-243	96.2
QAY24441.1\|2788656_2789601_-	hypothetical protein	A0A0U2SH76	Escherichia_phage	1.3e-172	99.7
QAY24442.1\|2789587_2790028_-	hypothetical protein	A0A0U2RTA8	Escherichia_phage	2.2e-82	98.6
QAY24443.1\|2790024_2790465_-	hypothetical protein	A0A0U2S646	Escherichia_phage	4.0e-76	97.9
QAY24444.1\|2790464_2790935_-	hypothetical protein	A0A0U2SAX6	Escherichia_phage	2.5e-84	100.0
QAY24445.1\|2790992_2792021_-	hypothetical protein	A0A0U2QQI2	Escherichia_phage	1.9e-190	99.7
QAY24446.1\|2792035_2792653_-	hypothetical protein	A0A0U2S600	Escherichia_phage	1.0e-117	99.5
QAY24447.1\|2792645_2793968_-	DUF2213 domain-containing protein	A0A0U2QW61	Escherichia_phage	7.2e-190	95.9
QAY26343.1\|2793948_2794668_-	hypothetical protein	A0A0U2I1R8	Escherichia_phage	9.5e-136	98.7
QAY24448.1\|2794726_2796163_-	DUF1073 domain-containing protein	A0A0U2S5X9	Escherichia_phage	4.2e-268	97.3
QAY24449.1\|2796182_2797511_-\|terminase	terminase	A0A0U2JTW9	Escherichia_phage	2.4e-262	98.6
QAY24450.1\|2797500_2798580_-\|terminase	terminase small subunit	A0A0U2RXW9	Escherichia_phage	1.8e-146	92.2
QAY24451.1\|2798583_2798793_-	hypothetical protein	NA	NA	NA	NA
QAY24452.1\|2798770_2799703_-	hypothetical protein	A0A1B1INP7	uncultured_Mediterranean_phage	1.6e-82	54.9
QAY24453.1\|2799695_2800487_-	transcriptional regulator	R4TG31	Halovirus	1.3e-48	40.7
QAY24454.1\|2800891_2801074_-	hypothetical protein	NA	NA	NA	NA
QAY24455.1\|2801088_2801466_-	M15 family peptidase	Q9MBZ3	Enterobacteria_phage	1.3e-64	98.4
QAY24456.1\|2801468_2801744_-\|holin	phage holin family protein	Q9MBZ4	Enterobacteria_phage	3.6e-43	95.6
QAY24457.1\|2801733_2802126_-\|holin	holin	Q9MBZ5	Enterobacteria_phage	1.7e-46	83.8
QAY24458.1\|2803557_2804271_-	hypothetical protein	NA	NA	NA	NA
QAY24459.1\|2804724_2805267_-	DUF1133 family protein	A0A0U2S606	Escherichia_phage	4.9e-76	76.8
QAY24460.1\|2805263_2805554_-	DUF1364 domain-containing protein	A0A0U2KD41	Escherichia_phage	7.4e-47	88.5
QAY24461.1\|2805553_2806153_-	DUF1367 family protein	A0A0U2RT94	Escherichia_phage	3.8e-106	92.0
QAY24462.1\|2806606_2806819_-	type I toxin-antitoxin system Hok family toxin	A0A0U2QV81	Escherichia_phage	8.1e-27	92.9
QAY24463.1\|2807052_2807568_-	hypothetical protein	A0A076GCN9	Escherichia_phage	3.2e-37	77.6
QAY24464.1\|2807733_2807916_-	hypothetical protein	A0A2R2Z308	Escherichia_phage	2.0e-26	96.7
QAY26346.1\|2808006_2808408_-	hypothetical protein	A0A2R2Z307	Escherichia_phage	2.8e-52	91.2
QAY24465.1\|2808420_2808843_-	DUF977 family protein	A0A0U2QQN3	Escherichia_phage	9.7e-64	90.6
QAY26344.1\|2808858_2809620_-	DUF1627 domain-containing protein	A0A0U2SAW4	Escherichia_phage	2.1e-117	89.7
QAY24466.1\|2809652_2810195_-	replication protein	A0A0U2JGJ0	Escherichia_phage	3.4e-85	98.7
QAY26345.1\|2810106_2811021_-	hypothetical protein	A0A0U2RT81	Escherichia_phage	1.5e-101	92.1
QAY24467.1\|2811530_2811944_-	hypothetical protein	NA	NA	NA	NA
QAY24468.1\|2811963_2812386_-	hypothetical protein	A0A0U2RXZ9	Escherichia_phage	6.5e-68	93.6
QAY24469.1\|2812369_2812645_-	helix-turn-helix domain-containing protein	A0A0U2S629	Escherichia_phage	3.4e-41	100.0
QAY24470.1\|2812752_2813214_+	helix-turn-helix domain-containing protein	A0A0U2QW76	Escherichia_phage	3.4e-78	100.0
QAY24471.1\|2813464_2813599_+	hypothetical protein	NA	NA	NA	NA
QAY24472.1\|2813609_2813762_+	DUF1391 domain-containing protein	M4QQ57	Salicola_phage	3.5e-08	55.3
QAY24473.1\|2814184_2814457_+	hypothetical protein	NA	NA	NA	NA
QAY24474.1\|2814475_2814685_+	host cell division inhibitory peptide Kil	NA	NA	NA	NA
QAY24475.1\|2814605_2814842_+	DUF1482 family protein	NA	NA	NA	NA
QAY24476.1\|2814771_2814972_+	hypothetical protein	A0A0U2SHB5	Escherichia_phage	3.7e-21	86.8
QAY24477.1\|2815046_2815322_+	hypothetical protein	A0A0U2QW85	Escherichia_phage	1.5e-44	98.9
QAY24478.1\|2815421_2818568_+	exodeoxyribonuclease VIII	A0A0U2I1R6	Escherichia_phage	0.0e+00	98.4
QAY24479.1\|2819194_2819992_-	AAA family ATPase	U5N3V8	Enterobacteria_phage	1.9e-145	99.6
QAY24480.1\|2819991_2821164_-\|transposase	IS21-like element IS21 family transposase	U5N3F9	Enterobacteria_phage	8.3e-230	99.7
QAY24481.1\|2821869_2822064_+	type I toxin-antitoxin system endodeoxyribonuclease toxin RalR	A0A0U2QQP4	Escherichia_phage	9.0e-33	100.0
QAY24482.1\|2822056_2822245_+	DUF1187 family protein	A0A0U2QL97	Escherichia_phage	2.7e-26	96.8
QAY24483.1\|2822351_2822633_+	excisionase	A0A2H4J5E1	uncultured_Caudovirales_phage	1.7e-11	41.2
QAY24484.1\|2822598_2823675_+\|integrase	integrase	A0A2H4IYC8	uncultured_Caudovirales_phage	4.1e-98	51.7
QAY24485.1\|2824053_2824404_-	DUF2511 domain-containing protein	NA	NA	NA	NA
QAY24486.1\|2824420_2825296_-	copper resistance D family protein	NA	NA	NA	NA
QAY24487.1\|2825296_2825671_-	CopC domain-containing protein YobA	NA	NA	NA	NA
QAY24488.1\|2825808_2826039_+	DNA polymerase III subunit theta	H9C187	Pectobacterium_phage	2.9e-14	60.3
2829771:2829786	attR	NA	NA	NA	NA

DBSCAN-SWA_2

3171635 : 3181454

Enterobacteria_phage(28.57%)

protease,transposase

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
QAY24773.1\|3171635_3172433_-	AAA family ATPase	U5N3V8	Enterobacteria_phage	1.9e-145	99.6
QAY24774.1\|3172432_3173605_-\|transposase	IS21-like element IS21 family transposase	U5N3F9	Enterobacteria_phage	8.3e-230	99.7
QAY24775.1\|3173982_3174660_+	hydrolase	NA	NA	NA	NA
QAY24776.1\|3175081_3177358_-\|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	A0A223W0B1	Agrobacterium_phage	1.4e-164	42.1
QAY24777.1\|3177388_3177709_-\|protease	ATP-dependent Clp protease adapter ClpS	A0A1B1IT64	uncultured_Mediterranean_phage	3.5e-13	45.7
QAY24778.1\|3178032_3178254_+	cold shock-like protein CspD	A0A2H4N7Y6	Lake_Baikal_phage	9.3e-18	64.2
QAY24779.1\|3178392_3180339_-	macrolide ABC transporter ATP-binding protein/permease MacB	G9BWD6	Planktothrix_phage	2.9e-38	40.8
QAY24780.1\|3180335_3181454_-	macrolide transporter subunit MacA	A0A140XAI1	Dickeya_phage	1.1e-08	38.9

Anti-CRISPR protein detection

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