CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
NC_009053	Actinobacillus pleuropneumoniae serovar 5b str. L20, complete sequence	1 crisprs	cas3-cas2,cas1,cas6f,cas7f,cas5f,cas8f,csa3,DEDDh,DinG,PD-DExK,cas3	0	13	3	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_009053_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_009053_1

235633-237163

TypeI-F

I-F

Consensus_repeat	Method
TTTCTAAGCTGCCTATACGGCAGTGAAG	CRISPRCasFinder
TTTCTAAGCTGCCTATACGGCAGTGAAG	CRT
TTTCTAAGCTGCCTATACGGCAGTGAAG	PILER-CR

25 spacers

cas1,cas3-cas2,cas6f,cas7f,cas5f,cas8f

The CRISPR arrays of NC_009053_1

>merge|NC_009053|1|235633-237163|CRISPRCasFinder,CRT,PILER-CR
ATTTGTGGCTGCCTATACGGCAGTGAAGGCAGTCAGTCATCAGCTTGGACTTTTACTAGATTTCTAAGCTGCCTATACGGCAGTGAAGTTTTCCCCCACCAACCGAGTGTTTTCAACATTTTTCTAAGCTGCCTATACGGCAGTGAAGGGTATCAATAGAGTATTGAATCTTGTTCGGGCTTTCTAAGCTGCCTATACGGCAGTGAAGCTTTACACAAGGTATCTTCCGCTCCTTTAAATTTTCTAAGCTGCCTATACGGCAGTGAAGAGCGTAATCAGGTTGAGTCTTTACAACAATTTTTTCTAAGCTGCCTATACGGCAGTGAAGGGAGCAGTTAGAAATTTATCGTCGGGGCGAATTTTCTAAGCTGCCTATACGGCAGTGAAGATTTGATAAAATCGCTTTTAATACGTGCTTGTTTTTCTAAGCTGCCTATACGGCAGTGAAGTTATTTCTTTAAGAATCATTTTATCAGCATAATTTCTAAGTTGCCTATACGGCAGTGAAGAAGCGGTTCGCTTACGTCATGGGATTTTACACTTTCTAAGCTGCCTATACGGCAGTGAAGAAGAGTAGAATACGCCGCACTTGCGGCATAGATTTCTAAGCTGCCTATACGGCAGTGAAGGAAAAAATAATGTCATACCCTCGAAACCCAAATTTCTAAGCTGCCTATACGGCAGTGAAGAAAAATTCCACATTCCGTGTGAGCTTTCTGCTTTTCTAAGCTGCCTATACGGCAGTGAAGATCGGAAGATTCAACATCAGACTATTTTAAATATTTCTAAGCCTGCCTATACGGCAGTGAAGCTTGATTTCTGCAATGTGGATTGCACCCGCTATTTCTAAGCTGCCTATACGGCAGTGAAGGAAACCGGTGAAGTTAAAGATAAGCACAATTTTTTCTAAGCTGCCTATACGGCAGTGAAGCTGTAACTGTTGCTTGTTGGTAGGTTTTTTCATTTCTAAGCTGCCTATACGGCAGTGAAGATTTAATCGTTAAAGCACGCCAAGAACTACTTTTTCTAAGCTGCCTATACGGCAGTGAAGATTTTGGCTTAGTTGTAGCTGGCTCACTTGGATTTCTAAGCTGCCTATACGGCAGTGAAGTACCTTTGGCTTTTCCGCTTGCTTTTTCAGGATTTCTAAGCTGCCTATACGGCAGTGAAGACGAAAAACGAGCATTGATTACAGTTGTAACTTTTCTAAGCTGCCTATACGGCAGTGAAGACTAAACAGCTTTTAAATTCAATTCGCTACAATTTCTAAGCTGCCTATACGGCAGTGAAGCCATTGACTGGTAACTTTTATCAATTTCATCATTTCTAAGCTGCCTATACGGCAGTGAAGTTTTGATAAATTTCTCGCCAATCACAAAATGATTTCTAAGCTGCCTATACGGCAGTGAAGTTCAGGTTTTTATTGGTGAGGCTCGTTATCGCTTTCTAAGCTGCCTATACGGCAGTGAAGCGTTCTCAGCGCACTCAAATCACGCAAGACGATTTCTAAGCTGCCTATACGGCAGTGAAG

>NC_009053|1|1|235633-237163|CRISPRCasFinder
ATTTGTGGCTGCCTATACGGCAGTGAAG	GCAGTCAGTCATCAGCTTGGACTTTTACTAGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTTTCCCCCACCAACCGAGTGTTTTCAACATT
TTTCTAAGCTGCCTATACGGCAGTGAAG	GGTATCAATAGAGTATTGAATCTTGTTCGGGC
TTTCTAAGCTGCCTATACGGCAGTGAAG	CTTTACACAAGGTATCTTCCGCTCCTTTAAAT
TTTCTAAGCTGCCTATACGGCAGTGAAG	AGCGTAATCAGGTTGAGTCTTTACAACAATTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	GGAGCAGTTAGAAATTTATCGTCGGGGCGAAT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATTTGATAAAATCGCTTTTAATACGTGCTTGTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTATTTCTTTAAGAATCATTTTATCAGCATAA
TTTCTAAGTTGCCTATACGGCAGTGAAG	AAGCGGTTCGCTTACGTCATGGGATTTTACAC
TTTCTAAGCTGCCTATACGGCAGTGAAG	AAGAGTAGAATACGCCGCACTTGCGGCATAGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	GAAAAAATAATGTCATACCCTCGAAACCCAAA
TTTCTAAGCTGCCTATACGGCAGTGAAG	AAAAATTCCACATTCCGTGTGAGCTTTCTGCT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATCGGAAGATTCAACATCAGACTATTTTAAATAT
TTCTAAGCCTGCCTATACGGCAGTGAAG	CTTGATTTCTGCAATGTGGATTGCACCCGCTA
TTTCTAAGCTGCCTATACGGCAGTGAAG	GAAACCGGTGAAGTTAAAGATAAGCACAATTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	CTGTAACTGTTGCTTGTTGGTAGGTTTTTTCA
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATTTAATCGTTAAAGCACGCCAAGAACTACTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATTTTGGCTTAGTTGTAGCTGGCTCACTTGGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	TACCTTTGGCTTTTCCGCTTGCTTTTTCAGGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	ACGAAAAACGAGCATTGATTACAGTTGTAACT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ACTAAACAGCTTTTAAATTCAATTCGCTACAA
TTTCTAAGCTGCCTATACGGCAGTGAAG	CCATTGACTGGTAACTTTTATCAATTTCATCA
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTTTGATAAATTTCTCGCCAATCACAAAATGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTCAGGTTTTTATTGGTGAGGCTCGTTATCGC
TTTCTAAGCTGCCTATACGGCAGTGAAG	CGTTCTCAGCGCACTCAAATCACGCAAGACGA
TTTCTAAGCTGCCTATACGGCAGTGAAG

>NC_009053|1|1|235633-237163|CRT
ATTTGTGGCTGCCTATACGGCAGTGAAG	GCAGTCAGTCATCAGCTTGGACTTTTACTAGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTTTCCCCCACCAACCGAGTGTTTTCAACATT
TTTCTAAGCTGCCTATACGGCAGTGAAG	GGTATCAATAGAGTATTGAATCTTGTTCGGGC
TTTCTAAGCTGCCTATACGGCAGTGAAG	CTTTACACAAGGTATCTTCCGCTCCTTTAAAT
TTTCTAAGCTGCCTATACGGCAGTGAAG	AGCGTAATCAGGTTGAGTCTTTACAACAATTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	GGAGCAGTTAGAAATTTATCGTCGGGGCGAAT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATTTGATAAAATCGCTTTTAATACGTGCTTGTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTATTTCTTTAAGAATCATTTTATCAGCATAA
TTTCTAAGTTGCCTATACGGCAGTGAAG	AAGCGGTTCGCTTACGTCATGGGATTTTACAC
TTTCTAAGCTGCCTATACGGCAGTGAAG	AAGAGTAGAATACGCCGCACTTGCGGCATAGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	GAAAAAATAATGTCATACCCTCGAAACCCAAA
TTTCTAAGCTGCCTATACGGCAGTGAAG	AAAAATTCCACATTCCGTGTGAGCTTTCTGCT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATCGGAAGATTCAACATCAGACTATTTTAAATAT
TTCTAAGCCTGCCTATACGGCAGTGAAG	CTTGATTTCTGCAATGTGGATTGCACCCGCTA
TTTCTAAGCTGCCTATACGGCAGTGAAG	GAAACCGGTGAAGTTAAAGATAAGCACAATTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	CTGTAACTGTTGCTTGTTGGTAGGTTTTTTCA
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATTTAATCGTTAAAGCACGCCAAGAACTACTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATTTTGGCTTAGTTGTAGCTGGCTCACTTGGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	TACCTTTGGCTTTTCCGCTTGCTTTTTCAGGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	ACGAAAAACGAGCATTGATTACAGTTGTAACT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ACTAAACAGCTTTTAAATTCAATTCGCTACAA
TTTCTAAGCTGCCTATACGGCAGTGAAG	CCATTGACTGGTAACTTTTATCAATTTCATCA
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTTTGATAAATTTCTCGCCAATCACAAAATGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTCAGGTTTTTATTGGTGAGGCTCGTTATCGC
TTTCTAAGCTGCCTATACGGCAGTGAAG	CGTTCTCAGCGCACTCAAATCACGCAAGACGA
TTTCTAAGCTGCCTATACGGCAGTGAAG

>NC_009053|1|1|235693-237163|PILER-CR
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTTTCCCCCACCAACCGAGTGTTTTCAACATT
TTTCTAAGCTGCCTATACGGCAGTGAAG	GGTATCAATAGAGTATTGAATCTTGTTCGGGC
TTTCTAAGCTGCCTATACGGCAGTGAAG	CTTTACACAAGGTATCTTCCGCTCCTTTAAAT
TTTCTAAGCTGCCTATACGGCAGTGAAG	AGCGTAATCAGGTTGAGTCTTTACAACAATTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	GGAGCAGTTAGAAATTTATCGTCGGGGCGAAT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATTTGATAAAATCGCTTTTAATACGTGCTTGTT
TTTCTAAGCTGCCTATACGGCAGTGAAG	TTATTTCTTTAAGAATCATTTTATCAGCATAA
TTTCTAAGTTGCCTATACGGCAGTGAAG	AAGCGGTTCGCTTACGTCATGGGATTTTACAC
TTTCTAAGCTGCCTATACGGCAGTGAAG	AAGAGTAGAATACGCCGCACTTGCGGCATAGA
TTTCTAAGCTGCCTATACGGCAGTGAAG	GAAAAAATAATGTCATACCCTCGAAACCCAAA
TTTCTAAGCTGCCTATACGGCAGTGAAG	AAAAATTCCACATTCCGTGTGAGCTTTCTGCT
TTTCTAAGCTGCCTATACGGCAGTGAAG	ATCGGAAGATTCAACATCAGACTATTTTAAATATTTCTAAGC
CTGCCTATACGGCAGTGAAGCTTGATTT	CTGCAATGTGGATTGCACCCGCTATTTCTAAG
CTGCCTATACGGCAGTGAAGGAAACCGG	TGAAGTTAAAGATAAGCACAATTTTTTCTAAG
CTGCCTATACGGCAGTGAAGCTGTAACT	GTTGCTTGTTGGTAGGTTTTTTCATTTCTAAG
CTGCCTATACGGCAGTGAAGATTTAATC	GTTAAAGCACGCCAAGAACTACTTTTTCTAAG
CTGCCTATACGGCAGTGAAGATTTTGGC	TTAGTTGTAGCTGGCTCACTTGGATTTCTAAG
CTGCCTATACGGCAGTGAAGTACCTTTG	GCTTTTCCGCTTGCTTTTTCAGGATTTCTAAG
CTGCCTATACGGCAGTGAAGACGAAAAA	CGAGCATTGATTACAGTTGTAACTTTTCTAAG
CTGCCTATACGGCAGTGAAGACTAAACA	GCTTTTAAATTCAATTCGCTACAATTTCTAAG
CTGCCTATACGGCAGTGAAGCCATTGAC	TGGTAACTTTTATCAATTTCATCATTTCTAAG
CTGCCTATACGGCAGTGAAGTTTTGATA	AATTTCTCGCCAATCACAAAATGATTTCTAAG
CTGCCTATACGGCAGTGAAGTTCAGGTT	TTTATTGGTGAGGCTCGTTATCGCTTTCTAAG
CTGCCTATACGGCAGTGAAGCGTTCTCA	GCGCACTCAAATCACGCAAGACGATTTCTAAG
CTGCCTATACGGCAGTGAAG

Protein	Signature genes	Signature genes Name	Protein_function
NC_009053.1\|WP_009875014.1\|231295_234643_-\|type-I-F-CRISPR-associated-helicase-Cas3	cas3-cas2	cas3-cas2-CAS-I-F	gnl\|CDD\|274201
NC_009053.1\|WP_011848335.1\|228821_230087_-\|serine-hydroxymethyltransferase	unknown	unknown	gnl\|CDD\|234571
NC_009053.1\|WP_009875013.1\|237304_237874_-\|type-I-F-CRISPR-associated-endoribonuclease-Cas6/Csy4	cas6f	cd09674_cas6f_CAS-I-F	gnl\|CDD\|187870
NC_009053.1\|WP_005595987.1\|223488_224526_-\|rRNA-methyltransferase	unknown	unknown	gnl\|CDD\|236779
NC_009053.1\|WP_011848337.1\|244341_244689_+\|DUF4810-domain-containing-protein	unknown	unknown	gnl\|CDD\|379760
NC_009053.1\|WP_005596036.1\|244700_245360_+\|DUF799-domain-containing-protein	unknown	unknown	gnl\|CDD\|368539
NC_009053.1\|WP_005595989.1\|224691_225504_+\|inositol-1-monophosphatase	unknown	unknown	gnl\|CDD\|236753
NC_009053.1\|WP_005595991.1\|225624_227478_+\|1-deoxy-D-xylulose-5-phosphate-synthase	unknown	unknown	gnl\|CDD\|235470
NC_009053.1\|WP_005595985.1\|222803_223430_+\|LysE-family-transporter	unknown	unknown	gnl\|CDD\|236665
NC_009053.1\|WP_009875008.1\|241584_243516_+\|threonine--tRNA-ligase	unknown	unknown	gnl\|CDD\|234752
NC_009053.1\|WP_011848336.1\|238873_239833_-\|type-I-F-CRISPR-associated-protein-Csy2	cas5f	pfam09614_cas5f_CAS-I-F	gnl\|CDD\|378221
NC_009053.1\|WP_080512802.1\|245574_246117_+\|translation-initiation-factor-IF-3	unknown	unknown	gnl\|CDD\|234582
NC_009053.1\|WP_005600274.1\|234639_235596_-\|type-I-F-CRISPR-associated-endonuclease-Cas1	cas1	cd09718_cas1_CAS-I-F	gnl\|CDD\|187849
NC_009053.1\|WP_005603453.1\|230317_231205_-\|NAD(+)-kinase	unknown	unknown	gnl\|CDD\|167337
NC_009053.1\|WP_009875009.1\|239829_241179_-\|type-I-F-CRISPR-associated-protein-Csy1	cas8f	cd09675_cas8f_CAS-I-F	gnl\|CDD\|378220
NC_009053.1\|WP_005596065.1\|246365_246563_+\|50S-ribosomal-protein-L35	unknown	unknown	gnl\|CDD\|234676
NC_009053.1\|WP_005596031.1\|243657_244332_+\|CsgG/HfaB-family-protein	unknown	unknown	gnl\|CDD\|224379
NC_009053.1\|WP_005618774.1\|221343_222309_+\|thiamine-phosphate-kinase	unknown	unknown	gnl\|CDD\|235583
NC_009053.1\|WP_005595983.1\|222321_222795_+\|phosphatidylglycerophosphatase-A	unknown	unknown	gnl\|CDD\|368021
NC_009053.1\|WP_009875012.1\|237876_238872_-\|type-I-F-CRISPR-associated-protein-Csy3	cas7f	cd09677_cas7f_CAS-I-F	gnl\|CDD\|378222

Protein	Function_ID	Function_description	E-value
NC_009053.1\|WP_009875014.1\|231295_234643_-\|type-I-F-CRISPR-associated-helicase-Cas3	gnl\|CDD\|274201	TIGR02562, conserved_hypothetical_protein, CRISPR-associated helicase Cas3, subtype I-F/YPEST. The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.	0
NC_009053.1\|WP_011848335.1\|228821_230087_-\|serine-hydroxymethyltransferase	gnl\|CDD\|234571	PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.	0
NC_009053.1\|WP_009875013.1\|237304_237874_-\|type-I-F-CRISPR-associated-endoribonuclease-Cas6/Csy4	gnl\|CDD\|187870	cd09739, Cas6_I-F, CRISPR/Cas system-associated RAMP superfamily protein Cas6f. 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; Cas6f is an endoribonuclease that generates crRNA; This family is specific for CRISPR/Cas system I-F subtype; Possesses RRM fold; also known as Csy4 family.	2.03956e-64
NC_009053.1\|WP_005595987.1\|223488_224526_-\|rRNA-methyltransferase	gnl\|CDD\|236779	PRK10864, PRK10864, putative methyltransferase; Provisional.	7.56548e-77
NC_009053.1\|WP_011848337.1\|244341_244689_+\|DUF4810-domain-containing-protein	gnl\|CDD\|379760	pfam16068, DUF4810, Domain of unknown function (DUF4810). This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 134 amino acids in length. There is a conserved PES sequence motif. It is a putative lipoprotein.	8.48828e-33
NC_009053.1\|WP_005596036.1\|244700_245360_+\|DUF799-domain-containing-protein	gnl\|CDD\|368539	pfam05643, DUF799, Putative bacterial lipoprotein (DUF799). This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.	7.57253e-102
NC_009053.1\|WP_005595989.1\|224691_225504_+\|inositol-1-monophosphatase	gnl\|CDD\|236753	PRK10757, PRK10757, inositol-1-monophosphatase.	6.75423e-148
NC_009053.1\|WP_005595991.1\|225624_227478_+\|1-deoxy-D-xylulose-5-phosphate-synthase	gnl\|CDD\|235470	PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional.	0
NC_009053.1\|WP_005595985.1\|222803_223430_+\|LysE-family-transporter	gnl\|CDD\|236665	PRK10229, PRK10229, threonine efflux system; Provisional.	3.35261e-35
NC_009053.1\|WP_009875008.1\|241584_243516_+\|threonine--tRNA-ligase	gnl\|CDD\|234752	PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.	0
NC_009053.1\|WP_011848336.1\|238873_239833_-\|type-I-F-CRISPR-associated-protein-Csy2	gnl\|CDD\|378221	pfam09614, Cas_Csy2, CRISPR-associated protein (Cas_Csy2). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2464 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy2, for CRISPR/Cas Subtype Ypest protein 2.	6.09019e-137
NC_009053.1\|WP_080512802.1\|245574_246117_+\|translation-initiation-factor-IF-3	gnl\|CDD\|234582	PRK00028, infC, translation initiation factor IF-3; Reviewed.	6.14173e-94
NC_009053.1\|WP_005600274.1\|234639_235596_-\|type-I-F-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|187849	cd09718, Cas1_I-F, CRISPR/Cas system-associated protein Cas1. 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; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain.	1.82275e-179
NC_009053.1\|WP_005603453.1\|230317_231205_-\|NAD(+)-kinase	gnl\|CDD\|167337	PRK02231, ppnK, NAD(+) kinase.	0
NC_009053.1\|WP_009875009.1\|239829_241179_-\|type-I-F-CRISPR-associated-protein-Csy1	gnl\|CDD\|378220	pfam09611, Cas_Csy1, CRISPR-associated protein (Cas_Csy1). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy1, for CRISPR/Cas Subtype Ypest protein 1.	1.59888e-156
NC_009053.1\|WP_005596065.1\|246365_246563_+\|50S-ribosomal-protein-L35	gnl\|CDD\|234676	PRK00172, rpmI, 50S ribosomal protein L35; Reviewed.	3.48394e-21
NC_009053.1\|WP_005596031.1\|243657_244332_+\|CsgG/HfaB-family-protein	gnl\|CDD\|224379	COG1462, CsgG, Uncharacterized protein involved in formation of curli polymers [Cell envelope biogenesis, outer membrane].	2.87652e-67
NC_009053.1\|WP_005618774.1\|221343_222309_+\|thiamine-phosphate-kinase	gnl\|CDD\|235583	PRK05731, PRK05731, thiamine monophosphate kinase; Provisional.	6.12482e-142
NC_009053.1\|WP_005595983.1\|222321_222795_+\|phosphatidylglycerophosphatase-A	gnl\|CDD\|368021	pfam04608, PgpA, Phosphatidylglycerophosphatase A. This family represents a family of bacterial phosphatidylglycerophosphatases (EC:3.1.3.27), known as PgpA. It appears that bacteria possess several phosphatidylglycerophosphatases, and thus, PgpA is not essential in Escherichia coli.	2.26301e-51
NC_009053.1\|WP_009875012.1\|237876_238872_-\|type-I-F-CRISPR-associated-protein-Csy3	gnl\|CDD\|378222	pfam09615, Cas_Csy3, CRISPR-associated protein (Cas_Csy3). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2463 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy3, for CRISPR/Cas Subtype Ypest protein 3.	0

>NC_009053.1|WP_005600274.1|234639_235596_-|type-I-F-CRISPR-associated-endonuclease-Cas1
MKKTPYIPSSDLKTILHSKRANIYYLEHCRILLNGGRVEYVTDKGNESLYWNIPIANTICLLLGSGTSITQAAMRELSKAGVMVGFCSGGGTPLFNGTEAEIGCDFFSPQSEYRPVEYLQQWCRFWFDDNKRLNSAKTLQLARLQLLLRTWNKFDWEYAQDKLTALVQHYQEEFTNVKDSQSLLAAEGRLTAKLYALANQATLNDESFKRESGKEGANQFLDHGNYLAYGLGATACWVLGLPHGLAILHGKTRRGGLVFDAADIIKDAIILPQAFISAQNGDNEKQFRQACINNLIRFEALDIIINTLKQLASEGANI
>NC_009053.1|WP_009875014.1|231295_234643_-|type-I-F-CRISPR-associated-helicase-Cas3
MNILLISQCNKNALTETRRILDQFAERCGDRCWQTAITQAGLETLHNMLRQTARKNTAVACYWTHGKNLTELLWIVGDKSQFNAEGRVPTNRTQRNILRADDENGWLSAYSIQILTAIAALLHDIGKANIAFQQKLKPKAKFFPDCYRHEWISTRLFEAMISGCDTDEQWLARLANWQNYIEENPDWLPNLTLIADKSDHPHNFSHFPPLAKVVLWLILSHHKLPFTQKTLDCHSDQERILSEHFMLKTAVEPFYRFLAPVEHWVMNQSEHPQPENFWQFKTLVMESKAWQKAMQRWANKALNHAPLRELSQLNKTINDPFLLILSRLCLIVGDHNYSSAPADRLLGDLNFFEKLIANTDKKTKQPKQALDEHLLGVCKTSAKFARLLPKLAKELPHIQQHRPFTKRTNLDRFKWQNRAFELARSLQSESEQAGFFGVNMASTGCGKTLANAKIMYGLSNQDGARFTIALGLRVLTLQTGLALRQKLMLSSEQLAVLVGGSATKQLFELQNESVQSGSESAQEWFEDNEVYGMNFLESGIAEEEFGTLLADNKAKKLLYAPIVSCTLDHMIQATETIRGGKHIVPLLRLLTSDLVLDEPDDFSQSDLPALSRLVHLAGMFGSKVLLSSATLTPDLISGLFNAYQAGRKIYNRHQGINPELPICCAWIDEYKQQQQKCAAVKEFERYHALFTASRAEKLMQSPIRHKAEIIQLPPFSAVENQDINYTMLADSLIEQAITLHQRYAQQDPISKKFVSVGLIRFANIKPMIPLVETLFKTPLNTQFSDYKIHLCCYHSRQLLLLRSKLEEKLDRILNRHEPEALFSQPEIMSALTQDKAVHHIFIVLGSPVTEVGRDHDYDWAIVDPSSMRSIIQLAGRVWRHRPEKIATQANILLLPTNWRGLQTKNNGSEPIFCRPGFEDQSNKLTSHKTVGLIKQEHLASITAIPRIIKPLGLQAETNLADLEHKVIGDLLNNKGINRVNAYWQDNLTNRLNANLPLITPFRKNEGKWQTEVVCLPSEESHWEFMFKSSEKAWEDPYFENDYLAEISYQKLNCESPWITPWLTTPLNQALSELCEQLDEADQTQAALRFATVSLQHYGKTLPIWKFNETLGFWQP
>NC_009053.1|WP_005603453.1|230317_231205_-|NAD(+)-kinase
MKPEERFFECIAIVGKPRHEIALETHLAVYNWLKDRHYRVLVEKSIAQQLNLPEARSLEEIGQQANLVIVIGGDGNMLGMARRLAEYQVPLIGINRGNLGFLTDIAPHSTFEQLHNCIERGEFVIEERFLLEARIERNGKIIATNNALNEVVIHPTQVARIIEFEVYIDGKFAFSQRSDGLIISTPTGSTAYSLSAGGPILTPNMNAIALVPMHPHTLSSRPLVIDGDSQISLRFAQYNQPSLEVSCDGQYDLPFTPEDRIIVEKSPNKLRLLHLKDYNYFTVLGSKLGWSSKLF
>NC_009053.1|WP_011848335.1|228821_230087_-|serine-hydroxymethyltransferase
MFTANMNIQDYDPILWQAIENENRRQEEHIELIASENYASPRVMQAQGSQFTNKYAEGYPGKRYYGGCEYADIVEQLAIDRAKQLFGADYVNVQPHSGSQANAAVYGALIQPNDTILGMDLAHGGHLTHGAKVSFSGKIYNSVLYGITAEGLIDYEDVRQKALECKPKMIVAGFSAYSQIVDWAKMREIADEVGAYLFVDMAHVAGLIAAGVYPSPLPYAHVVTTTTHKTLGGPRGGLILSACGDEEIYKKLQSSVFPANQGGPLVHIIAAKAVCFKEALEPEYKIYQQNVVKNAKAMVEVFKQRSYEVISNGTENHLFLVSFVKQGLTGKAADAALGQANITVNKNSVPNDPQKPFITSGIRIGTPAVTRRGFKEADVQALAGWMCDVLDSIGKDNHEQVIAETKAKVLDICARLPVYAK
>NC_009053.1|WP_005595991.1|225624_227478_+|1-deoxy-D-xylulose-5-phosphate-synthase
MQNKYPLLSQINSPEDLRLLAKEQLQSVADELRAYLLESVSQTSGHLASGLGVVELTVALHYVYQTPFDQLIWDVGHQAYPHKILTGRRDQMHTIRQKNGIHPFPWREESLYDVLSVGHSSTSISAGVGIAVAAEKENAGRKTVCVIGDGAITAGMAFEAMNHAGALHTDMLVILNDNEMSISENVGALNNHLARIFSGSIYTTVRDGSKKVLDKVPTIKNFMKKSEEHMKGVISPESTLFEELGFNYIGPIDGHNIDELVKTLSNMRELKGPQFLHIRTKKGKGYEPAENDPIGYHGVPKFDPTCGQLPKSKTIPTYSDIFGNWLCEMAEQDSKLIGITPAMREGSGMVEFSKRFPEQYFDVAIAEQHAVTFGAGLAIAGYKPVVAIYSSFLQRAYDQLIHDVAIQNLPVIFAIDRAGIVGADGQTHQGAFDVSFMRCIPNMTIMCPSDENEMRQMLYTAYRMNTPTAVRYPRGNAQGVALAPMQALEVGKGKLIQQGQKVAILNFGPLLNEARIVAEKHNYTLADMRFVKPLDEQLVAELADSHELLVTLEENAIQGGAGSAVNEYLQKIGKIRPLVMLGIPDFFVPQATQAESYADLGLDAAGIEQRIQAVVNQ
>NC_009053.1|WP_005595989.1|224691_225504_+|inositol-1-monophosphatase
MNPMLNIAIRAARKAGNIIAKGYEQAASEIEVAQKGTNDYVTAIDKAAEAAIIEVIRKSYPDHAIVGEESGILAGENENVQWVIDPLDGTTNFVKRLPHFAVSIAVRENGRTTVGVVYDPIRNELFTAVRGEGAKLNEFRLRVETERRDLNGTVLATGFPFKAAKHRPAHLNMLEGLMNNGVADFRRTGSAALDLAYVAANRVDGYFEIGLKPWDCAAGDLIVREAGAIVTNFVGGTDYLKSGNVVAGQARVVKEILNAIQPTLTEDLKN
>NC_009053.1|WP_005595987.1|223488_224526_-|rRNA-methyltransferase
MKPKFNENKPRFQTVEERRDNKFQTKSNRFEDKPRFDKPKFGGDKACFDRKDHQEAREAIYPTIGKKAAGEGNVQISVKGGNNTMKEKKTGPLSPRAPEKIKKNRAEEMKVYGENACIALFKQRPDAIVRLWATVEGAKKLGDMLSYLAEHKKAYHVVDRAEMERVTGTEHHGDVCLLVKKAVPFSLEGYLQVPRKRDCLVLLDAVNNAQNVGGIIRTCAFYGVNGVIVESADTLNSSAAARVAEGGLEFVRPLETKNKQIALTQLRNAGYQVVHLTRNKQAAPLAKTKLAAKTVFVLSEIPAQDIEYPEDTTVQLSFENPLNSGLNVAVSTGILLNQWYQANII
>NC_009053.1|WP_005595985.1|222803_223430_+|LysE-family-transporter
MLTILLVHLAGLASPGPDFFYVVRQSASHSTKAGILAAIGISLGIIFWASFAIFGLAWLSNTIGTVFQFLIMVIGGIYLSYIGSLMVRVTKNATFTNEPTNLRVLDNVTEIKKGLLINIFNAKAGVYFTSVVSAFLAQFTQTSDLFLLLFLFVFSTLIYFILVALLFSRRPIQEFYTKYSRYIDNVAGVIFILFGMILIFDGIKGLIS
>NC_009053.1|WP_005595983.1|222321_222795_+|phosphatidylglycerophosphatase-A
MKNFNLKNPIHLFACGFGSGLLKPAPGTWGSLAGVLIAVLLWNLTESSLFFIGLTLVSFIAGCHICEKTSRDLNVHDDGRIVWDEIVAIFLMFAFLPEYNGLAYTLTFICFRFFDVLKPYPIRYFDEKLETGLGIMFDDILAAIYALIALHFIYWLI
>NC_009053.1|WP_005618774.1|221343_222309_+|thiamine-phosphate-kinase
MMEFEVIAQYFKRKNLRSDVDLSVGDDCAVTTLKPNERLAVTTDTLVSGTHFLPSISAADLAYKTLAVNLSDLAAMGAAPAWVSLALTLPKVDHQWLAEFSQSLFAVLDRYHVDLIGGDTTGGPLSLTLTAQGILPQDQGLFRHQAQVGDWIFVSGSLGDSAAGLSILLDNCKISDESDRYLVQRHLRPTPRVELGLALRAFSCCAIDISDGLLADLGHILERSQVGAEIELDNIPLSTHLTTKYSEKEALHFALTGGEDYELCFTVSDDKRSEMERILRSQGIKVSCIGRITPAASGLILRQNGKQVPLPTQSGFDHFKS
>NC_009053.1|WP_009875013.1|237304_237874_-|type-I-F-CRISPR-associated-endoribonuclease-Cas6/Csy4
MSELTHYIELKAIPQVDILQTDVIAHGLQILHKFLPLYQGQIGLSFPAYGLGRTLGGIIRVFGNEQHCTQIKTQLIGEGLQDYVLITSVTPVPEEIVEYHRYQRVHRKGQSAIRRTEKFLTQQGKWTEDVRKEMLIHQQNQKTFPHVKLKSSSTKQHFVLAIRQFRLAEPASGLFNAYGLSQVATVPHF
>NC_009053.1|WP_009875012.1|237876_238872_-|type-I-F-CRISPR-associated-protein-Csy3
MTKLTTASVLAFERKLDISDATFTQKNSTSSEPEIAVTIREKSVRGTISNRLKNALANDPAKLDAEIEKANLQRVDVATLNDDYDTLVARFTCKVLPFEGKPNVCNDPEYQAKLLSTIQNYLTAHGMSELAKRYATNLANARWLWRNRISAETIQVSIKVADDVIVFENAKQLPLNSFEQADEKLQKIASYIEKGLKGEEFIILEVEAQAKMGRGQEVYPSQELVLDTGTRKSKILYEINHKAGMHSQKIGNAIRTIDTWYAENAPFPIAAEPYGAVTNLGTAFRQPKEKIDFYTLFDNWVLKDVAPELEQQHYVISVLIRGGVFGASGKE
>NC_009053.1|WP_011848336.1|238873_239833_-|type-I-F-CRISPR-associated-protein-Csy2
MNYPNFYLLFDHVEIQAANTISSPITYGFPSLTGFTGAIHALSRKLFPQQVELGGVMIACHDYQILGYKNSDFSDLTFNQTRNPLKKNGDSPSIIEEGKIHLDISLVVEMEVKDPELYYALNSQDSEQKTQFLEHCKKLLMQQRIAGGSVFQIENVELFNLSDTKEIKLALMPAFVLMDAKQTLADITQSLQSGISNNEITIYPATPNANALDALLEVATLHHIPLSEHATSQEWETFNVNQGKGWLVPIPVGYQAISPLFTAGEMQNCRVTEYPSQYVETVYSLGKWVFPFSLPDDLSQCFWHYNTPQDNLYLITQGA
>NC_009053.1|WP_009875009.1|239829_241179_-|type-I-F-CRISPR-associated-protein-Csy1
MITPLQIRAKIIDFLQAQHLKKSENDYKKLEKATEPEEIAKIKAEISKSEEKYRLDTWLHIAATEMAQQLKFGTHIAKGIHPDAKGNNINFRANLNLPATLVGSQLIDKLVLDANGNAAALPLAAFFDIMVDEVNKRTLKDLLLTDEPCLDGCFSDDLSLSAQYKIAFQMALKGNLNSPETHERNKQVLWVNSSSAIEDNHYTCLIPLYPSSFTHAIYNKLNQARFSEENKQARENRYKNKAQNPYISIPHLAVTKLGGTKPQNVSLLTSKQGGRNYLLPSLPPIFSKGELRLTNAQNTIFNDRLAYVCRAGLYQLYQAVADSRKNYIVRVPRAEAVNLIVQMVLQQAYKLQKRTAGWSRDYQLAWCEKYWLDPQRAKLNGEEQFHSALTQQDWISEVEQRFAAWLNALLKKRFPKHQDDFTATEYNEWRKYFRKKLHRQLRCLYKEVL
>NC_009053.1|WP_009875008.1|241584_243516_+|threonine--tRNA-ligase
MPIITLPDGSQRQFDNPVSVMEVAQSIGAGLAKATIAGRVNGERRDACDIISEDSSLEIITAKDEDGLEIIRHSCAHLLGHAIKQLFPNVKMAIGPTIDNGFYYDVDLDRSLTQEDLDAIEKRMLELAKTNYDVVKKRVSWQEARDTFEKRGEPYKMAILDENIERTATPALYHHEEYIDMCRGPHVPNMRFCHHFKLQKVAGAYWRGDSKNKMLQRIYGTAWADKKQLAEYLTRLEEAAKRDHRRIGKALDLYHMQEEAPGLVFWHNDGWTIFRELETFVRTKLKEYDYQEVKGPFMMDRVLWERTGHWQNYADLMFTTQSENREYAIKPMNCPGHVQIFNQGLKSYRDLPIRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTEDQIESEVTSCIRMVYDIYSTFGFSNIQVKLSTRPENRIGDDAMWDRAEDGLAKALTANGLSYEIQEGEGAFYGPKIEFALRDCLDREWQCGTIQLDFALPGRLDASYVAEDNGRRTPVMIHRAILGSIERFIGIITEEYAGFFPTWLAPTQAVVMNITDSQADYVQKVTKALSDAGIRVKSDLRNEKVGFKVREHTLRRVPYMLVCGDKEIEAGKVSVRTRKGADLGTFTIDEFVEILKNQVKARGLKLLGEE
>NC_009053.1|WP_005596031.1|243657_244332_+|CsgG/HfaB-family-protein
MKKLLMTTLCVTALGLAGCATEGSRAIAPTVTQAASTATNYHGVKSAISVGKFDNKSSFQNGVFSDGQDQLGNQSKTILVSHLQQTGRFSVLDRTNMSEAAAEAKIKGQKQNLKGATYVITGDVTEFGRKTVGDHQLFGILGRGKEQVAYAKVTLNVVNVNTSEVVYSVQGAGEYNLSNREVLGFGGTAGYDSTLNGKVLDLAIREAVNNLVNGIEAGHWTPAK
>NC_009053.1|WP_011848337.1|244341_244689_+|DUF4810-domain-containing-protein
MKKINIIMFALITVVLSACSSRSVDTNTYYWGNYSDLIYSYYNEPGDFTKQENGFNEIIKMAKDAQKPVAPGVYGHLGLVLLKQGKTAEAQNAFLQEQQLFPESKTFMQYLQRKK
>NC_009053.1|WP_005596036.1|244700_245360_+|DUF799-domain-containing-protein
MKKLLILLSGILFLSGCAQQQKPSYDYSALKESKPKSILVLLPVNNSVDVKADTSVLARVTYPLAELGYYVYPVALVDEVFKQNGLTDGNAIRSANIKKIYDIFGADSILYLNVDKYGTSYKVFDSVTEVELEGKLIDLKTGKTLWDGTGRFAEGSTHSNDGALVALVKAAVSQVVDTTKDKGYEVSASAMSSLVHVGKNGGLLVGPRHSLYGKEDVKK
>NC_009053.1|WP_080512802.1|245574_246117_+|translation-initiation-factor-IF-3
MKPVKRVQTNRAHRLNDEIRGVKEVRLTDENGEQVGIVSIQDALARAEDAELDLVEISPNAEPPVCRIMNYGKFIYEKEKAAKEQKKKQKVVQMKEIKFRPGTDEGDYQIKLRSILRFLEDGDKVKITVRFRGREMAHQDIGLDVLDRVKTDTAEVAVVESAPGKLEGRQAVMVIAPKKK
>NC_009053.1|WP_005596065.1|246365_246563_+|50S-ribosomal-protein-L35
MPKIKTVRGAAKRFKKTASGGFKRKQSHLRHILTKKTTKRKRHLRHKSMVAKADQVLVVACLPYA

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_009053_1	1.10\|236202\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236202-236233	32	NC_007206	Haemophilus influenzae biotype aegyptius plasmid pF1947, complete sequence	848-879	2	0.938
NC_009053_1	1.10\|236202\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236202-236233	32	NC_007206	Haemophilus influenzae biotype aegyptius plasmid pF1947, complete sequence	6966-6997	2	0.938
NC_009053_1	1.7\|236021\|33\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236021-236053	33	MK721190	Enterococcus phage vB_EfaS_Ef6.4, complete genome	20805-20837	8	0.758
NC_009053_1	1.7\|236021\|33\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236021-236053	33	JX193904	Enterococcus phage EfaCPT1, complete genome	19650-19682	8	0.758
NC_009053_1	1.8\|236082\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236082-236113	32	NC_014389	Butyrivibrio proteoclasticus B316 plasmid pCY360, complete sequence	247497-247528	8	0.75
NC_009053_1	1.8\|236082\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236082-236113	32	NZ_CP010126	Escherichia coli strain C8 plasmid A, complete genome	56628-56659	8	0.75
NC_009053_1	1.12\|236322\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236322-236353	32	NZ_CP049297	Bacillus megaterium strain S188 plasmid pS188, complete sequence	59532-59563	8	0.75
NC_009053_1	1.16\|236564\|32\|NC_009053\|CRISPRCasFinder,CRT	236564-236595	32	NZ_CP015332	Borrelia hermsii HS1 isolate Browne Mountain plasmid lpT28, complete sequence	26709-26740	8	0.75
NC_009053_1	1.19\|236744\|32\|NC_009053\|CRISPRCasFinder,CRT	236744-236775	32	MN694207	Marine virus AFVG_250M554, complete genome	18-49	8	0.75
NC_009053_1	1.19\|236744\|32\|NC_009053\|CRISPRCasFinder,CRT	236744-236775	32	MN694207	Marine virus AFVG_250M554, complete genome	38569-38600	8	0.75
NC_009053_1	1.19\|236744\|32\|NC_009053\|CRISPRCasFinder,CRT	236744-236775	32	MN693727	Marine virus AFVG_250M555, complete genome	39009-39040	8	0.75
NC_009053_1	1.29\|236572\|32\|NC_009053\|PILER-CR	236572-236603	32	NZ_CP015332	Borrelia hermsii HS1 isolate Browne Mountain plasmid lpT28, complete sequence	26709-26740	8	0.75
NC_009053_1	1.32\|236752\|32\|NC_009053\|PILER-CR	236752-236783	32	MN694207	Marine virus AFVG_250M554, complete genome	18-49	8	0.75
NC_009053_1	1.32\|236752\|32\|NC_009053\|PILER-CR	236752-236783	32	MN694207	Marine virus AFVG_250M554, complete genome	38569-38600	8	0.75
NC_009053_1	1.32\|236752\|32\|NC_009053\|PILER-CR	236752-236783	32	MN693727	Marine virus AFVG_250M555, complete genome	39009-39040	8	0.75
NC_009053_1	1.8\|236082\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236082-236113	32	NZ_KX833210	Salmonella enterica subsp. enterica serovar Typhi strain Salmonella Typhi Ty031 plasmid pTy031_01 plasmid pTy031_01, complete sequence	27548-27579	9	0.719
NC_009053_1	1.8\|236082\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236082-236113	32	NZ_CP040996	Klebsiella pneumoniae strain FDAARGOS_775 plasmid unnamed4	7610-7641	9	0.719
NC_009053_1	1.8\|236082\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236082-236113	32	NZ_CP032206	Klebsiella pneumoniae strain AR_0109 plasmid unnamed1, complete sequence	14174-14205	9	0.719
NC_009053_1	1.8\|236082\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	236082-236113	32	MH341453	Listeria phage PSU-VKH-LP041, complete genome	45990-46021	9	0.719
NC_009053_1	1.15\|236504\|32\|NC_009053\|CRISPRCasFinder,CRT	236504-236535	32	NZ_CP024244	Escherichia coli O128:H27 strain 90-9281 plasmid unnamed, complete sequence	134250-134281	9	0.719
NC_009053_1	1.19\|236744\|32\|NC_009053\|CRISPRCasFinder,CRT	236744-236775	32	NZ_CP038615	Arsenophonus nasoniae strain FIN plasmid pArsFIN3, complete sequence	27023-27054	9	0.719
NC_009053_1	1.19\|236744\|32\|NC_009053\|CRISPRCasFinder,CRT	236744-236775	32	NZ_CP038616	Arsenophonus nasoniae strain FIN plasmid pArsFIN4, complete sequence	3677-3708	9	0.719
NC_009053_1	1.28\|236512\|32\|NC_009053\|PILER-CR	236512-236543	32	NZ_CP024244	Escherichia coli O128:H27 strain 90-9281 plasmid unnamed, complete sequence	134250-134281	9	0.719
NC_009053_1	1.32\|236752\|32\|NC_009053\|PILER-CR	236752-236783	32	NZ_CP038615	Arsenophonus nasoniae strain FIN plasmid pArsFIN3, complete sequence	27023-27054	9	0.719
NC_009053_1	1.32\|236752\|32\|NC_009053\|PILER-CR	236752-236783	32	NZ_CP038616	Arsenophonus nasoniae strain FIN plasmid pArsFIN4, complete sequence	3677-3708	9	0.719
NC_009053_1	1.2\|235721\|32\|NC_009053\|CRISPRCasFinder,CRT,PILER-CR	235721-235752	32	NZ_CP019039	Bacillus velezensis strain GH1-13 plasmid unnamed, complete sequence	3941-3972	10	0.688
NC_009053_1	1.20\|236804\|32\|NC_009053\|CRISPRCasFinder,CRT	236804-236835	32	NC_049935	Enterococcus phage vB_EfaP_Efmus4, complete genome	16508-16539	10	0.688
NC_009053_1	1.33\|236812\|32\|NC_009053\|PILER-CR	236812-236843	32	NC_049935	Enterococcus phage vB_EfaP_Efmus4, complete genome	16508-16539	10	0.688

1. spacer 1.10|236202|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NC_007206 (Haemophilus influenzae biotype aegyptius plasmid pF1947, complete sequence) position: , mismatch: 2, identity: 0.938

aagagtagaatacgccgcacttgcggcataga	CRISPR spacer
aaaagtagagtacgccgcacttgcggcataga	Protospacer
**.******.**********************

2. spacer 1.10|236202|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NC_007206 (Haemophilus influenzae biotype aegyptius plasmid pF1947, complete sequence) position: , mismatch: 2, identity: 0.938

aagagtagaatacgccgcacttgcggcataga	CRISPR spacer
aaaagtagagtacgccgcacttgcggcataga	Protospacer
**.******.**********************

3. spacer 1.7|236021|33|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to MK721190 (Enterococcus phage vB_EfaS_Ef6.4, complete genome) position: , mismatch: 8, identity: 0.758

atttgataaaatcgcttttaatacgtgcttgtt	CRISPR spacer
atttgatacaatcgcttttgatactttcatacc	Protospacer
******** **********.**** * * *...

4. spacer 1.7|236021|33|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to JX193904 (Enterococcus phage EfaCPT1, complete genome) position: , mismatch: 8, identity: 0.758

atttgataaaatcgcttttaatacgtgcttgtt	CRISPR spacer
atttgatacaatcgcttttgatactttcatacc	Protospacer
******** **********.**** * * *...

5. spacer 1.8|236082|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NC_014389 (Butyrivibrio proteoclasticus B316 plasmid pCY360, complete sequence) position: , mismatch: 8, identity: 0.75

ttatttctttaagaatcattttatcagcataa	CRISPR spacer
atattgctttaagactcattttatatacctca	Protospacer
 **** ******** *********  .* * *

6. spacer 1.8|236082|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP010126 (Escherichia coli strain C8 plasmid A, complete genome) position: , mismatch: 8, identity: 0.75

ttatttctttaagaatcattttatcagcataa-	CRISPR spacer
atatatctttaagagtcattttatta-tgtgat	Protospacer
 *** *********.*********.* ..*.*

7. spacer 1.12|236322|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP049297 (Bacillus megaterium strain S188 plasmid pS188, complete sequence) position: , mismatch: 8, identity: 0.75

aaaaattccacattccgtgtgagctttctgct	CRISPR spacer
tgtaattccacattcattgtgagctttatatt	Protospacer
 . ************  ********** *..*

8. spacer 1.16|236564|32|NC_009053|CRISPRCasFinder,CRT matches to NZ_CP015332 (Borrelia hermsii HS1 isolate Browne Mountain plasmid lpT28, complete sequence) position: , mismatch: 8, identity: 0.75

ctgtaactgttgcttgttggtaggttttttca	CRISPR spacer
cttgtgttggtgcttgttggtaggtttttttg	Protospacer
**   ..** ********************..

9. spacer 1.19|236744|32|NC_009053|CRISPRCasFinder,CRT matches to MN694207 (Marine virus AFVG_250M554, complete genome) position: , mismatch: 8, identity: 0.75

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
tacctctagcttttccgcttgcttctgctttt	Protospacer
*****.*.****************.* *

10. spacer 1.19|236744|32|NC_009053|CRISPRCasFinder,CRT matches to MN694207 (Marine virus AFVG_250M554, complete genome) position: , mismatch: 8, identity: 0.75

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
tacctctagcttttccgcttgcttctgctttt	Protospacer
*****.*.****************.* *

11. spacer 1.19|236744|32|NC_009053|CRISPRCasFinder,CRT matches to MN693727 (Marine virus AFVG_250M555, complete genome) position: , mismatch: 8, identity: 0.75

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
tacctctagcttttccgcttgcttctgctttt	Protospacer
*****.*.****************.* *

12. spacer 1.29|236572|32|NC_009053|PILER-CR matches to NZ_CP015332 (Borrelia hermsii HS1 isolate Browne Mountain plasmid lpT28, complete sequence) position: , mismatch: 8, identity: 0.75

ctgtaactgttgcttgttggtaggttttttca	CRISPR spacer
cttgtgttggtgcttgttggtaggtttttttg	Protospacer
**   ..** ********************..

13. spacer 1.32|236752|32|NC_009053|PILER-CR matches to MN694207 (Marine virus AFVG_250M554, complete genome) position: , mismatch: 8, identity: 0.75

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
tacctctagcttttccgcttgcttctgctttt	Protospacer
*****.*.****************.* *

14. spacer 1.32|236752|32|NC_009053|PILER-CR matches to MN694207 (Marine virus AFVG_250M554, complete genome) position: , mismatch: 8, identity: 0.75

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
tacctctagcttttccgcttgcttctgctttt	Protospacer
*****.*.****************.* *

15. spacer 1.32|236752|32|NC_009053|PILER-CR matches to MN693727 (Marine virus AFVG_250M555, complete genome) position: , mismatch: 8, identity: 0.75

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
tacctctagcttttccgcttgcttctgctttt	Protospacer
*****.*.****************.* *

16. spacer 1.8|236082|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NZ_KX833210 (Salmonella enterica subsp. enterica serovar Typhi strain Salmonella Typhi Ty031 plasmid pTy031_01 plasmid pTy031_01, complete sequence) position: , mismatch: 9, identity: 0.719

ttatttctttaagaatcattttatcagcataa	CRISPR spacer
tgacagctttaagcatcatgttatcagcaagt	Protospacer
* *.  ******* ***** ********* .

17. spacer 1.8|236082|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP040996 (Klebsiella pneumoniae strain FDAARGOS_775 plasmid unnamed4) position: , mismatch: 9, identity: 0.719

ttatttctttaagaatcattttatcagcataa	CRISPR spacer
tgacagctttaagcatcatgttatcagcaagc	Protospacer
* *.  ******* ***** ********* .

18. spacer 1.8|236082|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP032206 (Klebsiella pneumoniae strain AR_0109 plasmid unnamed1, complete sequence) position: , mismatch: 9, identity: 0.719

ttatttctttaagaatcattttatcagcataa	CRISPR spacer
tgacagctttaagcatcatgttatcagcaagc	Protospacer
* *.  ******* ***** ********* .

19. spacer 1.8|236082|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to MH341453 (Listeria phage PSU-VKH-LP041, complete genome) position: , mismatch: 9, identity: 0.719

ttatttctttaagaatcattttatcagcataa	CRISPR spacer
ctatttctttgataatcattttatttcctcca	Protospacer
.*********.* ***********.  * . *

20. spacer 1.15|236504|32|NC_009053|CRISPRCasFinder,CRT matches to NZ_CP024244 (Escherichia coli O128:H27 strain 90-9281 plasmid unnamed, complete sequence) position: , mismatch: 9, identity: 0.719

gaaaccggtgaagttaaagataagcacaattt	CRISPR spacer
cataccggtgaagttatcgataagcagataaa	Protospacer
 * *************  ******** *

21. spacer 1.19|236744|32|NC_009053|CRISPRCasFinder,CRT matches to NZ_CP038615 (Arsenophonus nasoniae strain FIN plasmid pArsFIN3, complete sequence) position: , mismatch: 9, identity: 0.719

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
aaaaatcggcttttccactttctttttcagtt	Protospacer
 *   *.*********.*** *********

22. spacer 1.19|236744|32|NC_009053|CRISPRCasFinder,CRT matches to NZ_CP038616 (Arsenophonus nasoniae strain FIN plasmid pArsFIN4, complete sequence) position: , mismatch: 9, identity: 0.719

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
aaaaatcggcttttccactttctttttcagtt	Protospacer
 *   *.*********.*** *********

23. spacer 1.28|236512|32|NC_009053|PILER-CR matches to NZ_CP024244 (Escherichia coli O128:H27 strain 90-9281 plasmid unnamed, complete sequence) position: , mismatch: 9, identity: 0.719

gaaaccggtgaagttaaagataagcacaattt	CRISPR spacer
cataccggtgaagttatcgataagcagataaa	Protospacer
 * *************  ******** *

24. spacer 1.32|236752|32|NC_009053|PILER-CR matches to NZ_CP038615 (Arsenophonus nasoniae strain FIN plasmid pArsFIN3, complete sequence) position: , mismatch: 9, identity: 0.719

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
aaaaatcggcttttccactttctttttcagtt	Protospacer
 *   *.*********.*** *********

25. spacer 1.32|236752|32|NC_009053|PILER-CR matches to NZ_CP038616 (Arsenophonus nasoniae strain FIN plasmid pArsFIN4, complete sequence) position: , mismatch: 9, identity: 0.719

tacctttggcttttccgcttgctttttcagga	CRISPR spacer
aaaaatcggcttttccactttctttttcagtt	Protospacer
 *   *.*********.*** *********

26. spacer 1.2|235721|32|NC_009053|CRISPRCasFinder,CRT,PILER-CR matches to NZ_CP019039 (Bacillus velezensis strain GH1-13 plasmid unnamed, complete sequence) position: , mismatch: 10, identity: 0.688

ttttcccccaccaaccgagtgttttcaacatt	CRISPR spacer
aataaaataaccaacccagttttttcaacatt	Protospacer
  *    . ******* *** ***********

27. spacer 1.20|236804|32|NC_009053|CRISPRCasFinder,CRT matches to NC_049935 (Enterococcus phage vB_EfaP_Efmus4, complete genome) position: , mismatch: 10, identity: 0.688

acgaaaaacgagcattgattacagttgtaact	CRISPR spacer
caagtaaacgagctttgatttcagttgtcgtt	Protospacer
  .. ******** ****** ******* ..*

28. spacer 1.33|236812|32|NC_009053|PILER-CR matches to NC_049935 (Enterococcus phage vB_EfaP_Efmus4, complete genome) position: , mismatch: 10, identity: 0.688

acgaaaaacgagcattgattacagttgtaact	CRISPR spacer
caagtaaacgagctttgatttcagttgtcgtt	Protospacer
  .. ******** ****** ******* ..*

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

435746 : 442382

Staphylococcus_phage(50.0%)

The bacterium proteins that are colored denote the protein is present at specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin' and 'tRNA')

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_005600488.1\|435746_436841_+	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	A0A1V0SE20	Indivirus	7.1e-50	33.9
WP_005596391.1\|436963_437611_+	riboflavin synthase	A0A2H4PQS5	Staphylococcus_phage	3.1e-45	43.7
WP_009875161.1\|437671_438877_+	bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	A0A2H4PQS2	Staphylococcus_phage	1.5e-96	46.7
WP_011848365.1\|438987_439449_+	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	1.3e-40	57.4
WP_009875159.1\|439537_440026_-	transcription elongation factor GreB	NA	NA	NA	NA
WP_011848366.1\|440035_440971_-	KpsF/GutQ family sugar-phosphate isomerase	A0A2P0VNK5	Tetraselmis_virus	2.7e-37	34.2
WP_042655142.1\|441098_442382_-	aminopeptidase PepB	Q6GYZ8	Mycoplasma_phage	1.1e-30	32.9

DBSCAN-SWA_2

557222 : 599389

Mannheimia_phage(44.44%)

protease,tail,integrase,portal,terminase

attL 550941:550956|attR 598953:598968

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
550941:550956	attL	NA	NA	NA	NA
WP_005620278.1\|557222_558263_-\|integrase	tyrosine-type recombinase/integrase	A0A0M3LQJ3	Mannheimia_phage	3.7e-173	85.3
WP_005607263.1\|558272_558500_-	DUF4224 domain-containing protein	NA	NA	NA	NA
WP_005607265.1\|558524_559046_-	hypothetical protein	NA	NA	NA	NA
WP_005620280.1\|559663_560173_-	MazG-like family protein	A0A0M3LTD8	Mannheimia_phage	2.6e-31	47.7
WP_011848388.1\|560156_560363_-	hypothetical protein	NA	NA	NA	NA
WP_011848389.1\|560397_561120_-	hypothetical protein	Q7Y5X4	Haemophilus_phage	2.8e-26	33.1
WP_011848390.1\|561318_562221_-	recombination-associated protein RdgC	A0A2I7RNT5	Vibrio_phage	2.2e-57	41.3
WP_043880787.1\|562305_562620_-	hypothetical protein	NA	NA	NA	NA
WP_043880760.1\|562642_562939_-	hypothetical protein	NA	NA	NA	NA
WP_043880761.1\|562928_563198_-	hypothetical protein	NA	NA	NA	NA
WP_043880762.1\|563207_563426_-	hypothetical protein	NA	NA	NA	NA
WP_043880763.1\|564076_564358_+	hypothetical protein	NA	NA	NA	NA
WP_043880764.1\|564768_565119_+	hypothetical protein	NA	NA	NA	NA
WP_011848391.1\|565374_566190_-	DNA adenine methylase	NA	NA	NA	NA
WP_011848392.1\|566234_567878_-	AAA family ATPase	NA	NA	NA	NA
WP_043880765.1\|567933_568590_-	helix-turn-helix domain-containing protein	A0A0M3LSL8	Mannheimia_phage	6.8e-40	42.0
WP_011848394.1\|568719_568908_+	Cro/Cl family transcriptional regulator	A5VW97	Enterobacteria_phage	2.9e-12	60.0
WP_011848395.1\|568966_569662_+	phage antirepressor KilAC domain-containing protein	A0A2I7RHG4	Vibrio_phage	2.5e-48	48.0
WP_080512805.1\|569658_570690_+	conserved phage C-terminal domain-containing protein	A0A0P0IKQ2	Acinetobacter_phage	3.7e-16	48.1
WP_011848397.1\|570692_571217_+	DNA methylase	A0A0M3LNW2	Mannheimia_phage	2.5e-29	41.8
WP_011848398.1\|571411_572434_+	DUF968 domain-containing protein	S5MW46	Escherichia_phage	4.8e-56	38.3
WP_011848399.1\|572505_572874_+	RusA family crossover junction endodeoxyribonuclease	A0A0M3LPZ2	Mannheimia_phage	2.2e-40	63.1
WP_011848400.1\|572866_573379_+	antitermination protein	A0A1P8DTF1	Proteus_phage	5.7e-10	32.7
WP_043880766.1\|573518_573758_+	hypothetical protein	NA	NA	NA	NA
WP_011848401.1\|573750_574293_+	lysozyme	A0A0M3LPQ1	Mannheimia_phage	1.7e-44	51.7
WP_011848402.1\|574384_574756_+	DUF2570 domain-containing protein	NA	NA	NA	NA
WP_043880767.1\|575227_575704_+	DUF1441 family protein	K7PJY2	Enterobacterial_phage	3.5e-38	54.3
WP_011848404.1\|575706_577824_+\|terminase	phage terminase large subunit family protein	K7PH52	Enterobacterial_phage	2.0e-274	66.8
WP_043877954.1\|577820_578045_+	hypothetical protein	NA	NA	NA	NA
WP_011848405.1\|578044_579565_+\|portal	phage portal protein	S5MW34	Escherichia_phage	2.4e-160	58.0
WP_043877971.1\|579530_581525_+\|protease	Clp protease ClpP	A0A1W6JT88	Pseudomonas_phage	7.5e-199	54.9
WP_005596673.1\|581598_581922_+	DUF2190 family protein	K7PJY3	Enterobacterial_phage	3.3e-11	41.7
WP_011848407.1\|581914_582217_+\|tail	phage tail protein	NA	NA	NA	NA
WP_005596676.1\|582219_582747_+\|tail	phage tail protein	Q8VNN3	Enterobacteria_phage	1.1e-08	30.6
WP_011848408.1\|582743_583157_+\|tail	phage tail protein	NA	NA	NA	NA
WP_011848409.1\|583156_583813_+	hypothetical protein	NA	NA	NA	NA
WP_011848410.1\|583871_584264_+	hypothetical protein	NA	NA	NA	NA
WP_011848411.1\|584287_584563_+	DUF4035 domain-containing protein	NA	NA	NA	NA
WP_012478371.1\|584634_584871_+	hypothetical protein	NA	NA	NA	NA
WP_011848412.1\|584928_588360_+	tape measure protein	A0A0E3JPV7	Enterobacteria_phage	4.8e-60	26.2
WP_011848413.1\|588611_588947_+\|tail	phage tail protein	NA	NA	NA	NA
WP_043880768.1\|589024_589261_+	hypothetical protein	NA	NA	NA	NA
WP_043880769.1\|589257_589500_+	hypothetical protein	NA	NA	NA	NA
WP_011848414.1\|589799_590663_+	phage antirepressor N-terminal domain-containing protein	Q0H8C7	Salmonella_phage	1.3e-62	45.8
WP_011848415.1\|590783_591521_+\|tail	phage minor tail protein L	A0A0M3LPR8	Mannheimia_phage	1.2e-69	53.3
WP_043880770.1\|591522_592296_+	C40 family peptidase	A0A0M3LQI5	Mannheimia_phage	2.4e-60	47.0
WP_011848417.1\|592319_592841_+\|tail	tail assembly protein	A0A0M3LQC4	Mannheimia_phage	5.4e-32	50.0
WP_043880771.1\|592829_593012_-	hypothetical protein	A0A0M3LSW7	Mannheimia_phage	3.5e-10	51.7
WP_011848418.1\|593158_598756_+	DUF1983 domain-containing protein	A0A0M3LQ61	Mannheimia_phage	4.4e-305	46.9
WP_011848419.1\|598814_599156_+	hypothetical protein	NA	NA	NA	NA
598953:598968	attR	NA	NA	NA	NA
WP_043880772.1\|599155_599389_+	hypothetical protein	A0A0M3LSI9	Mannheimia_phage	2.3e-27	71.6

DBSCAN-SWA_3

1285600 : 1294711

uncultured_Caudovirales_phage(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_005608326.1\|1285600_1286233_+	repressor LexA	A0A2H4JG58	uncultured_Caudovirales_phage	1.2e-09	48.5
WP_009875487.1\|1286292_1286973_+	DNA mismatch repair endonuclease MutH	NA	NA	NA	NA
WP_005597990.1\|1287058_1287790_+	TerC family protein	A0A0R6PEZ3	Moraxella_phage	3.6e-42	48.0
WP_011848533.1\|1287904_1288942_+	beta-N-acetylhexosaminidase	A0A1B1IVS3	uncultured_Mediterranean_phage	6.8e-18	42.9
WP_009875490.1\|1289022_1290198_+	23S rRNA (uracil(747)-C(5))-methyltransferase RlmC	A0A2P1ELP3	Moumouvirus	3.0e-14	32.1
WP_005597992.1\|1290404_1291715_+	phosphopyruvate hydratase	W6LP63	Streptococcus_phage	1.2e-131	59.4
WP_009875491.1\|1291790_1292420_+	NUDIX hydrolase	NA	NA	NA	NA
WP_005597994.1\|1292433_1292844_+	DUF2251 domain-containing protein	NA	NA	NA	NA
WP_005597995.1\|1292902_1294711_-	ATP-dependent DNA helicase RecQ	A0A1V0SBK0	Catovirus	2.1e-86	37.7

Anti-CRISPR protein detection

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