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
CP028491	Carboxydocella thermautotrophica strain 019 chromosome, complete genome	1 crisprs	cas5,cas8c,cas7,cas4,cas1,cas2,cas3,cas3HD,RT,DEDDh,csa3,DinG,cas14k,cas14i	0	5	6	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: CP028491_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

CP028491_1

66454-68282

TypeI

I-C

Consensus_repeat	Method
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	PILER-CR
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CRISPRCasFinder
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CRT

27 spacers

cas2,cas1,cas4,cas7,cas8c,cas5,cas3

The CRISPR arrays of CP028491_1

>merge|CP028491|1|66454-68282|PILER-CR,CRISPRCasFinder,CRT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAACACCCGGCAGCTGTTCTAACTAATATCCTGGAGGCGTCGCACCCCGCAGGGGTGCGTGGATTGAAACCCGTTTTCACTTTTATTATATTCGGTAATAACCGTCGCACCCCGCAGGGGTGCGTGGATTGAAACGCCAGCATGGAGATGAAGTGGGATGCCATCGTTGAGTCGCACCCCGCAGGGGTGCGTGGATTGAAACGCTGGTGCGAAGAAAACGGCATACCAATAGAGGGTCGCACCCCGCAGGGGTGCGTGGATTGAAACAGAATAACCTGCCCAGAAAACCGTAGCAGCGGGTAGTCGCACCCCGCAGGGGTGCGTGGATTGAAACTGAGCCTATTCCGGCAAAGGGCGAAAATACAGTATCGTCGCACCCCGCAGGGGTGCGTGGATTGAAACTTGAAGCTGGCTGGCACTGGAACTTGGGTATAGTGTCGCACCCCGCAGGGGTGCGTGGATTGAAACTCTCTCTGCCCAGCCGTCTGCCAGATCGGTCTGAGTCGCACCCCGCAGGGGTGCGTGGATTGAAACTGAGTTGAACGGAGGTGAATAAATGTCAACGTATCAGCAGGTCGCACCCCGCAGGGGTGCGTGGATTGAAACTATTATAATTGAATTCGGTGCCCACCCAGGCACCGGTCGCACCCCGCAGGGGTGCGTGGATTGAAACGGGTCCTAATCCGCATGGTGCGGGACGAAAAACTGTCGCACCCCGCAGGGGTGCGTGGATTGAAACAGCAAAATATGCAAAAGCCAGGATTGCCCTGGCTGTCGCACCCCGCAGGGGTGCGTGGATTGAAACTAAGGAGGGACAAGCCATGTTGGAGCAACCCGGGGGTCGCACCCCGCAGGGGTGCGTGGATTGAAACAGCCGGGTGATACCCTCTGGTCTATAGCCAGAAAGTCGCACCCCGCAGGGGTGCGTGGATTGAAACAGCACAAAGTCTGCCTTGACACCTTCTGGCAGGCGTCGCACCCCGCAGGGGTGCGTGGATTGAAACAATGCGCCAGATAGCAGCCTCCCCTACTCCGGCTTGTCGCACCCCGCAGGGGTGCGTGGATTGAAACAGGTAGCGCTTGAGGGCATCAATCTTGGCCTTATGTCGCACCCCGCAGGGGTGCGTGGATTGAAACATGGAGTGCTGATACAAAAGCCCCCAGCTCTAAGTCGCACCCCGCAGGGGTGCGTGGATTGAAACTTCGTATTTTTGCTGCATTTCCCGCTCCAATTTGTCGCACCCCGCAGGGGTGCGTGGATTGAAACATCGAGACGATAGCTATTTGTTTTACCATGCTTGGTCGCACCCCGCAGGGGTGCGTGGATTGAAACATCTTCATCATTATAACAAACGTCATTTGCAGATAGTCGCACCCCGCAGGGGTGCGTGGATTGAAACCCGTTTTTGCGGGAAATCCTGCAAGAAAAAGAAACAGTCGCACCCCGCAGGGGTGCGTGGATTGAAACAGGGCTACCGACAGGACAAGAGCTGTTTTCCCCATGTCGCACCCCGCAGGGGTGCGTGGATTGAAACCATATACTTAGGTGAAAGAGGAATTAATAAGCAGGTCGCACCCCGCAGGGGTGCGTGGATTGAAACATTTTCCTTTTCAAAGATATTATTGCCATTCTCTGTGTCGCACCCCGCAGGGGTGCGTGGATTGAAACTATGTAAAGCCTGCTCCCCAGCGGGACAACAGCGTCGCACCCCGCAGGGGTGCGTGGATTGAAACGAAATATTGGTTGGCAGGGTAAAAAATCTGGATGAGTCGCACCCCGCAGGGGTGCGTGGATTGAAAG

>CP028491|1|1|66454-68282|PILER-CR
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ACCCGGCAGCTGTTCTAACTAATATCCTGGAGGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CCGTTTTCACTTTTATTATATTCGGTAATAACC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GCCAGCATGGAGATGAAGTGGGATGCCATCGTTGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GCTGGTGCGAAGAAAACGGCATACCAATAGAGG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGAATAACCTGCCCAGAAAACCGTAGCAGCGGGTA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TGAGCCTATTCCGGCAAAGGGCGAAAATACAGTATC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TTGAAGCTGGCTGGCACTGGAACTTGGGTATAGT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TCTCTCTGCCCAGCCGTCTGCCAGATCGGTCTGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TGAGTTGAACGGAGGTGAATAAATGTCAACGTATCAGCAG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TATTATAATTGAATTCGGTGCCCACCCAGGCACCG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GGGTCCTAATCCGCATGGTGCGGGACGAAAAACT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCAAAATATGCAAAAGCCAGGATTGCCCTGGCT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TAAGGAGGGACAAGCCATGTTGGAGCAACCCGGGG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCCGGGTGATACCCTCTGGTCTATAGCCAGAAA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCACAAAGTCTGCCTTGACACCTTCTGGCAGGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AATGCGCCAGATAGCAGCCTCCCCTACTCCGGCTT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGGTAGCGCTTGAGGGCATCAATCTTGGCCTTAT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATGGAGTGCTGATACAAAAGCCCCCAGCTCTAA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TTCGTATTTTTGCTGCATTTCCCGCTCCAATTT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATCGAGACGATAGCTATTTGTTTTACCATGCTTG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATCTTCATCATTATAACAAACGTCATTTGCAGATA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CCGTTTTTGCGGGAAATCCTGCAAGAAAAAGAAACA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGGGCTACCGACAGGACAAGAGCTGTTTTCCCCAT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CATATACTTAGGTGAAAGAGGAATTAATAAGCAG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATTTTCCTTTTCAAAGATATTATTGCCATTCTCTGT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TATGTAAAGCCTGCTCCCCAGCGGGACAACAGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GAAATATTGGTTGGCAGGGTAAAAAATCTGGATGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAG

>CP028491|1|1|66454-68282|CRISPRCasFinder
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ACCCGGCAGCTGTTCTAACTAATATCCTGGAGGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CCGTTTTCACTTTTATTATATTCGGTAATAACC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GCCAGCATGGAGATGAAGTGGGATGCCATCGTTGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GCTGGTGCGAAGAAAACGGCATACCAATAGAGG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGAATAACCTGCCCAGAAAACCGTAGCAGCGGGTA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TGAGCCTATTCCGGCAAAGGGCGAAAATACAGTATC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TTGAAGCTGGCTGGCACTGGAACTTGGGTATAGT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TCTCTCTGCCCAGCCGTCTGCCAGATCGGTCTGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TGAGTTGAACGGAGGTGAATAAATGTCAACGTATCAGCAG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TATTATAATTGAATTCGGTGCCCACCCAGGCACCG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GGGTCCTAATCCGCATGGTGCGGGACGAAAAACT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCAAAATATGCAAAAGCCAGGATTGCCCTGGCT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TAAGGAGGGACAAGCCATGTTGGAGCAACCCGGGG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCCGGGTGATACCCTCTGGTCTATAGCCAGAAA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCACAAAGTCTGCCTTGACACCTTCTGGCAGGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AATGCGCCAGATAGCAGCCTCCCCTACTCCGGCTT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGGTAGCGCTTGAGGGCATCAATCTTGGCCTTAT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATGGAGTGCTGATACAAAAGCCCCCAGCTCTAA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TTCGTATTTTTGCTGCATTTCCCGCTCCAATTT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATCGAGACGATAGCTATTTGTTTTACCATGCTTG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATCTTCATCATTATAACAAACGTCATTTGCAGATA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CCGTTTTTGCGGGAAATCCTGCAAGAAAAAGAAACA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGGGCTACCGACAGGACAAGAGCTGTTTTCCCCAT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CATATACTTAGGTGAAAGAGGAATTAATAAGCAG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATTTTCCTTTTCAAAGATATTATTGCCATTCTCTGT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TATGTAAAGCCTGCTCCCCAGCGGGACAACAGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GAAATATTGGTTGGCAGGGTAAAAAATCTGGATGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAG

>CP028491|1|1|66454-68282|CRT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ACCCGGCAGCTGTTCTAACTAATATCCTGGAGGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CCGTTTTCACTTTTATTATATTCGGTAATAACC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GCCAGCATGGAGATGAAGTGGGATGCCATCGTTGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GCTGGTGCGAAGAAAACGGCATACCAATAGAGG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGAATAACCTGCCCAGAAAACCGTAGCAGCGGGTA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TGAGCCTATTCCGGCAAAGGGCGAAAATACAGTATC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TTGAAGCTGGCTGGCACTGGAACTTGGGTATAGT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TCTCTCTGCCCAGCCGTCTGCCAGATCGGTCTGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TGAGTTGAACGGAGGTGAATAAATGTCAACGTATCAGCAG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TATTATAATTGAATTCGGTGCCCACCCAGGCACCG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GGGTCCTAATCCGCATGGTGCGGGACGAAAAACT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCAAAATATGCAAAAGCCAGGATTGCCCTGGCT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TAAGGAGGGACAAGCCATGTTGGAGCAACCCGGGG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCCGGGTGATACCCTCTGGTCTATAGCCAGAAA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGCACAAAGTCTGCCTTGACACCTTCTGGCAGGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AATGCGCCAGATAGCAGCCTCCCCTACTCCGGCTT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGGTAGCGCTTGAGGGCATCAATCTTGGCCTTAT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATGGAGTGCTGATACAAAAGCCCCCAGCTCTAA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TTCGTATTTTTGCTGCATTTCCCGCTCCAATTT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATCGAGACGATAGCTATTTGTTTTACCATGCTTG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATCTTCATCATTATAACAAACGTCATTTGCAGATA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CCGTTTTTGCGGGAAATCCTGCAAGAAAAAGAAACA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	AGGGCTACCGACAGGACAAGAGCTGTTTTCCCCAT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	CATATACTTAGGTGAAAGAGGAATTAATAAGCAG
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	ATTTTCCTTTTCAAAGATATTATTGCCATTCTCTGT
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	TATGTAAAGCCTGCTCCCCAGCGGGACAACAGC
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAC	GAAATATTGGTTGGCAGGGTAAAAAATCTGGATGA
GTCGCACCCCGCAGGGGTGCGTGGATTGAAAG

Protein	Signature genes	Signature genes Name	Protein_function
CP028491.1\|AVX19278.1\|64622_64937_+\|protein-of-unknown-function-DUF83	cas4	COG1468_cas4_CAS-I-A:CAS-I-B:CAS-I-C:CAS-I-D:CAS-II-B	gnl\|CDD\|224385
CP028491.1\|AVX19283.1\|68780_68969_+\|hypothetical-protein	unknown	unknown	unknown
CP028491.1\|AVX19279.1\|64941_65973_+\|CRISPR-associated-protein,-Cas1-family	cas1	cd09721_cas1_CAS-I-C	gnl\|CDD\|188360
CP028491.1\|AVX19272.1\|56742_57612_+\|transposase,-IS605-OrfB-family,-central-region	unknown	unknown	gnl\|CDD\|273793
CP028491.1\|AVX19290.1\|76828_77791_+\|stage-II-sporulation-protein-D	unknown	unknown	gnl\|CDD\|274252
CP028491.1\|AVX19275.1\|60960_61617_+\|CRISPR-associated-protein,-Cas5d-family	cas5	cd09752_cas5_CAS-I-C	gnl\|CDD\|187534
CP028491.1\|AVX19291.1\|77893_78172_+\|sporulation-protein-YabP	unknown	unknown	gnl\|CDD\|274341
CP028491.1\|AVX19288.1\|76151_76424_+\|bacterial-nucleoid-protein-Hbs	unknown	unknown	gnl\|CDD\|259853
CP028491.1\|AVX19271.1\|56044_56746_+\|transposase,-putative,-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|130826
CP028491.1\|AVX19284.1\|69014_72551_+\|transcription-repair-coupling-factor	cas3	cd09639_cas3_CAS-I	gnl\|CDD\|224118
CP028491.1\|AVX19282.1\|68419_68803_+\|hypothetical-protein	unknown	unknown	unknown
CP028491.1\|AVX19287.1\|74575_76069_+\|tetrapyrrole-methylase-family-protein-/-MazG-family-protein	unknown	unknown	gnl\|CDD\|226465
CP028491.1\|AVX19280.1\|65987_66278_+\|CRISPR-associated-protein,-Cas2-family	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|187856
CP028491.1\|AVX19277.1\|63408_64275_+\|CRISPR-associated-protein,-Csd2-family	cas7	cd09689_cas7_CAS-I-C	gnl\|CDD\|377458
CP028491.1\|AVX19286.1\|73946_74510_+\|AbrB-family-transcriptional-regulator,-stage-V-sporulation-protein-T	unknown	unknown	gnl\|CDD\|131898
CP028491.1\|AVX19285.1\|72584_73676_+\|peptidyl-prolyl-cis-trans-isomerase-C	unknown	unknown	gnl\|CDD\|234605
CP028491.1\|AVX19273.1\|57923_58496_+\|peptidyl-tRNA-hydrolase,-PTH1-family	unknown	unknown	gnl\|CDD\|235457
CP028491.1\|AVX19274.1\|58731_60942_+\|CRISPR-associated-helicase,-Cas3-family	cas3	COG1203_cas3_CAS-I	gnl\|CDD\|350688
CP028491.1\|AVX19289.1\|76494_76764_+\|Ribosomal-50S-subunit-recycling-heat-shock-protein,-contains-S4-domain	unknown	unknown	gnl\|CDD\|224109
CP028491.1\|AVX19276.1\|61620_63405_+\|CRISPR-associated-protein,-Csd1-family	cas8c	cd09757_cas8c_CAS-I-C	gnl\|CDD\|378245

Protein	Function_ID	Function_description	E-value
CP028491.1\|AVX19278.1\|64622_64937_+\|protein-of-unknown-function-DUF83	gnl\|CDD\|224385	COG1468, COG1468, CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms].	1.54942e-12
CP028491.1\|AVX19288.1\|76151_76424_+\|bacterial-nucleoid-protein-Hbs	gnl\|CDD\|259853	cd13831, HU, histone-like DNA-binding protein HU. This subfamily includes HU and HU-like domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. HU can induce DNA bends, condense DNA in a fiber and also interact with single stranded DNA. It contains two homologous subunits, alpha and beta, typically forming homodimers (alpha-alpha and beta-beta), except in E. coli and other enterobacteria, which form heterodimers (alpha-beta). In E. coli, HU binds uniformly to the chromosome, with a preference for damaged or distorted DNA structures and can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Anabaena HU (AHU) shows preference for A/T-rich region in the center of its DNA binding site.	7.67481e-44
CP028491.1\|AVX19279.1\|64941_65973_+\|CRISPR-associated-protein,-Cas1-family	gnl\|CDD\|188360	TIGR03640, cas1_DVULG, CRISPR-associated endonuclease Cas1, subtype I-C/DVULG. 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 DVULG subtype of CRISPR/Cas system.	0
CP028491.1\|AVX19272.1\|56742_57612_+\|transposase,-IS605-OrfB-family,-central-region	gnl\|CDD\|273793	TIGR01766, Putative_transposase_MJ0751, transposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam01385, and other proteins. [Mobile and extrachromosomal element functions, Transposon functions].	1.61781e-08
CP028491.1\|AVX19290.1\|76828_77791_+\|stage-II-sporulation-protein-D	gnl\|CDD\|274252	TIGR02669, stage_II_sporulation_protein_D, SpoIID/LytB domain. This model describes a domain found typically in two or three proteins per genome in Cyanobacteria and Firmicutes, and sporadically in other genomes. One member is SpoIID of Bacillus subtilis. Another in B. subtilis is the C-terminal half of LytB, encoded immediately upstream of an amidase, the autolysin LytC, to which its N-terminus is homologous. Gene neighborhoods are not well conserved for members of this family, as many, such as SpoIID, are monocistronic. One early modelling-based study suggests a DNA-binding role for SpoIID, but the function of this domain is unknown. [Unknown function, General].	4.04703e-61
CP028491.1\|AVX19284.1\|69014_72551_+\|transcription-repair-coupling-factor	gnl\|CDD\|224118	COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription].	0
CP028491.1\|AVX19291.1\|77893_78172_+\|sporulation-protein-YabP	gnl\|CDD\|274341	TIGR02892, conserved_hypothetical_protein, sporulation protein YabP. Members of this protein family are the YabP protein of the bacterial sporulation program, as found in Bacillus subtilis, Clostridium tetani, and other spore-forming members of the Firmicutes. In Bacillus subtilis, a yabP single mutant appears to sporulate and germinate normally (), but is in an operon with yabQ (essential for formation of the spore cortex), it near-universal among endospore-forming bacteria, and is found nowhere else. It is likely, therefore, that YabP does have a function in sporulation or germination, one that is either unappreciated or partially redundant with that of another protein. [Cellular processes, Sporulation and germination].	6.37581e-20
CP028491.1\|AVX19271.1\|56044_56746_+\|transposase,-putative,-N-terminal-domain-containing-protein	gnl\|CDD\|130826	TIGR01765, COG0675:_Transposase_and_inactivated_derivatives, transposase, putative, N-terminal domain. This model represents the N-terminal region of a family of putative transposases found in the largest copy number in Thermoanaerobacter tengcongensis. The three homologs in Bacillus anthracis are each split into two ORFs and this model represents the upstream ORF. [Mobile and extrachromosomal element functions, Transposon functions].	1.91362e-06
CP028491.1\|AVX19275.1\|60960_61617_+\|CRISPR-associated-protein,-Cas5d-family	gnl\|CDD\|187534	cd09752, Cas5_I-C, 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; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family.	7.31396e-121
CP028491.1\|AVX19287.1\|74575_76069_+\|tetrapyrrole-methylase-family-protein-/-MazG-family-protein	gnl\|CDD\|226465	COG3956, COG3956, Protein containing tetrapyrrole methyltransferase domain and MazG-like (predicted pyrophosphatase) domain [General function prediction only].	4.24588e-180
CP028491.1\|AVX19280.1\|65987_66278_+\|CRISPR-associated-protein,-Cas2-family	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.	2.41961e-34
CP028491.1\|AVX19277.1\|63408_64275_+\|CRISPR-associated-protein,-Csd2-family	gnl\|CDD\|377458	pfam05107, Cas_Cas7, CRISPR-associated protein Cas7. CRISPR-associated protein Cas7 is one of the components of the type I-B cascade-like antiviral defense complex. In Haloferax volcanii, Cas5, Cas6 and Cas7 form a small complex that aids the stability of CRISPR-derived RNA.	7.50112e-163
CP028491.1\|AVX19286.1\|73946_74510_+\|AbrB-family-transcriptional-regulator,-stage-V-sporulation-protein-T	gnl\|CDD\|131898	TIGR02851, stage_V_sporulation_protein_T, stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See pfam04014). [Regulatory functions, DNA interactions, Cellular processes, Sporulation and germination].	6.71957e-98
CP028491.1\|AVX19285.1\|72584_73676_+\|peptidyl-prolyl-cis-trans-isomerase-C	gnl\|CDD\|234605	PRK00059, prsA, peptidylprolyl isomerase; Provisional.	1.99165e-60
CP028491.1\|AVX19273.1\|57923_58496_+\|peptidyl-tRNA-hydrolase,-PTH1-family	gnl\|CDD\|235457	PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.	5.69543e-102
CP028491.1\|AVX19274.1\|58731_60942_+\|CRISPR-associated-helicase,-Cas3-family	gnl\|CDD\|350688	cd17930, DEXHc_cas3, DEXH/Q-box helicase domain of Cas3. CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.	3.04857e-60
CP028491.1\|AVX19289.1\|76494_76764_+\|Ribosomal-50S-subunit-recycling-heat-shock-protein,-contains-S4-domain	gnl\|CDD\|224109	COG1188, COG1188, Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis].	4.5287e-29
CP028491.1\|AVX19276.1\|61620_63405_+\|CRISPR-associated-protein,-Csd1-family	gnl\|CDD\|378245	pfam09709, Cas_Csd1, CRISPR-associated protein (Cas_Csd1). CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins that tend to be found near CRISPR repeats. The species range, so far, is exclusively bacterial and mesophilic, although CRISPR loci are particularly common among the archaea and thermophilic bacteria. Clusters of short DNA repeats with nonhomologous 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.	0

>CP028491.1|AVX19280.1|65987_66278_+|CRISPR-associated-protein,-Cas2-family
MMVLITYDVNTTTEAGRKRLRRVAKQCTDYGQRVQNSVFECLVDPAQFAQLRHKLEKIIDVEQDSLRYYFLGKNWRNRVEHVGVKHGFDPEDSLIL
>CP028491.1|AVX19279.1|64941_65973_+|CRISPR-associated-protein,-Cas1-family
MRKMLNVLYVTTPEAFLAKEGENLIVKVQEKVIFRAPIHYLEGIVTFGYMGASPALLGMCAEKGVSVTFLNEHGKFLASVAGPVKGNVLLRRKQYRMADSVKDSSKIASRFIMGKIANSKTVLRRFISDHGNKHGVENIENICREMARSIINLNKVTSLEEIRGIEGNIAKHYFSSFNQMILHQKEHFFMNERNRRPPLDNLNSLLSFLYTLLVNETRSALETVGLDPYVGFLHRDRPGRPGLALDLMEELRAYLADRLALSLINRKQITEMDFTRKESGAVIIKEKGRKTILEAWQKRKREEITHPFLNEKIPIGLLPYAQALLLSRYLRGDLDDYPPFIWK
>CP028491.1|AVX19278.1|64622_64937_+|protein-of-unknown-function-DUF83
MCSSYLFGGNDGIQLDYGYLFYGETRHRHRVVFNEKLRERVIYLAERMHMIFEQGITPIAIKNIKCKNCSLVELCVPELGRKRNTVLNYLTELIREMEDEITGD
>CP028491.1|AVX19277.1|63408_64275_+|CRISPR-associated-protein,-Csd2-family
MADFVQNRYEFVLLFDVENGNPNGDPDAGNMPRIDAETGLGLVTDVCLKRKIRNYVDIVKNGIEGYDIYVREGAVLNAQHRKAYEFYGIEPESKKLPKEVEEARKITKFMCHHFFDIRAFGAVMTTEVNCGQVRGPVQLNFARSIDPIVQQEVTITRMAVTSEKDAEKKEREMGRKHIVPYALYRVEGYISAHLAEKTGFTEDDLEILWDALINMFDHDRSAARGKMASRKLIIFKHETALGNAPAHKLFDLVKISRKDPGRPARSFEDYEVIIDYSALPAGVNLIEK
>CP028491.1|AVX19276.1|61620_63405_+|CRISPR-associated-protein,-Csd1-family
MIINSLYQYYERLLEDPDSGVSRPGFNKVKVSFALIISNTGELLDIVDLREIKGKKLVLRELDVPEQIKRASGISANFMCDNCMYVLGIKRKKNDKKERIRDAFEAFTALHEKILGEVDDEGAIAILRFLRQWDIDNADKHPKIVEVIDDISEGGNLVFRLEGAQGYIHERKAIIEAWHSYRSRQSSEVISQCLVTGKKSSIARLHPNIKGVTGAQSSGASLVSFNLDAFTSYGKSQSYNAPVSENVAFGYTTALNYLLTNEKHRVRIGDTTTVFWAERSGGLEEDLLGALFFPANNTKKKEGDDQNIITIDPKTVKLLHDIFSRIRAGEPVNIGLDGIDPQVNFYILGLAPNASRLSVRFWHVDQYGKFIEKIAQHYIDLAIVKSFENEPDYISIDMILKETAPLGDYKKIPPLLGGALIRSILTGIPYPQTLYHLIISRIRADQKVNYTRAAIIKACLVRNQRYYKRGNEVKISMALEEQNTNVAYRLGRLFALLEKVQEDANPDLNSTIKDRYFGAASATPGSIFPILLRLAQHHIAKAKYGRLMDERIEEVINSITNFPAYLNLEEQGLFVLGYYHQRKALFTKNEKKEG
>CP028491.1|AVX19275.1|60960_61617_+|CRISPR-associated-protein,-Cas5d-family
MGYGIRLLVWGDYACFTRPEMKVERVSYDVITPSAARGILEAIHWKPAIRWIVDKIHVLNEIRFDNLRRNEVGSKIPAGNVKKAMKGEVIELCQYAANDRQQRATLLLRDVAYIIEAHFEMTDKAGSEDTPEKHYNIVLRRARLGQCYHQPYLGCREFPAKFRLIEDDEPLPHSLHKGEKDLGWMLLDIDYTDNMTPRFFRAVMKEGIIEVPRLEEGE
>CP028491.1|AVX19274.1|58731_60942_+|CRISPR-associated-helicase,-Cas3-family
MEDTKYYAHSIEGKSKSDWHLLKKHLEDTAKLAAEFASSFGMKKLGSVAGLLHDIGKYSHEFQRRLEGEKSKVDHSTAGALEVIEHYGVLGKILAYGIAGHHCGLPDWGSYVDESSLEGRLNKKDLPDYSAYKKEIELPKPEEISFQMKLAPVGQGFSVQFLIRFLYSALVDADFLDTEQALNNEKSSLRENKVSLEDMISTLDTFLKKKCANVPDTRINRTRAEILATCREKAVLNPGFFTLTVPTGGGKTLSSMAFALKHAVTHGMKRIIYVIPYTSIIEQNAAIFREIFGEEKVLEHHSNFTYSSKESMEDETEYDFRLAEKMRLAAENWDMPIVVTTNVQFFESLFAAKSSRCRKLHNIANSVVIIDEAQMIPTGFLYPCIYALVELVTNYNTSVVLCTATQPAINKLLPPEIKPLEIMDKPEELYKAFKRVQVKDIGEITDDELARELLRHEQVLCIVNSKKHARILYEKISGNWAYHLSTRMCPAHRSKILKTIKERLRSGEICRVVSTQLIEAGVDVDFPVVYRSYTGIDSIAQSAGRCNREGLLSEGKVFVFKPEKHGLPAGWLSRTASIGESILRRNEDPLDLKSVSDYFAILYDIEGEKLDKEKIMAEIKEQERMLNFSFRRIAEKFNLIDENTVGIIIPWDDECKKIIEKARWSRLSGKYFRQLQKYTVDVYQSELEEMQRLGLIENVGGMLFILREEVCETSYSMETGLLPCTESMFTRDIFII
>CP028491.1|AVX19273.1|57923_58496_+|peptidyl-tRNA-hydrolase,-PTH1-family
MKMLVGLGNPGPQYELTRHNVGFLVIDALADKVGVSSFKQQAGALVASVNYQGEKLLLVKPQTYMNLSGQAVGELARYYKIPAQDVLVIYDDMDNPFGQLRLRARGSSGGHNGIKSIISHLGTEEFPRLKVGIGRPRPGQSAADYVLEPFSSEERAALGRIIPAAVDRVLAVVDKGIVAAMNEFNGKRVT
>CP028491.1|AVX19272.1|56742_57612_+|transposase,-IS605-OrfB-family,-central-region
MKLPYAVELIRTLEGRCLVHLTFEVVRVQEPDFAKGCLAIDTNPDGVALCNVSASGQPEPWAEGLNIPSPGNLGKYEGEFQVIPYPNGFLYIRIPDLAHASSFRRSYLIGVLARVVVDIAFFSGKPIVLENLNFGKDRLDTNKKFNRMASNFPFAKMVGAMYRRAVKEGVPFKLVSPRHTSTIGYWKYMKRYTVPVHCAAALVIGRRAMGFRERVTIELRQLVSQIKQNLTRKDNPDRPGEGKGMTRGVRACLRRLEERLPVHNGLAPCEQEAYNSVWPDLKLLALSVR
>CP028491.1|AVX19271.1|56044_56746_+|transposase,-putative,-N-terminal-domain-containing-protein
MIVPNYFTIIKAWNIIHWRSNKVRQGFRELIRNARETREEQISITVCGEFFPEIYPAHRSSKWSRGEEDPLTTEMRLFCACMRWAFNRLLEGASRHEIKKSGQELFGLNSRYADDARLKAQALLDSQTELLKLENEETEKKLGRARKKLSLTVKGRNKRVVSLVKRLAELKDYREKGTIPEVVFGGRRLWEKVCQGRAAREKWRHARRNRLYSRGDESKGGNPNRNWCRYGWP
>CP028491.1|AVX19282.1|68419_68803_+|hypothetical-protein
MEMMAAALAAVIAWSVNRRTQTESGWRTAILLAPLIEELAKTGFAKILSAQVLPVHLYFGLIEAIYDAWAKPERHLLPALLSLLSHGFFGYLTVKSGILAALFAHFSWNGLIWYMQRRRQNAGNILL
>CP028491.1|AVX19283.1|68780_68969_+|hypothetical-protein
MRVIYYCELCQEIVDEWEIALTEPDNPSIMEMHMEPTLCPDCMTAMGKDEGWLGQIKYNYLH
>CP028491.1|AVX19284.1|69014_72551_+|transcription-repair-coupling-factor
MTRGLVGPLLQAKELQDLWRDLGVKKKTALVYGVSGAVSASLLAAWYRLRQQPLLAIVRDLADAKRLCDDLSTFLPEEEILLYPAQELLPWDIEASSRELLTARLKVLGALARGRTSLIVAPVAALSRAVTPPEQFKNYLVTLNKGQEIEPTALAAQLLQMGYERVSQVEVAGQFSWRGGIVDIFPASASEPVRLEFFDVEIDSLRLFDPVSQRSLREIEQAEILPARDYFATAADWQQAARVLEKEYQNLRKKLIGLQQREAVGRLDQKLKDLLSRLKEGLIPAGLDAFAAYVMPEKATLLDYLPTGALIAVEDPNRVREKALAWDDERGETFASWLERGMALPGQEALYFSWEDIWRQLTGRPLLGLALLPREQTGWRPELLLNLNSRTAPLYQGNLEELTRDLKNYKRQGYAVALLTTHTQRSQQLLDLLKEAEIEAVYLGRLQQEFRTGNIVITRGELSAGFEFPQSKILILTERELFGQSKKGRKAREIKPAGGQKISAFTDLKIGDYVVHVNHGIGVYEGVEQLSVGGITRDYLVVSYAGADRLYIPTEQISLLQKYIGTDGQKPRISKLGGQEWQKAKAKARSAVKEMAEELIKLYAAREALKGFAFSPDTVWQQEFEQAFPYEETPDQLQAIAEIKADMERPRPMDRLLCGDVGYGKTEVALRAAFKAVMDNKQVAILVPTTILAQQHYNTCLERFQGFPVSIDLLSRFRSAREQKATLKKLASGQVDIIIGTHRLLQDDVKFRDLGLLIVDEEQRFGVAHKEKLKQLKQTVDVLTLSATPIPRTLHMALAGVRDMSLLETPPEERYPVQTFVVEFNPLMIRDAILRELARGGQVYFVHNRIEDMDRIFAFLTQLVPEARIAIGHGQMREDELEKVMLDFFNQEYDVLLCTTIIETGLDIPNVNTIIIDNADTMGLAQLYQLRGRVGRSNRMAYAYLTYRKDKVLTEIAEKRLQTLREFTELGSGFKIAMRDLEIRGAGNLLGPEQHGHIMAIGFDLYTQMLEEAIRELKGEIKEEPLETTVEIAIDAYLPADYIEDGAVKMEIYRKIMLCRTEEQLLDLSDELVDRFGDPPLPVVNLLTIARIKILGQEAGITYIGKQQEHLIIKLAPDAPLEPVKILRLPGKIRGLNIVGGAEPVIRVPWSKRDPGLNWVEKIIREIKYCGIGSENLV
>CP028491.1|AVX19285.1|72584_73676_+|peptidyl-prolyl-cis-trans-isomerase-C
MYKLKKLVASVLTAAMLALVAGCGSNAVATVNGEDITKEQFERRLEKMKAVYKQNGANFDTEQGKAMLKAIQKQVLDGMIEETILLQEAKKQGVLPSDADVQKRVEETIKKFESKEKFLEALKNYNMDEKEFAEWTKQNLALDALYNKVTANIKVTDEEIKKYYEENKEQFKQPEQVRARHILIKFDTQQEKVGRTEEQAKKMAQDLIKELEKGADFAKLAKEKSEDPGSKDNGGEYTFSRGQMVQEFEDAAFSLKPGSFTKEPVKTQYGYHIIKVEERIPAKERTFEEVKGELALQLPMQKKQEAFAKYTAELKSKAKIEIKDKELAASPAPAPSNGSQLPPGHPSTSGGSSSAPQPAKPAQ
>CP028491.1|AVX19286.1|73946_74510_+|AbrB-family-transcriptional-regulator,-stage-V-sporulation-protein-T
MKATGIVRRIDDLGRVVIPKEIRRTLRIREGDPLEIFVDRDGEVILKKYSPIGELGDFAREYAESLHEAVGHICCITDRDNVIAVAGGSKKEFMNKPIGPAVEKAMEERKAVIINNPGEHPHCLGCPVDDEDDTCKFTAEVIAPIIAEGDQIGAVLILSKDPNVRMGELELKLAETAAGFLAKQMEQ
>CP028491.1|AVX19287.1|74575_76069_+|tetrapyrrole-methylase-family-protein-/-MazG-family-protein
MAEIYIVGLGPGDEQTFPLGNWQLLKGFTGPIIFRTYRHPIVDWLKQQGITGASCDHFYEEAEDFAAVYEKIVQELVGQATQKGQLAYCVPGHPLVAETSVQWLLKRCESEGITVRILPAMSFLDAIYAALKIDPAQGGLQIIDALALAQTRINPRNGLLLLQVYNQLVASETKLTLMEFYPDEYPVTVIRGAGLADEKKVVIPLYELDRLPWIDHLTSIYLAPNPEGKPEFGHYALEPLATVMEKLRSEQGCPWDREQTHQSLKPFLIEEAYEVLEAIDNQDMEALCEELGDVLLQVVFHTQIAREHEYFDLNDVIMVITEKMIRRHPHVFADTQVADSREVIRNWEQIKAQEKKEQGKEEKSLLAGVPRSLPALLQAYKLQAKAAKVGFDWDNWRGAWDKVQEELRELGQVLDDRQKRQEELGDLLFALVNLARFFDIDPEEALKGTCSKFRRRFAFIEQTVRERGQKLEELALAELDKIWELAKNHENISKKNG
>CP028491.1|AVX19288.1|76151_76424_+|bacterial-nucleoid-protein-Hbs
MNKTDLVNSVAEKAELTKKDAEKAVNAVFASIEEALKKGEKVQLVGFGTFEVRSRGERKGRNPQTGEEITIAAAKVPAFKAGKALKEAVM
>CP028491.1|AVX19289.1|76494_76764_+|Ribosomal-50S-subunit-recycling-heat-shock-protein,-contains-S4-domain
MRLDKFLKVSRIIKRRTLAKEVCDGGRIQINGRPAKASSEVKAGDILELDFGQRRLRVRVVEIKENVPAALAGQLYEILEEIKVRETTF
>CP028491.1|AVX19290.1|76828_77791_+|stage-II-sporulation-protein-D
MFRWGWQKILLSLLVVMTLIGGGCALRKPLPPGQPPGPAGREFTEEPTISLYDNKTKQTKKIKLEEYVAGVVAAEMDTSWPVNALGAQAILARTFTLENIKAGRVKKLYGADISTDIEESQAYAPEKINDNVRKAVQLTRGQVIRWQGKYVKAWFHACCGGKTASAKEGLAYEKEPTPYLSTVADGCMAITTPENKHWEVKLSGEELARAVKQATGQDPGQVTSVQIIKRGPSGRVESLKVGNVAISGPALRLAVGSEKMRSMMLEDIQNAGGTFIFKGRGFGHGVGLCQWGAKKMAAEGKQPWSIVKFYYKGVKIEKLW
>CP028491.1|AVX19291.1|77893_78172_+|sporulation-protein-YabP
MESKKTVTGQRLEVLNREEVIITGVEHVDSFDEQVISLKTNLGNLILKGEGLNITQLNMEEGKLVVQGYLYSLTYAETKGGKSKGIFDKLLK

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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
CP028491_1	1.2\|66552\|33\|CP028491\|PILER-CR,CRISPRCasFinder,CRT	66552-66584	33	AP014503	Uncultured Mediterranean phage uvMED isolate uvMED-GF-U-MedDCM-OCT-S42-C30, * SEQUENCING IN PROGRESS *, 2 ordered pieces	20042-20074	8	0.758
CP028491_1	1.3\|66617\|35\|CP028491\|PILER-CR,CRISPRCasFinder,CRT	66617-66651	35	NZ_CP032343	Azospirillum brasilense strain MTCC4038 plasmid p4, complete sequence	416071-416105	9	0.743
CP028491_1	1.3\|66617\|35\|CP028491\|PILER-CR,CRISPRCasFinder,CRT	66617-66651	35	NZ_CP012917	Azospirillum brasilense strain Sp 7 plasmid ABSP7_p3, complete sequence	312121-312155	9	0.743
CP028491_1	1.7\|66884\|34\|CP028491\|PILER-CR,CRISPRCasFinder,CRT	66884-66917	34	NZ_CP042263	Litoreibacter sp. LN3S51 plasmid unnamed2, complete sequence	273244-273277	9	0.735
CP028491_1	1.14\|67354\|34\|CP028491\|PILER-CR,CRISPRCasFinder,CRT	67354-67387	34	MT310865	Streptomyces phage Bmoc, complete genome	21404-21437	9	0.735
CP028491_1	1.25\|68083\|36\|CP028491\|PILER-CR,CRISPRCasFinder,CRT	68083-68118	36	NC_019690	Pseudanabaena sp. PCC 7367 plasmid pPSE7367.01, complete sequence	296379-296414	10	0.722
CP028491_1	1.14\|67354\|34\|CP028491\|PILER-CR,CRISPRCasFinder,CRT	67354-67387	34	HQ317390	Colwellia phage 9A, complete genome	52658-52691	11	0.676

1. spacer 1.2|66552|33|CP028491|PILER-CR,CRISPRCasFinder,CRT matches to AP014503 (Uncultured Mediterranean phage uvMED isolate uvMED-GF-U-MedDCM-OCT-S42-C30, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces) position: , mismatch: 8, identity: 0.758

ccgttttcacttttattatattcggtaataacc	CRISPR spacer
acatcttcacttttattatattcaataattgct	Protospacer
 *.*.******************..**** .*.

2. spacer 1.3|66617|35|CP028491|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP032343 (Azospirillum brasilense strain MTCC4038 plasmid p4, complete sequence) position: , mismatch: 9, identity: 0.743

gccagcatggagatgaagtgggatgccatcgttga	CRISPR spacer
gccagcatggcgatgaagtgggttgcccacacgcc	Protospacer
********** *********** ****  *..

3. spacer 1.3|66617|35|CP028491|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP012917 (Azospirillum brasilense strain Sp 7 plasmid ABSP7_p3, complete sequence) position: , mismatch: 9, identity: 0.743

gccagcatggagatgaagtgggatgccatcgttga	CRISPR spacer
gccagcatggcgatgaagtgggttgcccacacgcc	Protospacer
********** *********** ****  *..

4. spacer 1.7|66884|34|CP028491|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP042263 (Litoreibacter sp. LN3S51 plasmid unnamed2, complete sequence) position: , mismatch: 9, identity: 0.735

ttgaagctggctggcactggaacttgggtatagt	CRISPR spacer
cggaagctggctggcgctggaacctgacgatcgc	Protospacer
. *************.*******.**.  ** *.

5. spacer 1.14|67354|34|CP028491|PILER-CR,CRISPRCasFinder,CRT matches to MT310865 (Streptomyces phage Bmoc, complete genome) position: , mismatch: 9, identity: 0.735

agccgggtgataccctctggtctatagccagaaa	CRISPR spacer
ttaagggtgataccctgtggtctattgctgaaaa	Protospacer
    ************ ******** **...***

6. spacer 1.25|68083|36|CP028491|PILER-CR,CRISPRCasFinder,CRT matches to NC_019690 (Pseudanabaena sp. PCC 7367 plasmid pPSE7367.01, complete sequence) position: , mismatch: 10, identity: 0.722

attttccttttcaaagatattattgccattctctgt	CRISPR spacer
tatctgtgtttcagagatattattaccattctctaa	Protospacer
  *.* . *****.**********.*********.

7. spacer 1.14|67354|34|CP028491|PILER-CR,CRISPRCasFinder,CRT matches to HQ317390 (Colwellia phage 9A, complete genome) position: , mismatch: 11, identity: 0.676

agccgggtgataccctctggtctatagccagaaa	CRISPR spacer
tcaaagactttaccctctggactatatccagaaa	Protospacer
    .*..  ********** ***** *******

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

143695 : 156572

Synechococcus_phage(22.22%)

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
AVX19355.1\|143695_147469_+	phosphoribosylformylglycinamidine synthase	A6N228	Microbacterium_phage	4.7e-32	25.0
AVX19356.1\|147889_149260_+	putative MFS transporter, AGZA family, xanthine/uracil permease	A0A0R6PHV4	Moraxella_phage	8.3e-56	33.9
AVX19357.1\|149286_149811_+	5-(carboxyamino)imidazole ribonucleotide mutase	A0A2P0VNU7	Tetraselmis_virus	1.3e-25	45.8
AVX19358.1\|149927_151220_+	adenylosuccinate lyase	A0A1B3B081	Gordonia_phage	2.3e-23	33.4
AVX19359.1\|151245_151953_+	phosphoribosylaminoimidazole-succinocarboxamide synthase	A0A0E3HI61	Synechococcus_phage	1.9e-40	42.8
AVX19360.1\|151971_153381_+	amidophosphoribosyltransferase	A0A0M3SGR2	Mollivirus	3.8e-64	37.0
AVX19361.1\|153377_154406_+	phosphoribosylformylglycinamidine cyclo-ligase	Q58MH8	Prochlorococcus_phage	1.4e-68	45.6
AVX19362.1\|154407_155034_+	formyltetrahydrofolate-dependent phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	1.4e-29	42.5
AVX19363.1\|155033_156572_+	IMP cyclohydrolase /phosphoribosylaminoimidazolecarboxamideformyltransferase	Q58MG4	Prochlorococcus_phage	1.7e-81	53.7

DBSCAN-SWA_2

328708 : 336503

Pseudomonas_phage(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVX19532.1\|328708_329776_+	bacterial peptide chain release factor 1 (bRF-1)	W8EDB3	Pseudomonas_phage	7.8e-09	45.2
AVX19533.1\|329787_330657_+	[protein release factor]-glutamine N5-methyltransferase	NA	NA	NA	NA
AVX19534.1\|330661_331690_+	translation factor SUA5	A0A291ATS8	Pandoravirus	5.3e-55	43.1
AVX19535.1\|331691_332144_+	protein-tyrosine phosphatase	A0A2H4PQT9	Staphylococcus_phage	5.8e-06	32.8
AVX19536.1\|332168_332618_+	ribose-5-phosphate isomerase	NA	NA	NA	NA
AVX19537.1\|332643_333891_+	serine hydroxymethyltransferase	A0A219Y950	Aeromonas_phage	6.6e-100	54.8
AVX19538.1\|333912_334542_+	uracil phosphoribosyltransferase	NA	NA	NA	NA
AVX19539.1\|334554_335013_+	dCMP deaminase	A0A1D8ESY8	Mycobacterium_phage	4.8e-24	48.0
AVX19540.1\|335009_335339_+	MazG nucleotide pyrophosphohydrolase domain-containing protein	NA	NA	NA	NA
AVX19541.1\|335399_336503_+	UDP-N-Acetylglucosamine 2-epimerase	A0A1V0SAG5	Catovirus	7.5e-23	29.3

DBSCAN-SWA_3

1123076 : 1134204

Staphylococcus_phage(42.86%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVX20324.1\|1123076_1124951_+	serine/threonine protein kinase	W5S4J6	Pithovirus	1.7e-19	33.2
AVX20325.1\|1124961_1125828_+	ribosome biogenesis GTPase	NA	NA	NA	NA
AVX20326.1\|1125830_1126484_+	ribulose-5-phosphate 3-epimerase	NA	NA	NA	NA
AVX20327.1\|1126485_1127511_+	Acetoin utilization deacetylase AcuC	A0A2K9L473	Tupanvirus	1.2e-38	38.1
AVX20328.1\|1127768_1128932_+	diaminohydroxyphosphoribosylaminopyrimidine deaminase	A0A1V0SE20	Indivirus	1.0e-46	34.8
AVX20329.1\|1128934_1129591_+	riboflavin synthase alpha chain	A0A2H4PQS5	Staphylococcus_phage	5.4e-37	41.7
AVX20330.1\|1129603_1130815_+	3,4-dihydroxy 2-butanone 4-phosphate synthase / GTP cyclohydrolase II	A0A2H4PQS2	Staphylococcus_phage	1.0e-105	49.9
AVX20331.1\|1130839_1131313_+	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	5.8e-41	59.3
AVX20332.1\|1131458_1132958_+	hypothetical protein	NA	NA	NA	NA
AVX20333.1\|1133031_1134204_+	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5/6)	B6DZZ7	Stx2-converting_phage	5.0e-33	31.9

DBSCAN-SWA_4

1335422 : 1344367

Halovirus(14.29%)

protease

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVX20542.1\|1335422_1336157_+	Organic radical activating enzyme	R4TAH8	Halovirus	6.3e-10	30.4
AVX20543.1\|1336170_1336731_+	GTP cyclohydrolase I	E7DN69	Pneumococcus_phage	1.4e-49	57.1
AVX20544.1\|1336752_1336932_+	Protein of unknown function (DUF4264)	NA	NA	NA	NA
AVX20545.1\|1336946_1338224_+	putative tyrosine transporter P-protein	NA	NA	NA	NA
AVX20546.1\|1338235_1339003_+	5'-nucleotidase /3'-nucleotidase /exopolyphosphatase	A0A1B1ITZ2	uncultured_Mediterranean_phage	6.7e-47	40.4
AVX20547.1\|1339114_1339576_+	hypothetical protein	NA	NA	NA	NA
AVX20548.1\|1339599_1341081_+\|protease	ATP-dependent metalloprotease FtsH	E5ESM9	Bathycoccus_sp._RCC1105_virus	1.7e-75	41.5
AVX20549.1\|1341152_1341659_+	nicotinamide-nucleotide amidase	B5TK85	Pseudomonas_phage	1.1e-21	41.5
AVX20550.1\|1341662_1343267_+	ATP-dependent RNA helicase DeaD	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	1.7e-68	39.8
AVX20551.1\|1343341_1344367_+	recombination protein RecA	A0A0S2MVG1	Bacillus_phage	1.0e-122	66.9

DBSCAN-SWA_5

1778461 : 1785432

Tupanvirus(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVX20966.1\|1778461_1778812_-	Cupin domain-containing protein	A0A2K9L322	Tupanvirus	1.3e-05	27.5
AVX20967.1\|1778964_1779762_+	DNA end-binding protein Ku	A0A249XRB2	Mycobacterium_phage	2.4e-47	40.9
AVX20968.1\|1779761_1780631_+	bifunctional non-homologous end joining protein LigD	A0A291AUP8	Sinorhizobium_phage	9.4e-21	29.8
AVX20969.1\|1780627_1781485_+	bifunctional non-homologous end joining protein LigD	NA	NA	NA	NA
AVX20970.1\|1781553_1781841_+	transcriptional regulator, ArsR family	A0A218MNF3	uncultured_virus	3.1e-05	41.2
AVX20971.1\|1781821_1782475_+	putative membrane protein	NA	NA	NA	NA
AVX20972.1\|1782452_1782755_-	hypothetical protein	NA	NA	NA	NA
AVX20973.1\|1782873_1783296_+	hypothetical protein	NA	NA	NA	NA
AVX20974.1\|1783334_1784252_-	cysteine synthase A	A0A1X9I5F1	Streptococcus_phage	1.2e-103	62.7
AVX20975.1\|1784370_1785432_-	PAS domain S-box-containing protein	A0A2K9L0Z8	Tupanvirus	7.0e-10	23.5

DBSCAN-SWA_6

2370679 : 2438221

Streptococcus_phage(13.33%)

capsid,portal,tail,terminase,tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
AVX21552.1\|2370679_2371465_-\|tRNA	tRNA(Ile)-lysidine synthase TilS/MesJ	NA	NA	NA	NA
AVX21553.1\|2371489_2371822_-	bacillithiol system protein YtxJ	NA	NA	NA	NA
AVX21554.1\|2371800_2372259_-	Nucleoside recognition	NA	NA	NA	NA
AVX21555.1\|2372269_2372689_-	hypothetical protein	NA	NA	NA	NA
AVX21556.1\|2372704_2372986_-	hypothetical protein	NA	NA	NA	NA
AVX21557.1\|2373051_2374221_-	LL-diaminopimelate aminotransferase apoenzyme	NA	NA	NA	NA
AVX21558.1\|2374271_2376425_-	Cd2+/Zn2+-exporting ATPase	E4ZFI9	Streptococcus_phage	8.1e-114	36.1
AVX21559.1\|2376443_2376791_-	transcriptional regulator, ArsR family	E4ZFI8	Streptococcus_phage	1.1e-12	39.3
AVX21560.1\|2376898_2378500_-	drug resistance transporter, EmrB/QacA subfamily	NA	NA	NA	NA
AVX21561.1\|2378505_2378937_-	DNA-binding transcriptional regulator, MarR family	NA	NA	NA	NA
AVX21562.1\|2379048_2379633_-	RNA polymerase, sigma-24 subunit, RpoE	NA	NA	NA	NA
AVX21563.1\|2379678_2380356_-	putative membrane protein YphA, DoxX/SURF4 family	NA	NA	NA	NA
AVX21564.1\|2380604_2380967_+	transcriptional regulator, HxlR family	NA	NA	NA	NA
AVX21565.1\|2380967_2382719_+	Signal transduction histidine kinase	NA	NA	NA	NA
AVX21566.1\|2382798_2385960_-	Fe-S oxidoreductase	NA	NA	NA	NA
AVX21567.1\|2386227_2386440_+	4Fe-4S binding domain-containing protein	NA	NA	NA	NA
AVX21568.1\|2386663_2386885_+	hypothetical protein	NA	NA	NA	NA
AVX21569.1\|2386891_2387653_-	hypothetical protein	NA	NA	NA	NA
AVX21570.1\|2387983_2389279_-	Transposase domain (DUF772)	NA	NA	NA	NA
AVX21571.1\|2389534_2389804_+	hypothetical protein	NA	NA	NA	NA
AVX21572.1\|2390435_2391080_-\|portal	phage portal protein, HK97 family	A0A2K5B287	Erysipelothrix_phage	6.7e-64	63.5
AVX21573.1\|2391214_2391469_-	prevent-host-death family protein	NA	NA	NA	NA
AVX21574.1\|2391894_2393082_+	putative arabinose efflux permease, MFS family	NA	NA	NA	NA
AVX21575.1\|2393065_2393518_+	transcriptional regulator, MarR family	NA	NA	NA	NA
AVX21576.1\|2393532_2393829_+	alkylhydroperoxidase AhpD family core domain-containing protein	NA	NA	NA	NA
AVX21577.1\|2394050_2394473_-	hypothetical protein	NA	NA	NA	NA
AVX21578.1\|2394497_2395031_-	hypothetical protein	NA	NA	NA	NA
AVX21579.1\|2395175_2395478_-	hypothetical protein	NA	NA	NA	NA
AVX21580.1\|2395478_2397065_-	hypothetical protein	NA	NA	NA	NA
AVX21581.1\|2397077_2397512_-	hypothetical protein	G9FHA5	Rhodococcus_phage	4.8e-42	59.7
AVX21582.1\|2397495_2397759_-	hypothetical protein	NA	NA	NA	NA
AVX21583.1\|2397760_2398411_-	N-acetylmuramoyl-L-alanine amidase	A0A0A7RTQ5	Clostridium_phage	2.0e-15	37.6
AVX21584.1\|2398412_2398655_-	hypothetical protein	NA	NA	NA	NA
AVX21585.1\|2398690_2399047_-	protein of unknown function (DUF4907)	NA	NA	NA	NA
AVX21586.1\|2399064_2400417_-	hypothetical protein	NA	NA	NA	NA
AVX21587.1\|2400424_2400616_-	hypothetical protein	NA	NA	NA	NA
AVX21588.1\|2400620_2401769_-	hypothetical protein	A0A0M5M1G2	Caulobacter_phage	2.3e-06	40.0
AVX21589.1\|2401771_2403664_-	hypothetical protein	NA	NA	NA	NA
AVX21590.1\|2403663_2404020_-	hypothetical protein	NA	NA	NA	NA
AVX21591.1\|2404024_2406838_-	tape measure domain-containing protein	U5PSU7	Bacillus_virus	6.8e-28	31.1
AVX21592.1\|2406841_2406988_-	hypothetical protein	NA	NA	NA	NA
AVX21593.1\|2407055_2407412_-	hypothetical protein	NA	NA	NA	NA
AVX21594.1\|2407434_2407839_-\|tail	Phage tail tube protein	A0A1B0XTL5	Freshwater_phage	9.4e-32	55.6
AVX21595.1\|2407853_2408573_-	hypothetical protein	A0A1B0XTM3	Freshwater_phage	1.9e-35	40.3
AVX21596.1\|2408572_2408725_-	hypothetical protein	NA	NA	NA	NA
AVX21597.1\|2408721_2409114_-	hypothetical protein	NA	NA	NA	NA
AVX21598.1\|2409126_2409480_-\|tail	Bacteriophage HK97-gp10, putative tail-component	A0A1J0MCP5	Streptomyces_phage	2.7e-06	30.0
AVX21599.1\|2409490_2409787_-	hypothetical protein	NA	NA	NA	NA
AVX21600.1\|2409780_2410248_-	hypothetical protein	NA	NA	NA	NA
AVX21601.1\|2410263_2410395_-	hypothetical protein	NA	NA	NA	NA
AVX21602.1\|2410441_2411395_-\|capsid	phage major capsid protein, HK97 family	D2J006	Enterococcus_phage	2.7e-98	59.4
AVX21603.1\|2411416_2412001_-	protein of unknown function (DUF4355)	NA	NA	NA	NA
AVX21604.1\|2412099_2412276_-	hypothetical protein	NA	NA	NA	NA
AVX21605.1\|2412281_2413703_-	Phage Mu protein F like protein	B5LPR2	Bacillus_virus	7.7e-12	21.0
AVX21606.1\|2413702_2415142_-\|portal	Phage portal protein, SPP1 Gp6-like	A0A0N7GFE4	Paenibacillus_phage	3.1e-45	34.6
AVX21607.1\|2415141_2416401_-\|terminase	phage terminase, large subunit, PBSX family	B6CXD2	Clostridium_phage	2.7e-117	51.0
AVX21608.1\|2416390_2416837_-\|terminase	phage terminase small subunit	A0A0A8WDX8	Clostridium_phage	5.3e-36	61.6
AVX21609.1\|2416899_2417100_-	hypothetical protein	NA	NA	NA	NA
AVX21610.1\|2417135_2417282_-	hypothetical protein	NA	NA	NA	NA
AVX21611.1\|2417288_2417504_-	hypothetical protein	NA	NA	NA	NA
AVX21612.1\|2417516_2417801_-	hypothetical protein	NA	NA	NA	NA
AVX21613.1\|2418007_2418490_-	phage transcriptional activator, RinA family	NA	NA	NA	NA
AVX21614.1\|2418490_2419072_-	hypothetical protein	NA	NA	NA	NA
AVX21615.1\|2419130_2419277_-	hypothetical protein	NA	NA	NA	NA
AVX21616.1\|2419267_2419654_-	Holliday junction resolvase RusA (prophage-encoded endonuclease)	M4ZS69	Bacillus_phage	8.2e-09	34.7
AVX21617.1\|2419628_2419757_-	hypothetical protein	NA	NA	NA	NA
AVX21618.1\|2419753_2420074_-	hypothetical protein	NA	NA	NA	NA
AVX21619.1\|2420093_2420894_-	hypothetical protein	NA	NA	NA	NA
AVX21620.1\|2420897_2421200_-	hypothetical protein	NA	NA	NA	NA
AVX21621.1\|2421317_2421779_-	hypothetical protein	Q6JIG5	Burkholderia_virus	4.9e-45	60.5
AVX21622.1\|2421775_2421976_-	single stranded DNA-binding protein (ssb)	A0A141DZL2	Streptococcus_phage	5.7e-14	63.5
AVX21623.1\|2421992_2422811_-	DNA replication protein DnaC	A0A0A0RNN8	Bacillus_phage	2.0e-28	33.7
AVX21624.1\|2422851_2423679_-	replicative DNA helicase loader DnaB	A0A1L2JY26	Aeribacillus_phage	1.1e-21	43.1
AVX21625.1\|2423686_2423986_-	LysM domain-containing protein	NA	NA	NA	NA
AVX21626.1\|2423955_2424192_-	hypothetical protein	NA	NA	NA	NA
AVX21627.1\|2424247_2425201_-	3'-5' exoribonuclease	NA	NA	NA	NA
AVX21628.1\|2425200_2426028_-	recombination protein RecT	S6AVW6	Thermus_phage	2.0e-76	61.1
AVX21629.1\|2426043_2426982_-	putative phage-type endonuclease	S6C475	Thermus_phage	8.7e-97	61.3
AVX21630.1\|2426978_2427098_-	hypothetical protein	NA	NA	NA	NA
AVX21631.1\|2427099_2427270_-	hypothetical protein	NA	NA	NA	NA
AVX21632.1\|2427374_2427923_-	helix-turn-helix protein	NA	NA	NA	NA
AVX21633.1\|2428147_2428486_-	hypothetical protein	NA	NA	NA	NA
AVX21634.1\|2428501_2428750_-	hypothetical protein	NA	NA	NA	NA
AVX21635.1\|2428763_2428973_-	helix-turn-helix protein	NA	NA	NA	NA
AVX21636.1\|2429101_2429407_+	Transcriptional regulator, contains XRE-family HTH domain	I3VYY8	Thermoanaerobacterium_phage	9.6e-05	35.1
AVX21637.1\|2429409_2429724_+	hypothetical protein	NA	NA	NA	NA
AVX21638.1\|2429842_2430070_-	putative transcriptional regulator	I3VYY8	Thermoanaerobacterium_phage	4.2e-05	38.5
AVX21639.1\|2430220_2430694_+	helix-turn-helix protein	A0A0A8WFJ2	Clostridium_phage	2.5e-12	46.2
AVX21640.1\|2430776_2431088_+	hypothetical protein	NA	NA	NA	NA
AVX21641.1\|2431172_2432315_+	hypothetical protein	A0A1S5SAB0	Streptococcus_phage	8.5e-54	38.5
AVX21642.1\|2432561_2433077_+	hypothetical protein	NA	NA	NA	NA
AVX21643.1\|2433161_2433500_+	proteic killer suppression protein	NA	NA	NA	NA
AVX21644.1\|2433492_2434593_+	addiction module antidote protein, HigA family	A0A075BTZ7	Microcystis_phage	1.5e-10	42.0
AVX21645.1\|2434735_2436163_+	site-specific DNA recombinase	A0A097BY75	Enterococcus_phage	4.4e-100	43.8
AVX21646.1\|2436159_2437509_-	23S rRNA m(5)U-1939 methyltransferase	A0A2K5B251	Erysipelothrix_phage	1.1e-79	40.3
AVX21647.1\|2437510_2438221_-	N-acylneuraminate cytidylyltransferase/CMP-N,N'-diacetyllegionaminic acid synthase	A0A1B1IVD3	uncultured_Mediterranean_phage	4.2e-11	32.5

Anti-CRISPR protein detection

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