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_013768	Listeria monocytogenes 08-5923, complete sequence	3 crisprs	casR,cas3,DEDDh,DinG,WYL,csa3	3	10	7	3

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_013768_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_013768_1

162147-162255

Orphan

Consensus_repeat	Method
TAAATCAAAATAAAGTACATTTTGAAAGTTCT	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_013768_1

>merge|NC_013768|1|162147-162255|CRISPRCasFinder
TAAATCAAAATAAAGTACATTTTGAAAGTTCTGGGAAGGATTAAATCATCGCTGCGCTCAGATTTATATTGAAGAACTAAATCAAAATAAAGTACATTTTGAAAGTTCT

>NC_013768|1|1|162147-162255|CRISPRCasFinder
TAAATCAAAATAAAGTACATTTTGAAAGTTCT	GGGAAGGATTAAATCATCGCTGCGCTCAGATTTATATTGAAGAAC
TAAATCAAAATAAAGTACATTTTGAAAGTTCT

Protein	Signature genes	Signature genes Name	Protein_function
NC_013768.1\|WP_012951102.1\|168665_169262_-\|dihydroxyacetone-kinase-subunit-L	unknown	unknown	gnl\|CDD\|274099
NC_013768.1\|WP_003722063.1\|164081_164399_+\|YbaB/EbfC-family-nucleoid-associated-protein	unknown	unknown	gnl\|CDD\|234669
NC_013768.1\|WP_009931588.1\|159036_159192_-\|hypothetical-protein	unknown	unknown	unknown
NC_013768.1\|WP_003722074.1\|153567_154515_+\|LPXTG-cell-wall-anchor-domain-containing-protein	unknown	unknown	gnl\|CDD\|273478
NC_013768.1\|WP_003728590.1\|161133_161355_+\|hypothetical-protein	unknown	unknown	unknown
NC_013768.1\|WP_003732087.1\|155611_157126_+\|gluconokinase	unknown	unknown	gnl\|CDD\|212659
NC_013768.1\|WP_009931159.1\|165409_166252_-\|aldo/keto-reductase	unknown	unknown	gnl\|CDD\|223729
NC_013768.1\|WP_009913205.1\|168287_168662_-\|PTS-dependent-dihydroxyacetone-kinase-phosphotransferase-subunit-DhaM	unknown	unknown	gnl\|CDD\|184702
NC_013768.1\|WP_003732089.1\|151687_153427_+\|thiol-reductant-ABC-exporter-subunit-CydC	unknown	unknown	gnl\|CDD\|227320
NC_013768.1\|WP_003732084.1\|162312_164052_+\|DNA-polymerase-III-subunit-gamma/tau	unknown	unknown	gnl\|CDD\|235505
NC_013768.1\|WP_012951100.1\|166372_167212_-\|Cof-type-HAD-IIB-family-hydrolase	unknown	unknown	gnl\|CDD\|319818
NC_013768.1\|WP_003722073.1\|154557_155496_+\|GW-domain-containing-glycosaminoglycan-binding-protein	unknown	unknown	gnl\|CDD\|226309
NC_013768.1\|WP_009925039.1\|157823_158465_+\|hypothetical-protein	unknown	unknown	unknown
NC_013768.1\|WP_003728591.1\|159634_160999_+\|PTS-sugar-transporter-subunit-IIC	unknown	unknown	gnl\|CDD\|224372
NC_013768.1\|WP_003722065.1\|161557_162022_+\|DUF3284-domain-containing-protein	unknown	unknown	gnl\|CDD\|378692
NC_013768.1\|WP_003732079.1\|169283_170273_-\|dihydroxyacetone-kinase-subunit-DhaK	unknown	unknown	gnl\|CDD\|237724
NC_013768.1\|WP_003722062.1\|164507_165104_+\|recombination-protein-RecR	unknown	unknown	gnl\|CDD\|234616
NC_013768.1\|WP_003722061.1\|165118_165364_+\|YaaL-family-protein	unknown	unknown	gnl\|CDD\|378478
NC_013768.1\|WP_012951101.1\|167330_168182_-\|MurR/RpiR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224651
NC_013768.1\|WP_003728589.1\|161357_161540_+\|DUF3188-domain-containing-protein	unknown	unknown	gnl\|CDD\|371501

Protein	Function_ID	Function_description	E-value
NC_013768.1\|WP_012951102.1\|168665_169262_-\|dihydroxyacetone-kinase-subunit-L	gnl\|CDD\|274099	TIGR02365, dha_L_ycgS, dihydroxyacetone kinase, phosphoprotein-dependent, L subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the subunit homologous to the E. coli YcgS subunit.	1.69543e-82
NC_013768.1\|WP_003722074.1\|153567_154515_+\|LPXTG-cell-wall-anchor-domain-containing-protein	gnl\|CDD\|273478	TIGR01167, Zinc_metalloprotease_ZmpB, LPXTG-motif cell wall anchor domain. This model describes the LPXTG motif-containing region found at the C-terminus of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall. Hits that do not lie at the C-terminus or are not found in Gram-positive bacteria are probably false-positive. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region. [Cell envelope, Other].	1.13667e-05
NC_013768.1\|WP_003722063.1\|164081_164399_+\|YbaB/EbfC-family-nucleoid-associated-protein	gnl\|CDD\|234669	PRK00153, PRK00153, YbaB/EbfC family nucleoid-associated protein.	3.53269e-41
NC_013768.1\|WP_003732087.1\|155611_157126_+\|gluconokinase	gnl\|CDD\|212659	cd07770, FGGY_GntK, Gluconate kinases; a subfamily of the FGGY family of carbohydrate kinases. This subfamily is composed of a group of gluconate kinases (GntK, also known as gluconokinase; EC 2.7.1.12) encoded by the gntK gene, which catalyzes the ATP-dependent phosphorylation of D-gluconate and produce 6-phospho-D-gluconate and ADP. The presence of Mg2+ might be required for catalytic activity. The prototypical member of this subfamily is GntK from Lactobacillus acidophilus. Unlike Escherichia coli GntK, which belongs to the superfamily of P-loop containing nucleoside triphosphate hydrolases, members in this subfamily are homologous to glycerol kinase, xylulose kinase, and rhamnulokinase from Escherichia coli. They have been classified as members of the FGGY family of carbohydrate kinases, which contain two large domains separated by a deep cleft that forms the active site. This model spans both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. Some uncharacterized homologous sequences are also included in this subfamily. The Lactobacillus gnt operon contains a single gntK gene. The gnt operons of some bacteria, such as Corynebacterium glutamicum, have two gntK genes. For example, the C. glutamicum gnt operon has both a gluconate kinase gntV gene (also known as gntK) and a second hypothetical gntK gene (also known as gntK2). Both gluconate kinases encoded by these genes belong to this family, however the protein encoded by C. glutamicum gntV is not included in this model as it is truncated in the C-terminal domain.	0
NC_013768.1\|WP_009931159.1\|165409_166252_-\|aldo/keto-reductase	gnl\|CDD\|223729	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only].	6.97706e-130
NC_013768.1\|WP_009913205.1\|168287_168662_-\|PTS-dependent-dihydroxyacetone-kinase-phosphotransferase-subunit-DhaM	gnl\|CDD\|184702	PRK14484, PRK14484, phosphotransferase mannnose-specific family component IIA; Provisional.	2.28713e-49
NC_013768.1\|WP_003732089.1\|151687_153427_+\|thiol-reductant-ABC-exporter-subunit-CydC	gnl\|CDD\|227320	COG4987, CydC, ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones].	0
NC_013768.1\|WP_003732084.1\|162312_164052_+\|DNA-polymerase-III-subunit-gamma/tau	gnl\|CDD\|235505	PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated.	0
NC_013768.1\|WP_012951100.1\|166372_167212_-\|Cof-type-HAD-IIB-family-hydrolase	gnl\|CDD\|319818	cd07516, HAD_Pase, phosphatase, similar to Escherichia coli Cof and Thermotoga maritima TM0651; belongs to the haloacid dehalogenase-like superfamily. Escherichia coli Cof is involved in the hydrolysis of HMP-PP (4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate, an intermediate in thiamin biosynthesis), Cof also has phosphatase activity against the coenzymes pyridoxal phosphate (PLP) and FMN. Thermotoga maritima TM0651 acts as a phosphatase with a phosphorylated carbohydrate molecule as a possible substrate. Escherichia coli YbhA is also a member of this family and catalyzes the dephosphorylation of PLP, YbhA can also hydrolyze erythrose-4-phosphate and fructose-1,6-bis-phosphate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.	1.59066e-84
NC_013768.1\|WP_003722073.1\|154557_155496_+\|GW-domain-containing-glycosaminoglycan-binding-protein	gnl\|CDD\|226309	COG3786, COG3786, Uncharacterized protein conserved in bacteria [Function unknown].	6.39605e-99
NC_013768.1\|WP_003728591.1\|159634_160999_+\|PTS-sugar-transporter-subunit-IIC	gnl\|CDD\|224372	COG1455, CelB, Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism].	1.91509e-162
NC_013768.1\|WP_003722065.1\|161557_162022_+\|DUF3284-domain-containing-protein	gnl\|CDD\|378692	pfam11687, DUF3284, Domain of unknown function (DUF3284). This family of proteins with unknown function appears to be restricted to Firmicutes.	5.35099e-31
NC_013768.1\|WP_003732079.1\|169283_170273_-\|dihydroxyacetone-kinase-subunit-DhaK	gnl\|CDD\|237724	PRK14481, PRK14481, dihydroxyacetone kinase subunit DhaK; Provisional.	0
NC_013768.1\|WP_003722062.1\|164507_165104_+\|recombination-protein-RecR	gnl\|CDD\|234616	PRK00076, recR, recombination protein RecR; Reviewed.	7.77001e-132
NC_013768.1\|WP_003722061.1\|165118_165364_+\|YaaL-family-protein	gnl\|CDD\|378478	pfam10704, DUF2508, Protein of unknown function (DUF2508). This family is conserved in Firmicutes. Several members are annotated as being the protein YaaL. The function is not known.	2.68189e-15
NC_013768.1\|WP_012951101.1\|167330_168182_-\|MurR/RpiR-family-transcriptional-regulator	gnl\|CDD\|224651	COG1737, RpiR, Transcriptional regulators [Transcription].	3.97147e-62
NC_013768.1\|WP_003728589.1\|161357_161540_+\|DUF3188-domain-containing-protein	gnl\|CDD\|371501	pfam11384, DUF3188, Protein of unknown function (DUF3188). This bacterial family of proteins has no known function.	4.70726e-11

>NC_013768.1|WP_003722065.1|161557_162022_+|DUF3284-domain-containing-protein
MNVTQKLYISQKECFDTLVSSAIYDVKNATGKTLQVRKLEGYKYQRTMSNGALATTKIVKVQPNELYQFETSSRVNTHTTTYTIKSTSETTCEVTYNELIETEKALNKMNNIIVGFMFGFFRKKRVKNLLKSIELSVINESKQKQEKLAAKSEQ
>NC_013768.1|WP_003728589.1|161357_161540_+|DUF3188-domain-containing-protein
MKIVNALFIISIGLIIIMFSPSYGKDGMASVPLLVTGLAVVLIGCVFIVLKIRKDKKEKN
>NC_013768.1|WP_003728590.1|161133_161355_+|hypothetical-protein
MIILNCPMKRDYITELLETHDKDGVTFKKIAEQGMKLTFETNIEDEEKAAKIAKETIKATEIGSVLYFQVSVG
>NC_013768.1|WP_003728591.1|159634_160999_+|PTS-sugar-transporter-subunit-IIC
MNGLTAFLEKYFVPVAAKIGSQKHLVALRDAFISTMPITMAGSIAVLLNAFFRDFPTDWGWTGFVEAMQPLIDINGYVYNGTLAIVSIIFAFSLGYNLSKAYEVDRLAGGLVSLAAFVMNLTVTVSLDAVKAAIAASNANFDVATLPKEFAGIYGFFSLSQVNGTGLFTAMIFGFISTIIYAKLMRRNIIIKMPDSVPPAVSKAFAAIIPALVALYVVGIIDWAFFKITNMDVITWISKTIQEPLLSLSQGYGAVLLVTFLVQLLWFFGIHGPNVLAPVLESLWGTAQLQNISAAQDGAKLPFEWVRGSFDAYVWMGGSGGTLVLIIALLMFSKRADARTVAKLSLAPGIFNINEPIMFGLPIVLNTIYLIPFLIAPMVMVTIAYFATTLGIVGPVKIAVVWVMPPLLNSFLATGGDWMAPVISLINMVVAFLIWVPFVITANRVGVPEEEMKA
>NC_013768.1|WP_009931588.1|159036_159192_-|hypothetical-protein
MAVKRDMPEESKNSKVVKKEHFSIVFPDDIKEPATVEEKKKQDAEKKTDDN
>NC_013768.1|WP_009925039.1|157823_158465_+|hypothetical-protein
MQQLKSKKKWLPALIVAVFVGIIVILAIMFGFFQRQEVFDKYEVAYEIDGKLYEVFPISATDIGVDKKSKDKNLYFRVNSYYNIDYLFRLAYKQYEINEPSTNKYYSGLIDYSVADNAYVTQKDVYITNNESYATYDFFDKNGKKIYTYNPEETSNDDYIVRIKPTILQGYEKSDIGSYDDYLNITALFKDKLGMDVNVRIDEDKEMVIFSIK
>NC_013768.1|WP_003732087.1|155611_157126_+|gluconokinase
MTSKPYIMGVDIGTSSTKAVLFNQRGEVIFRQATHYELITDETGKAEESPTEIFDAVLTSIQAVMKNINTEELAGISFSSAMHSLIMVGSNGELLTECITWADGRSSETLEKVKRDNYLFQLYEATGTPIHPMSPFAKICWLKEEKPTLFKRTEKFVDIKSYILYRLFGVWVMDESLASGTGLYNIMEHDWEFEAMEIVKLTPDFLPKVVPETYQLAGVKKEYAELMGIPENLPFIIGGSDGALANIGIQATGQNDVTITVGTSGAVRKLTDQFQIDSRGRTFCYGAGDGYFIAGGAVNNGGKVVEWGLQQFGSEAEISRRDFASFIAKIEEVPPGAAGLLFQPYLLGERAPFWTNDIRGGFVGLTINHTKAHFIRAILEGVAFNLAEVYEAVSAPDDIIYVTGGISAHDAWCKLLADILNREIRVPHTIEGSSLGAAIIGMRSLGILKDLNLKHTLPIKAVYHPSENVLKYAELRLIFKQVTTQLMSSYSQLNSWQKKFDINS
>NC_013768.1|WP_003722073.1|154557_155496_+|GW-domain-containing-glycosaminoglycan-binding-protein
MKKLLSGLIVVLMVSLLGHSFNAEAASYEKIIYDKAVNLKGVVNQSKRNDGINSKMYKTSSSVKYLGSAKKYDKKTLIITREGKTARAKWYYCKLGNTTIGWIDSRAFTNIGKPTIADTVPALWNSKKAIITTKPKSTTATTYFFQKNSAGNWYEVRHFTSHIGKWGFDPKFSEKSSGTPVGVYRTGIAFGQKGNPGTKLTFRAITNRSYWISNSNDKAYNTWQERNSSSSADEKMKIPQYKYGMEVKYNAKRVKGKGSAVFYHVDSPKYNYTLGCVAQSEANTKEVLKFADKNTLIVLGEESRIKTFYGIN
>NC_013768.1|WP_003722074.1|153567_154515_+|LPXTG-cell-wall-anchor-domain-containing-protein
MKKFHGLILTALVTCLIIPFSLAASAETNENGNNSTPTEEKTTDTTENIITEEKTEPAEPTKDTTVTPPQKSKVQTTIDITDSQEVYSYEQNSKIDLKDFTATLTDYTDTKLTNYRLAANSKLSTAQTGIQEVTLLGDNEDGKTTAVKLNYLVKEKTAQLTITDMNFDLETKIFTGKTKPFASVYMSSPADENFGEGTTTADKDGYFYAEWATTPKQITAYAFDESGNYSEEVTYQVPAKKQNEAVVTAPDKVKKIETKNAVKSATTKPTDVTKVTKDDKTDLPSTGDKGTEWIFVVAGVIVILVAVLLLRKRKK
>NC_013768.1|WP_003732089.1|151687_153427_+|thiol-reductant-ABC-exporter-subunit-CydC
MRKSSWIIPYIKENRGLFLLVIFLGTLTFASAGALMFTSGHLISKSSLMPESIMAVYISTVGVRAFGIMRSVSRYVERLSSHSLVLRILEKMRVRLYRLLEPQALLLKSRYKTGDILGLLAGDIEHLQNFYLTTMLPAIVSLVLYAGVVIALGAFSIPFAALFVLLIGLLVLVLPWVSLLYARGKNAYLKQGRNSLYQKFTDAVFGISDWKFSGREKTFISNYEKDEADMLRTENKQFHFVNWRDFFSQLVVGFMVIVMVYWSTAESRDGAFSGTMIAAFVLAIMALAEAFVPVSSAISDKSLYQDSLARLDKIEDPALPTFEEETKEIERINTENVVLKAENLTFAYDEKSPEILNGFDFTLQQGEKVAIIGRSGTGKSTFLKLVQGALLPTAGKVTMNDVEVEKLRPQIPELTSMLNQKAHLFSTTVLNNIRLGNQDASDEEVYEAAKKVQLHDFIMSMPDGYHTQMSEMGERFSGGERGRIALARILLQNTPIVILDEPTVGLDPITERDLLATIFETLADKSLIWVTHHLVGAEKMDRVLFLEEGKTLMEGPHAELMAEEPRYKRLYQLDRPIEL
>NC_013768.1|WP_003732084.1|162312_164052_+|DNA-polymerase-III-subunit-gamma/tau
MAYQALYRVFRPQSFQDVVGQEHVTKTLKNAIVQNKTSHAYLFSGPRGTGKTSAAKIFAKAINCEHGHDGEPCNECEICKGTTDGSIPDVLEIDAASNNGVEEIRDIREKVKYAPTVAKYKVYIIDEVHMLSTGAFNALLKTLEEPPKHVIFILATTEPHKLPLTIISRVQRFDFKRITTQDIIGRLKFILEEEKIPYDEKALMIVARAAEGGMRDALSLLDQVISYGSEEVTVEDALEITGSVAQNLLTKLVSAAFDGDAAEAISTLTALLAEGKDPVRLVEDLLVFFRDVLLYQKAPNLEETMERALIDDDFVALAKRADSLKVYEFVKILNTAQQQMRFSNHPGIYVEVALVQLTQAGQSVAGGGNVPADAASGSDVSDLKRQMEQMHQEIQTLKKQIASGAGAAPADKPTQNRGGSKKAINNGKQFKAPIGKINHVLGEAKKENLQLIRGCWGELLSMLMASQAALLNDAEPVAASQDTFVLKFKHEIHCQMAMDNPNFVETITSSIARLTQVNYTFIGIPEDQWADVRENFLHSHGSDADAEDGANPEAKKPAEDPFVAEAAKLVGEDLLEIKD
>NC_013768.1|WP_003722063.1|164081_164399_+|YbaB/EbfC-family-nucleoid-associated-protein
MRGMGNMQGMMKQMQKMQKEMAKAQADLEAQEFTGTAGGGMVTVKATGKRVITDVVINEEVVDPEDIEMLQDLVLAATNDVLKQIEDTTSQTMGKFTQGLNIPGM
>NC_013768.1|WP_003722062.1|164507_165104_+|recombination-protein-RecR
MHYPEPITKLIDSFMKLPGIGPKSAARLAFYVLDMKEDDVLDFAKALVDAKRNLSFCSVCGHITDKDPCYICADTSRDRSVICVVQESKDVIAMEKMRDFHGLYHVLHGTISPMDGIGPEDINIPDLLKRLQDDTIEEVILATNPNVEGEATAMYISRLLKPSGIKVTRIAHGLPVGGDLEYADEVTLSKAMEGRREV
>NC_013768.1|WP_003722061.1|165118_165364_+|YaaL-family-protein
MESRSNKFGRKKNKKIGKLHKSYDAYLMELIEVTQENWHKQKVLMRKSFEYDPNLEYEEKKAEARYFYLFKEARTRQLKNK
>NC_013768.1|WP_009931159.1|165409_166252_-|aldo/keto-reductase
MTLSFSDTYRLNNGIEMPRHGFGVYKLTDEARMRTALETAVDVGYRLFDTASFYHNEKELGDFFASSGLKRDEFFVTTKMWNTEQGYDETLRAFEKSQKKLQLDQIDLYLVHWPKQDTFFDTWRAVEKLYDEGLVRAIGVSNFEAHHLDRLRTSANVLPVVDQLETHPHFPNHLLHRYLEELHIVHQAWSPLGRGGVLQEQILIDLAEKHGKSPAQIVLRWHLQNNISIIPKSETPSRIRENAAIYDFELSEADMRQVERLNTGERVSHAPDVMYVRSEI
>NC_013768.1|WP_012951100.1|166372_167212_-|Cof-type-HAD-IIB-family-hydrolase
MTTQAIILDIDGTLLNDDKQISPETKKALITAQENGVKLILASGRPTTGMHVYAEQLEMEKHHGLLVSYNGAKVVDCATNEELFNQALTVEEGKAVLEHMKQFEVKVMIDKEDYMYTNDVYDCYVPYRGEEINIIQYESRGGNFKLCEKDDLAAFLDYRLSKILTAGDPAYMQKNYQAMMAPFKDTLNCVFTADFYFEFTAQGIDKAKALDTVLTPMGIHAENIVAFGDGHNDITMVEYAGTGIAMQNAVVELKAAASSVTLSNNEDGIAHVLNSLIPS
>NC_013768.1|WP_012951101.1|167330_168182_-|MurR/RpiR-family-transcriptional-regulator
MNILIKIRELTNLTNSEKELANYILVNPKKTLQFKPKELAAAAFVSAATIYRLINKLGLNGIGELKIEIASSLRETNAEKDINYDYPILESDTPYQIMTNLNQIYKGTIDETLNNADPEELVKIGEKLINAKTIDVYAASANLFFAQNFKFQMQEIGVLVNVPEEDYIQSLSAANSDENHIAIVVSYGGRSRTLQRVVKILSENNVDIILITSMQDNPLVEFATHKIYMASAENHYNKVSSFSTRQSLLSIFDTLYSIYFNQNYEKNIQYKTTNYQKMNTELE
>NC_013768.1|WP_009913205.1|168287_168662_-|PTS-dependent-dihydroxyacetone-kinase-phosphotransferase-subunit-DhaM
MTKPYGVVIISHSKDVAKGVHDIIKEIAPDVSITHAGGTEDGRIGTSFDAVNEAIESNEADKVYTFYDLGSAKMNIETVEEISEKEIILFNAPILEGAYATAAQVQMDEKPEVIAANLKTIEIK
>NC_013768.1|WP_012951102.1|168665_169262_-|dihydroxyacetone-kinase-subunit-L
MTYDKDWALRWLNDFGERVQENKQLLSDLDQAIGDGDHGINMARGLSELKKVFTEKEPADLKDVFKTAGMTMVSKVGGASGPLYGTAFLNMSKAVDADTIDAVGLTKVIEAGLEGIEKRGKSHAGEKTMIDVWEPVVHALHQEDLTDDVVDAALQKTKDLKATKGRASYLGERSIGHLDPGAYSSALLFHAMLQTEVS
>NC_013768.1|WP_003732079.1|169283_170273_-|dihydroxyacetone-kinase-subunit-DhaK
MKKILNGTDQVVEQMVEGLVKSHADVVHRVEGTRVIARNDKRPGKVGLVSGGGSGHEPAHAGYVGRGMLSAAVCGDVFTSPTPDQIYEGIKAADQGAGVLLIVKNYTGDVMNFEMAADLADADDIKVEQIVVDDDIAVEDSTFTTGRRGVAGTVLVHKIIGAAAEAGASLDELKALGEKVIASVKTLGVALSPCTVPEVGHPGFELGDDEIELGIGIHGEPGFTREKIMPSASLAKQLYERISNESKLLAGDKVVVLVNGMGATPLMEQYVFANDVHELLKNAGVQVAKTLVGDYMTSLEMAGLSLTILKLEDEKWVDMLKLPVDTIAW

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Crispr_ID: NC_013768_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_013768_2

539209-539686

Orphan

I-A

Consensus_repeat	Method
GTTTTAGTTACTTATTGTGAAATGTAAAT	PILER-CR
GTTTTAGTTACTTATTGTGAAATGTAAAT	CRT
TTTTAGTTACTTATTGTGAAATGTAAAT	CRISPRCasFinder

7 spacers

The CRISPR arrays of NC_013768_2

>merge|NC_013768|2|539209-539686|PILER-CR,CRT,CRISPRCasFinder
GTTTTAGTTACTTATTGTGAAATGTAAATACAGATCAAACTCCGGAAGGGTGATTGTAAATGGCGTTTTAGTTACTTATTGTGAAATGTAAATTGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGCGTTTTAGTTACTTATTGTGAAATGTAAATGCGATTTTTGTCAAAGGGACAGCGATGGGTTACAAGTTTTAGTTACTTATTGTGAAATGTAAATTTTTCTACTCCTGCTTCTAAAATGTCGTTTATAAGTTTTAGTTACTTATTGTGAAATGTAAATCTAAAACATCCTTCACTGTATCAACTCCTTTCTATATTTTAGTTACTTATTGTGAAATGTAAATAAAATAGGAGGAAATAAATTATGACTATCAAATTAAGTTTTAGTTACTTATTGTGAAATGTAAATTTTGTTGAATCAACGGATATAGATTTTACAATTTCGTTTTAGTTACTTATTGTGAAATGTAAAT

>NC_013768|2|1|539209-539686|PILER-CR
GTTTTAGTTACTTATTGTGAAATGTAAAT	ACAGATCAAACTCCGGAAGGGTGATTGTAAATGGC
GTTTTAGTTACTTATTGTGAAATGTAAAT	TGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGC
GTTTTAGTTACTTATTGTGAAATGTAAAT	GCGATTTTTGTCAAAGGGACAGCGATGGGTTACAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TTTTCTACTCCTGCTTCTAAAATGTCGTTTATAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	CTAAAACATCCTTCACTGTATCAACTCCTTTCTAT
ATTTTAGTTACTTATTGTGAAATGTAAAT	AAAATAGGAGGAAATAAATTATGACTATCAAATTAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TTTGTTGAATCAACGGATATAGATTTTACAATTTC
GTTTTAGTTACTTATTGTGAAATGTAAAT

>NC_013768|2|1|539209-539686|CRT
GTTTTAGTTACTTATTGTGAAATGTAAAT	ACAGATCAAACTCCGGAAGGGTGATTGTAAATGGC
GTTTTAGTTACTTATTGTGAAATGTAAAT	TGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGC
GTTTTAGTTACTTATTGTGAAATGTAAAT	GCGATTTTTGTCAAAGGGACAGCGATGGGTTACAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TTTTCTACTCCTGCTTCTAAAATGTCGTTTATAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	CTAAAACATCCTTCACTGTATCAACTCCTTTCTAT
ATTTTAGTTACTTATTGTGAAATGTAAAT	AAAATAGGAGGAAATAAATTATGACTATCAAATTAA
GTTTTAGTTACTTATTGTGAAATGTAAAT	TTTGTTGAATCAACGGATATAGATTTTACAATTTC
GTTTTAGTTACTTATTGTGAAATGTAAAT

>NC_013768|2|2|539210-539686|CRISPRCasFinder
TTTTAGTTACTTATTGTGAAATGTAAAT	ACAGATCAAACTCCGGAAGGGTGATTGTAAATGGCG
TTTTAGTTACTTATTGTGAAATGTAAAT	TGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGCG
TTTTAGTTACTTATTGTGAAATGTAAAT	GCGATTTTTGTCAAAGGGACAGCGATGGGTTACAAG
TTTTAGTTACTTATTGTGAAATGTAAAT	TTTTCTACTCCTGCTTCTAAAATGTCGTTTATAAG
TTTTAGTTACTTATTGTGAAATGTAAAT	CTAAAACATCCTTCACTGTATCAACTCCTTTCTATA
TTTTAGTTACTTATTGTGAAATGTAAAT	AAAATAGGAGGAAATAAATTATGACTATCAAATTAAG
TTTTAGTTACTTATTGTGAAATGTAAAT	TTTGTTGAATCAACGGATATAGATTTTACAATTTCG
TTTTAGTTACTTATTGTGAAATGTAAAT

Protein	Signature genes	Signature genes Name	Protein_function
NC_013768.1\|WP_012951245.1\|534607_535258_+\|ribulose-phosphate-3-epimerase	unknown	unknown	gnl\|CDD\|223114
NC_013768.1\|WP_003721297.1\|540762_541443_+\|type-1-glutamine-amidotransferase	unknown	unknown	gnl\|CDD\|153212
NC_013768.1\|WP_012951247.1\|540077_540656_+\|hypothetical-protein	unknown	unknown	unknown
NC_013768.1\|WP_012951251.1\|545087_546518_-\|CapA-family-protein	unknown	unknown	gnl\|CDD\|225399
NC_013768.1\|WP_003721303.1\|546638_547454_-\|histidine-phosphatase-family-protein	unknown	unknown	gnl\|CDD\|223483
NC_013768.1\|WP_003733193.1\|531020_533081_+\|BglG-family-transcription-antiterminator	unknown	unknown	gnl\|CDD\|226234
NC_013768.1\|WP_003721293.1\|536316_536610_+\|PTS-sugar-transporter-subunit-IIB	unknown	unknown	gnl\|CDD\|99908
NC_013768.1\|WP_014601718.1\|541467_541827_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|131113
NC_013768.1\|WP_012951243.1\|530261_530912_+\|transaldolase	unknown	unknown	gnl\|CDD\|223254
NC_013768.1\|WP_003721294.1\|536624_537896_+\|PTS-galactitol-transporter-subunit-IIC	unknown	unknown	gnl\|CDD\|226298
NC_013768.1\|WP_003721301.1\|544609_545041_+\|universal-stress-protein	unknown	unknown	gnl\|CDD\|366180
NC_013768.1\|WP_012951246.1\|535254_536301_+\|galactitol-1-phosphate-5-dehydrogenase	unknown	unknown	gnl\|CDD\|176198
NC_013768.1\|WP_003733187.1\|541833_542292_-\|MarR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|378956
NC_013768.1\|WP_003727295.1\|548249_549665_+\|multidrug-efflux-MFS-transporter	unknown	unknown	gnl\|CDD\|129794
NC_013768.1\|WP_003721290.1\|534198_534597_+\|hypothetical-protein	unknown	unknown	unknown
NC_013768.1\|WP_012951252.1\|547734_548103_-\|DUF1304-domain-containing-protein	unknown	unknown	gnl\|CDD\|226282
NC_013768.1\|WP_003733190.1\|538035_538971_+\|ribose-phosphate-pyrophosphokinase	unknown	unknown	gnl\|CDD\|234929
NC_013768.1\|WP_003733191.1\|533714_534182_+\|PTS-sugar-transporter-subunit-IIA	unknown	unknown	gnl\|CDD\|238129
NC_013768.1\|WP_012951250.1\|542673_544509_+\|lmo0514-family-class-1-internalin	unknown	unknown	gnl\|CDD\|380190
NC_013768.1\|WP_012951244.1\|533084_533687_+\|SIS-domain-containing-protein	unknown	unknown	gnl\|CDD\|223865

Protein	Function_ID	Function_description	E-value
NC_013768.1\|WP_012951245.1\|534607_535258_+\|ribulose-phosphate-3-epimerase	gnl\|CDD\|223114	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism].	8.25352e-108
NC_013768.1\|WP_003721293.1\|536316_536610_+\|PTS-sugar-transporter-subunit-IIB	gnl\|CDD\|99908	cd05566, PTS_IIB_galactitol, PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.	3.06007e-27
NC_013768.1\|WP_012951244.1\|533084_533687_+\|SIS-domain-containing-protein	gnl\|CDD\|223865	COG0794, GutQ, Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane].	5.57544e-75
NC_013768.1\|WP_012951251.1\|545087_546518_-\|CapA-family-protein	gnl\|CDD\|225399	COG2843, PgsA, Putative enzyme of poly-gamma-glutamate biosynthesis (capsule formation) [Cell envelope biogenesis, outer membrane].	7.01384e-100
NC_013768.1\|WP_003733193.1\|531020_533081_+\|BglG-family-transcription-antiterminator	gnl\|CDD\|226234	COG3711, BglG, Transcriptional antiterminator [Transcription].	3.95572e-80
NC_013768.1\|WP_003721297.1\|540762_541443_+\|type-1-glutamine-amidotransferase	gnl\|CDD\|153212	cd01741, GATase1_1, Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved. GATase activity can be found in a range of biosynthetic enzymes, including: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase , anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides, as in glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase.	7.71833e-60
NC_013768.1\|WP_014601718.1\|541467_541827_-\|hypothetical-protein	gnl\|CDD\|131113	TIGR02058, lin0512_fam, conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus. [Hypothetical proteins, Conserved].	4.36834e-66
NC_013768.1\|WP_012951243.1\|530261_530912_+\|transaldolase	gnl\|CDD\|223254	COG0176, MipB, Transaldolase [Carbohydrate transport and metabolism].	1.0547e-61
NC_013768.1\|WP_003721294.1\|536624_537896_+\|PTS-galactitol-transporter-subunit-IIC	gnl\|CDD\|226298	COG3775, GatC, Phosphotransferase system, galactitol-specific IIC component [Carbohydrate transport and metabolism].	7.01085e-178
NC_013768.1\|WP_003721301.1\|544609_545041_+\|universal-stress-protein	gnl\|CDD\|366180	pfam00582, Usp, Universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, though UspA lacks ATP-binding activity.	4.03126e-27
NC_013768.1\|WP_012951246.1\|535254_536301_+\|galactitol-1-phosphate-5-dehydrogenase	gnl\|CDD\|176198	cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This group contains proteins identified as sorbitol dehydrogenases and other sugar dehydrogenases of the medium-chain dehydrogenase/reductase family (MDR), which includes zinc-dependent alcohol dehydrogenase and related proteins. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Related proteins include threonine dehydrogenase, formaldehyde dehydrogenase, and butanediol dehydrogenase. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Horse liver alcohol dehydrogenase is a dimeric enzyme and each subunit has two domains. The NAD binding domain is in a Rossmann fold and the catalytic domain contains a zinc ion to which substrates bind. There is a cleft between the domains that closes upon formation of the ternary complex.	0
NC_013768.1\|WP_003733187.1\|541833_542292_-\|MarR-family-transcriptional-regulator	gnl\|CDD\|378956	pfam12802, MarR_2, MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.	1.03599e-12
NC_013768.1\|WP_003727295.1\|548249_549665_+\|multidrug-efflux-MFS-transporter	gnl\|CDD\|129794	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Other].	3.97112e-80
NC_013768.1\|WP_003721303.1\|546638_547454_-\|histidine-phosphatase-family-protein	gnl\|CDD\|223483	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only].	5.01016e-50
NC_013768.1\|WP_012951252.1\|547734_548103_-\|DUF1304-domain-containing-protein	gnl\|CDD\|226282	COG3759, COG3759, Predicted membrane protein [Function unknown].	8.73125e-42
NC_013768.1\|WP_003733190.1\|538035_538971_+\|ribose-phosphate-pyrophosphokinase	gnl\|CDD\|234929	PRK01259, PRK01259, ribose-phosphate diphosphokinase.	1.26262e-153
NC_013768.1\|WP_012951250.1\|542673_544509_+\|lmo0514-family-class-1-internalin	gnl\|CDD\|380190	NF033186, internalin_K, class 1 internalin InlK. Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface-anchored proteins with an N-terminal signal peptide, leucine-rich repeats, and a C-terminal LPXTG processing and cell surface anchoring site. Members of this family are internalin K (InlK), a virulence factor. See articles PMID:17764999. for a general discussion of internalins, and PMID:21829365, PMID:22082958, and PMID:23958637 for more information about internalin K.	8.58129e-120
NC_013768.1\|WP_003733191.1\|533714_534182_+\|PTS-sugar-transporter-subunit-IIA	gnl\|CDD\|238129	cd00211, PTS_IIA_fru, PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.	2.76446e-37

>NC_013768.1|WP_003733190.1|538035_538971_+|ribose-phosphate-pyrophosphokinase
MAGKMKLFSVTSERPLATKIADYLDIPLCEVELQKFSDGEVKINIEESIRGTNAYVVQSMNSNVNERLMELLIMVDALKRASVHSINIIMPYYGYARQDRKARSREPITAKLMANLIQRAGANRLITVDLHAAQIQGFFNIPIDHLSAIPLIGDYLIENYGEKDVVVVAPDHSGVVRARRIADRLNAPIAILNRKPRPHEDEIMSVIGDVKGKVAIVVDDIIDTGVRATTSADILLEKGAVEVIACATHSVMAGNATERLQNSNIKEVITSDSIDLPEDKQFDKLTTISIGRILGRAIEGVQENRSLHPLF
>NC_013768.1|WP_003721294.1|536624_537896_+|PTS-galactitol-transporter-subunit-IIC
MDIILDFFKYIIGLGVTVMMPIIITILGVIFRKKISVAFKAGLTVGVGFVGLGVITSLMLTTITPVTKALVENYNFKLTATDIGWGVGSSLAWGTEVVPFVFVAIIATNILMIAFKWTKTMDVDIWNYWQPLFIASALYLTTGSMIIAVLSSIINMAIIFKIADWTQKDVEDVLGLEGISLPQIQTTGWALVGYPMNWLLGKIPGVRKINWSTEKVQSRLGIFGEPMLMGLIIGGGLAAIAQMPLSQVLQTGVTIAASLVLIPRMVSLLMDGLTVISEAAHEFMEKRFPGRELFIGLDSAVGIGHPFVLSLGLLMIPITLILAFILPGNKVLPLADLTALPFYMIFAIVPSKGNLFRGIFTGIVIVIITLYLSGAAAPLMTELAGQIGYNIPKDAVEVTSLAVGTQWYTWIVYYGLHWFGGIL
>NC_013768.1|WP_003721293.1|536316_536610_+|PTS-sugar-transporter-subunit-IIB
MKKKRIYVCCGTGIATSTVISKKVRAVLDEKRIPYEISQCTVQEVASKVSTSKPDIIVSSTTVTGDVGDVPVVIGRSFLTGLKKQETIDEILAILQD
>NC_013768.1|WP_012951246.1|535254_536301_+|galactitol-1-phosphate-5-dehydrogenase
MKALKLYGKRDLRYEEADMPTIEEPDDVILKVKTVGICGSDISRYSKLGPYVPGMVWGHEFSGEVIEVGSEVTDIEIGDRAAGCPALYCGECEYCKKGEFARCRKLTVIGARHPGAYAEYIKLPAENVVKIPDELDYEAAALVEPSAVVVHGFYHTKLQAGDDVVVVGSGNIGLLAIQWAKVFGARRVIAIDVDDKKLALAKEVGADVVINSLKEDPLEVVAAHTDGLNADLVVEAAGSPITSAQVFAYAKKGGGVVFLGIPYADVTIERFYFEKIVRSELTVWGSWNAISAPFPGKEWQTTIHFLANKQINIEPMITHRLSLAEGPEVFERIYERNEFFGKILFFPE
>NC_013768.1|WP_012951245.1|534607_535258_+|ribulose-phosphate-3-epimerase
MAKIVPSVFGADIGRINEQLQVLEKNDIDLLHVDMMDGSFVPNIAFGPDQIKMMKKGTKLQFDVHMMVYEPDRYIPRLVEAGAHMITVHQEATTHLHRTIQLIKSYGVRAGVVLNPGTPPSTLEYVLDDIDCILLMTVNPGLGGQKFFQSSLEKIRKTKAYIGNRPIQIEVDGGVNAELAKECTLAGADLIVVGSYLFEGDIEANLEKLAKGVLTE
>NC_013768.1|WP_003721290.1|534198_534597_+|hypothetical-protein
MGSFFASFVDWLIGSPGRFVVNLIEDNMLIFMVVVMIYATTILYAKWTLAYYLPKKMSQLAEMKTWELDELYAAWQTEKKALPWYILVPSRNEFWVKSARNAPESTKLLHFSQQKLKLSDKEKLQKIIEIQS
>NC_013768.1|WP_003733191.1|533714_534182_+|PTS-sugar-transporter-subunit-IIA
MDVLEYFKEEMVRFSNEQNKEKLLAEMAEQLCEVGAVKPSYKDAVIKREKVFPTGLLTAHAGVAIPHTDSEHVIRPVVAVRILKKPVSFIEMASDNEAIDVRIVFMMALRSADEQLDMLQTLIQLIQDEEVMTTLLKAQETGDVLSAIEHFSKNN
>NC_013768.1|WP_012951244.1|533084_533687_+|SIS-domain-containing-protein
MDKQAILNNIHQTWQEEANAISRLPEVTSEEALVKTVEKIAECTGKIVVAGCGTSGVAAKKLVYSFNCIERPAVFLTPSDAVHGTLGVLQKEDILILISKGGNTGELLNLIPACKTKGSTLIGVTENPDSVIAKEADIFFPVSVSKEPDPFNMLATASTMAVIASFDAVIVCLMTYMNYTKEQFSVIHPGGAVGNKLLNK
>NC_013768.1|WP_003733193.1|531020_533081_+|BglG-family-transcription-antiterminator
MYLDNRSKTLFQEVIKNPNITNKQLEVKYKLSRYQISYSFQKVNEWLKWKNYPEVKRSKNGRFILEPELTALFSEKETRDPSVEYLPSENERANLILLMLLTSKEELSLAHFTTKIQVSKNTILRDLKVAQKLLPKETTVTYSRASGYQLAGSEWELRKVLTQVVSSVKEMFRGEHYFLSYSGIEKVQLMEIRRTLEEAEAMMQIKFTYEQIELLPYLLSVMFLRIRDRRLIDTAFHIDEKSLSDTREYHITDILLEKTGPVPEQERLFITLQLLTTNIFSGEILTEKLTEDLEKVVLTCLDLFEKKALVSLKNKHILIEKLLLHLKPAYYRIKYQMNLEDTLYEKFNQEFEALNFIVKEAFDPLAKFIGREIPAGEIFFISLFIGSDMIPQNDIYHKQKRAIVLCPSGVTFSKIMENILVKLFPEIHFYPTISVREYAFFKAEVDIVFSSIPLKDGENVFVVQPFMNDIEKTQLRQHVLQNLFGMGNQLTSIDKIMEVVERNADIKDPNAIRDGIIDILSANTATDENKRVKKVYLHDLITEDNIMICEDVKNYQEAIRLASQPLLLQQAITANYVKTMIDNHKFHDPYIIIGEDIAIPHAMPNAGVNRLAMSLLVVKNGVYFSETEQVHFVIVIAPVDKEQHIEALYQIVHLAENHQILDDLLENVTKEKIMQTINQLVIREDE
>NC_013768.1|WP_012951243.1|530261_530912_+|transaldolase
MHLDSANLDDVKKIQASSIFKGITTNPTILVKEKCNRQTAINRILELTDKQVFVQTVGFTYEEILADARMLLTMFGKDKIAIKIPAHEAGTNVIDTLKKEDKTIQILGTAIYSADQAITAALVGADFVAPYVNRMSAANIDPFKEIRQMRHFFDKKALKTQIMAASFKHSGQVMQAYESGADTVTIPYEIYLQMTNKVLAVEAIRVFNEDAVLYEK
>NC_013768.1|WP_012951247.1|540077_540656_+|hypothetical-protein
MKKILVPILLLATILASCSSPNEKITKDTKISKTNTIRADYKVPKDIKELEDDSANIVKVKFLQNKTIGKDGSTISEIEILTSYKGNLEKGSKVDISEPWYLSDGKYVAVENYIALDKEQEYTIFLGEKDKDTYPLSSLGYGKFGGSLKEDQAVLADFNILGEVQKFDFISENTEEVKNYQLIKEQVAGKYK
>NC_013768.1|WP_003721297.1|540762_541443_+|type-1-glutamine-amidotransferase
MIIDVLQHVPHEGPGLIANWARENQHQLKIHSLFEENAHVPNDSDFLIVLGGPMGINDTAEFPWLKDERKLIKRLSEQHKPVFGVCLGAQQIAATFGSEITVNKEKEVGWFPVKRTSDKLLFFPESLNVFHWHQDTFALPTGSTRLFASEGCLNQAFLYGENIIGLQFHFEMEKAGIETILRIDEAFITPGKYVQSVEVMREKDVPEDNKQMLEAILDYLINPKTI
>NC_013768.1|WP_014601718.1|541467_541827_-|hypothetical-protein
MEQILFIQTGFGVDVHGQNITNAAERAVRNAIFTNSMPGIQGLLPDGDLQNMVVNIKLALPCDADQLDEDTIRAIIPYGTVTIEKMAGGMMTTSGIFLEDKEDKNDLMYIVNASVETGY
>NC_013768.1|WP_003733187.1|541833_542292_-|MarR-family-transcriptional-regulator
MNNEQNMNQQIALFYFGYKAFTETADLIIAKHSLKRLHHRILFFTARMPGLTINELLTFLEISKQALHQPLAELKERELLTIEQGRRDKRQRCIFLTAAGKELENELGAAQRKQMSEIFTNSADTDGMHFTEVMEGYAKNRPGAAFIKDFKE
>NC_013768.1|WP_012951250.1|542673_544509_+|lmo0514-family-class-1-internalin
MKKALKLFLATICMFIMIYPSTAAHAEETNIVNIPDANLKTYLNGLLKQASDAPITKTQMNTIQTVTLSGSTYTDLTGLEEAGNLVTLSLNNTNIQTLEPIKNQTSLTYLTVGGDNVKDSLFVDLNGLVNLQSLSISGSEVTHNVFKTFNKLPKLTYLYAQNSMKITDISALASLPALTTLFLQFDGIDDFRPLNDFESFKNGNLKALAAFGQNTGRTNPRITLKSGKLDYNETNQTLYLPFSMMPKPLTSFDGTVAPFSKSTSASNTYLGFNDVALPSSRLSITDDGITVSGVTKEEFDNLDEIEYNARYDFPTGSYPTPPSMTSYTISSGTYDQYFDISHTLDLTADESFDYNQYDTTSEEQFLKDVHAETDDGTAVKSDFDQVVKLDVPGEYTVTLNAENAAGLKATPVTVKVTVHEKPVITSDSQISYKKETTKSVDEFLKEIHGSVTGNAVLTSDFDKVVDLNTPGEYTVTLNAINDRGQKADPVTVVVTVTTSDSGHVDPVPPTPEIKPTPQEETDQTIIPEPQSETTEDSVKEDQAKDGQAKSEEKADKTSLTTKENKVEKSEKTNQPKTKALPQTGDTNKTALPIAGVMLSLAALLIFRKSKS
>NC_013768.1|WP_003721301.1|544609_545041_+|universal-stress-protein
MEKYHRILVAVDGSEPAKLAFEKGLELALKLDGVLGIASIVDLRAFSPNVSYDGSLEEKAELELKTSVNEYAEKARTAGVKQVETFVAKGNPKILLSTDIPAEFQADLIICGATGMNRVEKLVLGSVSSYIMAHAICDTLIAR
>NC_013768.1|WP_012951251.1|545087_546518_-|CapA-family-protein
MKKLTYVIITGLVLVFIAGAFWITNSTNQSDQKATQTEPIKKISPANVKTISSEAKKTLNSLASSGADKASISDLKQLIKELKSYPTEKNDSGVYLQNLTACLEAVKSYTTGKTDEKTLGKVYPAFLASEQKLSAIEKTNQYDWFYAAAATNQQGLKEKGVVTLTMVGDNSFGTYPETPEHLKFDNVFQKNNGNNTYVYKNCLPWFKSDDYTVINAESAFTNATKAENKKWRIKSDPAHVAFLPASGVDAANLANNHTMDYFQVGYDDTLKAFKENNIPVFNADAPLETTIKGMKTVLLGYDCRMSQQSPAYLERIVKDVKKYKKEDTLVIVNMHWGVEYRETPTDYQTQFGHAILDAGADIIMGSHPHRLESVEKYKDKYIVYSMGDFAFGADPTLLSRMTSMFQLRFTKEDNKIVLKDISIVPTYENSDGSTTENNYQPLPVFGDDAKKIVDELNRISKPIEGGVTEYTYFDPF
>NC_013768.1|WP_003721303.1|546638_547454_-|histidine-phosphatase-family-protein
MKKNIFKLLMALCAVLLIAGCGNSTSADKKETKETKEDGTVTFYVVRHGKTMLNTTDRVQGWSDAVLTPAGEEVVKSAGKGLKDVDFSAAYSSDSGRAIQTANLILKESDKSADKEVQTDPRFREFNFGSYEGDLNENMWTDIAKSQGKTLEEWQKAGLSPKDFANSVAALDKTRVKEGENWPAEDYATIQARLKEGLTDVAKKESKNGDSNVLLVSHGLSIGALLDTIEPGYKLPAEGIKNASVTKITYKDGKFTIGDVNDLSYVEKGSK
>NC_013768.1|WP_012951252.1|547734_548103_-|DUF1304-domain-containing-protein
MAILAFILTFIVMIEHIYIMILEMFFANTKLAAKTFGVEKELLANKKVQTLFANQGLYNGFLAAGLVWGLFFAGAGMAETVQIFFLSCVVVAALFGGATSSKGILVKQGLPAVLALVAVLLV
>NC_013768.1|WP_003727295.1|548249_549665_+|multidrug-efflux-MFS-transporter
MQQEATGGQKIRPIPIIASFLMAGFIGLFSETALNMALSDLIQVFDISSATVQWLTTGYLLTLGILVPISGLLLQWFTTRGLFFTAVSFSIAGTLIAALSPTFAMLMIGRVVQAVGTALLLPLMFNTILLIFPEHKRGSAMGMIGLVIMFAPAVGPTISGLILENLTWNWIFWISLPFLIIALLFGMKFMQNVSVVTKPKIDILSIILSTLGFGGVVFAFSSAGESGWGSATVLVSIIVGGLALGLFVWRQLTMEKPLMDLKVFKYPMFTLGLILVFISFMMILSTMILLPLYLQNSLALAAFSAGLVLLPGGVLNGLMSPFTGRLFDAYGPRALVIPGFIVAVVALFFLTRIEVGTSALTIIVLHSVLMIGISMVMMPAQTNGLNQLPPKLYPDGTAIMNTLQQVSGAIGTAVAITIMSAGQKAYMETAQGVGPEQMVASLTAGIQNAFVFGLIMACIGLLCSLFIRKAK

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Crispr_ID: NC_013768_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_013768_3

2785489-2785640

Unclear

Consensus_repeat	Method
GAGCTCGGTTCCGATGTAGCAGGAGCATTAAAACCAAGAAGCATTGG	CRISPRCasFinder

1 spacers

cas3

The CRISPR arrays of NC_013768_3

>merge|NC_013768|3|2785489-2785640|CRISPRCasFinder
GAGCTCGGTTCCGATGTAGCAGGAGCATTAAAACCAAGAAGCATTGGCGTCTCTGGCAAAGCAAGTCTTAACTCTTCATCCGTAGGTGGTGGTGGAAATTCGAATGAGCTCGGTTCTGATGTAGCAGGAGCATTAAAACCAAGAAGCATTGG

>NC_013768|3|3|2785489-2785640|CRISPRCasFinder
GAGCTCGGTTCCGATGTAGCAGGAGCATTAAAACCAAGAAGCATTGG	CGTCTCTGGCAAAGCAAGTCTTAACTCTTCATCCGTAGGTGGTGGTGGAAATTCGAAT
GAGCTCGGTTCTGATGTAGCAGGAGCATTAAAACCAAGAAGCATTGG

Protein	Signature genes	Signature genes Name	Protein_function
NC_013768.1\|WP_003722729.1\|2791599_2792313_+\|listeriolysin-transcriptional-regulator-PrfA	unknown	unknown	gnl\|CDD\|223736
NC_013768.1\|WP_012952052.1\|2782667_2783129_-\|YehR-family-lipoprotein	unknown	unknown	gnl\|CDD\|227145
NC_013768.1\|WP_009931069.1\|2796543_2797752_-\|FtsX-like-permease-family-protein	unknown	unknown	gnl\|CDD\|182528
NC_013768.1\|WP_003722735.1\|2783263_2783587_-\|DUF5502-family-protein	unknown	unknown	gnl\|CDD\|340321
NC_013768.1\|WP_003722725.1\|2795550_2795859_-\|septation-protein-SpoVG	unknown	unknown	gnl\|CDD\|237321
NC_013768.1\|WP_003722726.1\|2795122_2795431_-\|septation-protein-SpoVG	unknown	unknown	gnl\|CDD\|237321
NC_013768.1\|WP_003722727.1\|2793362_2794736_-\|bifunctional-UDP-N-acetylglucosamine-diphosphorylase/glucosamine-1-phosphate-N-acetyltransferase-GlmU	unknown	unknown	gnl\|CDD\|184643
NC_013768.1\|WP_012952055.1\|2786681_2788214_-\|zinc-metalloproteinase-Mpl	unknown	unknown	gnl\|CDD\|225768
NC_013768.1\|WP_012952053.1\|2783658_2784528_-\|phosphatidylcholine-phospholipase-C	unknown	unknown	gnl\|CDD\|214813
NC_013768.1\|WP_012952051.1\|2778934_2779519_-\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|379228
NC_013768.1\|WP_003722742.1\|2778267_2778828_-\|aminoacyl-tRNA-hydrolase	unknown	unknown	gnl\|CDD\|235457
NC_013768.1\|WP_003722731.1\|2788544_2790134_-\|cholesterol-dependent-cytolysin-listeriolysin-O	unknown	unknown	gnl\|CDD\|366559
NC_013768.1\|WP_009930499.1\|2781543_2782218_+\|DNA-alkylation-repair-protein	unknown	unknown	gnl\|CDD\|378033
NC_013768.1\|WP_003722728.1\|2792355_2793312_-\|ribose-phosphate-diphosphokinase	unknown	unknown	gnl\|CDD\|234929
NC_013768.1\|WP_003722723.1\|2797748_2798441_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|213222
NC_013768.1\|WP_010989376.1\|2774613_2778153_-\|transcription-repair-coupling-factor	cas3	cd09639_cas3_CAS-I	gnl\|CDD\|224118
NC_013768.1\|WP_003722740.1\|2779608_2780232_-\|50S-ribosomal-protein-L25/general-stress-protein-Ctc	unknown	unknown	gnl\|CDD\|235534
NC_013768.1\|WP_003725735.1\|2782284_2782617_+\|putative-heavy-metal-binding-protein	unknown	unknown	gnl\|CDD\|179228
NC_013768.1\|WP_003722739.1\|2780525_2781467_+\|L-lactate-dehydrogenase	unknown	unknown	gnl\|CDD\|178836
NC_013768.1\|WP_012952056.1\|2790375_2791329_+\|phosphatidylinositol-specific-phospholipase-C	unknown	unknown	gnl\|CDD\|176497

Protein	Function_ID	Function_description	E-value
NC_013768.1\|WP_003722729.1\|2791599_2792313_+\|listeriolysin-transcriptional-regulator-PrfA	gnl\|CDD\|223736	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].	9.59942e-12
NC_013768.1\|WP_012952052.1\|2782667_2783129_-\|YehR-family-lipoprotein	gnl\|CDD\|227145	COG4808, COG4808, Uncharacterized protein conserved in bacteria [Function unknown].	1.58576e-57
NC_013768.1\|WP_009931069.1\|2796543_2797752_-\|FtsX-like-permease-family-protein	gnl\|CDD\|182528	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB.	2.47504e-62
NC_013768.1\|WP_003722735.1\|2783263_2783587_-\|DUF5502-family-protein	gnl\|CDD\|340321	pfam17606, DUF5502, Family of unknown function (DUF5502). This is a family of unknown function found in Listeria.	5.76244e-49
NC_013768.1\|WP_003722725.1\|2795550_2795859_-\|septation-protein-SpoVG	gnl\|CDD\|237321	PRK13259, PRK13259, septation regulator SpoVG.	2.92652e-53
NC_013768.1\|WP_003722726.1\|2795122_2795431_-\|septation-protein-SpoVG	gnl\|CDD\|237321	PRK13259, PRK13259, septation regulator SpoVG.	5.03804e-54
NC_013768.1\|WP_003722727.1\|2793362_2794736_-\|bifunctional-UDP-N-acetylglucosamine-diphosphorylase/glucosamine-1-phosphate-N-acetyltransferase-GlmU	gnl\|CDD\|184643	PRK14354, glmU, bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU.	0
NC_013768.1\|WP_012952055.1\|2786681_2788214_-\|zinc-metalloproteinase-Mpl	gnl\|CDD\|225768	COG3227, LasB, Zinc metalloprotease (elastase) [Amino acid transport and metabolism].	9.42667e-139
NC_013768.1\|WP_012952053.1\|2783658_2784528_-\|phosphatidylcholine-phospholipase-C	gnl\|CDD\|214813	smart00770, Zn_dep_PLPC, Zinc dependent phospholipase C (alpha toxin). This domain conveys a zinc dependent phospholipase C activity (EC 3.1.4.3). It is found in a monomeric phospholipase C of Bacillus cereus as well as in the alpha toxin of Clostridium perfringens and Clostridium bifermentans, which is involved in haemolysis and cell rupture. It is also found in a lecithinase of Listeria monocytogenes, which is involved in breaking the 2-membrane vacuoles that surround the bacterium. Structure information: PDB 1ca1.	7.07052e-87
NC_013768.1\|WP_012952051.1\|2778934_2779519_-\|GNAT-family-N-acetyltransferase	gnl\|CDD\|379228	pfam13508, Acetyltransf_7, Acetyltransferase (GNAT) domain. This domain catalyzes N-acetyltransferase reactions.	9.33654e-10
NC_013768.1\|WP_003722742.1\|2778267_2778828_-\|aminoacyl-tRNA-hydrolase	gnl\|CDD\|235457	PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.	4.98809e-109
NC_013768.1\|WP_003722731.1\|2788544_2790134_-\|cholesterol-dependent-cytolysin-listeriolysin-O	gnl\|CDD\|366559	pfam01289, Thiol_cytolysin, Thiol-activated cytolysin.	1.50399e-178
NC_013768.1\|WP_009930499.1\|2781543_2782218_+\|DNA-alkylation-repair-protein	gnl\|CDD\|378033	pfam08713, DNA_alkylation, DNA alkylation repair enzyme. Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.	1.81561e-21
NC_013768.1\|WP_003722728.1\|2792355_2793312_-\|ribose-phosphate-diphosphokinase	gnl\|CDD\|234929	PRK01259, PRK01259, ribose-phosphate diphosphokinase.	0
NC_013768.1\|WP_003722723.1\|2797748_2798441_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|213222	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein. This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of lipoproteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyzes the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.	7.27113e-121
NC_013768.1\|WP_010989376.1\|2774613_2778153_-\|transcription-repair-coupling-factor	gnl\|CDD\|224118	COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription].	0
NC_013768.1\|WP_003722740.1\|2779608_2780232_-\|50S-ribosomal-protein-L25/general-stress-protein-Ctc	gnl\|CDD\|235534	PRK05618, PRK05618, 50S ribosomal protein L25/general stress protein Ctc; Reviewed.	2.38585e-63
NC_013768.1\|WP_003725735.1\|2782284_2782617_+\|putative-heavy-metal-binding-protein	gnl\|CDD\|179228	PRK01119, PRK01119, putative heavy metal-binding protein.	8.98192e-61
NC_013768.1\|WP_003722739.1\|2780525_2781467_+\|L-lactate-dehydrogenase	gnl\|CDD\|178836	PRK00066, ldh, L-lactate dehydrogenase; Reviewed.	0
NC_013768.1\|WP_012952056.1\|2790375_2791329_+\|phosphatidylinositol-specific-phospholipase-C	gnl\|CDD\|176497	cd00137, PI-PLCc, Catalytic domain of prokaryotic and eukaryotic phosphoinositide-specific phospholipase C. This subfamily corresponds to the catalytic domain present in prokaryotic and eukaryotic phosphoinositide-specific phospholipase C (PI-PLC), which is a ubiquitous enzyme catalyzing the cleavage of the sn3-phosphodiester bond in the membrane phosphoinositides (phosphatidylinositol, PI; Phosphatidylinositol-4-phosphate, PIP; phosphatidylinositol 4,5-bisphosphate, PIP2) to yield inositol phosphates (inositol monosphosphate, InsP; inositol diphosphate, InsP2; inositol trisphosphate, InsP3) and diacylglycerol (DAG). The higher eukaryotic PI-PLCs (EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. They play a critical role in most signal transduction pathways, controlling numerous cellular events, such as cell growth, proliferation, excitation and secretion. These PI-PLCs strictly require Ca2+ for their catalytic activity. They display a clear preference towards the hydrolysis of the more highly phosphorylated PI-analogues, PIP2 and PIP, to generate two important second messengers, InsP3 and DAG. InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. In contrast, bacterial PI-PLCs contain a single catalytic domain. Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. They participate in Ca2+-independent PI metabolism. They are characterized as phosphatidylinositol-specific phospholipase C (EC 4.6.1.13) that selectively hydrolyze PI, not PIP or PIP2. The TIM-barrel type catalytic domain in bacterial PI-PLCs is very similar to the one in eukaryotic PI-PLCs, in which the catalytic domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. The catalytic mechanism of both prokaryotic and eukaryotic PI-PLCs is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes a distinctly different type of eukaryotic PLC, glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC), an integral membrane protein characterized in the protozoan parasite Trypanosoma brucei. T. brucei GPI-PLC hydrolyzes the GPI-anchor on the variant specific glycoprotein (VSG), releasing dimyristyl glycerol (DMG), which may facilitate the evasion of the protozoan to the host#s immune system. It does not require Ca2+ for its activity and is more closely related to bacterial PI-PLCs, but not mammalian PI-PLCs.	6.12448e-116

>NC_013768.1|WP_012952053.1|2783658_2784528_-|phosphatidylcholine-phospholipase-C
MKFKKVVLGMCLTASVLVFPVTIKANACCDEYLQTPAAPHDIDSKLPHKLSWSADNPTNTDVNTHYWLFKQAEKILAKDVNHMRANLMNELKKFDKQIAQGIYDADHKNPYYDTSTFLSHFYNPDRDNTYLPGFANAKITGAKYFNQSVTDYREGKFDTAFYKLGLAIHYYTDISQPMHANNFTAISYPPGYHCAYENYVDTIKHNYQATEDMVAKRFCSDDVKDWLYENAKRAKADYPKIVNAKTKKSYLVGNSEWKKDTVKPTGARLRDSQQTLAGFLEFWSKKTNE
>NC_013768.1|WP_003722735.1|2783263_2783587_-|DUF5502-family-protein
MYIKGRLIFFFVMFVIALCSVLILLIIKISVWKDEPFHLSDAKEIECLGSCEIKNTNQKIHFFSIKENLFEEKGDIAGILNEDEQKVADKSIFIVILDDEKGIANEE
>NC_013768.1|WP_012952052.1|2782667_2783129_-|YehR-family-lipoprotein
MKMLKKGTAVLFVMIMAVMLVACGDKEETKTYTLSQKGVDSKLTYTYKGDKVTKQTAENTMSYASLGVASKEDAEKMLKATSDKFQGIDGLKEKIEYKDDKAIETLEVDYTKISSEDMNKIPGMSSNGDTSKGISMEESAKMLESQGYKEVSK
>NC_013768.1|WP_003725735.1|2782284_2782617_+|putative-heavy-metal-binding-protein
MIVTTSPNIEGKQIIEYKKIVFGEVITGVNFMKDIGAGLRNFFGGRSQGYEDELINAREEAIREMEQRAKDIGANAVIGVDIDYEVLGADNGMLMVTASGTAVVIEAQDY
>NC_013768.1|WP_009930499.1|2781543_2782218_+|DNA-alkylation-repair-protein
MITFDQLDTELQALENPNTIKIFRNHGCPDSLDLYGLKIGDLKKIIRREKLTKNHELAVKLIESNNSDLIYLGLLAINPNKITTEQIEKWNIAFRETWSQLTFGLASIVSKRDDALLFAKTWIESDYDLTKSMGWQIYSEHINNLPEAETLLQRAKETLQTETNRTRYSMNGFIITCGIYKDDLHEKAMEAAKSVGKVHVNLGNTACKVPDAISYIEKARNRTK
>NC_013768.1|WP_003722739.1|2780525_2781467_+|L-lactate-dehydrogenase
MKDHQKIILVGDGAVGSSYAFACVNLSIGQEFGIIDIDKDRTIGDAMDLSHAVPFSTPKKIYSANYSDCHDADLVVVTAGTAQKPGETRLDLVNRNIKIMKGIVDEVMASGFDGIFLIASNPVDILTYATWKFSGLPKERVIGSGTSLDTARFRMSIADYLKVDARNVHGYILGEHGDTEFPAWSHTTVGGLPITEWISEDEQGAMDTIFVSVRDAAYEIINKKGATFYGVAAALARITKAILNNENAILPLSVYLDGHYGMNDIYIGAPAVVNRQGVRHIVEMNLNDKEKEQMKNSADTLKKVLDDAMKQID
>NC_013768.1|WP_003722740.1|2779608_2780232_-|50S-ribosomal-protein-L25/general-stress-protein-Ctc
MATTLEVQKRETTQHSEVTRLRSEGKVPGIIYGYKSENVPVSVDSLELIKAVRDNGRNAVFSVTVDGKKLNVLLHEYQVDPLKDVLVHVDLLAVDMNEEVETDVRVVLVGDAPGVKAGGVLQQIIHDVKVSATPEKLPETIELDISSLEIGDVLTTNDLPENKDYVVQAEEEETVVTVSAPRAEEEPTTTEAPEPEAVHGKDEEPVE
>NC_013768.1|WP_012952051.1|2778934_2779519_-|GNAT-family-N-acetyltransferase
MLDKSVPHISVIMVNHDATNYPEFHLPAGYFFCFYKDGLEEDWCRLQLETGQVLSMDSIRARFETEFGNEKEKLTKRCIFVKAPNGEIIGTAMLWDGNTFGKMESRIHWVAVLDSHGGKGIAKALLSKILGLNKSKFVYLTTQTGSYQAIYLYRKFGFEKYVGKTPENWKTVNFQEEKETAWQIIENKIAEHQA
>NC_013768.1|WP_003722742.1|2778267_2778828_-|aminoacyl-tRNA-hydrolase
MKLIAGLGNPGKKYERTRHNVGFMVVDELSFRHQTPWKKSKFNGMTSEIIVGGEKMILVKPLTFMNASGECIRPLMDYYNIPIEDVVIVYDDLDLPVGKIRLRQKGSAGGHNGMKSIIQHVKTQEFNRIRVGVSRPLKGEVINYVLGDFPKAEQPDIIAAIQKSADAIEDFAQTPFIEVMNKYNQK
>NC_013768.1|WP_010989376.1|2774613_2778153_-|transcription-repair-coupling-factor
MKGLQQLIYEQKDIRAVLNALDEKEKAQLVTGLTGSSRALFASVVEGASKRPVVFVTHNLYHAQKLYDDLLSLMDVDRLFLYPADELISSELSISSPELRGQRVEALDFLLSGKPGIVIVPVAGLRKMLPPVSLWKHFNISIVEGEEIDPDVLRQKLVTMGYTMSGMVNTPGEFSVRGGIIDIYPITEEFPIRIELFDTEVDSLRFFDVETQRSTTRVEEFRLLPATEIILDQSYYPDIVKRLEKKMMLTLNELKEQEDKQALIENLEEDLEMLRSGVKPDMFFKYIGLAYPDPASLFDYLPKNTAILLDEFGRILETEESLEREEAEWQTETLSRMETVRDVQVSHSFKKLLEGNHSPKIYLSLFQKQMASMRVSKTTNIVYKQMQQFHGQMNVLKTELESWHKNNYAVVILAPNLERAEKMQQTLTDYDMESTILKKESDVPKYGMVQFVIGTFQNGFELPLAKVAIISETELFNKKIKKVKKRQKLSNAERIQSYSELKVGDYVVHVNHGIARYVGMETLDINGVHKDYLLLVYQGEDKLFIPVDQLDLVQKYVGAEGKSPRLNKLGGAEWKRVKKKVQASVQDIADDLIKLYAEREAEKGYAFSADDEMQREFEEAFPYQETEDQLRSISEIKKDMERPRPMDRLLVGDVGYGKTEVALRAAFKAIMDGKQVAFLVPTTILAQQHFETMKERFQGFPIEIGLLSRFRTKKQQTETLKGMKNGTVDVVVGTHRLLSKDVEYQDLGLLIVDEEQRFGVTHKEKIKQMRSKIDVLTLTATPIPRTLHMSMLGVRDLSVIETPPANRFPVQTYVAEQNNVLVREAIERELARDGQVYYLYNRVESITQKADEISAMVPDARVATAHGQMGESELESVILSFLEGEFDVLVTTTIIETGVDIPNVNTLFVQDADRMGLSQLYQLRGRVGRWNRIAYAYFMYQKDKILREEAEKRLSAIKEFTELGSGFKIAMRDLSIRGAGNILGAQQHGFIDSVGFDLYSQMLKEAIEAKKPKEEQKQIVPVEIDIQADAYIPEYYITDGRQKIEMYKRFRNIETLSELEDLQSDMIDRFGEYPEEVEYLFTMTELKVRALEVGIESVKQEQNKITMLFSESGTAGIRGDIVMQIIGEFGRMVGVGMEGTQLKITINVQNKPLKEWLYQVKSLAEKLRGAMKEKASTEN
>NC_013768.1|WP_012952055.1|2786681_2788214_-|zinc-metalloproteinase-Mpl
MKSKLICIIMVIAFQAHFTMTVKADSVGEEKLQNNTQAKKTPADLKALPDSCEAKDFYKNFKILDMTKDKLGVTHYTLALSSGGYLTDNDEIKVHVTPDNKITFINGDLQQGQLRITNQIKITEKNAIEKAFEAIGQSEAHVKSYVGNPVKEKEIILNSRTKRLVYNIKLIFAEPEVASWIVQVDVETGAILKKQNMLSEVERADTHKDFQALGKGANRLLQRPLHVMKINDLFYLVDRTHKGLIRTFDLKHNTDTSFGKVVSNKTNMFTDPEFSSAVDAHFYASEVYEYYKNVHQLESLDGKGGEIDSFVHYGLNCNNAFWDGQEILYGDGDKKNFKPFSCAKTIVGHELTHAVIQYSAGLEYEGQSGALNESFADVFGYFIAPNHWLIGEDVCVRGSRDGRIRSIKDPDKYNQAAHMKDYESLPITEEGDWGGVHYNSGIPNKAAYNTITKLGKEKTEQLYFRALKYYLTKKSQFTDAKKALQQAAKDLYGEDASKKVAEAWEAVGVN
>NC_013768.1|WP_003722731.1|2788544_2790134_-|cholesterol-dependent-cytolysin-listeriolysin-O
MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSMAPPASPPASPKTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYPNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYDPEGNEIVQHKNWSENNKSKLAHFTSSIYLPGNARNINVYAKECTGLAWEWWRTVIDDRNLPLVKNRNISIWGTTLYPKYSNKVDNPIE
>NC_013768.1|WP_012952056.1|2790375_2791329_+|phosphatidylinositol-specific-phospholipase-C
MYKIYLRRTLVLVLCFILCFFTFPLGGKAYSLNNWNKPIKNSVTTKQWMSALPDTTNLAALSIPGTHDTMSYNGDITWTLTKPLAQTQTMSLYQQLEAGIRYIDIRAKDNLNIYHGPIFLNASLSGVLETITQFLKKNPKETIIMRLKDEQNSNDSFDYRIQPLINIYKDYFYTTPRTDTSNKIPTLKDVRGKILLLSENHTKKPLVINSRKFGMQFGAPNQVIQDDYNGPSVKTKFKEIVQTAYQASKADNKLFLNHISATSLTFTPRQYAAALNNKVEQFVLNLTSEKVRGLGILIMDFPEKQTIKNIIKNNKFN
>NC_013768.1|WP_003722729.1|2791599_2792313_+|listeriolysin-transcriptional-regulator-PrfA
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN
>NC_013768.1|WP_003722728.1|2792355_2793312_-|ribose-phosphate-diphosphokinase
MSNEYFDPKLKIFSLNSNRELAEEIAKEVGIELGKSSVTHFSDGEIQINIEESIRGCHVYVIQSTSNPVNQNLMELLIMIDALKRASAATINIVMPYYGYARQDRKARSREPITAKLVANLIETAGATRMITLDMHAPQIQGFFDIPIDHLNAVRLLSDYFSERHLGDDLVVVSPDHGGVTRARKMADRLKAPIAIIDKRRPRPNVAEVMNIVGNVEGKVCIIIDDIIDTAGTITLAAKALREAGATKVYACCSHPVLSGPAMKRIEESPIEKLVVTNSIALPEEKWIDKMEQLSVAALLGEAIVRVHENASVSSLFE
>NC_013768.1|WP_003722727.1|2793362_2794736_-|bifunctional-UDP-N-acetylglucosamine-diphosphorylase/glucosamine-1-phosphate-N-acetyltransferase-GlmU
MSKRYAVVLAAGQGTRMKSKLYKVLHPVCGKPMVEHVVDQISTLNVDKVVTIVGHGAEKVQEHLAGKSEFVKQDEQLGTAHAVLQAKAELAGKDGVTLVVCGDTPLIEASTMEALLKYHHEKRAKATILTTVIEDPTGYGRIIRDDLGIVEKIVEHKDATEKEQRISEINTGTYCFDNKALFEALENVSNDNVQGEYYLPDVIKILKDSDEVVAAYRMESFEESLGVNDRIALAEASKLMQRRINENHMRNGVTLVNPESTYIDIDVKIGQDTVIEPGVMLRGKTVIGDDCVVTSGSEIVNSVIGERVHVRTSSIFESKVGDDVQIGPYAHLRPESDIHDHVKIGNYVETKKAVVGEGTKLPHFIYMGDAEIGKNVNVGCGSIAVNYDGKNKAKTIIGDNVFVGCNSNLIAPVKVGDRAFIAAGSTITKDVPEDALGIARAKQDNKLGYAKHLNHGK
>NC_013768.1|WP_003722726.1|2795122_2795431_-|septation-protein-SpoVG
MQVTDVRLRRVETDGRMRAIASITLDEEFVVHDIRVIDGNNGLFVAMPSKRGVDGEFRDIAHPINSDTRAKIQEVVLAEYERVGEEEATAVTEEESESVSAE
>NC_013768.1|WP_003722725.1|2795550_2795859_-|septation-protein-SpoVG
MEITDVRLRRVETDGRMKAISSITIDGEFVIHDIRVIDGNEGLFVAMPSKRTPDGEFRDIAHPINSGTRAKIQEAVLAAYEVADEPAVNEESSADESIVEEN
>NC_013768.1|WP_009931069.1|2796543_2797752_-|FtsX-like-permease-family-protein
MNVLQSMKMAWKQLKASKLRSFLTMLGIIIGVASVILLVSLGNGVTQEVDDQMGDLGSNLITVVNSSVNPNDKYTYDEVMKYQNIDGVKSVSPELSGQVNATFDYKNSSNKVIGTNDQYKAARSLEMKEGRFLLPIDTEYGQKVAVIGSTVASDLFGFGDPIGETIRLNGMPYKVVGVLKEKGASMMGSSDDQIFIPISSAQRLLKDTNVRTIYVETKSAEDVDFVVNTLESRLAIKFGDEKEQEKNASSAQMGPSYQVINQQEILNAFNTISTTLTTALGAIAAISLVVGGIGIMNIMLVSVSERTREIGIRKALGAKKRAILLQFLIESIVISVCGGVIGIIIGVSGALIFGSVAGISSGITAGTIIFSFVFSLCIGVIFGIAPANKASKLRPIDALRSE
>NC_013768.1|WP_003722723.1|2797748_2798441_-|ABC-transporter-ATP-binding-protein
MPKPLIDMKNLTKTYTLGGETFKALDDVTFTVEQGEFLSIVGPSGSGKSTLMNMIGCLDVPDEGSYHLDDVDVFKLSDNKLSEIRNKKIGFIFQQFNLLPKLSAFENVELPLIYAGLSVSAREKAAIECLEKVGLLEKRRNLPTQLSGGQQQRVAIARALAGKPQILLADEPTGALDSKTGKEVMGILQELNRAGNTIVMITHDPTIASYGTRSIRIQDGKLFHEEATQA

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
NC_013768_2	2.1\|539238\|35\|NC_013768\|PILER-CR,CRT	539238-539272	35	NC_013768.1	1285751-1285785	0	1.0
NC_013768_2	2.7\|539623\|35\|NC_013768\|PILER-CR,CRT	539623-539657	35	NC_013768.1	2451852-2451886	0	1.0
NC_013768_2	2.6\|539558\|36\|NC_013768\|PILER-CR,CRT	539558-539593	36	NC_013768.1	1284603-1284638	1	0.972

1. spacer 2.1|539238|35|NC_013768|PILER-CR,CRT matches to position: 1285751-1285785, mismatch: 0, identity: 1.0

acagatcaaactccggaagggtgattgtaaatggc	CRISPR spacer
acagatcaaactccggaagggtgattgtaaatggc	Protospacer
***********************************

2. spacer 2.7|539623|35|NC_013768|PILER-CR,CRT matches to position: 2451852-2451886, mismatch: 0, identity: 1.0

tttgttgaatcaacggatatagattttacaatttc	CRISPR spacer
tttgttgaatcaacggatatagattttacaatttc	Protospacer
***********************************

3. spacer 2.6|539558|36|NC_013768|PILER-CR,CRT matches to position: 1284603-1284638, mismatch: 1, identity: 0.972

aaaataggaggaaataaattatgactatcaaattaa	CRISPR spacer
aaaataggaggaaatagattatgactatcaaattaa	Protospacer
****************.*******************

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_013768_2	2.1\|539238\|35\|NC_013768\|PILER-CR,CRT	539238-539272	35	NZ_LR134403	Listeria monocytogenes strain NCTC7974 plasmid 6, complete sequence	214611-214645	0	1.0
NC_013768_2	2.1\|539238\|35\|NC_013768\|PILER-CR,CRT	539238-539272	35	MT500540	Listeria phage LP-HM00113468, complete genome	39834-39868	0	1.0
NC_013768_2	2.1\|539238\|35\|NC_013768\|PILER-CR,CRT	539238-539272	35	KJ094023	Listeria phage LP-101, complete genome	5084-5118	0	1.0
NC_013768_2	2.6\|539558\|36\|NC_013768\|PILER-CR,CRT	539558-539593	36	MT500540	Listeria phage LP-HM00113468, complete genome	683-718	0	1.0
NC_013768_2	2.6\|539558\|36\|NC_013768\|PILER-CR,CRT	539558-539593	36	NC_009812	Listeria phage B025, complete genome	3896-3931	0	1.0
NC_013768_2	2.6\|539558\|36\|NC_013768\|PILER-CR,CRT	539558-539593	36	KJ094023	Listeria phage LP-101, complete genome	3936-3971	0	1.0
NC_013768_2	2.7\|539623\|35\|NC_013768\|PILER-CR,CRT	539623-539657	35	DQ003642	Listeria phage A006, complete genome	15712-15746	0	1.0
NC_013768_2	2.3\|539367\|35\|NC_013768\|PILER-CR,CRT	539367-539401	35	MH341453	Listeria phage PSU-VKH-LP041, complete genome	10139-10173	1	0.971
NC_013768_2	2.5\|539494\|35\|NC_013768\|PILER-CR,CRT	539494-539528	35	NC_021539	Listeria phage LP-030-2, complete genome	18926-18960	1	0.971
NC_013768_2	2.5\|539494\|35\|NC_013768\|PILER-CR,CRT	539494-539528	35	KJ094023	Listeria phage LP-101, complete genome	22882-22916	1	0.971
NC_013768_2	2.6\|539558\|36\|NC_013768\|PILER-CR,CRT	539558-539593	36	NZ_LR134403	Listeria monocytogenes strain NCTC7974 plasmid 6, complete sequence	213463-213498	1	0.972
NC_013768_2	2.8\|539238\|36\|NC_013768\|CRISPRCasFinder	539238-539273	36	NZ_LR134403	Listeria monocytogenes strain NCTC7974 plasmid 6, complete sequence	214611-214646	1	0.972
NC_013768_2	2.8\|539238\|36\|NC_013768\|CRISPRCasFinder	539238-539273	36	MT500540	Listeria phage LP-HM00113468, complete genome	39833-39868	1	0.972
NC_013768_2	2.8\|539238\|36\|NC_013768\|CRISPRCasFinder	539238-539273	36	KJ094023	Listeria phage LP-101, complete genome	5084-5119	1	0.972
NC_013768_2	2.10\|539367\|36\|NC_013768\|CRISPRCasFinder	539367-539402	36	MH341453	Listeria phage PSU-VKH-LP041, complete genome	10139-10174	1	0.972
NC_013768_2	2.12\|539494\|36\|NC_013768\|CRISPRCasFinder	539494-539529	36	NC_021539	Listeria phage LP-030-2, complete genome	18926-18961	1	0.972
NC_013768_2	2.12\|539494\|36\|NC_013768\|CRISPRCasFinder	539494-539529	36	KJ094023	Listeria phage LP-101, complete genome	22882-22917	1	0.972
NC_013768_2	2.13\|539558\|37\|NC_013768\|CRISPRCasFinder	539558-539594	37	NC_009812	Listeria phage B025, complete genome	3896-3932	1	0.973
NC_013768_2	2.13\|539558\|37\|NC_013768\|CRISPRCasFinder	539558-539594	37	KJ094023	Listeria phage LP-101, complete genome	3936-3972	1	0.973
NC_013768_2	2.13\|539558\|37\|NC_013768\|CRISPRCasFinder	539558-539594	37	MT500540	Listeria phage LP-HM00113468, complete genome	682-718	1	0.973
NC_013768_2	2.14\|539623\|36\|NC_013768\|CRISPRCasFinder	539623-539658	36	DQ003642	Listeria phage A006, complete genome	15711-15746	1	0.972
NC_013768_2	2.1\|539238\|35\|NC_013768\|PILER-CR,CRT	539238-539272	35	NC_009812	Listeria phage B025, complete genome	5044-5078	2	0.943
NC_013768_2	2.3\|539367\|35\|NC_013768\|PILER-CR,CRT	539367-539401	35	NC_009813	Listeria phage B054, complete genome	10139-10173	2	0.943
NC_013768_2	2.5\|539494\|35\|NC_013768\|PILER-CR,CRT	539494-539528	35	NC_009812	Listeria phage B025, complete genome	23381-23415	2	0.943
NC_013768_2	2.10\|539367\|36\|NC_013768\|CRISPRCasFinder	539367-539402	36	NC_009813	Listeria phage B054, complete genome	10139-10174	2	0.944
NC_013768_2	2.12\|539494\|36\|NC_013768\|CRISPRCasFinder	539494-539529	36	NC_009812	Listeria phage B025, complete genome	23381-23416	2	0.944
NC_013768_2	2.13\|539558\|37\|NC_013768\|CRISPRCasFinder	539558-539594	37	NZ_LR134403	Listeria monocytogenes strain NCTC7974 plasmid 6, complete sequence	213463-213499	2	0.946
NC_013768_2	2.8\|539238\|36\|NC_013768\|CRISPRCasFinder	539238-539273	36	NC_009812	Listeria phage B025, complete genome	5044-5079	3	0.917
NC_013768_2	2.6\|539558\|36\|NC_013768\|PILER-CR,CRT	539558-539593	36	JN700520	Staphylococcus phage StB12, complete genome	6832-6867	5	0.861
NC_013768_2	2.13\|539558\|37\|NC_013768\|CRISPRCasFinder	539558-539594	37	JN700520	Staphylococcus phage StB12, complete genome	6832-6868	6	0.838
NC_013768_2	2.6\|539558\|36\|NC_013768\|PILER-CR,CRT	539558-539593	36	MW084976	Bacillus phage Kirov, complete genome	27565-27600	8	0.778
NC_013768_2	2.13\|539558\|37\|NC_013768\|CRISPRCasFinder	539558-539594	37	MW084976	Bacillus phage Kirov, complete genome	27565-27601	9	0.757
NC_013768_2	2.7\|539623\|35\|NC_013768\|PILER-CR,CRT	539623-539657	35	NZ_CP029455	Bacillus cereus strain FORC087 plasmid pFORC087.1, complete sequence	130632-130666	11	0.686
NC_013768_2	2.7\|539623\|35\|NC_013768\|PILER-CR,CRT	539623-539657	35	NZ_CP015592	Bacillus cereus strain AR156 plasmid pAR460, complete sequence	17622-17656	11	0.686
NC_013768_2	2.7\|539623\|35\|NC_013768\|PILER-CR,CRT	539623-539657	35	NZ_CP009368	Bacillus cereus strain FM1 plasmid unnamed, complete sequence	31860-31894	11	0.686
NC_013768_2	2.7\|539623\|35\|NC_013768\|PILER-CR,CRT	539623-539657	35	NZ_CP009336	Bacillus thuringiensis strain HD1011 plasmid 1, complete sequence	338888-338922	11	0.686

1. spacer 2.1|539238|35|NC_013768|PILER-CR,CRT matches to NZ_LR134403 (Listeria monocytogenes strain NCTC7974 plasmid 6, complete sequence) position: , mismatch: 0, identity: 1.0

acagatcaaactccggaagggtgattgtaaatggc	CRISPR spacer
acagatcaaactccggaagggtgattgtaaatggc	Protospacer
***********************************

2. spacer 2.1|539238|35|NC_013768|PILER-CR,CRT matches to MT500540 (Listeria phage LP-HM00113468, complete genome) position: , mismatch: 0, identity: 1.0

acagatcaaactccggaagggtgattgtaaatggc	CRISPR spacer
acagatcaaactccggaagggtgattgtaaatggc	Protospacer
***********************************

3. spacer 2.1|539238|35|NC_013768|PILER-CR,CRT matches to KJ094023 (Listeria phage LP-101, complete genome) position: , mismatch: 0, identity: 1.0

acagatcaaactccggaagggtgattgtaaatggc	CRISPR spacer
acagatcaaactccggaagggtgattgtaaatggc	Protospacer
***********************************

4. spacer 2.6|539558|36|NC_013768|PILER-CR,CRT matches to MT500540 (Listeria phage LP-HM00113468, complete genome) position: , mismatch: 0, identity: 1.0

aaaataggaggaaataaattatgactatcaaattaa	CRISPR spacer
aaaataggaggaaataaattatgactatcaaattaa	Protospacer
************************************

5. spacer 2.6|539558|36|NC_013768|PILER-CR,CRT matches to NC_009812 (Listeria phage B025, complete genome) position: , mismatch: 0, identity: 1.0

aaaataggaggaaataaattatgactatcaaattaa	CRISPR spacer
aaaataggaggaaataaattatgactatcaaattaa	Protospacer
************************************

6. spacer 2.6|539558|36|NC_013768|PILER-CR,CRT matches to KJ094023 (Listeria phage LP-101, complete genome) position: , mismatch: 0, identity: 1.0

aaaataggaggaaataaattatgactatcaaattaa	CRISPR spacer
aaaataggaggaaataaattatgactatcaaattaa	Protospacer
************************************

7. spacer 2.7|539623|35|NC_013768|PILER-CR,CRT matches to DQ003642 (Listeria phage A006, complete genome) position: , mismatch: 0, identity: 1.0

tttgttgaatcaacggatatagattttacaatttc	CRISPR spacer
tttgttgaatcaacggatatagattttacaatttc	Protospacer
***********************************

8. spacer 2.3|539367|35|NC_013768|PILER-CR,CRT matches to MH341453 (Listeria phage PSU-VKH-LP041, complete genome) position: , mismatch: 1, identity: 0.971

gcgatttttgtcaaagggacagcgatgggttacaa	CRISPR spacer
gcgatttttgtcaaaggaacagcgatgggttacaa	Protospacer
*****************.*****************

9. spacer 2.5|539494|35|NC_013768|PILER-CR,CRT matches to NC_021539 (Listeria phage LP-030-2, complete genome) position: , mismatch: 1, identity: 0.971

ctaaaacatccttcactgtatcaactcctttctat	CRISPR spacer
ctaaaacatccttcactgtctcaactcctttctat	Protospacer
******************* ***************

10. spacer 2.5|539494|35|NC_013768|PILER-CR,CRT matches to KJ094023 (Listeria phage LP-101, complete genome) position: , mismatch: 1, identity: 0.971

ctaaaacatccttcactgtatcaactcctttctat	CRISPR spacer
ctaaaacatccttcactgtctcaactcctttctat	Protospacer
******************* ***************

11. spacer 2.6|539558|36|NC_013768|PILER-CR,CRT matches to NZ_LR134403 (Listeria monocytogenes strain NCTC7974 plasmid 6, complete sequence) position: , mismatch: 1, identity: 0.972

aaaataggaggaaataaattatgactatcaaattaa	CRISPR spacer
aaaataggaggaaatagattatgactatcaaattaa	Protospacer
****************.*******************

12. spacer 2.8|539238|36|NC_013768|CRISPRCasFinder matches to NZ_LR134403 (Listeria monocytogenes strain NCTC7974 plasmid 6, complete sequence) position: , mismatch: 1, identity: 0.972

acagatcaaactccggaagggtgattgtaaatggcg	CRISPR spacer
acagatcaaactccggaagggtgattgtaaatggct	Protospacer
***********************************

13. spacer 2.8|539238|36|NC_013768|CRISPRCasFinder matches to MT500540 (Listeria phage LP-HM00113468, complete genome) position: , mismatch: 1, identity: 0.972

acagatcaaactccggaagggtgattgtaaatggcg	CRISPR spacer
acagatcaaactccggaagggtgattgtaaatggct	Protospacer
***********************************

14. spacer 2.8|539238|36|NC_013768|CRISPRCasFinder matches to KJ094023 (Listeria phage LP-101, complete genome) position: , mismatch: 1, identity: 0.972

acagatcaaactccggaagggtgattgtaaatggcg	CRISPR spacer
acagatcaaactccggaagggtgattgtaaatggct	Protospacer
***********************************

15. spacer 2.10|539367|36|NC_013768|CRISPRCasFinder matches to MH341453 (Listeria phage PSU-VKH-LP041, complete genome) position: , mismatch: 1, identity: 0.972

gcgatttttgtcaaagggacagcgatgggttacaag	CRISPR spacer
gcgatttttgtcaaaggaacagcgatgggttacaag	Protospacer
*****************.******************

16. spacer 2.12|539494|36|NC_013768|CRISPRCasFinder matches to NC_021539 (Listeria phage LP-030-2, complete genome) position: , mismatch: 1, identity: 0.972

ctaaaacatccttcactgtatcaactcctttctata	CRISPR spacer
ctaaaacatccttcactgtctcaactcctttctata	Protospacer
******************* ****************

17. spacer 2.12|539494|36|NC_013768|CRISPRCasFinder matches to KJ094023 (Listeria phage LP-101, complete genome) position: , mismatch: 1, identity: 0.972

ctaaaacatccttcactgtatcaactcctttctata	CRISPR spacer
ctaaaacatccttcactgtctcaactcctttctata	Protospacer
******************* ****************

18. spacer 2.13|539558|37|NC_013768|CRISPRCasFinder matches to NC_009812 (Listeria phage B025, complete genome) position: , mismatch: 1, identity: 0.973

aaaataggaggaaataaattatgactatcaaattaag	CRISPR spacer
aaaataggaggaaataaattatgactatcaaattaaa	Protospacer
************************************.

19. spacer 2.13|539558|37|NC_013768|CRISPRCasFinder matches to KJ094023 (Listeria phage LP-101, complete genome) position: , mismatch: 1, identity: 0.973

aaaataggaggaaataaattatgactatcaaattaag	CRISPR spacer
aaaataggaggaaataaattatgactatcaaattaaa	Protospacer
************************************.

20. spacer 2.13|539558|37|NC_013768|CRISPRCasFinder matches to MT500540 (Listeria phage LP-HM00113468, complete genome) position: , mismatch: 1, identity: 0.973

aaaataggaggaaataaattatgactatcaaattaag	CRISPR spacer
aaaataggaggaaataaattatgactatcaaattaaa	Protospacer
************************************.

21. spacer 2.14|539623|36|NC_013768|CRISPRCasFinder matches to DQ003642 (Listeria phage A006, complete genome) position: , mismatch: 1, identity: 0.972

tttgttgaatcaacggatatagattttacaatttcg	CRISPR spacer
tttgttgaatcaacggatatagattttacaatttct	Protospacer
***********************************

22. spacer 2.1|539238|35|NC_013768|PILER-CR,CRT matches to NC_009812 (Listeria phage B025, complete genome) position: , mismatch: 2, identity: 0.943

acagatcaaactccggaagggtgattgtaaatggc	CRISPR spacer
gcagaacaaactccggaagggtgattgtaaatggc	Protospacer
.**** *****************************

23. spacer 2.3|539367|35|NC_013768|PILER-CR,CRT matches to NC_009813 (Listeria phage B054, complete genome) position: , mismatch: 2, identity: 0.943

gcgatttttgtcaaagggacagcgatgggttacaa	CRISPR spacer
gcgatttttgtcaaaggaacggcgatgggttacaa	Protospacer
*****************.**.**************

24. spacer 2.5|539494|35|NC_013768|PILER-CR,CRT matches to NC_009812 (Listeria phage B025, complete genome) position: , mismatch: 2, identity: 0.943

ctaaaacatccttcactgtatcaactcctttctat	CRISPR spacer
ctaaaacatccttcactatctcaactcctttctat	Protospacer
*****************.* ***************

25. spacer 2.10|539367|36|NC_013768|CRISPRCasFinder matches to NC_009813 (Listeria phage B054, complete genome) position: , mismatch: 2, identity: 0.944

gcgatttttgtcaaagggacagcgatgggttacaag	CRISPR spacer
gcgatttttgtcaaaggaacggcgatgggttacaag	Protospacer
*****************.**.***************

26. spacer 2.12|539494|36|NC_013768|CRISPRCasFinder matches to NC_009812 (Listeria phage B025, complete genome) position: , mismatch: 2, identity: 0.944

ctaaaacatccttcactgtatcaactcctttctata	CRISPR spacer
ctaaaacatccttcactatctcaactcctttctata	Protospacer
*****************.* ****************

27. spacer 2.13|539558|37|NC_013768|CRISPRCasFinder matches to NZ_LR134403 (Listeria monocytogenes strain NCTC7974 plasmid 6, complete sequence) position: , mismatch: 2, identity: 0.946

aaaataggaggaaataaattatgactatcaaattaag	CRISPR spacer
aaaataggaggaaatagattatgactatcaaattaaa	Protospacer
****************.*******************.

28. spacer 2.8|539238|36|NC_013768|CRISPRCasFinder matches to NC_009812 (Listeria phage B025, complete genome) position: , mismatch: 3, identity: 0.917

acagatcaaactccggaagggtgattgtaaatggcg	CRISPR spacer
gcagaacaaactccggaagggtgattgtaaatggct	Protospacer
.**** *****************************

29. spacer 2.6|539558|36|NC_013768|PILER-CR,CRT matches to JN700520 (Staphylococcus phage StB12, complete genome) position: , mismatch: 5, identity: 0.861

aaaataggaggaaataaattatgact-atcaaattaa	CRISPR spacer
taaataggaggaagtaaataatgactaatcaaacta-	Protospacer
 ************.***** ****** ******.**

30. spacer 2.13|539558|37|NC_013768|CRISPRCasFinder matches to JN700520 (Staphylococcus phage StB12, complete genome) position: , mismatch: 6, identity: 0.838

aaaataggaggaaataaattatgact-atcaaattaag	CRISPR spacer
taaataggaggaagtaaataatgactaatcaaactat-	Protospacer
 ************.***** ****** ******.**

31. spacer 2.6|539558|36|NC_013768|PILER-CR,CRT matches to MW084976 (Bacillus phage Kirov, complete genome) position: , mismatch: 8, identity: 0.778

aaaataggaggaaataaattatgactatcaaattaa	CRISPR spacer
ttaataggaggaaataaataatggctatcgtaagaa	Protospacer
  ***************** ***.*****. *  **

32. spacer 2.13|539558|37|NC_013768|CRISPRCasFinder matches to MW084976 (Bacillus phage Kirov, complete genome) position: , mismatch: 9, identity: 0.757

aaaataggaggaaataaattatgactatcaaattaag	CRISPR spacer
ttaataggaggaaataaataatggctatcgtaagaaa	Protospacer
  ***************** ***.*****. *  **.

33. spacer 2.7|539623|35|NC_013768|PILER-CR,CRT matches to NZ_CP029455 (Bacillus cereus strain FORC087 plasmid pFORC087.1, complete sequence) position: , mismatch: 11, identity: 0.686

tttgttgaatcaacggatatagattttacaatttc	CRISPR spacer
agaaaaaaatcaaccgatatagattttaaaatctt	Protospacer
   .  .******* ************* ***.*.

34. spacer 2.7|539623|35|NC_013768|PILER-CR,CRT matches to NZ_CP015592 (Bacillus cereus strain AR156 plasmid pAR460, complete sequence) position: , mismatch: 11, identity: 0.686

tttgttgaatcaacggatatagattttacaatttc	CRISPR spacer
aagaaaaaatcaaccgatatagattttaaaatctt	Protospacer
   .  .******* ************* ***.*.

35. spacer 2.7|539623|35|NC_013768|PILER-CR,CRT matches to NZ_CP009368 (Bacillus cereus strain FM1 plasmid unnamed, complete sequence) position: , mismatch: 11, identity: 0.686

tttgttgaatcaacggatatagattttacaatttc	CRISPR spacer
agaaaaaaatcaaccgatatagattttaaaatctt	Protospacer
   .  .******* ************* ***.*.

36. spacer 2.7|539623|35|NC_013768|PILER-CR,CRT matches to NZ_CP009336 (Bacillus thuringiensis strain HD1011 plasmid 1, complete sequence) position: , mismatch: 11, identity: 0.686

tttgttgaatcaacggatatagattttacaatttc	CRISPR spacer
agaaaaaaatcaaccgatatagattttaaaatctt	Protospacer
   .  .******* ************* ***.*.

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

98064 : 108096

Tupanvirus(33.33%)

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_009924391.1\|98064_99519_-	glycoside hydrolase family 1 protein	A0A0B5JD41	Pandoravirus	1.9e-50	30.3
WP_072215787.1\|99546_99855_-	hypothetical protein	NA	NA	NA	NA
WP_012951082.1\|100033_101644_+	ABC-F family ATP-binding cassette domain-containing protein	A0A2K9L3Z8	Tupanvirus	1.2e-45	29.5
WP_012951083.1\|101701_102232_+	ADP-ribose-binding protein	A0A0K1L687	Scale_drop_disease_virus	3.4e-29	49.3
WP_003722118.1\|102519_103986_+	IMP dehydrogenase	A0A1V0SHK8	Klosneuvirus	8.0e-97	40.0
WP_003732117.1\|104146_105919_+	DNA helicase RecQ	A0A2K9L3P7	Tupanvirus	6.3e-80	37.1
WP_012951084.1\|105942_108096_+	DNA topoisomerase III	A0A1X9I6W8	Streptococcus_phage	6.7e-44	34.1

DBSCAN-SWA_2

1126760 : 1136313

Hokovirus(28.57%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_003721506.1\|1126760_1127144_+	glycerol-3-phosphate cytidylyltransferase	A0A1V0SGE7	Hokovirus	1.4e-16	40.7
WP_003732709.1\|1127165_1128149_+	glycosyltransferase family 2 protein	A0A1V0SAH6	Catovirus	4.1e-12	34.6
WP_010989660.1\|1128163_1129177_+	glycosyltransferase	A0A1V0SAH6	Catovirus	7.9e-11	32.0
WP_003721509.1\|1129385_1130876_+	nicotinate phosphoribosyltransferase	G3MA18	Bacillus_virus	9.5e-114	49.7
WP_003727000.1\|1130887_1131712_+	ammonia-dependent NAD(+) synthetase	G3MA24	Bacillus_virus	9.7e-68	52.6
WP_012951453.1\|1131724_1132033_+	antibiotic biosynthesis monooxygenase	NA	NA	NA	NA
WP_003730540.1\|1132092_1132497_+	PTS sugar transporter subunit IIB	NA	NA	NA	NA
WP_012951454.1\|1132625_1134182_+	glutamine-hydrolyzing GMP synthase	A0A1V0SH76	Hokovirus	3.0e-17	28.1
WP_012951455.1\|1134399_1136313_+	site-specific DNA-methyltransferase	A0A2K5B2C1	Erysipelothrix_phage	1.3e-59	36.9

DBSCAN-SWA_3

1233093 : 1340176

116

Listeria_phage(68.85%)

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

attL 1257727:1257748|attR 1302474:1302495

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_012951511.1\|1233093_1235502_+\|tRNA	phenylalanine--tRNA ligase subunit beta	NA	NA	NA	NA
WP_003721621.1\|1235662_1236364_+	ABC transporter ATP-binding protein	G9BWD6	Planktothrix_phage	3.0e-33	35.8
WP_012951512.1\|1236377_1239788_+	FtsX-like permease family protein	NA	NA	NA	NA
WP_003721623.1\|1239885_1240338_+	winged helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_003721624.1\|1240353_1243554_+	MMPL family transporter	NA	NA	NA	NA
WP_003732773.1\|1243660_1244335_+	uracil-DNA glycosylase	A0A172DS90	Canid_alphaherpesvirus	7.5e-50	47.7
WP_072215733.1\|1244372_1245299_-	ribonuclease HIII	NA	NA	NA	NA
WP_003740576.1\|1245452_1245716_+	cell division protein ZapA	NA	NA	NA	NA
WP_012951513.1\|1245715_1246258_+	CvpA family protein	NA	NA	NA	NA
WP_003723851.1\|1246350_1248063_+	DNA polymerase/3'-5' exonuclease PolX	A0A2H4UV14	Bodo_saltans_virus	5.1e-18	24.8
WP_010989713.1\|1248085_1250443_+	endonuclease MutS2	Q94M10	Lactobacillus_phage	1.0e-21	50.4
WP_003723853.1\|1250523_1250835_+	thioredoxin	A0A1X9I9P5	Staphylococcus_phage	5.4e-19	39.6
WP_003733800.1\|1250910_1252722_+	excinuclease ABC subunit UvrC	NA	NA	NA	NA
WP_003732778.1\|1252910_1254125_+	aspartate kinase	NA	NA	NA	NA
WP_003733801.1\|1254180_1254675_-	YslB family protein	NA	NA	NA	NA
WP_003723856.1\|1254822_1255623_+	glutamate racemase	NA	NA	NA	NA
WP_003726032.1\|1255635_1256382_+	ribonuclease PH	NA	NA	NA	NA
WP_012951514.1\|1256385_1256997_+	XTP/dITP diphosphatase	NA	NA	NA	NA
WP_012951515.1\|1257033_1257558_+	metallophosphoesterase	NA	NA	NA	NA
1257727:1257748	attL	NA	NA	NA	NA
WP_012951516.1\|1257843_1258998_-\|integrase	site-specific integrase	A0A059T688	Listeria_phage	1.6e-209	95.8
WP_012951517.1\|1259139_1259796_-	DUF4352 domain-containing protein	NA	NA	NA	NA
WP_012951518.1\|1259847_1260300_-	ImmA/IrrE family metallo-endopeptidase	R4IBK9	Listeria_phage	1.1e-78	91.3
WP_012951519.1\|1260316_1260640_-	helix-turn-helix transcriptional regulator	R4IDX0	Listeria_phage	6.3e-39	75.7
WP_003730994.1\|1261040_1261244_-	hypothetical protein	NA	NA	NA	NA
WP_012951520.1\|1261310_1261502_+	helix-turn-helix transcriptional regulator	Q8W5X9	Listeria_phage	1.6e-21	84.1
WP_003730996.1\|1261523_1261766_+	hypothetical protein	A8ATD2	Listeria_phage	3.9e-41	93.8
WP_003730997.1\|1261768_1261954_+	hypothetical protein	A8ATD3	Listeria_phage	3.7e-28	98.4
WP_012951522.1\|1262706_1262949_+	hypothetical protein	NA	NA	NA	NA
WP_012951524.1\|1263765_1264230_+	methyltransferase domain-containing protein	A0A059T693	Listeria_phage	2.9e-85	94.8
WP_012951525.1\|1264226_1264940_+	SAM-dependent DNA methyltransferase	A8ATD5	Listeria_phage	4.5e-130	97.9
WP_012951526.1\|1264950_1265895_+\|integrase	site-specific integrase	A8ATD6	Listeria_phage	1.1e-176	97.8
WP_012951527.1\|1265907_1266588_+	hypothetical protein	A8ATD7	Listeria_phage	9.0e-120	95.6
WP_012951528.1\|1266584_1266818_+	DUF1642 domain-containing protein	B6D7L5	Listeria_phage	6.8e-11	55.6
WP_012951529.1\|1266820_1267264_+	hypothetical protein	NA	NA	NA	NA
WP_012951530.1\|1267456_1267936_+	hypothetical protein	NA	NA	NA	NA
WP_012951531.1\|1267936_1268566_+	hypothetical protein	A0A191KBJ8	Streptococcus_virus	1.1e-66	58.4
WP_012951532.1\|1268584_1268818_+	hypothetical protein	NA	NA	NA	NA
WP_012951533.1\|1268814_1269033_+	hypothetical protein	NA	NA	NA	NA
WP_012951534.1\|1269002_1269194_+	hypothetical protein	NA	NA	NA	NA
WP_003731668.1\|1269396_1269660_+	hypothetical protein	Q8W5W6	Listeria_phage	8.8e-23	67.1
WP_012951535.1\|1269832_1270216_+	hypothetical protein	A8ATE8	Listeria_phage	5.3e-61	92.9
WP_003731665.1\|1270217_1270697_+	siphovirus Gp157 family protein	R4IBM0	Listeria_phage	7.6e-57	76.7
WP_012951536.1\|1270716_1271406_+	AAA family ATPase	R4IDY8	Listeria_phage	3.1e-128	96.9
WP_074471730.1\|1271484_1272726_+	DEAD/DEAH box helicase	A8ATF1	Listeria_phage	1.2e-213	96.1
WP_009918373.1\|1272750_1273233_+	DUF669 domain-containing protein	A8ATF2	Listeria_phage	5.5e-87	98.8
WP_012951538.1\|1273255_1275544_+	primase	R4IBW2	Listeria_phage	0.0e+00	95.4
WP_012951539.1\|1275877_1276195_+	VRR-NUC domain-containing protein	A8ATF4	Listeria_phage	7.3e-48	89.3
WP_003731659.1\|1276196_1276409_+	hypothetical protein	NA	NA	NA	NA
WP_012951540.1\|1276856_1277396_+	DUF3310 domain-containing protein	A8ATF5	Listeria_phage	9.2e-75	77.1
WP_003731657.1\|1277392_1277662_+	hypothetical protein	NA	NA	NA	NA
WP_009917712.1\|1277881_1278307_+	DUF722 domain-containing protein	A0A059T6H4	Listeria_phage	8.0e-74	100.0
WP_012951542.1\|1278404_1279148_+	DUF559 domain-containing protein	NA	NA	NA	NA
WP_014930130.1\|1279616_1279943_+	hypothetical protein	A0A059T5G5	Listeria_phage	2.2e-55	100.0
WP_009931610.1\|1279942_1280257_+	HNH endonuclease	A8ATF8	Listeria_phage	5.0e-57	98.1
WP_012951543.1\|1280306_1280663_+	hypothetical protein	A0A059T7Y1	Listeria_phage	2.0e-46	98.0
WP_012951544.1\|1280659_1282303_+\|terminase	terminase large subunit	A0A059T7Q8	Listeria_phage	0.0e+00	99.3
WP_009917707.1\|1282312_1282702_-	DUF2513 domain-containing protein	A0A1Q1PVT8	Staphylococcus_phage	3.7e-17	39.8
WP_012951545.1\|1282752_1283883_+\|portal	phage portal protein	A0A059T6F0	Listeria_phage	2.8e-214	99.5
WP_012951546.1\|1283879_1284596_+\|protease	Clp protease ClpP	A0A1S5SFF8	Streptococcus_phage	9.3e-67	59.0
WP_012951547.1\|1284622_1285774_+\|capsid	phage major capsid protein	A0A059T678	Listeria_phage	3.1e-213	99.5
WP_009934007.1\|1285960_1286260_+	hypothetical protein	A8ATA0	Listeria_phage	9.9e-47	98.0
WP_009934006.1\|1286243_1286609_+	hypothetical protein	A0A059T6F2	Listeria_phage	1.6e-62	96.7
WP_012951550.1\|1286605_1287007_+	hypothetical protein	A0A059T5F3	Listeria_phage	2.1e-68	100.0
WP_009931623.1\|1287003_1287387_+	hypothetical protein	A0A059T681	Listeria_phage	6.1e-65	96.1
WP_012951551.1\|1287407_1287995_+\|tail	phage tail protein	A0A059T7Y4	Listeria_phage	1.7e-106	99.0
WP_012951552.1\|1288065_1288398_+	hypothetical protein	A8ATA5	Listeria_phage	2.8e-50	96.4
WP_012951553.1\|1288613_1293545_+\|tail	phage tail tape measure protein	A0A059T5F4	Listeria_phage	0.0e+00	95.1
WP_012951554.1\|1293532_1295182_+\|tail	phage tail protein	A0A059T682	Listeria_phage	0.0e+00	99.1
WP_012951555.1\|1295194_1297489_+	hypothetical protein	A0A059T7Y6	Listeria_phage	0.0e+00	94.0
WP_031644619.1\|1297478_1298573_+	hypothetical protein	A0A059T7R4	Listeria_phage	2.2e-184	87.9
WP_012951557.1\|1298620_1298923_+	hypothetical protein	A0A059T5E6	Listeria_phage	1.7e-38	93.0
WP_012951558.1\|1298922_1299180_+\|holin	phage holin	A8ATB7	Listeria_phage	3.2e-25	69.0
WP_012951559.1\|1299179_1300025_+	M15 family metallopeptidase	A0A059T7Y8	Listeria_phage	5.4e-130	83.7
WP_012951560.1\|1300128_1301127_+	DUF3644 domain-containing protein	A0A0N9RUA4	Staphylococcus_phage	3.9e-71	44.8
WP_012951561.1\|1301351_1301534_-	hypothetical protein	A0A059T7Z0	Listeria_phage	2.3e-22	96.6
WP_012951563.1\|1301974_1302208_+	hypothetical protein	A8ATC5	Listeria_phage	1.6e-36	98.7
WP_012951565.1\|1302855_1304214_+	DUF1254 domain-containing protein	NA	NA	NA	NA
1302474:1302495	attR	NA	NA	NA	NA
WP_012951566.1\|1304254_1304848_-	hypothetical protein	NA	NA	NA	NA
WP_009914084.1\|1305001_1305409_-	glyoxalase/bleomycin resistance/extradiol dioxygenase family protein	NA	NA	NA	NA
WP_009924169.1\|1305573_1306173_+	histidine phosphatase family protein	A0A1X9IGJ2	Lactococcus_phage	5.8e-30	41.0
WP_003723543.1\|1306204_1306465_-	hypothetical protein	NA	NA	NA	NA
WP_010989717.1\|1306588_1308001_+	DEAD/DEAH box helicase	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	8.3e-51	31.8
WP_003723545.1\|1308025_1308289_+	DUF3116 family protein	NA	NA	NA	NA
WP_003723546.1\|1308456_1308933_+	8-oxo-dGTP diphosphatase	NA	NA	NA	NA
WP_012951567.1\|1308970_1309216_-	hypothetical protein	NA	NA	NA	NA
WP_012951568.1\|1309212_1310418_-	MFS transporter	NA	NA	NA	NA
WP_003723549.1\|1310622_1311282_+	Crp/Fnr family transcriptional regulator	NA	NA	NA	NA
WP_003723550.1\|1311323_1311518_-	hypothetical protein	NA	NA	NA	NA
WP_003723551.1\|1311584_1312433_-	YitT family protein	NA	NA	NA	NA
WP_009931701.1\|1313052_1313766_+	trehalose operon repressor	NA	NA	NA	NA
WP_012951570.1\|1313796_1315443_-	alpha,alpha-phosphotrehalase	NA	NA	NA	NA
WP_003723556.1\|1315461_1316946_-	PTS system trehalose-specific EIIBC component	NA	NA	NA	NA
WP_003723557.1\|1317061_1317514_+	NUDIX domain-containing protein	NA	NA	NA	NA
WP_012951571.1\|1317560_1318025_-	hypothetical protein	NA	NA	NA	NA
WP_003723559.1\|1318213_1319134_+	alpha/beta hydrolase	NA	NA	NA	NA
WP_003723560.1\|1319153_1320401_-	glutamate-5-semialdehyde dehydrogenase	A0A1X9I5D4	Streptococcus_phage	1.2e-106	51.8
WP_003723561.1\|1320384_1321215_-	glutamate 5-kinase	A0A1X9I5D0	Streptococcus_phage	4.3e-47	42.4
WP_003723562.1\|1321350_1322490_-\|protease	PrsW family intramembrane metalloprotease	NA	NA	NA	NA
WP_003723563.1\|1322570_1322966_-	helix-turn-helix transcriptional regulator	A9D9J6	Lactobacillus_prophage	1.3e-14	57.4
WP_003727524.1\|1323116_1323332_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_010989719.1\|1323450_1323984_+\|protease	matrixin family metalloprotease	NA	NA	NA	NA
WP_003732795.1\|1324001_1324667_+	hypothetical protein	NA	NA	NA	NA
WP_003732796.1\|1324928_1325867_+	hypothetical protein	NA	NA	NA	NA
WP_003723884.1\|1325981_1327265_+	trigger factor	NA	NA	NA	NA
WP_003723886.1\|1327449_1328709_+\|protease	ATP-dependent protease ATP-binding subunit ClpX	G3M9Z9	Bacillus_virus	1.4e-145	63.2
WP_003723887.1\|1328827_1329394_+	type I signal peptidase SipX	NA	NA	NA	NA
WP_009924619.1\|1329428_1329998_+	type I signal peptidase SipY	NA	NA	NA	NA
WP_003723889.1\|1330099_1330642_+	type I signal peptidase SipZ	NA	NA	NA	NA
WP_003723890.1\|1330651_1331515_+	ribosome biogenesis GTPase YlqF	NA	NA	NA	NA
WP_003723891.1\|1331511_1332297_+	ribonuclease HII	G4YAY0	Emiliania_huxleyi_virus	3.0e-26	39.2
WP_003723892.1\|1332430_1333291_+	DNA-protecting protein DprA	NA	NA	NA	NA
WP_012951572.1\|1333562_1335641_+	type I DNA topoisomerase	A0A1V0SB35	Catovirus	3.2e-107	37.5
WP_009924616.1\|1335703_1337008_+\|tRNA	FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO	NA	NA	NA	NA
WP_009911635.1\|1337290_1338193_+	tyrosine recombinase XerC	A0A097EYL9	Mycobacterium_phage	1.2e-13	28.6
WP_003724001.1\|1338213_1338753_+\|protease	ATP-dependent protease subunit HslV	NA	NA	NA	NA
WP_003732800.1\|1338766_1340176_+\|protease	ATP-dependent protease ATPase subunit HslU	W6AS21	Erwinia_phage	3.7e-43	28.7

DBSCAN-SWA_4

1923241 : 1931527

Synechococcus_phage(33.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_003722243.1\|1923241_1923808_-	phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	7.0e-25	35.9
WP_012951771.1\|1923804_1924854_-	phosphoribosylformylglycinamidine cyclo-ligase	Q58MH8	Prochlorococcus_phage	4.6e-62	43.5
WP_003722245.1\|1924872_1926300_-	amidophosphoribosyltransferase	A0A0M3SGR2	Mollivirus	1.1e-53	34.6
WP_012951772.1\|1926284_1928504_-	phosphoribosylformylglycinamidine synthase subunit PurL	A6N228	Microbacterium_phage	5.0e-159	41.1
WP_003722247.1\|1928496_1929180_-	phosphoribosylformylglycinamidine synthase subunit PurQ	NA	NA	NA	NA
WP_003722248.1\|1929183_1929429_-	phosphoribosylformylglycinamidine synthase subunit PurS	NA	NA	NA	NA
WP_012951773.1\|1929440_1930154_-	phosphoribosylaminoimidazolesuccinocarboxamide synthase	A0A0E3F9V5	Synechococcus_phage	1.2e-42	38.3
WP_003729814.1\|1930234_1931527_-	adenylosuccinate lyase	A0A1B3B081	Gordonia_phage	2.5e-17	33.0

DBSCAN-SWA_5

2444790 : 2484021

Listeria_phage(98.11%)

terminase,holin,tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_012951924.1\|2444790_2445024_-	hypothetical protein	A0A059T6E1	Listeria_phage	8.0e-36	94.8
WP_012951925.1\|2445464_2445674_+	hypothetical protein	A0A059T7Z0	Listeria_phage	5.5e-28	97.1
WP_012951926.1\|2445775_2446180_+	hypothetical protein	NA	NA	NA	NA
WP_012951927.1\|2446181_2446610_+	transcriptional regulator	A8ATJ2	Listeria_phage	3.9e-28	87.3
WP_012951928.1\|2446621_2447119_+	AP2 domain-containing protein	A8ATW6	Listeria_phage	4.9e-83	90.9
WP_003722520.1\|2447393_2448167_+	DUF3825 domain-containing protein	A8ATW5	Listeria_phage	9.5e-150	100.0
WP_012951929.1\|2448207_2449053_-	peptidase M15	A0A059T7Y8	Listeria_phage	1.4e-133	92.6
WP_003722522.1\|2449052_2449334_-\|holin	holin	A8ASL4	Listeria_phage	3.4e-41	94.6
WP_003722523.1\|2449346_2449712_-	hypothetical protein	Q9T1A0	Listeria_phage	7.4e-12	100.0
WP_012951930.1\|2449750_2451913_-	hypothetical protein	A8ATW1	Listeria_phage	0.0e+00	98.8
WP_012951931.1\|2451925_2453494_-	hypothetical protein	A8ATW0	Listeria_phage	2.0e-303	99.2
WP_012951932.1\|2453490_2458290_-\|tail	phage tail tape measure protein	A8ATV9	Listeria_phage	0.0e+00	89.1
WP_074046934.1\|2458294_2458606_-	hypothetical protein	A0A0B5D116	Listeria_phage	1.3e-41	96.7
WP_012951934.1\|2458602_2459034_-	hypothetical protein	A8ATV7	Listeria_phage	3.2e-70	95.8
WP_012951935.1\|2459089_2459776_-	Ig domain-containing protein	A0A0B5CYK8	Listeria_phage	2.6e-114	97.4
WP_010991155.1\|2459780_2460152_-	hypothetical protein	A0A0B5CTY4	Listeria_phage	5.5e-63	99.2
WP_012951936.1\|2460148_2460466_-	HK97 gp10 family phage protein	A8ATV4	Listeria_phage	2.4e-51	98.1
WP_003733695.1\|2460455_2460821_-	hypothetical protein	A8ATV3	Listeria_phage	9.9e-65	99.2
WP_012951937.1\|2460820_2461174_-	hypothetical protein	A8ATV2	Listeria_phage	7.6e-62	100.0
WP_012951939.1\|2461355_2462228_-	hypothetical protein	A8ATV0	Listeria_phage	3.0e-160	99.0
WP_003744996.1\|2462250_2462805_-	hypothetical protein	A8ATU9	Listeria_phage	1.1e-88	99.5
WP_012951940.1\|2462900_2463944_-	hypothetical protein	A0A0B5D111	Listeria_phage	1.9e-193	96.5
WP_012951941.1\|2463948_2465505_-	hypothetical protein	A8ATU7	Listeria_phage	9.4e-298	97.9
WP_012951942.1\|2465519_2466839_-\|terminase	PBSX family phage terminase large subunit	A8ATU6	Listeria_phage	2.9e-263	99.3
WP_012951943.1\|2466831_2467572_-	hypothetical protein	A0A0B5CTX0	Listeria_phage	2.4e-134	99.6
WP_012951944.1\|2467611_2467839_-	hypothetical protein	A8AU06	Listeria_phage	1.5e-34	100.0
WP_012951945.1\|2468124_2468559_-	hypothetical protein	A8AU03	Listeria_phage	1.6e-74	97.2
WP_012951946.1\|2468699_2469083_-	DUF2481 family protein	A0A0B5CYS3	Listeria_phage	5.7e-63	96.1
WP_012951947.1\|2469086_2469491_-	DUF1064 domain-containing protein	A8ASP7	Listeria_phage	1.9e-61	89.6
WP_031645468.1\|2469435_2469618_-	hypothetical protein	A8ASP6	Listeria_phage	2.9e-17	81.0
WP_012951948.1\|2469645_2470023_-	hypothetical protein	NA	NA	NA	NA
WP_012951949.1\|2470044_2470524_-	single-stranded DNA-binding protein	A8ATZ7	Listeria_phage	1.4e-74	91.2
WP_012951950.1\|2470520_2470922_-	hypothetical protein	A8ATZ6	Listeria_phage	1.4e-48	75.9
WP_012951951.1\|2470918_2471278_-	hypothetical protein	A0A059T801	Listeria_phage	6.6e-45	92.0
WP_031645470.1\|2471299_2471530_-	DUF3850 domain-containing protein	A0A059T699	Listeria_phage	1.1e-18	73.8
WP_012951953.1\|2471665_2472196_-	hypothetical protein	A0A059T5F9	Listeria_phage	8.4e-97	95.5
WP_012951954.1\|2472192_2472480_-	hypothetical protein	A0A059T7V3	Listeria_phage	1.7e-40	88.4
WP_012951955.1\|2472476_2473460_-	DnaD domain protein	A8ASN4	Listeria_phage	1.4e-166	91.7
WP_012951956.1\|2473476_2474136_-	ERF family protein	A8ASN3	Listeria_phage	5.3e-93	94.1
WP_012951957.1\|2474141_2474618_-	siphovirus Gp157 family protein	A0A059T5F1	Listeria_phage	9.5e-76	100.0
WP_003734953.1\|2474614_2474809_-	hypothetical protein	A0A059T6E8	Listeria_phage	1.6e-29	100.0
WP_157862701.1\|2474904_2475045_-	hypothetical protein	A0A059T7Q6	Listeria_phage	9.4e-16	97.6
WP_003722564.1\|2475114_2475303_-	hypothetical protein	Q9T175	Listeria_phage	1.8e-22	82.3
WP_012951958.1\|2475411_2475627_-	hypothetical protein	Q9T176	Listeria_phage	9.7e-28	93.0
WP_012951959.1\|2475623_2476157_-	hypothetical protein	A0A059T5F0	Listeria_phage	1.5e-77	87.9
WP_012951960.1\|2476280_2477057_-	phage antirepressor Ant	A0A0B5D0I2	Listeria_phage	9.6e-142	99.2
WP_003733685.1\|2477038_2477314_-	hypothetical protein	NA	NA	NA	NA
WP_012951961.1\|2477319_2477601_-	hypothetical protein	A8ATX8	Listeria_phage	3.6e-38	96.7
WP_012951962.1\|2477597_2477834_-	hypothetical protein	A0A059T5E9	Listeria_phage	2.8e-36	97.4
WP_012951963.1\|2477898_2478258_+	DUF2513 domain-containing protein	A0A2H4J4K9	uncultured_Caudovirales_phage	2.1e-06	26.3
WP_003733687.1\|2478216_2478411_-	hypothetical protein	A0A059T6E5	Listeria_phage	1.4e-25	95.3
WP_012951964.1\|2478414_2478666_-	helix-turn-helix transcriptional regulator	A8ASM3	Listeria_phage	9.3e-22	76.7
WP_012951965.1\|2478828_2479134_+	helix-turn-helix transcriptional regulator	A8ASM2	Listeria_phage	1.8e-27	68.5
WP_012951966.1\|2479164_2479656_+	hypothetical protein	A8ATX4	Listeria_phage	2.9e-91	99.4
WP_012951967.1\|2479682_2480390_+	hypothetical protein	A0A0B5CTT6	Listeria_phage	5.3e-123	99.1
WP_012951968.1\|2480448_2480883_+	hypothetical protein	NA	NA	NA	NA
WP_012951969.1\|2481087_2482602_+	ATP-dependent DNA helicase RecG	NA	NA	NA	NA
WP_012951970.1\|2482662_2484021_+	recombinase family protein	Q8LTD8	Listeria_phage	1.1e-257	99.8

DBSCAN-SWA_6

2625930 : 2633774

Streptococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_003722604.1\|2625930_2626902_-	DNA-binding protein WhiA	Q7AWZ3	Streptococcus_phage	5.2e-52	39.4
WP_003722605.1\|2626909_2627878_-	YvcK family protein	A1IMD5	Streptococcus_phage	6.7e-68	43.3
WP_003722606.1\|2627879_2628755_-	RNase adapter RapZ	A0A0R8VB27	Thermobifida_phage	1.9e-08	29.7
WP_012952017.1\|2628862_2630593_-	phospho-sugar mutase	A0A1X9I671	Streptococcus_phage	3.0e-175	54.0
WP_012952018.1\|2630634_2631696_-	galactose mutarotase	NA	NA	NA	NA
WP_012952019.1\|2631712_2632696_-	UDP-glucose 4-epimerase GalE	A0A2K9L1R4	Tupanvirus	5.8e-51	37.2
WP_003722610.1\|2632814_2633774_-	thioredoxin-disulfide reductase	G3MA85	Bacillus_virus	2.0e-88	53.7

DBSCAN-SWA_7

2868729 : 2875254

Streptococcus_pyogenes_phage(33.33%)

tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_003734720.1\|2868729_2869548_-\|tail	phage tail family protein	A0A060AFE1	Staphylococcus_phage	7.2e-39	35.0
WP_012952081.1\|2869544_2871413_-	membrane protein	A0A097PAU2	Streptococcus_pyogenes_phage	3.5e-20	45.8
WP_012952082.1\|2871399_2871804_-	hypothetical protein	NA	NA	NA	NA
WP_003721745.1\|2871845_2872148_-	hypothetical protein	NA	NA	NA	NA
WP_003721744.1\|2872195_2872708_-\|tail	phage major tail protein, TP901-1 family	A0A097PBF4	Streptococcus_pyogenes_phage	1.2e-47	62.7
WP_012952083.1\|2872720_2873110_-	DUF5072 domain-containing protein	NA	NA	NA	NA
WP_003732220.1\|2873387_2873804_-	hypothetical protein	A8ASQ1	Listeria_phage	1.3e-20	39.3
WP_003732219.1\|2873815_2874244_-	hypothetical protein	NA	NA	NA	NA
WP_003721740.1\|2874460_2874796_+	helix-turn-helix transcriptional regulator	A0A2H4JAR9	uncultured_Caudovirales_phage	4.0e-20	52.5
WP_003721739.1\|2874801_2875254_+	ImmA/IrrE family metallo-endopeptidase	A0A059T7S0	Listeria_phage	4.0e-31	47.9

Anti-CRISPR protein detection

Acr_ID: NC_013768.1|WP_003723550.1|1311323_1311518_-|hypothetical-protein

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Acr_ID: NC_013768.1|WP_012951967.1|2479682_2480390_+|hypothetical-protein

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Acr_ID: NC_013768.1|WP_003733687.1|2478216_2478411_-|hypothetical-protein

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Acr ID

Acr position

Acr size

Homology with known anti

Neighbor HTH/AcRanker

Neighbor Aca

In prophage

Protospacer in prophage

NC_013768.1|WP_003723550.1|1311323_1311518_-|hypothetical-protein

1311323_1311518_-

64 aa aa

1233093-1340176

yes

CRISPR ID	CRISPR type	Spacer info	Spacer location	Spacer length	Protospacer location	Mismatch
NC_013768_2	Orphan	2.1\|539238\|35\|NC_013768\|PILER-CR,CRT	539238-539272	35	1285751-1285785	0
NC_013768_2	Orphan	2.6\|539558\|36\|NC_013768\|PILER-CR,CRT	539558-539593	36	1284603-1284638	1

1. spacer 2.1|539238|35|NC_013768|PILER-CR,CRT matches to NC_013768 position: 1285751-1285785, mismatch: 0

acagatcaaactccggaagggtgattgtaaatggc	CRISPR spacer
acagatcaaactccggaagggtgattgtaaatggc	Protospacer
***********************************

2. spacer 2.6|539558|36|NC_013768|PILER-CR,CRT matches to NC_013768 position: 1284603-1284638, mismatch: 1

aaaataggaggaaataaattatgactatcaaattaa	CRISPR spacer
aaaataggaggaaatagattatgactatcaaattaa	Protospacer
****************.*******************

NC_013768.1|WP_012951967.1|2479682_2480390_+|hypothetical-protein

2479682_2480390_+

235 aa aa

2444790-2484021

yes

CRISPR ID	CRISPR type	Spacer info	Spacer location	Spacer length	Protospacer location	Mismatch
NC_013768_2	Orphan	2.7\|539623\|35\|NC_013768\|PILER-CR,CRT	539623-539657	35	2451852-2451886	0

1. spacer 2.7|539623|35|NC_013768|PILER-CR,CRT matches to NC_013768 position: 2451852-2451886, mismatch: 0

tttgttgaatcaacggatatagattttacaatttc	CRISPR spacer
tttgttgaatcaacggatatagattttacaatttc	Protospacer
***********************************

NC_013768.1|WP_003733687.1|2478216_2478411_-|hypothetical-protein

2478216_2478411_-

64 aa aa

2444790-2484021

yes

CRISPR ID	CRISPR type	Spacer info	Spacer location	Spacer length	Protospacer location	Mismatch
NC_013768_2	Orphan	2.7\|539623\|35\|NC_013768\|PILER-CR,CRT	539623-539657	35	2451852-2451886	0

1. spacer 2.7|539623|35|NC_013768|PILER-CR,CRT matches to NC_013768 position: 2451852-2451886, mismatch: 0

tttgttgaatcaacggatatagattttacaatttc	CRISPR spacer
tttgttgaatcaacggatatagattttacaatttc	Protospacer
***********************************

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NC_013768

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CRISPR-Cas detection and classification

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Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

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