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
NZ_LT635479	Lachnoclostridium phocaeense strain Marseille-P3177T chromosome contig00001	3 crisprs	RT,csa3,cas3,DinG,c2c10_CAS-V-U3,c2c4_V-U1,Cas14u_CAS-V,cas14j,DEDDh,csn2,cas2,cas1,cas9,WYL	0	12	5	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NZ_LT635479_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_LT635479_1

1498379-1498613

Unclear

Consensus_repeat	Method
CACTTGACACCCGTGTAAATCTTCATAGGTCTCAAAC	CRISPRCasFinder

3 spacers

c2c4_V-U1

The CRISPR arrays of NZ_LT635479_1

>merge|NZ_LT635479|1|1498379-1498613|CRISPRCasFinder
TCCCTGACACCCGTGTATAAATGCAAAGGTCTCAACAAAAACAGACAACAATGCAAAATGATCAATACTTGACACCTGTGTAAATCATCACGGGTCTCAAACGCATCCCCTGTGTCTGTCGGCAGCGCAAACACTTGACACCCGTGTAAATCTTCATAGGTCTCAAACGGTAATGATGCCTTGGAGTGCGGCTAATGCACTTGACACCCGTGTAAATCTTCATAGGTCTCAAACC

>NZ_LT635479|1|1|1498379-1498613|CRISPRCasFinder
TCCCTGACACCCGTGTATAAATGCAAAGGTCTCAACA	AAAACAGACAACAATGCAAAATGATCAA
TACTTGACACCTGTGTAAATCATCACGGGTCTCAAAC	GCATCCCCTGTGTCTGTCGGCAGCGCAAA
CACTTGACACCCGTGTAAATCTTCATAGGTCTCAAAC	GGTAATGATGCCTTGGAGTGCGGCTAATG
CACTTGACACCCGTGTAAATCTTCATAGGTCTCAAACC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_LT635479.1\|WP_076777802.1\|1503233_1503479_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777804.1\|1504263_1505739_-\|hypothetical-protein	c2c4_V-U1	-	unknown
NZ_LT635479.1\|WP_076777789.1\|1493238_1493640_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777800.1\|1502477_1502729_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777792.1\|1495645_1495909_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_157888412.1\|1500050_1500488_-\|GIY-YIG-nuclease-family-protein	unknown	unknown	gnl\|CDD\|198380
NZ_LT635479.1\|WP_173829275.1\|1498756_1499596_-\|HNH-endonuclease	unknown	unknown	gnl\|CDD\|372995
NZ_LT635479.1\|WP_076777798.1\|1500554_1500800_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|197632
NZ_LT635479.1\|WP_076777795.1\|1497796_1498243_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777788.1\|1491559_1493035_-\|hypothetical-protein	c2c4_V-U1	-	unknown
NZ_LT635479.1\|WP_076777799.1\|1500996_1502421_+\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076780900.1\|1496652_1496868_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777790.1\|1493734_1494115_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777805.1\|1505789_1506080_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777791.1\|1494585_1495317_-\|phosphoadenosine-phosphosulfate-reductase	unknown	unknown	gnl\|CDD\|238846
NZ_LT635479.1\|WP_157888410.1\|1494161_1494317_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777801.1\|1502725_1503244_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|380121
NZ_LT635479.1\|WP_076777793.1\|1495931_1496408_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_083582520.1\|1496928_1497426_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_157888413.1\|1503622_1504051_-\|hypothetical-protein	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NZ_LT635479.1\|WP_173829275.1\|1498756_1499596_-\|HNH-endonuclease	gnl\|CDD\|372995	pfam14279, HNH_5, HNH endonuclease. This domain is related to other HNH domain families such as pfam01844. Suggesting that these proteins have a nucleic acid cleaving function.	1.31593e-11
NZ_LT635479.1\|WP_076777791.1\|1494585_1495317_-\|phosphoadenosine-phosphosulfate-reductase	gnl\|CDD\|238846	cd01713, PAPS_reductase, This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) . It is also found in NodP nodulation protein P from Rhizobium meliloti which has ATP sulphurylase activity (sulphate adenylate transferase) .	0.00138381
NZ_LT635479.1\|WP_076777801.1\|1502725_1503244_-\|hypothetical-protein	gnl\|CDD\|380121	pfam18143, HAD_SAK_2, HAD domain in Swiss Army Knife RNA repair proteins. Family of HAD domain phophoesterases observed in large eukaryotic proteins with predicted role in RNA repair, the so-called 'Swiss Army Knife' repair proteins. May be involved in phosphate group removal during RNA re-ligation.	1.26964e-27
NZ_LT635479.1\|WP_076777798.1\|1500554_1500800_-\|hypothetical-protein	gnl\|CDD\|197632	smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.	0.00449719
NZ_LT635479.1\|WP_157888412.1\|1500050_1500488_-\|GIY-YIG-nuclease-family-protein	gnl\|CDD\|198380	cd00719, GIY-YIG_SF, GIY-YIG nuclease domain superfamily. The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions.	1.89147e-07

>NZ_LT635479.1|WP_076777795.1|1497796_1498243_-|hypothetical-protein
MAKVTMENGCIARGKYRYREGENVFVKYISGGRTYWCYGEIAAASGPVFDEDKHSFRAFPVCMIENNGSVYLTDRNIIYIMHRTPEGYTEEEIGNLKAGRIIVADDRNDFQHTDYAGAKAAEHERERCGETTEDLEEDRDFSDEDTEN
>NZ_LT635479.1|WP_083582520.1|1496928_1497426_-|hypothetical-protein
MWYSDDLIVKRVSRQVRERTRENMEIYNMSLSDAFEEAARNYAKRGSDLYLAFYTSDFREYIPSAYQEEYLDFEKYPLSYTPSGKVQLDLQTVHSIDNPPFIRCPYCGSEEFFVKEHVSGPVHMKFRFDGEEADNGDMYEGTTTTETGVFAYCSGCRKRIFRYRR
>NZ_LT635479.1|WP_076780900.1|1496652_1496868_-|hypothetical-protein
MDQVCKILGLDFFEKFNIISRYPNALHIKIYGKIRNPYYFTDEGLQNRDGVLDNHKLADLITGYYDYEKVK
>NZ_LT635479.1|WP_076777793.1|1495931_1496408_-|hypothetical-protein
MAKGIIVVDMPEICENCLFSRTHAAPLQDCLYCTVLTRGVIRKNQIKRPNWCPIKPMPEIAYRHEKGEPGQRNYRIVDDLIGRKAAYKAFSDYLNRNYIGEISSQTELSIGEIASVIKSIPTAYDQEKVIEQLKEEGCIVDDEAGHRVVEIIEKGGLN
>NZ_LT635479.1|WP_076777792.1|1495645_1495909_-|hypothetical-protein
MKIPKEIREKIEQKIKLDEEIKDWMKESIDVDDMYFPSMEITEKPKGEFQGEGEWCDQSVGYCGDDFYGHYYWEMDNGKYLCMYYEC
>NZ_LT635479.1|WP_076777791.1|1494585_1495317_-|phosphoadenosine-phosphosulfate-reductase
MKEKLKVCWLSAGVSSFVAGYLSEGVDKYIYIDIENQHPDSMRFVRDCEAALKRPVEILRSPYRNVENVIKQFQYINGAYGAKCTQILKKRVRKEWEDRHKDYDITYVWGFDIDEKSRAERLNESMVEINQEYPLIDRCLTKQDAHAILDRLGIKRPVMYDLGYQNNNCIGCVKGGMGYWNKIRKDFPDVFERRAKLEREIGHSCIKGVFLDELEPDRGRMEDEIMQDCGIMCYLETIDKIDL
>NZ_LT635479.1|WP_157888410.1|1494161_1494317_-|hypothetical-protein
MRKIIYTADDEEPKCGQCDNFADGDAICEHCGPAFGWAGYTREEFIDERSL
>NZ_LT635479.1|WP_076777790.1|1493734_1494115_-|hypothetical-protein
MRTVSKKKDGNLPGQISFTMLTSETPAEDKPKEKPRKTESAPVKKDTVAEKKRNQVPLLAKEVPVEMYQAAKELLEGYYRITAGILVNHLRISANKALAIMDRLQKDGLIMEDGKRVSQKGKKWGK
>NZ_LT635479.1|WP_076777789.1|1493238_1493640_-|hypothetical-protein
MSENIIKVLDELGKRFGIAIDWSSENVTPYLQSLMSRFITNEIITSAILIVVSIVIILGLVIAIKQINKYETKVLKENKYYPDWLDYKYLIIIIFIVIIVVVLLFLVSMVLNIVTCCTVPEKIIIDYINTSIS
>NZ_LT635479.1|WP_076777788.1|1491559_1493035_-|hypothetical-protein
MARTRTDSFILELKLKTSPEDAAYLAKCFFAGHGIYNILVRHCRRRIASLRQDQAYRELLAEYRTLKDENERKAVSEQLKAIVASYGLTEYSLHSFVKVQQKKHKKYINSLVAQKIASSVWKGVEKVLYGNGKLLHFRKYTEFVSLEGKNNSTGLIFQDGILKVNGRPVYVSRHKRDGSTSRWYEDEALKHRVKYCRLVRKPVGSSWHYYVQLVLEGTAPVKHSLGSGRAGLDIGTSTAAMATRQECILTVLGESVEDIEKEQRRLLRKMDRSRRAMNPWNYNPDGTVRKGRKKWINSAHYRRMRMEYASLRRKRAAALKQWQEAMANRIVSQCDTLYVEKMNFKALQRRAKPSSVKENGKHTRRKRFGKSLQTRAPAQFCRTLKRKLEALGGQYLEVDTRAFRASQYDHVTDTYTKKKLSRRHNIIDGRWVQRDLYSAFLLSNSAEDLAHADRDRCNETFNLFLKNHDACVAKIRNTKTKIPRSFGFQAA
>NZ_LT635479.1|WP_173829275.1|1498756_1499596_-|HNH-endonuclease
MTMDHIIPLSRGGKNEAENLVALCEDCNKKKGNMLYLPYGYYNALNGISDSELIKMEKYVEAWFQQIKDQFDIQRFPLIAPVTNVQVIPFHTRAVKKVQYNPQLTYRWSLIGKDYYDEIEAVTGLDLRKVRSTISKYRRVEKEDPEAGELPVALYSFRKLTNDKIIAVTAVRIEPDSHHMTIYFPWCISTKKYAPEILRSLAEVLIRTVDRIAKLDLLAYTMISDIPDVLVNIRTEGRLYDPKAVYTDGGSYINMDTGEWGSDILTVCRHEPLQEYYNT
>NZ_LT635479.1|WP_157888412.1|1500050_1500488_-|GIY-YIG-nuclease-family-protein
MSYVIAHPTKAIFVLVIVGILVPVGETVTSAVTRRRVLRGQWHSPNWLGEFQRRPGCYVIVIYNDNGVMENLYVGQSVDVRRRIKEHITGHGNKRVYQDVLQKKQIRIFPVYCKEKQLNRLEKKLIRVFRARKSYNIQRGGAKKR
>NZ_LT635479.1|WP_076777798.1|1500554_1500800_-|hypothetical-protein
MRGAMIVLVLVALATTVNPYNQFISPVSSDVLESSEASTAYAGEMDNLYMCVECGEVVNARFYGMEIHSEQSGHYGFAKYV
>NZ_LT635479.1|WP_076777799.1|1500996_1502421_+|hypothetical-protein
MKKRMCPCGGTEFKATRIFQADVICDGAGKPINHIGFYEDHTTGPYTCQKCGTQYESLADLVTVHQYMTLTVGFPREAPTKLSVASDGTITENVKVAITGFYKALGNDLSKTEGIHPICVDDGEDTILYGLLCVKPDNVSIKLGNLEDGMPSEWEPIPLDEPEESGIDNQYQCKEVLLSMEALSHHKLLCGLKVIKDYEGDLYCGIVKPGGAVFYSPRIVRAKILAEAGSFIAVDIPNETGYTFMLTQKEFEDAVIRYKGLRLYANYHLRKSYEKERLYLGINLSYEEWMEEREAPNPITREDIESAKSEVYQSKRTIDPRRILSLMPSMPPEEKVSMRTLAQLTLTYGGFFVHDKTSNQYSFKYLAEEEDPEKWFRKITWAKIIEEEGDKVRLLLKNTKGDYLIDLLLTPQEFEKCRIKYSLPKAWGILPGWDELLSEYDLRQYYREKVRTSSRPLPPYEKWRDGPFDVIKLH
>NZ_LT635479.1|WP_076777800.1|1502477_1502729_-|hypothetical-protein
MTKLSSVRSLGKKRVAVRVRRIGGSNKYEVVPGSITMLSGEVKVGERDGALIVDENGEAMQPTGKFLWTAETIDPFHLVTDFF
>NZ_LT635479.1|WP_076777801.1|1502725_1503244_-|hypothetical-protein
MQSEKIVFLDIDGVLNYCGWYDEVRGLSGYHELCPRKLALLKELIDQTGAKIVLSSSWRDLAKEGKGEPHPMYRYLVETLGDCGLEIVDHTPHINDDRPREILEWIKRNAGNQARFISLDDDFSLLDYERYGIGDCLVRTSFYEPDGGLRQEHIEKAVGILSGNMQQGGSLS
>NZ_LT635479.1|WP_076777802.1|1503233_1503479_-|hypothetical-protein
MQEFREVALERDAANTSEEEDAYESAAYVTVFVCEKCGSTLTNTERVATHKAETGHEIYRVVTKKVVTQEEAASGVDYNAK
>NZ_LT635479.1|WP_157888413.1|1503622_1504051_-|hypothetical-protein
MESSQGKIGAKPLYESRVREYATQSFPDSGVKVFSDIRNSGQGTDRQSVTEENVLQKVSAVTYIFISDTVCTKEQFQDFIEDCAKWMEGQCQGVAAQFCLRLTDVAQWETIYMFNYEDKLREDIFSAEAECGITAAGEVTIY
>NZ_LT635479.1|WP_076777804.1|1504263_1505739_-|hypothetical-protein
MARTRTDSFILELKLKTSPADVAYLEKCFSAGHSIYNILVRHCRGRIASLRQDQTYRELLAEYRTLQEGNERKAVAERLKVLVAAYGLTEYSLHSFVKGQQKKHKNYINSLVAQKIASSVWKGVEKVLYGNGKFLHFRKYTEFVSLEGKNNSTGFIFQDGILKVNSRPIYVSRHKRDGSTSRLYEDEALKQRVKYCRLVRRPIGSSWHYYVQLVLEGTAPVKHRLGSGRAGLDIGTSTAAVATRQECILTVLGESVEDIEKEQRRLLRKMDRSRRAMNPWNYNPDGTVRKGRKKWINSAHYRRMRMEYASLRRKRAAALKQWQEAMANRIVSQCDTLYVEKMNFKSLQRRAKTSKVKENGKHTRRKRFGKSLQARAPAQFCRTLKRKLEALGGQYLEVDTRAFRASQYDHVTDTYTKKKLSRRHNIIDGRWVQRDLYSAFLLSNSAEDLAHADRDRCNETFDLFLKNHDACVAKIRNTKTKIPRSFGFQAA
>NZ_LT635479.1|WP_076777805.1|1505789_1506080_-|hypothetical-protein
MGLPTEYDSLTDSQKNAITSIEDCLTYLEDKYHEEFRYLSYAKAGPLEEEHLEAYPASETPSDVVTVYRTYEDGEYHYEDDYNNQAGKLPLVTVCR

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Crispr_ID: NZ_LT635479_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_LT635479_2

1499869-1499972

Unclear

Consensus_repeat	Method
CACTTGACACCCGTGTAAATCTTCATAGGTCTCAAAC	CRISPRCasFinder

1 spacers

c2c4_V-U1

The CRISPR arrays of NZ_LT635479_2

>merge|NZ_LT635479|2|1499869-1499972|CRISPRCasFinder
ACCTTGACACCTGTGTAATTTGTCACAGGTCTCAAACGCTCAGAACGCCCTTACACATGCTTGCAACCCCTTGACACCTGTGTAATTTGTCACAGGTCTCAAAC

>NZ_LT635479|2|2|1499869-1499972|CRISPRCasFinder
ACCTTGACACCTGTGTAATTTGTCACAGGTCTCAAAC	GCTCAGAACGCCCTTACACATGCTTGCAAC
CCCTTGACACCTGTGTAATTTGTCACAGGTCTCAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_LT635479.1\|WP_076777802.1\|1503233_1503479_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777804.1\|1504263_1505739_-\|hypothetical-protein	c2c4_V-U1	-	unknown
NZ_LT635479.1\|WP_076777789.1\|1493238_1493640_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777800.1\|1502477_1502729_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777792.1\|1495645_1495909_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_157888412.1\|1500050_1500488_-\|GIY-YIG-nuclease-family-protein	unknown	unknown	gnl\|CDD\|198380
NZ_LT635479.1\|WP_173829275.1\|1498756_1499596_-\|HNH-endonuclease	unknown	unknown	gnl\|CDD\|372995
NZ_LT635479.1\|WP_076777798.1\|1500554_1500800_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|197632
NZ_LT635479.1\|WP_076777795.1\|1497796_1498243_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777801.1\|1502725_1503244_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|380121
NZ_LT635479.1\|WP_076777799.1\|1500996_1502421_+\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076780900.1\|1496652_1496868_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777790.1\|1493734_1494115_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777806.1\|1506234_1507155_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777805.1\|1505789_1506080_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777791.1\|1494585_1495317_-\|phosphoadenosine-phosphosulfate-reductase	unknown	unknown	gnl\|CDD\|238846
NZ_LT635479.1\|WP_157888410.1\|1494161_1494317_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076777793.1\|1495931_1496408_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_083582520.1\|1496928_1497426_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_157888413.1\|1503622_1504051_-\|hypothetical-protein	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NZ_LT635479.1\|WP_173829275.1\|1498756_1499596_-\|HNH-endonuclease	gnl\|CDD\|372995	pfam14279, HNH_5, HNH endonuclease. This domain is related to other HNH domain families such as pfam01844. Suggesting that these proteins have a nucleic acid cleaving function.	1.31593e-11
NZ_LT635479.1\|WP_076777791.1\|1494585_1495317_-\|phosphoadenosine-phosphosulfate-reductase	gnl\|CDD\|238846	cd01713, PAPS_reductase, This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) . It is also found in NodP nodulation protein P from Rhizobium meliloti which has ATP sulphurylase activity (sulphate adenylate transferase) .	0.00138381
NZ_LT635479.1\|WP_076777801.1\|1502725_1503244_-\|hypothetical-protein	gnl\|CDD\|380121	pfam18143, HAD_SAK_2, HAD domain in Swiss Army Knife RNA repair proteins. Family of HAD domain phophoesterases observed in large eukaryotic proteins with predicted role in RNA repair, the so-called 'Swiss Army Knife' repair proteins. May be involved in phosphate group removal during RNA re-ligation.	1.26964e-27
NZ_LT635479.1\|WP_076777798.1\|1500554_1500800_-\|hypothetical-protein	gnl\|CDD\|197632	smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.	0.00449719
NZ_LT635479.1\|WP_157888412.1\|1500050_1500488_-\|GIY-YIG-nuclease-family-protein	gnl\|CDD\|198380	cd00719, GIY-YIG_SF, GIY-YIG nuclease domain superfamily. The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions.	1.89147e-07

>NZ_LT635479.1|WP_173829275.1|1498756_1499596_-|HNH-endonuclease
MTMDHIIPLSRGGKNEAENLVALCEDCNKKKGNMLYLPYGYYNALNGISDSELIKMEKYVEAWFQQIKDQFDIQRFPLIAPVTNVQVIPFHTRAVKKVQYNPQLTYRWSLIGKDYYDEIEAVTGLDLRKVRSTISKYRRVEKEDPEAGELPVALYSFRKLTNDKIIAVTAVRIEPDSHHMTIYFPWCISTKKYAPEILRSLAEVLIRTVDRIAKLDLLAYTMISDIPDVLVNIRTEGRLYDPKAVYTDGGSYINMDTGEWGSDILTVCRHEPLQEYYNT
>NZ_LT635479.1|WP_076777795.1|1497796_1498243_-|hypothetical-protein
MAKVTMENGCIARGKYRYREGENVFVKYISGGRTYWCYGEIAAASGPVFDEDKHSFRAFPVCMIENNGSVYLTDRNIIYIMHRTPEGYTEEEIGNLKAGRIIVADDRNDFQHTDYAGAKAAEHERERCGETTEDLEEDRDFSDEDTEN
>NZ_LT635479.1|WP_083582520.1|1496928_1497426_-|hypothetical-protein
MWYSDDLIVKRVSRQVRERTRENMEIYNMSLSDAFEEAARNYAKRGSDLYLAFYTSDFREYIPSAYQEEYLDFEKYPLSYTPSGKVQLDLQTVHSIDNPPFIRCPYCGSEEFFVKEHVSGPVHMKFRFDGEEADNGDMYEGTTTTETGVFAYCSGCRKRIFRYRR
>NZ_LT635479.1|WP_076780900.1|1496652_1496868_-|hypothetical-protein
MDQVCKILGLDFFEKFNIISRYPNALHIKIYGKIRNPYYFTDEGLQNRDGVLDNHKLADLITGYYDYEKVK
>NZ_LT635479.1|WP_076777793.1|1495931_1496408_-|hypothetical-protein
MAKGIIVVDMPEICENCLFSRTHAAPLQDCLYCTVLTRGVIRKNQIKRPNWCPIKPMPEIAYRHEKGEPGQRNYRIVDDLIGRKAAYKAFSDYLNRNYIGEISSQTELSIGEIASVIKSIPTAYDQEKVIEQLKEEGCIVDDEAGHRVVEIIEKGGLN
>NZ_LT635479.1|WP_076777792.1|1495645_1495909_-|hypothetical-protein
MKIPKEIREKIEQKIKLDEEIKDWMKESIDVDDMYFPSMEITEKPKGEFQGEGEWCDQSVGYCGDDFYGHYYWEMDNGKYLCMYYEC
>NZ_LT635479.1|WP_076777791.1|1494585_1495317_-|phosphoadenosine-phosphosulfate-reductase
MKEKLKVCWLSAGVSSFVAGYLSEGVDKYIYIDIENQHPDSMRFVRDCEAALKRPVEILRSPYRNVENVIKQFQYINGAYGAKCTQILKKRVRKEWEDRHKDYDITYVWGFDIDEKSRAERLNESMVEINQEYPLIDRCLTKQDAHAILDRLGIKRPVMYDLGYQNNNCIGCVKGGMGYWNKIRKDFPDVFERRAKLEREIGHSCIKGVFLDELEPDRGRMEDEIMQDCGIMCYLETIDKIDL
>NZ_LT635479.1|WP_157888410.1|1494161_1494317_-|hypothetical-protein
MRKIIYTADDEEPKCGQCDNFADGDAICEHCGPAFGWAGYTREEFIDERSL
>NZ_LT635479.1|WP_076777790.1|1493734_1494115_-|hypothetical-protein
MRTVSKKKDGNLPGQISFTMLTSETPAEDKPKEKPRKTESAPVKKDTVAEKKRNQVPLLAKEVPVEMYQAAKELLEGYYRITAGILVNHLRISANKALAIMDRLQKDGLIMEDGKRVSQKGKKWGK
>NZ_LT635479.1|WP_076777789.1|1493238_1493640_-|hypothetical-protein
MSENIIKVLDELGKRFGIAIDWSSENVTPYLQSLMSRFITNEIITSAILIVVSIVIILGLVIAIKQINKYETKVLKENKYYPDWLDYKYLIIIIFIVIIVVVLLFLVSMVLNIVTCCTVPEKIIIDYINTSIS
>NZ_LT635479.1|WP_157888412.1|1500050_1500488_-|GIY-YIG-nuclease-family-protein
MSYVIAHPTKAIFVLVIVGILVPVGETVTSAVTRRRVLRGQWHSPNWLGEFQRRPGCYVIVIYNDNGVMENLYVGQSVDVRRRIKEHITGHGNKRVYQDVLQKKQIRIFPVYCKEKQLNRLEKKLIRVFRARKSYNIQRGGAKKR
>NZ_LT635479.1|WP_076777798.1|1500554_1500800_-|hypothetical-protein
MRGAMIVLVLVALATTVNPYNQFISPVSSDVLESSEASTAYAGEMDNLYMCVECGEVVNARFYGMEIHSEQSGHYGFAKYV
>NZ_LT635479.1|WP_076777799.1|1500996_1502421_+|hypothetical-protein
MKKRMCPCGGTEFKATRIFQADVICDGAGKPINHIGFYEDHTTGPYTCQKCGTQYESLADLVTVHQYMTLTVGFPREAPTKLSVASDGTITENVKVAITGFYKALGNDLSKTEGIHPICVDDGEDTILYGLLCVKPDNVSIKLGNLEDGMPSEWEPIPLDEPEESGIDNQYQCKEVLLSMEALSHHKLLCGLKVIKDYEGDLYCGIVKPGGAVFYSPRIVRAKILAEAGSFIAVDIPNETGYTFMLTQKEFEDAVIRYKGLRLYANYHLRKSYEKERLYLGINLSYEEWMEEREAPNPITREDIESAKSEVYQSKRTIDPRRILSLMPSMPPEEKVSMRTLAQLTLTYGGFFVHDKTSNQYSFKYLAEEEDPEKWFRKITWAKIIEEEGDKVRLLLKNTKGDYLIDLLLTPQEFEKCRIKYSLPKAWGILPGWDELLSEYDLRQYYREKVRTSSRPLPPYEKWRDGPFDVIKLH
>NZ_LT635479.1|WP_076777800.1|1502477_1502729_-|hypothetical-protein
MTKLSSVRSLGKKRVAVRVRRIGGSNKYEVVPGSITMLSGEVKVGERDGALIVDENGEAMQPTGKFLWTAETIDPFHLVTDFF
>NZ_LT635479.1|WP_076777801.1|1502725_1503244_-|hypothetical-protein
MQSEKIVFLDIDGVLNYCGWYDEVRGLSGYHELCPRKLALLKELIDQTGAKIVLSSSWRDLAKEGKGEPHPMYRYLVETLGDCGLEIVDHTPHINDDRPREILEWIKRNAGNQARFISLDDDFSLLDYERYGIGDCLVRTSFYEPDGGLRQEHIEKAVGILSGNMQQGGSLS
>NZ_LT635479.1|WP_076777802.1|1503233_1503479_-|hypothetical-protein
MQEFREVALERDAANTSEEEDAYESAAYVTVFVCEKCGSTLTNTERVATHKAETGHEIYRVVTKKVVTQEEAASGVDYNAK
>NZ_LT635479.1|WP_157888413.1|1503622_1504051_-|hypothetical-protein
MESSQGKIGAKPLYESRVREYATQSFPDSGVKVFSDIRNSGQGTDRQSVTEENVLQKVSAVTYIFISDTVCTKEQFQDFIEDCAKWMEGQCQGVAAQFCLRLTDVAQWETIYMFNYEDKLREDIFSAEAECGITAAGEVTIY
>NZ_LT635479.1|WP_076777804.1|1504263_1505739_-|hypothetical-protein
MARTRTDSFILELKLKTSPADVAYLEKCFSAGHSIYNILVRHCRGRIASLRQDQTYRELLAEYRTLQEGNERKAVAERLKVLVAAYGLTEYSLHSFVKGQQKKHKNYINSLVAQKIASSVWKGVEKVLYGNGKFLHFRKYTEFVSLEGKNNSTGFIFQDGILKVNSRPIYVSRHKRDGSTSRLYEDEALKQRVKYCRLVRRPIGSSWHYYVQLVLEGTAPVKHRLGSGRAGLDIGTSTAAVATRQECILTVLGESVEDIEKEQRRLLRKMDRSRRAMNPWNYNPDGTVRKGRKKWINSAHYRRMRMEYASLRRKRAAALKQWQEAMANRIVSQCDTLYVEKMNFKSLQRRAKTSKVKENGKHTRRKRFGKSLQARAPAQFCRTLKRKLEALGGQYLEVDTRAFRASQYDHVTDTYTKKKLSRRHNIIDGRWVQRDLYSAFLLSNSAEDLAHADRDRCNETFDLFLKNHDACVAKIRNTKTKIPRSFGFQAA
>NZ_LT635479.1|WP_076777805.1|1505789_1506080_-|hypothetical-protein
MGLPTEYDSLTDSQKNAITSIEDCLTYLEDKYHEEFRYLSYAKAGPLEEEHLEAYPASETPSDVVTVYRTYEDGEYHYEDDYNNQAGKLPLVTVCR
>NZ_LT635479.1|WP_076777806.1|1506234_1507155_-|hypothetical-protein
MIYALTMTQNQASVFQKACSEYEELRWNKWKAFVEDVGSSVGQSTREQALEAFEGAMRTAFGNIPTRPTDEMEHAFSLSFYMMPQLLEMDEDDYITLEMDQDQTEFVQMVLEEYFRLRLNQWFDFATEVACNGYVYDKEDPDNGKKFSAYIKRRDASKDKFEKAMQMLVPRYGRQTEDMLIAQDIWQVIRYRLYLDKGGDPNGAVVDARPPMQISQEPLPEFIRKKKEYRMADKDGNRQLTLAEKWAIDAMAYESGAKVKTGKQPCNGCMYQIKGDALHCGIYTKERKPKPVLFGHEKCPKYREEK

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Crispr_ID: NZ_LT635479_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_LT635479_3

2368437-2369523

TypeII

Consensus_repeat	Method
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CRT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CRISPRCasFinder
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	PILER-CR

16 spacers

csn2,cas2,cas1,cas9

The CRISPR arrays of NZ_LT635479_3

>merge|NZ_LT635479|3|2368437-2369523|CRT,CRISPRCasFinder,PILER-CR
TTATGTATTACTCATAAATTTGCACCAGGCTCAAACCCATGAGATCCCGCCAGAAATTCTACGATTTAATTACCCCATAATTTGCACTACTCTCAAACGGCACTGGTATCAGAAACCCAACGGGCAGGGTTTCATTACCCTATAGATTTACACTACTCTCAAACTCTCTATTCTTTTAAAAACTATTTGACGATGTTTCATTACCCTATAGATTTACACTACTCTCAAACGGTTTGATGGTGTTCCTGCTCTTTGGAATTGTTTCATTACCCTATAGATTTACACTACTCTCAAACTGGCGAAGATTACAGCGTGATCATTCTGGAGTTTCATTACCCTATAGATTTACACTACTCTCAAACCACCTTTGCAGCCTGCTCCAGTTTTGGCGCGTTTCATTACCCTATAGATTTACACTACTCTCAAACCTCCATATTCTTTATAGGGATGTAATTTTTGTTTCATTACCCTATAGATTTACACTACTCTCAAACATATTGCTTATCATTTGGCTGATATTCGGGGTTTCATTACCCTATAGATTTACACTACTCTCAAACCATCGTGGAGCCGGACAATTCACTCGGCGTGTTTCATTACCCTATAGATTTACACTACTCTCAAACATCTGCCGGCCCGCAATGAGGAAGAGACAGGTTTCATTACCCTATAGATTTACACTACTCTCAAACAGTTTAACGACTTCATCCAGGCGGTTCACCGTTTCATTACCCTATAGATTTACACTACTCTCAAACCTCAACAAAATGTCAGTTTAATTCATCAAGGTTTCATTACCCTATAGATTTACACTACTCTCAAACCACAACTGTCAGAGGGTAGTACAGGGCTTTGTTTCATTACCCTATAGATTTACACTACTCTCAAACCCGCAAAGCGACCGATATATGAGAGAGGATGTTTCATTACCCTATAGATTTACACTACTCTCAAACAAATGTTGGTTCGCCCACTCATCTGATAGGTTTCATTACCCTATAGATTTACACTACTCTCAAACGGCTTTGCAACATATTCAGCAAACATAGCCGTTTCATTACCCTATAGATTTACACTACTCTCAAAC

>NZ_LT635479|3|1|2368437-2369523|CRT
TTATGTATTACTCATAAATTTGCACCAGGCTCAAAC	CCATGAGATCCCGCCAGAAATTCTAC
GATTTAATTACCCCATAATTTGCACTACTCTCAAAC	GGCACTGGTATCAGAAACCCAACGGGCAGG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	TCTCTATTCTTTTAAAAACTATTTGACGAT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	GGTTTGATGGTGTTCCTGCTCTTTGGAATT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	TGGCGAAGATTACAGCGTGATCATTCTGGA
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CACCTTTGCAGCCTGCTCCAGTTTTGGCGC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CTCCATATTCTTTATAGGGATGTAATTTTT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	ATATTGCTTATCATTTGGCTGATATTCGGG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CATCGTGGAGCCGGACAATTCACTCGGCGT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	ATCTGCCGGCCCGCAATGAGGAAGAGACAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	AGTTTAACGACTTCATCCAGGCGGTTCACC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CTCAACAAAATGTCAGTTTAATTCATCAAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CACAACTGTCAGAGGGTAGTACAGGGCTTT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CCGCAAAGCGACCGATATATGAGAGAGGAT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	AAATGTTGGTTCGCCCACTCATCTGATAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	GGCTTTGCAACATATTCAGCAAACATAGCC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC

>NZ_LT635479|3|3|2368499-2369523|CRISPRCasFinder
GATTTAATTACCCCATAATTTGCACTACTCTCAAAC	GGCACTGGTATCAGAAACCCAACGGGCAGG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	TCTCTATTCTTTTAAAAACTATTTGACGAT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	GGTTTGATGGTGTTCCTGCTCTTTGGAATT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	TGGCGAAGATTACAGCGTGATCATTCTGGA
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CACCTTTGCAGCCTGCTCCAGTTTTGGCGC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CTCCATATTCTTTATAGGGATGTAATTTTT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	ATATTGCTTATCATTTGGCTGATATTCGGG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CATCGTGGAGCCGGACAATTCACTCGGCGT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	ATCTGCCGGCCCGCAATGAGGAAGAGACAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	AGTTTAACGACTTCATCCAGGCGGTTCACC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CTCAACAAAATGTCAGTTTAATTCATCAAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CACAACTGTCAGAGGGTAGTACAGGGCTTT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CCGCAAAGCGACCGATATATGAGAGAGGAT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	AAATGTTGGTTCGCCCACTCATCTGATAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	GGCTTTGCAACATATTCAGCAAACATAGCC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC

>NZ_LT635479|3|1|2368565-2369523|PILER-CR
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	TCTCTATTCTTTTAAAAACTATTTGACGAT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	GGTTTGATGGTGTTCCTGCTCTTTGGAATT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	TGGCGAAGATTACAGCGTGATCATTCTGGA
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CACCTTTGCAGCCTGCTCCAGTTTTGGCGC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CTCCATATTCTTTATAGGGATGTAATTTTT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	ATATTGCTTATCATTTGGCTGATATTCGGG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CATCGTGGAGCCGGACAATTCACTCGGCGT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	ATCTGCCGGCCCGCAATGAGGAAGAGACAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	AGTTTAACGACTTCATCCAGGCGGTTCACC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CTCAACAAAATGTCAGTTTAATTCATCAAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CACAACTGTCAGAGGGTAGTACAGGGCTTT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	CCGCAAAGCGACCGATATATGAGAGAGGAT
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	AAATGTTGGTTCGCCCACTCATCTGATAG
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC	GGCTTTGCAACATATTCAGCAAACATAGCC
GTTTCATTACCCTATAGATTTACACTACTCTCAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_LT635479.1\|WP_087252738.1\|2376631_2376835_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|224323
NZ_LT635479.1\|WP_076779123.1\|2360913_2362518_-\|amidohydrolase	unknown	unknown	gnl\|CDD\|224490
NZ_LT635479.1\|WP_076779125.1\|2363924_2364575_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076776434.1\|2364660_2366331_-\|IS66-family-transposase	unknown	unknown	gnl\|CDD\|376980
NZ_LT635479.1\|WP_076779133.1\|2371416_2375475_-\|type-II-CRISPR-RNA-guided-endonuclease-Cas9	cas9	mkCas0193_cas9_CAS-II-A:CAS-II-B:CAS-II-C	gnl\|CDD\|374653
NZ_LT635479.1\|WP_076779129.1\|2370236_2370542_-\|CRISPR-associated-endonuclease-Cas2	cas2	mkCas0206_cas2_CAS-I:CAS-II:CAS-III	gnl\|CDD\|226043
NZ_LT635479.1\|WP_076779140.1\|2378713_2379025_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_033125183.1\|2362672_2363779_-\|PTS-sugar-transporter-subunit-IIC	unknown	unknown	gnl\|CDD\|379113
NZ_LT635479.1\|WP_076779127.1\|2369574_2370240_-\|type-II-A-CRISPR-associated-protein-Csn2	csn2	cd09644_csn2_CAS-II-A	gnl\|CDD\|213407
NZ_LT635479.1\|WP_076779118.1\|2356300_2356804_-\|transcription-elongation-factor-GreA	unknown	unknown	gnl\|CDD\|234693
NZ_LT635479.1\|WP_157888443.1\|2376050_2376227_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076779137.1\|2376921_2377779_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076779121.1\|2359611_2360724_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|341026
NZ_LT635479.1\|WP_076776436.1\|2366477_2366831_-\|IS66-family-insertion-sequence-element-accessory-protein-TnpB	unknown	unknown	gnl\|CDD\|377551
NZ_LT635479.1\|WP_157888493.1\|2376249_2376378_-\|Sec23/Sec24-zinc-finger-containing-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076779131.1\|2370553_2371420_-\|type-II-CRISPR-associated-endonuclease-Cas1	cas1	cd09720_cas1_CAS-II-A:CAS-II-B:CAS-II-C	gnl\|CDD\|274694
NZ_LT635479.1\|WP_157888442.1\|2367244_2367391_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_076779120.1\|2356877_2359592_-\|NYN-domain-containing-protein	unknown	unknown	gnl\|CDD\|223556
NZ_LT635479.1\|WP_076779139.1\|2377794_2378622_-\|hypothetical-protein	unknown	unknown	unknown
NZ_LT635479.1\|WP_173829249.1\|2366823_2367192_-\|hypothetical-protein	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NZ_LT635479.1\|WP_076779129.1\|2370236_2370542_-\|CRISPR-associated-endonuclease-Cas2	gnl\|CDD\|226043	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms].	4.00932e-27
NZ_LT635479.1\|WP_076779131.1\|2370553_2371420_-\|type-II-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|274694	TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype II/NMENI. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is a prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 variant of the NMENI subtype of CRISPR/Cas system.	5.14268e-101
NZ_LT635479.1\|WP_076776434.1\|2364660_2366331_-\|IS66-family-transposase	gnl\|CDD\|376980	pfam03050, DDE_Tnp_IS66, Transposase IS66 family. Transposase proteins are necessary for efficient DNA transposition. This family includes IS66 from Agrobacterium tumefaciens.	7.28635e-102
NZ_LT635479.1\|WP_076779133.1\|2371416_2375475_-\|type-II-CRISPR-RNA-guided-endonuclease-Cas9	gnl\|CDD\|374653	pfam16592, Cas9_REC, REC lobe of CRISPR-associated endonuclease Cas9. The REC lobe of Cas9 - the CRISPR-associated endonuclease Cas9 - includes the REC1 and REC2 domains. REC1 forms an elongated, alpha-helical structure consisting of 25 alpha helices and two beta-sheets, whereas REC2 inserted within REC1 adopts a six-helix bundle structure. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defense against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive.	6.6104e-123
NZ_LT635479.1\|WP_033125183.1\|2362672_2363779_-\|PTS-sugar-transporter-subunit-IIC	gnl\|CDD\|379113	pfam13303, PTS_EIIC_2, Phosphotransferase system, EIIC. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyzes the transfer of a phosphoryl group from IIB to the sugar substrate.	4.51536e-85
NZ_LT635479.1\|WP_076779127.1\|2369574_2370240_-\|type-II-A-CRISPR-associated-protein-Csn2	gnl\|CDD\|213407	cd09644, Csn2, CRISPR/Cas system-associated protein Csn2. Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Csn2 has been predicted to be a functional analog of Cas4 based on anti-correlated phyletic patterns; also known as SPy1049 family.	1.01985e-45
NZ_LT635479.1\|WP_076779123.1\|2360913_2362518_-\|amidohydrolase	gnl\|CDD\|224490	COG1574, COG1574, Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only].	4.85685e-130
NZ_LT635479.1\|WP_076779118.1\|2356300_2356804_-\|transcription-elongation-factor-GreA	gnl\|CDD\|234693	PRK00226, greA, transcription elongation factor GreA; Reviewed.	2.68768e-44
NZ_LT635479.1\|WP_076779121.1\|2359611_2360724_-\|MFS-transporter	gnl\|CDD\|341026	cd17473, MFS_arabinose_efflux_permease_like, Putative arabinose efflux permease family transporters of the Major Facilitator Superfamily. This family includes a group of putative arabinose efflux permease family transporters, such as alpha proteobacterium quinolone resistance protein NorA (characterized Staphylococcus aureus Quinolone resistance protein NorA belongs to a different group), Desulfovibrio dechloracetivorans bacillibactin exporter, Vibrio aerogenes antiseptic resistance protein. The biological function of those transporters remain unclear. They belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement.	6.25026e-63
NZ_LT635479.1\|WP_076776436.1\|2366477_2366831_-\|IS66-family-insertion-sequence-element-accessory-protein-TnpB	gnl\|CDD\|377551	pfam05717, TnpB_IS66, IS66 Orf2 like protein. This protein is found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition.	6.66991e-43
NZ_LT635479.1\|WP_087252738.1\|2376631_2376835_-\|hypothetical-protein	gnl\|CDD\|224323	COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription].	0.00131264
NZ_LT635479.1\|WP_076779120.1\|2356877_2359592_-\|NYN-domain-containing-protein	gnl\|CDD\|223556	COG0480, FusA, Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis].	1.10462e-123

>NZ_LT635479.1|WP_157888442.1|2367244_2367391_-|hypothetical-protein
MAGLREMLLKEQSRLEQILKKTEERMKDAPDGSLRLSRSGKSVQYYRK
>NZ_LT635479.1|WP_173829249.1|2366823_2367192_-|hypothetical-protein
MMEVLPMDMNNNVVSKTDLWAERIHAFQESGLSRKDWCQQNEIPPSTLGYWIRKIQSESPGTEPASDSVFAKLPSEQELQFNAGTGNHSVTILLPENIRIEIGADCPARLMTTLFQALKNYA
>NZ_LT635479.1|WP_076776436.1|2366477_2366831_-|IS66-family-insertion-sequence-element-accessory-protein-TnpB
MLDFSGSATVYLACGVTDLRKSYTGLAAIIKLKFHLDPYSRCMFAFCNRRRTLIKILQWDGSGFWILMKRLDRNSFHWPDTPDELRKVTLKEIHWLCDGLSLNPSGAFEERHPKIVV
>NZ_LT635479.1|WP_076776434.1|2364660_2366331_-|IS66-family-transposase
MDPVFTEEQLNRMSREDMLSLLKIMQEHRQKQEETLQKQESRIQILEEKTKELEFLNAMLSDRLTLAQRKRFGASSEKYADGYTQLNLFNEAEQKADPNAPEPDLEEVHPSSYKRKKRSGKKEEDLSSFETTEVIEYKLTGADRHCPDCNTKYKVVTKETVKRLKFIPARFEVVEEVTFVYSCPKCGAMKRPEKAPSLLKGSVATPSLVAGIMNAKYVNGMPLARQEREFARYDLNLSTKTMANWIIQCADRYLQPLYDLMKEELLRSKYLHGDETRIQVIDEPDQKGSTQNWMWVYLTDEYSGSPRMVLFQYERTRAGYHPAEFLGDQFEGSFTCDGYQAYHSLPERITVTGCMAHARRRFNEALTVLKKDFTKEQLKETTAYQAMARIGMLYKIEEMIRDKSPKERYEERQKQAKPLLEAFFEWLHTLEDSVDRSSLIGEAVLYTLNQEVYLKRYLEDGHLSIDNLAAERALKNFATGRRNWLFAKSIRGAQASATVYSITETAMLNRLKPYNYLTYVMEQMKDLGPLPEKEAMLELLPWSTSLPADCHSKPKK
>NZ_LT635479.1|WP_076779125.1|2363924_2364575_-|hypothetical-protein
MPGKQKNGEYLPKAEGEMIRRLAQKSYDQKVAKLAGRRLAQIKRMVKDYEDDEIESLFLNEHMERKKLIRPVEPTWEQRLEAWINEEYLQKEFREDVPVILTERGERVRSKSEKLLADYFWRSGILYKYERPLHLKGFGIVHPDFTFLSRKTRQEVYWEHDGRMDDPVYAQRAIRKIQAYEQNEIYPGEKLILTFETEKSVLDLRMVKRLAEKYLI
>NZ_LT635479.1|WP_033125183.1|2362672_2363779_-|PTS-sugar-transporter-subunit-IIC
MEKVKSFLKRKNIVISAKRYGIDALGAMAQGLFCSLLIGTILNTIGSQFHIGFLTAQIITINGVGYTIGGMASFMSGAAMAVAIGYALQAPPLVLFSLATVGYACNALGQAGGPLAVLFVAIIAAEVGKAVSKETKIDILVTPIVTTLAGIGAAWVIAPPIGLAASAFGQLIMQATELQPFLMGVVVSVLVGVALTLPISSAAICSVLGLTGLAGGAAVAGCCAQMVGFAVMSFKENRWGGLVSQGLGTSMLQMPNIVKNPRIWIAPTVTSAITGPIATCIFKLQMNGDAINSGMGTCGLCGQLGVWTGWIAPSDAAVANGAVAMAPSAFDWLGLILISFVLPAILAPAINQVCRRMGWVKDGDLTLS
>NZ_LT635479.1|WP_076779123.1|2360913_2362518_-|amidohydrolase
MDSCIYENGKIFTADKDNLYGEAMLVEDGLIRKVGTAEEVEEMAPAGCGRIDLGGRRVIPGFVDAHMHPVMLADFSRQISALPPKIHSIEELVEAVREKRQEQGPDKWIQGWGYDEGKFAERRSITRWDLDRGCSDAPVSVIRTCGHIRCVNSRALEMAGIDRNTPDPDGGEIERDENGEPTGVLKENARNLVLPFMPVPDKQEKVENLTELGRLLTSQGIVAVTDMGNLDSGDNYPLYQEAAEKGFLQEVGVYYMWDFFMDDPDFSIPRERFDRRQQIFVCGLKLIGDGSVSGRTAWMAESYLGTDSCGISVCSDRQMETAIRFCKENRCQLSMHAMGGRAIERVVDRAAKEEKWNDGPEPYVRVEHITDPSADSVRKAARKGIGFVTQPIFLYAEIESYLNNLGPAWMKRCYPVRDLLDSQVKLCFSTDAPATSWAVPSDPFPNLKGAVTRRAWDGTDCGQEQTVDIETAIILYTKEAAQMAGFDRLGQLREGYKADFLILDRDILEIPAEEIDQVQVEQTYIGGQCAYQRS
>NZ_LT635479.1|WP_076779121.1|2359611_2360724_-|MFS-transporter
MSDQTNHGKTLTVSILSLSLLTVMAGAAVAPALGVIQAHFSDTNPLFVQMIISVPALFIVITNFIFPKLCKVFSAKTLVLMGLLLYTAGGCASGLFDNIFAVLVMRALVGIGVGIIMPLSTGLLSYYFPPEKQVGLMGYSSAMNQMGGVIATLLSGLLANISWRVSFLVYLMGLISIVLCLFYLPNDKITQETQAKEDRGEKETAGGVGVFRVNIMYILAMFLLMSTFFIYPANFAMETISEGIIPQNYIAVIMAGMDFVAFCGGLLFVRAKRLLGGKTKFLAPLCFLIGYLLLALLGGWTGTLLGSVFVGFANGAGIPYIMSEASMKAGKAAATTVMPLISADSKRKSRVKIALSTYAPFCAMIIQSLS
>NZ_LT635479.1|WP_076779120.1|2356877_2359592_-|NYN-domain-containing-protein
MENTSENIEKNAEMQTAGHLCVGLVAHVDAGKTTLAEGILYTTGQIRRLGRVDHRDAFLDTDQMEKDRGITIFSKQAETVIGDKKVTLLDTPGHVDFSAEMERTLQVLDYAVLVISGADGVQGHVETLWHLLERYHIPVFLFVNKMDQEGTDEEKLMEELKKRLSDECEDFSDPEEFDERMALHDEELLEHFLEGKAPDRGSIRRLIRERRIFPCFFGSALKMEGVEAFLEGLGMYMEYPGCQSAFGARVYKITRDASGQRLTHLKVTGGCLRVKMNMDAYMADPGEEGAAGQRVTGQKIDQIRIYAGNSFQTVQEAGAGMVCAVTGLEGTYSGQGMGCETASVLPVLEPVLTYRMQPPGACDVHGLYLKLKTLEEEIPELHIVWREETKEIHTQIMGEVQIDVLKSLIRERFGAEVSFDEGSIVYKETIEDSVEGVGHFEPLRHYAEVHLLLEPGERGSGLEFDVSCSRDMLDVNWQRLILTHLEEKQHRGVLTGAQITDMKITLIAGRAHQKHTEGGDFRQATYRAVRQGLMKARSVLLEPWYEYRIEVPQEMIGRAMNDVQRMNGRFDAPLVGEETAVLTGSAPVATMQGYMREVLSYTGGRGRFSCRLQGYEPCHNPEEVISASLYDPEADLDNPSSSVFCSHGAGFVVPWYQVEDYMHVEGMETGEEEPQEEILTGIEERKRRIHSEVIDEEELKAIFAQTYGNAGQKRTGWKRTVRTQDSTYKAKGTPKKQGREYLLVDGYNIIFAWEDLKELAKDNIEAARNKLMDVLCDYQGYRRMTLILVFDAYKVPGNPGEVQKYHNIHVVYTREAETADQYIEKAVHDMAREHQVTVATSDGMEQIIIMGQGARRISARDLLTEIHEARKELRALHLDPTPKMKRYLLEDVSPEVLKELKKKE
>NZ_LT635479.1|WP_076779118.1|2356300_2356804_-|transcription-elongation-factor-GreA
MREQLTMQDVEKIEKEIEYRKLVVRKNAIEAVKEARSHGDLSENFEYHAAKKDKNQNESRIRYLERMLKTARIVKDDAADDEVGLDKKVEVYFEDDDETEVFKLVTSVRGSSLNGKISIESPIGRAIMKHRAGDRVYVKVNDNAGYYVVIRSVEKTDGEDEDAIRKY
>NZ_LT635479.1|WP_076779127.1|2369574_2370240_-|type-II-A-CRISPR-associated-protein-Csn2
MKVVHPKISSRIEISDQRINVLVIEAPEFLYELLTDIKRQMDNLDGDTVLSIHDEPVSIHKCVELVTDPLAVEMNNRTIIKKVLAAMEKCGQDDVYYERTQKLMAEIETYINDLSLNFDADIECHDISLQQILKAAELTVADEYDRLVDKIYAYMELVREFEGDKLFVFVNLSSYIGREQLQEFVATVIGHSFQVLLIDSHDFERLESENRLIVDRDLCEF
>NZ_LT635479.1|WP_076779129.1|2370236_2370542_-|CRISPR-associated-endonuclease-Cas2
MRILVFFDLPVQTSEDIRNYRSFRKILLKNGFFMMQESVYCRMVLNPSIEKSVIETIRKAKPPAGLVQVLSVTEKQFSKMEFLVGKSNKEVIDTDERLVIL
>NZ_LT635479.1|WP_076779131.1|2370553_2371420_-|type-II-CRISPR-associated-endonuclease-Cas1
MSFRTVVITKRCKLDYKMNFLEVRKEDTKRILLDDIHTIIIENPAVSLTGCLIEALMQKKIKVIFCDSKRNPQSELVPYYGCHDCSSKVKLQISWSEELKGEIWTRIVKEKIRKQADFLADLQKDEEALLRGYIDEMEYRDATNREGHAAKVYFNALFGKEFTRNDDNPVNAALNYGYSLILSTINREVVANGYLTQLGFFHDNMFNQFNLSCDLMEPFRVLVDRYVYASGFTEFSVEEKHRMLELLQQEIGINNTRQVMNNGIKIYVKSVFDAINEKDLSLITFYGL
>NZ_LT635479.1|WP_076779133.1|2371416_2375475_-|type-II-CRISPR-RNA-guided-endonuclease-Cas9
MKENYYVGLDIGTNSIGYAVTDEHFNLLKYKGEPMWGSHVFEEGKQCAERRAYRTARRRLNRRQQRVHLTQQIFAKAIGEIDKHFFIRLKESALFREDTSGRDTYIFFQDKTYTDKEYHRDYPTIHHLIKELMEDKTPHDVRLVYLAVAWLMAHRGHFLSEVNKDNIAALLDFDSIYGNFMELFSEKPWMCDDKEKFKSILLLNQTVRNKERQFWDLLYAGKKPKTEEEDHISKEGIIKLLAGGTVEAGKLFCQKDFEEKISVSLRKSEEDFQLILSEMDEEDAEYLIRLRALYDWALLVDSLHGCSSISEAKVKDYDQHKSDLNVLKNFVHKYCPDEFNAIFKNIDKENYAAYVYNIPKEKRTKEYKKKATQEEFCDYLKRKLKDIACEPEDQKVYQEIMLRLETYTFMPKQVNGDNRVIPYQLYYYELKKILENTETYLPFLSETDEDGISDKEKLLSVFEFRIPYFVGPLCSASEHAWLKRKAEGKIYPWNFEEKVDLDQSEDAFIDRMTNNCSYLPEETVLPQNSLLYCKFAVLNEINNIKINGNPITVECKQEIYGLFEENKKVTVDKIKKYLISNNYMRPGDTLGGIDIMIKSSLKPQHDFKRLLRSGILKEGEVERVIEYITYSEDRGRILRRLEREFPKLSEEDRKYLSKLKYNGFGRLSKKLLTGIRAANKETGESFNIIQALWETNDNLMQLLSDRYTFKELIEEEQRAYYAEHPMTIDSLLDEMYVSNAVKRPIYRTLDVIKDIKSVCKTAPKKIYVEMARGQEEEKNRKKSRKEQILELYKNMDKSEVRELSKQLEDREERELRSEVLFLYFMQLGKSMYSGKPIDIEKLKTDAYNVDHIYPQCRVKDDSLSNKVLVLSEENGVKGDKYPISAEIQEKMADMWRVYHKKGLISDEKYLRLTRKTSFSNTEKMEFINRQLVETRQSTKAVTRILQYVFPETEIVFVKAGLVSDFRNQVLESVKSRSVNDLHHAKDAYLNIVAGEVYNARFTTKFFKIDQDDYSVKTKVIFGNKVWCGKELVWNGGKDIARVKKVLAKNSVHYTRYAFERKGGLFDQQPLRAAAGLIERKGGLDTEKYGGYNKSTASYFLLAKYTEAGKKPKKDVMFVPIDLMETKRIMDNKTYAEEYVGKTIAQIIGKPRETVQEVSFPLGIRKLKVNMLLSLDGFDVAIAGKSSGGQKLLFRSMMPLIVDSEKERYIKRLENFSKKKKQSNELHVDETYDKITKEKNDALYLFFIRKLETKPYDAIFGGQLKVLKNGEDPFEKLTLEEQVEVLLNILSLFQTGRTTGCDLKALGGVGQAAIFTTNSKLSNWKKSFKDIRIVDISAAGLHRKVSQNLLELL
>NZ_LT635479.1|WP_157888443.1|2376050_2376227_-|hypothetical-protein
MDKRDVEEFIEEMEEMGDVWQEEDVERVYGEYTLAEALADRKASIGIFGDIISKVLNR
>NZ_LT635479.1|WP_157888493.1|2376249_2376378_-|Sec23/Sec24-zinc-finger-containing-protein
MDWYCDECGAHLNDQLNFNPYDNEWTCTECGYVNDITKDNVW
>NZ_LT635479.1|WP_087252738.1|2376631_2376835_-|hypothetical-protein
MPDVCPECGGDIIITEDWDEGVCYYECTDCDYSEYAYDIDENYVPEGCAACGGPYPQCKTSCKIFDD
>NZ_LT635479.1|WP_076779137.1|2376921_2377779_-|hypothetical-protein
MNKKKITIAVVLAIIVAGISGILFYMCYHRWDKATCTTAKTCSICGKTEGEPLGHKWTEATCEEPQICSACGETEGTALGHKWEEATCEMPKICSVCGKTQGEALGHVLEEYTVVKEATCSEQGEKEAVCSRCKKTIVETIDKVEHTPGEWEVKEDYSISAQAIITPGKQIKKCTVCNKELESKEYTVELSTSQRNAVLKAYQEIQNWHCGRDFLINDVLVGFDGYSIEDATFAVDHIDVDWDYQAILYAKENGVGESENQITEMMQYYGFNQDQIAKALKEIGY
>NZ_LT635479.1|WP_076779139.1|2377794_2378622_-|hypothetical-protein
MKKKLLVSVLLFAMGASVLTGCGGGEKQEEPEEIVYLEESEIDSLFTNPEEYAGKYVKLSGQLLDAPETDGETTAIQAWHDVENYTQNFIAHTDAADGIQNQDYVWVDGKIDGTFSGENAFGGSVECPLIVDATVTKGSYMEIVVPTIAEISPAVSQDQNGIVVTVDKVEYAEDETRVYVTINNGTDYNFSCGTYSAKLLIDGKQMDQDTMSQTLYNSPELSELSYEVMAGTSSSGTLIFPAIEQGVAFQFILPDAYSDNYDLMFTNYMIDVPAQ
>NZ_LT635479.1|WP_076779140.1|2378713_2379025_-|hypothetical-protein
MNVDKIFERATIRGVADYLLFGLGPDEDDRSYEERLDEIYMRFEKTVGKYDENPTSELLDLCNELSSETASVYMEIGLQAGILLMVDMVRNIERKITPEKKIV

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NZ_LT635479_3	3.11\|2369129\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369129-2369158	30	MK291444	Paracoccus phage vB_PthS_Pthi1, complete genome	4360-4389	3	0.9
NZ_LT635479_3	3.1\|2368473\|26\|NZ_LT635479\|CRT	2368473-2368498	26	NC_010580	Beijerinckia indica subsp. indica ATCC 9039 plasmid pBIND01, complete sequence	144658-144683	5	0.808
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	KJ019089	Synechococcus phage ACG-2014j isolate Syn7803US23, complete genome	91454-91483	6	0.8
NZ_LT635479_3	3.5\|2368733\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368733-2368762	30	NZ_LN907828	Erwinia gerundensis isolate E_g_EM595 plasmid pEM01, complete sequence	258522-258551	6	0.8
NZ_LT635479_3	3.6\|2368799\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368799-2368828	30	NZ_CP030264	Ensifer adhaerens strain Corn53 plasmid AB, complete sequence	369022-369051	6	0.8
NZ_LT635479_3	3.6\|2368799\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368799-2368828	30	NZ_CP032695	Rhizobium jaguaris strain CCGE525 plasmid pRCCGE525c, complete sequence	1513241-1513270	6	0.8
NZ_LT635479_3	3.6\|2368799\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368799-2368828	30	NZ_CP022999	Rhizobium sp. 11515TR strain 10195 plasmid p11515TR-A, complete sequence	179215-179244	6	0.8
NZ_LT635479_3	3.3\|2368601\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368601-2368630	30	NZ_AP019824	Leptotrichia hofstadii strain JCM16775 plasmid pJCM16775-1, complete sequence	24899-24928	7	0.767
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	MN813698	Gordonia phage Volt, complete genome	1403-1432	7	0.767
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	MH479925	Gordonia phage Ronaldo, complete genome	1403-1432	7	0.767
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	MK919478	Gordonia phage Ziko, complete genome	1417-1446	7	0.767
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	MH552560	Microviridae sp. isolate ctcf390, complete genome	404-433	7	0.767
NZ_LT635479_3	3.5\|2368733\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368733-2368762	30	NZ_CP015231	Epibacterium mobile F1926 plasmid unnamed1, complete sequence	1019553-1019582	7	0.767
NZ_LT635479_3	3.5\|2368733\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368733-2368762	30	KY653122	Morganella phage IME1369_03, complete genome	1417-1446	7	0.767
NZ_LT635479_3	3.7\|2368865\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368865-2368894	30	LN835295	Clostridium perfringens plasmid pJIR4150, complete sequence, strain JIR12708	38427-38456	7	0.767
NZ_LT635479_3	3.8\|2368931\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368931-2368960	30	MN830257	Lactobacillus phage JNU_P11, complete genome	9821-9850	7	0.767
NZ_LT635479_3	3.16\|2369458\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369458-2369487	30	CP002509	Bacillus thuringiensis serovar finitimus YBT-020 plasmid pBMB26, complete sequence	134262-134291	7	0.767
NZ_LT635479_3	3.2\|2368535\|30\|NZ_LT635479\|CRT,CRISPRCasFinder	2368535-2368564	30	NZ_CP040452	Halomonas sp. PA16-9 plasmid p_unnamed1, complete sequence	1788786-1788815	8	0.733
NZ_LT635479_3	3.3\|2368601\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368601-2368630	30	NZ_AP017970	Fusobacterium varium strain Fv113-g1 plasmid pFV113-g1-2, complete sequence	65401-65430	8	0.733
NZ_LT635479_3	3.3\|2368601\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368601-2368630	30	MN693585	Marine virus AFVG_25M418, complete genome	38471-38500	8	0.733
NZ_LT635479_3	3.9\|2368997\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368997-2369026	30	NZ_CP022994	Paraburkholderia aromaticivorans strain BN5 plasmid pBN4, complete sequence	71718-71747	8	0.733
NZ_LT635479_3	3.12\|2369195\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369195-2369224	30	MN013084	Klebsiella phage vB_KaeM_KaAlpha, complete genome	138345-138374	8	0.733
NZ_LT635479_3	3.12\|2369195\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369195-2369224	30	KJ101592	Enterobacter phage PG7, complete genome	137236-137265	8	0.733
NZ_LT635479_3	3.12\|2369195\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369195-2369224	30	GU323318	Enterobacteria phage CC31, complete genome	129650-129679	8	0.733
NZ_LT635479_3	3.12\|2369195\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369195-2369224	30	MN617835	Enterobacter phage prasa_myo, complete genome	139227-139256	8	0.733
NZ_LT635479_3	3.12\|2369195\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369195-2369224	30	MG999954	Enterobacter phage myPSH1140, complete genome	139227-139256	8	0.733
NZ_LT635479_3	3.12\|2369195\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369195-2369224	30	LT614807	Cronobacter phage Pet-CM3-4 genome assembly, chromosome: I	135819-135848	8	0.733
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	MN732883	Acinetobacter phage Kimel, complete genome	31143-31172	9	0.7
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	MN662249	Acinetobacter phage Stupor, complete genome	30161-30190	9	0.7
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	NC_049511	Acinetobacter phage AM101, complete genome	29658-29687	9	0.7
NZ_LT635479_3	3.4\|2368667\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2368667-2368696	30	NC_049492	Acinetobacter phage vB_AbaP_Kimel, complete genome	31143-31172	9	0.7
NZ_LT635479_3	3.12\|2369195\|30\|NZ_LT635479\|CRT,CRISPRCasFinder,PILER-CR	2369195-2369224	30	AP013478	Uncultured Mediterranean phage uvMED DNA, complete genome, group G18, isolate: uvMED-CGR-U-MedDCM-OCT-S26-C62	6448-6477	9	0.7

1. spacer 3.11|2369129|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MK291444 (Paracoccus phage vB_PthS_Pthi1, complete genome) position: , mismatch: 3, identity: 0.9

agtttaacgacttcatccaggcggttcacc	CRISPR spacer
agttcaacgacttcatccaggcggtccatc	Protospacer
****.********************.**.*

2. spacer 3.1|2368473|26|NZ_LT635479|CRT matches to NC_010580 (Beijerinckia indica subsp. indica ATCC 9039 plasmid pBIND01, complete sequence) position: , mismatch: 5, identity: 0.808

ccatgagatcccgccagaaattctac	CRISPR spacer
ccatgagatccggcccgaaattcagg	Protospacer
*********** *** ******* .

3. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to KJ019089 (Synechococcus phage ACG-2014j isolate Syn7803US23, complete genome) position: , mismatch: 6, identity: 0.8

ggtttgatggtgttcctgctctt-tggaatt	CRISPR spacer
tatttgatgttgttcctgctcttgtagtat-	Protospacer
 .******* ************* *.* **

4. spacer 3.5|2368733|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NZ_LN907828 (Erwinia gerundensis isolate E_g_EM595 plasmid pEM01, complete sequence) position: , mismatch: 6, identity: 0.8

tggcg-aagattacagcgtgatcattctgga	CRISPR spacer
-gtcgcatccttacagcctgatcattctgga	Protospacer
 * ** *   ******* *************

5. spacer 3.6|2368799|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NZ_CP030264 (Ensifer adhaerens strain Corn53 plasmid AB, complete sequence) position: , mismatch: 6, identity: 0.8

cacctttgcagcctgctccagttttggcgc	CRISPR spacer
cgcctttgcagcctgcgccagtgttgtggt	Protospacer
*.************** ***** ***  *.

6. spacer 3.6|2368799|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NZ_CP032695 (Rhizobium jaguaris strain CCGE525 plasmid pRCCGE525c, complete sequence) position: , mismatch: 6, identity: 0.8

cacctttgcagcctgctccagttttggcgc	CRISPR spacer
cacctttgcagcctcatccagttccagcgg	Protospacer
**************  *******...***

7. spacer 3.6|2368799|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NZ_CP022999 (Rhizobium sp. 11515TR strain 10195 plasmid p11515TR-A, complete sequence) position: , mismatch: 6, identity: 0.8

cacctttgcagcctgctccagttttggcgc	CRISPR spacer
cgccgctgcagcctcctccagtttcggcgg	Protospacer
*.** .******** *********.****

8. spacer 3.3|2368601|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NZ_AP019824 (Leptotrichia hofstadii strain JCM16775 plasmid pJCM16775-1, complete sequence) position: , mismatch: 7, identity: 0.767

tctctattcttttaaaaactatttgacgat	CRISPR spacer
catctattcttttaaaaaatattttaaaag	Protospacer
. **************** ***** * .*

9. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MN813698 (Gordonia phage Volt, complete genome) position: , mismatch: 7, identity: 0.767

ggtttgatggtgttcctgctctttggaatt	CRISPR spacer
ggggcaatcgtgttccggctctttggaatc	Protospacer
**  ..** ******* ************.

10. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MH479925 (Gordonia phage Ronaldo, complete genome) position: , mismatch: 7, identity: 0.767

ggtttgatggtgttcctgctctttggaatt	CRISPR spacer
ggggcaatcgtgttccggctctttggaatc	Protospacer
**  ..** ******* ************.

11. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MK919478 (Gordonia phage Ziko, complete genome) position: , mismatch: 7, identity: 0.767

ggtttgatggtgttcctgctctttggaatt	CRISPR spacer
ggggcaatcgtgttccggctctttggaatc	Protospacer
**  ..** ******* ************.

12. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MH552560 (Microviridae sp. isolate ctcf390, complete genome) position: , mismatch: 7, identity: 0.767

ggtttgatggtgttcctgctctttggaatt	CRISPR spacer
aggctaatggtgttcctgctatttcgaatg	Protospacer
.* .*.************** *** ****

13. spacer 3.5|2368733|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NZ_CP015231 (Epibacterium mobile F1926 plasmid unnamed1, complete sequence) position: , mismatch: 7, identity: 0.767

tggcgaagattacagcgtgatcattctgga	CRISPR spacer
gggcgatgattacagcgcgatcatggtcaa	Protospacer
 ***** **********.******  * .*

14. spacer 3.5|2368733|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to KY653122 (Morganella phage IME1369_03, complete genome) position: , mismatch: 7, identity: 0.767

tggcgaagattacagcgtgatcattctgga	CRISPR spacer
aggcgaagattacaacgtgatcccgatggg	Protospacer
 *************.******* .  ***.

15. spacer 3.7|2368865|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to LN835295 (Clostridium perfringens plasmid pJIR4150, complete sequence, strain JIR12708) position: , mismatch: 7, identity: 0.767

ctccatattctttatagggatgtaattttt	CRISPR spacer
aaaaatattctttttagggatgtattttta	Protospacer
    ********* ********** ****

16. spacer 3.8|2368931|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MN830257 (Lactobacillus phage JNU_P11, complete genome) position: , mismatch: 7, identity: 0.767

atattgcttatcatttggctgatattcggg	CRISPR spacer
ttaatgcttatcgtttggctgataacaagg	Protospacer
 ** ********.*********** . .**

17. spacer 3.16|2369458|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to CP002509 (Bacillus thuringiensis serovar finitimus YBT-020 plasmid pBMB26, complete sequence) position: , mismatch: 7, identity: 0.767

ggctttgcaacatattcagcaaacatagcc	CRISPR spacer
tgaaatgcatcatattcaggaaacatagcg	Protospacer
 *   **** ********* *********

18. spacer 3.2|2368535|30|NZ_LT635479|CRT,CRISPRCasFinder matches to NZ_CP040452 (Halomonas sp. PA16-9 plasmid p_unnamed1, complete sequence) position: , mismatch: 8, identity: 0.733

ggcactggtatcagaaacccaacgggcagg	CRISPR spacer
gtgggcggtatcagaaacccagcgggcgcg	Protospacer
*  . .***************.*****. *

19. spacer 3.3|2368601|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NZ_AP017970 (Fusobacterium varium strain Fv113-g1 plasmid pFV113-g1-2, complete sequence) position: , mismatch: 8, identity: 0.733

tctctattcttttaaaaactatttgacgat	CRISPR spacer
cacctattcttttaaaaagtatttcataaa	Protospacer
. .*************** ***** *..*

20. spacer 3.3|2368601|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MN693585 (Marine virus AFVG_25M418, complete genome) position: , mismatch: 8, identity: 0.733

tctctattcttttaaaaactatttgacgat	CRISPR spacer
actctatacctttaaaaactatttctatac	Protospacer
 ****** *.**************    *.

21. spacer 3.9|2368997|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NZ_CP022994 (Paraburkholderia aromaticivorans strain BN5 plasmid pBN4, complete sequence) position: , mismatch: 8, identity: 0.733

catcgtggagccggacaattcactcggcgt	CRISPR spacer
gtacgtgcaggcggacaattcactcgggcg	Protospacer
   **** ** ****************

22. spacer 3.12|2369195|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MN013084 (Klebsiella phage vB_KaeM_KaAlpha, complete genome) position: , mismatch: 8, identity: 0.733

ctcaacaaaatgtcagtttaattcatcaag	CRISPR spacer
ccattgaagatgtcagttaaattcatcaaa	Protospacer
*.    **.********* **********.

23. spacer 3.12|2369195|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to KJ101592 (Enterobacter phage PG7, complete genome) position: , mismatch: 8, identity: 0.733

ctcaacaaaatgtcagtttaattcatcaag	CRISPR spacer
ccatcgaagatgtcagttaaattcatcaaa	Protospacer
*.    **.********* **********.

24. spacer 3.12|2369195|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to GU323318 (Enterobacteria phage CC31, complete genome) position: , mismatch: 8, identity: 0.733

ctcaacaaaatgtcagtttaattcatcaag	CRISPR spacer
ccatcgaagatgtcagttaaattcatcaaa	Protospacer
*.    **.********* **********.

25. spacer 3.12|2369195|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MN617835 (Enterobacter phage prasa_myo, complete genome) position: , mismatch: 8, identity: 0.733

ctcaacaaaatgtcagtttaattcatcaag	CRISPR spacer
ccatcgaagatgtcagttaaattcatcaaa	Protospacer
*.    **.********* **********.

26. spacer 3.12|2369195|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MG999954 (Enterobacter phage myPSH1140, complete genome) position: , mismatch: 8, identity: 0.733

ctcaacaaaatgtcagtttaattcatcaag	CRISPR spacer
ccatcgaagatgtcagttaaattcatcaaa	Protospacer
*.    **.********* **********.

27. spacer 3.12|2369195|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to LT614807 (Cronobacter phage Pet-CM3-4 genome assembly, chromosome: I) position: , mismatch: 8, identity: 0.733

ctcaacaaaatgtcagtttaattcatcaag	CRISPR spacer
ccattgaagatgtcagttaaattcatcaaa	Protospacer
*.    **.********* **********.

28. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MN732883 (Acinetobacter phage Kimel, complete genome) position: , mismatch: 9, identity: 0.7

ggtttgatggtgttcctgctctttggaatt	CRISPR spacer
aatttgatggtgttcatgccctttgctgcc	Protospacer
..************* ***.*****  ...

29. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to MN662249 (Acinetobacter phage Stupor, complete genome) position: , mismatch: 9, identity: 0.7

ggtttgatggtgttcctgctctttggaatt	CRISPR spacer
aatttgatggtgttcatgccctttgctgcc	Protospacer
..************* ***.*****  ...

30. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NC_049511 (Acinetobacter phage AM101, complete genome) position: , mismatch: 9, identity: 0.7

ggtttgatggtgttcctgctctttggaatt	CRISPR spacer
aatttgatggtgttcatgccctttgctgcc	Protospacer
..************* ***.*****  ...

31. spacer 3.4|2368667|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to NC_049492 (Acinetobacter phage vB_AbaP_Kimel, complete genome) position: , mismatch: 9, identity: 0.7

ggtttgatggtgttcctgctctttggaatt	CRISPR spacer
aatttgatggtgttcatgccctttgctgcc	Protospacer
..************* ***.*****  ...

32. spacer 3.12|2369195|30|NZ_LT635479|CRT,CRISPRCasFinder,PILER-CR matches to AP013478 (Uncultured Mediterranean phage uvMED DNA, complete genome, group G18, isolate: uvMED-CGR-U-MedDCM-OCT-S26-C62) position: , mismatch: 9, identity: 0.7

ctcaacaaaatgtcagtttaattcatcaag	CRISPR spacer
aaaaacataatgtctgtttaattcatagtc	Protospacer
   **** ****** *********** .

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1279410 : 1300958

Klosneuvirus(20.0%)

transposase

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_162274328.1\|1279410_1280001_-\|transposase	PD-(D/E)XK nuclease family transposase	NA	NA	NA	NA
WP_157888406.1\|1280331_1280475_-	hypothetical protein	NA	NA	NA	NA
WP_076777584.1\|1280478_1281321_-	hypothetical protein	NA	NA	NA	NA
WP_076777585.1\|1281327_1282146_-	ImmA/IrrE family metallo-endopeptidase	NA	NA	NA	NA
WP_076777586.1\|1282148_1282523_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_076777587.1\|1282849_1284028_-	UDP-N-acetyl glucosamine 2-epimerase	A0A1V0SJE0	Klosneuvirus	4.7e-108	52.1
WP_076777588.1\|1284044_1285235_-	capsular polysaccharide biosynthesis protein CapF	NA	NA	NA	NA
WP_083582680.1\|1285274_1286279_-	polysaccharide biosynthesis protein	A0A2P1ELS8	Moumouvirus	5.9e-35	35.7
WP_076777589.1\|1286381_1287944_+\|transposase	IS21 family transposase	NA	NA	NA	NA
WP_076777590.1\|1287940_1288717_+	ATP-binding protein	NA	NA	NA	NA
WP_076777591.1\|1289381_1290698_+\|transposase	ISL3 family transposase	NA	NA	NA	NA
WP_076777592.1\|1290694_1291027_+	hypothetical protein	NA	NA	NA	NA
WP_083582506.1\|1291277_1293077_-	glutamine--fructose-6-phosphate transaminase (isomerizing)	M1H1Z3	Paramecium_bursaria_Chlorella_virus	4.1e-95	36.6
WP_076776416.1\|1293539_1294343_-	ATP-binding protein	NA	NA	NA	NA
WP_076776417.1\|1294335_1295655_-\|transposase	IS21 family transposase	U5N3F9	Enterobacteria_phage	3.8e-21	26.1
WP_076777593.1\|1297009_1298326_+\|transposase	ISL3 family transposase	NA	NA	NA	NA
WP_076777594.1\|1298322_1298655_+	hypothetical protein	NA	NA	NA	NA
WP_044925077.1\|1299142_1299679_-	VanZ family protein	NA	NA	NA	NA
WP_076777595.1\|1300043_1300958_-\|transposase	IS3 family transposase	A0A1P8CWQ3	Bacillus_phage	4.1e-43	37.4

DBSCAN-SWA_2

1313234 : 1407653

Erysipelothrix_phage(54.55%)

transposase,tRNA,capsid,protease,head,terminase,holin,portal,tail

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_076777599.1\|1313234_1314551_+\|transposase	ISL3 family transposase	NA	NA	NA	NA
WP_076777600.1\|1314547_1314880_+	hypothetical protein	NA	NA	NA	NA
WP_076777601.1\|1315423_1316410_-	peptidoglycan bridge formation glycyltransferase FemA/FemB family protein	NA	NA	NA	NA
WP_076777602.1\|1316422_1317433_-	hypothetical protein	NA	NA	NA	NA
WP_076777603.1\|1317437_1318427_-	GNAT family N-acetyltransferase	NA	NA	NA	NA
WP_155961780.1\|1318428_1319061_-	sugar transferase	NA	NA	NA	NA
WP_076777604.1\|1319107_1320391_-	DegT/DnrJ/EryC1/StrS family aminotransferase	NA	NA	NA	NA
WP_076780878.1\|1320434_1322351_-	SDR family NAD(P)-dependent oxidoreductase	L7Y3T9	Megavirus	6.9e-24	30.3
WP_076777605.1\|1322432_1322945_-	hypothetical protein	NA	NA	NA	NA
WP_076777606.1\|1323192_1323828_-	sugar transferase	NA	NA	NA	NA
WP_076777607.1\|1324063_1324588_-	hypothetical protein	NA	NA	NA	NA
WP_076777608.1\|1324754_1325261_-	hypothetical protein	NA	NA	NA	NA
WP_076777609.1\|1325583_1326462_-	hypothetical protein	NA	NA	NA	NA
WP_076780880.1\|1326692_1327505_-\|tRNA	tRNA (guanosine(37)-N1)-methyltransferase TrmD	NA	NA	NA	NA
WP_076777610.1\|1327504_1328017_-	ribosome maturation factor RimM	NA	NA	NA	NA
WP_076777611.1\|1328101_1328332_-	KH domain-containing protein	NA	NA	NA	NA
WP_033125421.1\|1328350_1328596_-	30S ribosomal protein S16	NA	NA	NA	NA
WP_076777612.1\|1328659_1330021_-	signal recognition particle protein	NA	NA	NA	NA
WP_076777613.1\|1330051_1330396_-	YlxM family DNA-binding protein	NA	NA	NA	NA
WP_076777614.1\|1330537_1330777_+	chorion class high-cysteine HCB protein 13	NA	NA	NA	NA
WP_076777615.1\|1330901_1331432_+	hypothetical protein	NA	NA	NA	NA
WP_076777616.1\|1331388_1331676_+	hypothetical protein	NA	NA	NA	NA
WP_076777617.1\|1331740_1332205_-	acyl-CoA thioesterase	NA	NA	NA	NA
WP_076777618.1\|1332323_1333064_+\|tRNA	tRNA pseudouridine(38-40) synthase TruA	NA	NA	NA	NA
WP_076777619.1\|1333057_1334416_-	YjiH family protein	NA	NA	NA	NA
WP_076777620.1\|1334415_1335495_-	iron-containing alcohol dehydrogenase family protein	NA	NA	NA	NA
WP_076777621.1\|1335491_1336670_-	pyridoxal phosphate-dependent aminotransferase	NA	NA	NA	NA
WP_076777622.1\|1336770_1337631_+	MerR family transcriptional regulator	NA	NA	NA	NA
WP_076777623.1\|1337680_1338427_-	DeoR/GlpR transcriptional regulator	A0A077SK06	Escherichia_phage	3.2e-25	33.9
WP_076777624.1\|1338459_1339863_-	gluconate permease	NA	NA	NA	NA
WP_076777625.1\|1339893_1340892_-	4-hydroxythreonine-4-phosphate dehydrogenase PdxA	NA	NA	NA	NA
WP_076777626.1\|1340943_1342248_-	four-carbon acid sugar kinase family protein	NA	NA	NA	NA
WP_076777627.1\|1342484_1343909_-	hydroxyacid dehydrogenase	NA	NA	NA	NA
WP_076777628.1\|1343923_1344811_-	2-hydroxy-3-oxopropionate reductase	NA	NA	NA	NA
WP_076777629.1\|1345189_1345834_+	GntR family transcriptional regulator	NA	NA	NA	NA
WP_076777630.1\|1345830_1346397_-	HD domain-containing protein	NA	NA	NA	NA
WP_076777631.1\|1346403_1346808_-	YjbQ family protein	NA	NA	NA	NA
WP_076777632.1\|1346824_1347682_-	patatin family protein	NA	NA	NA	NA
WP_076777633.1\|1347852_1349487_+	ATP-binding cassette domain-containing protein	A0A2K9L3Z8	Tupanvirus	3.8e-55	28.5
WP_076777634.1\|1349675_1351430_-\|transposase	IS1182 family transposase	A0ZS58	Staphylococcus_virus	4.2e-44	27.6
WP_076777635.1\|1351591_1353064_-	polysaccharide deacetylase family protein	NA	NA	NA	NA
WP_076777636.1\|1353240_1354404_-	phosphoglycerate dehydrogenase	M1NSB9	Streptococcus_phage	8.3e-89	43.6
WP_076777637.1\|1354406_1355489_-	3-phosphoserine/phosphohydroxythreonine transaminase	M1Q1P2	Streptococcus_phage	5.0e-104	53.0
WP_076777638.1\|1355526_1357209_-	biosynthetic-type acetolactate synthase large subunit	A0A0P0CDR3	Ostreococcus_lucimarinus_virus	7.8e-56	30.4
WP_076777639.1\|1357257_1358937_-	dihydroxy-acid dehydratase	NA	NA	NA	NA
WP_076777640.1\|1359079_1360165_-	3-isopropylmalate dehydrogenase	NA	NA	NA	NA
WP_076777641.1\|1360348_1363384_-	glucosaminidase domain-containing protein	G3MBP9	Bacillus_virus	1.3e-13	36.5
WP_076777642.1\|1363555_1363861_-	preprotein translocase subunit YajC	NA	NA	NA	NA
WP_076777643.1\|1363963_1365094_-\|tRNA	tRNA guanosine(34) transglycosylase Tgt	A0A1B1IVQ4	uncultured_Mediterranean_phage	6.6e-91	46.3
WP_076777644.1\|1365116_1366781_-	peptidoglycan binding domain-containing protein	NA	NA	NA	NA
WP_076777645.1\|1367420_1369145_-	recombinase family protein	NA	NA	NA	NA
WP_083582510.1\|1369211_1369463_-	hypothetical protein	NA	NA	NA	NA
WP_083582511.1\|1369619_1371317_-	SpoIID/LytB domain-containing protein	H7BV89	unidentified_phage	8.5e-18	28.0
WP_076777646.1\|1371313_1371742_-\|holin	phage holin family protein	A0A2K5B2A2	Erysipelothrix_phage	2.6e-48	64.0
WP_076777647.1\|1371805_1374274_-	glycosyl hydrolase	A0A2K5B2A1	Erysipelothrix_phage	0.0e+00	67.0
WP_076777648.1\|1374270_1374849_-	hypothetical protein	A0A2K5B2A0	Erysipelothrix_phage	1.1e-52	51.6
WP_076777649.1\|1374859_1375054_-	hypothetical protein	A0A2K5B299	Erysipelothrix_phage	6.9e-17	55.4
WP_076777650.1\|1375072_1377595_-\|tail	phage tail protein	A0A2K5B298	Erysipelothrix_phage	0.0e+00	65.3
WP_076777651.1\|1377598_1378366_-\|tail	phage tail family protein	A0A2I4R672	Erysipelothrix_phage	2.3e-71	53.3
WP_076777652.1\|1378378_1380988_-\|tail	phage tail protein	A0A2K5B297	Erysipelothrix_phage	8.2e-28	59.8
WP_076780886.1\|1381206_1381593_-	hypothetical protein	A0A2K5B295	Erysipelothrix_phage	1.9e-42	70.2
WP_076777653.1\|1381592_1382186_-\|tail	phage tail protein	A0A2K5B294	Erysipelothrix_phage	5.7e-78	74.1
WP_076777654.1\|1382190_1382532_-	hypothetical protein	A0A2K5B293	Erysipelothrix_phage	5.5e-33	60.6
WP_076777655.1\|1382528_1382960_-	HK97 gp10 family phage protein	A0A2K5B292	Erysipelothrix_phage	5.5e-46	62.2
WP_076777656.1\|1382952_1383288_-\|head,tail	head-tail adaptor protein	A0A2K5B291	Erysipelothrix_phage	1.1e-33	64.0
WP_076777657.1\|1383291_1383603_-\|head,tail	phage gp6-like head-tail connector protein	A0A2K5B290	Erysipelothrix_phage	1.4e-40	81.0
WP_076777658.1\|1383618_1383846_-	Head fiber protein	A0A2K5B289	Erysipelothrix_phage	5.1e-19	69.3
WP_076777659.1\|1383859_1385062_-\|capsid	phage major capsid protein	A0A2I4R671	Erysipelothrix_phage	1.7e-177	77.6
WP_076780887.1\|1385075_1385795_-\|protease	Clp protease ClpP	A0A2K5B288	Erysipelothrix_phage	2.8e-79	74.1
WP_076777660.1\|1385760_1387056_-\|portal	phage portal protein	A0A2K5B287	Erysipelothrix_phage	2.9e-191	76.0
WP_076780889.1\|1387052_1388654_-\|terminase	terminase large subunit	A0A2K5B285	Erysipelothrix_phage	1.3e-249	77.7
WP_076777661.1\|1388746_1389682_-	hypothetical protein	NA	NA	NA	NA
WP_076777662.1\|1389674_1390154_-	hypothetical protein	NA	NA	NA	NA
WP_076777663.1\|1390165_1390477_-	hypothetical protein	NA	NA	NA	NA
WP_076777664.1\|1390575_1390839_-	hypothetical protein	NA	NA	NA	NA
WP_076777665.1\|1390843_1391245_-	hypothetical protein	NA	NA	NA	NA
WP_076777666.1\|1391234_1391600_-	hypothetical protein	NA	NA	NA	NA
WP_076777667.1\|1391596_1391836_-	DUF4314 domain-containing protein	Q6DMU8	Streptococcus_phage	1.9e-08	52.5
WP_076777668.1\|1391832_1392243_-	hypothetical protein	NA	NA	NA	NA
WP_076777669.1\|1392232_1392415_-	hypothetical protein	NA	NA	NA	NA
WP_076777670.1\|1392517_1392889_-	hypothetical protein	NA	NA	NA	NA
WP_076777671.1\|1392973_1394266_-	DNA modification methylase	A0A2I4R670	Erysipelothrix_phage	6.0e-56	35.4
WP_076777672.1\|1394216_1394654_-	hypothetical protein	NA	NA	NA	NA
WP_076777673.1\|1394816_1395566_-	hypothetical protein	A0A0A0YWF4	Pseudomonas_phage	6.6e-23	33.5
WP_076777674.1\|1396283_1396871_-	ParB N-terminal domain-containing protein	Q938L7	Temperate_phage	2.8e-37	58.8
WP_076777675.1\|1396902_1397445_-\|terminase	P27 family phage terminase small subunit	A0A2K5B277	Erysipelothrix_phage	4.1e-67	67.2
WP_076777676.1\|1397569_1397923_-	HNH endonuclease	A0A2K5B276	Erysipelothrix_phage	6.9e-47	71.2
WP_076777677.1\|1398105_1398525_-	DUF1492 domain-containing protein	A0A2K5B275	Erysipelothrix_phage	2.0e-13	36.4
WP_076777678.1\|1398521_1398812_-	VRR-NUC domain-containing protein	I3VYX6	Thermoanaerobacterium_phage	1.4e-21	55.2
WP_076777679.1\|1398974_1401488_-	DNA primase	A0A2D1GP66	Streptomyces_phage	2.5e-29	30.2
WP_076777680.1\|1401484_1401913_-	DUF4406 domain-containing protein	A0A2K5B270	Erysipelothrix_phage	4.0e-41	55.4
WP_076777681.1\|1401909_1402323_-	HNH endonuclease	NA	NA	NA	NA
WP_076777682.1\|1402316_1404236_-	bifunctional 3'-5' exonuclease/DNA polymerase	G8CTD0	Vibrio_phage	2.4e-40	27.7
WP_076777683.1\|1404369_1405119_-	hypothetical protein	I3VYY1	Thermoanaerobacterium_phage	2.9e-50	46.2
WP_076777684.1\|1405140_1405557_-	hypothetical protein	I3VYY4	Thermoanaerobacterium_phage	2.1e-26	47.7
WP_076777685.1\|1405570_1406911_-	DEAD/DEAH box helicase	I3VYY6	Thermoanaerobacterium_phage	7.7e-115	50.8
WP_083582512.1\|1406907_1407216_-	HNH endonuclease	A0A2I7QIM4	Bacillus_phage	1.9e-16	47.4
WP_076777686.1\|1407274_1407463_-	hypothetical protein	NA	NA	NA	NA
WP_076777687.1\|1407449_1407653_-	hypothetical protein	A0A2I4R673	Erysipelothrix_phage	1.0e-10	51.7

DBSCAN-SWA_3

2325231 : 2335094

Streptococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_076781026.1\|2325231_2327094_-	cadmium-translocating P-type ATPase	E4ZFI9	Streptococcus_phage	6.6e-96	34.3
WP_076779082.1\|2327125_2327485_-	helix-turn-helix transcriptional regulator	E4ZFI8	Streptococcus_phage	6.2e-11	34.8
WP_076779084.1\|2327607_2329905_-	cadmium-translocating P-type ATPase	E4ZFI9	Streptococcus_phage	1.6e-112	33.0
WP_076779086.1\|2330043_2331474_-	dihydrolipoyl dehydrogenase	A0A2K5B2C5	Erysipelothrix_phage	7.2e-34	24.5
WP_076779088.1\|2331485_2332154_-	uracil-DNA glycosylase	A0A2K9QQR6	Equid_alphaherpesvirus	1.5e-47	46.6
WP_076779089.1\|2332187_2332949_-	imidazole glycerol phosphate synthase subunit HisF	NA	NA	NA	NA
WP_076779091.1\|2332966_2333572_-	imidazole glycerol phosphate synthase subunit HisH	NA	NA	NA	NA
WP_076779094.1\|2333636_2335094_-	HAMP domain-containing protein	W8CYF6	Bacillus_phage	7.3e-26	27.5

DBSCAN-SWA_4

2815454 : 2876473

Staphylococcus_phage(18.18%)

tRNA,transposase,integrase

attL 2815389:2815405|attR 2823054:2823070

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
2815389:2815405	attL	NA	NA	NA	NA
WP_083582586.1\|2815454_2816294_-\|integrase	site-specific integrase	Q4ZE80	Staphylococcus_phage	4.2e-18	28.1
WP_005612369.1\|2816463_2816748_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_076777595.1\|2816744_2817659_+\|transposase	IS3 family transposase	A0A1P8CWQ3	Bacillus_phage	4.1e-43	37.4
WP_076779705.1\|2817680_2818004_-	hypothetical protein	NA	NA	NA	NA
WP_076779707.1\|2818076_2818289_-	excisionase family DNA-binding protein	NA	NA	NA	NA
WP_157888458.1\|2818306_2818447_-	hypothetical protein	NA	NA	NA	NA
WP_157888459.1\|2818468_2819341_-	hypothetical protein	NA	NA	NA	NA
WP_076779711.1\|2819431_2820115_-	hypothetical protein	NA	NA	NA	NA
WP_076779714.1\|2820126_2820408_-	hypothetical protein	NA	NA	NA	NA
WP_076779716.1\|2820705_2821593_+	hypothetical protein	NA	NA	NA	NA
WP_076779718.1\|2822600_2822753_+	toxin-antitoxin system protein	NA	NA	NA	NA
WP_076779721.1\|2823346_2824021_+	hypothetical protein	NA	NA	NA	NA
2823054:2823070	attR	NA	NA	NA	NA
WP_076779723.1\|2824141_2829340_-	Ig-like domain repeat protein	NA	NA	NA	NA
WP_076779726.1\|2829585_2830833_+	FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_076779728.1\|2830892_2833091_+	sigma-70 family RNA polymerase sigma factor	NA	NA	NA	NA
WP_076779730.1\|2833239_2835324_+	hypothetical protein	NA	NA	NA	NA
WP_076779732.1\|2835435_2836389_-	hypothetical protein	NA	NA	NA	NA
WP_076779735.1\|2836499_2837180_-	D-lyxose/D-mannose family sugar isomerase	NA	NA	NA	NA
WP_076779737.1\|2837160_2838120_-	alpha/beta hydrolase	A0A223FN69	NY_014_poxvirus	5.2e-12	24.5
WP_076779739.1\|2838130_2839507_-	citrate/2-methylcitrate synthase	NA	NA	NA	NA
WP_076781103.1\|2839529_2840426_-	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))- dimethyltransferase RsmA	E4ZFQ0	Streptococcus_phage	1.4e-16	33.0
WP_076779741.1\|2840447_2841215_-	TatD family hydrolase	NA	NA	NA	NA
WP_076779743.1\|2841324_2842251_-\|transposase	Rpn family recombination-promoting nuclease/putative transposase	NA	NA	NA	NA
WP_076779745.1\|2842573_2844493_-\|tRNA	methionine--tRNA ligase	A0A1V0SEZ7	Hokovirus	1.8e-96	34.0
WP_076779747.1\|2845037_2845679_+	superoxide dismutase	Q56AR7	Bacillus_thuringiensis_phage	3.3e-39	45.1
WP_076779752.1\|2846248_2847502_-	DUF2399 domain-containing protein	NA	NA	NA	NA
WP_076779754.1\|2847546_2850903_-	AAA family ATPase	NA	NA	NA	NA
WP_076779756.1\|2850853_2851498_-	DUF4194 domain-containing protein	NA	NA	NA	NA
WP_076779757.1\|2851505_2852834_-	hypothetical protein	NA	NA	NA	NA
WP_076779759.1\|2853120_2854836_+	DUF885 domain-containing protein	NA	NA	NA	NA
WP_076779761.1\|2854907_2855801_-	ribokinase	NA	NA	NA	NA
WP_076779763.1\|2855892_2856540_-	class II aldolase/adducin family protein	NA	NA	NA	NA
WP_076779765.1\|2856562_2857645_-	sugar ABC transporter substrate-binding protein	NA	NA	NA	NA
WP_076781104.1\|2857695_2858616_-	hypothetical protein	NA	NA	NA	NA
WP_076779767.1\|2858648_2860148_-	sugar ABC transporter ATP-binding protein	A0A2H4PQG7	Staphylococcus_phage	1.7e-17	30.5
WP_076779769.1\|2860152_2861583_-	rhamnulokinase	NA	NA	NA	NA
WP_076779771.1\|2861593_2862502_-	glycyl-radical enzyme activating protein	NA	NA	NA	NA
WP_076779773.1\|2862507_2864919_-	pyruvate formate-lyase	H6X4X8	Enterobacteria_phage	2.4e-05	50.0
WP_076779775.1\|2865250_2866273_+	LacI family DNA-binding transcriptional regulator	C6ZCU4	Enterobacteria_phage	7.4e-17	27.6
WP_083582594.1\|2866408_2866705_+\|transposase	transposase	NA	NA	NA	NA
WP_157888460.1\|2866765_2867086_+	helix-turn-helix domain-containing protein	A0A0C5AJ29	Paenibacillus_phage	4.1e-30	64.8
WP_157888461.1\|2867115_2867448_+\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_076779777.1\|2868080_2869247_-	pyridoxal phosphate-dependent aminotransferase	NA	NA	NA	NA
WP_076779779.1\|2869253_2870432_-	GNAT family N-acetyltransferase	A0A2R8FG22	Brazilian_cedratvirus	2.6e-13	28.8
WP_076779781.1\|2870443_2871109_-	amino acid ABC transporter permease	NA	NA	NA	NA
WP_076779783.1\|2871126_2871951_-	transporter substrate-binding domain-containing protein	NA	NA	NA	NA
WP_076779786.1\|2872231_2872699_+	ATPase P	NA	NA	NA	NA
WP_076779789.1\|2872933_2873464_-	spore maturation protein	NA	NA	NA	NA
WP_076779791.1\|2873590_2874982_+	MATE family efflux transporter	NA	NA	NA	NA
WP_076776291.1\|2875168_2876473_-\|transposase	IS4 family transposase	NA	NA	NA	NA

DBSCAN-SWA_5

2946332 : 2965690

Streptococcus_phage(93.33%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_076779897.1\|2946332_2946752_-	RNA polymerase subunit sigma-70	A0A1S5SEW0	Streptococcus_phage	2.6e-24	43.8
WP_076779900.1\|2947275_2947638_+	helix-turn-helix transcriptional regulator	A0A1S5SFA6	Streptococcus_phage	1.1e-20	45.9
WP_076779902.1\|2947743_2947932_-	cysteine-rich KTR domain-containing protein	D0R0F6	Streptococcus_phage	4.1e-14	59.6
WP_076779904.1\|2947946_2948384_-	GyrI-like domain-containing protein	NA	NA	NA	NA
WP_076779907.1\|2948540_2948765_-	hypothetical protein	NA	NA	NA	NA
WP_076779909.1\|2948767_2949511_-	ABC transporter permease	NA	NA	NA	NA
WP_076779912.1\|2949497_2950229_-	ABC transporter ATP-binding protein	A0A2H4PQG7	Staphylococcus_phage	3.7e-18	31.3
WP_076779914.1\|2950303_2951044_-	MerR family transcriptional regulator	NA	NA	NA	NA
WP_076779916.1\|2951192_2952086_-	conjugal transfer protein	A0A1S5SF22	Streptococcus_phage	6.0e-79	52.9
WP_076779918.1\|2952107_2953115_-	lysozyme family protein	A0A1S5SEZ8	Streptococcus_phage	3.6e-125	71.9
WP_076779920.1\|2953111_2955253_-	YtxH domain-containing protein	A0A1S5SF30	Streptococcus_phage	8.1e-183	61.0
WP_076779921.1\|2955252_2957700_-	ATP-binding protein	A0A1S5SF64	Streptococcus_phage	0.0e+00	76.1
WP_070087533.1\|2957686_2958076_-	conjugal transfer protein	A0A1S5SEX7	Streptococcus_phage	1.8e-48	73.8
WP_076779923.1\|2958183_2958687_-	antirestriction protein ArdA	A0A1S5SF25	Streptococcus_phage	8.6e-51	56.0
WP_076779925.1\|2958704_2959202_-	antirestriction protein ArdA	NA	NA	NA	NA
WP_076779926.1\|2959208_2959412_-	hypothetical protein	NA	NA	NA	NA
WP_076779928.1\|2959535_2959949_-	DUF3788 domain-containing protein	NA	NA	NA	NA
WP_010817892.1\|2959975_2960422_-	GNAT family N-acetyltransferase	NA	NA	NA	NA
WP_010817891.1\|2960438_2960849_-	ester cyclase	NA	NA	NA	NA
WP_010817890.1\|2961044_2961266_-	hypothetical protein	A0A1S5SEY0	Streptococcus_phage	6.2e-30	91.8
WP_021374764.1\|2961262_2961403_-	DUF3789 domain-containing protein	NA	NA	NA	NA
WP_083582725.1\|2961418_2962609_-	XRE family transcriptional regulator	A0A1S5SEX3	Streptococcus_phage	3.6e-148	63.0
WP_076779932.1\|2962799_2964194_-	DUF87 domain-containing protein	A0A1S5SFB5	Streptococcus_phage	2.8e-168	62.6
WP_083582598.1\|2964253_2964859_-	VanZ family protein	NA	NA	NA	NA
WP_076779934.1\|2964960_2965347_-	YdcP family protein	A0A1S5SF96	Streptococcus_phage	1.3e-38	65.4
WP_076779936.1\|2965363_2965690_-	YdcP family protein	A0A1S5SF38	Streptococcus_phage	3.3e-35	65.7

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NZ_LT635479

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection