CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Target MGE spacer number	Prophage number
NC_011960	Rhodobacter sphaeroides KD131 plasmid pRSKD131B, complete sequence	2 crisprs	NA	2	1
NC_011962	Rhodobacter sphaeroides KD131 plasmid pRSKD131A, complete sequence	0 crisprs	NA	0	0
NC_011958	Rhodobacter sphaeroides KD131 chromosome 2, complete sequence	2 crisprs	DEDDh	0	3
NC_011963	Rhodobacter sphaeroides KD131 chromosome 1, complete sequence	3 crisprs	csa3,DEDDh,cas3,cas5,cas8c,cas7,cas4,cas1,cas2	18	5

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_011960_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011960_1

63076-63162

Orphan

Consensus_repeat	Method
GAGCTCGCCCAGCAGCTCCGGCAG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_011960_1

>merge|NC_011960|1|63076-63162|CRISPRCasFinder
GAGCTCGCCCAGCAGCTCCGGCAGAAGACGCAGCACGCGGCCGAACTGGAGCGCCATGCGGAAGAGCTCGCCGAGCAGCTCCGGCAG

>NC_011960|1|1|63076-63162|CRISPRCasFinder
GAGCTCGCCCAGCAGCTCCGGCAG	AAGACGCAGCACGCGGCCGAACTGGAGCGCCATGCGGAA
GAGCTCGCCGAGCAGCTCCGGCAG

Protein	Signature genes	Signature genes Name	Protein_function
NC_011960.1\|WP_009565042.1\|75832_76771_+\|glycosyltransferase	unknown	unknown	gnl\|CDD\|133039
NC_011960.1\|WP_041671112.1\|54375_54639_+\|hypothetical-protein	unknown	unknown	unknown
NC_011960.1\|WP_002724800.1\|70271_71093_+\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|213187
NC_011960.1\|WP_012642359.1\|71430_72546_-\|ParB-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|274586
NC_011960.1\|WP_012642355.1\|64247_65252_-\|hypothetical-protein	unknown	unknown	unknown
NC_011960.1\|WP_002724803.1\|74818_75781_+\|replication-initiator-protein-A	unknown	unknown	gnl\|CDD\|370826
NC_011960.1\|WP_012642343.1\|50205_50571_-\|AtpZ/AtpI-family-protein	unknown	unknown	gnl\|CDD\|378198
NC_011960.1\|WP_009565066.1\|50567_51008_-\|F0F1-ATP-synthase-subunit-epsilon	unknown	unknown	gnl\|CDD\|184057
NC_011960.1\|WP_041671109.1\|51004_52399_-\|F0F1-ATP-synthase-subunit-beta	unknown	unknown	gnl\|CDD\|183615
NC_011960.1\|WP_012642357.1\|67571_68372_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224596
NC_011960.1\|WP_011840036.1\|69115_70255_+\|sugar-transporter	unknown	unknown	gnl\|CDD\|226055
NC_011960.1\|WP_041671123.1\|63434_64151_-\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|369777
NC_011960.1\|WP_012642349.1\|57602_58907_-\|hypothetical-protein	unknown	unknown	unknown
NC_011960.1\|WP_041671120.1\|60145_61447_-\|DUF2793-domain-containing-protein	unknown	unknown	gnl\|CDD\|371324
NC_011960.1\|WP_011836238.1\|54883_55888_+\|NAD-dependent-epimerase/dehydratase-family-protein	unknown	unknown	gnl\|CDD\|187563
NC_011960.1\|WP_049764010.1\|72667_74074_-\|AAA-family-ATPase	unknown	unknown	gnl\|CDD\|274585
NC_011960.1\|WP_012642350.1\|59022_59964_-\|calcium-binding-protein	unknown	unknown	gnl\|CDD\|380205
NC_011960.1\|WP_041671125.1\|65252_67508_-\|glycoside-hydrolase-family-99-like-domain-containing-protein	unknown	unknown	gnl\|CDD\|379549
NC_011960.1\|WP_012642348.1\|56838_57528_-\|hypothetical-protein	unknown	unknown	unknown
NC_011960.1\|WP_041671116.1\|55991_56828_+\|hypothetical-protein	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NC_011960.1\|WP_009565042.1\|75832_76771_+\|glycosyltransferase	gnl\|CDD\|133039	cd04196, GT_2_like_d, Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.	5.0911e-72
NC_011960.1\|WP_002724800.1\|70271_71093_+\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|213187	cd03220, ABC_KpsT_Wzt, ATP-binding cassette component of polysaccharide transport system. The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenza) and a cytoplasmic membrane protein MPA2.	1.78218e-89
NC_011960.1\|WP_012642359.1\|71430_72546_-\|ParB-N-terminal-domain-containing-protein	gnl\|CDD\|274586	TIGR03454, partition_RepB, plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently. [Mobile and extrachromosomal element functions, Plasmid functions].	7.35995e-11
NC_011960.1\|WP_002724803.1\|74818_75781_+\|replication-initiator-protein-A	gnl\|CDD\|370826	pfam10134, RPA, Replication initiator protein A. Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination.	2.32126e-121
NC_011960.1\|WP_012642343.1\|50205_50571_-\|AtpZ/AtpI-family-protein	gnl\|CDD\|378198	pfam09527, ATPase_gene1, Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophobic stretches and is presumed to be a subunit of the enzyme. It carries two transmembrane helices and is a magnesium or calcium uniporter. The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein with 2 TMSs. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI.	2.19208e-10
NC_011960.1\|WP_009565066.1\|50567_51008_-\|F0F1-ATP-synthase-subunit-epsilon	gnl\|CDD\|184057	PRK13447, PRK13447, F0F1 ATP synthase subunit epsilon; Provisional.	2.52274e-59
NC_011960.1\|WP_041671109.1\|51004_52399_-\|F0F1-ATP-synthase-subunit-beta	gnl\|CDD\|183615	PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.	0
NC_011960.1\|WP_012642357.1\|67571_68372_-\|ABC-transporter-permease	gnl\|CDD\|224596	COG1682, TagG, ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane].	1.20685e-33
NC_011960.1\|WP_041671123.1\|63434_64151_-\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|369777	pfam08241, Methyltransf_11, Methyltransferase domain. Members of this family are SAM dependent methyltransferases.	6.85196e-10
NC_011960.1\|WP_011836238.1\|54883_55888_+\|NAD-dependent-epimerase/dehydratase-family-protein	gnl\|CDD\|187563	cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended (e) SDRs. This subgroup contains UDP-D-glucuronic acid 4-epimerase, an extended SDR, which catalyzes the conversion of UDP-alpha-D-glucuronic acid to UDP-alpha-D-galacturonic acid. This group has the SDR's canonical catalytic tetrad and the TGxxGxxG NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.	3.34107e-167
NC_011960.1\|WP_041671120.1\|60145_61447_-\|DUF2793-domain-containing-protein	gnl\|CDD\|371324	pfam10983, DUF2793, Protein of unknown function (DUF2793). This is a bacterial family of proteins with unknown function.	1.21105e-31
NC_011960.1\|WP_049764010.1\|72667_74074_-\|AAA-family-ATPase	gnl\|CDD\|274585	TIGR03453, partition_RepA, plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error. [Mobile and extrachromosomal element functions, Plasmid functions].	2.26018e-59
NC_011960.1\|WP_012642350.1\|59022_59964_-\|calcium-binding-protein	gnl\|CDD\|380205	NF033203, entero_EhxA, enterohemolysin EhxA. Members of this family are the RTX toxin called enterohemolysin or EhxA, because it is found in enterohemorrhagic Escherichia coli (EHEC) strains such as O157:H7.	1.65286e-15
NC_011960.1\|WP_041671125.1\|65252_67508_-\|glycoside-hydrolase-family-99-like-domain-containing-protein	gnl\|CDD\|379549	pfam14307, Glyco_tran_WbsX, Glycosyltransferase WbsX. Members of this family are found in within O-antigen biosynthesis clusters in Gram negative bacteria, where they are predicted to function as glycosyltransferases.	9.32622e-149
NC_011960.1\|WP_011840036.1\|69115_70255_+\|sugar-transporter	gnl\|CDD\|226055	COG3524, KpsE, Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane].	1.23505e-72

>NC_011960.1|WP_041671120.1|60145_61447_-|DUF2793-domain-containing-protein
MSDASPILSLPYILPSQAQKHVTHNEALQRLDVLVQPAVLDRDRSAPPAAPAAGARHLVGPGAEGAWVGREEAFAVWDAEAAVWRFLAPQPGWQTFVLAEGAGLVFTAQGWRTLIGLLPEFPSLGIATPADATNRLAVAGPATLFTHAGAGHRIKVNKAAEAETASLLFQSDWSGRAEIGLAGSDDFSLKVSPDGTSFRTALSADRASGRVALPQGAVVTGSLTGSAVQASAADATPGRLLTVGAFGLGAPAPLVGNAGAVDGALAPGFYGYDSAQGSSGGPAGVQAGLLLHQSRGAGEVQLFLVEAGGGGLMPGILFSRARGEGAWSPWVAGGIVESAGNVNGRYIRHQDGTQSCWQKVTTSASADVVAPFPAAFSTATGLVTVSSVVSNGAQALSPRLTGRTTTSVGVSVFSATNTRLAAQVELISMGRWY
>NC_011960.1|WP_012642350.1|59022_59964_-|calcium-binding-protein
MPEVSPFPSVSPLSAPLAQSALAQTPAGTPGNDLLNGGPGADRLVGGDGNDTINGRDGVDRLYGGDGDDLLDGGFYHDACYGQAGNDTFRIRGVDLADDVYGGAGTDTLDLSGYTNLRLGFRVDLAAGRYDFRPEPFGPYVVKSIEIVKGSARADVLLGSRLAETLSGGLGNDRLEGRGGADVLRGMEGADALFGGTGNDLLVGGAGNDRLDGQWERDVLVGGAGNDILIGGGGADRFVFAGNFGRDRIRDFSPDMEGERIDLRGVGAITGFGDLMANHLSEVNGHVVIEVGANRITLEGISSEMLTRDDFLF
>NC_011960.1|WP_012642349.1|57602_58907_-|hypothetical-protein
MTLLRTTLLTALLSLALGAGAEAAPEAIYGPGPRALDNREIFAAANLPLWQELDRAGVEGIVLNASLLMAYDFRGLTRRGAEIPRPEGSYLTDADLASLAQIVSRTGLDVTYVAGIALSGDRCDPSLDPAEVGRAAAGFEVDRNVTRLLEAGIPISAINVDGPMLRLLPDSGKAASCKASAGIGFDPMTAAEAVQAYMIELRDRIEAAQGGRPVEMRWLVNLPNWQVGRVPRLGNGRGAPTTDLSQAFEAFTRVQAEGRSSGRPLEISEIVIDYPYAYVRQNPGHFSARLRTLWNVSRDLNPSGRQPPLGIIVNSRSYANPCLKREGQPDAAFLTFRRGQGAISAACQRAQIGEDTRANAEDGVFDNDTDYLRDSFAYADGLKPGGELAKQLVLRDGTRIADHIAHLYYQSWGVNPLSNAWYMERLIERLEDVR
>NC_011960.1|WP_012642348.1|56838_57528_-|hypothetical-protein
MPYHLVHVGKCAGESVIRSLRPQVPDLHVYHVRDANLRLADAVLRRDPSDIFIVLTRDPVARFVSAFEWDLHSKSIDGDGRRLRNEVWGRIFEAFRTANDLAEALTDPASDRRQLALSAFTASKLHMQFDLGWYLPPHIAAELPAGRTHLIRTERLGADLARFLVSQDLREVEAPVTKNAYKQRLPEDRVTKTLSDLARRNIRLASPATYATLALIESRLADPEATVLG
>NC_011960.1|WP_041671116.1|55991_56828_+|hypothetical-protein
MARIWLHIGHGKTGTSSIQWAMAERSRLRRDVIYPARGRSNQMAHHGLFPLKGEAYGPETVQTLRQISERLASVTVPALLSSEHLCHASERKVTQISKAFAGHDLRVVYYIRRQDDLLESAFRQRQSAQPGACPDPALFLERFAKGFDFENRLQPWRTVFGDEAITLRLYHPTIIGSDVVADIERLLGLPDWPERTAGQKNPSLTAAGTRKVMEAALTSPETALRLAQELRGVDTEGDNSPFYDAPTRQTIMERYRASNQRIAEQFLDEEAAALFLKA
>NC_011960.1|WP_011836238.1|54883_55888_+|NAD-dependent-epimerase/dehydratase-family-protein
MRRILVTGTAGFIGFHLARLLLAEGFRVHGYDGMTDYYDVALKRRRHAMLLQDPNFSATEGMLEDQALFDRVADEFAPEVIVHLAAQAGVRYSVENPRAYLDANVIGSFTVMEAARRLKVAHLMMASTSSVYGANEEMPFRETDKADRQLTIYAATKKANESMGHAWAHVHGLPITMFRFFTVYGPWGRPDLALFRFVEAILEDRPIEIYNHGEMWRDFTYVDDLVRAIRLLIEAVPGGPETAVEEDSLSPAAPFRIVNIGNSDKVRLLDFVEAIEESLGRRAIRSYLPMQVGDVPATWADAGLLQRLTGYRPQTDIRDGIAQFVSWYRDYTGK
>NC_011960.1|WP_041671112.1|54375_54639_+|hypothetical-protein
MRPLALRNGHRLLAVEAAYLLFVLALAATGLNNEPEGASFVTLILALTSGGVVALLAVTHLASDPSGSLVLPPLLLVLFGAIYPILQ
>NC_011960.1|WP_041671109.1|51004_52399_-|F0F1-ATP-synthase-subunit-beta
MTGRVTSVRGPVLDIRVEGPLPAIGDVVEVGSLPVVAEIQAHLGAADVRAIALHSTQGIARGERVRTTGGPLRVPTGPAVLGRLLDVAGRPADLGPPIPAEAPRAPILHPAPPLAAQDARFQVFSTGIKVLDLLAPLAQGGKTAMFGGAGVGKTVLVMELIRAMVSGYDGISVFAGVGERSREGHEMLGEMKASGVLDRTVLVYGQMNEPPGARWRVPLTALTIAEGFRDGEGRNVLLLIDNVFRFVQAGAEVSGLLGRMPSRVGYQPTLETEVAALQERIASVGRASVTAIEAVYVPADDFTDPAVTAISAHVDSTVVLSRQLAAEGIYPAIDPLATTSVLLDPAVVGEEHARVAGRLKEAIEHYHELRDVIALLGIEELGREEQLMVGRARKLQRFLTQPFFVAAAYTGMEGRSVPVAETVQGCAAILGGECDDWDEGSLYMIGTLAEARAREEARRRKGAA
>NC_011960.1|WP_009565066.1|50567_51008_-|F0F1-ATP-synthase-subunit-epsilon
MSLTLRVTTPLAAVLEEEGLASIRAEDASGGFGLLPGHVDLLTVIEAGVLRFRRAEGPWRFCAIRGGVLRATGGRTVTVACREAVPGEDLARLEAGLKRQAEAADQAARRARGEQVRLHANAIRSLMRHLDRAPGADLSGIVEAFE
>NC_011960.1|WP_012642343.1|50205_50571_-|AtpZ/AtpI-family-protein
MTGPGSRPAPPGAGPGPDPAVPPAISPPAPPGASPDPLAEAVRRSAVRAEAGRRDPEPSLARRFGQIGVLGWVIVLPTLGGVLAGGWLDRLLGTGITFAAALTMAGAALGLWLALRWMHAQ
>NC_011960.1|WP_041671123.1|63434_64151_-|class-I-SAM-dependent-methyltransferase
MTAVYAHQGFCNACGSPAEFRSQSHWFRDNLFCSVCGSIPRERALATVLERVRPDWRDRRIHESSPADRSISARLARECRSYVASQFFPGEPLGTVVRGFRNENLEAQTFEDGRFDLVVTLDVMEHVNEPDKVFREVFRTLVPGGAYLFSVPTYKERVTSERRARYRPDGGIDHLAEPEYHGNPVSDAGSLVTFHYGYDLPELIHAWAGFDVELFRFHHHHLGLIGEFTEIYLATRPA
>NC_011960.1|WP_012642355.1|64247_65252_-|hypothetical-protein
MARVVLHIGTHKTATTTIQDMFAHNADLLRQHGVIYPRLSRVAGHHGLVMDWNKLPAAYALPNGSLGTLRQLAAQYGKGEGTVVLSSEEFSRGLEGRRVDFRAVREALAGFESFSIVCVLREQWQYAQSIYLETSKNRVPVKPGLLVQSILNRDMIDGLWTDYNLLYDHLLEAFAPEEIAFLDFEACRRHSGGVVGAMLEHLGCDLPASALEVVHDGQSNVSPLSLPAWAASLIAEPERAPRWLVESTTGAFRAEHGEEARPCLWTRVEFAALSRYAQERNARFLERLAPVQPDFTIRQSTPGDAAIYRDDIKGSFWLRCSRWTYRGKMSAGEG
>NC_011960.1|WP_041671125.1|65252_67508_-|glycoside-hydrolase-family-99-like-domain-containing-protein
MLKLHRLRRFARILVLTGEERRYLRAIRKSGLFDRTYYRGAYPGLNPIYLKYPEKHYIAYGERLGYRPNPDFSPQAYLRYHPDVAEAGVPPFLHYVRVGHAEQRLTKELPEVVALPARGMPQVRFEHGRQTAPYAVAVHVYYPDLWPEFAARLRRLRIPFDLYVTLTYRGEETDALAQEIRADFPGAFVTPMPNRGRDILPFVTLLNAGAFDGYRAVCKFHTKKSPHRQDGDLWRKHLIEGILPETGLEEKLEAFVEAPEAGFWVADGQHYTGTQWWGSNVEATRHLLQRIEIPLDREALSFPAGSIYWVKPLVLGLLRSLQLRLEDFDIEEGQVDGTLAHAIERVLGYLTARAGQKVLQTSELRPAAAAAPAKPAFVSAFYLPQFHPVPENDAWWGRGFTEWRSVVKAPSMFEGHLQPMLPADLGFYDLRATEVMGEQAAMAREAGIDAFCVYHYWFDGRRILEAPIDRLMARPEIDFPFYLCWANESWRRNWDGLSGTVLLEQTYGAGFEEKLAADTAPYLRDPRYARPDGRRPRFVIYRPEDMPDPQASVARLREGWRRAGIGEVELGAVRFHVEGAHPVPEALFDFWVEMPPHGLVKGPDYLFGGPDGNRMPAAMNPAFSGLIYDYAAVARRALSETYVRTLPKATIAGVMPGWDNTARRGAAGHVAYGANPATFNVWLAGALERRVPASYRRELFVNAWNEWAEKAVLEPSLTFGDLNLQVMRQHLGAAEPATHLAEPPAHGMRSH
>NC_011960.1|WP_012642357.1|67571_68372_-|ABC-transporter-permease
MTGLSGLLAGRRFLWGRSVLSLMLREMATSYGRSPGGYLWAVAEPVAALTLLTVVFSFLMRSPPLGNNFPLFYATGYLPFMYYSALTAKIGQAIRFSRPLLAYPAVSFFDAILSRFLLNTLTNLVVFVIVMVGIIAFYDLNVSLDLPAILEAFSMAAALAMGVGTLNCYLFSVAPVWERVWAILNRPMFLLSGIFFLMETVPEPFRTLLSYNPLTHVIAKMRQGFFATYDARLVDPLYAYSVSLVCLFFGMLLLNRHHRMLLNEGA
>NC_011960.1|WP_011840036.1|69115_70255_+|sugar-transporter
MPAAAPRAAARLRHHGLLASFLGLVLAPTLASGLYLFAIAEDQYTSTVGFSVRTEEMGSALDLLGGLSSFGLTGGGSASDSDILYQFIQSQELVQRINERIDLRAIYSKPGFDPVFSFDPDGGIEDLVDYWKDMVRISYDSTTGLIELRVHAFTPEDAQAVAQGILDESNRMINDLSAIARADATRYAREELDNAVERLRVQRVAMTEFRSRTQIVDPSADIQAQMGLLNTLQQQLASASIDLNLLRQTTQPSDPRIAQNERRIGVIEELIQREREKFGLGGGTGTGASTYSTMIAEFERLTVDLDFAEKAYIAALTNHDAAIAEAQRMSRYLATYVRPTLAQQSLYPQRGLLTLMIGGFALMLWAIGMLIYYSVRDRR
>NC_011960.1|WP_002724800.1|70271_71093_+|ABC-transporter-ATP-binding-protein
MIELRNVSKSYVLNGTRKVVARDLNFTFPSGESVGLLGRNGAGKSSLLRMLAGTMLPDTGEILSSGTISWPVGFSGSFHPELTGAQNVRFVARLYGVDTEAMIAFVRDFAEIGQHFHLPVRSYSSGMRSRLAFGISMAVPFDTYLIDEVTAVGDAAFSAKSNAILRARLEESGAVIVSHSMPLLKKLCRSGAVLHDGQLFYYERIEQAIRHHESMMRGALPRWMRGDLDEGEGEEAGAAAPGPRARARAGAARAGGGRAARPGPASGTSEPRG
>NC_011960.1|WP_012642359.1|71430_72546_-|ParB-N-terminal-domain-containing-protein
MAKRKRLTLPPLGGFAPGPTSASEASPAPAPASASALGPGLAPAPISRVTGEAAATAALREVAEELGAARSEGRLVLRLELDRIEEGWLVRDRIGLEAEELASLMTSLSAHGQRSPIEVTDMGEGRFGLISGWRRVTALRRLHAETGEERFATVLALLRRPDTAAAAYVAMVEENEIRAGLSYFERARIAAKAVEAGVFATDKLALQQLYGSASRAKRSKIGSFLGIYRALEGALRYPSALPERLGLALARRLEEEAAFAAEVAAALAAATPDSAEAELALIADLLAPAAEAAPELARPSAPDPVPEAPAPAPAPDPAPANPRSARAQAPAAELRPGLFLKAEGAGSLHLYGPAVDEAFRARLRDWLASEE
>NC_011960.1|WP_049764010.1|72667_74074_-|AAA-family-ATPase
MRKSPPAREPQVPLPPYFNISPDAALAELEAPLTTAGFAEIARSCAQGRDDLAARGLDAEGRRSLRLFSTWEITRYLIPVATAHFRRVLKANPDLPQGVSETEGGAKWFTLDEVLRLRAHFAAEGSKAKEYRPYRPAGLPAKLVAVANFKGGVGKTSTAAHLAMSAALDGYRVLVIDLDSQGSMTSIFGGRVADEWGTVFPLLARHYAAHLQAENRARVARGDPPVPMDETLTEAQKIRAGDLIAKTHWPNIDLIGAQLNLYWAEFQIPVWRMQGRSWKLWDALTDVLAEDGVLDRYDVIFLDTPPALGYLTINGLAAADILLVPLGASFLEFDSTGRFFDMLHSTFRSIEEGENIAARALGREELAFEWDAVRAVLTRYDGAQQAEMAALMQAYMGRTMAPERQDFTALIGQAGEQVNGIYEADYRDFNRDTYIRGRETFDATYAAFKRLLVGIWRREELAAADAAE
>NC_011960.1|WP_002724803.1|74818_75781_+|replication-initiator-protein-A
MADFFICDILDALPKDDMASMEHPVFSLATRPDLRVLDYAHNGVRITVTPSVRGLATLFDKDILIYCVSQLMAALNAGRAISRTLHLTAHDLMTATHRETSGDGYQRLREAFERLAGTRITTNMEVGGREITTGFGLIESWQIVRRSRGGRMVQVMVTLSEWLFQAVLTKSVLTLSRDYFRLRKPLERRIYELARKHCGQQPEWRVSIATLAKKSGSASPLRVFRKMIRDMIAADSLPGYSLAEEPGDLLCVTRRAAVLAPGLAPALRDTTLERVRARMPGWDVHALVAEWHAFWHSSGQPRLRSADAAFLGWIERRVPG
>NC_011960.1|WP_009565042.1|75832_76771_+|glycosyltransferase
MTDAPPPRIALLLATYNGAANLEAQLESFAAQTLRPTWLVVSDDGSTDATRALLAAFAARHPWLALRLVEGPCRGSAQNFLHLLGQVPPEADMAALSDQDDVWLPGKLARGAAAMADLPADLPVLYGGSSWICDAELGNRRPYPLPARPPGFRHALVQNIAGGNTMMLNRGAIALLAAASREPERIVVHDWWIYQIVSGAGGRVIFDPVPLLLYRQHGGNLIGANDGFRAKYRRLRMLLSGGFRQWNAINIRALSASAHRFTPENRRLLAEFEALRRAGPWGRLRQLKRIGLYRQGLPGRLSLWLAAVLGRI

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Crispr_ID: NC_011960_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011960_2

72575-72653

Orphan

Consensus_repeat	Method
GGTTTGTTTCGCGCGCGAAACAA	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_011960_2

>merge|NC_011960|2|72575-72653|CRISPRCasFinder
GGTTTGTTTCGCGCGCGAAACAATTTGCCCCCGCCGTGCCGCCCTGCCGGCCCCCGGATTTGTTTCGCGCGCGAAACAA

>NC_011960|2|2|72575-72653|CRISPRCasFinder
GGTTTGTTTCGCGCGCGAAACAA	TTTGCCCCCGCCGTGCCGCCCTGCCGGCCCCCG
GATTTGTTTCGCGCGCGAAACAA

Protein	Signature genes	Signature genes Name	Protein_function
NC_011960.1\|WP_009565042.1\|75832_76771_+\|glycosyltransferase	unknown	unknown	gnl\|CDD\|133039
NC_011960.1\|WP_002724800.1\|70271_71093_+\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|213187
NC_011960.1\|WP_012642359.1\|71430_72546_-\|ParB-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|274586
NC_011960.1\|WP_012642363.1\|78438_79290_+\|dTDP-4-dehydrorhamnose-reductase	unknown	unknown	gnl\|CDD\|367904
NC_011960.1\|WP_011840032.1\|76834_77398_+\|dTDP-4-dehydrorhamnose-3,5-epimerase	unknown	unknown	gnl\|CDD\|376414
NC_011960.1\|WP_012642355.1\|64247_65252_-\|hypothetical-protein	unknown	unknown	unknown
NC_011960.1\|WP_002724803.1\|74818_75781_+\|replication-initiator-protein-A	unknown	unknown	gnl\|CDD\|370826
NC_011960.1\|WP_012642357.1\|67571_68372_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224596
NC_011960.1\|WP_002724637.1\|82197_83034_+\|3-deoxy-8-phosphooctulonate-synthase	unknown	unknown	gnl\|CDD\|235363
NC_011960.1\|WP_012642353.1\|62049_63408_+\|sulfotransferase	unknown	unknown	gnl\|CDD\|226081
NC_011960.1\|WP_041671123.1\|63434_64151_-\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|369777
NC_011960.1\|WP_002724812.1\|79286_80177_+\|glucose-1-phosphate-thymidylyltransferase-RfbA	unknown	unknown	gnl\|CDD\|130274
NC_011960.1\|WP_041671120.1\|60145_61447_-\|DUF2793-domain-containing-protein	unknown	unknown	gnl\|CDD\|371324
NC_011960.1\|WP_041671132.1\|81270_81996_-\|sulfotransferase	unknown	unknown	gnl\|CDD\|379204
NC_011960.1\|WP_009565040.1\|77401_78442_+\|dTDP-glucose-4,6-dehydratase	unknown	unknown	gnl\|CDD\|224013
NC_011960.1\|WP_049764010.1\|72667_74074_-\|AAA-family-ATPase	unknown	unknown	gnl\|CDD\|274585
NC_011960.1\|WP_012642350.1\|59022_59964_-\|calcium-binding-protein	unknown	unknown	gnl\|CDD\|380205
NC_011960.1\|WP_041671125.1\|65252_67508_-\|glycoside-hydrolase-family-99-like-domain-containing-protein	unknown	unknown	gnl\|CDD\|379549
NC_011960.1\|WP_041671130.1\|80151_80934_-\|sulfotransferase	unknown	unknown	gnl\|CDD\|366246
NC_011960.1\|WP_011840036.1\|69115_70255_+\|sugar-transporter	unknown	unknown	gnl\|CDD\|226055

Protein	Function_ID	Function_description	E-value
NC_011960.1\|WP_009565042.1\|75832_76771_+\|glycosyltransferase	gnl\|CDD\|133039	cd04196, GT_2_like_d, Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.	5.0911e-72
NC_011960.1\|WP_002724800.1\|70271_71093_+\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|213187	cd03220, ABC_KpsT_Wzt, ATP-binding cassette component of polysaccharide transport system. The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenza) and a cytoplasmic membrane protein MPA2.	1.78218e-89
NC_011960.1\|WP_012642359.1\|71430_72546_-\|ParB-N-terminal-domain-containing-protein	gnl\|CDD\|274586	TIGR03454, partition_RepB, plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently. [Mobile and extrachromosomal element functions, Plasmid functions].	7.35995e-11
NC_011960.1\|WP_012642363.1\|78438_79290_+\|dTDP-4-dehydrorhamnose-reductase	gnl\|CDD\|367904	pfam04321, RmlD_sub_bind, RmlD substrate binding domain. L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesized by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucleotide.	1.1592e-122
NC_011960.1\|WP_011840032.1\|76834_77398_+\|dTDP-4-dehydrorhamnose-3,5-epimerase	gnl\|CDD\|376414	pfam00908, dTDP_sugar_isom, dTDP-4-dehydrorhamnose 3,5-epimerase. This family catalyze the isomerisation of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13.	3.65992e-99
NC_011960.1\|WP_002724803.1\|74818_75781_+\|replication-initiator-protein-A	gnl\|CDD\|370826	pfam10134, RPA, Replication initiator protein A. Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination.	2.32126e-121
NC_011960.1\|WP_012642357.1\|67571_68372_-\|ABC-transporter-permease	gnl\|CDD\|224596	COG1682, TagG, ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane].	1.20685e-33
NC_011960.1\|WP_002724637.1\|82197_83034_+\|3-deoxy-8-phosphooctulonate-synthase	gnl\|CDD\|235363	PRK05198, PRK05198, 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional.	0
NC_011960.1\|WP_012642353.1\|62049_63408_+\|sulfotransferase	gnl\|CDD\|226081	COG3551, COG3551, Uncharacterized protein conserved in bacteria [Function unknown].	7.39736e-51
NC_011960.1\|WP_041671123.1\|63434_64151_-\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|369777	pfam08241, Methyltransf_11, Methyltransferase domain. Members of this family are SAM dependent methyltransferases.	6.85196e-10
NC_011960.1\|WP_002724812.1\|79286_80177_+\|glucose-1-phosphate-thymidylyltransferase-RfbA	gnl\|CDD\|130274	TIGR01207, Glucose-1-phosphate_thymidylyltransferase_1, glucose-1-phosphate thymidylyltransferase, short form. Alternate name: dTDP-D-glucose synthase homotetramer This model describes a tightly conserved but broadly distributed subfamily (here designated as short form) of known and putative bacterial glucose-1-phosphate thymidylyltransferases. It is well characterized in several species as the first of four enzymes involved in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides].	2.32712e-162
NC_011960.1\|WP_041671120.1\|60145_61447_-\|DUF2793-domain-containing-protein	gnl\|CDD\|371324	pfam10983, DUF2793, Protein of unknown function (DUF2793). This is a bacterial family of proteins with unknown function.	1.21105e-31
NC_011960.1\|WP_041671132.1\|81270_81996_-\|sulfotransferase	gnl\|CDD\|379204	pfam13469, Sulfotransfer_3, Sulfotransferase family.	2.10745e-11
NC_011960.1\|WP_009565040.1\|77401_78442_+\|dTDP-glucose-4,6-dehydratase	gnl\|CDD\|224013	COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane].	0
NC_011960.1\|WP_049764010.1\|72667_74074_-\|AAA-family-ATPase	gnl\|CDD\|274585	TIGR03453, partition_RepA, plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error. [Mobile and extrachromosomal element functions, Plasmid functions].	2.26018e-59
NC_011960.1\|WP_012642350.1\|59022_59964_-\|calcium-binding-protein	gnl\|CDD\|380205	NF033203, entero_EhxA, enterohemolysin EhxA. Members of this family are the RTX toxin called enterohemolysin or EhxA, because it is found in enterohemorrhagic Escherichia coli (EHEC) strains such as O157:H7.	1.65286e-15
NC_011960.1\|WP_041671125.1\|65252_67508_-\|glycoside-hydrolase-family-99-like-domain-containing-protein	gnl\|CDD\|379549	pfam14307, Glyco_tran_WbsX, Glycosyltransferase WbsX. Members of this family are found in within O-antigen biosynthesis clusters in Gram negative bacteria, where they are predicted to function as glycosyltransferases.	9.32622e-149
NC_011960.1\|WP_041671130.1\|80151_80934_-\|sulfotransferase	gnl\|CDD\|366246	pfam00685, Sulfotransfer_1, Sulfotransferase domain.	5.76817e-12
NC_011960.1\|WP_011840036.1\|69115_70255_+\|sugar-transporter	gnl\|CDD\|226055	COG3524, KpsE, Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane].	1.23505e-72

>NC_011960.1|WP_012642359.1|71430_72546_-|ParB-N-terminal-domain-containing-protein
MAKRKRLTLPPLGGFAPGPTSASEASPAPAPASASALGPGLAPAPISRVTGEAAATAALREVAEELGAARSEGRLVLRLELDRIEEGWLVRDRIGLEAEELASLMTSLSAHGQRSPIEVTDMGEGRFGLISGWRRVTALRRLHAETGEERFATVLALLRRPDTAAAAYVAMVEENEIRAGLSYFERARIAAKAVEAGVFATDKLALQQLYGSASRAKRSKIGSFLGIYRALEGALRYPSALPERLGLALARRLEEEAAFAAEVAAALAAATPDSAEAELALIADLLAPAAEAAPELARPSAPDPVPEAPAPAPAPDPAPANPRSARAQAPAAELRPGLFLKAEGAGSLHLYGPAVDEAFRARLRDWLASEE
>NC_011960.1|WP_002724800.1|70271_71093_+|ABC-transporter-ATP-binding-protein
MIELRNVSKSYVLNGTRKVVARDLNFTFPSGESVGLLGRNGAGKSSLLRMLAGTMLPDTGEILSSGTISWPVGFSGSFHPELTGAQNVRFVARLYGVDTEAMIAFVRDFAEIGQHFHLPVRSYSSGMRSRLAFGISMAVPFDTYLIDEVTAVGDAAFSAKSNAILRARLEESGAVIVSHSMPLLKKLCRSGAVLHDGQLFYYERIEQAIRHHESMMRGALPRWMRGDLDEGEGEEAGAAAPGPRARARAGAARAGGGRAARPGPASGTSEPRG
>NC_011960.1|WP_011840036.1|69115_70255_+|sugar-transporter
MPAAAPRAAARLRHHGLLASFLGLVLAPTLASGLYLFAIAEDQYTSTVGFSVRTEEMGSALDLLGGLSSFGLTGGGSASDSDILYQFIQSQELVQRINERIDLRAIYSKPGFDPVFSFDPDGGIEDLVDYWKDMVRISYDSTTGLIELRVHAFTPEDAQAVAQGILDESNRMINDLSAIARADATRYAREELDNAVERLRVQRVAMTEFRSRTQIVDPSADIQAQMGLLNTLQQQLASASIDLNLLRQTTQPSDPRIAQNERRIGVIEELIQREREKFGLGGGTGTGASTYSTMIAEFERLTVDLDFAEKAYIAALTNHDAAIAEAQRMSRYLATYVRPTLAQQSLYPQRGLLTLMIGGFALMLWAIGMLIYYSVRDRR
>NC_011960.1|WP_012642357.1|67571_68372_-|ABC-transporter-permease
MTGLSGLLAGRRFLWGRSVLSLMLREMATSYGRSPGGYLWAVAEPVAALTLLTVVFSFLMRSPPLGNNFPLFYATGYLPFMYYSALTAKIGQAIRFSRPLLAYPAVSFFDAILSRFLLNTLTNLVVFVIVMVGIIAFYDLNVSLDLPAILEAFSMAAALAMGVGTLNCYLFSVAPVWERVWAILNRPMFLLSGIFFLMETVPEPFRTLLSYNPLTHVIAKMRQGFFATYDARLVDPLYAYSVSLVCLFFGMLLLNRHHRMLLNEGA
>NC_011960.1|WP_041671125.1|65252_67508_-|glycoside-hydrolase-family-99-like-domain-containing-protein
MLKLHRLRRFARILVLTGEERRYLRAIRKSGLFDRTYYRGAYPGLNPIYLKYPEKHYIAYGERLGYRPNPDFSPQAYLRYHPDVAEAGVPPFLHYVRVGHAEQRLTKELPEVVALPARGMPQVRFEHGRQTAPYAVAVHVYYPDLWPEFAARLRRLRIPFDLYVTLTYRGEETDALAQEIRADFPGAFVTPMPNRGRDILPFVTLLNAGAFDGYRAVCKFHTKKSPHRQDGDLWRKHLIEGILPETGLEEKLEAFVEAPEAGFWVADGQHYTGTQWWGSNVEATRHLLQRIEIPLDREALSFPAGSIYWVKPLVLGLLRSLQLRLEDFDIEEGQVDGTLAHAIERVLGYLTARAGQKVLQTSELRPAAAAAPAKPAFVSAFYLPQFHPVPENDAWWGRGFTEWRSVVKAPSMFEGHLQPMLPADLGFYDLRATEVMGEQAAMAREAGIDAFCVYHYWFDGRRILEAPIDRLMARPEIDFPFYLCWANESWRRNWDGLSGTVLLEQTYGAGFEEKLAADTAPYLRDPRYARPDGRRPRFVIYRPEDMPDPQASVARLREGWRRAGIGEVELGAVRFHVEGAHPVPEALFDFWVEMPPHGLVKGPDYLFGGPDGNRMPAAMNPAFSGLIYDYAAVARRALSETYVRTLPKATIAGVMPGWDNTARRGAAGHVAYGANPATFNVWLAGALERRVPASYRRELFVNAWNEWAEKAVLEPSLTFGDLNLQVMRQHLGAAEPATHLAEPPAHGMRSH
>NC_011960.1|WP_012642355.1|64247_65252_-|hypothetical-protein
MARVVLHIGTHKTATTTIQDMFAHNADLLRQHGVIYPRLSRVAGHHGLVMDWNKLPAAYALPNGSLGTLRQLAAQYGKGEGTVVLSSEEFSRGLEGRRVDFRAVREALAGFESFSIVCVLREQWQYAQSIYLETSKNRVPVKPGLLVQSILNRDMIDGLWTDYNLLYDHLLEAFAPEEIAFLDFEACRRHSGGVVGAMLEHLGCDLPASALEVVHDGQSNVSPLSLPAWAASLIAEPERAPRWLVESTTGAFRAEHGEEARPCLWTRVEFAALSRYAQERNARFLERLAPVQPDFTIRQSTPGDAAIYRDDIKGSFWLRCSRWTYRGKMSAGEG
>NC_011960.1|WP_041671123.1|63434_64151_-|class-I-SAM-dependent-methyltransferase
MTAVYAHQGFCNACGSPAEFRSQSHWFRDNLFCSVCGSIPRERALATVLERVRPDWRDRRIHESSPADRSISARLARECRSYVASQFFPGEPLGTVVRGFRNENLEAQTFEDGRFDLVVTLDVMEHVNEPDKVFREVFRTLVPGGAYLFSVPTYKERVTSERRARYRPDGGIDHLAEPEYHGNPVSDAGSLVTFHYGYDLPELIHAWAGFDVELFRFHHHHLGLIGEFTEIYLATRPA
>NC_011960.1|WP_012642353.1|62049_63408_+|sulfotransferase
MTSDQTPARPALLVLGMHRSGTSALAGVLGRAGFALPQELMPPTEHNPRGYFESTRIFRLNDALLAAAGSSWDDWRAFDADWHLSPAAEPFHAEAQEALAAEFPGTAPIVLKDPRICRLLPFWTRALTEAGFRPLAVCTHRPAREVGASLARRNGWPEARGLLLWLRHVLDAEAQTRGRPRVFVSYDGLLADWRGTLGRIAEAFDLALPRPLDEAAPEIEAFLSADLRHAPETLAAAAGLSDWIARPEEILDRKAAGEDRPGDRETLDRIAAEVAAAAPLLADLSGAVEELGTRLEREAALRQEAQTILHQERQRLDDLTAELQLQLHHRTLHVAELERHAGELAQQLRQKTQHAAELERHAEELAEQLRQQRSHAAELERHAGELSALTHELRQQVHHKGRHVAELERHAGALQTAVTRLEAERSALLDSASWRVTGPLRRVSEALRRPKS
>NC_011960.1|WP_041671120.1|60145_61447_-|DUF2793-domain-containing-protein
MSDASPILSLPYILPSQAQKHVTHNEALQRLDVLVQPAVLDRDRSAPPAAPAAGARHLVGPGAEGAWVGREEAFAVWDAEAAVWRFLAPQPGWQTFVLAEGAGLVFTAQGWRTLIGLLPEFPSLGIATPADATNRLAVAGPATLFTHAGAGHRIKVNKAAEAETASLLFQSDWSGRAEIGLAGSDDFSLKVSPDGTSFRTALSADRASGRVALPQGAVVTGSLTGSAVQASAADATPGRLLTVGAFGLGAPAPLVGNAGAVDGALAPGFYGYDSAQGSSGGPAGVQAGLLLHQSRGAGEVQLFLVEAGGGGLMPGILFSRARGEGAWSPWVAGGIVESAGNVNGRYIRHQDGTQSCWQKVTTSASADVVAPFPAAFSTATGLVTVSSVVSNGAQALSPRLTGRTTTSVGVSVFSATNTRLAAQVELISMGRWY
>NC_011960.1|WP_012642350.1|59022_59964_-|calcium-binding-protein
MPEVSPFPSVSPLSAPLAQSALAQTPAGTPGNDLLNGGPGADRLVGGDGNDTINGRDGVDRLYGGDGDDLLDGGFYHDACYGQAGNDTFRIRGVDLADDVYGGAGTDTLDLSGYTNLRLGFRVDLAAGRYDFRPEPFGPYVVKSIEIVKGSARADVLLGSRLAETLSGGLGNDRLEGRGGADVLRGMEGADALFGGTGNDLLVGGAGNDRLDGQWERDVLVGGAGNDILIGGGGADRFVFAGNFGRDRIRDFSPDMEGERIDLRGVGAITGFGDLMANHLSEVNGHVVIEVGANRITLEGISSEMLTRDDFLF
>NC_011960.1|WP_049764010.1|72667_74074_-|AAA-family-ATPase
MRKSPPAREPQVPLPPYFNISPDAALAELEAPLTTAGFAEIARSCAQGRDDLAARGLDAEGRRSLRLFSTWEITRYLIPVATAHFRRVLKANPDLPQGVSETEGGAKWFTLDEVLRLRAHFAAEGSKAKEYRPYRPAGLPAKLVAVANFKGGVGKTSTAAHLAMSAALDGYRVLVIDLDSQGSMTSIFGGRVADEWGTVFPLLARHYAAHLQAENRARVARGDPPVPMDETLTEAQKIRAGDLIAKTHWPNIDLIGAQLNLYWAEFQIPVWRMQGRSWKLWDALTDVLAEDGVLDRYDVIFLDTPPALGYLTINGLAAADILLVPLGASFLEFDSTGRFFDMLHSTFRSIEEGENIAARALGREELAFEWDAVRAVLTRYDGAQQAEMAALMQAYMGRTMAPERQDFTALIGQAGEQVNGIYEADYRDFNRDTYIRGRETFDATYAAFKRLLVGIWRREELAAADAAE
>NC_011960.1|WP_002724803.1|74818_75781_+|replication-initiator-protein-A
MADFFICDILDALPKDDMASMEHPVFSLATRPDLRVLDYAHNGVRITVTPSVRGLATLFDKDILIYCVSQLMAALNAGRAISRTLHLTAHDLMTATHRETSGDGYQRLREAFERLAGTRITTNMEVGGREITTGFGLIESWQIVRRSRGGRMVQVMVTLSEWLFQAVLTKSVLTLSRDYFRLRKPLERRIYELARKHCGQQPEWRVSIATLAKKSGSASPLRVFRKMIRDMIAADSLPGYSLAEEPGDLLCVTRRAAVLAPGLAPALRDTTLERVRARMPGWDVHALVAEWHAFWHSSGQPRLRSADAAFLGWIERRVPG
>NC_011960.1|WP_009565042.1|75832_76771_+|glycosyltransferase
MTDAPPPRIALLLATYNGAANLEAQLESFAAQTLRPTWLVVSDDGSTDATRALLAAFAARHPWLALRLVEGPCRGSAQNFLHLLGQVPPEADMAALSDQDDVWLPGKLARGAAAMADLPADLPVLYGGSSWICDAELGNRRPYPLPARPPGFRHALVQNIAGGNTMMLNRGAIALLAAASREPERIVVHDWWIYQIVSGAGGRVIFDPVPLLLYRQHGGNLIGANDGFRAKYRRLRMLLSGGFRQWNAINIRALSASAHRFTPENRRLLAEFEALRRAGPWGRLRQLKRIGLYRQGLPGRLSLWLAAVLGRI
>NC_011960.1|WP_011840032.1|76834_77398_+|dTDP-4-dehydrorhamnose-3,5-epimerase
MQIEETELPGVLILTPRVFGDARGSFCEAWNRATLQGLGIDLDFVQDNQSISAPVGTVRGLHYQAPPHAQDKLVRVGHGAILDVAVDVRVGSPTYGRWVGVELTAGNARQLLVPKGFLHGFVTREPDTVVLYKTTDVYAPDCDGAVHFADPDLGIDWGIDPASAVLSDKDARAPRFADWTSPFSIEA
>NC_011960.1|WP_009565040.1|77401_78442_+|dTDP-glucose-4,6-dehydratase
MKLIVTGGAGFIGSAVVRKAVADGHHVVNLDCLTYAACLDNLASVAGAPNYVFEKADIRDAEAMARVFATHRPDAVMHLAAESHVDRSIDGPGAFIDTNVRGTYVLLEAARAYWVGQGKPQGFRFHHISTDEVFGTLGETGQFTEETPYAPNSPYSASKAASDHLVRAWGETYGLPYVLTNCSNNYGPFHFPEKLIPVVILKALAGAPIPVYGKGENVRDWLYVEDHADALLTVLARGENHRSYNIGGENEAKNIDIVRKICAILDARRPKATPYADQIAFVTDRPGHDLRYAIDPTRIRTELGWRPSVTLDEGLERTVDWYLANEPWWRALQDRAGVGERLGVKA
>NC_011960.1|WP_012642363.1|78438_79290_+|dTDP-4-dehydrorhamnose-reductase
MILVFGRTGQVARELARQAPDARFLGRDEADLADPEACARAIREAKPDAVINAAAWTAVDRAEEEEAPATVVNGEAPGAMARACAALGIPFVQISTDYVFDGSGTRPWQPGDPVGPLGAYGRSKLAGEEAVRAAGGPHAILRTSWVFSAHGANFVKTMLRLGATRDRLTVVCDQVGGPTPAADIAAACLAMARGLAARPDLSGTYHLSGGPDVSWADFAREIFRQAELACLVADIASADYPQKAHRPANSRMDCSDLARFGLSRPDWRQGLARVLADLQEVSE
>NC_011960.1|WP_002724812.1|79286_80177_+|glucose-1-phosphate-thymidylyltransferase-RfbA
MSVRKGIILAGGSGTRLYPLTIGVSKQLMPVYDKPMIYYPLSVLMLAGIREIAIITTPQDQEQFRRALGTGAQWGISLTYLVQPRPEGLAQAYTIAEEFLAGSPSCMVLGDNIFFGHGLPDLLALADAKTEGGTVFGYHVADPERYGVVAMDERGRVTQIVEKPKVAPSNYAVTGIYFLDARAPDLVHGIRPSERGELEIVSLLEIYLEEGLLDVQRMGRGFAWLDTGTHASLLDAGNFVRTLQLRQGMQTGCPEEIAFARGWVDAEALTGMAAQLSKNDYGRYLQGLLTDRMMEG
>NC_011960.1|WP_041671130.1|80151_80934_-|sulfotransferase
MRAASPRVRFLVAGAQKCGTTALHRFLSAHPDLFLPAGKELHFFDRPLPDDWSGPEGPLYETAFAEARPDQLCGEATPVYLFHTPSLQRIRAYNPAMRLILLLRDPVLRAYSHWRMERTRGAETLPFPEAIRTGRARVAEDWRTFSYVERGFYGAQLTRLERLFPREQRLVLWTDEMQRDHAGTLARIWRFLGCAAPSVPPPPAEIRPLDPAPGLAPLAEEDARYLRALYAPDIALTETLTGRDLSLWREGALSPPSSGR
>NC_011960.1|WP_041671132.1|81270_81996_-|sulfotransferase
MDRDLPETPALVLGASGGSGTRVAGQLLRAAGGYLGGARNEAGDSLALVAAIEALAARGARLLEGGRPEEADLALWRAALRQHLALHAGEPFWGWKNPRSMFLLPFSVALVPGLRFIHMVRDGRDMALSGNRRQYERHVPGGPGTPADRARFWAESNLRVKRHAEAVLGDRYAILRFEDLCRDPEGCMARLGRQFGLRLEPAGAGIEVRPPDGVGRHRALPAADRAAVEAAAAPAMEAFGY
>NC_011960.1|WP_002724637.1|82197_83034_+|3-deoxy-8-phosphooctulonate-synthase
MTETPTIVTIGDIAIGGGHPIALITGPCQLESLDHARMMAERIAEACAPTGTKFIFKASYDKANRSSLSTARGLGMEKGLEILGRIREEFGVPVLTDVHEPGHCATAAEVCDVLQIPAFLCRQTDLLLAAGETGRAVNVKKGQFLAPWDMKNVADKVASTGNRRILLCERGTSFGYNTLVTDFRGLPTMAATGWPVVFDATHSVQQPGGLGGSSGGQREFAPVLARAACAVGVSALFIETHEDPDRAPSDGPNMIPVDRMGRLIADLCAFDALAKSLA

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	NC_011960	Rhodobacter sphaeroides KD131 plasmid pRSKD131B, complete sequence	63100-63138	0	1.0
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NC_011960	Rhodobacter sphaeroides KD131 plasmid pRSKD131B, complete sequence	72598-72630	0	1.0
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	CP036421	Rhodobacter sphaeroides strain HJ plasmid unnamed1, complete sequence	28105-28137	0	1.0
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	NZ_CP030273	Rhodobacter sphaeroides 2.4.1 plasmid pA, complete sequence	75966-76004	1	0.974
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	CP047033	Rhodobacter sphaeroides strain DSM 158 plasmid pEA, complete sequence	69648-69686	1	0.974
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	NC_009040	Rhodobacter sphaeroides ATCC 17029 plasmid pRSPH01, complete sequence	30261-30299	1	0.974
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	NZ_CP047039	Rhodobacter sphaeroides strain 2.4.1 substr. H2 plasmid pEA, complete sequence	69619-69657	1	0.974
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	NZ_CP015213	Rhodobacter sphaeroides strain MBTLJ-13 plasmid b, complete sequence	113436-113474	1	0.974
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	NZ_CP051470	Rhodobacter sphaeroides strain CH10 plasmid pRspCH10A, complete sequence	10724-10762	1	0.974
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	NZ_CP015290	Rhodobacter sphaeroides strain MBTLJ-20 plasmid b, complete sequence	119408-119446	1	0.974
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NZ_CP030273	Rhodobacter sphaeroides 2.4.1 plasmid pA, complete sequence	67220-67252	2	0.939
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	CP047033	Rhodobacter sphaeroides strain DSM 158 plasmid pEA, complete sequence	60898-60930	2	0.939
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NC_009040	Rhodobacter sphaeroides ATCC 17029 plasmid pRSPH01, complete sequence	21550-21582	2	0.939
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NZ_CP047039	Rhodobacter sphaeroides strain 2.4.1 substr. H2 plasmid pEA, complete sequence	60874-60906	2	0.939
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NZ_CP015213	Rhodobacter sphaeroides strain MBTLJ-13 plasmid b, complete sequence	104690-104722	2	0.939
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NZ_CP051470	Rhodobacter sphaeroides strain CH10 plasmid pRspCH10A, complete sequence	19476-19508	2	0.939
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NZ_CP015290	Rhodobacter sphaeroides strain MBTLJ-20 plasmid b, complete sequence	3847-3879	2	0.939
NC_011960_1	1.1\|63100\|39\|NC_011960\|CRISPRCasFinder	63100-63138	39	CP036421	Rhodobacter sphaeroides strain HJ plasmid unnamed1, complete sequence	18781-18819	4	0.897
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NZ_CP045374	Sulfitobacter sp. THAF37 plasmid pTHAF37_b, complete sequence	70638-70670	7	0.788
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NZ_AP022593	Mycolicibacterium arabiense strain JCM 18538 plasmid pJCM18538, complete sequence	4332115-4332147	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MN284907	Gordonia phage Fireball, complete genome	8624-8656	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MK864264	Gordonia phage VanDeWege, complete genome	8812-8844	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MH479910	Gordonia phage Danyall, complete genome	8520-8552	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MT639651	Gordonia phage Portcullis, complete genome	8580-8612	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MH479917	Gordonia phage KimmyK, complete genome	8648-8680	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MH669015	Gordonia phage TillyBobJoe, complete genome	8335-8367	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MK814761	Gordonia phage SmokingBunny, complete genome	8499-8531	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	KX557286	Gordonia phage Twister6, complete genome	8431-8463	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MK864267	Gordonia phage Valary, complete genome	8884-8916	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MK967381	Gordonia phage RogerDodger, complete genome	8884-8916	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MT310872	Gordonia phage Evamon, complete genome	8501-8533	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MT521998	Gordonia phage Jambalaya, complete genome	8332-8364	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MK864265	Gordonia phage Barb, complete genome	8648-8680	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	NC_030913	Gordonia phage Wizard, complete genome	8624-8656	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MK305889	Gordonia phage Mutzi, complete genome	8520-8552	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MN010760	Gordonia phage Nubi, complete genome	8521-8553	9	0.727
NC_011960_2	2.1\|72598\|33\|NC_011960\|CRISPRCasFinder	72598-72630	33	MK864266	Gordonia phage Arri, complete genome	8692-8724	10	0.697

1. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to NC_011960 (Rhodobacter sphaeroides KD131 plasmid pRSKD131B, complete sequence) position: , mismatch: 0, identity: 1.0

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcacgcggccgaactggagcgccatgcggaa	Protospacer
***************************************

2. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NC_011960 (Rhodobacter sphaeroides KD131 plasmid pRSKD131B, complete sequence) position: , mismatch: 0, identity: 1.0

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccggcccccg	Protospacer
*********************************

3. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to CP036421 (Rhodobacter sphaeroides strain HJ plasmid unnamed1, complete sequence) position: , mismatch: 0, identity: 1.0

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccggcccccg	Protospacer
*********************************

4. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to NZ_CP030273 (Rhodobacter sphaeroides 2.4.1 plasmid pA, complete sequence) position: , mismatch: 1, identity: 0.974

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcacgcggccgaactcgagcgccatgcggaa	Protospacer
*********************** ***************

5. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to CP047033 (Rhodobacter sphaeroides strain DSM 158 plasmid pEA, complete sequence) position: , mismatch: 1, identity: 0.974

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcacgcggccgaactcgagcgccatgcggaa	Protospacer
*********************** ***************

6. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to NC_009040 (Rhodobacter sphaeroides ATCC 17029 plasmid pRSPH01, complete sequence) position: , mismatch: 1, identity: 0.974

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcacgaggccgaactggagcgccatgcggaa	Protospacer
************* *************************

7. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to NZ_CP047039 (Rhodobacter sphaeroides strain 2.4.1 substr. H2 plasmid pEA, complete sequence) position: , mismatch: 1, identity: 0.974

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcacgcggccgaactcgagcgccatgcggaa	Protospacer
*********************** ***************

8. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to NZ_CP015213 (Rhodobacter sphaeroides strain MBTLJ-13 plasmid b, complete sequence) position: , mismatch: 1, identity: 0.974

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcacgcggccgaactcgagcgccatgcggaa	Protospacer
*********************** ***************

9. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to NZ_CP051470 (Rhodobacter sphaeroides strain CH10 plasmid pRspCH10A, complete sequence) position: , mismatch: 1, identity: 0.974

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcacgcggccgaactcgagcgccatgcggaa	Protospacer
*********************** ***************

10. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to NZ_CP015290 (Rhodobacter sphaeroides strain MBTLJ-20 plasmid b, complete sequence) position: , mismatch: 1, identity: 0.974

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcacgcggccgaactcgagcgccatgcggaa	Protospacer
*********************** ***************

11. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NZ_CP030273 (Rhodobacter sphaeroides 2.4.1 plasmid pA, complete sequence) position: , mismatch: 2, identity: 0.939

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccgacccccc	Protospacer
**************************.*****

12. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to CP047033 (Rhodobacter sphaeroides strain DSM 158 plasmid pEA, complete sequence) position: , mismatch: 2, identity: 0.939

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccgacccccc	Protospacer
**************************.*****

13. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NC_009040 (Rhodobacter sphaeroides ATCC 17029 plasmid pRSPH01, complete sequence) position: , mismatch: 2, identity: 0.939

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccgacccccc	Protospacer
**************************.*****

14. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NZ_CP047039 (Rhodobacter sphaeroides strain 2.4.1 substr. H2 plasmid pEA, complete sequence) position: , mismatch: 2, identity: 0.939

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccgacccccc	Protospacer
**************************.*****

15. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NZ_CP015213 (Rhodobacter sphaeroides strain MBTLJ-13 plasmid b, complete sequence) position: , mismatch: 2, identity: 0.939

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccgacccccc	Protospacer
**************************.*****

16. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NZ_CP051470 (Rhodobacter sphaeroides strain CH10 plasmid pRspCH10A, complete sequence) position: , mismatch: 2, identity: 0.939

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccgacccccc	Protospacer
**************************.*****

17. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NZ_CP015290 (Rhodobacter sphaeroides strain MBTLJ-20 plasmid b, complete sequence) position: , mismatch: 2, identity: 0.939

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
tttgcccccgccgtgccgccctgccgacccccc	Protospacer
**************************.*****

18. spacer 1.1|63100|39|NC_011960|CRISPRCasFinder matches to CP036421 (Rhodobacter sphaeroides strain HJ plasmid unnamed1, complete sequence) position: , mismatch: 4, identity: 0.897

aagacgcagcacgcggccgaactggagcgccatgcggaa	CRISPR spacer
aagacgcagcaggcggccgaactcgagcgccatgccgga	Protospacer
*********** *********** *********** *.*

19. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NZ_CP045374 (Sulfitobacter sp. THAF37 plasmid pTHAF37_b, complete sequence) position: , mismatch: 7, identity: 0.788

--tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
aggttg--cccgccgtgtcgccctgctggcccttg	Protospacer
   ***  *********.********.*****..*

20. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NZ_AP022593 (Mycolicibacterium arabiense strain JCM 18538 plasmid pJCM18538, complete sequence) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gacggcaccgccgggccgccctgctggccccgc	Protospacer
  .* * ****** **********.******

21. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MN284907 (Gordonia phage Fireball, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

22. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MK864264 (Gordonia phage VanDeWege, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

23. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MH479910 (Gordonia phage Danyall, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

24. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MT639651 (Gordonia phage Portcullis, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

25. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MH479917 (Gordonia phage KimmyK, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

26. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MH669015 (Gordonia phage TillyBobJoe, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

27. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MK814761 (Gordonia phage SmokingBunny, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

28. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to KX557286 (Gordonia phage Twister6, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

29. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MK864267 (Gordonia phage Valary, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

30. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MK967381 (Gordonia phage RogerDodger, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

31. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MT310872 (Gordonia phage Evamon, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

32. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MT521998 (Gordonia phage Jambalaya, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

33. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MK864265 (Gordonia phage Barb, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

34. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to NC_030913 (Gordonia phage Wizard, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

35. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MK305889 (Gordonia phage Mutzi, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

36. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MN010760 (Gordonia phage Nubi, complete genome) position: , mismatch: 9, identity: 0.727

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaggagtct	Protospacer
 ************ .**********.*   .*

37. spacer 2.1|72598|33|NC_011960|CRISPRCasFinder matches to MK864266 (Gordonia phage Arri, complete genome) position: , mismatch: 10, identity: 0.697

tttgcccccgccgtgccgccctgccggcccccg	CRISPR spacer
gttgcccccgccggaccgccctgccaaggatct	Protospacer
 ************ .**********..   .*

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

72667 : 83034

Enterobacteria_phage(42.86%)

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_049764010.1\|72667_74074_-	AAA family ATPase	A0A0K2FLP4	Brevibacillus_phage	2.1e-06	26.6
WP_002724803.1\|74818_75781_+	replication initiator protein A	A0A0K1Y6J9	Rhodobacter_phage	1.3e-58	39.1
WP_009565042.1\|75832_76771_+	glycosyltransferase	NA	NA	NA	NA
WP_011840032.1\|76834_77398_+	dTDP-4-dehydrorhamnose 3,5-epimerase	A0A291LA62	Escherichia_phage	1.0e-31	43.5
WP_009565040.1\|77401_78442_+	dTDP-glucose 4,6-dehydratase	I7HTA3	Enterobacteria_phage	1.6e-91	51.8
WP_012642363.1\|78438_79290_+	dTDP-4-dehydrorhamnose reductase	I7HXC9	Enterobacteria_phage	1.5e-31	38.5
WP_002724812.1\|79286_80177_+	glucose-1-phosphate thymidylyltransferase RfbA	I7I009	Enterobacteria_phage	7.7e-87	54.9
WP_041671130.1\|80151_80934_-	sulfotransferase	NA	NA	NA	NA
WP_041671132.1\|81270_81996_-	sulfotransferase	NA	NA	NA	NA
WP_002724637.1\|82197_83034_+	3-deoxy-8-phosphooctulonate synthase	E3T537	Cafeteria_roenbergensis_virus	6.0e-49	41.1

Anti-CRISPR protein detection

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

2. NC_011958

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Crispr_ID: NC_011958_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011958_1

191804-191907

Orphan

Consensus_repeat	Method
TTGACAGCTGTCAACCAGTGGCACG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_011958_1

>merge|NC_011958|1|191804-191907|CRISPRCasFinder
TTGACAGCTGTCAACCAGTGGCACGGAGGCCAGGCTCTGCTCTCTGACACTCCGAACGCTCAGCCGGCAAGCGCGGGCATTGACAGCTGTCAACCAGTGGCACG

>NC_011958|1|1|191804-191907|CRISPRCasFinder
TTGACAGCTGTCAACCAGTGGCACG	GAGGCCAGGCTCTGCTCTCTGACACTCCGAACGCTCAGCCGGCAAGCGCGGGCA
TTGACAGCTGTCAACCAGTGGCACG

Protein	Signature genes	Signature genes Name	Protein_function
NC_011958.1\|WP_009561297.1\|191469_191742_-\|metal/formaldehyde-sensitive-transcriptional-repressor	unknown	unknown	gnl\|CDD\|197388
NC_011958.1\|WP_012640909.1\|185781_186159_-\|hypothetical-protein	unknown	unknown	unknown
NC_011958.1\|WP_011842692.1\|196794_197493_+\|glutathione-S-transferase-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|198316
NC_011958.1\|WP_009561298.1\|193714_195403_-\|methyl-accepting-chemotaxis-protein	unknown	unknown	gnl\|CDD\|223910
NC_011958.1\|WP_041670342.1\|186293_186932_+\|SRPBCC-family-protein	unknown	unknown	gnl\|CDD\|176859
NC_011958.1\|WP_011842681.1\|182099_182612_-\|CopD-family-protein	unknown	unknown	gnl\|CDD\|367596
NC_011958.1\|WP_041670344.1\|196106_196763_+\|glutathione-S-transferase-family-protein	unknown	unknown	gnl\|CDD\|223698
NC_011958.1\|WP_009561306.1\|201107_201362_-\|GlsB/YeaQ/YmgE-family-stress-response-membrane-protein	unknown	unknown	gnl\|CDD\|225170
NC_011958.1\|WP_080517732.1\|188148_190335_-\|PAS-domain-containing-protein	unknown	unknown	gnl\|CDD\|226434
NC_011958.1\|WP_012640913.1\|190487_191462_-\|CDF-family-Co(II)/Ni(II)-efflux-transporter-DmeF	unknown	unknown	gnl\|CDD\|224151
NC_011958.1\|WP_080517681.1\|182749_185068_-\|bifunctional-diguanylate-cyclase/phosphodiesterase	unknown	unknown	gnl\|CDD\|238923
NC_011958.1\|WP_041670346.1\|198107_199418_-\|D-amino-acid-dehydrogenase	unknown	unknown	gnl\|CDD\|234819
NC_011958.1\|WP_002723610.1\|201419_202586_-\|AI-2E-family-transporter	unknown	unknown	gnl\|CDD\|223701
NC_011958.1\|WP_012640911.1\|186935_188120_+\|glutathione-dependent-formaldehyde-dehydrogenase	unknown	unknown	gnl\|CDD\|176243
NC_011958.1\|WP_012640917.1\|197503_197980_+\|VOC-family-protein	unknown	unknown	gnl\|CDD\|226383
NC_011958.1\|WP_049763991.1\|199898_200978_-\|putative-zinc-binding-metallopeptidase	unknown	unknown	gnl\|CDD\|379751
NC_011958.1\|WP_012640908.1\|185535_185727_-\|twin-arginine-translocase-TatA/TatE-family-subunit	unknown	unknown	gnl\|CDD\|234822
NC_011958.1\|WP_012640907.1\|185158_185434_-\|hypothetical-protein	unknown	unknown	unknown
NC_011958.1\|WP_012640915.1\|195555_196020_-\|MarR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|197670
NC_011958.1\|WP_080517733.1\|203369_204053_+\|metal-binding-protein-ZinT	unknown	unknown	gnl\|CDD\|370371

Protein	Function_ID	Function_description	E-value
NC_011958.1\|WP_009561297.1\|191469_191742_-\|metal/formaldehyde-sensitive-transcriptional-repressor	gnl\|CDD\|197388	cd10153, RcnR-FrmR-like_DUF156, Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156. This domain family includes various transcriptional regulators that respond to different stressors. It includes Escherichia coli RncR (formally known as YohL, nickel and cobalt-sensitive), and E. coli FrmR (formally known as YaiN, formaldehyde sensitive). Escherichia coli RncR represses expression of the gene encoding the nickel and cobalt-efflux protein RcnA; RcnA may act through modulating NikR, to repress the NIkABCDE nickel transporter. In vitro, purified RncR binds to the rncA promoter DNA fragment in the absence of Ni2+ or Co2+, and the affinity of RncR for this promoter is reduced in the presence of excess nickel. Escherichia coli FrmR regulates the formaldehyde degradation frmRAB operon. This family belongs to a larger superfamily that includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved; in E.coli RcnR and FrmR there is a His or a Thr instead of the second Cys (C-H-H or C-H-T) respectively. For E. coli FrmR, an N-terminal His residue, not conserved in all members of this family, is also involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are poorly conserved in this family.	9.30938e-34
NC_011958.1\|WP_011842692.1\|196794_197493_+\|glutathione-S-transferase-N-terminal-domain-containing-protein	gnl\|CDD\|198316	cd03207, GST_C_8, C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 8; composed of Agrobacterium tumefaciens GST and other uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The three-dimensional structure of Agrobacterium tumefaciens GST has been determined but there is no information on its functional characterization.	4.03364e-29
NC_011958.1\|WP_009561298.1\|193714_195403_-\|methyl-accepting-chemotaxis-protein	gnl\|CDD\|223910	COG0840, Tar, Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms].	1.00155e-52
NC_011958.1\|WP_041670342.1\|186293_186932_+\|SRPBCC-family-protein	gnl\|CDD\|176859	cd07817, SRPBCC_8, Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins.	1.43261e-53
NC_011958.1\|WP_011842681.1\|182099_182612_-\|CopD-family-protein	gnl\|CDD\|367596	pfam03653, UPF0093, Uncharacterized protein family (UPF0093).	3.99959e-09
NC_011958.1\|WP_041670344.1\|196106_196763_+\|glutathione-S-transferase-family-protein	gnl\|CDD\|223698	COG0625, Gst, Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones].	1.80632e-33
NC_011958.1\|WP_009561306.1\|201107_201362_-\|GlsB/YeaQ/YmgE-family-stress-response-membrane-protein	gnl\|CDD\|225170	COG2261, COG2261, Predicted membrane protein [Function unknown].	8.96532e-12
NC_011958.1\|WP_080517732.1\|188148_190335_-\|PAS-domain-containing-protein	gnl\|CDD\|226434	COG3920, COG3920, Signal transduction histidine kinase [Signal transduction mechanisms].	6.50779e-47
NC_011958.1\|WP_012640913.1\|190487_191462_-\|CDF-family-Co(II)/Ni(II)-efflux-transporter-DmeF	gnl\|CDD\|224151	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism].	3.07976e-77
NC_011958.1\|WP_080517681.1\|182749_185068_-\|bifunctional-diguanylate-cyclase/phosphodiesterase	gnl\|CDD\|238923	cd01948, EAL, EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria.	4.21624e-87
NC_011958.1\|WP_041670346.1\|198107_199418_-\|D-amino-acid-dehydrogenase	gnl\|CDD\|234819	PRK00711, PRK00711, D-amino acid dehydrogenase.	0
NC_011958.1\|WP_002723610.1\|201419_202586_-\|AI-2E-family-transporter	gnl\|CDD\|223701	COG0628, yhhT, Predicted permease, member of the PurR regulon [General function prediction only].	2.68862e-49
NC_011958.1\|WP_012640911.1\|186935_188120_+\|glutathione-dependent-formaldehyde-dehydrogenase	gnl\|CDD\|176243	cd08283, FDH_like_1, Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc-dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. 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.	0
NC_011958.1\|WP_012640917.1\|197503_197980_+\|VOC-family-protein	gnl\|CDD\|226383	COG3865, COG3865, Uncharacterized protein conserved in bacteria [Function unknown].	8.52293e-66
NC_011958.1\|WP_012640908.1\|185535_185727_-\|twin-arginine-translocase-TatA/TatE-family-subunit	gnl\|CDD\|234822	PRK00720, tatA, twin-arginine translocase TatA/TatE family subunit.	1.79835e-12
NC_011958.1\|WP_049763991.1\|199898_200978_-\|putative-zinc-binding-metallopeptidase	gnl\|CDD\|379751	pfam15887, Peptidase_Mx, Putative zinc-binding metallo-peptidase. This family has a highly conserved HHExxH motif with a highly conserved ED pairing downstream. HExxH is indicative of a zinc-binding metallo-peptidase.	1.74664e-127
NC_011958.1\|WP_012640915.1\|195555_196020_-\|MarR-family-transcriptional-regulator	gnl\|CDD\|197670	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein.	6.7954e-18
NC_011958.1\|WP_080517733.1\|203369_204053_+\|metal-binding-protein-ZinT	gnl\|CDD\|370371	pfam09223, ZinT, ZinT (YodA) periplasmic lipocalin-like zinc-recruitment. ZinT plays a critical role in recruiting periplasmic zinc to the bacterial zinc-uptake complex ZnuABC, consisting of families pfam01297,pfam00950, pfam00005, regulated by the transcription-regulator FUR, pfam01475. ZinT acts as a Zn2+-buffering protein that delivers Zn2+ to ZnuA (TroA), pfam01297. Members of this family of prokaryotic domains were first identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium, and ensure its subsequent elimination.	7.28179e-110

>NC_011958.1|WP_009561297.1|191469_191742_-|metal/formaldehyde-sensitive-transcriptional-repressor
MAHLTKDKSKTLARVRRLKGQIEAVERAIEAEADCAAILQLVAAVRGAAGGLTAELLEEHLEHHVAGVEDAAARKRGAEEMIAAFRTYMK
>NC_011958.1|WP_012640913.1|190487_191462_-|CDF-family-Co(II)/Ni(II)-efflux-transporter-DmeF
MSDHAAHPHDHDHDHDHDHDHDHDHVFLGARHARNERRTWAVIALTSVMMVIEIAAGTLYGSMALVADGWHMSTHAAALLITALAYLLARRHARDRRFTFGTGKFGDLAGFASAVVLAVVALLIGWESAMRLLDPVPIDFGQATVVAVIGLLVNLGSAALLHEGHGHDHGHGHGHGHDHGPSHHAHDNNLRAAYLHVLADALTSVLAIAALIGGRIGGWVWLDPLIGLLGALVIARWSLGLLRSAGGVLVDFIPEEEELPAEIRAALETGCDRITDLHVWQLGPGHHGAIVALRSGDPRPPDHYRGKLSHLHEISHLTLEVRPA
>NC_011958.1|WP_080517732.1|188148_190335_-|PAS-domain-containing-protein
MAQGTVEARHGALDEAALGIGRWRWDLRSQELVWSEEERAIFGLAPGAPVPGFAAFSAMIHPDDRARVVAAVSETLAQRRLRHSIGFRILRPDGTMRQILSHGRLVMGLDGKPISLEGVDLDLTDTQADPALERPQRAPCPDRTPHIAALRPGEEQDALLRVALEAGRMTVWQLDLQKRLVQVDGDVARLIGLSHVPPELPVAVFENHVDPEDLPLLRAAEAAALRGEPMQVELRLVLETGGRRWLRLMGEPRPDAMGRPQRLVGVAYDISARKEAEEKLRESEAHYRAVFAAIDEGFCTCEMIVDETGAPVDYRFLEANPLFESMTGLVNAVGRTALELVPNLERHWIEIYARVGLGGETLRFELPSDAMGRWFNVFAAPLAAPGRFALVFKDVTDRRRSEEALRESEAMFRSLTEAMPQLVWSARPDGSCDFFNRRWTDCTGASTEMAMGDGWRAFYHPDDQPAIDRLWPQALRTGEPYEIEYRLRHRDGSYRWMLARGVPVRDEAGGILRWMGTCTDIHDLKLAHQRQQILLGEMEHRVKNILALVQAVARQTFGRIPEASSALEAYGGRLQSLAGAYSHLNHESWERASLRHIVATSIGGCGARAEAWSLDGPEVMLPPRSAVPVSMAVHELCTNAVKYGALSVPEGRVTIHWSLGPGDRLTLVWAEADGPHVVPPARAGFGMRMIETVLAVEAGGTVRLDFLPEGVRCEIEVPIRPEPGLRVE
>NC_011958.1|WP_012640911.1|186935_188120_+|glutathione-dependent-formaldehyde-dehydrogenase
MRALTWHGKHDVRVETHPDPEIVNPRDAIIEVTATAICGSDLHLYDGVIPGLMSGDILGHEFMGRVVETGPKSTLKKGQRVVVPFTISCGKCFFCEHQLFSACDNSNPAEKQDLSEPLYGHAVSGLFGYSHLTGGYPGGQAEYVRVPYSDVGPIVIPDGLDDEQVLFLSDILPTGWMAAENAGIEEGDTVAVWGCGPVGLFAIQSALLMGAGKVIAIDEYPKRLALARKLGAEVIDFRRTKVLEALMEMSGGLGPDAVIDAVGMEAHGFMPDTLMDNMKQRVGIGADSAHALREAILAVRKGGRVSVPGVYGGFLDKFPLGALMEKGLTVKTGQTHVQRYTEELLRRIGEGEIDTTFLISHRLPLEEAARGYENFRFNQNEWTKVVLKPGLTGA
>NC_011958.1|WP_041670342.1|186293_186932_+|SRPBCC-family-protein
MPLHRTPRTGPEPRTLALLAGAGLAAGAAVWAVSRSRENPVVFRPNDDAPDRASRHPGGTMPVGRTITINRPRSELFAFWRDFSNLPQFMESVEHVTVVGDVSRWTLAAPFGRKVTLETRIVEEVPDRLIAWRSTDGSDVRAEGAVTFRDAPAGRGTEVEAVVAYVPAGGEAGRLIARLFRLVPAMQGRRELRRFKMLMEAGEIATSRNRKD
>NC_011958.1|WP_012640909.1|185781_186159_-|hypothetical-protein
MRPGPANFGTTQGRLSACLVSLVLTVLLVLLPPQSERPLPGVAASQSDTLRALQSLEPALAPAGRSDRPVLPGGAQPAHGAPDAALLPPPPGRRAAATLPHAGPAPQPFARAFQARAPPNRPFAI
>NC_011958.1|WP_012640908.1|185535_185727_-|twin-arginine-translocase-TatA/TatE-family-subunit
MLNNIGLPGLLVIAAAIIVLFGKGKVSSMMGELGRGISAFKQGLQDTPAEPAAAEPPREIKDA
>NC_011958.1|WP_012640907.1|185158_185434_-|hypothetical-protein
MSLDPAALGGLLPAAGALTLLFQGGRRSLRRRADRRAARAANLPTPAPAPSGTPTSDPELGASRSERRQVLLHWILLVLGLGAIFALGKLI
>NC_011958.1|WP_080517681.1|182749_185068_-|bifunctional-diguanylate-cyclase/phosphodiesterase
MNAARSRLDGSEIRRRDQAARSSASTGRSAAPVGRQEVRMDKPRAPASFSAQLVAAILFACLVATLSVLFLSSTAVKAVDADAEARQIRFAQRALLRETRELLQQQQASTVWDESVVHVRAGDRDWIDSNLGTWMHEEYGQDETYIVDPASRIVYVARERVTGQPGPRATLPPAVEEMVEEMRPMMRAATRNRADSTADVAGLSLSRFVLLGGKPALVSVVPIVPDTPAVMQAAGTEYLHVAVQMADADMAARLSNTYEFDRGSFSVQPGPEDRLSVPLRDGAGRPIAWFVWRADRPGHRIVDEMLPVVGLFAAFGAALLTWLLRTLWTASRRLHQSEEEARYLAMHDPLAGIPNRTLFEDRLDQALKAERRGGPPVALLCLDLDRFKAVNDTMGHQAGDELIRQMAARLRSHVRETDTVARLGGDEFGVILIGMASDETLGRYCSGLVHLLAAPCDLKCGQVQIGASIGAVRAASVDGGREAILRSADTALYRAKAEGRGRYCIATPEMNDIFRRRHEIERDLREAVAEGGQIHVLYQPIFDAEERIVAAEALVRWNHPILGQMGPETFLSIAEETGLIDRIGHHVLEQACILAATSGIPRVSVNVSPVQLRQETFADEVLAVMAAHSLSGERLVLELTEKFTLDAGPATLANLARLRAAGVSIALDDFATGQSLLRYVRDYQIDTIKIDRSYVARLGTGDGTDQIVRAILDLGRAMGIEVTAEGVERASQREALLGMGCHGFQGYLLGRPMDPLRLAALSARKGVAQKSA
>NC_011958.1|WP_011842681.1|182099_182612_-|CopD-family-protein
MIDLLEPAIPHLKALHIAMLVLWCGGLFALPLMLSLHDDAIGQADYSRVRRATHYGYTLVVTPAAVAAIASGTALIFLREVFVAWMFAKLVFVALLVAFHAWVGHTLVSVAETEGTHRPPAALLPLILLLVPVLGILTLVLAKPDLGRIPLPAWLETPRELQLPFDVPSR
>NC_011958.1|WP_009561298.1|193714_195403_-|methyl-accepting-chemotaxis-protein
MSIKLKLAAAFLFVFLLFAVATALTLMRLGTMDREVERMVRVEQPAAQLGVQLVNDQQAESLALRDHIIASEDEQRRSAEEALLAARKRRNETYERLMPLLTDADDAAMLKRLGEVMATGTERIDRALASSKAGDTSGAARILAEPSSKTSRAERSKLLADLQDRRARNIAEAAANADASFSKAQRDLILSLAIAVVLGGIAVTLIVRSISRGLDQALVLAERVAEGDLTLTARTHARDEIGRLLDANNRMVIKLREMVGTITGAVNRVSSGSSSMASTSEELSQGAQEQASATAEASASVEQMAANIRQTADNAGNTETVARTSADRAQASGSAVNEAVDAMQAIAERILVVQEIARQTDLLALNAAVEAARAGEHGRGFAVVAAEVRKLAERSRGAAEEISALSARTLRTASAAGEMLGQLLPDIERTSTLVSGISVASRELALGAQQVAAAIQQLDSVTQQTSSAATGLASGAEALSTQADDLRRTMGHFRVGSGSGPMAETAPSPPDEAEAPARKPARAPLGATGRARPVTAGGFDFDMGESAGGDPVDREFRRHDAA
>NC_011958.1|WP_012640915.1|195555_196020_-|MarR-family-transcriptional-regulator
MHLMSKEPAAPFSMTPLIRDRCLCLGAQRAARTLARHFDEAFRPLGLRSGQFSLLVALNRPEPPAMAEVAEVLAVDRTTLTAALKPLERRGLLQVRPDAGDRRLRRLALTEAGRGLLGRAIPVWEETMAALERGIGRDPSDLAAGLEALRRAAV
>NC_011958.1|WP_041670344.1|196106_196763_+|glutathione-S-transferase-family-protein
MLELFAHPFSSYCQKVWIALHEYGLEARHRMLSPEEPENIELLAGFWPFRKMPLLLDDGRPVSEASIIVEHLTLHHARGPRLIPEDPVAALEVRFWDRFFDNYVATPQQKIVFDAMRPEEARDPAGVAEARAMLETAYGLLERHLPGRTWVAGERFSLADCSAAPQLFYADWTHPIGEGFPLVAAYRARLNVRPSMARCIEAARPWRPYFPLGAPDRD
>NC_011958.1|WP_011842692.1|196794_197493_+|glutathione-S-transferase-N-terminal-domain-containing-protein
MDRPGLTVTAFDWVPGFAQGQVRDLRPRWALEEAELPYEVELLPQGAQETPEHLARQPFGQVPVLTLDGRSMFESGACVWRIAERSERLLPRDPGLRDSCLSWVIAALNTLEPPIMMMGMLWFFERWPDTFGLEDREAPGKVRGPARGMLDKRLAQFGRALAGRETIVGDGFTVADLMLTCVLLPAAQMDLLGAHPEVKAYYDRHSARPGFRKAQADQIAAFAENAGKYRAA
>NC_011958.1|WP_012640917.1|197503_197980_+|VOC-family-protein
MDTDTLTTCLWFDGQAEEAARFYCDLLPRSEITEVLHAPTDYPAGRTGDVLDVSFTLMGRPFLALNGGAYTQFTEAVSLMIPCRTQEEVDRYWQALSARPEAEACGWVKDRWGLSWQIVPLVLPRLLSDPDRAKAGRVMRAMMEMKKIDIAALEAAAA
>NC_011958.1|WP_041670346.1|198107_199418_-|D-amino-acid-dehydrogenase
MRIVVLGAGVVGVTSAYELARAGHEVTVVDRQPAAALETSFANAGEISPGYASPWAAPGIPAKALRWMFMKHAPLVIRPRLDAAQVRFLLAILRNCTPAAYAQNKGRMVRLAEYSRDCLTDLRAATGLAFDERQQGTLQLFRSQKQLDAAARDIEVLRAGGVPFELLDADGCLAAEPGLWAARDRIAGGLRLTGDETGDCFKFTQGLAGLAEEGGVRFRYGTGVERLRVEGGRVTGVETTKGTFLADAVVVALGSHSPALVAPLGLRLPVYPVKGYSITVPIVDADRAPVSTVMDETYKIAITRLGTRIRVGGMAEVAGFSATLPPARRETLGMSVNDLFGGAGDLSRASFWTGLRPMTPDGTPVVGRTPVAGLWLNTGHGTLGWTMAAGSARVLSDLIDGRAPEIESADLGIERYAAPGRRARPAVRLNPARQAG
>NC_011958.1|WP_049763991.1|199898_200978_-|putative-zinc-binding-metallopeptidase
MLSPAVGRGPFPTPVGPVQRYRCPSCHQEIFFRNTVCLACGIQLLFDPDRGFSDMAETGHPCANRGQINCNWSADEPGALCLSCQHTTVVPDLSVPANIDRWERIETVKRPLILMLHRLGLPLFDEAGMPVPRFELKGETGDATAPRVLTGHAEGTITLNIAEADDAERERIRAEMNEPYRTLTGHLRHEVAHHYWDVLTEERPDRLETLRAIFGDDRQDYGAALQAHYAEGAPPDWAESYISAYATAHPWEDFAETWAHVFHLLDGLETAQAFGLKAPQDLPEGLERLVREPMPRLAQAWVELTIALNAVNEAMGHETFYPFVLAPPVVAKQEAIRSLIVEANSGDAAAAPSGSALPR
>NC_011958.1|WP_009561306.1|201107_201362_-|GlsB/YeaQ/YmgE-family-stress-response-membrane-protein
MTIIWTIIIGFIAGVIAKFLHPGDNEPSGFILTTILGIVGALVATWLGQAVGWYGPGEGAGFIGAIVGAIVLLVIWGAVTRKRG
>NC_011958.1|WP_002723610.1|201419_202586_-|AI-2E-family-transporter
MQNERIGEAGTLLEPEAPDVPSENEISRLNHLIAIRRLLGIILLVLVVMGFYFARDVVLPLMIGLLLALTFSPVVRALQRIGIAPPITATALITALAAVIAVSAFLLSGPVSDWINQAPRLGDQLRERAQTILDSFEAVRNASEQVSEITDSEDPTVQRVAVQTPGILSSAVGSVASILTTIIVTLVLALFLLASGDLFYIKLIEGFPRFGDKKRALRIVYGIERRVSRYLLSVTIINAGLGVVIGLLMWGTGMPSPLVWAMAAFLLNFLPYIGAIAGVALSAAVAIVHYDHLTQALLVPALYLTATAIEGQLVTPIVLGRRLELNTVSVFVTVIFWGWLWGIPGALVAVPFLVCIKVVCDNVESLHAVGNFLGARAPLPDLEQDTPE
>NC_011958.1|WP_080517733.1|203369_204053_+|metal-binding-protein-ZinT
MQTVLSRPLSILAASVALAVAAPALAEKPHDHGHDHAHGHGHDEAHSHASDEIAKGVFKDEQVADRPLSDWQGDWQSVYPLLEDGTLAPVMAHKAEHGDKTAEEYRAYYRTGYETEVNRIVIDGDRVTFHGKGEPVSGQYEDDGHEVLTYKAGNRGVRFIFEKVNGDEAAPKFIQFSDHRIAPSTSDHYHLYWGDDRAALLQEVTHWPTYYPAELSAGEIVEEMLAH

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Crispr_ID: NC_011958_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011958_2

1246234-1246445

Orphan

Consensus_repeat	Method
CACCGGCGACACCGCGAGGCCTGACCGGGCGGAGACGG	PILER-CR

2 spacers

The CRISPR arrays of NC_011958_2

>merge|NC_011958|2|1246234-1246445|PILER-CR
CACCGGCGACACCGCGAGGCCTGACCGGGCGGCGGCGGACAAGTCGAGGCGGGGCGCTCGCCGACAAGGCGCGGGCCCCGCCGTGGACGAGCTGACCCGATCGCGGCGGACACCGCGAGGCCGGGGCCTTCGCCGACGAGGCGGCGGCCCTGCCCCGGGCAAGGCACCCGCAGCCACCGGCGACACCGCGAGGCCTGACCGGGCGGAGACGG

>NC_011958|2|1|1246234-1246445|PILER-CR
CACCGGCGACACCGCGAGGCCTGACCGGGCGGCGGCGG	ACAAGTCGAGGCGGGGCGCTCGCCGACAAGGCGCGGGCCCCGCCGTGGACGAGCTGACCCGATCGCGGCG
GACACCGCGAGGCCGGGGCCTTCGCCGACGAGGCGGCG	GCCCTGCCCCGGGCAAGGCACCCGCAGCCACCGGCGACACCGCGAGGCCTGA
CCGGGCGGAGACGG

Protein	Signature genes	Signature genes Name	Protein_function
NC_011958.1\|WP_015923202.1\|1242751_1243504_+\|metal-ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224046
NC_011958.1\|WP_015923196.1\|1238207_1239863_+\|PepSY-domain-containing-protein	unknown	unknown	gnl\|CDD\|377164
NC_011958.1\|WP_009563501.1\|1252582_1253371_+\|alpha/beta-fold-hydrolase	unknown	unknown	gnl\|CDD\|131480
NC_011958.1\|WP_015923212.1\|1255665_1255890_-\|ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|173855
NC_011958.1\|WP_041670706.1\|1241283_1241838_+\|hypothetical-protein	unknown	unknown	unknown
NC_011958.1\|WP_015923198.1\|1240139_1240967_+\|DUF3325-domain-containing-protein	unknown	unknown	gnl\|CDD\|371735
NC_011958.1\|WP_015923195.1\|1235624_1238135_+\|TonB-dependent-siderophore-receptor	unknown	unknown	gnl\|CDD\|227114
NC_011958.1\|WP_015923201.1\|1241834_1242755_+\|zinc-ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|238499
NC_011958.1\|WP_049763998.1\|1249573_1250572_-\|AAA-family-ATPase	unknown	unknown	gnl\|CDD\|234896
NC_011958.1\|WP_041670704.1\|1240963_1241287_+\|hypothetical-protein	unknown	unknown	unknown
NC_011958.1\|WP_015923206.1\|1246513_1247968_-\|cobyric-acid-synthase	unknown	unknown	gnl\|CDD\|234838
NC_011958.1\|WP_009563503.1\|1251548_1251689_-\|DUF3768-domain-containing-protein	unknown	unknown	gnl\|CDD\|372214
NC_011958.1\|WP_161601254.1\|1251185_1251476_+\|DUF1289-domain-containing-protein	unknown	unknown	gnl\|CDD\|377738
NC_011958.1\|WP_015923210.1\|1253540_1254362_-\|NAD(P)H-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|225158
NC_011958.1\|WP_041670716.1\|1254453_1255377_+\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176114
NC_011958.1\|WP_015923203.1\|1243500_1244388_+\|metal-ABC-transporter-permease	unknown	unknown	gnl\|CDD\|224033
NC_011958.1\|WP_041670709.1\|1244384_1245344_+\|zinc-ABC-transporter-substrate-binding-protein	unknown	unknown	gnl\|CDD\|223874
NC_011958.1\|WP_015923197.1\|1239846_1240143_+\|DUF3649-domain-containing-protein	unknown	unknown	unknown
NC_011958.1\|WP_015923207.1\|1248014_1249577_-\|cobyric-acid-synthase	unknown	unknown	gnl\|CDD\|234838
NC_011958.1\|WP_009563502.1\|1252081_1252498_-\|MerR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|133388

Protein	Function_ID	Function_description	E-value
NC_011958.1\|WP_015923202.1\|1242751_1243504_+\|metal-ABC-transporter-ATP-binding-protein	gnl\|CDD\|224046	COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism].	1.94562e-75
NC_011958.1\|WP_015923196.1\|1238207_1239863_+\|PepSY-domain-containing-protein	gnl\|CDD\|377164	pfam03929, PepSY_TM, PepSY-associated TM region. The PepSY_TM family is so named because it is an alignment of up to five transmembranes helices found in bacterial species some of which carry a nested PepSY domain, pfam03413.	3.37844e-59
NC_011958.1\|WP_015923212.1\|1255665_1255890_-\|ABC-transporter-substrate-binding-protein	gnl\|CDD\|173855	cd08490, PBP2_NikA_DppA_OppA_like_3, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.	1.97656e-05
NC_011958.1\|WP_009563501.1\|1252582_1253371_+\|alpha/beta-fold-hydrolase	gnl\|CDD\|131480	TIGR02427, b-ketoadipate_enol-lactone_hydrolase, 3-oxoadipate enol-lactonase. Members of this family are 3-oxoadipate enol-lactonase. Note that the substrate is known as 3-oxoadipate enol-lactone, 2-oxo-2,3-dihydrofuran-5-acetate, 4,5-Dihydro-5-oxofuran-2-acetate, and 5-oxo-4,5-dihydrofuran-2-acetate. The enzyme the catalyzes the fourth step in the protocatechuate degradation to beta-ketoadipate and then to succinyl-CoA and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate, and vanillate all can be converted in one step to protocatechuate. This enzyme also acts in catechol degradation. In genomes that catabolize both catechol and protocatechuate, two forms of this enzyme may be found. All members of the seed alignment for this model were chosen from within protocatechuate degradation operons of at least three genes of the pathway, from genomes with the complete pathway through beta-ketoadipate. [Energy metabolism, Other].	1.11703e-20
NC_011958.1\|WP_015923198.1\|1240139_1240967_+\|DUF3325-domain-containing-protein	gnl\|CDD\|371735	pfam11804, DUF3325, Protein of unknown function (DUF3325). This family of short proteins are functionally uncharacterized. This family is restricted to Alpha-, Beta- and Gamma-proteobacteria.	1.05281e-13
NC_011958.1\|WP_015923195.1\|1235624_1238135_+\|TonB-dependent-siderophore-receptor	gnl\|CDD\|227114	COG4773, FhuE, Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism].	0
NC_011958.1\|WP_015923201.1\|1241834_1242755_+\|zinc-ABC-transporter-substrate-binding-protein	gnl\|CDD\|238499	cd01017, AdcA, Metal binding protein AdcA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AdcA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).	4.07411e-92
NC_011958.1\|WP_015923206.1\|1246513_1247968_-\|cobyric-acid-synthase	gnl\|CDD\|234838	PRK00784, PRK00784, cobyric acid synthase.	0
NC_011958.1\|WP_049763998.1\|1249573_1250572_-\|AAA-family-ATPase	gnl\|CDD\|234896	PRK01077, PRK01077, cobyrinate a,c-diamide synthase.	2.55284e-93
NC_011958.1\|WP_009563503.1\|1251548_1251689_-\|DUF3768-domain-containing-protein	gnl\|CDD\|372214	pfam12599, DUF3768, Protein of unknown function (DUF3768). This family of proteins is found in bacteria. Proteins in this family are typically between 108 and 129 amino acids in length. There are two conserved sequence motifs: NDP and RVLT.	2.46297e-11
NC_011958.1\|WP_161601254.1\|1251185_1251476_+\|DUF1289-domain-containing-protein	gnl\|CDD\|377738	pfam06945, DUF1289, Protein of unknown function (DUF1289). This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N-terminus. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids.	2.05574e-05
NC_011958.1\|WP_015923210.1\|1253540_1254362_-\|NAD(P)H-dependent-oxidoreductase	gnl\|CDD\|225158	COG2249, MdaB, Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only].	7.27208e-65
NC_011958.1\|WP_041670716.1\|1254453_1255377_+\|LysR-family-transcriptional-regulator	gnl\|CDD\|176114	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	2.8961e-65
NC_011958.1\|WP_015923203.1\|1243500_1244388_+\|metal-ABC-transporter-permease	gnl\|CDD\|224033	COG1108, ZnuB, ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism].	5.87392e-46
NC_011958.1\|WP_041670709.1\|1244384_1245344_+\|zinc-ABC-transporter-substrate-binding-protein	gnl\|CDD\|223874	COG0803, LraI, ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism].	6.02971e-10
NC_011958.1\|WP_015923207.1\|1248014_1249577_-\|cobyric-acid-synthase	gnl\|CDD\|234838	PRK00784, PRK00784, cobyric acid synthase.	0
NC_011958.1\|WP_009563502.1\|1252081_1252498_-\|MerR-family-transcriptional-regulator	gnl\|CDD\|133388	cd01282, HTH_MerR-like_sg3, Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.	5.2163e-46

>NC_011958.1|WP_041670709.1|1244384_1245344_+|zinc-ABC-transporter-substrate-binding-protein
MSLTRRSALGHALLAMTALPLGARPVDAKATAAPRILTALPAAAALAQALLEGTGAEVMPVQPDRLPPSRLPSYLSGRGADALAQLAPQADAVLSLRSLWPGDPLYPQARRSNLRITEIDMATPLDGALPGIAQRDPARNDAVYRAMDLTPMGALEVEMAPWLSPAALTHMAAITAADLQRLHPDAADRIASNRDTLAARLRDLRAEAEQGLLAAPDLGCLTLTPAASYLAADLGLDLLAEIIAAPREWTPARAARLTGWLRRNAVAAVLTDKPAEGDLRTAIADAGAREILLTPIGGSDATPLPALKASIDGIIAGFA
>NC_011958.1|WP_015923203.1|1243500_1244388_+|metal-ABC-transporter-permease
MSFETFRHSVQALAEAGWLPAALAWGFAVNALLAGLIAGPLLGALGALVVIKRHAFFSEAVGHAALTGVAIGILAGEPYTGPYGALFGYCLIFGIALNYLRNRTGLSADTLIGVFLSMSLAMGAAILLVLAGRINVHILENVLFGSILTVSGRDIAVLAAVALPVAGLIVVFFNRLVGASFNPMLARARGIDAATLDYLFVIMVTLVTVAGVKIIGAVLVGALLVIPAAAARILARSLAGYVMLSVAIASVATLAGIFLPMQFDLPVPSGPAVILIAGIIFLICAALRGLKGASA
>NC_011958.1|WP_015923202.1|1242751_1243504_+|metal-ABC-transporter-ATP-binding-protein
MNAPAPISAALQGPAVRFEGVGLRYGAARILDGIDLRAEPGRIHAVVGPNGGGKSSLLRCLMGQAPFSGTIALDWPAVPGRIGYVPQVVEFDRNLPMTVTDFLICFMARRPAFLRPRAVLRDRVARLLDRVGLAGKARRRMGDLSGGERQRVLLAQALDDGHGREPDLMVLDEPMAALDAVGAQVFETILTGLRDRGATLIWVEHDLAAVRRLADGVSAIDGQLLFQGAPQAELTPDRVLALFSHRRTQP
>NC_011958.1|WP_015923201.1|1241834_1242755_+|zinc-ABC-transporter-substrate-binding-protein
MISRRLVLAAPAILWAARARAAEPLRVGVTLHPYHSWLSNILGPHGEAVPLIPEGFNPHAYEPRAEDIRRIDRLDVVVLNGIGHDDFAERMIAASSQPDMPVIEANRDVPLLAAVGGLSSRMGNNRAIGGKVVNSHTFLSVTGAIQQIQTIARALSAQRPDLAEPLRDNARAYARRLRQMRAEAMAGLADLPAASFRIATIHGAYDYLLREFGLEVTAVVEPAHGIEPSPSQLAKTIAAIRDLDVRVIFSELDFPSPYVATIERETGIRLYPLSHIIYGPYRPEKFEVEMAQNYATILRAIREQAA
>NC_011958.1|WP_041670706.1|1241283_1241838_+|hypothetical-protein
MTTRVVRPASARRESLLVGALCLAVLAASAAVIGLHRRADDIPGLPAWQIDARSDLTPGEQGVLAELTIAAGEIAWLSEGGALPDVADLAAEGLPPFAPQASDGLRGGHVWSLSGGLYLGRSGDSRVAGSFLLIPGDPPAIWLAPGAADAPADPSQDALRGAGWRQVVSRYEASVTRHDPGAAE
>NC_011958.1|WP_041670704.1|1240963_1241287_+|hypothetical-protein
MIRLHATALGLAMLCATPALAHNPIAECAAAEGRIIDCRGGFSDGSGAAGVTLDVISYDEDILIPGKLGDDWRLQFERPEGEFYILFDAGPGHVVEIDYHDIEGLEH
>NC_011958.1|WP_015923198.1|1240139_1240967_+|DUF3325-domain-containing-protein
MTAIWLNAAMLLASTGGFLALALASEKPGAALLGQKPAPARRWGLRLLGWPLLALALVEGTVGWGPSVGWVTWLGWLTVAGAGLVFAFPYWERARAAAPARERRAAAPVPLLPPLRARPLRAAVLAAVVIAPPAYLAAVALAHEQPVLRADAIAGQAGPWRFTLAEADRRVPRILLGDFPTKSYQIRFCDTCDDQIRAAYLKVNKPRSLRGAGLVFGSDRWNRSVEIQLPNSTGPDSEIWLTVEGKDGSLHHASFPIRQISPATADWLQHRRQEP
>NC_011958.1|WP_015923197.1|1239846_1240143_+|DUF3649-domain-containing-protein
MNLPSDLPARLSVASRIAAAALGGYALASAAASALALSLPGPRHEAALWGMLLSFLFYALAVIWVMHARSATRAWIGMALPTATLGLACWLLGAGGGA
>NC_011958.1|WP_015923196.1|1238207_1239863_+|PepSY-domain-containing-protein
MHSSFRQSMAWLHTWTGLVVGWVLFLVFVTGTAGYVQYEISRWMRPELPMEARGDLPSVDVLIGHALARLKANAPEAKSWQIVLPHAARQPRGWQPLSIRWEEMPPDRQDFGRTGSEVLDAVTGQALASPEPRDTWGGAGLYRMHYALHYVPYWVGYYIVGICTMLMLMAVFSGVITHKKIIADFFTFRPGKGQRSWLDAHNVISVMCLPFFTMITYSGLVFFTTWYAPAPVAAVYGTGDAAMNRYWDDRSPVHRAGYQPARAEAALLARLVTQAEADWGTGRVAELRIEHPRGEPAFVELSGIAGDRMGGLRPAHLRFDAVEGAPLPPDDREGAAARTERLLFDLHEGIFAGWVLRWLYVVSGLLGCGVIATGLVLWTVKRRQKHIKGASAGARFGLRLVEVLNAGTIIGLPFGIALFFLANRLLPLQMEGRAEWEFHALFLGWGWALLWASVRPLKRAWIDLCRLAAAACLAIPLVNALTTDRHLGASLPAGDWALAGFDLSMLGFAAFFALMAGKLRRKWAVPDEDGASAGTPVHSAGHGRVRHEPAE
>NC_011958.1|WP_015923195.1|1235624_1238135_+|TonB-dependent-siderophore-receptor
MRQSFPDSRAKTGLGMSISLALLASTALVSGNGLSRPAAAQEASTLYAVPAGPLGLAITRFGERSGLQILYPADLVRGKQSPGVSGALTAPEALSRLLAGSGLTYRYTATDTVTIVALGATGASNTGPDGSILLDTISVSGGGAATEGSGSYATGAASVARGADSLKEVPQSVTVMTDKVLEDQNLTMMSEAMAKAPGVVAATDGSGNPQFFSRGFTITNYQVDNLGTAYESTFRPDFDLSIYDRVEVLRGAEGLFSAAGEPGGTVNLARKRPTDERQSSVSLAYGSWNNRRLEADLSGPLTEDGRLRGRMIGAWQDREYFYSPADEEKQVAYGILEYDLTPDTTIHAGATYQHQNGIRWAKGLPTYTDGTQLGLDRGIALNTDWSTRETTTWDMFIGAEHRFSEDWTLQFSAMRQRFDYRYTELSVGGPVDPATGVIGDPGAFSEDAGNHSDAVDLSISGRFEAWGREHKLVAGADWRRSDGKQIRNLYETSFPDGSLTIGDFPGLDLPPATLTGATTGWPAYGAKQQGVYARLDMAVSDRAHVIVGGRYGNYTHREIAENRDEDGNVTYRDSSFRWRETGIFTPYVGVTYDLTPDWTTYASLTEIYKPQGNTYAGPPENPTQLDPITGRNFELGAKGELMEGRLNVAAALYRIERNGEAVEDTRYGDEDGTFYLPLGKVVSQGVELEASGEIAPGWQVFAGYTYNQNKNENADAPYHALTPKHMFKLWTEYTLPGDLSKWTVGSGVTVKSKHANTGTYWLMGENGWTQPDFEIRQGGYAVWDAHVNYQVDDRWSVALNVNNLLDKTYYATLGVPNGGNWYGEPRNATLTLRGRF
>NC_011958.1|WP_015923206.1|1246513_1247968_-|cobyric-acid-synthase
MRARRLMVLGTGSDVGKSLLVAGLCRAYARRGLKVAPFKAQNMSNNAAVTADGGEIGRAQALQARAAGLPPVTDMNPVLLKPDTDVTAQVVVQGRVHARLSAADYQRRKPALRPRVVESLDRLSEGRDLVLIEGAGSGAERYLRPQDISNMGLATAADLPAVLLADDSRGGVTAAVLGHHLLWTPAERARVAGVIVNKFRGDPAIFAPAAEDIRQATGWPVLGLLRWSEAARALPAEDSLALDATRAPGRGLVVAVPELPRIANADDLDPLAVEPGVDLRWVRPGHPLPAEAAVVVLPGSKSTGAALDALRAEGWDIDLRAHVRRGGRVLGICAGFQMLGRRVCDPDGIEGPPGETAGLGLLDVETVIGPAKRLSEIAATDAISGTRVSGYEMHMGVTTGAELRRPWLRLDGRAEGALSADGRIAGTYLHGIFGSGAFRAQWLHAMGGAGTAEDHAARIESMLDRLADGIEADLDLDALLDLAH
>NC_011958.1|WP_015923207.1|1248014_1249577_-|cobyric-acid-synthase
MTIRIDTCPPLPEIDVPRLDPPPPRRARALMIQGTSSDVGKSLLVAGLCRAYARRGLKVAPFKAQNMSNNAAVAADSDLPPGPDGPRFGEIGRAQALQARAAGVPPSIHMNPVLLKPQALVGSQVVLRGRALGNWPAKHYHELKPLMMPAIMDSFARVAAEADLMIVEGAGAATEVHLRRSDIANMLLAEAADLPVVLLTDNDRGGALAAVVGSWMLHSEAERARIRGYIVNKFRGDFALYAPGCEVMTAHTGWPLLGVVRWFDAATLLPAEDALALARPLRSEGAGLRVAVPQLSRVANFDDLDPLSSEPGVDLRWVRPGEPIPEGTDVVLLPGSKTTRQALEELRANGWDTDIRAHHRRGGRVVGICAGFQMLGHRVRDPDGIEGPPGETAGLGLLDVETVIGPSKQLLTLSATDLLSGARVTGYEMHMGVTTGAGLARPWLSLDGRAEGAVSADGRAMGSYVHGLFGADGFRAHWLGAMGGRASGLDHAAQVEAALDALAAHLEATLDLDALLALAR
>NC_011958.1|WP_049763998.1|1249573_1250572_-|AAA-family-ATPase
MRKDGLPSAGEAGAWRPGALPPRLRIGVPGSGSGKTTVTLGLLRAFRDTGLAVQPFKNGPDYVDPASPSAAAGRASFNLDGWAMGEDLLGALARRTAGADLLVAEGSMGLYDGTSAPGRSGRGAASEIARRFGWPVVLALDVGGQAQAAAATALGFAQHPEAPDVAGVILNNVSGARHEVMIRREMARLGLTVLGALPRRSDLVLPERHLGFVQGGEHPDLETAVARPAALLRYHDDLGAVRAAARRTLAPGAGPLPAASGLPHRPSAAPLPRHGAGARLAGHEVHYSTILEQPDPPLARATDADGNPVPETGSGRGPVTSRFFHPITAETP
>NC_011958.1|WP_161601254.1|1251185_1251476_+|DUF1289-domain-containing-protein
MQRSDGRTPRARGGQPRQPGRSLHRPLQADPESGICLGCARSREEIGLWGSASEAEGAAGRGRPLPPIRSETCALIQSRAARGTGPRKARSRAATR
>NC_011958.1|WP_009563503.1|1251548_1251689_-|DUF3768-domain-containing-protein
MTYGGERVKLHWKIDLCDPGYAFATDDAADVTKTRHLLTVLLASEY
>NC_011958.1|WP_009563502.1|1252081_1252498_-|MerR-family-transcriptional-regulator
MKIGDVSDRSGISVRMLRFYEAEGLLRPHRTGSGYRDYGPADLEQACIIRQLADAGLTVEAMRDLLPCIISPEPTFHPCERLRARLADELAKLDRRLADISRSRSQVAAYLAGLPAMDPRAVGPEGSGRDPGVAGARL
>NC_011958.1|WP_009563501.1|1252582_1253371_+|alpha/beta-fold-hydrolase
MSKIEYVHHNGARVGYRDDGAGKPLILVHGTGGDGEANFEGLLPHLSRRRLLRPDYAGSGLTEDPTEVLTLDHLVQQVIAAADHAGIDRFDLAGFSLGSAVAVRLAALHSGRVDRLVLIGGFVHASDPRSRLQFGLWADLARKDPATLARLMMLTGFSHAFLAGVADMEAVVSDMVSGGNWEGVALQAELDLRVDVSPDLRLIRAPTLVIGNRCDQMVDPAASTTLAAGIAGATLAWLEGPHLALMERPEAAAELLLRHLAD
>NC_011958.1|WP_015923210.1|1253540_1254362_-|NAD(P)H-dependent-oxidoreductase
MNVLIVHAHPEPRSLGAALRDVAIAELTAGGHAVELSDLHAMGWKAVVDRADFPALDPGARLRVPSASGQAMATATLTEDVAAEQEKLRRADLLILQFPLWWFTMPAILKGWVDRVYAHGFAYGVGEHSDRRWGDRYGEGTFAGKRAMLIVTAGGWETHYSARGINGPIEDLLFPIHHGILHYPGYDVLPPFLVYRADRLDQAGFQEVAERLRQRMRMLDSLRPIPFRRQNGGDYLISELTLRAELAAPGASGFALHLTAEDGGDPRDPDPTR
>NC_011958.1|WP_041670716.1|1254453_1255377_+|LysR-family-transcriptional-regulator
MDESEVTLDRMRTFVRVAERGSLSAVARDMRIGQSSVTRHLNELERAVGVALLSRTTRRVTLTEEGHRYYLQAVQILRLVAEASDEARRAGAASSGLVRLSCTAALGVRHIGRLIHRFQDRHPEIEVDLGLTDERIDLVREGVDLAIRLGTLGDSRLKLRPLGRSRRILVASPGYLDRRGRPQTPADLERHEGIRMFNIAGSERLTLEGPDGTTRVVPFGGRLRVDHGLAAREAYRAGRGLGPAHLWLVDDLLTDGQLERILPDHALPSIPLSLLIAPERARIARIRLMVEFLAQEVAGIPGIGRDR
>NC_011958.1|WP_015923212.1|1255665_1255890_-|ABC-transporter-substrate-binding-protein
MLEQDGRRFGVELMTCPDRPELPLIAAALPQKSAETGLPRRLSRVFISACIGWSEIHLTAGYLGLTLMLALLPA

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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

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

714052 : 780660

Burkholderia_virus(20.0%)

integrase,tRNA,transposase

attL 719765:719816|attR 752512:752563

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_012641276.1\|714052_715105_+\|tRNA	tRNA 2-selenouridine(34) synthase MnmH	NA	NA	NA	NA
WP_012641277.1\|715105_716206_+	FAD-dependent oxidoreductase	NA	NA	NA	NA
WP_012641278.1\|716293_717592_+	RNA polymerase factor sigma-54	NA	NA	NA	NA
WP_012641279.1\|717691_719719_+	hydantoinase/oxoprolinase family protein	NA	NA	NA	NA
719765:719816	attL	NA	NA	NA	NA
WP_161601256.1\|719827_720910_-\|integrase	tyrosine-type recombinase/integrase	F8TUV0	EBPR_podovirus	5.0e-104	54.4
WP_012641281.1\|720893_721094_-	hypothetical protein	NA	NA	NA	NA
WP_012641282.1\|721090_721462_-	hypothetical protein	NA	NA	NA	NA
WP_012641283.1\|721458_723270_-	ParB/RepB/Spo0J family partition protein	G8DH78	Emiliania_huxleyi_virus	5.4e-95	39.6
WP_012641284.1\|723393_723789_-	DUF2312 domain-containing protein	A0A1X9HX62	Ruegeria_phage	1.3e-22	51.5
WP_012641285.1\|723788_724121_-	hypothetical protein	NA	NA	NA	NA
WP_012641286.1\|724117_724315_-	hypothetical protein	NA	NA	NA	NA
WP_041670511.1\|724613_725021_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_041670513.1\|725019_725250_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_002719110.1\|725375_725588_+	hypothetical protein	NA	NA	NA	NA
WP_012641287.1\|725584_725863_+	hypothetical protein	NA	NA	NA	NA
WP_012641288.1\|725859_726417_+	DUF1937 family protein	H6WBR3	Rhodobacter_phage	2.7e-21	40.8
WP_012641289.1\|726457_727093_+	hypothetical protein	NA	NA	NA	NA
WP_012641290.1\|727322_727901_+	hypothetical protein	NA	NA	NA	NA
WP_012641291.1\|728106_728646_+	hypothetical protein	NA	NA	NA	NA
WP_012641292.1\|729203_729935_-	Crp/Fnr family transcriptional regulator	NA	NA	NA	NA
WP_012641293.1\|730112_730352_+	hypothetical protein	NA	NA	NA	NA
WP_012641295.1\|730896_731241_-	hypothetical protein	NA	NA	NA	NA
WP_161601252.1\|731850_732255_+	hypothetical protein	NA	NA	NA	NA
WP_041670515.1\|733017_734646_+	chaperonin GroEL	A0A240F779	uncultured_virus	2.8e-159	56.3
WP_012641298.1\|734768_734915_+	hypothetical protein	NA	NA	NA	NA
WP_011339464.1\|735288_735639_+	hypothetical protein	NA	NA	NA	NA
WP_012641300.1\|735754_744067_-	glycosyl transferase	NA	NA	NA	NA
WP_041670517.1\|744902_745175_-	hypothetical protein	NA	NA	NA	NA
WP_012641303.1\|745566_745950_-	hypothetical protein	NA	NA	NA	NA
WP_012641305.1\|746523_746730_-	cold-shock protein	A0A1W6JNX5	Morganella_phage	3.0e-10	52.4
WP_011840461.1\|747540_747747_+	cold-shock protein	A0A1W6JNX5	Morganella_phage	4.6e-11	54.0
WP_080517700.1\|747780_748131_+	DUF982 domain-containing protein	NA	NA	NA	NA
WP_080517701.1\|749483_750086_-	AAA family ATPase	A0A097BYE2	Leuconostoc_phage	1.4e-31	37.0
WP_012641311.1\|750853_751228_-	hypothetical protein	NA	NA	NA	NA
WP_012641312.1\|751977_752187_+	hypothetical protein	NA	NA	NA	NA
WP_012641313.1\|752515_754135_-	recombinase family protein	R9TP69	Rhizobium_phage	4.9e-132	48.6
752512:752563	attR	NA	NA	NA	NA
WP_012641316.1\|756364_757000_+	hypothetical protein	NA	NA	NA	NA
WP_012641317.1\|757047_757356_-	hypothetical protein	NA	NA	NA	NA
WP_009564280.1\|757554_757875_+	multidrug efflux SMR transporter	NA	NA	NA	NA
WP_009564281.1\|758230_758650_+	VOC family protein	NA	NA	NA	NA
WP_012641319.1\|758972_759845_-	EamA family transporter	NA	NA	NA	NA
WP_145975089.1\|760450_760864_+	DUF1801 domain-containing protein	NA	NA	NA	NA
WP_009564286.1\|761698_761917_+	hypothetical protein	A0A218M799	Flavobacterium_phage	3.4e-12	47.1
WP_009564290.1\|762106_762322_+	hypothetical protein	NA	NA	NA	NA
WP_009564292.1\|762312_762684_+	hypothetical protein	F8TVB7	EBPR_siphovirus	3.5e-09	53.5
WP_080517703.1\|762739_763102_+	hypothetical protein	NA	NA	NA	NA
WP_012641323.1\|763208_765332_+	TonB-dependent siderophore receptor	NA	NA	NA	NA
WP_012641324.1\|765333_766230_+	alpha/beta hydrolase	NA	NA	NA	NA
WP_012641325.1\|766428_767832_+	PepSY domain-containing protein	NA	NA	NA	NA
WP_145975090.1\|768803_769385_-	hypothetical protein	NA	NA	NA	NA
WP_085990727.1\|769650_770864_-\|transposase	IS3 family transposase	Q8W6R2	Burkholderia_virus	3.3e-104	66.5
WP_085990722.1\|770860_772089_-\|transposase	IS3 family transposase	Q8W6R2	Burkholderia_virus	5.6e-104	66.5
WP_049763994.1\|772235_772613_-\|transposase	transposase	A0A0P0ZBS5	Stx2-converting_phage	1.8e-13	43.9
WP_080517742.1\|772536_772704_-\|transposase	transposase	NA	NA	NA	NA
WP_012641334.1\|774446_775496_+	glycosyltransferase	NA	NA	NA	NA
WP_009565934.1\|775492_776239_+	polysaccharide deacetylase family protein	NA	NA	NA	NA
WP_012641335.1\|776555_777467_-	glycosyl transferase	NA	NA	NA	NA
WP_012641336.1\|777562_778477_-	lipopolysaccharide 3-alpha-galactosyltransferase	NA	NA	NA	NA
WP_085990728.1\|779432_780660_+\|transposase	IS3 family transposase	Q8W6R2	Burkholderia_virus	6.2e-103	66.5

DBSCAN-SWA_2

935400 : 961550

Acidithiobacillus_phage(20.0%)

head,transposase,portal,terminase,capsid

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_015922954.1\|935400_935553_+\|transposase	IS3 family transposase	A0A0N7BVE9	Escherichia_phage	6.0e-08	57.1
WP_015922955.1\|935553_935706_+\|transposase	IS3 family transposase	NA	NA	NA	NA
WP_080517716.1\|936081_937140_+	DNA cytosine methyltransferase	M1PSQ0	Streptococcus_phage	1.1e-23	28.6
WP_145975094.1\|937127_938342_-	hypothetical protein	NA	NA	NA	NA
WP_015922957.1\|938338_940243_-	ATP-binding protein	NA	NA	NA	NA
WP_015922958.1\|940664_941138_-	hypothetical protein	F8TVB7	EBPR_siphovirus	5.7e-12	51.2
WP_015922959.1\|941150_941960_-	M15 family metallopeptidase	A0A0B5A5A2	Paracoccus_phage	6.8e-66	51.3
WP_015922960.1\|942014_942821_-	DNA adenine methylase	A0A291AUP9	Sinorhizobium_phage	1.6e-83	57.0
WP_049764001.1\|943238_943601_-	hypothetical protein	NA	NA	NA	NA
WP_015922962.1\|943852_944170_-	hypothetical protein	I3UM16	Rhodobacter_phage	4.8e-23	58.9
WP_015922963.1\|944301_944616_-	hypothetical protein	NA	NA	NA	NA
WP_041670563.1\|944640_944958_-	hypothetical protein	NA	NA	NA	NA
WP_015922965.1\|944964_946284_-	hypothetical protein	A0A1S5R1J5	Pseudomonas_phage	9.9e-14	28.5
WP_015922966.1\|946299_947190_-	hypothetical protein	A0A2H4J8C7	uncultured_Caudovirales_phage	2.4e-27	32.8
WP_015922967.1\|947189_952364_-	hypothetical protein	F1C5E9	Cronobacter_phage	1.7e-08	25.9
WP_041670823.1\|952413_952776_-	hypothetical protein	NA	NA	NA	NA
WP_015922969.1\|952838_953279_-	hypothetical protein	NA	NA	NA	NA
WP_011339606.1\|953380_953851_-	hypothetical protein	M4QQ74	Salicola_phage	1.2e-17	38.9
WP_015922970.1\|953962_954385_-	hypothetical protein	NA	NA	NA	NA
WP_015922971.1\|954381_954708_-	hypothetical protein	NA	NA	NA	NA
WP_002723262.1\|954718_955741_-\|capsid	major capsid protein	K4I3Z3	Acidithiobacillus_phage	9.5e-105	55.7
WP_015922972.1\|955821_956211_-\|head	head decoration protein	K4ICP8	Acidithiobacillus_phage	3.2e-21	47.3
WP_015922973.1\|956351_957695_-	S49 family peptidase	A0A068CE01	Rhizobium_phage	5.1e-58	47.2
WP_041670566.1\|957691_959182_-\|portal	phage portal protein	K4I1F2	Acidithiobacillus_phage	8.5e-179	68.8
WP_002723266.1\|959181_959391_-	hypothetical protein	NA	NA	NA	NA
WP_015922975.1\|959387_961550_-\|terminase	phage terminase large subunit family protein	A0A291AUS9	Sinorhizobium_phage	2.1e-101	35.3

DBSCAN-SWA_3

974898 : 1029300

Acidithiobacillus_phage(23.33%)

integrase,head,tail,transposase,portal,terminase,capsid

attL 983728:983744|attR 1001259:1001275

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_015923003.1\|974898_975897_+\|integrase	site-specific integrase	U5P434	Shigella_phage	8.6e-10	25.9
WP_009565105.1\|976808_976976_+	hypothetical protein	NA	NA	NA	NA
WP_085990731.1\|978246_978882_+	DUF882 domain-containing protein	A0A0K1LLY2	Rhodobacter_phage	3.9e-24	46.6
WP_085990730.1\|979611_980839_+\|transposase	IS3 family transposase	Q8W6R2	Burkholderia_virus	2.5e-104	66.9
WP_015923008.1\|981399_982740_-	hypothetical protein	NA	NA	NA	NA
WP_049764002.1\|982820_984419_-	hypothetical protein	A0A0R6PHP9	Moraxella_phage	1.8e-25	37.9
983728:983744	attL	NA	NA	NA	NA
WP_041670843.1\|984433_985402_-	hypothetical protein	NA	NA	NA	NA
WP_041670587.1\|985419_985608_-	hypothetical protein	NA	NA	NA	NA
WP_015923011.1\|986108_986714_+	hypothetical protein	NA	NA	NA	NA
WP_041670596.1\|986738_988016_-\|integrase	site-specific integrase	G8C7K6	Escherichia_phage	7.1e-17	26.8
WP_041670846.1\|988673_988898_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_041670598.1\|988894_989146_+	hypothetical protein	NA	NA	NA	NA
WP_015923015.1\|989142_989538_+	nuclease	NA	NA	NA	NA
WP_015923016.1\|989534_990572_+	helix-turn-helix domain-containing protein	A0A068CE61	Rhizobium_phage	2.4e-15	43.5
WP_080517725.1\|990576_991725_+	DNA cytosine methyltransferase	A0A0C5AFC4	Paenibacillus_phage	5.4e-32	46.2
WP_015923018.1\|991737_992415_+	hypothetical protein	G8DGC1	Emiliania_huxleyi_virus	1.1e-37	41.2
WP_015923019.1\|992426_994484_-	DUF262 domain-containing protein	NA	NA	NA	NA
WP_015923020.1\|994683_995097_+	DUF2384 domain-containing protein	NA	NA	NA	NA
WP_041670851.1\|995090_995783_+	RES family NAD+ phosphorylase	NA	NA	NA	NA
WP_015923022.1\|995893_1000756_+	DEAD/DEAH box helicase	A0A2H4UTW8	Bodo_saltans_virus	6.2e-37	25.4
WP_145975105.1\|1000755_1001196_+	hypothetical protein	NA	NA	NA	NA
WP_162829288.1\|1001192_1002065_+	exonuclease	A0A0R6PHP9	Moraxella_phage	2.4e-40	40.1
1001259:1001275	attR	NA	NA	NA	NA
WP_145975097.1\|1002202_1003723_+	hypothetical protein	NA	NA	NA	NA
WP_015923029.1\|1005430_1006807_+	site-specific DNA-methyltransferase	K4I3Y2	Acidithiobacillus_phage	2.8e-128	55.2
WP_015923030.1\|1006803_1007013_+	hypothetical protein	K4I1E3	Acidithiobacillus_phage	2.4e-15	62.3
WP_080517727.1\|1007240_1007636_+	HNH endonuclease	NA	NA	NA	NA
WP_015923031.1\|1007636_1008203_-	DUF3489 domain-containing protein	K4HZZ2	Acidithiobacillus_phage	2.5e-14	38.3
WP_015923032.1\|1008297_1008567_-	hypothetical protein	NA	NA	NA	NA
WP_015923033.1\|1008669_1009032_-	hypothetical protein	NA	NA	NA	NA
WP_015923034.1\|1009028_1009334_-	hypothetical protein	A0A0K0PVG0	Roseobacter_phage	1.2e-10	41.4
WP_015923035.1\|1009344_1009563_-	hypothetical protein	NA	NA	NA	NA
WP_015923036.1\|1009575_1009788_-	hypothetical protein	NA	NA	NA	NA
WP_041670604.1\|1009790_1010009_-	hypothetical protein	NA	NA	NA	NA
WP_015923038.1\|1010149_1010698_+	hypothetical protein	A0A2H4JCL4	uncultured_Caudovirales_phage	3.0e-17	39.1
WP_041670607.1\|1010645_1012667_+\|terminase	phage terminase large subunit family protein	A0A2H4JIC6	uncultured_Caudovirales_phage	1.0e-211	58.7
WP_041670610.1\|1012678_1012888_+	hypothetical protein	K4HZB1	Acidithiobacillus_phage	9.2e-07	48.6
WP_041670854.1\|1012899_1014387_+\|portal	phage portal protein	K4I1F2	Acidithiobacillus_phage	2.2e-179	66.7
WP_015923042.1\|1014386_1015820_+	S49 family peptidase	A0A068CE01	Rhizobium_phage	8.1e-62	46.9
WP_015923043.1\|1015935_1016316_+\|head	head decoration protein	K4ICP8	Acidithiobacillus_phage	4.4e-23	54.0
WP_015923044.1\|1016400_1017423_+\|capsid	major capsid protein	K4I3Z3	Acidithiobacillus_phage	8.3e-101	54.8
WP_015923045.1\|1017434_1017746_+	hypothetical protein	NA	NA	NA	NA
WP_015923046.1\|1017742_1018375_+	hypothetical protein	G8DH49	Emiliania_huxleyi_virus	6.3e-51	51.5
WP_015923047.1\|1018371_1018791_+	hypothetical protein	G8DH50	Emiliania_huxleyi_virus	1.0e-36	56.6
WP_015923050.1\|1019765_1020203_+	hypothetical protein	NA	NA	NA	NA
WP_145975098.1\|1020196_1020439_+	hypothetical protein	NA	NA	NA	NA
WP_015923052.1\|1020435_1022898_+\|tail	phage tail tape measure protein	I6S2X0	Marinomonas_phage	2.3e-27	35.9
WP_015923053.1\|1022890_1024063_+	hypothetical protein	A0A0S0N058	Pseudomonas_phage	4.3e-37	30.5
WP_015923054.1\|1024059_1024926_+	phage BR0599 family protein	A0A0S0MV27	Pseudomonas_phage	1.1e-48	39.3
WP_015923055.1\|1024965_1025214_+	hypothetical protein	A0A0S0MV97	Pseudomonas_phage	2.0e-16	57.3
WP_015923056.1\|1025210_1025429_+	hypothetical protein	A0A2D0W9I0	Bordetella_phage	4.6e-09	50.9
WP_015923057.1\|1025415_1028547_+	VWA domain-containing protein	A0A2D0W9A4	Bordetella_phage	7.8e-166	41.1
WP_015923058.1\|1028622_1029300_+	DUF2793 domain-containing protein	A0A1V0DX32	Synechococcus_virus	5.1e-14	35.1

Anti-CRISPR protein detection

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

3. NC_011963

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Crispr_ID: NC_011963_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011963_1

314440-314553

Orphan

Consensus_repeat	Method
TGCCGCTCCGGCTCCGGCCCGTCAGGCG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_011963_1

>merge|NC_011963|1|314440-314553|CRISPRCasFinder
TGCCGCTCCGGCTCCGGCCCGTCAGGCGGTGCGATCCGTGGGGCGCCGCCGCGGCTGCGGCCGGTCATGCCTCCCGGCCCGTCAGGTGCCGCCCCGGCTCCGGCCCGTCAGGCG

>NC_011963|1|1|314440-314553|CRISPRCasFinder
TGCCGCTCCGGCTCCGGCCCGTCAGGCG	GTGCGATCCGTGGGGCGCCGCCGCGGCTGCGGCCGGTCATGCCTCCCGGCCCGTCAGG
TGCCGCCCCGGCTCCGGCCCGTCAGGCG

Protein	Signature genes	Signature genes Name	Protein_function
NC_011963.1\|WP_012643630.1\|318876_319590_-\|DUF3108-domain-containing-protein	unknown	unknown	gnl\|CDD\|378635
NC_011963.1\|WP_011337158.1\|320910_321201_+\|50S-ribosomal-protein-L28	unknown	unknown	gnl\|CDD\|234736
NC_011963.1\|WP_012643618.1\|300923_301736_-\|indole-3-glycerol-phosphate-synthase-TrpC	unknown	unknown	gnl\|CDD\|234710
NC_011963.1\|WP_002719160.1\|310892_311516_-\|GcrA-cell-cycle-regulator	unknown	unknown	gnl\|CDD\|227655
NC_011963.1\|WP_012643620.1\|303545_304979_+\|divergent-polysaccharide-deacteylase-family-protein	unknown	unknown	gnl\|CDD\|200562
NC_011963.1\|WP_012643626.1\|313396_314323_+\|ornithine-carbamoyltransferase	unknown	unknown	gnl\|CDD\|234835
NC_011963.1\|WP_012643621.1\|305142_306654_-\|anthranilate-synthase-component-I	unknown	unknown	gnl\|CDD\|184154
NC_011963.1\|WP_011337160.1\|321765_322248_+\|copper-chaperone-PCu(A)C	unknown	unknown	gnl\|CDD\|377298
NC_011963.1\|WP_009566587.1\|322806_323259_-\|STAS/SEC14-domain-containing-protein	unknown	unknown	gnl\|CDD\|378774
NC_011963.1\|WP_012643622.1\|306664_308530_-\|SurA-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|182731
NC_011963.1\|WP_012643628.1\|315450_315927_-\|NUDIX-hydrolase	unknown	unknown	gnl\|CDD\|239217
NC_011963.1\|WP_012643625.1\|312101_313283_+\|aspartate-aminotransferase-family-protein	unknown	unknown	gnl\|CDD\|179270
NC_011963.1\|WP_041669144.1\|319726_320698_+\|methylmalonyl-Co-A-mutase-associated-GTPase-MeaB	unknown	unknown	gnl\|CDD\|236515
NC_011963.1\|WP_011337161.1\|322287_322599_-\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_041669142.1\|308727_310710_+\|AsmA-family-protein	unknown	unknown	gnl\|CDD\|225529
NC_011963.1\|WP_002719170.1\|321376_321736_+\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_009566580.1\|314930_315425_-\|GreA/GreB-family-elongation-factor	unknown	unknown	gnl\|CDD\|180535
NC_011963.1\|WP_012643629.1\|316404_318831_-\|ATP-dependent-helicase-HrpB	unknown	unknown	gnl\|CDD\|273901
NC_011963.1\|WP_009566395.1\|302779_303367_-\|aminodeoxychorismate/anthranilate-synthase-component-II	unknown	unknown	gnl\|CDD\|235552
NC_011963.1\|WP_012643619.1\|301766_302783_-\|anthranilate-phosphoribosyltransferase	unknown	unknown	gnl\|CDD\|234682

Protein	Function_ID	Function_description	E-value
NC_011963.1\|WP_012643630.1\|318876_319590_-\|DUF3108-domain-containing-protein	gnl\|CDD\|378635	pfam11306, DUF3108, Protein of unknown function (DUF3108). This is a bacterial family of putative lipoproteins. Structure 3fzx, the first structural template for this large family including several homologs in the human gut microbiome and in metagenomic datasets, folds into a beta barrel that topologically looks like a small-scale porin (such as FepA). Bacteroides fragilis glyA is a putative exported protein, and this fold is of the YmcC-like type, with a predicted signal peptide SpI cleavage site AGAMA\|QNQDC, and a Phobius server prediction of non-cytoplasmic localization for amino acids 21-236. The possibility of it being a membrane protein can be ruled out by the hydrophilic nature of the solvent exposed surface outside the barrels. Analysis of sequence conservation suggests that an area near Glu172/Trp206 is potentially interesting. These two residues are also conserved in Dali hit Structure 2in5, a hypothetical lipoprotein classified as a new YmcC-like fold in SCOP (SCOP:159271, with a 12-stranded meander beta-sheet folded into a deformed beta-barrel) despite large structural differences between the two structures, suggesting similarity in function.	2.16728e-12
NC_011963.1\|WP_011337158.1\|320910_321201_+\|50S-ribosomal-protein-L28	gnl\|CDD\|234736	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed.	6.44569e-35
NC_011963.1\|WP_012643618.1\|300923_301736_-\|indole-3-glycerol-phosphate-synthase-TrpC	gnl\|CDD\|234710	PRK00278, trpC, indole-3-glycerol phosphate synthase TrpC.	3.24085e-139
NC_011963.1\|WP_002719160.1\|310892_311516_-\|GcrA-cell-cycle-regulator	gnl\|CDD\|227655	COG5352, COG5352, Uncharacterized protein conserved in bacteria [Function unknown].	3.37804e-43
NC_011963.1\|WP_012643620.1\|303545_304979_+\|divergent-polysaccharide-deacteylase-family-protein	gnl\|CDD\|200562	cd10936, CE4_DAC2, Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria. This family contains an uncharacterized protein BH1492 from Bacillus halodurans, an uncharacterized protein ATU2773 from Agrobacterium tumefaciens C58, and other bacterial hypothetical proteins. Although their functions are still unknown, structural superposition and sequence comparison suggest that BH1492 and ATU2773 might be divergently related to the 7-stranded barrel catalytic domain of polysaccharide deacetylases (DACs) from the carbohydrate esterase 4 (CE4) superfamily, which remove N-linked acetyl groups from cell wall polysaccharides. This family is designated as DAC family 2, a divergent DAC family.	1.48342e-48
NC_011963.1\|WP_012643626.1\|313396_314323_+\|ornithine-carbamoyltransferase	gnl\|CDD\|234835	PRK00779, PRK00779, ornithine carbamoyltransferase; Provisional.	0
NC_011963.1\|WP_012643621.1\|305142_306654_-\|anthranilate-synthase-component-I	gnl\|CDD\|184154	PRK13573, PRK13573, anthranilate synthase component I; Provisional.	0
NC_011963.1\|WP_011337160.1\|321765_322248_+\|copper-chaperone-PCu(A)C	gnl\|CDD\|377298	pfam04314, PCuAC, Copper chaperone PCu(A)C. PCu(A)C is a periplasmic copper chaperone. Its role may be to capture and transfer copper to two other copper chaperones, PrrC and Cox11, which in turn deliver Cu(I) to cytochrome c oxidase.	1.56575e-42
NC_011963.1\|WP_009566587.1\|322806_323259_-\|STAS/SEC14-domain-containing-protein	gnl\|CDD\|378774	pfam11964, SpoIIAA-like, SpoIIAA-like. These proteins adopt an alpha/beta SpoIIAA-like fold, similar to that found in STAT (pfam01740). They adopt open and closed conformations arising from different arrangements of their alpha-2 and alpha-3 helices. They may be membrane associated and may function as carriers of non-polar compounds.	1.06236e-17
NC_011963.1\|WP_012643622.1\|306664_308530_-\|SurA-N-terminal-domain-containing-protein	gnl\|CDD\|182731	PRK10788, PRK10788, periplasmic folding chaperone; Provisional.	6.13349e-39
NC_011963.1\|WP_012643628.1\|315450_315927_-\|NUDIX-hydrolase	gnl\|CDD\|239217	cd02883, Nudix_Hydrolase, Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.	8.86689e-21
NC_011963.1\|WP_012643625.1\|312101_313283_+\|aspartate-aminotransferase-family-protein	gnl\|CDD\|179270	PRK01278, argD, acetylornithine transaminase protein; Provisional.	0
NC_011963.1\|WP_041669144.1\|319726_320698_+\|methylmalonyl-Co-A-mutase-associated-GTPase-MeaB	gnl\|CDD\|236515	PRK09435, PRK09435, methylmalonyl Co-A mutase-associated GTPase MeaB.	4.50046e-179
NC_011963.1\|WP_041669142.1\|308727_310710_+\|AsmA-family-protein	gnl\|CDD\|225529	COG2982, AsmA, Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane].	4.5024e-30
NC_011963.1\|WP_009566580.1\|314930_315425_-\|GreA/GreB-family-elongation-factor	gnl\|CDD\|180535	PRK06342, PRK06342, transcription elongation factor GreA.	1.01423e-31
NC_011963.1\|WP_012643629.1\|316404_318831_-\|ATP-dependent-helicase-HrpB	gnl\|CDD\|273901	TIGR01970, ATP-dependent_RNA_helicase_HrpB, ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. [Unknown function, Enzymes of unknown specificity].	0
NC_011963.1\|WP_009566395.1\|302779_303367_-\|aminodeoxychorismate/anthranilate-synthase-component-II	gnl\|CDD\|235552	PRK05670, PRK05670, anthranilate synthase component II; Provisional.	5.50105e-127
NC_011963.1\|WP_012643619.1\|301766_302783_-\|anthranilate-phosphoribosyltransferase	gnl\|CDD\|234682	PRK00188, trpD, anthranilate phosphoribosyltransferase; Provisional.	1.35257e-177

>NC_011963.1|WP_012643626.1|313396_314323_+|ornithine-carbamoyltransferase
MNHFLDIHKTDTAELRQMMDSAHAMKAARKGRPKGQFDEDQPLAGRMVALIFEKPSTRTRVSFDVGVRQMGGQTMVLSGKEMQLGHGETIADTARVLSRYVDLIMIRTFEEATLLEMAEHATVPVINGLTNRTHPCQIMADVMTYEEHRGPIAGRKVVWAGDGNNVCASFLHAAGQFGFDFTFTGPPTLDPEAEFVGYAREKGRRVSIERDPAKAVAGADLVVTDTWVSMHDPQSARERRHNQLRPYQVNEALMAQAKPDALFMHCLPAHRDDEATSAVMDGPHSVIFDEAENRLHAQKAIMRWCLGL
>NC_011963.1|WP_012643625.1|312101_313283_+|aspartate-aminotransferase-family-protein
MISAVLPTYNRAPLAFVAGEGSWLTAEDGSRYLDLGAGIAVNALGHANPALVEVISAQAAKLWHVSNLYRIPEQERLAEKLVEATFADTVFFTNSGTEAAELSIKMVRKYWSEKGQPDRIEILCFEGAFHGRSTGAIAAAGSEKMTKGYGPLMPGFRQLPFGDHEALRAAISEKTAAVMLEPVQGEGGIRVLPDVCLKGLRDACDAVGALLVFDEVQCGMGRTGRLFAHEWAGIEPDIMMVAKGIGGGFPLGAVLAKEAAAAAMTAGTHGSTYGGNPLGCAVGAKVMEIVADPAFLAEVNRKAALFRQKLEGLVAAHPQVFEEVRGAGLMLGLKCRAPNADLVKAAYGQHLLTVPAADNVVRLLPALNIPDEDIAEAVARLDRAAGTLDAHAA
>NC_011963.1|WP_002719160.1|310892_311516_-|GcrA-cell-cycle-regulator
MSWTDERVETLKRMWAEGQSASQIAKELGGVTRNAVIGKVHRLGLSNRVGGNGSREEAEEEAAPAVGAAPASPPPAPPRPEPARPAEPPRAAEPRPAPERPAPAPAAPAAPVPIRKPVVAAGQPLPPQPSANEISPEALASVREVEKRARRLTLMELTERTCKWPIGDPATDDFWFCGLPSSAGKPYCEAHVGVAFQPMSARRDRRR
>NC_011963.1|WP_041669142.1|308727_310710_+|AsmA-family-protein
MRWLVRLAAVLFGLAALFLVALVLMPRERVAELAAREFEAATGRALTISGDVRPSIWPRLGVRTGPVTVANAPWTDEGPMLEARSLEIGLDTLALMSGAWRISRIALEEPVIRLERDAEGRANWDLSPPPRGTEAAAAEGQAGPAPASAQAGFPLFSLDEGLVTGGRVLWIDRAAGLRTEISGLDMRVSLPEAGGPADLTLSGQANGHGFAVEGRLAEAGTSLAGRVAPVRLSLVTGAARIGFDGEAGSAPPMAEGTIDAALGDLGDLAALFGQDRPTLPEGLGRRQIALTGGLTLAEGGTLHLRNGQVTADGNRLAVEADLIPQGERPKLEANLRAETLNLASLSAGGGGTGGGGGAGKGWSRQPIDVSALSALDLGLALSAGSVDFGRLKLGATKAILTLDRARLVADLREVAAYGGTLSGELIVNGRQGLSVGADLTLTGLQTEPFLGDLADFDRLATQGDLRLKLLASGPHEEALMQSLSGTGSVRFGKGELRGLDIARMVRTLDAGSVGQGTRTIFDRMGASFTLEKGVLRNEDLTLEAPLMRATGKGQVGIGARTLDYRLLPTLLPQADGTGGVSVPLLVSGPWASPRYRLDLDALVRQPVGQKVKERLEEEAAERLGVVPEEGESLEEAAKRRAREAVQGEAGRALNRLFGGN
>NC_011963.1|WP_012643622.1|306664_308530_-|SurA-N-terminal-domain-containing-protein
MSKLTSIEHHKPKKKGTQLVFWGLVGLMAVGLGGFGVTNFGGGLSTVGSVGDRDITTGAYARALQQEMRALGAQINQPVTMEMAKAFGLDQQVRRRLVTEAALSNEADRIGLSVGDARVAREITGTDAFHGPSGQFDRETYRLVLRQNNLSEGEFETGLREDMARSLLQGAVGGGFIAPAQMVDALHAYIAERRSFGLLRVTEANLAKPLAAPTDAELQAWYEAHPADFTAPETKRITYAALLPQDVAATLPTDEAALRRLYDERHAEFVQPERRLVERLVFPTAEAAAEARKRLDAGTPFETLVSERGLELADIDLGDASRDALGGAADAVFALTEPGIAGPVETDLGPALFRVNGVIAAHETSFEEVRDDLLTEYQQEAAGRAIAGRREQIDDLLAAGATLEDLAGEAGMKIATVDYAPGLDSDISGYEAFRTAADKLQKDDFPETILLNDGGLLAMRLDEVVAPKLKPFEEVRDDVAEAAHKDALTKALAARATEIAKAAEEGTDLGSFGPVEDLGPMTRDGFVEGVPETLVPAAFEMQQGAFRAIEGADFAGVLRLDAVEPAAADDEAAKALKASLSAQIEQALSQDALALFSSSLMQEAGITLNDAAISAVQAQFQ
>NC_011963.1|WP_012643621.1|305142_306654_-|anthranilate-synthase-component-I
MSLVTSFESFERGWKAGQNQIVYARLTADLDTPVSLMLKLAEARTDTFMLESVTGGEIRGRYSVVGMKPDLIWQCHGQDSRINREARFDRQAFQSLEGHPLETLRALIAESRIEMPADLPPIAAGLFGYLGYDMIRLVEHLPGINPDPLGLPDAVLMRPSVVAVLDGVKGEVTVVAPAWVSSGLSARAAYAQAAERVMDALRDLDRAPPVQRDFGEVAQVGEMRSNFTHEGYKAAVEKAKDYIRAGDIFQVVPSQRWAQDFRLPPFALYRSLRKTNPSPFMFFFNFGGFQVVGASPEILVRLRDREVTVRPIAGTRKRGATPEEDRALEADLLSDKKELAEHLMLLDLGRNDVGRVARIGTVRPTEKFIIERYSHVMHIVSNVVGEIAEGEDALSALLAGLPAGTVSGAPKVRAMEIIDELEPEKRGVYGGGVGYFAANGEMDFCIALRTAVLKEETLYIQSGGGVVYDSDPEAEYQETVNKARALRRAAEDAGLFARRAGNG
>NC_011963.1|WP_012643620.1|303545_304979_+|divergent-polysaccharide-deacteylase-family-protein
MSRGFLSGVVMGGIVGGIGLALASQMAPPPGTTWPEAQADEALAGTAPDEASRPQVAAEGARKSDTADPDASPAESVSAGARAAQTPGAATDLAPPPGSEFARPLPDAVPVVPSADRAPDRTDVSVVAAPEVPDGGAPDTETAARPQPLPLVPAAPVAPTAEAAAPAVPGLTAATPARSEGAARPGAPAAEADPSAADLPPPPPLTPEEEAMLAEAAGQPAPAEPRRIEPDPPRAPSEASRLPRIGDPAPAAEEEEPPLRRYAQPFENPGRKPLFSILLQDTGGPLLDREALAALPFPVTFVIDPQAPDAATAAGIYRAAGHEVLMLASGLPEGARPADAEVTLESAAAALPEAVGLIDLPAGGFQEARPLSTQVVEILAAQGRGLVTHDHGLNAADQVARREGLPAAVVFRRLDEGEADAASVRRALDRAAFKAAQDGRAMVLGDTRPETLKGLMEWSLEGRADGVALAPATALLR
>NC_011963.1|WP_009566395.1|302779_303367_-|aminodeoxychorismate/anthranilate-synthase-component-II
MLLLIDNYDSFTYNLVHYLGELGAEVVVRRNDALDVQAAMGMHPDAIVLSPGPCDPAAAGICLPLTAAAAEARIPLLGVCLGHQTIGQAFGGKVVRCHEIVHGKMGAMHHEGKGVFAGLPSPFLATRYHSLVVERDSLPDCLEVTAWLEDGTIMGLRHKSLPIEGVQFHPESIASEHGHQMLRTFLDSARAAVTA
>NC_011963.1|WP_012643619.1|301766_302783_-|anthranilate-phosphoribosyltransferase
MSDRLKPLIGTAATRPLSREEAEFAFECLFEGEATPAQMGGLLMALRTRGETVDEYAAAASVMRAKCHKVRAPHGAIDIVGTGGDGKGTLNISTATAFVVAGAGVPVAKHGNRNLSSKSGAADALTEMGLNVMIGPEQVEACLLEAGIGFMMAPMHHPAMRHVGPVRAELGTRTIFNILGPLTNPAGVKRQLTGAFSPDLIRPMAEVLSALGSEKAWLVHGGDGTDELAISAASKVAALEGGQIREFELHPEEAGLPVHPFEEIVGGTPAENAQAFHALLDGAPGAYRDAVLLNAAAALVVADRAADLREGVEIATDSILSGAAKAKVALLARLTNAA
>NC_011963.1|WP_012643618.1|300923_301736_-|indole-3-glycerol-phosphate-synthase-TrpC
MSTILDRIKAYKLEEIAARKAERPLVAVEDAARAAPAPRGFARALSTAAATGYGLIAEIKKASPSKGLIREDFDVPALARAYEAGGATCLSVLTDGPSFQGADDFLRQAREAVKLPCLRKDFLYDTYQVAEARALGADCILIIMASVTDSQALELEAAASHWGMDVLVEVHSRDELARAEHLKSRLIGINNRNLDTFEVSLDVTRDLARRVPEDRLIVSESGLYTPEDLADLARYGARCFLIGESLMRQADVEAATRAILADPLTSQGGV
>NC_011963.1|WP_009566580.1|314930_315425_-|GreA/GreB-family-elongation-factor
MSRAFVKEDGPDNTPLPDLPISPHPNLVTPRGLADLQARLLATQARLRALRAREDRLDRLPEAAAERDIRYLEARIASAILVDPAAQPLDEVAFGLAVTVEDEAGRRTVWEITGEDEAQATARRIAPQAPLARALMGARLGEKVVWTRPAGEVTLTVTGIAHPE
>NC_011963.1|WP_012643628.1|315450_315927_-|NUDIX-hydrolase
MDKARGACEGRDMRSPRLAVRALILHENRLLLVNAWPGGVSDLWCAPGGGVEPGASLPDNLVREVAEETGLTVAVDDPCLVNEFHDPGTGFHQVDVYFRCRILAGSLSAEWRDPAGIVTDRRFFAQAELARIRHKPDSLAGAAWGGGLLYDPLEVIVR
>NC_011963.1|WP_012643629.1|316404_318831_-|ATP-dependent-helicase-HrpB
MTETLPIDAALPGLIAALRAQRMAVLQAPPGAGKTTRVPLAILKAGLTAGRIVMLEPRRLAARAAAERMAATLGEPVGRTVGYRIRGEARVSRETRIEVVTEGILTRTLQDDPELTGIGALLFDEFHERSLNADLGLALALEVRGALREDLLLLVMSATLDAGPVAALMGGAPVVTSEGRAFPVETRWLSRPLPGGARLEPEVAALVRQAVAETEGDLLVFLPGEGEIRRVEGLLGGLGCEVAPLFGALDLAAQRRALEEGPGRRIVLATSIAETSLTIPGVRVVVDAGRARRARFDPSSGMSRLVTERVTRAEADQRRGRAGRVAEGICYRMWTRGEEGALAAFPPAEIEAADLTALALELAVWGSADLPFLTPPHPGVLAEARGLLEGLGALEDGRVTAHGQALARLPLHPRLGHMLTVAGPSAAPLAALMSDRDPVRGPPDLALRLAALADPKRFSDEHPHEVNRAALARIREEARRLARAVTTPEAGLSVGQMAALAYPDRVGLRRKGEAPRWVLSGGKGAAMEPGQPLAGVRLIVATDLDGDAREAKVRQAAPIPESDLRALFAPQIRWRDVCHWSRREGRVVARRQECFGALVLDDRTWPEVPPEALALAAVEGLRQIGLPWSASARRLRARVELLRAEGAPMPDMSDAALLEDPDWLLPFLGGRRTEAELRALDLTEALRARLGWEGMQLLDRLAPPQFETPLGRRVPIDYEGEAPGIEIRLQELFGVTEHPTVGPKRLPLRITLLSPGQRPVQVTMDLPGFWASSYADVRRDMRGRYPRHPWPEDPTVAEPTLRAKPRGT
>NC_011963.1|WP_012643630.1|318876_319590_-|DUF3108-domain-containing-protein
MRIGFGIAALMLLLAGPAAAQSDEAVFDLVLRGVRAGTLSFAGSEQDGRYAVNGRLQSGGLVSLLRTVRYDARASGRIVRGTPQASAYSEKADTGRRQSEVQLAWRNGRPVVERYEPARKPRSYDVDPAAQRGTVDPLTALYAALRDVDPGQECRTSLEIFDGRRRTQLVLGAPQAAEGGVACAGEFRRIAGYSEEDMAEKSRFPFTLRYEPTAEGRMRVVQVATDTIYGRATLRRR
>NC_011963.1|WP_041669144.1|319726_320698_+|methylmalonyl-Co-A-mutase-associated-GTPase-MeaB
MDLTDLASRLASGDRRALARAITLVESRRADHREAALALLADLARSGREALRIGLSGTPGVGKSTFIESFGLRLTGQGLKVAVLAVDPSSARSGGSILGDKTRMERLSRDPQAFIRPSPSQTHLGGVARRTREAVALCEAAGFDVILIETVGVGQSETVVAQLCDLFLLLLAPAGGDELQGVKRGIMEMADLILVNKADGDLKPAALRTVADYAGALRLLRRRPQDPEGFPKAMPVSALEEQGLADAWTEMQALVAWRRETGHFARRRAEQARHWFEEEVREGLLAVLTRPGPARERMARLGAAVTRGEITPEAAAAELLTTL
>NC_011963.1|WP_011337158.1|320910_321201_+|50S-ribosomal-protein-L28
MSRVCELSGKAPMTGNTVSHANNKSRRRFLPNLNDVTLISDVLGQSFKLRISAAALRTVDHRGGLDAFLAKAKDDELSVKARAIKKEIEKAQATAA
>NC_011963.1|WP_002719170.1|321376_321736_+|hypothetical-protein
MIGAMMRSLLACLLSLCLAAASLTVAEARGRAAGAQQVVICTGYGVTAVALDAQGRPVGPLHPCPDCLGGLTLLALPQAPALPALSLGRGEALAVPPPIRATAAASPVPCARDPPVSSA
>NC_011963.1|WP_011337160.1|321765_322248_+|copper-chaperone-PCu(A)C
MTPFQAILAAAAVTFALPAFADSELAVTDAYARVASPAAQSGAIFMVIENHGASDDRLVSAATDAAARVELHTHLAGQDGVMQMVEVKEGFPVPAHGSHALARGGDHVMLMGLTKPLKEGDEIALTLTFESGKVLEVAAPVDTSREAPMGDHMKGMTHGN
>NC_011963.1|WP_011337161.1|322287_322599_-|hypothetical-protein
MKKPALAAAAFAALVLPTIASAGGPIERACLRSDRQAANVATCNCIQQVADMTLPSGDQRRAAKFFANPDEAQDVRFSSRSSDTAFWKRYKSFGEAAQAYCGG
>NC_011963.1|WP_009566587.1|322806_323259_-|STAS/SEC14-domain-containing-protein
MRARTVLLGLGLLGLGAVALGAQSRGRPGWLRRLPSPAPHILAFELGGHVGRPEIRRMAETVLAAFDRFESVDMLVVLPEFTGLTPAAALDLKGLKAGFRSLGKVRRYAVVEPPKIAALMIETSDWFMPVQARTFPLTQRDAAEAWVARR

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Crispr_ID: NC_011963_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011963_2

1384998-1385140

Orphan

Consensus_repeat	Method
TCAGGCTCCGGCCCTGCCGTAGGCGTGGCGGAGGCGTTGGGTGCG	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_011963_2

>merge|NC_011963|2|1384998-1385140|CRISPRCasFinder
TCAGGCTCCGGCCCTGCCGTAGGCGTGGCGGAGGCGTTGGGTGCGATGCGCCGCGGGATCTTCCCCCGGCGCCCTCATGCCCTGCGCCGGTGTCCAGCTCAGGCTCCGGCCCTGCCGTAGGCGTGGCGGAGCCGTTGGGTGCG

>NC_011963|2|2|1384998-1385140|CRISPRCasFinder
TCAGGCTCCGGCCCTGCCGTAGGCGTGGCGGAGGCGTTGGGTGCG	ATGCGCCGCGGGATCTTCCCCCGGCGCCCTCATGCCCTGCGCCGGTGTCCAGC
TCAGGCTCCGGCCCTGCCGTAGGCGTGGCGGAGCCGTTGGGTGCG

Protein	Signature genes	Signature genes Name	Protein_function
NC_011963.1\|WP_015920676.1\|1380432_1381515_+\|flagellar-assembly-protein-T-N-terminal-domain-containing-protein	unknown	unknown	gnl\|CDD\|379857
NC_011963.1\|WP_015920684.1\|1386792_1390080_-\|Hpt-domain-containing-protein	unknown	unknown	gnl\|CDD\|223716
NC_011963.1\|WP_049763958.1\|1392407_1393133_-\|ParA-family-protein	unknown	unknown	gnl\|CDD\|224113
NC_011963.1\|WP_002720194.1\|1393136_1393646_-\|purine-binding-chemotaxis-protein-CheW	unknown	unknown	gnl\|CDD\|223905
NC_011963.1\|WP_002720181.1\|1382216_1382516_+\|flagellar-biosynthesis-anti-sigma-factor-FlgM	unknown	unknown	gnl\|CDD\|274802
NC_011963.1\|WP_002720184.1\|1383562_1383958_-\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_015920688.1\|1393664_1394765_-\|chemotaxis-specific-protein-glutamate-methyltransferase-CheB	unknown	unknown	gnl\|CDD\|234828
NC_011963.1\|WP_009563998.1\|1377600_1379715_-\|flagellar-biosynthesis-protein-FlhA	unknown	unknown	gnl\|CDD\|235672
NC_011963.1\|WP_015920685.1\|1390707_1392411_-\|methyl-accepting-chemotaxis-protein	unknown	unknown	gnl\|CDD\|214599
NC_011963.1\|WP_080517592.1\|1381511_1382180_+\|flagellar-basal-body-P-ring-formation-protein-FlgA	unknown	unknown	gnl\|CDD\|379039
NC_011963.1\|WP_015920690.1\|1395570_1396770_-\|chemotaxis-protein-CheW	unknown	unknown	gnl\|CDD\|223716
NC_011963.1\|WP_015920679.1\|1384124_1384610_+\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_041669482.1\|1384663_1384852_+\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_002720182.1\|1382544_1382916_+\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_015920689.1\|1394764_1395574_-\|protein-glutamate-O-methyltransferase-CheR	unknown	unknown	gnl\|CDD\|224271
NC_011963.1\|WP_002720183.1\|1382933_1383566_-\|sel1-repeat-family-protein	unknown	unknown	gnl\|CDD\|276807
NC_011963.1\|WP_002720178.1\|1379902_1380436_+\|flagellar-assembly-lipoprotein-FlgP	unknown	unknown	gnl\|CDD\|225563
NC_011963.1\|WP_080517593.1\|1386073_1386655_-\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_002720191.1\|1390104_1390509_-\|response-regulator	unknown	unknown	gnl\|CDD\|381096
NC_011963.1\|WP_015920682.1\|1385409_1385790_-\|flagellar-protein-FliS	unknown	unknown	gnl\|CDD\|294015

Protein	Function_ID	Function_description	E-value
NC_011963.1\|WP_015920676.1\|1380432_1381515_+\|flagellar-assembly-protein-T-N-terminal-domain-containing-protein	gnl\|CDD\|379857	pfam16548, FlgT_N, Flagellar assembly protein T, N-terminal domain. FlgT_N is the N-terminal domain of a family of flagellar proteins that make up part of the basal body of the flagellum. The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilize both ring structures. FlgT-N contributes to the construction of the H-ring structure, and adopts a two-layer alpha-beta sandwich architecture composed of a four-stranded anti-parallel beta-sheet and two alpha helices.	3.22699e-07
NC_011963.1\|WP_015920684.1\|1386792_1390080_-\|Hpt-domain-containing-protein	gnl\|CDD\|223716	COG0643, CheA, Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms].	5.68049e-19
NC_011963.1\|WP_049763958.1\|1392407_1393133_-\|ParA-family-protein	gnl\|CDD\|224113	COG1192, Soj, ATPases involved in chromosome partitioning [Cell division and chromosome partitioning].	7.78037e-46
NC_011963.1\|WP_002720194.1\|1393136_1393646_-\|purine-binding-chemotaxis-protein-CheW	gnl\|CDD\|223905	COG0835, CheW, Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms].	8.80075e-39
NC_011963.1\|WP_002720181.1\|1382216_1382516_+\|flagellar-biosynthesis-anti-sigma-factor-FlgM	gnl\|CDD\|274802	TIGR03824, FlgM_jcvi, flagellar biosynthesis anti-sigma factor FlgM. FlgM interacts with and inhibits the alternative sigma factor sigma(28) FliA. The C-terminus of FlgM contains the sigma(28)-binding domain.	4.90166e-16
NC_011963.1\|WP_015920685.1\|1390707_1392411_-\|methyl-accepting-chemotaxis-protein	gnl\|CDD\|214599	smart00283, MA, Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). Thought to undergo reversible methylation in response to attractants or repellants during bacterial chemotaxis.	3.75045e-50
NC_011963.1\|WP_015920688.1\|1393664_1394765_-\|chemotaxis-specific-protein-glutamate-methyltransferase-CheB	gnl\|CDD\|234828	PRK00742, PRK00742, chemotaxis-specific protein-glutamate methyltransferase CheB.	1.28042e-130
NC_011963.1\|WP_009563998.1\|1377600_1379715_-\|flagellar-biosynthesis-protein-FlhA	gnl\|CDD\|235672	PRK06012, flhA, flagellar type III secretion system protein FlhA.	0
NC_011963.1\|WP_080517592.1\|1381511_1382180_+\|flagellar-basal-body-P-ring-formation-protein-FlgA	gnl\|CDD\|379039	pfam13144, ChapFlgA, Chaperone for flagella basal body P-ring formation. ChapFlgA is a family similar to the SAF family, and includes chaperones for flagellar basal-body proteins and pilus-assembly proteins, FlgA, RcpB and CpaB. ChapFlgA is necessary for the formation of the P-ring of the flagellum, FlgI, which sits in the peptidoglycan layer of the outer membrane of the bacterium. FlgA plays an auxiliary role in P-ring assembly.	6.95584e-27
NC_011963.1\|WP_015920690.1\|1395570_1396770_-\|chemotaxis-protein-CheW	gnl\|CDD\|223716	COG0643, CheA, Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms].	1.8608e-124
NC_011963.1\|WP_002720183.1\|1382933_1383566_-\|sel1-repeat-family-protein	gnl\|CDD\|276807	sd00010, SLR, Sel1-like repeat. Sel1-like repeats (SLRs) share similar alpha-helical conformations with Tetratricopeptide repeats (TPRs), but with different consensus sequence lengths and superhelical topologies. SLRs contain 36 to 44 amino acids and are present in bacteria and eukaryotes but not in archaea. SLR proteins are involved in a variety of functions, and many serve as adaptor proteins for the assembly of macromolecular complexes. The SLR family was named after the Caenorhabditis elegans Sel1 protein which is predicted to fold into 11 SLRs, a transmembrane domain, and an N-terminal signal sequence. The human Sel1L protein contains an additional fibronectin type-II domain and an N-terminal PEST sequence. Its downregulation is associated with the development of breast and pancreatic carcinomas.	6.76849e-09
NC_011963.1\|WP_015920689.1\|1394764_1395574_-\|protein-glutamate-O-methyltransferase-CheR	gnl\|CDD\|224271	COG1352, CheR, Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms].	2.82349e-68
NC_011963.1\|WP_002720178.1\|1379902_1380436_+\|flagellar-assembly-lipoprotein-FlgP	gnl\|CDD\|225563	COG3018, COG3018, Uncharacterized protein conserved in bacteria [Function unknown].	2.2168e-11
NC_011963.1\|WP_002720191.1\|1390104_1390509_-\|response-regulator	gnl\|CDD\|381096	cd17541, REC_CheB-like, phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate methylesterase CheB and similar chemotaxis proteins. Methylesterase CheB is a chemotaxis response regulator with an N-terminal REC domain and a C-terminal methylesterase domain. Chemotaxis is a behavior known in motile bacteria that directs their movement in response to chemical gradients. CheB is a phosphorylation-activated response regulator involved in the reversible modification of bacterial chemotaxis receptors. It catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins) by CheR. The CheB REC domain packs against the active site of the C-terminal domain and inhibits methylesterase activity by directly restricting access to the active site. Also included in this family is chemotaxis response regulator CheY, which contains a stand-alone REC domain, and an uncharacterized subfamily composed of proteins containing an N-terminal REC domain and a C-terminal CheY-P phosphatase (CheC) domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.	7.54953e-41
NC_011963.1\|WP_015920682.1\|1385409_1385790_-\|flagellar-protein-FliS	gnl\|CDD\|294015	cd16098, FliS, flagellar export chaperone FliS. This family contains flagellar export chaperone FliS, a protein critical for flagellar assembly and bacterial colonization. FliS prevents premature polymerization of flagellins, the major protein of the filament, by regulating interactions between structural components of the bacterial flagellum in the cytosol. It binds specifically to FliC (flagellin) which is sequentially secreted in large numbers through the central channel of the flagellum and polymerized to form the tail filament. FliS protects FliC from degradation and aggregation by binding to the FliC C-terminal helical domain, which contributes to stabilization of flagellin subunit interactions during polymerization. FliS has been shown to interact specifically with FlgM, whose role is to inhibit FliA, a flagellum-specific RNA polymerase responsible for flagellin transcription; FliA competes with FliS for FlgM binding.	4.3025e-19

>NC_011963.1|WP_041669482.1|1384663_1384852_+|hypothetical-protein
MPIELQQSAPAFRRPPPVPEAVGAPLDGLMVETVHFDEDGREARRTRRPLHILLAPLRRRSA
>NC_011963.1|WP_015920679.1|1384124_1384610_+|hypothetical-protein
MTSRASSRLLFSLGLALPLGLFGAGLARLLDRPPVSLLPPAPVEEAGPRRPEGPLTYLPLPAPIHATIRGGRRQLTIQASFAVETGQIDLAEMASMLKTDLPLLTVELAEALRACDEAQPSLDAFRRALPEALRAAANARYATPEVPEPVFEALLTDFLVH
>NC_011963.1|WP_002720184.1|1383562_1383958_-|hypothetical-protein
MRLNLPQVLAPLARRLPAGPRPVREGDDADAFDLVRTETRLKNRAQVERYLPDILGRALARIWIDPIFRDRFAADPVATLAAYDVFLPETITIAFEIEGHARPRLVVYEQKGPLRPKQRMLYLQLVMKAGK
>NC_011963.1|WP_002720183.1|1382933_1383566_-|sel1-repeat-family-protein
MRGAALLCLALSVGAATASETGADPFDAAIAAFRAGDAGRAAVLFKTLAEAGEAEAQFNLALLYAEGAGLPQNPREALYWAWRAQIAGIPRAEALSQRLTAALPDEARADLAERLERVLAPGIAAGDARAMFGLARVLLQLRPEPDAKRAYEWLAIAAALGLPEAQGARDAALAEVPEPDRFAVQDGALAAFAEWCRAASHPAVACAAAG
>NC_011963.1|WP_002720182.1|1382544_1382916_+|hypothetical-protein
MSPLLVLSLALPAAAAGALAYVLMRRHRAGAPAAPPALEEQLAALEQRISDRLHDMDWRHASVLDRISATTDSLQSDIDWLTGERMIEQAIQLARKGAEPEAIAGEVGLELEEARAIARLRRH
>NC_011963.1|WP_002720181.1|1382216_1382516_+|flagellar-biosynthesis-anti-sigma-factor-FlgM
MVESVVPTPGPSRLERLKDTQTRVDRSLAGAATGSARASGETVELSAAALATPEELRSGPPVDLELVQKIKDAIAEGKYPVDLERITDALFADYLDLKL
>NC_011963.1|WP_080517592.1|1381511_1382180_+|flagellar-basal-body-P-ring-formation-protein-FlgA
MSVRLLPLLLLLAAPAAAQGLSGAETAALVAAAMARAGVPGAPPVPVRALPPCSHTPHVEALNGSWSTAELRCDAPAWKRALRTSAPASPAPRAPDAADATFAGVALIRPLARGSVIAAEDLASGPLSTRWHADLIGRRLKVALAPGQPVLPRHLEPDWLVTRGGPVALRVAAGPIEVLAPAEALEDGALGDLVEVRNLSSGAILRATVTARNLAEVRPNMR
>NC_011963.1|WP_015920676.1|1380432_1381515_+|flagellar-assembly-protein-T-N-terminal-domain-containing-protein
MKRLLLLLTLLLAPLAASADSPAVRVEAEGFAMVAGPGDRDAARRRAVSDALLAAALAAGADVSGHTAVNRGIVTSDVAIVRSVGRILRHRILSETLSGATWRVRIEALVGEGPGLLCPVRTLIVTAYPATLAVDPHAPAWSGELARTIAERLVERLALHPAASLSRVAERRPTRLGRGGEAFDYQSLTQGSVRLPANGHGFLPTIRLRRVAGPRLELALELKLVAADGTASVQQFVRRVPLPRPSLLGDLSVLVQPQREALASALLDGSDRALDALFDRAGCEPASARLVAAGGLLEVPVGQANGLTPGSLAFTADGGSTEILEIVALRSGSARLRPLDPTRPPAAFAGRRVQFVETGR
>NC_011963.1|WP_002720178.1|1379902_1380436_+|flagellar-assembly-lipoprotein-FlgP
MPVRPPSVRLAGLVLPMLAACAPGPRAVDALPADAGPRVAELARMKDANDRLDGRSAGRSAGLIAVTPKPLVTGIGFAAVAGQPGHTLNERRLMAIRAAKIEAMRDLAEQVHGLRLDARTTVRDAVAVDDQIAGAVAGTIRGARLVRVTPKGSDSYEVELALDADAVGYIVKAARLR
>NC_011963.1|WP_009563998.1|1377600_1379715_-|flagellar-biosynthesis-protein-FlhA
MSAVAARDGWGARLGGMTLPLGILAVVAMMVLPLPVALLDLFFVGNILLSLVILMVALHTFRPLDFSSFPSILLVATVLRLALNVASTRIVLSHGHTGHDAAGKVIEAFGSFVIGGNFVVGAFVFAILVIINLVVITKGAGRVSEVSARFTLDAMPGKQMAIDADLNAGLLNPDEARERRADVAAEADFYGAMDGASKFVKGDAMAGILILIINIVGGIIIGTLQHGLGVMQAAETYVLLSIGDGLVAQIPSLLLSIATAIIVTRVSSTTDMSVLIGKQMGIGRAWVPVAAVMLILGLTPGMPNLLFLLGGAAAAAMAWVAFAREGAGAKGTAAAGGAQPAVEAGAAPGPEAITTEDVTDYAPISLQIGYGLIPLAGDNGGALVARITAIRRDVSKALGFVVPGVRIRDDLGLAPNQYRIRVGQAILAEDTVYPDRKLALPGGASRRKLNGIAVRDPSFGLEASWILPHQVAEAEADDHVVVEPESVIATHLSQILVKHAAQLIGQDDVQGLVDALGRTAPTLVQSVVPKLVPLHVLTAVLKALLADRIPVSDMRRILEGLSDLAGRNLQPVEMAEALRPALVPLLLQQMGPISQPLPLITLEPDLEQLLLRSRRQGDEMLLVDNGLAQSLLTALSERLETASGQGKQAAVIVAQPLRRAFAAFVRPHLPDAVVIGMGELPEARRVEVLGTVGGAPALPPGAAR
>NC_011963.1|WP_015920682.1|1385409_1385790_-|flagellar-protein-FliS
MTFADARARYRRTETVDFQAVEDPHQIVLVTLRELERSLRALAAAAEAGGSYPDQHLNRAFTAIYILQSSLDFEKGGEIADNLFGVYEFCRLQVASAFRREHGQLTDAAGHIGAILEAWEQIGPRP
>NC_011963.1|WP_080517593.1|1386073_1386655_-|hypothetical-protein
MSRAVARPSAASLAVPGLRVLGEAADSLRQALPAPSARVLAGLRLGTIGDAASDALGGALRAMGASVASVALDGHRMPADRRPDAVVICWPGAAGTAAAEWEQVALMKLDNPRLIVVLLDGGRGLLEAPDHDLRIPRGSPGSEIRAALAELRRLRREQRLAASARSDVGAPVCSLFRRPAPSAQGASLFAHAA
>NC_011963.1|WP_015920684.1|1386792_1390080_-|Hpt-domain-containing-protein
MSDAFDEMDEIWALYADDGAQALDAMEASLLALQAGEDAAAHVGPLFRAVHTFKGNSRVLGLSVVESRAHLCEDLIGLVRDAGVPMDGEIVEILLFASDTLRAMLEETAASRADVEGTGSEALMDQLRSKIARCSGAGAATAEADAAPVEVDAATAEERAAATEAGAAPTETGAAATSAAEPSAAWEGSPETGVPAAAAEALPVAGKAFPSVADILDLLDDSALPDTGEAAEVPLEAGGGPAGEGHAPAGPPAEAGPAEAPVPPAAEPARPAARLADDPAYRAIFRDMATAALTRFRAQIDAFATDPGAAAQGARAEADGLCHAARQMGLEDWEAALAAFLSDSQGPERLAALVLELEALGDEPAPTPQVEAKPFFAAIAGPLAEVGRLGLRLATGERPGPAERAAAADPLGQAALAQGYVRVAEAAQALAAAEGAEPFGTARLRLYEELAAVEALMPEAAAAAGVSPVGLLRRLCAAEAAETLAALDATLNAFRSGPLAETFGRFERLMRCVHHACAHHALDAAAQLAMSLVDLFGRAEAKGAVPDAMLVHIARGFIETIELAFEALAQGETPAMEVLDRLFEEAANVCFVSDGLMTAGAIERRLGLPADFHRVLSPESVRAAVEEMEKGQQFYIVRTDINSDDRTAESFLDWLSGDQARSITNVTVFRGTETLFDFLISSRLGEADLIEALVRMDPSGRRLSLTQALRPRQDEPAPVEAPGEAPLAQGAAITPEMLETIGEISASQAMVQHLLTELAEADLAEATEALVRQAAGDWTAARGPVRALLEAHGARLQEIVQAGTQLTAQLAALQEETVTQRARPASTVLRPLRTFAETLARRRRREVCLTTSGDELALDLALLERLRGFLRGLVALRLDQDRGAPGTLHVSLWRDEERVTVLVQDDGAPESDSPALADLAAEVGQAGGALRSVPLPGGGMRFHLGLPLSMVVLEGMVVGVDGMRYVLPVESIRTILQADAAAAMTISAAGGQRVLRLSETEIVAIHSLRGHPQEGHRERPWPVSRRVYVVLGTGPRSVAIPVDELVGQQLVLLRPLRGVLARLTHLTGLALLAGGDVGMVLSANRICPPLPAEAG
>NC_011963.1|WP_002720191.1|1390104_1390509_-|response-regulator
MPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQPNVDLILLDIEMPVMDGMEFLRHAKLKTRAKICMLSSVAVSGSPHAARARELGADGVVAKPSGTVSHDLEEKTGGELARTMRTLMAA
>NC_011963.1|WP_015920685.1|1390707_1392411_-|methyl-accepting-chemotaxis-protein
MTRRPKTTAPTPAAAPRLTNDPLDWLAAPETEAEAEAPRPAVALEPAAPRKPRGARAAAPAAKAPKAARKRVAAKAVPAAAVRISADPAPAPAPAEAPAAPHGNEGEAARAVARLLAEVRIVSAAHAAGDLDRRIEASAYPGDLGEVAQALNGMVEGQVRSLEEAVGCFEAIGEGNFDAGIRQWPGRMAMVNRVIDRFRANMKAVTAEVAMLSDSIVDGRLDREVDLSKFSGEFVEIVRSFERTYASLNGVFRSLSVQLEQTAQTVSQVSQASQSLASNSAVQSSSVDEVSASAEETDSQVKANAAAARSASLLVEGAATVAAEGREKVTEMVQAMEGIRISSQGIAKIIKVIDEIAFQTNLLALNAAVEAARAGQHGRGFAVVAHEVRNLAGRSAKAARETSELIEDAGTRVQAGVRIATETSRSFVSIVDDIEKVKALVQDISRASDEQTRNVAQISTAIGEVAKSALSTSQQADELASSATQMQAAAEAMRTEIGRFKLREAHEGALTLPALDALPPEMLAQLQQMVAAQMGLPAARPIAAPAGAFRPAGAPCADRDERGFGDF
>NC_011963.1|WP_049763958.1|1392407_1393133_-|ParA-family-protein
MRAMICNQKGGVGKTTTAANLGAALARAGAGRVLLVDLDPQMHLTAALGLASEEPGWSVADWLAGRPGEPLAVPDEPGLWLVPGAPEAPAVVGEAFPDSGFDWVLIDAPPSWSEGLARLMQGADLVICPLEPDFLGLQGLNRLLRTMQGAGLDWSRLRLLATRVSDRLAVHREVRARLAERFGESFLPVAIRSSVKLAEAPGRGRTIFTHAPASTGASDHAALARLLMPSGRRARRKGTRT
>NC_011963.1|WP_002720194.1|1393136_1393646_-|purine-binding-chemotaxis-protein-CheW
MPEDLTRTARAEGQPLSETDNVEDMYLTFALGGEDYGVGIGGVTEIVGMQRIMGVPDVPAWIKGVINLRGKVIPLVDVRLRFGMAERAYDDRTVIIVLEVAAAPVGLIVDGVSEVLDIPPAQIDRPGQFGRSRSPVMGLARVGDRVTILLDAEVLVADGDLALPAELEA
>NC_011963.1|WP_015920688.1|1393664_1394765_-|chemotaxis-specific-protein-glutamate-methyltransferase-CheB
MKAAADRLMAARTREGRTRVLIVDDSAMVRQALALGLSTDPRLEVVGTASGAEAARAQMAALKPDVVTLDLEMPQMDGLTFLRSYMESAPVPTVVISSLTRTSGETAMRAMEAGAVDIISKPSLGAGQGLPAIMRDVCARVWAAARARLALPDGVAPAPVAPGASEDWIHALGASTGGVQALSRILPFFPAQSPGLLVVQHMPEGFTAAFARRLDALCRMRVREAADGDLVLPGLVLIAPGGLRHMDIERVGGVCRVRLVAGAPVSYSRPSVDRMFLSLAAAAGPRVSAALLTGMGRDGAAGLLAIRRAGGRTFAQDEGSSAVFGMPLAARELRAAEEILTLDDIPARMMLAAAADTRAPSLASND
>NC_011963.1|WP_015920689.1|1394764_1395574_-|protein-glutamate-O-methyltransferase-CheR
MTIREEAGYEAIRVWLSRRCGIAYPEHKGELLRQRLTRVRRAYDLGSLADIALRLDAQGSHELELAVMHAASTNHTYFCREPDVLDAFRAMVLPVLARREQIRIWSAACSSGDEVYTIAMMIAETLGPEGLARTQILGTDISAPMVEQAEQGIYRRRHLEQVPDAVLRRWFVPLGGGSYRVAPEIAAACTFRRMNLKTRPFPFRKPFQAIFCRNVLYYFDRADQAETLRALHAATEPGGWLVTSVTESLRGHETGWRSLGGGLHQKEAR
>NC_011963.1|WP_015920690.1|1395570_1396770_-|chemotaxis-protein-CheW
MSAPVEAGPDGGLLRVSSEKIGRLMDLVGELSLSVAETVHSPDLEGLELPAFDGAVHRLRMIVREVQDAATELRLVPVEEVFKRLRRMVRELERQTGKKIEMVFEGAETAIDKLVADQLYDPLLHVVRNSADHGLEPPEERRAAGKPETGRIVLAAAQAGSEVRISVSDDGRGLSRPKILKRARERGLFGPDEEPEPATLWKVIFEPGFSTAEAVTNLSGRGVGMDVLNATMTALRGRIGVDSRDGQGSEVSLHIPVSLAFLDCIILRLGARLYALPIDAVSEIVQPKPCDLMGVGAAGGSEMLRLRGHWIPVCRLERFYGEAPSAVSPPAGQVLAVVSTASGLIALPVDEVLDRQQVVMKPLTGRLAQVRASWGCALLGTGEVALVLDGNRLAAGGAA

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Crispr_ID: NC_011963_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011963_3

1994975-1997002

TypeI

I-C

Consensus_repeat	Method
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	PILER-CR
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CRISPRCasFinder
GTCGCCCCTCACGCGGGGGCGTGGATCGAAACN	CRT
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	PILER-CR

30 spacers

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

The CRISPR arrays of NC_011963_3

>merge|NC_011963|3|1994975-1997002|PILER-CR,CRISPRCasFinder,CRT,PILER-CR
GTCGCCCCTCACGCGGGGGCGTGGATCGAAACACGTCAACGTCAACTTTGATGGCGTCTGAGATCGATCCGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACAAGGCCATGCCGAGAGATGACCAGCGCGCCTTCATGTCGCCCCTCACGCGGGGGCGTGGATCGAAACGGGCTGATCTCGACCCCGGGCGGGATCACCGGAACGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCATGTGCAGGGCGAACGCGGTGACGCCCCACGCGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCGCCCGGCGGCGTTGTAGAGCGCGCCGACGCCGCGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCCCCTCGTCGCCCGCCGGGTGGACGTCGACAAGATGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCGTGGCGGGAGCGCGCATCAACCCACGTGGGGCGTGTCGCCCCTCACGCGGGGGCGTGGATCGAAACATCAGGCGGATGTTGGTCAGCATGTCCTCGATGGCGTCGCCCCTCACGCGGGGGCGTGGATCGAAACACGCACAAGGAATGGCCTGGCGACGAGGCGAAGCCGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACTGAAGATGCATGATGACTGAGGAGAAAACGACCATGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACGTCACCGATGGCCCCATGGGCCGTGTCGCCCGGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCGTGGTCTACGAGGCGCCCCTCGATCCGCGCTGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACTCGGCCACCGGCGAGACGATCACATTCCCGATGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACTCATCGGATCTCTTCCTGATGCCGCGAAAAGCCACGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCCAATCGTCCACGCCCAGCGCCCAGGCCAGCCACGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCTCGGGCATTAGGAGCCAATTCGGAACGATTTTACGTCGCCCCTCATGCGGGGGCGTGGATCGAAACATCGTGTTGATAATGGCCTGCACCGTCTGGCCGGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACACGCTGGGCCCGGCGTCCGAGCCGCTGCAGGGACGTCGCCCCTCACGCGGGGGCGTGGATCGAAACGGAAACATGCCCGATCATGTCGGACGTGATGAAAGTCGCCCCTCACGCGGGGGCGTGGATCGAAACACACAAAAAACAAAAGCCGTCATGCCGATAGGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACTTACACCTGCTCGACTGGCAGCACCGGTAAGATTGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCCCGTGCGAACCTCAAGCCAGGAACTCGGAACGGGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCGGGGCGATGGGAGCAAGCGGCGTGGCCTCGTCGCGTCGCCCCTCACGCGGGGGCGTGGATCGAAACACAGGTGGGACTATCTCATCGCCCCGCCCCGCACGTCGCCCCTCACGCGGGGGCGTGGATCGAAACAACCAGGTGGCGGTCGGCAATGCGCGGGTCCGCCGTCGCCCCTCACGCGGGGGCGTGGATCGAAACCCCACCAGAACTGGTACTTCTTGCCACTTCTATCGCGTCGCCCCTCACGCGGGGGCGTGGATCGAAACGTCGCGGGCCAGAAACACAACTGCGCCCTCGTGCGTCGCCCCTCACGCGGGGGCGTGGATCGAAACATCCCGACAATTCGCGCGGAATCGCAGGACGTGGCGTCGCCCCTCACGCGGGGGCGTGGATCGAAACTCGCTCGGCACGTAGCGGCCGGCGTAGGCCGCCGCGTCGCCCCTCACGCGGGGCGTGGATCGAAACCAGTAGGTCTGGTCGGCCTGCTCAAGCGTCATGGTTGCCCCTCACGCGGGGGAGGTCTACCATCT

>NC_011963|3|1|1994975-1996538|PILER-CR
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGTCAACGTCAACTTTGATGGCGTCTGAGATCGATCCG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	AAGGCCATGCCGAGAGATGACCAGCGCGCCTTCAT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GGGCTGATCTCGACCCCGGGCGGGATCACCGGAACG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CATGTGCAGGGCGAACGCGGTGACGCCCCACGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGCCCGGCGGCGTTGTAGAGCGCGCCGACGCCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCCTCGTCGCCCGCCGGGTGGACGTCGACAAGATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGTGGCGGGAGCGCGCATCAACCCACGTGGGGCGT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ATCAGGCGGATGTTGGTCAGCATGTCCTCGATGGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGCACAAGGAATGGCCTGGCGACGAGGCGAAGCCG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TGAAGATGCATGATGACTGAGGAGAAAACGACCATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GTCACCGATGGCCCCATGGGCCGTGTCGCCCGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGTGGTCTACGAGGCGCCCCTCGATCCGCGCTG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCGGCCACCGGCGAGACGATCACATTCCCGATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCATCGGATCTCTTCCTGATGCCGCGAAAAGCCAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCAATCGTCCACGCCCAGCGCCCAGGCCAGCCACG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CTCGGGCATTAGGAGCCAATTCGGAACGATTTTAC
GTCGCCCCTCATGCGGGGGCGTGGATCGAAAC	ATCGTGTTGATAATGGCCTGCACCGTCTGGCCGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGCTGGGCCCGGCGTCCGAGCCGCTGCAGGGAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GGAAACATGCCCGATCATGTCGGACGTGATGAAA
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACACAAAAAACAAAAGCCGTCATGCCGATAGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TTACACCTGCTCGACTGGCAGCACCGGTAAGATT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCGTGCGAACCTCAAGCCAGGAACTCGGAACGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGGGGCGATGGGAGCAAGCGGCGTGGCCTCGTCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAACACAGGTGGGACTATCTCATCGCCCCGCCCCGCACGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	AACCAGGTGGCGGTCGGCAATGCGCGGGTCCGC
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCACCAGAACTGGTACTTCTTGCCACTTCTATCG
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GTCGCGGGCCAGAAACACAACTGCGCCCTCGTG
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ATCCCGACAATTCGCGCGGAATCGCAGGACGTGG
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCGCTCGGCACGTAGCGGCCGGCGTAGGCCGCCG


>NC_011963|3|3|1994975-1996938|CRISPRCasFinder
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGTCAACGTCAACTTTGATGGCGTCTGAGATCGATCCG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	AAGGCCATGCCGAGAGATGACCAGCGCGCCTTCAT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GGGCTGATCTCGACCCCGGGCGGGATCACCGGAACG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CATGTGCAGGGCGAACGCGGTGACGCCCCACGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGCCCGGCGGCGTTGTAGAGCGCGCCGACGCCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCCTCGTCGCCCGCCGGGTGGACGTCGACAAGATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGTGGCGGGAGCGCGCATCAACCCACGTGGGGCGT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ATCAGGCGGATGTTGGTCAGCATGTCCTCGATGGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGCACAAGGAATGGCCTGGCGACGAGGCGAAGCCG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TGAAGATGCATGATGACTGAGGAGAAAACGACCATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GTCACCGATGGCCCCATGGGCCGTGTCGCCCGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGTGGTCTACGAGGCGCCCCTCGATCCGCGCTG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCGGCCACCGGCGAGACGATCACATTCCCGATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCATCGGATCTCTTCCTGATGCCGCGAAAAGCCAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCAATCGTCCACGCCCAGCGCCCAGGCCAGCCACG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CTCGGGCATTAGGAGCCAATTCGGAACGATTTTAC
GTCGCCCCTCATGCGGGGGCGTGGATCGAAAC	ATCGTGTTGATAATGGCCTGCACCGTCTGGCCGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGCTGGGCCCGGCGTCCGAGCCGCTGCAGGGAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GGAAACATGCCCGATCATGTCGGACGTGATGAAA
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACACAAAAAACAAAAGCCGTCATGCCGATAGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TTACACCTGCTCGACTGGCAGCACCGGTAAGATT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCGTGCGAACCTCAAGCCAGGAACTCGGAACGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGGGGCGATGGGAGCAAGCGGCGTGGCCTCGTCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACAGGTGGGACTATCTCATCGCCCCGCCCCGCAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	AACCAGGTGGCGGTCGGCAATGCGCGGGTCCGCC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCACCAGAACTGGTACTTCTTGCCACTTCTATCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GTCGCGGGCCAGAAACACAACTGCGCCCTCGTGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ATCCCGACAATTCGCGCGGAATCGCAGGACGTGGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCGCTCGGCACGTAGCGGCCGGCGTAGGCCGCCGC
GTCGCCCCTCACGCGGGGCGTGGATCGAAACC

>NC_011963|3|1|1994975-1997002|CRT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGTCAACGTCAACTTTGATGGCGTCTGAGATCGATCCG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	AAGGCCATGCCGAGAGATGACCAGCGCGCCTTCAT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GGGCTGATCTCGACCCCGGGCGGGATCACCGGAACG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CATGTGCAGGGCGAACGCGGTGACGCCCCACGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGCCCGGCGGCGTTGTAGAGCGCGCCGACGCCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCCTCGTCGCCCGCCGGGTGGACGTCGACAAGATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGTGGCGGGAGCGCGCATCAACCCACGTGGGGCGT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ATCAGGCGGATGTTGGTCAGCATGTCCTCGATGGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGCACAAGGAATGGCCTGGCGACGAGGCGAAGCCG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TGAAGATGCATGATGACTGAGGAGAAAACGACCATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GTCACCGATGGCCCCATGGGCCGTGTCGCCCGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGTGGTCTACGAGGCGCCCCTCGATCCGCGCTG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCGGCCACCGGCGAGACGATCACATTCCCGATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCATCGGATCTCTTCCTGATGCCGCGAAAAGCCAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCAATCGTCCACGCCCAGCGCCCAGGCCAGCCACG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CTCGGGCATTAGGAGCCAATTCGGAACGATTTTAC
GTCGCCCCTCATGCGGGGGCGTGGATCGAAAC	ATCGTGTTGATAATGGCCTGCACCGTCTGGCCGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGCTGGGCCCGGCGTCCGAGCCGCTGCAGGGAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GGAAACATGCCCGATCATGTCGGACGTGATGAAA
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACACAAAAAACAAAAGCCGTCATGCCGATAGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TTACACCTGCTCGACTGGCAGCACCGGTAAGATT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCGTGCGAACCTCAAGCCAGGAACTCGGAACGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGGGGCGATGGGAGCAAGCGGCGTGGCCTCGTCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACAGGTGGGACTATCTCATCGCCCCGCCCCGCAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	AACCAGGTGGCGGTCGGCAATGCGCGGGTCCGCC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCACCAGAACTGGTACTTCTTGCCACTTCTATCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GTCGCGGGCCAGAAACACAACTGCGCCCTCGTGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ATCCCGACAATTCGCGCGGAATCGCAGGACGTGGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCGCTCGGCACGTAGCGGCCGGCGTAGGCCGCCGC
GTCGCCCCTCACGCGGGGCGTGGATCGAAACC	AGTAGGTCTGGTCGGCCTGCTCAAGCGTCATG
GTTGCCCCTCACGCGGGGGAGGTCTACCATCT

>NC_011963|3|2|1996572-1996937|PILER-CR
	ACGTCAACGTCAACTTTGATGGCGTCTGAGATCGATCCG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	AAGGCCATGCCGAGAGATGACCAGCGCGCCTTCAT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GGGCTGATCTCGACCCCGGGCGGGATCACCGGAACG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CATGTGCAGGGCGAACGCGGTGACGCCCCACGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGCCCGGCGGCGTTGTAGAGCGCGCCGACGCCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCCTCGTCGCCCGCCGGGTGGACGTCGACAAGATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGTGGCGGGAGCGCGCATCAACCCACGTGGGGCGT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ATCAGGCGGATGTTGGTCAGCATGTCCTCGATGGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGCACAAGGAATGGCCTGGCGACGAGGCGAAGCCG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TGAAGATGCATGATGACTGAGGAGAAAACGACCATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GTCACCGATGGCCCCATGGGCCGTGTCGCCCGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGTGGTCTACGAGGCGCCCCTCGATCCGCGCTG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCGGCCACCGGCGAGACGATCACATTCCCGATG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCATCGGATCTCTTCCTGATGCCGCGAAAAGCCAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCAATCGTCCACGCCCAGCGCCCAGGCCAGCCACG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CTCGGGCATTAGGAGCCAATTCGGAACGATTTTAC
GTCGCCCCTCATGCGGGGGCGTGGATCGAAAC	ATCGTGTTGATAATGGCCTGCACCGTCTGGCCGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACGCTGGGCCCGGCGTCCGAGCCGCTGCAGGGAC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GGAAACATGCCCGATCATGTCGGACGTGATGAAA
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ACACAAAAAACAAAAGCCGTCATGCCGATAGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TTACACCTGCTCGACTGGCAGCACCGGTAAGATT
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCGTGCGAACCTCAAGCCAGGAACTCGGAACGG
GTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CGGGGCGATGGGAGCAAGCGGCGTGGCCTCGTCGC
GTCGCCCCTCACGCGGGGGCGTGGATCGAAACACAGGTGGGACTATCTCATCGCCCCGCCCCGCACGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	AACCAGGTGGCGGTCGGCAATGCGCGGGTCCGC
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	CCCACCAGAACTGGTACTTCTTGCCACTTCTATCG
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	GTCGCGGGCCAGAAACACAACTGCGCCCTCGTG
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	ATCCCGACAATTCGCGCGGAATCGCAGGACGTGG
CGTCGCCCCTCACGCGGGGGCGTGGATCGAAAC	TCGCTCGGCACGTAGCGGCCGGCGTAGGCCGCCG
CGTCGCCCCTCACGCGGGGCGTGGATCGAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_011963.1\|WP_041669676.1\|1989395_1990094_+\|type-I-C-CRISPR-associated-protein-Cas5	cas5	cd09752_cas5_CAS-I-C	gnl\|CDD\|187534
NC_011963.1\|WP_080517666.1\|1986682_1989013_+\|CRISPR-associated-helicase/endonuclease-Cas3	cas3	COG1203_cas3_CAS-I	gnl\|CDD\|350688
NC_011963.1\|WP_049763965.1\|1998983_1999367_-\|VOC-family-protein	unknown	unknown	gnl\|CDD\|319923
NC_011963.1\|WP_080517605.1\|1989012_1989342_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|198390
NC_011963.1\|WP_080517609.1\|2001833_2002346_+\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|366181
NC_011963.1\|WP_041669679.1\|1999411_2000218_-\|SDR-family-NAD(P)-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|187602
NC_011963.1\|WP_015921086.1\|1985763_1986303_+\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_080517607.1\|2000259_2000643_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224647
NC_011963.1\|WP_015921092.1\|1993467_1994502_+\|type-I-C-CRISPR-associated-endonuclease-Cas1	cas1	cd09721_cas1_CAS-I-C	gnl\|CDD\|187852
NC_011963.1\|WP_041669678.1\|1992820_1993471_+\|CRISPR-associated-protein-Cas4	cas4	cd09637_cas4_CAS-I:CAS-II:CAS-V	gnl\|CDD\|273040
NC_011963.1\|WP_015921095.1\|1997670_1998531_+\|sigma-70-family-RNA-polymerase-sigma-factor	unknown	unknown	gnl\|CDD\|236600
NC_011963.1\|WP_015921089.1\|1990090_1991941_+\|type-I-C-CRISPR-associated-protein-Cas8c/Csd1	cas8c	cd09757_cas8c_CAS-I-C	gnl\|CDD\|378245
NC_011963.1\|WP_015921098.1\|2000916_2001525_-\|LysE-family-translocator	unknown	unknown	gnl\|CDD\|224199
NC_011963.1\|WP_012643676.1\|1984979_1985558_+\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_015921101.1\|2003765_2004509_+\|helix-turn-helix-transcriptional-regulator	unknown	unknown	gnl\|CDD\|380379
NC_011963.1\|WP_015921093.1\|1994503_1994794_+\|CRISPR-associated-endonuclease-Cas2	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|187856
NC_011963.1\|WP_015921090.1\|1991945_1992821_+\|type-I-C-CRISPR-associated-protein-Cas7/Csd2	cas7	cd09689_cas7_CAS-I-C	gnl\|CDD\|377458
NC_011963.1\|WP_015921094.1\|1997207_1997681_+\|carboxymuconolactone-decarboxylase-family-protein	unknown	unknown	gnl\|CDD\|225039
NC_011963.1\|WP_041669683.1\|2004875_2005148_+\|hypothetical-protein	unknown	unknown	unknown
NC_011963.1\|WP_015921100.1\|2002755_2003673_-\|NADP-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|176191

Protein	Function_ID	Function_description	E-value
NC_011963.1\|WP_041669676.1\|1989395_1990094_+\|type-I-C-CRISPR-associated-protein-Cas5	gnl\|CDD\|187534	cd09752, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family.	1.78255e-109
NC_011963.1\|WP_080517666.1\|1986682_1989013_+\|CRISPR-associated-helicase/endonuclease-Cas3	gnl\|CDD\|350688	cd17930, DEXHc_cas3, DEXH/Q-box helicase domain of Cas3. CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.	4.23461e-52
NC_011963.1\|WP_080517605.1\|1989012_1989342_+\|hypothetical-protein	gnl\|CDD\|198390	cd10443, GIY-YIG_HE_Tlr8p_PBC-V_like, GIY-YIG domain of uncharacterized hypothetical protein found in phycodnavirus PBCV-1 DNA virus, T. thermophila Tlr element eoncoding protein Tlr8p, and similar proteins found in bacteria. The family includes a group of diverse uncharacterized hypothetical proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI. Similar to I-TevI, family members from phycodnavirus PBCV-1 DNA virus have nuclease-associated modular DNA-binding domains (NUMODs) and a helix-turn-helix (HTH) domain C-terminally fused to the GIY-YIG domain, which suggests that these PBCV-1 acquired the I-TevI-like homing endonucleases from phages by horizontal gene transfer. This family also includes proteins that appear to connect homing endonucleases with Penelope elements, such as Tetrahymena thermophila Tlr element encoding protein Tlr8p that possess additional N-terminal and central structural regions, followed by a putative superfamily 1 helicase domain and I-TevI-like GIY-YIG domain, but lacks the NUMOD domains and HTH domain. It is suggested that the Tlr8p element could have acquired its GIY-YIG domain w ithin the nucleus of the ciliate cell infected by the Phycodnavirus. Some family members only contain a standalone GIY-YIG domain and their biological functions are unclear.	5.53495e-11
NC_011963.1\|WP_015921094.1\|1997207_1997681_+\|carboxymuconolactone-decarboxylase-family-protein	gnl\|CDD\|225039	COG2128, COG2128, Uncharacterized conserved protein [Function unknown].	8.27179e-25
NC_011963.1\|WP_041669679.1\|1999411_2000218_-\|SDR-family-NAD(P)-dependent-oxidoreductase	gnl\|CDD\|187602	cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR. This subgroup resembles the SDR family, but does not have a perfect match to the NAD-binding motif or the catalytic tetrad characteristic of the SDRs. It includes the SDRs, Q9HYA2 from Pseudomonas aeruginosa PAO1 and APE0912 from Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent reduction of ACP in the first reductive step of de novo fatty acid synthesis (FAS). FAS consists of four elongation steps, which are repeated to extend the fatty acid chain through the addition of two-carbo units from malonyl acyl-carrier protein (ACP): condensation, reduction, dehydration, and a final reduction. Type II FAS, typical of plants and many bacteria, maintains these activities on discrete polypeptides, while type I FAS utilizes one or two multifunctional polypeptides. BKR resembles enoyl reductase, which catalyzes the second reduction step in FAS. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs.	1.2405e-70
NC_011963.1\|WP_015921101.1\|2003765_2004509_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|380379	cd06124, cupin_NimR-like_N, AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain. This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.	5.34607e-24
NC_011963.1\|WP_080517607.1\|2000259_2000643_+\|helix-turn-helix-transcriptional-regulator	gnl\|CDD\|224647	COG1733, COG1733, Predicted transcriptional regulators [Transcription].	1.25266e-31
NC_011963.1\|WP_015921092.1\|1993467_1994502_+\|type-I-C-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|187852	cd09721, Cas1_I-C, CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain.	0
NC_011963.1\|WP_041669678.1\|1992820_1993471_+\|CRISPR-associated-protein-Cas4	gnl\|CDD\|273040	TIGR00372, conserved_hypothetical_protein, CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.	8.46498e-40
NC_011963.1\|WP_015921095.1\|1997670_1998531_+\|sigma-70-family-RNA-polymerase-sigma-factor	gnl\|CDD\|236600	PRK09636, PRK09636, RNA polymerase sigma factor SigJ; Provisional.	6.2393e-145
NC_011963.1\|WP_080517609.1\|2001833_2002346_+\|GNAT-family-N-acetyltransferase	gnl\|CDD\|366181	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family. This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.	6.58859e-16
NC_011963.1\|WP_015921089.1\|1990090_1991941_+\|type-I-C-CRISPR-associated-protein-Cas8c/Csd1	gnl\|CDD\|378245	pfam09709, Cas_Csd1, CRISPR-associated protein (Cas_Csd1). CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins that tend to be found near CRISPR repeats. The species range, so far, is exclusively bacterial and mesophilic, although CRISPR loci are particularly common among the archaea and thermophilic bacteria. Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins.	0
NC_011963.1\|WP_015921098.1\|2000916_2001525_-\|LysE-family-translocator	gnl\|CDD\|224199	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism].	3.2793e-35
NC_011963.1\|WP_015921093.1\|1994503_1994794_+\|CRISPR-associated-endonuclease-Cas2	gnl\|CDD\|187856	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.	1.13693e-33
NC_011963.1\|WP_015921090.1\|1991945_1992821_+\|type-I-C-CRISPR-associated-protein-Cas7/Csd2	gnl\|CDD\|377458	pfam05107, Cas_Cas7, CRISPR-associated protein Cas7. CRISPR-associated protein Cas7 is one of the components of the type I-B cascade-like antiviral defense complex. In Haloferax volcanii, Cas5, Cas6 and Cas7 form a small complex that aids the stability of CRISPR-derived RNA.	3.45177e-146
NC_011963.1\|WP_049763965.1\|1998983_1999367_-\|VOC-family-protein	gnl\|CDD\|319923	cd07262, VOC_like, uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.	2.47104e-44
NC_011963.1\|WP_015921100.1\|2002755_2003673_-\|NADP-dependent-oxidoreductase	gnl\|CDD\|176191	cd05289, MDR_like_2, alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases. Members identified as zinc-dependent alcohol dehydrogenases and quinone oxidoreductase. QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction.	6.89151e-115

>NC_011963.1|WP_015921093.1|1994503_1994794_+|CRISPR-associated-endonuclease-Cas2
MLVLVTYDVNTLEPGGKKRLRQIAASCEDYGQRVQYSVFEIEVDPAQWTKLKSRLEAIIKPQHDSLRYYYLGSNWSRKVEHVGAKPATDLNGPLII
>NC_011963.1|WP_015921092.1|1993467_1994502_+|type-I-C-CRISPR-associated-endonuclease-Cas1
MKRLLNTVYVTTEGAALRKDGETLVAEVEGVEKTRVPLHMLASVVAFGPVLLTPALIATCAERGVTVALLSRNGRFQARIEGPVSGNVLLRREQYRRADVPEDIVRSFVLGKVSNQRAVLRRALRDYGEEMDVTARAALEAACDRMAQVMRRVQLSDRTVDEMRGSEGEAATLYFASFDLLIRSPDADMRWTGRSRRPPLDAMNALLSFLYTLLTHDCRSACEAVGLDPAVGFLHRDRPGRPSLALDLMEELRAPLADRLALSLVNRRQLRSRDFCRMDGGAVLLTDAARRGVLTAWQDRKREERQHGFLQEKAPFGLVPYLQAQLLARHLRGDIDAYPPWFWS
>NC_011963.1|WP_041669678.1|1992820_1993471_+|CRISPR-associated-protein-Cas4
MPQLPADEVPIPLSAVQHAIYCLRQAALIQVERLWDENRFTAEGDVLHAVADKGGRRKARGVRRVLALPLASARLNLTGVADLVEFQPIPGQGERPFPVEYKRGKPKLHRADEAQLCAQALCLEEMTDQPVPEGALFYSQTRRRVLVPFDADLRTLTEATVAELILLFATGRTPPPTPHRSRCRACSLLDLCRPDTVSRPVRRWRDQTLTRLLEAP
>NC_011963.1|WP_015921090.1|1991945_1992821_+|type-I-C-CRISPR-associated-protein-Cas7/Csd2
MTALTNRYEFVFLFDIRNGNPNGDPDNGNMPRIDTDTEHGLVTDVALKRKIRNYVDLKHGGEPPHAIYMREKAILNATHGEAYAALGLKPESKKLPKDEAKAREITRWMCRNFYDIRTFGAVMTTDVNAGQVRGPVQLSFSETVDPILPQEVTITRSSVTNEKDAAKERTMGRKYIVPYGLYRCHGFVSASLAGDATKGTGFSEEDLALLFEALTNMFEHDRSAARMEMNAQRLIVFRHDSALGNAPAQALFKRVAVARRDDVKVPRRFEDYDVTVDTENLPTGVEIRELL
>NC_011963.1|WP_015921089.1|1990090_1991941_+|type-I-C-CRISPR-associated-protein-Cas8c/Csd1
MSLLASLVRAYERLPDKTPYGYSTEKIGFCVVLTPEGAVTEVMDLRDSNKKRSPAPVQVPQAVKRTMGLAPNFLWDKSAYVLGVTGRAGKRTAEEHAKFSSRHQEWLAGTEDEGLRALLRFLDTWQPEDFRPPLWPEAAQDQNIVFRLLGERSFLHDRPAAVALWARIGTEGASAPRICLVSGQSAPIERLHPSIKGVWGAQSSGASLVSFNLDAFTSYGHKQGDNAPISEAAAFAYTTALNGFLADKAHRLQIGDSSTVFWADASDAALAEEAEAWGSFMLGNRSTSGATEALAETRIKANLQRLRDGRTLSEIEPSLALGVRFHVLGLAPNAARLSVRFYWEDSFGTFAHHYAEWMRDTALDGVGPPRDISIRNAVLRTAPAQEKNGHIAFDSDHVSPLLSGELLRAILTGGRFPRSLLSQLLMRIRSDHLLDRVRLSLIKAVILRDMRREGRLPPRPDGTVMEDYLMRPDPDDPNPARRLGRLFALIERAQLTALGDAINATVTDKFLGAAAATPGRVFPGLIRGAREHHLKRLRNGHADAKWITDADHARAVARGLEREIGVLWASFTEGAPSQHSTEEQGLFLVGYYQEKYARRGEAETDQPEAAETGSEE
>NC_011963.1|WP_041669676.1|1989395_1990094_+|type-I-C-CRISPR-associated-protein-Cas5
MAYGIRLHVWGRNALFTRPELKVERVSYDVMTPSAARGILEAIHWKPAIRWVIDRIHVLEPIRFQSIRRNEVGHKAPAGTIRQAMKRCDLDGLQLLVDEDRQQRASTVLVNPAYVIEAHFERTIKAGPEDTEGKHLDIFNRRAARGQCFHQPCLGTREFPAHFALLPPGNPLPSRDPATETAEHGFGSPRDLGLMLWDIDHAVPGRPSLFFRARLNEGVLDVPQPGSHEVLR
>NC_011963.1|WP_080517605.1|1989012_1989342_+|hypothetical-protein
MSGETATPLRYAVVYKVTWPNGKIYVGSDLTDSITYFGSPDRKLLESDFPAREERRKITVTREILWESSTATRSEVLSMERKLIIQLRANDPALGYNRRPKSAATAATY
>NC_011963.1|WP_080517666.1|1986682_1989013_+|CRISPR-associated-helicase/endonuclease-Cas3
MQASSASCKNLRLAFGRIRSIGQARFALTHQEVLVQFYAHSGHRDDRTDWQTLPDHLAAVERLARARAAPLGLSEAAGIAGRLHDLGKYDPAFDRVLRGENLHVDHSTAGGRALLDSVPAGLRPVAEVLAYAILGHHAGLPDKVSEDSACLERRIASAPHNLAPEWERHFPIDLAAAGTELRAHVRADPHKAPFDLSVAVRMIFSCLVDADFRDTETFYDQLEGRARSREWPTLQDCLPDLRQKFAAHMAGFERSTEVNRLRAEILAHVTVQAAMPPGLFTLSVPTGGGKTLASLGFALDHAALHGHRRIVYAIPYTSIIDQTAKVFRDLLGQEIVLEHHSAIETRDGGEAGRIKSHLAMEDWAAPVVVTTNVQLFESLFAARASRCRKLHNLAGAIIVLDEAQCLPRPMLLPTLAMIDTLATHYGCTVVLCTATQPAFDSSQLRHGGLLLSGRELAPEPQELARKLKRVNIARASTMDDTALISAMRGAPQSFVIVNSRRHALALYRAAVEEGIQNVVHLSTRQYPAHRRRIIETIKGRLTQSLPCRLISTSLIEAGVDLDFPRGWRAEAGLDSVIQAAGRVNREGKRTLSASTLTVFSAPENSPPPEVARLAEAMQATANKFNDLFDIDAIRDWFNEVYWRATPQRLGQGMTKSMIFDGAETGFPFRKLASDYRLIDSPMVPVIIPLGKAVAEVARLTVAEVPSGTIARAVQPYTVQIPSAAREILRRNGKGSFHAEELRGDQFFVLDELSLYQEDFGLWWKQAEYLSADQGVI
>NC_011963.1|WP_015921086.1|1985763_1986303_+|hypothetical-protein
MKGAKGRKAMKAKLVSLKLAPWDLGPLTPAQIAGKRIEEAAEVDPKTGKKSNPNRVIRTRRETWVDRYHRQGKLSVEQANIAAELFEAASGMLSRDPLAAMVKVDTSGTYDPEAERLDRRRKFFRMWEEIPSFAQPVVKHVVLDDQSLRSMPGRLNGRHEARQLDRLQRGLDALHKAWS
>NC_011963.1|WP_012643676.1|1984979_1985558_+|hypothetical-protein
MAMTKAEERARVKALVVDRLEQAGMVRRRGTAAAAHEAAMARLCEQLGYMGAENLMTLAEVLIDSAADGVWPSEVLIRQFARAIEEPPPAERRLVSSWLASVEGPKAEAGGHLVELYRWLLKHPRPPLAMDLREIRDQAQDNARRCELIRDRIDRETASREDRDWLELYLRDRAQARALVDAGRARKEGAAA
>NC_011963.1|WP_015921094.1|1997207_1997681_+|carboxymuconolactone-decarboxylase-family-protein
MTPRMTDHFKRIGQAFQGLVTFETELRKGPLEPALLHLVKMRASQLNGCAFCLQMHASEALKDGETHLRLHMLAGWQDSSLFSPRERAALAWTEAVTLIAHSHTPDADWEALRAEFSEDEAAYLTFAIAAINLWNRTQIAFRVAHATELPVERARVA
>NC_011963.1|WP_015921095.1|1997670_1998531_+|sigma-70-family-RNA-polymerase-sigma-factor
MSPDVYLQIFETRRPQLLRLAYRMLGSHAEAEDVVQEAWIRWQAADQAQIAIPAAWLNRVVSRLCLDLMRSARHRRESYIGPWLPEPLIEEEDADHRPDNLTLSLMMALERLSPLERAAFLLHDVFGQSFDDVARALDRSPSAARQLAVRARAHVHIDRPRYKVEREAAEDLTRAFFEACKTGDAAVLSGLLAEDAVLHSDGGGKVYNLLNVIVGAQKLLRMFTSLSRKRGDEMEFVRFTLIDALPGYVWRMGDQIQTTALEVEDGRITRVYTTRNPDKLTRIRLN
>NC_011963.1|WP_049763965.1|1998983_1999367_-|VOC-family-protein
MSIFDHVSLRTTRLEETLRFYDAVLATLGIDRRFYVERAEGNVAGFGRDRVELFLTGVQGTEPTPVHVAFRARSREEVQAFHAAGLTAGGTDNGAPGVRARYHDTYYAAFVIDPAGNNVEAVFQGSE
>NC_011963.1|WP_041669679.1|1999411_2000218_-|SDR-family-NAD(P)-dependent-oxidoreductase
MNLHLEGKIALVTGSSKGIGAGIARGLAREGAVVMVHGRDREQATAVARQIRQDGGTAHVVTGDLTEEAEVDTLLAEVRAIGDIDILVNNAGGSGGSSDWATTEAGAWASTYDANVLAAMRMAKAILPQMRQAGWGRIINISSLAALMPPAGNPDYSAAKAAMLAMSASMAKAVAADGVTVNTVSPGTIRSEKLDRKFREVAHQRGIALEAPWEVVEAEALPLFASVPTGRVGTLDEIADAVAFLASPRASYITGSNLRLDGGMLLTV
>NC_011963.1|WP_080517607.1|2000259_2000643_+|helix-turn-helix-transcriptional-regulator
MMDPSRTHKKVPVAELDRSACLGPDGAVAQVARCLKMISGRWKLPILFRLYADGMQRSSLLLRDIPDVSQKMLTQHLRELEDDGLVRRTDFGEKPPRVEYRLTDRGEALMPVLLAARQFSEDHDRAV
>NC_011963.1|WP_015921098.1|2000916_2001525_-|LysE-family-translocator
MFVSAVIVLTITPGPDLFLIVGRGISQGRAAALFTAFGFFLAGFIQVPLLAFGLANVVAGNPALFDVLRYGGGAYLMWRGIVMIRNAGHGDTVSADHASTGAAIKEGFIASLVNPKSHIFLLAFLPQFVRPEDGSVMAQFVFLGILMRVVALVVEGGMALLAGSIGYRLRRSLKLRGWLERTAGGLLVAVGLRLVLMERPQP
>NC_011963.1|WP_080517609.1|2001833_2002346_+|GNAT-family-N-acetyltransferase
MNFRTGQPSDAAALAAISIEVWLGTYMRKGVSAFFAEYALNEFTSTKMASRLKDPNEHVIVSENEGGIDAFIRLGQGRSAPVSGCSTLEIATLYVQPRHHRKGLGRALLEQGLAYARQASAPSVWLTTNSENAPAIAFYLEQGFEKVGTTHFNLGDQAYLNDVFRRIVST
>NC_011963.1|WP_015921100.1|2002755_2003673_-|NADP-dependent-oxidoreductase
MLTVLINAYGANDVVEVAEVERPSPQTGEVLIKVSAAGVNPIDWKIRDGAGERMGLTLPIHLGGEFVGAVEDMGPGAAGFERGEIVFGMVRTGAFSQYLTVNAADIVRKPGNLDITQAAALPLAGTTAWQAMFDEAKLCAGQRLLITGASGGVGSLAVQLAKAKGAHVTAMTSARNAEFVRGLGADEVVDYTARPFEEVVHDINVVLDTVGGDTFRRALATLRKGGIMVTIVAFPEGEEAKAHGVRVKRAFTVANAGSLRAITALVEAGRVTPHVEKTFPLVDVKTALALSAAGRVRGKIVLTIE
>NC_011963.1|WP_015921101.1|2003765_2004509_+|helix-turn-helix-transcriptional-regulator
MTRPFTLTRLRKPRGESLPDHSHDAAQLTFAASGMVQVRTEDGVWLVPPQLAAWIPAGAPHRLDILTDADLWMIFWEPAAMACWMPGAFPSRAFVSRVSPLLRSLLDAAMAADPASERVELMVRLILHELTATEEAPTFLPRPTSAEARRVADLALADHRNELDLDTLARRAATSIRTASRRFPEETGMTLKAWRQRARILWAMTQLGQGQPIARVARDAGFASTAAFSHAFRQVTTVTPSAFLSPP
>NC_011963.1|WP_041669683.1|2004875_2005148_+|hypothetical-protein
MGFLALDVTRTGVVLRKFNERGTRILERFNTHEVGMRRALITAQRELARDDDLTEVRANVQEPELAQRLKHCVTTEASDGGKLQALADAL

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_011963_3	3.15\|1995944\|35\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995944-1995978	35	NZ_CP041355	Pseudomonas aeruginosa strain AZPAE15042 plasmid pIHMA87, complete sequence	91513-91547	6	0.829
NC_011963_3	3.30\|1996939\|32\|NC_011963\|CRT	1996939-1996970	32	NZ_CP041652	Streptomyces sp. RLB1-9 plasmid pRLB1-9.2, complete sequence	69412-69443	6	0.812
NC_011963_3	3.31\|1996605\|33\|NC_011963\|PILER-CR	1996605-1996637	33	NZ_CP017750	Cupriavidus sp. USMAA2-4 plasmid unnamed1, complete sequence	310972-311004	6	0.818
NC_011963_3	3.31\|1996605\|33\|NC_011963\|PILER-CR	1996605-1996637	33	NZ_CP026545	Cupriavidus metallidurans strain Ni-2 plasmid unnamed1	3162-3194	6	0.818
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP013635	Rhizobium sp. N324 plasmid pRspN324e, complete sequence	593047-593080	7	0.794
NC_011963_3	3.25\|1996605\|34\|NC_011963\|CRISPRCasFinder,CRT	1996605-1996638	34	NZ_CP017750	Cupriavidus sp. USMAA2-4 plasmid unnamed1, complete sequence	310972-311005	7	0.794
NC_011963_3	3.25\|1996605\|34\|NC_011963\|CRISPRCasFinder,CRT	1996605-1996638	34	NZ_CP026545	Cupriavidus metallidurans strain Ni-2 plasmid unnamed1	3162-3195	7	0.794
NC_011963_3	3.33\|1996739\|33\|NC_011963\|PILER-CR	1996739-1996771	33	NZ_CP015007	Aminobacter aminovorans strain KCTC 2477 plasmid pAA02, complete sequence	307877-307909	7	0.788
NC_011963_3	3.4\|1995213\|33\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995213-1995245	33	NZ_CP035001	Rhizobium acidisoli strain FH23 plasmid pRapFH23c, complete sequence	114470-114502	8	0.758
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP021653	Ralstonia solanacearum strain RS 488 plasmid unnamed, complete sequence	1057277-1057310	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP021767	Ralstonia solanacearum strain RS 489 plasmid unnamed, complete sequence	1057265-1057298	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP012940	Ralstonia solanacearum strain UW163 plasmid unnamed, complete sequence	806494-806527	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP012944	Ralstonia solanacearum strain IBSBF1503 plasmid unnamed, complete sequence	1087939-1087972	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP012688	Ralstonia solanacearum strain UY031 plasmid unnamed, complete sequence	1057284-1057317	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NC_017575	Ralstonia solanacearum Po82 megaplasmid, complete sequence	1309882-1309915	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP026308	Ralstonia solanacearum strain IBSBF 2571 plasmid unnamed, complete sequence	1309826-1309859	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	CP047139	Ralstonia solanacearum strain CFBP 8695 plasmid unnamed, complete sequence	985873-985906	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP051295	Ralstonia solanacearum strain CIAT_078 plasmid megaplasmid, complete sequence	798219-798252	8	0.765
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	CP047137	Ralstonia solanacearum strain CFBP 8697 plasmid unnamed, complete sequence	943634-943667	8	0.765
NC_011963_3	3.12\|1995747\|33\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995747-1995779	33	NZ_CP013539	Rhizobium phaseoli strain R630 plasmid pRphaR630b, complete sequence	325617-325649	8	0.758
NC_011963_3	3.12\|1995747\|33\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995747-1995779	33	NZ_AP014705	Methylobacterium aquaticum strain MA-22A plasmid pMaq22A_1p, complete sequence	180059-180091	8	0.758
NC_011963_3	3.20\|1996276\|32\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1996276-1996307	32	NZ_CP018299	Photobacterium damselae strain Phdp Wu-1 plasmid plas1, complete sequence	196698-196729	8	0.75
NC_011963_3	3.27\|1996739\|34\|NC_011963\|CRISPRCasFinder,CRT	1996739-1996772	34	NZ_CP015007	Aminobacter aminovorans strain KCTC 2477 plasmid pAA02, complete sequence	307877-307910	8	0.765
NC_011963_3	3.11\|1995682\|33\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995682-1995714	33	NC_021289	Burkholderia insecticola plasmid p1, complete sequence	403478-403510	9	0.727
NC_011963_3	3.18\|1996144\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1996144-1996177	34	NZ_CP022366	Azospirillum sp. TSH58 plasmid TSH58_p04, complete sequence	274713-274746	9	0.735
NC_011963_3	3.30\|1996939\|32\|NC_011963\|CRT	1996939-1996970	32	NZ_CP025016	Rhizobium leguminosarum strain Norway plasmid pRLN4, complete sequence	26143-26174	9	0.719
NC_011963_3	3.30\|1996939\|32\|NC_011963\|CRT	1996939-1996970	32	NZ_CP010858	Marinovum algicola DG 898 plasmid pMaD3	14203-14234	9	0.719
NC_011963_3	3.3\|1995145\|36\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995145-1995180	36	CP000662	Rhodobacter sphaeroides ATCC 17025 plasmid pRSPA01, complete sequence	822457-822492	10	0.722
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_AP022571	Mycolicibacterium poriferae strain JCM 12603 plasmid pJCM12603, complete sequence	146612-146645	10	0.706
NC_011963_3	3.5\|1995278\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995278-1995311	34	NZ_CP040820	Paraoceanicella profunda strain D4M1 plasmid pD4M1B, complete sequence	14087-14120	10	0.706
NC_011963_3	3.15\|1995944\|35\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995944-1995978	35	NZ_LR594663	Variovorax sp. RA8 plasmid 2	403002-403036	10	0.714
NC_011963_3	3.15\|1995944\|35\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995944-1995978	35	NZ_CP034186	Deinococcus sp. S14-83 strain S14-83T plasmid unnamed2, complete sequence	69919-69953	10	0.714
NC_011963_3	3.18\|1996144\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1996144-1996177	34	NZ_AP022611	Mycolicibacterium madagascariense strain JCM 13574 plasmid pJCM13574	144216-144249	10	0.706
NC_011963_3	3.21\|1996340\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1996340-1996373	34	NZ_CP020443	Paracoccus yeei strain FDAARGOS_252 plasmid unnamed3, complete sequence	66035-66068	10	0.706
NC_011963_3	3.35\|1996872\|34\|NC_011963\|PILER-CR	1996872-1996905	34	NZ_CP040937	Hymenobacter sp. DG01 plasmid unnamed, complete sequence	239387-239420	10	0.706
NC_011963_3	3.35\|1996872\|34\|NC_011963\|PILER-CR	1996872-1996905	34	NZ_CP024314	Rhizobium sp. NXC24 plasmid pRspNXC24c, complete sequence	1909624-1909657	10	0.706
NC_011963_3	3.6\|1995344\|36\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995344-1995379	36	NC_021347	Rhodococcus phage E3, complete genome	64522-64557	11	0.694
NC_011963_3	3.8\|1995479\|35\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1995479-1995513	35	MN908685	Microbacterium phage PauloDiaboli, complete genome	57937-57971	11	0.686
NC_011963_3	3.19\|1996210\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1996210-1996243	34	NC_018696	Paraburkholderia phenoliruptrix BR3459a plasmid pSYMBR3459, complete sequence	569219-569252	11	0.676
NC_011963_3	3.21\|1996340\|34\|NC_011963\|PILER-CR,CRISPRCasFinder,CRT	1996340-1996373	34	NZ_CP032695	Rhizobium jaguaris strain CCGE525 plasmid pRCCGE525c, complete sequence	1917635-1917668	11	0.676

1. spacer 3.15|1995944|35|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP041355 (Pseudomonas aeruginosa strain AZPAE15042 plasmid pIHMA87, complete sequence) position: , mismatch: 6, identity: 0.829

ccaatcgtccacgcccagcgcccaggccagccacg	CRISPR spacer
ctcggcgcccacgcccagcgcgcaggccagccacg	Protospacer
*. . **.************* *************

2. spacer 3.30|1996939|32|NC_011963|CRT matches to NZ_CP041652 (Streptomyces sp. RLB1-9 plasmid pRLB1-9.2, complete sequence) position: , mismatch: 6, identity: 0.812

agtaggt-ctggtcggcctgctcaagcgtcatg	CRISPR spacer
-gtagctgctcgccggcctgctcaagcgtcagc	Protospacer
 **** * ** *.******************

3. spacer 3.31|1996605|33|NC_011963|PILER-CR matches to NZ_CP017750 (Cupriavidus sp. USMAA2-4 plasmid unnamed1, complete sequence) position: , mismatch: 6, identity: 0.818

aaccagg-tggcggtcggcaatgcgcgggtccgc	CRISPR spacer
-tcgaggctggtggtcggcaatgcgcggttcctc	Protospacer
  * *** ***.**************** *** *

4. spacer 3.31|1996605|33|NC_011963|PILER-CR matches to NZ_CP026545 (Cupriavidus metallidurans strain Ni-2 plasmid unnamed1) position: , mismatch: 6, identity: 0.818

aaccagg-tggcggtcggcaatgcgcgggtccgc	CRISPR spacer
-tcgaggctggtggtcggcaatgcgcggttcctc	Protospacer
  * *** ***.**************** *** *

5. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP013635 (Rhizobium sp. N324 plasmid pRspN324e, complete sequence) position: , mismatch: 7, identity: 0.794

--cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
atcgcctgat--cgttgttgagcgcggcgacgccgc	Protospacer
  ****.*..  ****** ******* *********

6. spacer 3.25|1996605|34|NC_011963|CRISPRCasFinder,CRT matches to NZ_CP017750 (Cupriavidus sp. USMAA2-4 plasmid unnamed1, complete sequence) position: , mismatch: 7, identity: 0.794

aaccagg-tggcggtcggcaatgcgcgggtccgcc	CRISPR spacer
-tcgaggctggtggtcggcaatgcgcggttcctct	Protospacer
  * *** ***.**************** *** *.

7. spacer 3.25|1996605|34|NC_011963|CRISPRCasFinder,CRT matches to NZ_CP026545 (Cupriavidus metallidurans strain Ni-2 plasmid unnamed1) position: , mismatch: 7, identity: 0.794

aaccagg-tggcggtcggcaatgcgcgggtccgcc	CRISPR spacer
-tcgaggctggtggtcggcaatgcgcggttcctct	Protospacer
  * *** ***.**************** *** *.

8. spacer 3.33|1996739|33|NC_011963|PILER-CR matches to NZ_CP015007 (Aminobacter aminovorans strain KCTC 2477 plasmid pAA02, complete sequence) position: , mismatch: 7, identity: 0.788

gtcgcgggccagaaacacaactgcgccctcgtg	CRISPR spacer
atcgccggccagaaaaacaactgcgcccatgat	Protospacer
.**** ********* ************ .*

9. spacer 3.4|1995213|33|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP035001 (Rhizobium acidisoli strain FH23 plasmid pRapFH23c, complete sequence) position: , mismatch: 8, identity: 0.758

catgtgcagggcgaacgcggtgacgccccacgc	CRISPR spacer
catgtacagggcgaccgcggtgacgtcggcgac	Protospacer
*****.******** **********.*    .*

10. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP021653 (Ralstonia solanacearum strain RS 488 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

11. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP021767 (Ralstonia solanacearum strain RS 489 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

12. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP012940 (Ralstonia solanacearum strain UW163 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

13. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP012944 (Ralstonia solanacearum strain IBSBF1503 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

14. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP012688 (Ralstonia solanacearum strain UY031 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

15. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NC_017575 (Ralstonia solanacearum Po82 megaplasmid, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

16. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP026308 (Ralstonia solanacearum strain IBSBF 2571 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

17. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to CP047139 (Ralstonia solanacearum strain CFBP 8695 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

18. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP051295 (Ralstonia solanacearum strain CIAT_078 plasmid megaplasmid, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

19. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to CP047137 (Ralstonia solanacearum strain CFBP 8697 plasmid unnamed, complete sequence) position: , mismatch: 8, identity: 0.765

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
ggcccggtcgcgttgtagagcgcgccggcatgcc	Protospacer
 ******. ******************.*..  *

20. spacer 3.12|1995747|33|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP013539 (Rhizobium phaseoli strain R630 plasmid pRphaR630b, complete sequence) position: , mismatch: 8, identity: 0.758

cgtggtctacgaggcgcccctcgatccgcgctg	CRISPR spacer
ccgggcgatcgaggcacccctcgatcctcgctg	Protospacer
*  **.   ******.*********** *****

21. spacer 3.12|1995747|33|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_AP014705 (Methylobacterium aquaticum strain MA-22A plasmid pMaq22A_1p, complete sequence) position: , mismatch: 8, identity: 0.758

cgtggtctacgaggcgcccctcgatccgcgctg	CRISPR spacer
ggcgctgctcgacgcgcccctcgatgcgcgctg	Protospacer
 *.* * . *** ************ *******

22. spacer 3.20|1996276|32|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP018299 (Photobacterium damselae strain Phdp Wu-1 plasmid plas1, complete sequence) position: , mismatch: 8, identity: 0.75

-acacaaaaaacaaaagccgtcatgccgatagg	CRISPR spacer
aatac-taaaacaaaagcggtcatgccaatgtc	Protospacer
 *.**  *********** ********.**.

23. spacer 3.27|1996739|34|NC_011963|CRISPRCasFinder,CRT matches to NZ_CP015007 (Aminobacter aminovorans strain KCTC 2477 plasmid pAA02, complete sequence) position: , mismatch: 8, identity: 0.765

gtcgcgggccagaaacacaactgcgccctcgtgc	CRISPR spacer
atcgccggccagaaaaacaactgcgcccatgatg	Protospacer
.**** ********* ************ .*

24. spacer 3.11|1995682|33|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NC_021289 (Burkholderia insecticola plasmid p1, complete sequence) position: , mismatch: 9, identity: 0.727

gtcaccgatggccccatgggccgtgtcgcccgg	CRISPR spacer
tcgcccgatggccccacgggccgtctcggtctg	Protospacer
 .  ************.******* *** .* *

25. spacer 3.18|1996144|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP022366 (Azospirillum sp. TSH58 plasmid TSH58_p04, complete sequence) position: , mismatch: 9, identity: 0.735

acgctgggcccggcgtccgagccgctgcagggac	CRISPR spacer
tcgctgtgcccggcgtcggagccgcggaaatcgc	Protospacer
 ***** ********** ******* * *.  .*

26. spacer 3.30|1996939|32|NC_011963|CRT matches to NZ_CP025016 (Rhizobium leguminosarum strain Norway plasmid pRLN4, complete sequence) position: , mismatch: 9, identity: 0.719

agtaggtctggtcggcctgctcaagcgtcatg	CRISPR spacer
catcgccacggtcggactgctcaagcgtaatg	Protospacer
 .* * . .****** ************ ***

27. spacer 3.30|1996939|32|NC_011963|CRT matches to NZ_CP010858 (Marinovum algicola DG 898 plasmid pMaD3) position: , mismatch: 9, identity: 0.719

agtaggtctggtcggcctgctcaagcgtcatg	CRISPR spacer
gcgcggtctggccggcctgctccagcgcctcg	Protospacer
.   *******.********** ****.* .*

28. spacer 3.3|1995145|36|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to CP000662 (Rhodobacter sphaeroides ATCC 17025 plasmid pRSPA01, complete sequence) position: , mismatch: 10, identity: 0.722

gggctgatctcgaccccgggcgggatcaccggaacg	CRISPR spacer
ctcatgacctcgaccgcgggcgggatcaccttctcg	Protospacer
    ***.******* **************    **

29. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_AP022571 (Mycolicibacterium poriferae strain JCM 12603 plasmid pJCM12603, complete sequence) position: , mismatch: 10, identity: 0.706

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
gggccggcggcgttgcacagcgcgccgcgacgat	Protospacer
 * ************.* *********  .* ..

30. spacer 3.5|1995278|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP040820 (Paraoceanicella profunda strain D4M1 plasmid pD4M1B, complete sequence) position: , mismatch: 10, identity: 0.706

cgcccggcggcgttgtagagcgcgccgacgccgc	CRISPR spacer
tccacggcggccttgtagagcgcgcggatctgcc	Protospacer
. * ******* ************* **. .  *

31. spacer 3.15|1995944|35|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_LR594663 (Variovorax sp. RA8 plasmid 2) position: , mismatch: 10, identity: 0.714

ccaatcgtccacgcccagcgcccaggccagccacg	CRISPR spacer
tgcagtgtccacgcacagcgccctggccagcctat	Protospacer
.  * .******** ******** ********

32. spacer 3.15|1995944|35|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP034186 (Deinococcus sp. S14-83 strain S14-83T plasmid unnamed2, complete sequence) position: , mismatch: 10, identity: 0.714

ccaatcgtccacgcccagcgcccaggccagccacg	CRISPR spacer
gatgctgtagacgcccagcacccaggccagccccg	Protospacer
   ...**  *********.************ **

33. spacer 3.18|1996144|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_AP022611 (Mycolicibacterium madagascariense strain JCM 13574 plasmid pJCM13574) position: , mismatch: 10, identity: 0.706

acgctgggcccggcgtccgagccgctgcagggac	CRISPR spacer
gtccttggcgcggcgtccgagccgctggccagcc	Protospacer
.. ** *** *****************   .* *

34. spacer 3.21|1996340|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP020443 (Paracoccus yeei strain FDAARGOS_252 plasmid unnamed3, complete sequence) position: , mismatch: 10, identity: 0.706

ttacacctgctcgactggcagcaccggtaagatt	CRISPR spacer
ggccacctgatcgactggctgcaccggggcgagg	Protospacer
   ****** ********* ******* . **

35. spacer 3.35|1996872|34|NC_011963|PILER-CR matches to NZ_CP040937 (Hymenobacter sp. DG01 plasmid unnamed, complete sequence) position: , mismatch: 10, identity: 0.706

tcgctcggcacgtagcggccggcgtaggccgccg	CRISPR spacer
aaggctggcacgtagcggccagcgtgggccacat	Protospacer
  * ..**************.****.****.*

36. spacer 3.35|1996872|34|NC_011963|PILER-CR matches to NZ_CP024314 (Rhizobium sp. NXC24 plasmid pRspNXC24c, complete sequence) position: , mismatch: 10, identity: 0.706

tcgctcggcacgtagcggccggcgtaggccgccg	CRISPR spacer
gtccgtggcacgtagcggccggcgtcgccctggg	Protospacer
 . * .******************* * **   *

37. spacer 3.6|1995344|36|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NC_021347 (Rhodococcus phage E3, complete genome) position: , mismatch: 11, identity: 0.694

cccctcgtcgcccgccgggtggacgtcgacaagatg	CRISPR spacer
gccctcgacgcccgccgcgtggacgtcgttggctga	Protospacer
 ****** ********* ********** ...   .

38. spacer 3.8|1995479|35|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to MN908685 (Microbacterium phage PauloDiaboli, complete genome) position: , mismatch: 11, identity: 0.686

atcaggcggatgttggtcagcatgtcctcgatggc	CRISPR spacer
gcagttccgatgttggtcagaatgtcctcggtgta	Protospacer
.. .  * ************ *********.**

39. spacer 3.19|1996210|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NC_018696 (Paraburkholderia phenoliruptrix BR3459a plasmid pSYMBR3459, complete sequence) position: , mismatch: 11, identity: 0.676

ggaaacatgcccgatcatgtcggacgtgatgaaa	CRISPR spacer
catgccgggctcgatcatgtcggccgtgatgatc	Protospacer
 . . *. **.************ ********

40. spacer 3.21|1996340|34|NC_011963|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP032695 (Rhizobium jaguaris strain CCGE525 plasmid pRCCGE525c, complete sequence) position: , mismatch: 11, identity: 0.676

ttacacctgctcgactggcagcaccggtaagatt	CRISPR spacer
cttgacctgctcgacatgcagcaccggtttcgcc	Protospacer
.*  ***********  ***********   ...

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

87161 : 96208

uncultured_Mediterranean_phage(50.0%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_041669063.1\|87161_89384_+	cadmium-translocating P-type ATPase	E4ZFI9	Streptococcus_phage	4.4e-115	41.3
WP_009563714.1\|89507_90029_-	single-stranded DNA-binding protein	A0A0U2C0X4	Paracoccus_phage	4.6e-47	77.6
WP_041669982.1\|90242_90857_+	lytic transglycosylase domain-containing protein	A0A0S2SXL7	Bacillus_phage	3.8e-24	45.3
WP_012643477.1\|90969_92262_-\|tRNA	serine--tRNA ligase	A0A1B1IVT2	uncultured_Mediterranean_phage	7.3e-94	45.6
WP_012643478.1\|92368_92926_-	superoxide dismutase family protein	NA	NA	NA	NA
WP_002722646.1\|93217_93544_+	preprotein translocase subunit YajC	A0A1B1IVR5	uncultured_Mediterranean_phage	4.3e-19	54.4
WP_012643480.1\|93559_95224_+	protein translocase subunit SecD	NA	NA	NA	NA
WP_012643481.1\|95233_96208_+	protein translocase subunit SecF	A0A1B1IVP7	uncultured_Mediterranean_phage	5.2e-52	43.3

DBSCAN-SWA_2

337842 : 345763

Gordonia_phage(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_041669162.1\|337842_338601_-	phage Gp37/Gp68 family protein	A0A2P1A0W3	Gordonia_phage	1.2e-59	44.3
WP_145975067.1\|339203_339743_+	hypothetical protein	NA	NA	NA	NA
WP_041669164.1\|339817_340300_-	hypothetical protein	F8TVB7	EBPR_siphovirus	7.5e-12	51.8
WP_012643651.1\|340312_341122_-	M15 family metallopeptidase	A0A0B5A5A2	Paracoccus_phage	1.4e-63	50.2
WP_041669165.1\|341173_341980_-	DNA adenine methylase	A0A291AUP9	Sinorhizobium_phage	1.6e-83	57.8
WP_145975068.1\|342462_343134_+	DUF2971 domain-containing protein	NA	NA	NA	NA
WP_009567184.1\|343167_343485_-	hypothetical protein	I3UM16	Rhodobacter_phage	2.8e-23	57.9
WP_041669171.1\|343615_343951_-	hypothetical protein	NA	NA	NA	NA
WP_041669172.1\|343954_344272_-	hypothetical protein	NA	NA	NA	NA
WP_012643656.1\|344278_345763_-	hypothetical protein	A0A0S3UG21	Pseudomonas_phage	2.1e-12	31.3

DBSCAN-SWA_3

352380 : 372207

Paracoccus_phage(23.08%)

head,integrase,terminase,capsid,portal

attL 364134:364151|attR 375800:375817

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_011337201.1\|352380_352824_-	hypothetical protein	A0A2P1N076	Streptomyces_phage	1.8e-07	33.3
WP_012643661.1\|352833_353214_-	DUF3168 domain-containing protein	A0A0U2BX31	Paracoccus_phage	1.7e-27	54.8
WP_012643662.1\|353218_353386_-	hypothetical protein	NA	NA	NA	NA
WP_012643663.1\|353382_353856_-	HK97 gp10 family phage protein	A0A0U2C0P4	Paracoccus_phage	6.0e-30	51.3
WP_041669174.1\|353852_354185_-\|head	phage head closure protein	NA	NA	NA	NA
WP_012643665.1\|354181_354688_-	hypothetical protein	NA	NA	NA	NA
WP_012643666.1\|354692_354977_-	hypothetical protein	NA	NA	NA	NA
WP_012643667.1\|355072_356398_-\|capsid	phage major capsid protein	Q6UAX6	Klebsiella_phage	4.1e-52	37.5
WP_009567369.1\|356652_357396_+	sulfite exporter TauE/SafE family protein	NA	NA	NA	NA
WP_012643668.1\|357406_358321_-	S49 family peptidase	I3ULZ8	Rhodobacter_phage	2.2e-20	36.7
WP_012643669.1\|358317_359553_-\|portal	phage portal protein	Q6DMU2	Streptococcus_phage	9.0e-25	26.3
WP_041669181.1\|359761_360262_-	N-acetyltransferase	NA	NA	NA	NA
WP_012643671.1\|360263_360527_-	YjhX family toxin	NA	NA	NA	NA
WP_012643672.1\|360857_362516_-\|terminase	terminase	A0A2H4JB64	uncultured_Caudovirales_phage	2.2e-79	32.3
WP_012643673.1\|362502_362940_-\|terminase	P27 family phage terminase small subunit	NA	NA	NA	NA
WP_012643674.1\|363202_363616_-	HNH endonuclease	A0A2D1GNP5	Pseudomonas_phage	1.9e-19	42.0
WP_012643675.1\|363720_364260_-	hypothetical protein	A0A0U2C0Z0	Paracoccus_phage	1.9e-08	32.6
364134:364151	attL	NA	NA	NA	NA
WP_012643676.1\|364465_365044_-	hypothetical protein	NA	NA	NA	NA
WP_174893312.1\|365247_365937_-	DUF1376 domain-containing protein	NA	NA	NA	NA
WP_012643678.1\|365943_366495_-	DUF1937 family protein	NA	NA	NA	NA
WP_012641287.1\|366491_366770_-	hypothetical protein	NA	NA	NA	NA
WP_002719110.1\|366766_366979_-	hypothetical protein	NA	NA	NA	NA
WP_009564704.1\|367095_367308_-	hypothetical protein	NA	NA	NA	NA
WP_157228015.1\|367395_367740_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_041669191.1\|368020_368218_+	hypothetical protein	NA	NA	NA	NA
WP_012643680.1\|368214_368547_+	hypothetical protein	NA	NA	NA	NA
WP_012643681.1\|368546_368942_+	DUF2312 domain-containing protein	A0A1X9HX62	Ruegeria_phage	1.7e-25	56.2
WP_012643682.1\|369064_370876_+	ParB/RepB/Spo0J family partition protein	G8DH78	Emiliania_huxleyi_virus	3.9e-85	37.1
WP_041669193.1\|370951_371182_+	helix-turn-helix domain-containing protein	I3UM25	Rhodobacter_phage	3.1e-16	62.9
WP_012643684.1\|371265_372207_+\|integrase	tyrosine-type recombinase/integrase	I3UM24	Rhodobacter_phage	3.2e-67	46.3
375800:375817	attR	NA	NA	NA	NA

DBSCAN-SWA_4

731042 : 801675

Paracoccus_phage(22.22%)

head,protease,tail,capsid,portal

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_002719573.1\|731042_731768_+\|protease	proteasome-type protease	NA	NA	NA	NA
WP_041669300.1\|731757_732711_-	alpha/beta hydrolase	NA	NA	NA	NA
WP_009562457.1\|732707_732992_-	SCP2 sterol-binding domain-containing protein	NA	NA	NA	NA
WP_080517573.1\|733067_733640_+	tetratricopeptide repeat protein	NA	NA	NA	NA
WP_041669302.1\|733649_736538_+	helicase	A0A248SJQ0	Salicola_phage	2.9e-26	28.6
WP_012643928.1\|736543_736840_+	RNA-binding S4 domain-containing protein	NA	NA	NA	NA
WP_002719579.1\|736894_737233_+	ferredoxin family protein	NA	NA	NA	NA
WP_002719580.1\|737512_738022_+	CarD family transcriptional regulator	NA	NA	NA	NA
WP_012643929.1\|738210_738960_-	adenosylcobinamide-GDP ribazoletransferase	NA	NA	NA	NA
WP_012643930.1\|739041_740058_+	nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase	NA	NA	NA	NA
WP_012643931.1\|740114_741983_-	cation:proton antiporter	NA	NA	NA	NA
WP_049763950.1\|742157_745034_-	hypothetical protein	NA	NA	NA	NA
WP_012643933.1\|745197_745890_+	SIMPL domain-containing protein	NA	NA	NA	NA
WP_012643934.1\|745935_747228_-	O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase	NA	NA	NA	NA
WP_012643935.1\|747473_747821_-	hypothetical protein	NA	NA	NA	NA
WP_009562470.1\|747817_748204_-	response regulator	Q56AR1	Bacillus_thuringiensis_phage	1.0e-06	32.3
WP_012643937.1\|748181_749099_-	protein-glutamate O-methyltransferase	NA	NA	NA	NA
WP_012643938.1\|749095_749554_-	chemotaxis protein CheW	NA	NA	NA	NA
WP_012643939.1\|749555_751616_-	chemotaxis protein CheA	NA	NA	NA	NA
WP_009565207.1\|751623_751992_-	response regulator	Q56AR1	Bacillus_thuringiensis_phage	1.7e-11	34.5
WP_041669307.1\|751982_752267_-	STAS domain-containing protein	NA	NA	NA	NA
WP_049763951.1\|752263_752863_-	chemotaxis protein CheD	NA	NA	NA	NA
WP_012643943.1\|752920_755299_-	chemotaxis protein	A0A2H4J162	uncultured_Caudovirales_phage	6.0e-09	62.7
WP_041669308.1\|755393_757181_-	hypothetical protein	NA	NA	NA	NA
WP_012643944.1\|757283_758966_-	methyl-accepting chemotaxis protein	A0A2H4J162	uncultured_Caudovirales_phage	1.0e-07	28.8
WP_002719598.1\|759054_759423_-	response regulator	Q56AR1	Bacillus_thuringiensis_phage	1.5e-12	38.5
WP_041669310.1\|759419_759749_-	STAS domain-containing protein	NA	NA	NA	NA
WP_049763952.1\|760081_762034_+	alpha-1,4-glucan--maltose-1-phosphate maltosyltransferase	NA	NA	NA	NA
WP_012643948.1\|762030_765339_+	maltose alpha-D-glucosyltransferase	NA	NA	NA	NA
WP_041669314.1\|765335_767522_+	1,4-alpha-glucan branching protein GlgB	NA	NA	NA	NA
WP_012643950.1\|767518_769585_+	glycogen debranching protein GlgX	NA	NA	NA	NA
WP_012643951.1\|769581_771360_+	malto-oligosyltrehalose trehalohydrolase	NA	NA	NA	NA
WP_012643952.1\|771356_773174_+	4-alpha-glucanotransferase	NA	NA	NA	NA
WP_012643953.1\|773170_775786_+	malto-oligosyltrehalose synthase	NA	NA	NA	NA
WP_012643954.1\|775859_776525_-	SDR family oxidoreductase	NA	NA	NA	NA
WP_002719608.1\|776644_778108_-	amidophosphoribosyltransferase	A0A0M3SGR2	Mollivirus	1.2e-47	32.0
WP_012643955.1\|778192_778807_-	CvpA family protein	NA	NA	NA	NA
WP_012643956.1\|778825_780184_-	DNA repair protein RadA	NA	NA	NA	NA
WP_002719611.1\|780356_780782_-	paraquat-inducible protein A	NA	NA	NA	NA
WP_002719612.1\|780782_781529_-	ATP-binding cassette domain-containing protein	F2Y1V5	Organic_Lake_phycodnavirus	8.7e-07	25.6
WP_009564495.1\|781525_782308_-	ABC transporter permease	NA	NA	NA	NA
WP_009564494.1\|782304_783354_-	alanine racemase	NA	NA	NA	NA
WP_012643959.1\|783582_784320_+	3-oxoacyl-ACP reductase FabG	NA	NA	NA	NA
WP_002719616.1\|784498_784732_+	acyl carrier protein	I1TR04	Pseudomonas_phage	7.3e-05	43.9
WP_002719617.1\|785225_786488_+	beta-ketoacyl-ACP synthase II	NA	NA	NA	NA
WP_012643960.1\|786487_787666_+	endolytic transglycosylase MltG	NA	NA	NA	NA
WP_161601241.1\|787736_788180_+	hypothetical protein	NA	NA	NA	NA
WP_012643961.1\|788172_789471_+	DNA-packaging protein	A0A0K1LMR9	Caulobacter_phage	2.3e-71	41.7
WP_041669323.1\|789543_790719_+\|portal	phage portal protein	W8ECU7	Geobacillus_phage	4.5e-58	38.3
WP_002719622.1\|790720_790954_+	hypothetical protein	NA	NA	NA	NA
WP_011840821.1\|790958_791522_+\|head,protease	HK97 family phage prohead protease	A0A0U2BX10	Paracoccus_phage	1.1e-30	49.3
WP_009564487.1\|791587_792784_+\|capsid	phage major capsid protein	B0VK33	Azospirillum_phage	3.6e-63	41.5
WP_009564486.1\|792879_793479_+	hypothetical protein	NA	NA	NA	NA
WP_012643963.1\|793478_793814_+\|head,tail	head-tail adaptor protein	NA	NA	NA	NA
WP_012643964.1\|793810_794209_+	DUF3168 domain-containing protein	NA	NA	NA	NA
WP_002719628.1\|794246_794660_+\|tail	phage major tail protein, TP901-1 family	NA	NA	NA	NA
WP_002719629.1\|794659_794977_+	gene transfer agent family protein	NA	NA	NA	NA
WP_012643965.1\|794978_795179_+\|tail	phage tail assembly chaperone	NA	NA	NA	NA
WP_012643966.1\|795171_795822_+\|tail	phage tail tape measure protein	D6PFD6	uncultured_phage	4.3e-10	28.1
WP_041670027.1\|795831_796464_+	DUF2460 domain-containing protein	A0A0B5A2K3	Paracoccus_phage	4.7e-62	51.9
WP_012643968.1\|796463_797348_+	DUF2163 domain-containing protein	A0A0B5A5B8	Paracoccus_phage	2.5e-61	43.9
WP_012643969.1\|797344_797785_+	peptidase	A0A1V0DYB6	Dinoroseobacter_phage	1.5e-27	47.1
WP_012643970.1\|797784_801675_+	glycoside hydrolase TIM-barrel-like domain-containing protein	A0A0B5A7K5	Paracoccus_phage	5.2e-220	39.3

DBSCAN-SWA_5

3080811 : 3108004

Paracoccus_phage(25.0%)

head,terminase,transposase,tail,capsid,portal

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_041669943.1\|3080811_3081174_-\|transposase	transposase	NA	NA	NA	NA
WP_145975079.1\|3082394_3083318_-	DUF4435 domain-containing protein	NA	NA	NA	NA
WP_080517639.1\|3083334_3084732_-	AAA family ATPase	NA	NA	NA	NA
WP_041669947.1\|3086490_3087297_-	DNA adenine methylase	A0A291AUP9	Sinorhizobium_phage	1.6e-83	58.2
WP_145975080.1\|3087474_3088251_-	hypothetical protein	A0A2H4EXG4	Aeromonas_phage	2.3e-10	43.2
WP_011336898.1\|3088366_3088684_-	hypothetical protein	I3UM16	Rhodobacter_phage	2.1e-23	58.9
WP_080517640.1\|3088919_3089255_-	hypothetical protein	NA	NA	NA	NA
WP_015921834.1\|3089258_3089576_-	hypothetical protein	NA	NA	NA	NA
WP_015920764.1\|3089582_3091067_-	hypothetical protein	A0A0S3UG21	Pseudomonas_phage	2.7e-12	30.7
WP_015921835.1\|3091082_3091973_-	hypothetical protein	NA	NA	NA	NA
WP_041669948.1\|3097020_3097266_-	hypothetical protein	NA	NA	NA	NA
WP_015921839.1\|3097340_3097733_-	hypothetical protein	NA	NA	NA	NA
WP_015921840.1\|3097729_3098170_-	hypothetical protein	A0A2P1N076	Streptomyces_phage	2.5e-06	34.4
WP_015921841.1\|3098179_3098560_-	DUF3168 domain-containing protein	A0A0U2BX31	Paracoccus_phage	3.8e-27	54.0
WP_015921842.1\|3098563_3099034_-	HK97 gp10 family phage protein	A0A0U2C0P4	Paracoccus_phage	1.5e-28	51.1
WP_041669952.1\|3099030_3099363_-\|head,tail	head-tail adaptor protein	A0A0U2BXJ0	Paracoccus_phage	7.0e-17	44.5
WP_015921844.1\|3099359_3099866_-	hypothetical protein	NA	NA	NA	NA
WP_015921845.1\|3099870_3100167_-	hypothetical protein	NA	NA	NA	NA
WP_015921846.1\|3100264_3101590_-\|capsid	phage major capsid protein	Q6UAX6	Klebsiella_phage	7.1e-52	37.2
WP_145975081.1\|3101940_3102345_-	hypothetical protein	NA	NA	NA	NA
WP_015921848.1\|3102669_3103587_-	S49 family peptidase	I3ULZ8	Rhodobacter_phage	5.8e-21	36.7
WP_041669954.1\|3103583_3104819_-\|portal	phage portal protein	Q6DMU2	Streptococcus_phage	5.8e-24	26.3
WP_145975082.1\|3105030_3105795_+	hypothetical protein	NA	NA	NA	NA
WP_012643672.1\|3105921_3107580_-\|terminase	terminase	A0A2H4JB64	uncultured_Caudovirales_phage	2.2e-79	32.3
WP_015921852.1\|3107566_3108004_-\|terminase	phage terminase small subunit P27 family	NA	NA	NA	NA

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. NC_011960

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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

2. NC_011958

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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

3. NC_011963

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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