CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Self targeting spacer number	Target MGE spacer number	Prophage number	Anti-CRISPR protein number
NC_011978	Thermotoga neapolitana DSM 4359, complete sequence	8 crisprs	cas14k,DEDDh,cas6,csx1,cas10,cas7,cas5,cas3HD,cas3,cas4,cas1,cas2,WYL,csa3	0	2	3	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_011978_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011978_1

75115-75482

Orphan

III-A

Consensus_repeat	Method
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CRISPRCasFinder
GTTTCCATACCTCNAAGGAAGNATTGAAAC	CRT
GTTTCCATACCTCTAAGGAAGGATTGAAAC	PILER-CR

5 spacers

DEDDh

The CRISPR arrays of NC_011978_1

>merge|NC_011978|1|75115-75482|CRISPRCasFinder,CRT,PILER-CR
AGGGTTATACCTCTAAGGAAGTATTGAAACCGAAATCGTGGTTTACTTCCAGAATGCCGGTGGATTGTTTCCATACCTCAAAGGAAGTATTGAAACGTGCTGTAATAGGATTTTTCCTCAGAAAGAAACTTTTTGGTTTCCATACCTCAAAGGAAGTATTGAAACCAAAAGAGACTTTCCCCAACCACTCTCCAAACCAGAAGTTTCCATACCTCTAAGGAAGGATTGAAACTTGGAAACTTGGGAAGGAGGAGTCTTGTTTGGTTTAGTTTCCATACCTCTAAGGAAGGATTGAAACCAAGAACGAATCGATGCCGTATTCGTTCCGTGTCAGAACGGTTTCCATACCTCTAAGGAAGGATTGAAAC

>NC_011978|1|1|75115-75482|CRISPRCasFinder
AGGGTTATACCTCTAAGGAAGTATTGAAAC	CGAAATCGTGGTTTACTTCCAGAATGCCGGTGGATT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GTGCTGTAATAGGATTTTTCCTCAGAAAGAAACTTTTTG
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CAAAAGAGACTTTCCCCAACCACTCTCCAAACCAGAA
GTTTCCATACCTCTAAGGAAGGATTGAAAC	TTGGAAACTTGGGAAGGAGGAGTCTTGTTTGGTTTA
GTTTCCATACCTCTAAGGAAGGATTGAAAC	CAAGAACGAATCGATGCCGTATTCGTTCCGTGTCAGAACG
GTTTCCATACCTCTAAGGAAGGATTGAAAC

>NC_011978|1|1|75115-75482|CRT
AGGGTTATACCTCTAAGGAAGTATTGAAAC	CGAAATCGTGGTTTACTTCCAGAATGCCGGTGGATT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GTGCTGTAATAGGATTTTTCCTCAGAAAGAAACTTTTTG
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CAAAAGAGACTTTCCCCAACCACTCTCCAAACCAGAA
GTTTCCATACCTCTAAGGAAGGATTGAAAC	TTGGAAACTTGGGAAGGAGGAGTCTTGTTTGGTTTA
GTTTCCATACCTCTAAGGAAGGATTGAAAC	CAAGAACGAATCGATGCCGTATTCGTTCCGTGTCAGAACG
GTTTCCATACCTCTAAGGAAGGATTGAAAC

>NC_011978|1|1|75181-75482|PILER-CR
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GTGCTGTAATAGGATTTTTCCTCAGAAAGAAACTTTTTG
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CAAAAGAGACTTTCCCCAACCACTCTCCAAACCAGAA
GTTTCCATACCTCTAAGGAAGGATTGAAAC	TTGGAAACTTGGGAAGGAGGAGTCTTGTTTGGTTTA
GTTTCCATACCTCTAAGGAAGGATTGAAAC	CAAGAACGAATCGATGCCGTATTCGTTCCGTGTCAGAACG
GTTTCCATACCTCTAAGGAAGGATTGAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_011978.1\|WP_012644974.1\|76868_77408_+\|GNAT-family-N-acetyltransferase	unknown	unknown	gnl\|CDD\|366181
NC_011978.1\|WP_038066286.1\|82073_83081_-\|tRNA-preQ1(34)-S-adenosylmethionine-ribosyltransferase-isomerase-QueA	unknown	unknown	gnl\|CDD\|234666
NC_011978.1\|WP_012644970.1\|71795_73628_-\|ATP-dependent-zinc-metalloprotease-FtsH	unknown	unknown	gnl\|CDD\|273520
NC_011978.1\|WP_012644963.1\|66059_66956_+\|DMT-family-transporter	unknown	unknown	gnl\|CDD\|223769
NC_011978.1\|WP_012644981.1\|87266_88151_+\|signal-recognition-particle-docking-protein-FtsY	unknown	unknown	gnl\|CDD\|236686
NC_011978.1\|WP_012644967.1\|68658_69963_-\|nucleotide-sugar-dehydrogenase	unknown	unknown	gnl\|CDD\|223749
NC_011978.1\|WP_038066311.1\|84520_85672_-\|DegT/DnrJ/EryC1/StrS-aminotransferase-family-protein	unknown	unknown	gnl\|CDD\|223476
NC_011978.1\|WP_012644973.1\|76100_76868_+\|pyrroline-5-carboxylate-reductase	unknown	unknown	gnl\|CDD\|223422
NC_011978.1\|WP_012644964.1\|66885_67965_+\|Gfo/Idh/MocA-family-oxidoreductase	unknown	unknown	gnl\|CDD\|223745
NC_011978.1\|WP_012644975.1\|77404_81508_-\|PolC-type-DNA-polymerase-III	DEDDh	cd06127_DEDDh_CAS-I	gnl\|CDD\|234767
NC_011978.1\|WP_038066255.1\|69956_71414_-\|radical-SAM-protein	unknown	unknown	gnl\|CDD\|188475
NC_011978.1\|WP_012644980.1\|85768_87151_-\|DegQ-family-serine-endoprotease	unknown	unknown	gnl\|CDD\|273938
NC_011978.1\|WP_012644982.1\|88147_88801_+\|DUF2225-domain-containing-protein	unknown	unknown	gnl\|CDD\|224569
NC_011978.1\|WP_038066252.1\|64414_66055_+\|putative-manganese-dependent-inorganic-diphosphatase	unknown	unknown	gnl\|CDD\|237843
NC_011978.1\|WP_038066259.1\|73614_74859_-\|tRNA-lysidine(34)-synthetase-TilS	unknown	unknown	gnl\|CDD\|274129
NC_011978.1\|WP_041437364.1\|83091_84528_-\|apolipoprotein-N-acyltransferase	unknown	unknown	gnl\|CDD\|223885
NC_011978.1\|WP_166426831.1\|63325_64357_-\|rod-shape-determining-protein-MreB	unknown	unknown	gnl\|CDD\|237564
NC_011978.1\|WP_038066274.1\|67964_68672_+\|rhomboid-family-intramembrane-serine-protease	unknown	unknown	gnl\|CDD\|366759
NC_011978.1\|WP_012644969.1\|71373_71799_-\|thioesterase-family-protein	unknown	unknown	gnl\|CDD\|227783
NC_011978.1\|WP_038066281.1\|81494_81992_-\|crossover-junction-endodeoxyribonuclease-RuvC	unknown	unknown	gnl\|CDD\|234587

Protein	Function_ID	Function_description	E-value
NC_011978.1\|WP_012644974.1\|76868_77408_+\|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.	2.21926e-19
NC_011978.1\|WP_038066286.1\|82073_83081_-\|tRNA-preQ1(34)-S-adenosylmethionine-ribosyltransferase-isomerase-QueA	gnl\|CDD\|234666	PRK00147, queA, S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional.	0
NC_011978.1\|WP_012644970.1\|71795_73628_-\|ATP-dependent-zinc-metalloprotease-FtsH	gnl\|CDD\|273520	TIGR01241, ATP-dependent_zinc_metalloprotease_FtsH, ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides].	0
NC_011978.1\|WP_012644963.1\|66059_66956_+\|DMT-family-transporter	gnl\|CDD\|223769	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only].	1.48463e-20
NC_011978.1\|WP_012644981.1\|87266_88151_+\|signal-recognition-particle-docking-protein-FtsY	gnl\|CDD\|236686	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional.	7.68247e-172
NC_011978.1\|WP_012644967.1\|68658_69963_-\|nucleotide-sugar-dehydrogenase	gnl\|CDD\|223749	COG0677, WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane].	0
NC_011978.1\|WP_038066311.1\|84520_85672_-\|DegT/DnrJ/EryC1/StrS-aminotransferase-family-protein	gnl\|CDD\|223476	COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane].	2.79552e-158
NC_011978.1\|WP_012644973.1\|76100_76868_+\|pyrroline-5-carboxylate-reductase	gnl\|CDD\|223422	COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism].	2.40396e-80
NC_011978.1\|WP_012644964.1\|66885_67965_+\|Gfo/Idh/MocA-family-oxidoreductase	gnl\|CDD\|223745	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only].	3.70892e-85
NC_011978.1\|WP_012644975.1\|77404_81508_-\|PolC-type-DNA-polymerase-III	gnl\|CDD\|234767	PRK00448, polC, DNA polymerase III PolC; Validated.	0
NC_011978.1\|WP_038066255.1\|69956_71414_-\|radical-SAM-protein	gnl\|CDD\|188475	TIGR03960, radical_SAM_domain_protein, radical SAM family uncharacterized protein. This model describes a radical SAM protein, or protein region, regularly found paired with or fused to a region described by TIGR03936. PSI-BLAST analysis of TIGR03936 suggests a relationship to the tRNA pseudouridine synthase TruA, suggesting that this system may act in RNA modification. [Unknown function, Enzymes of unknown specificity].	3.75285e-59
NC_011978.1\|WP_012644980.1\|85768_87151_-\|DegQ-family-serine-endoprotease	gnl\|CDD\|273938	TIGR02037, Probable_periplasmic_serine_protease_do/HhoA-like, periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides].	0
NC_011978.1\|WP_012644982.1\|88147_88801_+\|DUF2225-domain-containing-protein	gnl\|CDD\|224569	COG1655, COG1655, Uncharacterized protein conserved in bacteria [Function unknown].	2.49304e-70
NC_011978.1\|WP_038066252.1\|64414_66055_+\|putative-manganese-dependent-inorganic-diphosphatase	gnl\|CDD\|237843	PRK14869, PRK14869, putative manganese-dependent inorganic diphosphatase.	0
NC_011978.1\|WP_038066259.1\|73614_74859_-\|tRNA-lysidine(34)-synthetase-TilS	gnl\|CDD\|274129	TIGR02432, tRNAIle-lysidine_synthase, tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer). [Protein synthesis, tRNA and rRNA base modification].	4.56021e-83
NC_011978.1\|WP_041437364.1\|83091_84528_-\|apolipoprotein-N-acyltransferase	gnl\|CDD\|223885	COG0815, Lnt, Apolipoprotein N-acyltransferase [Cell envelope biogenesis, outer membrane].	2.06908e-85
NC_011978.1\|WP_166426831.1\|63325_64357_-\|rod-shape-determining-protein-MreB	gnl\|CDD\|237564	PRK13930, PRK13930, rod shape-determining protein MreB; Provisional.	0
NC_011978.1\|WP_038066274.1\|67964_68672_+\|rhomboid-family-intramembrane-serine-protease	gnl\|CDD\|366759	pfam01694, Rhomboid, Rhomboid family. This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite.	2.74163e-36
NC_011978.1\|WP_012644969.1\|71373_71799_-\|thioesterase-family-protein	gnl\|CDD\|227783	COG5496, COG5496, Predicted thioesterase [General function prediction only].	3.19431e-38
NC_011978.1\|WP_038066281.1\|81494_81992_-\|crossover-junction-endodeoxyribonuclease-RuvC	gnl\|CDD\|234587	PRK00039, ruvC, Holliday junction resolvase; Reviewed.	3.50846e-87

>NC_011978.1|WP_038066259.1|73614_74859_-|tRNA-lysidine(34)-synthetase-TilS
MIGEGDIVLVAVSGGIDSMTLLYILKKLSPLLKIEVLGAHLDHRIRESSERDRKFVEDICRQWNVPVETAVVDVPALWKGSGKTLEEVAREVRYSFLEKVAKKLGATKIALAHHKNDLLETVLHRLVRGTGPLGIACIPVKREKYIRPFLVFKRSEIEDYAQKQKIPFVVDETNYDIKYTRNFIRHRVVPLLKKLNPNVEDAVYRLVSISFMLREFVEETVQNFVKEKVHFYKDFAVFEEPKNQFLFLEVTRWVLKTLYGRTPDYEKLIESLKSRRVELWKDVFVERSFGYGAVGKTLFKKKYRLEVKDGIFDIEGFKIKVNLHGIERAFWLRNRRKGDRIIINGSEEKLKDIFIEKKVPVFYRDRVPLLVDEQGRVLWVPGIAFSDEFPPEVNVELLEFPIGYVKGGTSFEQV
>NC_011978.1|WP_012644970.1|71795_73628_-|ATP-dependent-zinc-metalloprotease-FtsH
MNRSSIWNLLFTILIIVSLFWLARFFYIESSPVSKLSYTSFVQMVEDDRGLVSEVVIRDDGVLRVYTKDGRVYEVDAPWVVNDSQFIEKLVSKGVKVSGERSGSSSFWINVLGTLIPTILFIIVWLFIMRSLSGRNSQAFTFTKSRATMYKPSGSKRVTFKDVGGADEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVDLEILAKRTPGFVGADLENLVNEAALLAARDGREKITMKDFEEAIDRVIAGPARKSRLISPKEKRIIAYHEAGHAVVSTVVPNGELVHRISIIPRGYKALGYTLHLPEEDKYLVTKNELLDKLTALLGGRAAEEVVFGDVTSGAANDIERATEIARNMVCQLGMSEELGPLAWGKEEQEVFLGKEITRLRNYSEEVASKIDEEVKKIVTNCYERAKEIIRKYRKQLDNIVEILLEKETIEGEELRKILSEEFEKVVE
>NC_011978.1|WP_012644969.1|71373_71799_-|thioesterase-family-protein
MMEFDFLEGKRLTEDVALDETMAWNEDVMMLDLHLVSTSALMGVVHRVSYDLLSRYLPDDYTAVVVESCVRHVKAIPTGTRVAVGVRVIGVTGNRVKFRGIVMSGDEKILEAEFVRAIVSRNYLRRVALEKTEKTPGFFGI
>NC_011978.1|WP_038066255.1|69956_71414_-|radical-SAM-protein
MRKPRRPQDFLEYEKVLGFKSKERQVENLKLEGDVRVALIVPNDYIVASSGLAFYYVQKLLNHHPRIRCERFFYDESFSKYYSLETQTPLDEFPIWLFSVSFENDLLNLLDLLKKKGIPLLWKDREEHHPLVVAGGAVTYLNTEFLLPVADAVYYGELEKHLEEFSEALTGEKKEDILKALAEIPSMNVPSLGKKHSEIATGVIVDEFLPHAHIVSDAGVFLGKLLVELGRGCIRRCAFCIFGKNLKPARFVRPDRFESLVEEIPWKEYGLISATITDYPWLNELLDVVERHQLKISVSSLRLDRLSERLLKVLKESGQRSFTIAPEAGSQKIRDILKKDITDEQIEIALKMARNVGFDRIKMYFIYGLEEETEEDLRAFRKIGELALQMGYREVHMSFNPLIPKPGTDFEERRMEPVDVLREKEKFLKEYLKGFRVDFESIRESVIQYTIARASREEIVEWVKSFENKKRFRKMIFNEGRKRLC
>NC_011978.1|WP_012644967.1|68658_69963_-|nucleotide-sugar-dehydrogenase
MLKEKLVSRTAVVGVIGLGYVGLPLAVEKAKAGYRVIGFDIQKKRVDMVNAGINYIGDVVDEELKDLVEKGMIRATTDFSELKNCDVATICVPTPLGKYKEPDLTYVINTAKEIAKYLHREMLVVLESTTYPGTTEEVVLPILESTGLKVGEDFYLAFSPERVDPGNRIYKTKNTPKVVGGVTEKCTELAKILYENVLEAPVHTVSSPRAAEMSKVLENTFRLVNISLINEVAILARRMGINIWEVIDAAATKPFGFMPFYPGPGAGGHCIPIDPFYLAYKAKEYDVRLDLVEMAGEINDFMPEYVVMRVQDILNERKKPLNGSKVLLLGVAYKGDIDDVRESPALKVWDHLEKKKAIVEFFDPYVPEVKRGEKIHRRVELTEEYLKSVDIVVITTAHKNGVDYNFVVKHAPVVFDTKNITKDVKENREKIILL
>NC_011978.1|WP_038066274.1|67964_68672_+|rhomboid-family-intramembrane-serine-protease
MRKRAVYFILLFNAFIFVLMALSGVFSTREPILQMLLLLRYGAQYGPRVDAGDWFRLITALFVHGGILHILFNSYALYYFGLIVEDIYGSEKFLFSYFFTGVVGNIATHIFYHDTISVGASGAIFGLIGVLFAAGFRKDTPFFMKPVTGVSLLPIILINVVYGFLPGTNINNAAHLGGFLSGMLLGYTMKPFSWKRRALWKAIAILTVSLVVLSYVFLIRQIPEIDEAIRRFRAG
>NC_011978.1|WP_012644964.1|66885_67965_+|Gfo/Idh/MocA-family-oxidoreductase
MKLRVALIGCGRIGQKKHVPALIETRDLFDTVAVCDLVEERMNVAADQFEKAGLKRPETVKDYREILRRDDIDVVSIATESGKHYQMTMEALESGKHVLVEKPMALSTRHMNEMVELSKRKNLKLGVFFQNRFNPPVQEVRKKLDSGAFGRVFYASVAVRWNRNEAYYRQAKWRGTWEMDGGVLMNQSTHAIDLLQWFLGGEIEEIYGHIANTNHPYIEAEDTGFAIVKFKGGKTGLIEATSNVFPRNLEETLAIFGEKGTVVVGGLAVNRILTWRFEKEESHPFMNLPDPDTVYGDSHKYVYRDFYEAVLKDRKPYISGEDGKKAVEIVLGIYKSFLEGRPVKYPFDFSTEEMKGVKL
>NC_011978.1|WP_012644963.1|66059_66956_+|DMT-family-transporter
MERFFAWLVIVLWGVSFLATKVVVQVLNPFLAGFLRFLLSFLFLSLVSGRPKIFNRDIFMAGFWGVFGYFAFENSALMFTEPTNAAIIVSSAPIFFLLFSHIVQKKKTTAGMYLGVLLSFLGVVLVILNGRFVLKLNPIGDLLAFGAALSWVFYTHHVERLGSLSFKENAGIMFWGMVLFLPFSAGKFHQVLDMNASVIVSLIYLGILCSGLAYFLWNRAIEKLGSRRTTNMIYYIPVVTAVVEHTVKMRFPSALLIGGVVLVVLGLSIFEREAEHETESSTDRMRKDRPEKARSCSD
>NC_011978.1|WP_038066252.1|64414_66055_+|putative-manganese-dependent-inorganic-diphosphatase
MERVYVVGHRNPDTDSVCSAIGYAHYKAEVEKKKQFIPARCGELTNEALFVLDYFKVRPPIFLETLEPTVEDLELKDPIFVSPDTPVYDVAMLMEGKGIKNVPVVSRGKMIGVVTESNLARVYVRRLKIEPLVIHPVPLEQLVRVLKAEVVCDHLKEKTISGKVHIAVDALHVLLGKIEIGDVVIVGDNEPSQIALLEKGAKLMIIVNNAPVSSRVLEIAKEKGAAVLRVKFDAFGAAKLINLALPVTLVMSKKFPTVTKRDTLEDVKNIVFTSKLRAAFVEDEKGKLLGVITRTDLMKDVRKKVILVDHNEITQAPEGVEKAEILEIIDHHRLGGLSTLNPVFFYNEPVGSTSTIVTEFFLRDGVKMEREIAGVLLAGIVSDTLFFKLSTTTEKDRAMAGFLARITKLDLEKFAKKVLKEGMKIPENVDPLDLLKRDVKVYEMGEESFAVSQIMTSDFSVLLKEKEKFATALKSLKGELGVTHCFVLFTNPIEEASLVMVEGDQRILEKAFDGAEKKDGLFLLKGVMSRKKDFVPRIGDILRRER
>NC_011978.1|WP_166426831.1|63325_64357_-|rod-shape-determining-protein-MreB
MVERGKKVLRKDIGIDLGTANTLVFLKGKGIVVNEPSVIAIDSSTGEILKVGLEAKNMLGKTPATIKAIRPMKDGVIADYTVALVMLKYFINKAKNGFNFLKPRVVIGVPIGITDVERRAILDAGLEAGASKVFLIEEPMAAAIGSNLNVEEPSGNMVVDIGGGTTEVAVISLGSIVTWESVRIAGDEMDEAIMQYVRETYRVAIGERTAERVKIEIGNVFPSKENDELETTVSGIDLSTGLPRKLTLKGGEVREALRSVVVTIVESVRTTLEKTPPELVSDIIERGIFLTGGGSLLRGLDTLLQKETGISVIRAEEPLTAVAKGAGMVLEKVNILKKLQGAG
>NC_011978.1|WP_012644973.1|76100_76868_+|pyrroline-5-carboxylate-reductase
MKVSVIGVGNMGSIFAEKLSEKAEKVLLVEKVPEKLARFKREPFEIVDIETAKLSDYIVLAVKPQDASSILEKLKGYSGVLISIVAGLKISTIEEYGILKVARVMPNVGVRVKEGVLAVSYSEKVRSEEKEGVKSLLESLGLVVEIEEKHFPAITALTGSGPAFVFVMTEAFLDAALKMGLSFEVARDLVYKLFEGSARLLFETKEHPAVWKHRVTSPAGTTIEGIVAMEKSAVRGGIIESLLASHRKALELEGK
>NC_011978.1|WP_012644974.1|76868_77408_+|GNAT-family-N-acetyltransferase
MFPKRVLLKDGSSLMIREANIWDAKRIVEYMKEVTSETDFLITRPDEVYDVSTERSYIKMYRNDPRKLMLLGEINREIVSMLTFTGFGRKRTRHVGELGISVKRRYWGLGIGTAMMTCAIEWAKENGFKRIQLEVLKSNERAIGLYRKLGFEVEGVKKKAVRKDDGSYEDVLIMALLFD
>NC_011978.1|WP_012644975.1|77404_81508_-|PolC-type-DNA-polymerase-III
MEKIENLRWKNITLKSLVIDPGTGVVTISVENYSEEVEDLVRSLEKETRFRVVLNGYHRDGSDLKEKILSILNGNVPYIKDVVLEGNRLVLKVLGDFARERIASKLRSMRRELNNILPSGVEIMLEVIEPSDDLLKKILPQIEPEDEKKSEGEEVKVEDSNHVFGQKPRKIVFTPSKVFEYNKKTSIKGKVFKMEKVDGKRTLLLLYLTDGEDSLICKAFNGIEEIEKGVSVGDVVVVTGDLAQENGEPVLYVKGVTKLPEEKRVDNSPIKRVELHAHTKFSDLDAIMDIESYVNRAKEWGFPAVAITDHGNVQAIPYFYDAAKSAGIKPIFGIEAYLVSDVEPILKNFSGNATFEDVTFVVFDFETTGLDPQVDEIIEIGAVKIKEGRIIDEYHTLIKPSGTISRKSAEITGITQEMLEGERAIEEVLPEFLEFLEDSILVAHNANFDYRFLRLWIKKVLGKDWEKPYVDTLALAKSLLRLKSYSLDSVVKKLGLGSFRHHRALDDARVTAQVFLRFIEMMKKIGITKLSEMEKLKDSVDFTAQKPYHCTILVQNRTGLKNLYRLVSDSYTKYFHSVPRILKSELIEKREGLIVGSACISGELARAALEGASDSELEEIAKFYDYIEIMPLDVIEEDEEVDRERLKEVYRKLYRIAKRLNKPVVMTGDVHFLDPEDAKGRSALLAPQSRNFERQPALYLRTTEEMLEKAMEIFEDEEIAKEVVVENPNRIAEMIEEVQPLEKKLHPPVIENADEIVRNLTMERAHELYGDPLPEIVEKRIKKELDAIINHGYAVLYLIAKELVQKSMSDGYVVGSRGSVGSSLVAHLLGITEVNPLPPHYRCPRCKYFEIVEDDRYGAGYDLPDKSCPKCGTPLKKDGHDIPFETFMGFEGDKVPDIDLNFSGEYQDQAHRFVEELFGKDHVYRAGTINTIAEKSAVGYVKSYEEKTGKKLRRAEMERLVSMITGVKRTTGQHPGGLMIIPKDKEVYDFTPIQYPANDREAGVFTTHFAYETIHDDLVKIDALGHDDPTFIKMLKDLTGIDPMSVPMDDPDTLAIFSSVKPLGVDPVELGSDVGTYGIPEFGTEFVRGMLVETRPKSFAELVRISGLSHGTDVWLNNARDWINLGYAKLSEVISCRDDIMNFLIHKGMEPSLAFKIMESVRKGKGITEEMEKEMRRLKTPEWFIESCKRIKYLFPKAHAVAYVSMAFRIAYFKVHYPLQFYAAYFTIKGDQFDPTLVLKGKEAIKARLRELKMMTGKDAQKKNEESVLEVALEMILRGFSFLPPDIFKSDAKKFLIEGNALRIPFNKLPGLGDSVAESIVRAREEKPFTSIEDLVRRTKVNKNHVELMKSLGVLRDLPETEQFTLF
>NC_011978.1|WP_038066281.1|81494_81992_-|crossover-junction-endodeoxyribonuclease-RuvC
MRILGVDPGYGIVGIGIIEISGNRISHVFHGAIETSKDLPRGKRLKQIHEEFLRILEKFSPDECAMETLFFVKNVTTAIGVGEARGVILLALEEKGVPVFEYAPNEVKISLTGYGRASKRQVQENVKRFLGLSEIPRPDDAADALAIAWCHALQSRMRRVTHGKD
>NC_011978.1|WP_038066286.1|82073_83081_-|tRNA-preQ1(34)-S-adenosylmethionine-ribosyltransferase-isomerase-QueA
MKVSEFDYELPPELIAQEPVEPRDASRLMVLHRKTKKIEHRIFREIVEYLEPGDLLVLNVSKVIPARLYAKKKTGAHIEILLLDRLEEGIWRCLVKPGQKVKKGTELLIDNNLSAVCLDRSEDGTRILEFRPKNDDLILKKGKAPLPPYIKKEVPLDRYQTVYAKENGSVAAPTAGLHFTPELIEKLKEKGVEFAEIVLHVGIGTFRPVKVEEVEKHRMHEEYYRVPREAVRKIRETKEKGKRVVAVGTTTVRTLETIARLPEQEEYAGKTDLFIYPPFEFKMVDALITNFHLPRSTLLMLVAAFAGKDFIMEAYREAVKRRYRFFSFGDAMLIL
>NC_011978.1|WP_041437364.1|83091_84528_-|apolipoprotein-N-acyltransferase
MASFFLSVLSGVLTALSMPGFLSGALIWFSLIPLLFAMERVGIWKKALLSFLYFFTHILITFFWVLPTLTENLPFVFGRYPSWLGVVVYLLMGVIEAAPFFGFGFLSHFAPRGTLLRSLYLASIYTMFEYIRGIGELGFTGGRISEALFRHTGLLQVVSVTGTLGLVFLIVFLNTVFYELLKKRKAVFIFVLIALVYILNATVEHLLPLPESGTFEVMALQPNVSTSLKYFTSSENMLNILEDMLKGKEDHVVITPEAFFLEDVRYSSVSNSLKEISRKNSIILGFPASGRNSVFLLENGEFKRVYSKVKLFPFVETLPYPKVFGVFSFLRGLSYYEPGEEFSVFKVRESPSFSVQICFESYFPEVSRNFVKNGSEFLVTVTNDGWFHYKVALINHFVQGVFRAAETRRQFLQVANTGITGLIDEYGRILRVLPSEERLLGLFHVKPRKGETFYVKFGDWFFYFSILLSGLSWVLSKL
>NC_011978.1|WP_038066311.1|84520_85672_-|DegT/DnrJ/EryC1/StrS-aminotransferase-family-protein
MIPLSRPDITEEDIEEVVEVLKSGRLSLGDHTRKFGEVVAQYVGAKYGWPVSSGTAALHLILESLDVKEGDIVLVPSFTFIASVNVILMKKAIPVFVDVDRRTLNVSSETLEDAIKRCLKGFKQGDVHIKGVPGFFMAVDVFGHPLDWDGVLEVCSRYGITVIEDSCEALGSEYKGKKTGTFGVAGAFAFYPNKQITTGEGGVVVTDSEQIFTLVKSMSNQGRGEDEKWLYHVRFGYNYRIDEMSAALGLSQMERIDRILEKRSEAADRYSKMLKDLPWVQVPVVEEYVTRMSWFVYVIRLNGPDRDRVMKYMEEKGVQVRNYFHPVHLQPFYEKTFGNMRGLLPVTEEESKKTLALPFFTNISPKEQERVVEILEEAVERVG
>NC_011978.1|WP_012644980.1|85768_87151_-|DegQ-family-serine-endoprotease
MKKFLALILTVVVLSSVFPYVNPDYESPIVKVVEACAPAVVKIDVTKTVRTSFFDPYFEDFFRKWFGELPPGFERQVSSLGSGFIFDPEGYILTNYHVVGGADNITVTLLDGSKYDAEYIGGDEELDIAVIKIKATDKKFPYLGFGDSDKVKIGEWAIAIGNPLGFQHTVTVGVVSATNRKIPKPDGSGYYVGLIQTDAAINPGNSGGPLLNIHGEVIGINTAIVNPQEAVNLGFAIPINTVKKFLDTILTKKKVEKAYLGVTVMTLTEETAKALGLETTSGALITSVQKGSPAEKAGLKEGDVILKVDDQDVRSHEELVSIIHTYKPGDTATLTIERKGKIMKVQVTFGSSSEEETAAAEGEKTIDVLGITVANITPADRETYSIPEEIRGVIVRESSGKFGIQKGDIIVAVYINGRRYDINSVEDLERVASGIKKGDYVALYIYRNGARVFVSFIYQR
>NC_011978.1|WP_012644981.1|87266_88151_+|signal-recognition-particle-docking-protein-FtsY
MGLFDFLKKGLQKTKDAFFGKVVSLLKGKKLDDETREKLEELLIQADVGIETTEYILERLEEKDGNALEALRETLLEILNFDTALNEPDNPPFVITVVGVNGTGKTTSCGKLAKMFADRGKSVVLAAADTFRAAAIEQLKLWGDRVGATVIAHSEGADPAAVAFDAVSHALARNKDVVIIDTAGRLHTKKNLMEELRKVHRVIKKKIPEAPHEVLLVIDATTGQNGLVQAKVFKDAVDVTGIILTKLDGTAKGGIVLAIAKELGIPIKFVGVGEKEDDLKPFDPNAFVEVLLSE
>NC_011978.1|WP_012644982.1|88147_88801_+|DUF2225-domain-containing-protein
MRTFWEKEFTCPFCGHRFKKKMVFFDAVKIKSRDIDLKPIFEDVNPMLYEVVTCPNCYFSAFDRDFETIKIKGEETEKKLKKLLEEARKKIKIKDEETPTEAIKRYALSGIVYSVLNQRKKVAISYLKIAWIFREMGKPEDEKRYLERALREFENHFKYDSYEESDEPMILFYLGVLNQILGNRKEAARWYERLLGKHRDSLYAKVGRERWQDLRRS

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Crispr_ID: NC_011978_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011978_2

271824-272186

Orphan

III-A

Consensus_repeat	Method
GTTTCCATACCTCTAAGGAAGTATTGAAACC	PILER-CR
GTTTCAATACTTCCTTAGAGGTATGGAAAC	CRISPRCasFinder
GTTTCAATACTTCCTTAGAGGTATGGAAAC	CRT

5 spacers

The CRISPR arrays of NC_011978_2

>merge|NC_011978|2|271824-272186|PILER-CR,CRISPRCasFinder,CRT
GGTTTCAATACTTCCTTAGAGGTATGGAAACCAGGAATTGTTCCAGACGGAGTGGCGGTAGAGACATGTTTCAATACTTCCTTAGAGGTATGGAAACTCCACGTCAAAGCCGTGCATTTTCAAAGCGAGTCTGGTTTCAATACTTCCTTAGAGGTATGGAAACGAAAAATTGGTTGGTGTTTCTGATGAAATAATTCTGGGTTTCAATACTTCCTTAGAGGTATGGAAACTTGTGAGTTCTGCTCTTTTTGCCTTTTTGTGATATACGTTTCAATACTTCCTTAGAGGTATGGAAACACTGGAGGGGGTAGAGGACAGCCTTCTTTTCACCTCGTTTCAATACTTCCTTTGAGGTATGAAAAC

>NC_011978|2|2|271824-272053|PILER-CR
GGTTTCAATACTTCCTTAGAGGTATGGAAAC	CAGGAATTGTTCCAGACGGAGTGGCGGTAGAGACA
TGTTTCAATACTTCCTTAGAGGTATGGAAAC	TCCACGTCAAAGCCGTGCATTTTCAAAGCGAGTCT
GGTTTCAATACTTCCTTAGAGGTATGGAAAC	GAAAAATTGGTTGGTGTTTCTGATGAAATAATTCTG
GGTTTCAATACTTCCTTAGAGGTATGGAAAC

>NC_011978|2|2|271825-272186|CRISPRCasFinder
GTTTCAATACTTCCTTAGAGGTATGGAAAC	CAGGAATTGTTCCAGACGGAGTGGCGGTAGAGACAT
GTTTCAATACTTCCTTAGAGGTATGGAAAC	TCCACGTCAAAGCCGTGCATTTTCAAAGCGAGTCTG
GTTTCAATACTTCCTTAGAGGTATGGAAAC	GAAAAATTGGTTGGTGTTTCTGATGAAATAATTCTGG
GTTTCAATACTTCCTTAGAGGTATGGAAAC	TTGTGAGTTCTGCTCTTTTTGCCTTTTTGTGATATAC
GTTTCAATACTTCCTTAGAGGTATGGAAAC	ACTGGAGGGGGTAGAGGACAGCCTTCTTTTCACCTC
GTTTCAATACTTCCTTTGAGGTATGAAAAC

>NC_011978|2|2|271825-272186|CRT
GTTTCAATACTTCCTTAGAGGTATGGAAAC	CAGGAATTGTTCCAGACGGAGTGGCGGTAGAGACAT
GTTTCAATACTTCCTTAGAGGTATGGAAAC	TCCACGTCAAAGCCGTGCATTTTCAAAGCGAGTCTG
GTTTCAATACTTCCTTAGAGGTATGGAAAC	GAAAAATTGGTTGGTGTTTCTGATGAAATAATTCTGG
GTTTCAATACTTCCTTAGAGGTATGGAAAC	TTGTGAGTTCTGCTCTTTTTGCCTTTTTGTGATATAC
GTTTCAATACTTCCTTAGAGGTATGGAAAC	ACTGGAGGGGGTAGAGGACAGCCTTCTTTTCACCTC
GTTTCAATACTTCCTTTGAGGTATGAAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_011978.1\|WP_038066445.1\|260883_261432_+\|thymidine-kinase	unknown	unknown	gnl\|CDD\|235272
NC_011978.1\|WP_081434631.1\|279008_279989_+\|diacylglycerol-kinase-family-lipid-kinase	unknown	unknown	gnl\|CDD\|224513
NC_011978.1\|WP_015918788.1\|276537_277524_-\|TolC-family-protein	unknown	unknown	gnl\|CDD\|224455
NC_011978.1\|WP_015918785.1\|273557_274262_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|213222
NC_011978.1\|WP_015918781.1\|268821_269937_-\|ROK-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224851
NC_011978.1\|WP_015918786.1\|274258_275266_-\|efflux-RND-transporter-periplasmic-adaptor-subunit	unknown	unknown	gnl\|CDD\|273776
NC_011978.1\|WP_015918795.1\|282056_282407_+\|nucleotide-pyrophosphohydrolase	unknown	unknown	gnl\|CDD\|212135
NC_011978.1\|WP_038066448.1\|261421_262636_-\|HAMP-domain-containing-histidine-kinase	unknown	unknown	gnl\|CDD\|223715
NC_011978.1\|WP_038066477.1\|272356_273571_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|182528
NC_011978.1\|WP_015918791.1\|278874_279081_+\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_041437420.1\|263692_264826_+\|glutamine-amidotransferase-family-protein	unknown	unknown	gnl\|CDD\|238888
NC_011978.1\|WP_015918777.1\|264818_266342_+\|alpha-hydroxy-acid-oxidizing-protein	unknown	unknown	gnl\|CDD\|223147
NC_011978.1\|WP_015918782.1\|269941_271162_-\|glycosyltransferase	unknown	unknown	gnl\|CDD\|340823
NC_011978.1\|WP_049750494.1\|266338_266794_+\|4Fe-4S-dicluster-domain-containing-protein	unknown	unknown	gnl\|CDD\|319885
NC_011978.1\|WP_081434650.1\|281187_282063_+\|biotin-synthase-BioB	unknown	unknown	gnl\|CDD\|273075
NC_011978.1\|WP_015918779.1\|266790_268068_+\|NAD(P)/FAD-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|224171
NC_011978.1\|WP_015918787.1\|275262_276522_-\|TolC-family-protein	unknown	unknown	gnl\|CDD\|224455
NC_011978.1\|WP_015918780.1\|268055_268793_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|238481
NC_011978.1\|WP_038066450.1\|262616_263288_-\|response-regulator-transcription-factor	unknown	unknown	gnl\|CDD\|223816
NC_011978.1\|WP_038066479.1\|280001_281072_-\|glycosyltransferase-family-4-protein	unknown	unknown	gnl\|CDD\|340831

Protein	Function_ID	Function_description	E-value
NC_011978.1\|WP_038066445.1\|260883_261432_+\|thymidine-kinase	gnl\|CDD\|235272	PRK04296, PRK04296, thymidine kinase; Provisional.	7.39803e-79
NC_011978.1\|WP_081434631.1\|279008_279989_+\|diacylglycerol-kinase-family-lipid-kinase	gnl\|CDD\|224513	COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].	3.21369e-88
NC_011978.1\|WP_015918788.1\|276537_277524_-\|TolC-family-protein	gnl\|CDD\|224455	COG1538, TolC, Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion].	4.0908e-15
NC_011978.1\|WP_015918785.1\|273557_274262_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|213222	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein. This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of lipoproteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyzes the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.	4.69179e-126
NC_011978.1\|WP_015918781.1\|268821_269937_-\|ROK-family-transcriptional-regulator	gnl\|CDD\|224851	COG1940, NagC, Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism].	1.13431e-39
NC_011978.1\|WP_015918786.1\|274258_275266_-\|efflux-RND-transporter-periplasmic-adaptor-subunit	gnl\|CDD\|273776	TIGR01730, COG0845:_Membrane-fusion_protein, RND family efflux transporter, MFP subunit. This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed functions imply outward transport. These functions include nodulation, acriflavin resistance, heavy metal efflux, and multidrug resistance proteins. Most members of this family are found in Gram-negative bacteria. The proposed function of MFP proteins is to bring the inner and outer membranes together and enable transport to the outside of the outer membrane. Note, however, that a few members of this family are found in Gram-positive bacteria, where there is no outer membrane. [Transport and binding proteins, Unknown substrate].	9.35921e-34
NC_011978.1\|WP_015918795.1\|282056_282407_+\|nucleotide-pyrophosphohydrolase	gnl\|CDD\|212135	cd11528, NTP-PPase_MazG_Nterm, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs. MazG is a NTP-PPase that hydrolyzes all canonical NTPs into their corresponding nucleoside monophosphates and pyrophosphate. The prototype of this family is MazG proteins from Escherichia coli (EcMazG) that represents the most abundant form consisting two sequence-related domains in tandem, this family corresponding to the N-terminal MazG-like domain. EcMazG functions as a regulator of cellular response to starvation by lowering the cellular concentration of guanosine 3',5'-bispyrophosphate (ppGpp). EcMazG exists as a dimer; each monomer contains two tandem MazG-like domains with similarly folded globular structures. However, only the C-terminal domain has well-ordered active site and exhibits an NTPase activity responsible for the regulation of bacterial cell survival under nutritional stress. Divalent ions, such as Mg2+ or Mn2+, are required for activity; however, this domain does not exhibit an NTPase activity despite containing structural features such as the EEXX(E/D) motif and key basic catalytic residues responsible for nucleotide pyrophosphohydrolysis activity. It is suggested that the N-terminal domain of EcMazG might have a house-cleaning function by hydrolyzing noncanonical NTPs whose incorporation into the nascent DNA leads to increased mutagenesis and DNA damage.	5.80048e-24
NC_011978.1\|WP_038066448.1\|261421_262636_-\|HAMP-domain-containing-histidine-kinase	gnl\|CDD\|223715	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms].	6.79421e-54
NC_011978.1\|WP_038066477.1\|272356_273571_-\|ABC-transporter-permease	gnl\|CDD\|182528	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB.	1.29202e-51
NC_011978.1\|WP_041437420.1\|263692_264826_+\|glutamine-amidotransferase-family-protein	gnl\|CDD\|238888	cd01907, GlxB, Glutamine amidotransferases class-II (Gn-AT)_GlxB-type. GlxB is a glutamine amidotransferase-like protein of unknown function found in bacteria and archaea. GlxB has a structural fold similar to that of other class II glutamine amidotransferases including glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). The GlxB fold is also somewhat similar to the Ntn (N-terminal nucleophile) hydrolase fold of the proteasomal alpha and beta subunits.	1.41697e-110
NC_011978.1\|WP_015918777.1\|264818_266342_+\|alpha-hydroxy-acid-oxidizing-protein	gnl\|CDD\|223147	COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport and metabolism].	0
NC_011978.1\|WP_015918782.1\|269941_271162_-\|glycosyltransferase	gnl\|CDD\|340823	cd03792, GT4_trehalose_phosphorylase, trehalose phosphorylase and similar proteins. Trehalose phosphorylase (TP) reversibly catalyzes trehalose synthesis and degradation from alpha-glucose-1-phosphate (alpha-Glc-1-P) and glucose. The catalyzing activity includes the phosphorolysis of trehalose, which produce alpha-Glc-1-P and glucose, and the subsequent synthesis of trehalose. This family is most closely related to the GT4 family of glycosyltransferases.	4.58523e-178
NC_011978.1\|WP_049750494.1\|266338_266794_+\|4Fe-4S-dicluster-domain-containing-protein	gnl\|CDD\|319885	cd10563, CooF_like, CooF, iron-sulfur subunit of carbon monoxide dehydrogenase. This family includes CooF, the iron-sulfur subunit of carbon monoxide dehydrogenase (CODH), found in anaerobic bacteria and archaea. Carbon monoxide dehydrogenase is a key enzyme for carbon monoxide (CO) metabolism, where CooF is the proposed mediator of electron transfer between CODH and the CO-induced hydrogenase, catalyzing the reaction that uses CO as a single carbon and energy source, and producing only H2 and CO2. The ion-sulfur subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons in the protein complex during reaction.	5.13853e-65
NC_011978.1\|WP_081434650.1\|281187_282063_+\|biotin-synthase-BioB	gnl\|CDD\|273075	TIGR00433, biotin_synthase, biotin synthase. Catalyzes the last step of the biotin biosynthesis pathway. All members of the seed alignment are in the immediate gene neighborhood of a bioA gene. [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin].	4.15113e-140
NC_011978.1\|WP_015918779.1\|266790_268068_+\|NAD(P)/FAD-dependent-oxidoreductase	gnl\|CDD\|224171	COG1251, NirB, NAD(P)H-nitrite reductase [Energy production and conversion].	7.54781e-85
NC_011978.1\|WP_015918787.1\|275262_276522_-\|TolC-family-protein	gnl\|CDD\|224455	COG1538, TolC, Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion].	7.12139e-16
NC_011978.1\|WP_015918780.1\|268055_268793_+\|hypothetical-protein	gnl\|CDD\|238481	cd00981, arch_gltB, Archaeal-type gltB domain. This domain shares sequence similarity with a region of unknown function found in the large subunit of glutamate synthase, which is encoded by gltB and found in most bacteria and eukaryotes. It is predicted to be homologous to the C-terminal domain of glutamate synthase based upon sequence similarity coupled with genome organization data, showing that this domain is found in a gene cluster with other domains of Glts, which are annotated. This domain is found primarily in archaea, but is also present in a few bacteria, likely as a result of lateral gene transfer.	8.63455e-124
NC_011978.1\|WP_038066450.1\|262616_263288_-\|response-regulator-transcription-factor	gnl\|CDD\|223816	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription].	2.17423e-86
NC_011978.1\|WP_038066479.1\|280001_281072_-\|glycosyltransferase-family-4-protein	gnl\|CDD\|340831	cd03801, GT4_PimA-like, phosphatidyl-myo-inositol mannosyltransferase. This family is most closely related to the GT4 family of glycosyltransferases and named after PimA in Propionibacterium freudenreichii, which is involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIM) which are early precursors in the biosynthesis of lipomannans (LM) and lipoarabinomannans (LAM), and catalyzes the addition of a mannosyl residue from GDP-D-mannose (GDP-Man) to the position 2 of the carrier lipid phosphatidyl-myo-inositol (PI) to generate a phosphatidyl-myo-inositol bearing an alpha-1,2-linked mannose residue (PIM1). Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found mainly in certain bacteria and archaea.	8.44757e-23

>NC_011978.1|WP_015918782.1|269941_271162_-|glycosyltransferase
MDARLRERNIEEYWPVIGEEVDEIKKLAEPLKGMKVLHVNATAYGGGVAEILHNLVPLMRSVGLDARWRVLEAPDEFFNVTKKFHNTLQGADIEITEEEWDLYERVCQENTKLIQDEEILVIHDPQPAAVRKYLDLNDRKWLWRCHIDLSTPNMTVWKRFFRYLEGYDKLIFHLEEYFPEGWKEKSVAFPPSIDPLSEKNSDLDEDFIKTTLERLEIDPKRPLITVVARFDPWKDLFSAIDVYRIVKEEISDVQLAIVSAMATDDPEGWFFYEKVLRYAGVDEDIKFCTNLKGVGNKEVNAIQRATTVALHTAIREGFGLVISEALYKKVPVVARPVGGVKIQVKHGENGYLAWEKEKLAEYVIRLIKDENLRKKMGENGKRTVVENFIITVHLKNYLKTFLNLLG
>NC_011978.1|WP_015918781.1|268821_269937_-|ROK-family-transcriptional-regulator
MPSPLLRKENKLKVLKHILENGKVTRGDLSNELELAQSTLSYIIDELNEENFLLIEEVKSKKGRPYQVLSVNPERFSVIGVKVGREEVHGVLFNASLNPIREHRVSILAPMRSNEGYTRALRETVENLFSENLLGIGICSSGLVRDHQVVVSHVMNVRNWNLRDVLGDFERVVVMNDADALCREVSQRIGSDFLLISYGIGIGASLFRNGRIEHLEMGHMIVSSEGKCYCGQTGCLEYHSSEYAVLKSYLGSEIDFEDFISNEEEKYRPFIEELRKKVRENFEAVRKHYEKAFRNLSVAVGDVVMSTGVSRVFLAGEGAVSEDIAKLLEKMVKERFNKEFVDDVEFHLASANWMLGAARAVVEEYLSDILK
>NC_011978.1|WP_015918780.1|268055_268793_+|hypothetical-protein
MVRIDAKGLHYKKLNDMIWEAIENGETEIVLDNVCGQRYIGAGIRKKVRIEINGVPGNDLGVFMDGPEITVNGNAQDGVGNTMNSGKIVVHGHAGDIIGYAMRGGHIYIKKSAGYRVGIHMKAYKENYPVIVIGGFARDFLGEYMAGGLLIVLGLEKDEDGNIAGNYVGTGMHGGEIFLRGNIEEHKLGKEVKIFQPSEEDMNRIRPYIEEFCRLFEYDPEEILSEEFILLKPYTHRPYGRLYAY
>NC_011978.1|WP_015918779.1|266790_268068_+|NAD(P)/FAD-dependent-oxidoreductase
MRYIVVGSGPAGLNAIEAIRELDKDGEILLTTAEKYVGYSRPLITYLLGRKVTEEKMYYRTEDYLKEMGVSIKPATRVERVIPKEKVVVTSTGEKIAYDKLLLAVGGKPFVPKIEGLEGKEGVFTFTTWEDEERVERYIKENDVREAVVLGGGLIGLKTTEALMELGVKVTIVELADRILSVTFDKKASEIITNALKKEGCDVITNDTIVAVKGEGSVSSVVLKSGKEIPTRLLIIAIGVRPNVDFLKDSGIEINRGIVVNEKMETSEKDIYAAGDCTEFYDLIDGQRKTIAIWPVAVAQGRVAGYNMAGGNVRYPGGIPMNSVELAGIPTISVGHTNVEGDEYEILTYEEGNTYKKMVIKDNKLIGAVLVNDIDRAGIYTGLILQKMDVSSFKDKLLDENFGLVYLPKEFRKKMLEGEVKIWLE
>NC_011978.1|WP_049750494.1|266338_266794_+|4Fe-4S-dicluster-domain-containing-protein
MITVRRILIREEYCMGCKLCEINCVAAQVGTGNLIKIYRYVPELPEPNVIVEEHDYITFALQCRNCDDPSCLKACMTGAMHRDPETGAIKVNQEKCVGCWMCVMACPFGVVRRSTKEKKVASKCDLCIDRGTPACVEGCPNEALVLVEVRG
>NC_011978.1|WP_015918777.1|264818_266342_+|alpha-hydroxy-acid-oxidizing-protein
MAKRKVPAEFVVERDDYKCIRCLACVRVCSYGANYYDENANRVYTENYKCVGCHFCEAICPTEAITVRRNNFDIRPLAHWTPEHLIGIMKQADTGGVLLTSMGNDRPYFSYFDRIVLNASQVTNPSIDPLREPMEIRTYIGRKEAKLEIEEDGEGNVALKTEIAPQLKLEVPVMFTAMSYGSISLNALLSLARAARTIGTFFNTGEGGLPKELREFKDNMIVQVASGRFGVSADYLNAGSAVEIKIGQGAKPGIGGHLPGEKVTEPISETRMIPVGTDALSPAPHHDIYSIEDLRQLIYAIKEATRYEKPVGVKIAAVHNVAPIAAGMVRAGADYIVIDGIRGGTGAAPKVTRDHVGIPIEFAIAVVDQRLREEGIRHMASIVVAGGIRNSADVIKAIALGADAVYIGTAALVALGCHLCQTCYLGKCNWGIATQDPKLTKRLNPEIGARRAANLLRAWAHEIKEILGGMGINAIESLRGNREALRGVGLHEYELKLLGIKPAGEAW
>NC_011978.1|WP_041437420.1|263692_264826_+|glutamine-amidotransferase-family-protein
MPYDLPRLIPDRDFKVPSACGVSGIMNTSGKRFSGSTIVETMALMRERGNGLGAGYAAYGIYPELKDFYCFHMLYDSELDKKNAEEYIKSHYEIIESEPIPTRKNPHIKEVHILWRYFLKPKSIPEGFTEEDFVVDTVMFINEKIKGAFVMSSGKNMGVFKGVGFPEDIADFYRIDEYKGYIWTAHNRFPTNTVGWWGGAHPFGILDWTVVHNGEISSYGINRRFLEAYGYKCTLMTDTEVVAYLVDLFMRRFGYSPKITAKILAAPLWKDIDLMPEEERKLYTALRMNYGGALLNGPFAIIVANSNMMMGLNDRIKLRPLVAATKDDFLYIASEESAIRVVCPEPDEVWAPKAGEPVVGVLKSTEKVRVALEGENG
>NC_011978.1|WP_038066450.1|262616_263288_-|response-regulator-transcription-factor
MRVLLVEDEKDLADLIAEALKKEMFTVDVCYDGEEGMYMALNEDFDVVILDVLLPVHDGWEILKAMREKGINTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVKALIRRKAENKNVKLVCGDLILDTATRKVFRGGKEIDLTKKEYQILEYLMMNKNRVVTKEELQEHLWSFDDTVFSDTLRSHIKNLRKKIDRGFKKKIIHTVRGIGYVVRDE
>NC_011978.1|WP_038066448.1|261421_262636_-|HAMP-domain-containing-histidine-kinase
MLSVMNEKKAFRKTHLTWTLIFTLSIVFVVAVVAGAVFMVEKNRITRQFDGDLVRTAEFIEKRLSAPGMMGMLRMMKGMPPLFVPRGEAFQLLLSSGEVFLEVGEQLDTPEMPVKEGFSTEGNYRVFTKKIDLGDTTIFLRVGKDISDLMERSRRLLSMYLLLIVFTAGGAWIFGYFISKLALLPVKNAYDSLKRFSMDASHELKTPLSVLKTSLDVLKYQDVPEEVKNKLSIMEKNVEKMRKQVEQLLLLVKSGEMFKDTVKERINLKVFLEELVEAFAPKAEAKNLKLKIECPDDLFVETEKDVLRVVLENLIDNAIKFTEKGEVIVGAVSDGRVTIYVKDTGPGIPKKEQKKIFERFYRISRNTEGSGLGLSIVKELVARLKAKIVLESEEGKGSTFKIIF
>NC_011978.1|WP_038066445.1|260883_261432_+|thymidine-kinase
MSGKLTVITGPMYSGKTTELLSFVEIYRLGRKKVAVFKPKIDNRYHSTKIVSHSGDGVEAFTVERPEEMWKYIDEETRGVFVDEVQFFSRDLFDVVRELLNRGIDVFCAGLDLTHKQNPFETTAMLLSLADTVIKKKAVCQRCGEYSATLTLKIAGGEEEIDVGGQEKYIAVCRDCYNALKK
>NC_011978.1|WP_038066477.1|272356_273571_-|ABC-transporter-permease
MEILKEVLRSLLANKMRTFLSMLGIVIGVTAVIMVMSLGAGMRESVTERLTSLGSNIIMVTPGFIGGRGGTIAQSVESLSEEDVSDILSMCPSVDRAIGLVNGNFLVQYRETNSRANVYAAPYEIFQILNLKVSSGRTFTEEDSAANVAIIGQEIAYNLFENENPVGKKIYLVQGNRKLVFEIIGVFERTGSILMFNPDNMILIPYETGKFRVFQTHGNISMILATSKSPQVAQRAVMEIDHLLYTKFHEEESYYNIISQQAILNVVSESVSIINLVLVAIAAVSLVVGGIGIMNIMLVSVVERTREIGIKMAIGASRIRILMEFLVESVVITFVAGAIGVALGILGSNTIVNTFGSSYGLKAFVDPFSVIIAFGVSASVGLFFGFYPAYRASRLSPIEALRYE
>NC_011978.1|WP_015918785.1|273557_274262_-|ABC-transporter-ATP-binding-protein
MKKVMELVDVWKVYDLGEVKVEALRGVSFEVFQGEYVIIIGPSGSGKSTLLHILGCLDRPTKGKVLIEGEDVSKMSDRKLAQVRNRKIGFVFQSYNLLPRLNALENVELPMIYAGVPARERRKRAKELLELVGLGDRLHHRPNQLSGGQQQRVAIARALANDPVFILADEPTGNLDTKTGEEILELFRKLHEMGKTLVVVTHNLEMVDEGTCIVRIRDGRIEDVERRGVVYGDT
>NC_011978.1|WP_015918786.1|274258_275266_-|efflux-RND-transporter-periplasmic-adaptor-subunit
MKKWITLLIIAILVVLLIVVIFLNRASAQSVSERTATSTQLPVYLTYTVTKENETVEIVGQVTADTRSVASKVSGDVLELYVQEGDYVQSGQRIAKIDDTDYQIEYLSALNNYKTSPTEINRLNLEVAKKNLENTIVTSPVNGVVQSVDVSEGDRVSVGTAIVEIVETDTLRVEGSIDEYDLKNVKEGMKAVFTFEQLGLTLTGKVKRISPVAETSGGVTVIPVEFSFDQTPPEIVIPGLTCNVEIIIREATSSFFVPKEAVRQDQNGYYVMKQTSEGPQKVYVEIGEEVNEKIEIKKGVSEGDVLLLVPSQEEIQRLRTRQGLPVFGPGGGRAR
>NC_011978.1|WP_015918787.1|275262_276522_-|TolC-family-protein
MKRFLLLFLVFPVFLAGNVFDLFEENMNRSSDYWSAVESFKEKDLSYRQYTSFWNPEVSVSLGTNGIIITEDGVQNFSVIPRVNFVNIYGFKLGLSFPISVNMKDWSANFEGTQLSVSRGLKEDYMVSRLQAEASYLSALYSLKSVKNSIFIQTIQDVFDWYYYTRKIEILSQRLQVLREKLSKTVDEDEKESLEKQILSVEQTLRNTKLNLEAIHEGINEEIYRETKELLSNITLPATTLEHREDLKALEIQKKAEEIKKKTWFLPYLPDLTFSFNYDFEKSTWSIGIGLQLTLWDFGERKLEAEKRKFQIVSLEYEEKIKEINDSINKSLTSIDNLRSQMKQEDIELNDLREVYETNRQLFEKGFLSEEDFILSELDYTEGKLTMENLENSLILEKLKYISTLGYDLEKFLKEGDLN
>NC_011978.1|WP_015918788.1|276537_277524_-|TolC-family-protein
MKNLFVALVLVVSVAGFSASLNDVLQTALASSTDYQIAQIDLETATMDYEKAKLEATNRKSELSAELSYYNNLQNYRSSLKSVYQDVLGRIFDLLIAEVSYESAQINFENAQEDHRTNQELFKKNLISENDLKDSELTLEEASNNLLSAKYDLDEAKKNYEELFSVEASEIELPLVDFHDLVSEDEYLDNLLSVKIAETNMKIAEYDLNNLSAAASKYERRTAELAYQKAKMNYEKTLKEAKDTYRSTINSLEVMLSNLKVLKERIDLNESILKDYQDRYEKGLISKKELNAQKINLLNARKNYLNSLQNYYNTIITLLIDAGKDVSF
>NC_011978.1|WP_015918791.1|278874_279081_+|hypothetical-protein
MRIISDLFFFTGFGTLFVSIVFFDLGTRAIKKKQPRKKKFYDKRGWQFLTASLASFAVSIILALFGRG
>NC_011978.1|WP_081434631.1|279008_279989_+|diacylglycerol-kinase-family-lipid-kinase
MAVSHCKSCFLCSINNTCTFWKGIGVFLVYNPAAGGGKARKLWMKVKDLLERYEIDCEVAFTEKPGHAMELSRKAFESGHRKIVAFGGDGTMNEVVNGIFLGGFNLEEVTFGWIPFGSGKDWARTIGVPLMIEEAVKTLKDGRVFVQDLGVAEYESSNGEMKKRVFVNVAGLFFDGFVTHRTNLLRKKNRVSYFSRIFSSIIKYKPPVARIQVDERVWEKKIFSMNVGICKYNGGGMNQLPHAVPDDGLLAVTVINDIGKIRILANLYRVFNGTLLEHPGVEGYQAKKVTVEFQKKEPVELDGESFWTRKISFSVVPRVLRVLVKK
>NC_011978.1|WP_038066479.1|280001_281072_-|glycosyltransferase-family-4-protein
MKIGFLSRWGATCGVGMHAEILAREFVNMGHEVVVFAPTEESAKKEVKYYKRTEATDPDFVKREIYTEVDNVTEEGWVKEEEILKENLDLLIVETFWRVPVKPLTKLIEKLKIPVISVFHEANIFKAREVVKLPCDKIVVFDRRFYDEILEFYGIPREKVEVISYPVMKPYEVEPERPVGEDKFLFFSFGRQPVEEYCDFLNVLKKLKKRFDNVHYWIIRSDGKIEYEAEWITQWQKRPTVEKLYSYLKGSNVHLLPKGNTPNVVVSSTLYQVIASETPIVIRDSRFVETIETDAYGFGPIVKYRNIHDLAHKLELLMLDSELVEDIKKEARIFVEKYSGEKVAREFLELAKSINK
>NC_011978.1|WP_081434650.1|281187_282063_+|biotin-synthase-BioB
METRELILKASTMVRNSRLDICSIVNAKSGICDQDCKFCAQSSLYNTGVKRYPLLDEESILEKAKEAEKMGAVRFGIVTSGKRPTRDELLKIASIIEFLKVTTSLRICASLGTLEKDELSYLKDHGLDRYHHNLETSPGFFQNICTTHTFYDRVKTVENAKSIGLEVCSGGIFGVGESFEDRLELARILKDLEVDSVPINFLIPIKGTPFENFPELDVVERIKTIAAFRIVLGENVTIKIAAGREKLGDFQALAFFAGANGMIVGGYLTVKGRSYDDDRKLVEGLKELMGW
>NC_011978.1|WP_015918795.1|282056_282407_+|nucleotide-pyrophosphohydrolase
MVEKLLEIIEKSLEKCPWLERQSIDSLLDALASEVEEIRDAVKKKDLTNLEEEIGDLIYDAFLVGAVAQRDYGVDLERAIQRVVEKISHRKPWLFWDEKISLEEAERIWKERKSRG

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Crispr_ID: NC_011978_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011978_3

311329-311756

Orphan

III-A

Consensus_repeat	Method
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CRISPRCasFinder
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CRT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	PILER-CR

6 spacers

The CRISPR arrays of NC_011978_3

>merge|NC_011978|3|311329-311756|CRISPRCasFinder,CRT,PILER-CR
TTTCCTATACCTCTAAGAAAGGATTGAAACTTGACATTGTCAAAAGAACGTGGCACTAAACAACGGTTTCCATACCTCTAAGGAAGTATTGAAACGATTAGTTTTTACCATGTATTGGTAATCTTGTCAATGTTTCCATACCTCAAAGGAAGTATTGAAACGGGAGTCCTACGTTGGATATCCACAGACGGCAGAGTACAGTTTCCATACCTCAAAGGAAGTATTGAAACGTGGAGAAGGCTTTTATCTCAATGGATATCGTTGGTAGTTTCCATACCTCAAAGGAAGTATTGAAACCGCGAAAGCAAAACTCCACGCCCTCAAAGCGCCTTTGTTTCCATACCTCAAAGGAAGTATTGAAACTCAGTTCGAACACAACCTGGCGACGTTTGTCTCGTGTTTCCATACCTCAAAGGAAGTATTGAAAC

>NC_011978|3|3|311329-311756|CRISPRCasFinder
TTTCCTATACCTCTAAGAAAGGATTGAAAC	TTGACATTGTCAAAAGAACGTGGCACTAAACAACG
GTTTCCATACCTCTAAGGAAGTATTGAAAC	GATTAGTTTTTACCATGTATTGGTAATCTTGTCAAT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GGGAGTCCTACGTTGGATATCCACAGACGGCAGAGTACA
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GTGGAGAAGGCTTTTATCTCAATGGATATCGTTGGTA
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CGCGAAAGCAAAACTCCACGCCCTCAAAGCGCCTTT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	TCAGTTCGAACACAACCTGGCGACGTTTGTCTCGT
GTTTCCATACCTCAAAGGAAGTATTGAAAC

>NC_011978|3|3|311329-311756|CRT
TTTCCTATACCTCTAAGAAAGGATTGAAAC	TTGACATTGTCAAAAGAACGTGGCACTAAACAACG
GTTTCCATACCTCTAAGGAAGTATTGAAAC	GATTAGTTTTTACCATGTATTGGTAATCTTGTCAAT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GGGAGTCCTACGTTGGATATCCACAGACGGCAGAGTACA
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GTGGAGAAGGCTTTTATCTCAATGGATATCGTTGGTA
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CGCGAAAGCAAAACTCCACGCCCTCAAAGCGCCTTT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	TCAGTTCGAACACAACCTGGCGACGTTTGTCTCGT
GTTTCCATACCTCAAAGGAAGTATTGAAAC

>NC_011978|3|3|311394-311756|PILER-CR
GTTTCCATACCTCTAAGGAAGTATTGAAAC	GATTAGTTTTTACCATGTATTGGTAATCTTGTCAAT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GGGAGTCCTACGTTGGATATCCACAGACGGCAGAGTACA
GTTTCCATACCTCAAAGGAAGTATTGAAAC	GTGGAGAAGGCTTTTATCTCAATGGATATCGTTGGTA
GTTTCCATACCTCAAAGGAAGTATTGAAAC	CGCGAAAGCAAAACTCCACGCCCTCAAAGCGCCTTT
GTTTCCATACCTCAAAGGAAGTATTGAAAC	TCAGTTCGAACACAACCTGGCGACGTTTGTCTCGT
GTTTCCATACCTCAAAGGAAGTATTGAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_011978.1\|WP_015918829.1\|316707_317973_-\|3-phosphoshikimate-1-carboxyvinyltransferase	unknown	unknown	gnl\|CDD\|235037
NC_011978.1\|WP_038066529.1\|308405_308741_-\|carboxymuconolactone-decarboxylase-family-protein	unknown	unknown	gnl\|CDD\|223672
NC_011978.1\|WP_004083125.1\|318727_319744_-\|3-deoxy-7-phosphoheptulonate-synthase	unknown	unknown	gnl\|CDD\|181535
NC_011978.1\|WP_015918822.1\|308765_310097_-\|FAD-dependent-oxidoreductase	unknown	unknown	gnl\|CDD\|163244
NC_011978.1\|WP_038066527.1\|307013_308360_-\|dihydrolipoyl-dehydrogenase	unknown	unknown	gnl\|CDD\|273568
NC_011978.1\|WP_004083127.1\|317969_318731_-\|prephenate-dehydrogenase	unknown	unknown	gnl\|CDD\|223364
NC_011978.1\|WP_015918831.1\|320000_321242_-\|MFS-transporter	unknown	unknown	gnl\|CDD\|340863
NC_011978.1\|WP_038066515.1\|302208_303174_-\|nitroreductase-family-protein	unknown	unknown	gnl\|CDD\|380315
NC_011978.1\|WP_011943194.1\|314822_315953_-\|chorismate-synthase	unknown	unknown	gnl\|CDD\|272865
NC_011978.1\|WP_162828737.1\|321254_321431_-\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_038066533.1\|312380_313004_+\|LysE-family-transporter	unknown	unknown	gnl\|CDD\|280058
NC_011978.1\|WP_015918815.1\|301201_302212_+\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|223912
NC_011978.1\|WP_011943195.1\|315949_316711_-\|shikimate-dehydrogenase	unknown	unknown	gnl\|CDD\|223247
NC_011978.1\|WP_038066519.1\|305849_306350_-\|nitroreductase-family-protein	unknown	unknown	gnl\|CDD\|380325
NC_011978.1\|WP_015918817.1\|303255_305208_-\|anaerobic-ribonucleoside-triphosphate-reductase	unknown	unknown	gnl\|CDD\|181342
NC_011978.1\|WP_015918818.1\|305179_305725_-\|anaerobic-ribonucleoside-triphosphate-reductase-activating-protein	unknown	unknown	gnl\|CDD\|274317
NC_011978.1\|WP_041437436.1\|313396_314875_-\|bifunctional-shikimate-kinase-AroK/3-dehydroquinate-synthase-AroB	unknown	unknown	gnl\|CDD\|172457
NC_011978.1\|WP_015918826.1\|312962_313400_-\|type-II-3-dehydroquinate-dehydratase	unknown	unknown	gnl\|CDD\|376496
NC_011978.1\|WP_015918823.1\|310205_311171_-\|NAD(P)H-dependent-glycerol-3-phosphate-dehydrogenase	unknown	unknown	gnl\|CDD\|223318
NC_011978.1\|WP_038066522.1\|306377_307037_+\|endonuclease-III-domain-containing-protein	unknown	unknown	gnl\|CDD\|225140

Protein	Function_ID	Function_description	E-value
NC_011978.1\|WP_015918829.1\|316707_317973_-\|3-phosphoshikimate-1-carboxyvinyltransferase	gnl\|CDD\|235037	PRK02427, PRK02427, 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional.	0
NC_011978.1\|WP_038066529.1\|308405_308741_-\|carboxymuconolactone-decarboxylase-family-protein	gnl\|CDD\|223672	COG0599, COG0599, Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown].	5.82489e-21
NC_011978.1\|WP_004083125.1\|318727_319744_-\|3-deoxy-7-phosphoheptulonate-synthase	gnl\|CDD\|181535	PRK08673, PRK08673, 3-deoxy-7-phosphoheptulonate synthase; Reviewed.	0
NC_011978.1\|WP_015918822.1\|308765_310097_-\|FAD-dependent-oxidoreductase	gnl\|CDD\|163244	TIGR03385, Coenzyme_A_disulfide_reductase, CoA-disulfide reductase. Members of this protein family are CoA-disulfide reductase (EC 1.8.1.14), as characterized in Staphylococcus aureus, Pyrococcus horikoshii, and Borrelia burgdorferi, and inferred in several other species on the basis of high levels of CoA and an absence of glutathione as a protective thiol. [Cellular processes, Detoxification].	3.56844e-79
NC_011978.1\|WP_038066527.1\|307013_308360_-\|dihydrolipoyl-dehydrogenase	gnl\|CDD\|273568	TIGR01350, Dihydrolipoyl_dehydrogenase, dihydrolipoamide dehydrogenase. This model describes dihydrolipoamide dehydrogenase, a flavoprotein that acts in a number of ways. It is the E3 component of dehydrogenase complexes for pyruvate, 2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can also serve as the L protein of the glycine cleavage system. This family includes a few members known to have distinct functions (ferric leghemoglobin reductase and NADH:ferredoxin oxidoreductase) but that may be predicted by homology to act as dihydrolipoamide dehydrogenase as well. The motif GGXCXXXGCXP near the N-terminus contains a redox-active disulfide.	0
NC_011978.1\|WP_004083127.1\|317969_318731_-\|prephenate-dehydrogenase	gnl\|CDD\|223364	COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and metabolism].	9.77158e-66
NC_011978.1\|WP_015918831.1\|320000_321242_-\|MFS-transporter	gnl\|CDD\|340863	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters. This family is composed of Streptococcus pyogenes macrolide efflux protein A (MefA) and similar transporters, many of which remain uncharacterized. Some members may be multidrug resistance (MDR) transporters, which are drug/H+ antiporters (DHAs) that mediate the efflux of a variety of drugs and toxic compounds, conferring resistance to these compounds. MefA confers resistance to 14-membered macrolides including erythromycin and to 15-membered macrolides. It functions as an efflux pump to regulate intracellular macrolide levels. The MefA-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement.	6.93031e-72
NC_011978.1\|WP_038066515.1\|302208_303174_-\|nitroreductase-family-protein	gnl\|CDD\|380315	cd02138, TdsD-like, nitroreductase similar to Burkholderia pseudomallei TdsD. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to Burkholderia pseudomallei TdsD, may be involved in the processing of organosulfur compounds. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer.	1.76755e-80
NC_011978.1\|WP_011943194.1\|314822_315953_-\|chorismate-synthase	gnl\|CDD\|272865	TIGR00033, Chorismate_synthase, chorismate synthase. Homotetramer (noted in E.coli) suggests reason for good conservation. [Amino acid biosynthesis, Aromatic amino acid family].	6.61219e-168
NC_011978.1\|WP_038066533.1\|312380_313004_+\|LysE-family-transporter	gnl\|CDD\|280058	pfam01810, LysE, LysE type translocator. This family consists of various hypothetical proteins and an l-lysine exporter LysE from Corynebacterium glutamicum which is proposed to be the first of a novel family of translocators. LysE exports l-lysine from the cell into the surrounding medium and is predicted to span the membrane six times. The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances or peptide hydrolysis; and also after artificial deregulation of l-Lysine biosynthesis as used by the biotechnology. industry for the production of l-lysine.	3.84796e-28
NC_011978.1\|WP_015918815.1\|301201_302212_+\|ABC-transporter-permease	gnl\|CDD\|223912	COG0842, COG0842, ABC-type multidrug transport system, permease component [Defense mechanisms].	1.01879e-16
NC_011978.1\|WP_011943195.1\|315949_316711_-\|shikimate-dehydrogenase	gnl\|CDD\|223247	COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and metabolism].	1.6478e-82
NC_011978.1\|WP_038066519.1\|305849_306350_-\|nitroreductase-family-protein	gnl\|CDD\|380325	cd02150, nitroreductase, nitroreductase family protein. A subfamily of the nitroreductase family containing uncharacterized proteins. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer.often found to be homodimers.	1.27914e-93
NC_011978.1\|WP_015918817.1\|303255_305208_-\|anaerobic-ribonucleoside-triphosphate-reductase	gnl\|CDD\|181342	PRK08271, PRK08271, anaerobic ribonucleoside triphosphate reductase; Provisional.	0
NC_011978.1\|WP_015918818.1\|305179_305725_-\|anaerobic-ribonucleoside-triphosphate-reductase-activating-protein	gnl\|CDD\|274317	TIGR02826, hypothetical_protein, anaerobic ribonucleoside-triphosphate reductase activating protein. Members of this family represent a set of radical SAM enzymes related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR) as described in model TIGR02491. Members of this family are found paired with members of a similarly divergent set of anaerobic ribonucleoside-triphosphate reductases. Identification of this protein as an RNR activitating protein is partly from pairing with a candidate RNR. It is further supported by our finding that upstream of these operons are examples of a conserved regulatory element (described Rodionov and Gelfand) that is found in nearly all bacteria and that occurs specifically upstream of operons for all three classes of RNR genes. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism].	1.27009e-63
NC_011978.1\|WP_041437436.1\|313396_314875_-\|bifunctional-shikimate-kinase-AroK/3-dehydroquinate-synthase-AroB	gnl\|CDD\|172457	PRK13951, PRK13951, bifunctional shikimate kinase AroK/3-dehydroquinate synthase AroB.	0
NC_011978.1\|WP_015918826.1\|312962_313400_-\|type-II-3-dehydroquinate-dehydratase	gnl\|CDD\|376496	pfam01220, DHquinase_II, Dehydroquinase class II.	5.26872e-88
NC_011978.1\|WP_015918823.1\|310205_311171_-\|NAD(P)H-dependent-glycerol-3-phosphate-dehydrogenase	gnl\|CDD\|223318	COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy production and conversion].	1.95713e-151
NC_011978.1\|WP_038066522.1\|306377_307037_+\|endonuclease-III-domain-containing-protein	gnl\|CDD\|225140	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair].	6.40243e-83

>NC_011978.1|WP_015918823.1|310205_311171_-|NAD(P)H-dependent-glycerol-3-phosphate-dehydrogenase
MRFFVLGAGSWGTVFAQLLKENGEEVILWARRKEIADLINNSHTSPYIDEMEISVRATNNLDELKSTDILVIAIPVQHVREHLSRLSKKPSMVLNLSKGLEIKTGKRISEIVKEILGCPYAVLSGPSHAEEVARKLPTAVTLAGDNARELQRRISNEYFRVYTCEDVVGVEIAGALKNVIAIAAGILDGLGGWDNAKAALETRGIYEIARFGRHFGADQKTFMGLAGIGDLMVTCNSKYSRNRRFGELIAKGFDPQKLLESSHQVVEGAFTVKAVVKKADELEIDMPISEEVYRVIYGGKSPFQSMKDLMKRSLKDEFWAD
>NC_011978.1|WP_015918822.1|308765_310097_-|FAD-dependent-oxidoreductase
MKYDVVIVGGGPAGLVAAFTTKRFYKDKKILVVKKTEKETVPCGIPYIFHTLSGVENDYMGIEERFKSAGIDLLIDEVVDGNTDEKKLLTKTGKEIFYEKLIIATGSTPNVPNIPGVDLEGVFTVPKDANYLKMLYEKIKDSKNVVIIGGGFIGVEVADELKKSGKNVTLVEIMDSLLPVSFDPDFGEIARKEIEAENLKVLTGRKVTEIYGSKRVEGVRLDNAETILADAVILATGYRPNSDLARKLGLKVTEYGFIETDEYMRTSKPDVFAAGDCVQHRDFLTGKPSRLMLASAAVFDARIAASNLYGLKVIRTNKGSLNAYSTVIGSKAFGSVGITERVAKEEGFEIVVGRAEAPDRHPGKFEDTTKLIVKLIFSEDSKILLGAQVCGGKSVGEIVNILSLGMQKGITANDLFTMQIGTHPLLTSAPTVYPLAKAAEMVL
>NC_011978.1|WP_038066529.1|308405_308741_-|carboxymuconolactone-decarboxylase-family-protein
MAAKEKLEQIRKQLQEVIGKAPEIGKFAEYVHAAESPKALDTKTKELISLGIAVAVRCEPCIVWHTEAAVRAGATEEEILDAIKVAVCMGGGPALMYGLKAYEVALEFLGK
>NC_011978.1|WP_038066527.1|307013_308360_-|dihydrolipoyl-dehydrogenase
MYDAVIIGGGPGGYVCAIKLAQLGKRVALVEKEALGGTCTNKGCIPTKAMLTVSHLMSEIKDKSSKYGLKVSGVEFDVSSIMKHVEKSVLMSRKGIEYLMKKNNVDVFIGTGIVENRNTVVVEETGTKLETKNLVLAHGSIPSVFPPFDVEGVWTSDDVFRLKEFPESLLIVGGGVIGVEFATFFSSFGVNVTIVEVANHILPYEDEDVAEEVKKSLKRKGVKILEKAKITSLNKIENGFEATLETGETLRAEKVLLAVGRKPNIPEDVKALGVEIKRGVVTDRKMRTNIEGVYAIGDIRGEIMLAHVAMYEGIVAAKNIAGMEEEMDYSAVPNIIFSSPEVASVGLKEKDVNPEEVVISKFPVSANGRARTMLENIGFVKVVADKNGVVLGMSIVSPSATDMIMEGVIAVKHRMKAEDLEKAIHPHPTLTETILGALEGVSGKPIHL
>NC_011978.1|WP_038066522.1|306377_307037_+|endonuclease-III-domain-containing-protein
MKLEELHEELRSIHGPVGKWWPGTPEEIMVTAILTQNTNWKNVERAMRNIEEALGKDDILEKLSSLSTERIAHLIRPAGFFNIKAKRLKALLEFLREYNFNLKLLKRMPLGALRELLLKIKGIGKETADAILLYALEKPIFVVDSYTKRLLARIFNIELKDYDEIQKLFMSCYPHDVRLYQELHGLIVEHAKRFCSKNPKCRECPLKKKCFYSQMNGLS
>NC_011978.1|WP_038066519.1|305849_306350_-|nitroreductase-family-protein
MSIVYKRRSIRKYQRKDVPDELVKEVIRAAMHAPSACNQQPWHFVVIRDAETRKKVAEIHPHAKMILEAPVAILVCGDPSLEKCKGFWVQDCSAAVENLLLRAAELGLGAVWCGVYPREDRVKSFQKLLGIPEHVIPFALVPMGYPAEQPTPEDRFKPERIHYEKW
>NC_011978.1|WP_015918818.1|305179_305725_-|anaerobic-ribonucleoside-triphosphate-reductase-activating-protein
MYINRIGTLRDHPDLYGVSVYFQGCDAMPKCHMCHNPETWHLSERFKRDPEDVVKTIDEKLSDLLRYFPKVALVLLGGEPLAPYNREDTLLLSKTFKEKFKDRLVVVLFTWRLPKDIVRENLLEYVQYVDEFVMGRYLHTYRREGFPASRNQLHVNRETFEKMIRAVKRREHHGSSLFVRK
>NC_011978.1|WP_015918817.1|303255_305208_-|anaerobic-ribonucleoside-triphosphate-reductase
MVVRYSFESDFEELLKELLSRYGYEMFQMDGLGDQLDVVKFTEDFVRRGIIESTIDANANVRVTNISTYFIEISKPHTYLYSLYRIWQKMKEMYGKSVADEFVESQINGAIYLHDRHHAALMPYCFAYTLKPIVERGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLEEGIIPEDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFDGERYPDGSLITDHVEDIIRLQKHYWEWVSRERERQMFTFPVLTASLLYRDGKFLDEDSARFINRVNMKWQDTNWYISDSIDAVASCCRLTSSTQTLKKFSLSSEDEKLKGRMNSIGGSDLNIGSFKVITINLPRIALESNGDRDRFLQILRRRVDLVKKSLASIREIIKERISEGLLPLYENELMLLNRQYGTIGITGVWESATIMGLTTEDVDGLKYTKEGERFVDTVLDLIKEEAEKGYSEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFTIYSNQWVPLAANTDVLNRIRYSGMWDRKVSGGAILHINLGEPFKTEEEYFNMVKMIADMGVMYFAFNTKISVCEHNHAFYGERCPVCGKKKVDEYVRIVGYLVPVSAFNKERREIEYPRRQFYSSTIVRK
>NC_011978.1|WP_038066515.1|302208_303174_-|nitroreductase-family-protein
MRVKPFELLTDEGKPFTHVDLYGRYTILFFFPKAGTSGCTREAVEFSRENFEKTQVVGISRDSVESLKRFKEKNNLKVVLLSDPEGELHEFFDVLENGKTVRSTFILDRWGFVRREWRKVKVEGHVQEVKEALDQLLKEDLSLNRHIEWRRARRALKKDRIPRDEVETLIKAAHLAPSCMNNQPWRFVVVDSEDVLKRLHEALPGGNYWMKNAPVLIAVHSKRDFDCVLSDNREYFLFDTGLAVGNLLVQATQMGLVAHPVAGYDPVKVKEILGIPEDHVLITLIAVGYLGDENELSEKHREIERSERVRKDLSEIVRWNL
>NC_011978.1|WP_015918815.1|301201_302212_+|ABC-transporter-permease
MSEFFSLFSAMWKESWRDRIATFFSVAFPVMFLLIFGFIFGGSGESVKTAVVTVEYDLSDFGDVYSSLEEVEGYYHEVAVVERDRIVFIRNTTDEYYQSLLDSWEMSLKTKVERLFNRLNPVIVVKKKPLETTRQLTAFDYTLTGVIAISLLSIGLFGTVDVFSHYRERGFLKRLRATPVGNFSFVFGLVSARMAYGILSTTIIMVLGVLLFKAKYELNVLLFLLSVVSSVLCFIAFGALVSILFKKSEVATQVSVILFTIMMFLSGVYFPISFLPDYLRTVALFLPVKYGVEVIRYSLGFEIFTFTRYLFAVSIMFGAGLVFVFYTSSLILRKED
>NC_011978.1|WP_038066533.1|312380_313004_+|LysE-family-transporter
MLSIFFGSFLVGLSGAMAPGPLMAIAISKSTKDWKASLKLITGHVLLEALLVMLLLVGVRTIPPVLMRAISLAGGIFLLYMGISQLFEAKDPSLISNTGNSRFPLPVQGALVSFSNPYFLLWWFSVGSAFLFRAREHLLSGVLLFYSGHILSDISWYTFLGVAGQFLHKPSWKGVYRIVLVSMSFVLIGFGVYFLLAAFRGDFSHVL
>NC_011978.1|WP_015918826.1|312962_313400_-|type-II-3-dehydroquinate-dehydratase
MKLLVVNGPNLNMLGKRDRNVYGNFTYDDLVRMIEDWAKRNGVEVEVFQSNHEGEIIDRLHRLDFDGLVINPGAFTHYSYAIRDALEIVKVPKVEVHISNIHGREEFRRKSVTAEVCDGQISGLGAYGYILALEYVRKVSSESSK
>NC_011978.1|WP_041437436.1|313396_314875_-|bifunctional-shikimate-kinase-AroK/3-dehydroquinate-synthase-AroB
MRIFLVGMMGSGKSTIGKRVSEVLDLQFIDMDEEIERREGRRVRRIFEEDGEEYFRLKEKELLRELVERDNVVVATGGGVVIDPENRELLKKEKTLFLYAPPEVLMERVTTENRPLLREGKERIREIWERRKQFYTEFRGIDTSKLNEWETTALVVLEALDEKEISTIEKPHLVKIILGGFKRVRNEELVFTTERVEKIYGRYLPENRLLFPDGEEVKTLEHVSRAYYELVRMDFPRGKTIAGVGGGALTDFTGFVASTFKRGVGLSFYPTTLLAQVDASVGGKNAIDFAGVKNIVGTFRMPDYVIIDPVVTLSMDEGRFEEGVVEAFKMALLSGRGLELFDDPEKIERRNLRILSEMVRLSVEEKAKIVMEDPYDKGLRHALNLGHTLGHVYEMLEGVPHGIAVAWGLEKETMYLYRKGIVPKDTFRWIVEKIKEIVPIPVPAVDREKARTLILNDKKIMKGSRVRLPYVREPGKVEFLEVDPLELLEVVD
>NC_011978.1|WP_011943194.1|314822_315953_-|chorismate-synthase
MRLTIAGDSHGKYMIAVLEGIPAGLKIDEEIIRRELFRRRNCYGRGKRMSMEEDAFEIVSGVWGGITTGAPVTILVPNKAGNPVKDVRSVPRPGHIDYAAFVKYKLPDLNVYVERSSARWTVALTAAGALLKSLLREFNIDVLGFVTRLGNVEAKNIPDNFEELRRKRDESAVFCPDPEATEGMISEIDRAKEEGNTLGGKVKVIARGVPAGIGSYSDLFKKLDSKIGSLFFAIPAVKGVVIGSEEMWYGFDYLDEFELEDGRIKRRTNNLGGIEGGITNGEDVWVNVFVKPIPTTGKPLNSVDLRTMEPAKTPYVRSDVTAVPPASVVCEAALAVVISDALLEHLGDGNIDDLKRRFGNENLPRWDDGFWKEYDR
>NC_011978.1|WP_011943195.1|315949_316711_-|shikimate-dehydrogenase
MKFCIIGYPVSHSISPRLYNEYFKRAGMNHSYGMEEIPPESFDTEIRRILEEYDGFNATIPHKERVMRYVEPSEDAQRIKAVNCVFRGKGYNTDWVGVVKSLEGVEVKEPVVVVGAGGAARAVIYALLQMGVKDIWVVNRTIERAKALDFPVKIFSLDQLDEVVKKAKSLFNTTSVGMKGEKLTVSEASLKGLYLVYDVVYFETPLVSDAKRLGVEHVVKGNLMFYYQAMENLKIWGIYDERSFKEVFEEVLR
>NC_011978.1|WP_015918829.1|316707_317973_-|3-phosphoshikimate-1-carboxyvinyltransferase
MKVLPAKKVEGVLSVPPDKSITHRALILSALAESESTLYNLLRCLDTERTHDILEKLGTRFEGDWEKMKVFPKPFAEPIEPLFCGNSGTTTRLMSGVLASYEMFTVLYGDSSLSRRPMRRVIEPLEMMGARFMARQNNYLPMAIKGNHLSGISYKTPVASAQVKSAVLLAGLRASGRTIVIEPAKSRDHTERMLKNLGVPVEVEGTRVVLEPATFRGFTMKVPGDISSAAFFVVLGAIHPNARITVTDVGLNPTRTGLLEVMKLMGANLEWEITEENLEPIGTVRVETSPNLKGVVVPEHLVPLMIDELPLVALLGVFAEGETVVRNAEELRKKESDRIRVLVENFKRLGVEIEEFKDGFKIVGKQSIKGGSVDPEGDHRMAMLFSIAGLVSEEGVDVKDHECVAVSFPNFYELLERVVIS
>NC_011978.1|WP_004083127.1|317969_318731_-|prephenate-dehydrogenase
MKISVLGAGCIGGSIALKLKEKHHVTAFDRDEETMKALEENGIETVSKESDLYDTDLLVLALPMSVEERFLKETDFSGKILDVASVKTPFMEIARERGLNFTGGHPMAGNERKGKSGWDREMFDGKIFFLCSLDGKEDGMIENIVKDLGARPLWIDYRIHDEIVAAVSHVQYLISLSARYVGKPFEEYAGPGYLSNTRLSKQNMEMALDMIRYNKENILKYLENARNFLNVLYHLTEKEDFENLKKVIREVIS
>NC_011978.1|WP_004083125.1|318727_319744_-|3-deoxy-7-phosphoheptulonate-synthase
MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN
>NC_011978.1|WP_015918831.1|320000_321242_-|MFS-transporter
MNELLHWKRNFFLLALGRFVSILGSSIQAVAIPLFVLDLTHSGSAVALMTVAYMVPRILFTPIAGIVGDRGDRKFLMVSMDFLRGFLICFLALLAFRNSVTLPVLYVSQIAMAVMDNLFDIPTGAMFPDIVPQDFLMRANSIMGMVRIFPQILGPALGGVIYGFYGIAIVFLVNGVSFVLSAISEIFIVYSRKVEKKPAKFSQILEDLKEGFLFIWNHELIRTILIFALFLNLLISPLFMVVYPYTIREVMKFSAQEFGFLETSFTLGALLGNFLIASYLSKKNMWKAMKISIFLFELPIVFLGFLVMPDFSLSRLVIFSLFFITFLIMGFLNPIINVPLDTAFQRMTPSHIRARAFSFLILVANGVTPLGSVLYGYLVDRVPVHFLYYIVGALSFLVAVLLLVALRGKELPT
>NC_011978.1|WP_162828737.1|321254_321431_-|hypothetical-protein
MKVYLMVSTILVVMLFSLIWLYVLFFSPVETASSSPAVWELGVTETSSAMVPGSLQDR

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Crispr_ID: NC_011978_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011978_4

704816-705245

III-A

Consensus_repeat	Method
TTTCCATACCTCTAAGGAAGTATTGAAAC	PILER-CR
GTTTCAATACTTCCTTAGAGGTATGGAAAC	CRISPRCasFinder
GTTTCAATACTTCCTTAGAGGTATGGAAA	CRT

6 spacers

cas10,csx1,cas6,cas7,cas5,cas3HD,cas3,cas4,cas1,cas2

The CRISPR arrays of NC_011978_4

>merge|NC_011978|4|704816-705245|PILER-CR,CRISPRCasFinder,CRT
GTTTCAATACTTCCTTAGAGGTATGGAAACCGTAGTTCCTCACGGTGCCGGAGCAAACCTCGAACTCGTTTCAATACTTCCTTAGAGGTATGGAAACTGTTTCGTGTAAGTGTGAATCTCAGAACGTTGCCTTGTTTCAATACTTCCTTAGAGGTATGGAAACTCTTGAGGGGGTGAGGGTTGATCTTCTTTCCACCTCGTTTCAATACTTCCTTAGAGGTATGGAAACAAAGGACACTGTCGTATATGGTAGGACATGACGGCACCGAGTTTCAATACTTCCTTAGAGGTATGGAAACTTTTTCTTTGCGTGAAGTAAGCGTTTGGGAATTCTGTTTCAATACTTCCTTAGAGGTATGGAAATTGAGCCATGAGCCAGGCTTCTCTTTTACAATTAGCAGTTTCAATACATCCTCAGAGGTATGATTTA

>NC_011978|4|4|704816-705178|PILER-CR
GTTTCAATACTTCCTTAGAGGTATGGAAA	CCGTAGTTCCTCACGGTGCCGGAGCAAACCTCGAACTC
GTTTCAATACTTCCTTAGAGGTATGGAAA	CTGTTTCGTGTAAGTGTGAATCTCAGAACGTTGCCTT
GTTTCAATACTTCCTTAGAGGTATGGAAA	CTCTTGAGGGGGTGAGGGTTGATCTTCTTTCCACCTC
GTTTCAATACTTCCTTAGAGGTATGGAAA	CAAAGGACACTGTCGTATATGGTAGGACATGACGGCACCGA
GTTTCAATACTTCCTTAGAGGTATGGAAA	CTTTTTCTTTGCGTGAAGTAAGCGTTTGGGAATTCT
GTTTCAATACTTCCTTAGAGGTATGGAAA

>NC_011978|4|4|704816-705245|CRISPRCasFinder
GTTTCAATACTTCCTTAGAGGTATGGAAAC	CGTAGTTCCTCACGGTGCCGGAGCAAACCTCGAACTC
GTTTCAATACTTCCTTAGAGGTATGGAAAC	TGTTTCGTGTAAGTGTGAATCTCAGAACGTTGCCTT
GTTTCAATACTTCCTTAGAGGTATGGAAAC	TCTTGAGGGGGTGAGGGTTGATCTTCTTTCCACCTC
GTTTCAATACTTCCTTAGAGGTATGGAAAC	AAAGGACACTGTCGTATATGGTAGGACATGACGGCACCGA
GTTTCAATACTTCCTTAGAGGTATGGAAAC	TTTTTCTTTGCGTGAAGTAAGCGTTTGGGAATTCT
GTTTCAATACTTCCTTAGAGGTATGGAAAT	TGAGCCATGAGCCAGGCTTCTCTTTTACAATTAGCA
GTTTCAATACATCCTCAGAGGTATGATTTA

>NC_011978|4|4|704816-705244|CRT
GTTTCAATACTTCCTTAGAGGTATGGAAA	CCGTAGTTCCTCACGGTGCCGGAGCAAACCTCGAACTC
GTTTCAATACTTCCTTAGAGGTATGGAAA	CTGTTTCGTGTAAGTGTGAATCTCAGAACGTTGCCTT
GTTTCAATACTTCCTTAGAGGTATGGAAA	CTCTTGAGGGGGTGAGGGTTGATCTTCTTTCCACCTC
GTTTCAATACTTCCTTAGAGGTATGGAAA	CAAAGGACACTGTCGTATATGGTAGGACATGACGGCACCGA
GTTTCAATACTTCCTTAGAGGTATGGAAA	CTTTTTCTTTGCGTGAAGTAAGCGTTTGGGAATTCT
GTTTCAATACTTCCTTAGAGGTATGGAAA	TTGAGCCATGAGCCAGGCTTCTCTTTTACAATTAGCA
GTTTCAATACATCCTCAGAGGTATGATTT

Protein	Signature genes	Signature genes Name	Protein_function
NC_011978.1\|WP_038067006.1\|703840_704182_-\|J-domain-containing-protein	unknown	unknown	gnl\|CDD\|365959
NC_011978.1\|WP_015919213.1\|715624_716464_+\|GGDEF-domain-containing-protein	unknown	unknown	gnl\|CDD\|143635
NC_011978.1\|WP_015919206.1\|709205_710366_+\|CRISPR-associated-endonuclease-Cas3''	cas3HD	cd09641_cas3HD_CAS-I	gnl\|CDD\|350688
NC_011978.1\|WP_038067041.1\|712076_713057_+\|type-I-B-CRISPR-associated-endonuclease-Cas1	cas1	cd09722_cas1_CAS-I-B	gnl\|CDD\|274695
NC_011978.1\|WP_081434635.1\|701130_702531_+\|type-III-A-CRISPR-associated-protein-Cas10/Csm1	cas10	cd09680_cas10_CAS-III	gnl\|CDD\|187811
NC_011978.1\|WP_015919207.1\|710352_711546_+\|CRISPR-associated-helicase-Cas3'	cas3	COG1203_cas3_CAS-I	gnl\|CDD\|273707
NC_011978.1\|WP_015919199.1\|703379_703850_-\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_015919196.1\|699499_701110_+\|CRISPR-associated-DxTHG-motif-protein	csx1	cd09671_csx1_CAS-III	gnl\|CDD\|187802
NC_011978.1\|WP_144399156.1\|706200_707415_+\|type-I-B-CRISPR-associated-protein-Cas8b1/Cst1	unknown	unknown	gnl\|CDD\|187796
NC_011978.1\|WP_038066994.1\|694204_695242_+\|dipeptide-epimerase	unknown	unknown	gnl\|CDD\|239435
NC_011978.1\|WP_038067003.1\|702570_703380_-\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_041437564.1\|698734_699487_+\|CRISPR-associated-endoribonuclease-Cas6	cas6	COG1583_cas6_CAS-I:CAS-III:CAS-IV	gnl\|CDD\|224499
NC_011978.1\|WP_015919204.1\|707407_708424_+\|type-I-B-CRISPR-associated-protein-Cas7/Cst2/DevR	cas7	cd09687_cas7_CAS-I-B	gnl\|CDD\|274215
NC_011978.1\|WP_015919208.1\|711548_712067_+\|CRISPR-associated-protein-Cas4	cas4	pfam01930_cas4_CAS-I	gnl\|CDD\|366863
NC_011978.1\|WP_038067033.1\|705328_706057_+\|CRISPR-associated-endoribonuclease-Cas6	cas6	cd09652_cas6_CAS-I:CAS-III	gnl\|CDD\|273848
NC_011978.1\|WP_038066997.1\|697710_698115_+\|DUF1232-domain-containing-protein	unknown	unknown	gnl\|CDD\|225876
NC_011978.1\|WP_015919189.1\|695238_697191_+\|IGHMBP2-family-helicase	unknown	unknown	gnl\|CDD\|273041
NC_011978.1\|WP_015919205.1\|708420_709203_+\|type-I-B-CRISPR-associated-protein-Cas5	cas5	cd09658_cas5_CAS-I-B	gnl\|CDD\|273860
NC_011978.1\|WP_144399088.1\|713059_713344_+\|CRISPR-associated-endonuclease-Cas2	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|187856
NC_011978.1\|WP_038067000.1\|698151_698574_+\|hypothetical-protein	unknown	unknown	unknown

Protein	Cas_name	Cas_description	E-value	Identity	Coverage
NC_011978.1\|WP_015919204.1\|707407_708424_+\|type-I-B-CRISPR-associated-protein-Cas7/Cst2/DevR	cas7	cd09687_cas7_CAS-I-B	1.3e-90	298.4	0.4
NC_011978.1\|WP_041437564.1\|698734_699487_+\|CRISPR-associated-endoribonuclease-Cas6	cas6	COG1583_cas6_CAS-I:CAS-III:CAS-IV	1.1e-78	259.2	7.1
NC_011978.1\|WP_038067041.1\|712076_713057_+\|type-I-B-CRISPR-associated-endonuclease-Cas1	cas1	cd09722_cas1_CAS-I-B	1.4e-138	456.2	9.0
NC_011978.1\|WP_015919208.1\|711548_712067_+\|CRISPR-associated-protein-Cas4	cas4	pfam01930_cas4_CAS-I	1.1e-50	166.7	3.3
NC_011978.1\|WP_038067033.1\|705328_706057_+\|CRISPR-associated-endoribonuclease-Cas6	cas6	cd09652_cas6_CAS-I:CAS-III	4.7e-30	100.1	1.3
NC_011978.1\|WP_081434635.1\|701130_702531_+\|type-III-A-CRISPR-associated-protein-Cas10/Csm1	cas10	cd09680_cas10_CAS-III	6.7e-115	379.7	2.6
NC_011978.1\|WP_015919207.1\|710352_711546_+\|CRISPR-associated-helicase-Cas3'	cas3	COG1203_cas3_CAS-I	1.3e-55	183.6	6.0
NC_011978.1\|WP_015919206.1\|709205_710366_+\|CRISPR-associated-endonuclease-Cas3''	cas3HD	cd09641_cas3HD_CAS-I	1.3e-25	85.1	0.0
NC_011978.1\|WP_015919196.1\|699499_701110_+\|CRISPR-associated-DxTHG-motif-protein	csx1	cd09671_csx1_CAS-III	7.3e-89	293.2	6.8
NC_011978.1\|WP_144399088.1\|713059_713344_+\|CRISPR-associated-endonuclease-Cas2	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	9.5e-26	84.6	0.3
NC_011978.1\|WP_015919205.1\|708420_709203_+\|type-I-B-CRISPR-associated-protein-Cas5	cas5	cd09658_cas5_CAS-I-B	1.1e-70	232.3	0.3

Protein	Function_ID	Function_description	E-value
NC_011978.1\|WP_038067006.1\|703840_704182_-\|J-domain-containing-protein	gnl\|CDD\|365959	pfam00226, DnaJ, DnaJ domain. DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature.	5.44802e-24
NC_011978.1\|WP_015919213.1\|715624_716464_+\|GGDEF-domain-containing-protein	gnl\|CDD\|143635	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain. Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.	8.8737e-64
NC_011978.1\|WP_038067041.1\|712076_713057_+\|type-I-B-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|274695	TIGR03641, cas1_HMARI, CRISPR-associated endonuclease Cas1, subtype I-B/HMARI/TNEAP. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes Cas1 subgroup that includes Cas1 proteins of the related HMARI and TNEAP subtypes of CRISPR/Cas system.	1.34446e-174
NC_011978.1\|WP_015919204.1\|707407_708424_+\|type-I-B-CRISPR-associated-protein-Cas7/Cst2/DevR	gnl\|CDD\|274215	TIGR02585, conserved_protein, CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This clade is a member of the DevR family (TIGR01875) and includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to be regulated through a number of means, including both location and autorepression; DevR mutants are incapable of fruiting body development.	1.10332e-99
NC_011978.1\|WP_015919207.1\|710352_711546_+\|CRISPR-associated-helicase-Cas3'	gnl\|CDD\|273707	TIGR01587, CRISPR-associated_endonuclease/helicase_Cas3, CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.	2.8195e-42
NC_011978.1\|WP_015919196.1\|699499_701110_+\|CRISPR-associated-DxTHG-motif-protein	gnl\|CDD\|187802	cd09671, Csx1_III-U, CRISPR/Cas system-associated protein Csx1. 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; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as DxTHG family.	9.78663e-71
NC_011978.1\|WP_144399156.1\|706200_707415_+\|type-I-B-CRISPR-associated-protein-Cas8b1/Cst1	gnl\|CDD\|187796	cd09665, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1. 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; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as CXXC_CXXC family.	0.000126133
NC_011978.1\|WP_081434635.1\|701130_702531_+\|type-III-A-CRISPR-associated-protein-Cas10/Csm1	gnl\|CDD\|187811	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10. 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; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; signature gene for type III; also known as Csm1 family.	4.27338e-132
NC_011978.1\|WP_041437564.1\|698734_699487_+\|CRISPR-associated-endoribonuclease-Cas6	gnl\|CDD\|224499	COG1583, COG1583, CRISPR system related protein, RAMP superfamily [Defense mechanisms].	1.40814e-70
NC_011978.1\|WP_015919208.1\|711548_712067_+\|CRISPR-associated-protein-Cas4	gnl\|CDD\|366863	pfam01930, Cas_Cas4, Domain of unknown function DUF83. This domain has no known function. The domain contains three conserved cysteines at its C-terminus.	6.9859e-52
NC_011978.1\|WP_038067033.1\|705328_706057_+\|CRISPR-associated-endoribonuclease-Cas6	gnl\|CDD\|273848	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This broadly distributed, highly divergent Cas family is now characterized as an endoribonuclease that generates guide RNAs for host defense against phage and other invaders. The family contains a C-terminal motif GXGXXXXXGXG, where the each X between two Gly is hydrophobic and the spacer XXXXX contains (usually) one Arg or Lys. The seed alignment for the current version of this model has gappy columns removed. Members of this protein family are found associated with several different CRISPR/cas system subtypes, and consequently we designate this family Cas6.	4.80581e-30
NC_011978.1\|WP_038066997.1\|697710_698115_+\|DUF1232-domain-containing-protein	gnl\|CDD\|225876	COG3339, COG3339, Uncharacterized conserved protein [Function unknown].	2.0246e-17
NC_011978.1\|WP_015919189.1\|695238_697191_+\|IGHMBP2-family-helicase	gnl\|CDD\|273041	TIGR00376, DNA-binding_protein_SMUBP-2, DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair].	0
NC_011978.1\|WP_015919206.1\|709205_710366_+\|CRISPR-associated-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.	1.38438e-33
NC_011978.1\|WP_144399088.1\|713059_713344_+\|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.	1.40083e-27
NC_011978.1\|WP_038066994.1\|694204_695242_+\|dipeptide-epimerase	gnl\|CDD\|239435	cd03319, L-Ala-DL-Glu_epimerase, L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of the murein peptide of peptidoglycan, of which L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a member of the enolase-superfamily, which is characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.	4.84758e-120
NC_011978.1\|WP_015919205.1\|708420_709203_+\|type-I-B-CRISPR-associated-protein-Cas5	gnl\|CDD\|273860	TIGR01895, conserved_hypothetical_protein, CRISPR-associated protein Cas5, subtype I-B/TNEAP. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family is represented by TM1800 from Thermotoga maritima. It is related to TIGR01868 (CRISPR-associated protein, CT1976 family).	2.68051e-92

>NC_011978.1|WP_038067006.1|703840_704182_-|J-domain-containing-protein
MNPYEVLGVEPGASKEEIERAYRELVKKYHPDRYKDHPLRDLAEEKMKQINEAYQMLMNEEPEKNYSEEDSRFFSYSMGYRNNECRDILACLGCAWCTDTCCEACGGDCIPCM
>NC_011978.1|WP_015919199.1|703379_703850_-|hypothetical-protein
MHVKKISYGGLISALVVLLLYTGNFTKSKIFFAALCSVFVGFLVELFGKGAIPLIAALNLLSFLLVPNPGYVSIFLVLSFYSFVRKKSLLYRLFYLNAGFFFLLIVAIRFFKVELPEVSPILYIPGIAGLQIAFLAYDYLYTRILDYLLHLVRERR
>NC_011978.1|WP_038067003.1|702570_703380_-|hypothetical-protein
MFGYIKPLKCELKVREYEEFRRYYCGVCRALKRYSIVPRLLLTYEAASLSLLLSSLKGEHVERKRNFCFFTLKKVEYYQSESINRVAEIFVALLSEKMRDNYLDTKNPIYLLVKSFLKKDPKISKLFDRFYTLERKKANFEELAKEQGRILGKILESTVEEEDQRRILYHLGVHLGEWLYIVDALDDFEKDKKKGVYNPLVEEYRDFERAKNAVKDVLEMCINEIWKAYDLLNLKRNRSILDNIMYLGAPAVTERIFMKQRESSPAGKT
>NC_011978.1|WP_081434635.1|701130_702531_+|type-III-A-CRISPR-associated-protein-Cas10/Csm1
MNDRKELVVGALIHDVGKVVRRAGDSRAHQLAGYDFTNKVKKFAKFQKYIHYHHEKDLKEKNLEDEKVWYVCFADNLSSSERMTDGNVFDEYRRLENLLSKIPEKEQKKPTYFPIRSADKITEAVTEMEEEKESYASLYESFVEDAEKISLSPDDVNFLVYKYFSFIPQETRVEGDMDISLYDHLKVTAMLSLALYDYAKENHLDFKTYDEMKRYFEDPSVKPFLLVGGDVSGIQNFISSVSSKGALRSYRGRSFFIEILQEVVVDEILSRTGFYRTNVHYIGGGHFHLVLSNTEKVKETIEKIRKELNAWFRKRGLSLHLVTEYTEFSTKDVKDMGSIFESIAKKVNLRKLRMYTEEDLEELFPDDLSSIAEKGGFTCKVCGNRVEKLFALGDSEEEIACDFCRKMYELGRDLLKKDEEGNYTYIYLVEKDNGRFEIFNKRFDFSRKPGEDCVVWERTEDLVWGM
>NC_011978.1|WP_015919196.1|699499_701110_+|CRISPR-associated-DxTHG-motif-protein
MHEFVKLVTFLGVGNYRESLVKISPDFCVRQKVFPLAIVDYLHHLGKSVEVLFFLTEESRQSETWLECRNYLENKNVSYKFFSIPERVSSEVVMNSLVRTLVENLKEDENIILDITHSFRSFPLMAGVVALYLKEAKRIDVRVIYGKFDPETNTTECEDLTPLTRATEWIYAVRLFREYGYAKELAHLIRKRNEEIHRKNSSKKPRILNSLSSSLQNISFSLRIGSIKAIRKNLSNFFEFFDGKRNQIRSEVKEFVPEIAALLDVLEKSYRVFHIERGGLKLNEEELESERKLLNFYLQTGDLGMALRLAREYLINAYLMMSGEETNFLERDVRESVNLSKLGYDIILQARNHVARFGFNKVDLPSLNKIEKAIKSLVSSHPERILISSEKSYQSRKAALLTPLGTTKGALYTVLKHFSPDLLLIVTSKQGKEILPEILEKVKYKNDYKVILLEDPFTGVNEINRVISEAREYLADSDEIIVNLTGGTTLLTYLVECIKNHLRYGRKIKTVLAVDRRSYEEQIKNPFVVGEILELE
>NC_011978.1|WP_041437564.1|698734_699487_+|CRISPR-associated-endoribonuclease-Cas6
MRIKINFQTTKARIPLNYNYFLSSFIYKRLAAQNENFARFLHESGYGKRFKFFTFSQLFFENSKVDGDKIVIFPGRGWWHISSPVVDFVRYMFSSLSEDPVIRVGKTEFFVQSITVEESLPALSEYNFVMISPLVVSVPEEKNGKLVHRYLHPCEEEFYEAFKKNLYKKYRIFYGKDPEGDVEIIPDWNYIKSRERITKRIKLKDVFVRAVVFPFRMRGDRKLVEIGYETGFGEKNSMGFGMVALKENKP
>NC_011978.1|WP_038067000.1|698151_698574_+|hypothetical-protein
MPVLQKRRIRSELKQFVGKTVEVVGNVKRFGSTRHPSCKYPIVLLTSVTVRYKNKSVKIDHLWMVIKRLPHTLDIATGDILGFKADIVRYKVLPDFKSKNAILRPRYNYGVTNPRNFRIINHSMNLEKSMTLYDALLKVL
>NC_011978.1|WP_038066997.1|697710_698115_+|DUF1232-domain-containing-protein
MEGREYLNRFLKGKSEEEIIEKSRKYVENEEEILEGAFRNIAEVFEEFKTFLSMLKDFFTGEYKDVPGGTIAAASLAIFYYVFPFDIIPDIIPVAGWIDDITVIKFLWNLVREDLQKYMAWKGKQRKRKQKVFA
>NC_011978.1|WP_015919189.1|695238_697191_+|IGHMBP2-family-helicase
MTVHQFVKKLIKLVELERNAEISAMLDEIKRLSGEEREKKGRAILGLTGKFVGEELGYFFVRFGRRKEIDTEIGVGDLVLISKGTPLKSDYTGTVVEKGTRFITVAVDRLPPWKLKNVRIDLFASDITFRRQIENLMGLSPEGKRCLEFLLGKREPEESVEEEFVPFDEGLNESQREAVSLALGSSDFFLIHGPFGTGKTRTLVEYIRQETARGRKLLVTAESNLAVDNLVERLWGSVSLVRIGHPSRVSPHLKESTLAHQIETHDEYTKVKEMKENLSKLIEKRDRFTKPSPQWRRGLSDEKILEYAEKNWSARGVPKERIKEMAEWIKLNNQIQEMRELIEEKEEAIARSIVRKAQVVLSTNSSAALDIVSGILFDVVVVDEASQATIPSILIPISRGKKFVLAGDHKQLPPTILSEEARDLSRTLFEELIRLYPEKSVLLDTQYRMNEILMEFPSREFYDGKLKADDSVKNITLLDLGVESPNFDKLWDVILSPKNVLVFVDTRNRPDRFERQRKDSPSRENPLEARLVKEIVEKLISMGVKEEWIGVITPYDDQVDLVRTLLEEKVEVHSVDGFQGREKEVIIISFVRSNKNGEIGFLEDLRRLNVSLTRAKRKLIAIGDSSTLSVHPTYRRFVEFARKKGTYVIL
>NC_011978.1|WP_038066994.1|694204_695242_+|dipeptide-epimerase
MSKIVDVKFTLRRHEYEKPFHITGSISSESRNVEVEITLESGIRGYGEASPSFRVNGERVEALLAVENVVKDMITGFDVRNYAKIFEITDKLFAFPSLKAAVQFAVLDALAQELDVQVCHLLGGAKSRIETDKTVGIDSIEKRVEEARKIFEEGFRVIKIKVGENLKEDIEAMMEIAKVTKGAKYIVDANMGYSPKEAVEFVKKIYQAGIDISVYEQPVRREDIDGLKFVRFHSPFPVAADESARTKFDVMRLVKEEAVDYVNIKLMKSGISDALAIVKIAEASGLKLMIGCMGESSLGINQSVHFALGTGAFEYHDLDSHLMLKEEKFRGKFIQEGPEMRVREE
>NC_011978.1|WP_038067033.1|705328_706057_+|CRISPR-associated-endoribonuclease-Cas6
MRIFVKIQPESGSEGKFPADYRRIFMSLLKQVYKRTPFEEIVNSHDRIPKPYVFSVGFNKIKDISGDSIIFESPIFFNFSSSIPQMVGYLYNYIVSQDSIMNGLKVAGVDLPVPKIITSKTVTFKIMGSAVLTRAEKDRYYVLPEDNDFEEALNHSIQVRLNLSRELFETFGVRIPNFKPVKVVNKNLRKVPAKHYGGYIEAFSGTITLDGDPDVLSFLHENGLGVRTGQGFGMLKVVREWH
>NC_011978.1|WP_144399156.1|706200_707415_+|type-I-B-CRISPR-associated-protein-Cas8b1/Cst1
MLDELYLIDNFDNLSLPRLFVFILEETARIEGDIRKAYNYFKGNVGYYENYVAQVKEKQFMENLSKIVHYIFRKPSLEGTDRCFFCGNSLKTDEDRSILQRKQFSRILFKDFSSSEGKFPNSFWNMSNEFYLCDVCSQMALFRHFVFPKSGESIFVNVPSFKAIWYLNEAIKAYRDLSLELSVSRAISEVHLKLQRLLGIWERQNVEVIYYNSKSYRIYYMPQRVINLLLNTRISSILNSLNSIKIFEAVIYQERLNEILECEYLLLKYLFDVSSSGRSHLAENVKQYVGDVKRNAGYYMNTLPDLFQEVRSVMGVKQMVPVWRMRELGKEASQLFERTRYRLLELIRLAKKDEVYHLILKTYMANNKPFPEDLNRVFSAKDEDFKNLMFAYVSGMISGGEENE
>NC_011978.1|WP_015919204.1|707407_708424_+|type-I-B-CRISPR-associated-protein-Cas7/Cst2/DevR
MSNPKAITATIVFESSAVNRDENIANNIQSLKKLRREDGVYTFFSRASMRHHVFNALVRKHGWKPARVAKDGDVIQFDVLEESILTSEELDFFGYMRTFESASLSRKAPVGMTKAVSLEKWEGDMAFYANHDLVQRAREIGESADPNPFSKEEHLSLYKYSVVVDLENIGKEKVIINEKQCEKLNRLFGIDLKELKEKESIANDKGTISLESVGEKSYRILVTLNDPEKQKRLKQFFDIIINGFEIHSSTESWCVSPVFIVIATTRLPVTLFNPYIKLDDGKIDVDLVAKIAEENTNVIDYRIWGVPFILKGEVDKLCKGPKDLNDWVTGVIGGKENS
>NC_011978.1|WP_015919205.1|708420_709203_+|type-I-B-CRISPR-associated-protein-Cas5
MKLLRIEIKASTGHFAIPFLIFERKTFPIPMYSTMIGFVCNILADEAKISRFLSSNFSMAVVGDHDGVVEEYTWFRNLSKESHTKKFICSFNREANNEIEHPGGQSPVKIQTLINPKINLFLKAEEWILEMVKESFENPQCISRPHLGRSEDVVDDIKVELIDCEKKQVFDTNGYTWMPSPEFVDDVSDSYEELYKRISGSVYRVSSVYIIQNNRRIFEFVHAKLHRGAIPMVGFKVPEVLSWNGTPIFLARIRFPDKGG
>NC_011978.1|WP_015919206.1|709205_710366_+|CRISPR-associated-endonuclease-Cas3''
MPILAKSNGISLREHVEDVLKVLNNFSIEPDLKEFLRKAVFYHDLGKVSYEFQKKVGGNVPEDGIPEVPHSFLSIAFVPENTLEEMGEDLSKVFLSAILYHHWRETYLDYLFGSKQGNVREAFKRLLEVGNNLIRMIKEEMKDFLEYDVELNRSLCEYLSQNSILDSGLILPPHLISLLPSIVLKELNLKDDVYRCYILTLGTLMRADRFASCAEGVGKKDLLERADIEFKEDTFEVIESDLKRRYEKVWQSDVVKEIRGKNVVLVAPTGAGKTEFALMWSKGKTVFTLPLQSATNMMYERVKKYFGEENVGLLHSDAAIHLFLTSLYRKDFEDREGEILEIAEQSRFFSYPFVVATGDQVFPATLKYPGYEMIYSVMANSFLGDR
>NC_011978.1|WP_015919207.1|710352_711546_+|CRISPR-associated-helicase-Cas3'
MVIDEIQAYSPEAAAIIVKTVEDVNTLGGKFLIMTATLPGFIKDEIIKRTDLDEGVKDVYDSIPQGRLRRNVLKFKDSSDPTEEAVKLYEEGWKVLVVRNTVKKAIETYQKLVEKIGKERVLLVHSRMTLEDRKEVERILENYRPGMNGESIVLVSTQVVEASMDIDFDILLTDVAPADSLVQRMGRIFRKREWTENNPNTFIYIGKSKKEFDSLIKGVYSKDIVENTLKALSEVILGLGEEKIDVLFKNLPKQQPFSLNESQKRTWVEKTYEKLELEKGYMERFRKTLDVLDSGYSSEKKHEAHRIFRRISSMSIVPENLKEDLVEELKGASNYFEFKQITSRYLVDVPLYDMDGSLLEPLKVEAQDEKVLRWTSSLYVLKGSKYEKGIGIFLKEK
>NC_011978.1|WP_015919208.1|711548_712067_+|CRISPR-associated-protein-Cas4
MEELDILNISGTMVSYYFTCKRKLWLFAKNIDMEQSQPTTDLIIGKLLNFKSFKQEKHKEIEIEDCVIDFITFRGEIIIHETKKSRKFEEAHVWQTKYYMFVLRKYGLDITHGVIHYPKLMRKEEINFEKDDEEKIRNALLEIKRITHEKIPPPVLNKSFCKRCSYYELCYV
>NC_011978.1|WP_038067041.1|712076_713057_+|type-I-B-CRISPR-associated-endonuclease-Cas1
MGKNYYVFSSGRVKRHENTILIEYQKAGMQQRKFIPVENIDQIFFLGEVDLNSKFLDFAAKNNIVLHFFNYYGYYTGSFYPREKFISGELLVRQVEHYLDSEKRLTLARKFVEGAVHNFKRNIEKRGFDITDKISEYLERTKYAKTIPELMSCEAHARKLYYSTWEEITGWPFEERSMQPPLNELNALISFGNSLTYSIVLKELYFTHLNPTISYLHEPGTKRFSLALDIAEIFKPIFVDRIIFKLINLKKIDREKHFLQEARGVFLNEEGRRLFIEEFENMLQQTILHRKLKRKIKYQSLIRLEAYKIIKHLLGEDEYRPLKVWW
>NC_011978.1|WP_144399088.1|713059_713344_+|CRISPR-associated-endonuclease-Cas2
MVKVILVYDISTETKEGVKRLNKVRKIARRYLDHIQKSVFEGELTEGEVEKLKFELSCVIDKNEDFVIIYKMPPSIMMERDFLTNTEDPSSNFI
>NC_011978.1|WP_015919213.1|715624_716464_+|GGDEF-domain-containing-protein
MKNGRFEFLKRVLGSIQSIRGFVLFESVGGELSVKTSVGKVPLFFKEGFSFTTDEIFELLKFQCDTAVVSVMKDREWSKMLVLFLEKPLEKETLSLIQSLMSVSECEDLFFDMKELEYMAYHDPLTGLPNRRYFFELGGKYLDIAKREDKKVFILFLDLSGFKKINDTYGHPFGDEVLKTVSKRILDRIRKSDVISRFGGDEFTLLLYDMKEDYLDSFLKRLFSAFKMPVKIGNTEISVSANVGVARFPEDGTNLEELLKMADSRMYEAKKMKIPYVFV

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Crispr_ID: NC_011978_5

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011978_5

713422-715291

Consensus_repeat	Method
GTTTTTATCTTCCTAAGAGGAATATGAAC	PILER-CR
GTTTTTATCTTCCTAAGAGGAATATGAAC	CRISPRCasFinder
GTTTTTATCTTCCTAAGAGGAATATGAAC	CRT

28 spacers

cas2,cas1,cas4,cas3,cas3HD,cas5,cas7,cas6

The CRISPR arrays of NC_011978_5

>merge|NC_011978|5|713422-715291|PILER-CR,CRISPRCasFinder,CRT
GTTTTTATCTTCCTAAGAGGAATATGAACGCACAAATGTGTGTGTGTCGGCGTTTTTGTGGCGCCAGGTTTTTATCTTCCTAAGAGGAATATGAACGAAACTGCCCACGCCGTACCAGAGCGTTGGCGCCAGGTTTTTATCTTCCTAAGAGGAATATGAACGGGGATTACTCCCCGCTAAACTCTACCGCTATCCAGGTTTTTATCTTCCTAAGAGGAATATGAACAAGCCATCAGGACAGAAATAGACACGATAGCGCTCAGTTTTTATCTTCCTAAGAGGAATATGAACATGACATTTATAAACTATTTCATTCCAGGGGATTACTCGTTTTTATCTTCCTAAGAGGAATATGAACAGCTCTTTCGATGCGACAGTCGGCGAGTATGGAGTGTGTTTTTATCTTCCTAAGAGGAATATGAACCTCTACCCTCAATTAAGATCGACTGTCACATATCAAGTTTTTATCTTCCTAAGAGGAATATGAACTTGTAACCAGCCACGGCGATCTATCTGCCCTGTGAAAGTTTTTATCTTCCTAAGAGGAATATGAACCAATCTAGAAGGAGGGGATTGAGATGGTCAAGTATGAGTTTTTATCTTCCTAAGAGGAATATGAACATTCACAACTATATCTATGTGTTCGAGTGTAATCTCGTTTTTATCTTCCTAAGAGGAATATGAACAAGATAAGAATCTTCACCTTAAATCTCCTCCCACACCAGTTTTTATCTTCCTAAGAGGAATATGAACGGCGACAGAAGCCGCCAGTGTCGTTTGCAAACTGCGGTTTTTATCTTCCTAAGAGGAATATGAACGTAGGGAAGCTAGAGGTGGTAGGATGAGTGAATGGAGTTTTTATCTTCCTAAGAGGAATATGAACCAATCTTCTCTAACTCATTGGCGTTCTGAAAGATTTCAGTTTTTATCTTCCTAAGAGGAATATGAACATCTAGATAGAGGACATTTATAGGGTCTCGTGTTTTGTTTTTATCTTCCTAAGAGGAATATGAACCGTTCTGCAGGGGGTCTTTTTCAATCTCCCTGTCCAGGTTTTTATCTTCCTAAGAGGAATATGAACCTATATGGACAGACTCCTATATCCGCTTCCTGTATGAAAGTTTTTATCTTCCTAAGAGGAATATGAACTTCCTCCCTTACCTCATCGTGATGCGCACACCTTTCTGGTTTTTATCTTCCTAAGAGGAATATGAACTTTTCTTGAAGTCTTCCTCTACTCTTTTTTTATATCGTTTTTATCTTCCTAAGAGGAATATGAACTGATAAAAAAGGAGTTCGTTGAAAAGCTGATGAAAAGTTTTTATCTTCCTAAGAGGAATATGAACCTTTACCTCGTGATGAAGGCGGGGGTAGGTATATCCGGTTTTTATCTTCCTAAGAGGAATATGAACTCTATACAATTTTATCTCTTTGAGGGTGTTGGCGCAGTTTTTATCTTCCTAAGAGGAATATGAACTGTCTTCTCTCCTATCCGCCTGCCGTTTTTGGGAATGTTTTTATCTTCCTAAGAGGAATATGAACTGCTATCACTTCCTTACCTCTGTATCTCGTACTCGATCGTTTTTATCTTCCTAAGAGGAATATGAACCTTGAGAAGGCTGCTGCACAGGCTGACGCATGGATCGGTTTTTATCTTCCTAAGAGGAATATGAACATGGTCGGGTCATTCCCCTCCTTGTCTCTGAACAACGTTTTTATCTTCCTAAGAGGAATATGAACCAGAACTCCTTCCACCTGTTCACCGCTGCTTTGAACGTTTTTATCTTCCTAAGAGGAATATGAACTGCGGTGTGATAGGTCACACTCCCACCTCACACAACGTTTTTATCTTCCTAAGAGGAATATAGTA

>NC_011978|5|5|713422-715226|PILER-CR
GTTTTTATCTTCCTAAGAGGAATATGAAC	GCACAAATGTGTGTGTGTCGGCGTTTTTGTGGCGCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GAAACTGCCCACGCCGTACCAGAGCGTTGGCGCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GGGGATTACTCCCCGCTAAACTCTACCGCTATCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	AAGCCATCAGGACAGAAATAGACACGATAGCGCTCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATGACATTTATAAACTATTTCATTCCAGGGGATTACTC
GTTTTTATCTTCCTAAGAGGAATATGAAC	AGCTCTTTCGATGCGACAGTCGGCGAGTATGGAGTGT
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTCTACCCTCAATTAAGATCGACTGTCACATATCAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTGTAACCAGCCACGGCGATCTATCTGCCCTGTGAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAATCTAGAAGGAGGGGATTGAGATGGTCAAGTATGA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATTCACAACTATATCTATGTGTTCGAGTGTAATCTC
GTTTTTATCTTCCTAAGAGGAATATGAAC	AAGATAAGAATCTTCACCTTAAATCTCCTCCCACACCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	GGCGACAGAAGCCGCCAGTGTCGTTTGCAAACTGCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GTAGGGAAGCTAGAGGTGGTAGGATGAGTGAATGGA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAATCTTCTCTAACTCATTGGCGTTCTGAAAGATTTCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATCTAGATAGAGGACATTTATAGGGTCTCGTGTTTT
GTTTTTATCTTCCTAAGAGGAATATGAAC	CGTTCTGCAGGGGGTCTTTTTCAATCTCCCTGTCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTATATGGACAGACTCCTATATCCGCTTCCTGTATGAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTCCTCCCTTACCTCATCGTGATGCGCACACCTTTCTG
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTTTCTTGAAGTCTTCCTCTACTCTTTTTTTATATC
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGATAAAAAAGGAGTTCGTTGAAAAGCTGATGAAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTTTACCTCGTGATGAAGGCGGGGGTAGGTATATCCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	TCTATACAATTTTATCTCTTTGAGGGTGTTGGCGCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGTCTTCTCTCCTATCCGCCTGCCGTTTTTGGGAAT
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGCTATCACTTCCTTACCTCTGTATCTCGTACTCGATC
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTTGAGAAGGCTGCTGCACAGGCTGACGCATGGATCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATGGTCGGGTCATTCCCCTCCTTGTCTCTGAACAAC
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAGAACTCCTTCCACCTGTTCACCGCTGCTTTGAAC
GTTTTTATCTTCCTAAGAGGAATATGAAC

>NC_011978|5|5|713422-715291|CRISPRCasFinder
GTTTTTATCTTCCTAAGAGGAATATGAAC	GCACAAATGTGTGTGTGTCGGCGTTTTTGTGGCGCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GAAACTGCCCACGCCGTACCAGAGCGTTGGCGCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GGGGATTACTCCCCGCTAAACTCTACCGCTATCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	AAGCCATCAGGACAGAAATAGACACGATAGCGCTCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATGACATTTATAAACTATTTCATTCCAGGGGATTACTC
GTTTTTATCTTCCTAAGAGGAATATGAAC	AGCTCTTTCGATGCGACAGTCGGCGAGTATGGAGTGT
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTCTACCCTCAATTAAGATCGACTGTCACATATCAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTGTAACCAGCCACGGCGATCTATCTGCCCTGTGAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAATCTAGAAGGAGGGGATTGAGATGGTCAAGTATGA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATTCACAACTATATCTATGTGTTCGAGTGTAATCTC
GTTTTTATCTTCCTAAGAGGAATATGAAC	AAGATAAGAATCTTCACCTTAAATCTCCTCCCACACCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	GGCGACAGAAGCCGCCAGTGTCGTTTGCAAACTGCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GTAGGGAAGCTAGAGGTGGTAGGATGAGTGAATGGA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAATCTTCTCTAACTCATTGGCGTTCTGAAAGATTTCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATCTAGATAGAGGACATTTATAGGGTCTCGTGTTTT
GTTTTTATCTTCCTAAGAGGAATATGAAC	CGTTCTGCAGGGGGTCTTTTTCAATCTCCCTGTCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTATATGGACAGACTCCTATATCCGCTTCCTGTATGAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTCCTCCCTTACCTCATCGTGATGCGCACACCTTTCTG
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTTTCTTGAAGTCTTCCTCTACTCTTTTTTTATATC
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGATAAAAAAGGAGTTCGTTGAAAAGCTGATGAAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTTTACCTCGTGATGAAGGCGGGGGTAGGTATATCCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	TCTATACAATTTTATCTCTTTGAGGGTGTTGGCGCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGTCTTCTCTCCTATCCGCCTGCCGTTTTTGGGAAT
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGCTATCACTTCCTTACCTCTGTATCTCGTACTCGATC
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTTGAGAAGGCTGCTGCACAGGCTGACGCATGGATCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATGGTCGGGTCATTCCCCTCCTTGTCTCTGAACAAC
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAGAACTCCTTCCACCTGTTCACCGCTGCTTTGAAC
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGCGGTGTGATAGGTCACACTCCCACCTCACACAAC
GTTTTTATCTTCCTAAGAGGAATATAGTA

>NC_011978|5|5|713422-715291|CRT
GTTTTTATCTTCCTAAGAGGAATATGAAC	GCACAAATGTGTGTGTGTCGGCGTTTTTGTGGCGCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GAAACTGCCCACGCCGTACCAGAGCGTTGGCGCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GGGGATTACTCCCCGCTAAACTCTACCGCTATCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	AAGCCATCAGGACAGAAATAGACACGATAGCGCTCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATGACATTTATAAACTATTTCATTCCAGGGGATTACTC
GTTTTTATCTTCCTAAGAGGAATATGAAC	AGCTCTTTCGATGCGACAGTCGGCGAGTATGGAGTGT
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTCTACCCTCAATTAAGATCGACTGTCACATATCAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTGTAACCAGCCACGGCGATCTATCTGCCCTGTGAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAATCTAGAAGGAGGGGATTGAGATGGTCAAGTATGA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATTCACAACTATATCTATGTGTTCGAGTGTAATCTC
GTTTTTATCTTCCTAAGAGGAATATGAAC	AAGATAAGAATCTTCACCTTAAATCTCCTCCCACACCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	GGCGACAGAAGCCGCCAGTGTCGTTTGCAAACTGCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	GTAGGGAAGCTAGAGGTGGTAGGATGAGTGAATGGA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAATCTTCTCTAACTCATTGGCGTTCTGAAAGATTTCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATCTAGATAGAGGACATTTATAGGGTCTCGTGTTTT
GTTTTTATCTTCCTAAGAGGAATATGAAC	CGTTCTGCAGGGGGTCTTTTTCAATCTCCCTGTCCAG
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTATATGGACAGACTCCTATATCCGCTTCCTGTATGAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTCCTCCCTTACCTCATCGTGATGCGCACACCTTTCTG
GTTTTTATCTTCCTAAGAGGAATATGAAC	TTTTCTTGAAGTCTTCCTCTACTCTTTTTTTATATC
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGATAAAAAAGGAGTTCGTTGAAAAGCTGATGAAAA
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTTTACCTCGTGATGAAGGCGGGGGTAGGTATATCCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	TCTATACAATTTTATCTCTTTGAGGGTGTTGGCGCA
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGTCTTCTCTCCTATCCGCCTGCCGTTTTTGGGAAT
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGCTATCACTTCCTTACCTCTGTATCTCGTACTCGATC
GTTTTTATCTTCCTAAGAGGAATATGAAC	CTTGAGAAGGCTGCTGCACAGGCTGACGCATGGATCG
GTTTTTATCTTCCTAAGAGGAATATGAAC	ATGGTCGGGTCATTCCCCTCCTTGTCTCTGAACAAC
GTTTTTATCTTCCTAAGAGGAATATGAAC	CAGAACTCCTTCCACCTGTTCACCGCTGCTTTGAAC
GTTTTTATCTTCCTAAGAGGAATATGAAC	TGCGGTGTGATAGGTCACACTCCCACCTCACACAAC
GTTTTTATCTTCCTAAGAGGAATATAGTA

Protein	Signature genes	Signature genes Name	Protein_function
NC_011978.1\|WP_038067006.1\|703840_704182_-\|J-domain-containing-protein	unknown	unknown	gnl\|CDD\|365959
NC_011978.1\|WP_015919213.1\|715624_716464_+\|GGDEF-domain-containing-protein	unknown	unknown	gnl\|CDD\|143635
NC_011978.1\|WP_038067045.1\|718399_719590_+\|M20-family-metallo-hydrolase	unknown	unknown	gnl\|CDD\|237578
NC_011978.1\|WP_038067041.1\|712076_713057_+\|type-I-B-CRISPR-associated-endonuclease-Cas1	cas1	cd09722_cas1_CAS-I-B	gnl\|CDD\|274695
NC_011978.1\|WP_015919215.1\|716957_718292_-\|xylose-isomerase	unknown	unknown	gnl\|CDD\|274238
NC_011978.1\|WP_015919204.1\|707407_708424_+\|type-I-B-CRISPR-associated-protein-Cas7/Cst2/DevR	cas7	cd09687_cas7_CAS-I-B	gnl\|CDD\|274215
NC_011978.1\|WP_015919207.1\|710352_711546_+\|CRISPR-associated-helicase-Cas3'	cas3	COG1203_cas3_CAS-I	gnl\|CDD\|273707
NC_011978.1\|WP_015919218.1\|720139_720775_+\|class-I-SAM-dependent-methyltransferase	unknown	unknown	gnl\|CDD\|225370
NC_011978.1\|WP_015919221.1\|722237_722732_+\|peptide-deformylase	unknown	unknown	gnl\|CDD\|237761
NC_011978.1\|WP_144399156.1\|706200_707415_+\|type-I-B-CRISPR-associated-protein-Cas8b1/Cst1	unknown	unknown	gnl\|CDD\|187796
NC_011978.1\|WP_015919219.1\|720755_721520_+\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|213192
NC_011978.1\|WP_015919220.1\|721494_722250_+\|5'/3'-nucleotidase-SurE	unknown	unknown	gnl\|CDD\|237566
NC_011978.1\|WP_015919222.1\|722745_723717_+\|M23-family-metallopeptidase	unknown	unknown	gnl\|CDD\|366703
NC_011978.1\|WP_038067049.1\|719594_720143_+\|ATP-binding-protein	unknown	unknown	gnl\|CDD\|340391
NC_011978.1\|WP_144399089.1\|716472_716940_-\|DUF192-domain-containing-protein	unknown	unknown	gnl\|CDD\|224347
NC_011978.1\|WP_015919208.1\|711548_712067_+\|CRISPR-associated-protein-Cas4	cas4	pfam01930_cas4_CAS-I	gnl\|CDD\|366863
NC_011978.1\|WP_038067033.1\|705328_706057_+\|CRISPR-associated-endoribonuclease-Cas6	cas6	cd09652_cas6_CAS-I:CAS-III	gnl\|CDD\|273848
NC_011978.1\|WP_015919206.1\|709205_710366_+\|CRISPR-associated-endonuclease-Cas3''	cas3HD	cd09641_cas3HD_CAS-I	gnl\|CDD\|350688
NC_011978.1\|WP_144399088.1\|713059_713344_+\|CRISPR-associated-endonuclease-Cas2	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|187856
NC_011978.1\|WP_015919205.1\|708420_709203_+\|type-I-B-CRISPR-associated-protein-Cas5	cas5	cd09658_cas5_CAS-I-B	gnl\|CDD\|273860

Protein	Function_ID	Function_description	E-value
NC_011978.1\|WP_038067006.1\|703840_704182_-\|J-domain-containing-protein	gnl\|CDD\|365959	pfam00226, DnaJ, DnaJ domain. DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature.	5.44802e-24
NC_011978.1\|WP_015919213.1\|715624_716464_+\|GGDEF-domain-containing-protein	gnl\|CDD\|143635	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain. Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.	8.8737e-64
NC_011978.1\|WP_038067045.1\|718399_719590_+\|M20-family-metallo-hydrolase	gnl\|CDD\|237578	PRK13983, PRK13983, M20 family metallo-hydrolase.	0
NC_011978.1\|WP_038067041.1\|712076_713057_+\|type-I-B-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|274695	TIGR03641, cas1_HMARI, CRISPR-associated endonuclease Cas1, subtype I-B/HMARI/TNEAP. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes Cas1 subgroup that includes Cas1 proteins of the related HMARI and TNEAP subtypes of CRISPR/Cas system.	1.34446e-174
NC_011978.1\|WP_015919215.1\|716957_718292_-\|xylose-isomerase	gnl\|CDD\|274238	TIGR02630, Xylose_isomerase, xylose isomerase. Members of this family are the enzyme xylose isomerase (5.3.1.5), which interconverts D-xylose and D-xylulose. [Energy metabolism, Sugars].	0
NC_011978.1\|WP_015919204.1\|707407_708424_+\|type-I-B-CRISPR-associated-protein-Cas7/Cst2/DevR	gnl\|CDD\|274215	TIGR02585, conserved_protein, CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This clade is a member of the DevR family (TIGR01875) and includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to be regulated through a number of means, including both location and autorepression; DevR mutants are incapable of fruiting body development.	1.10332e-99
NC_011978.1\|WP_015919207.1\|710352_711546_+\|CRISPR-associated-helicase-Cas3'	gnl\|CDD\|273707	TIGR01587, CRISPR-associated_endonuclease/helicase_Cas3, CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.	2.8195e-42
NC_011978.1\|WP_015919218.1\|720139_720775_+\|class-I-SAM-dependent-methyltransferase	gnl\|CDD\|225370	COG2813, RsmC, 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis].	1.01504e-79
NC_011978.1\|WP_015919221.1\|722237_722732_+\|peptide-deformylase	gnl\|CDD\|237761	PRK14597, PRK14597, peptide deformylase; Provisional.	3.70139e-101
NC_011978.1\|WP_144399156.1\|706200_707415_+\|type-I-B-CRISPR-associated-protein-Cas8b1/Cst1	gnl\|CDD\|187796	cd09665, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1. 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; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as CXXC_CXXC family.	0.000126133
NC_011978.1\|WP_015919219.1\|720755_721520_+\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|213192	cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding cassette component of cobalt transport system. Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.	2.21568e-88
NC_011978.1\|WP_015919220.1\|721494_722250_+\|5'/3'-nucleotidase-SurE	gnl\|CDD\|237566	PRK13935, PRK13935, stationary phase survival protein SurE; Provisional.	1.02783e-177
NC_011978.1\|WP_015919222.1\|722745_723717_+\|M23-family-metallopeptidase	gnl\|CDD\|366703	pfam01551, Peptidase_M23, Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.	9.96168e-22
NC_011978.1\|WP_038067049.1\|719594_720143_+\|ATP-binding-protein	gnl\|CDD\|340391	cd00075, HATPase, Histidine kinase-like ATPase domain. This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.	4.53136e-21
NC_011978.1\|WP_144399089.1\|716472_716940_-\|DUF192-domain-containing-protein	gnl\|CDD\|224347	COG1430, COG1430, Uncharacterized conserved protein [Function unknown].	6.89875e-45
NC_011978.1\|WP_015919208.1\|711548_712067_+\|CRISPR-associated-protein-Cas4	gnl\|CDD\|366863	pfam01930, Cas_Cas4, Domain of unknown function DUF83. This domain has no known function. The domain contains three conserved cysteines at its C-terminus.	6.9859e-52
NC_011978.1\|WP_038067033.1\|705328_706057_+\|CRISPR-associated-endoribonuclease-Cas6	gnl\|CDD\|273848	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This broadly distributed, highly divergent Cas family is now characterized as an endoribonuclease that generates guide RNAs for host defense against phage and other invaders. The family contains a C-terminal motif GXGXXXXXGXG, where the each X between two Gly is hydrophobic and the spacer XXXXX contains (usually) one Arg or Lys. The seed alignment for the current version of this model has gappy columns removed. Members of this protein family are found associated with several different CRISPR/cas system subtypes, and consequently we designate this family Cas6.	4.80581e-30
NC_011978.1\|WP_015919206.1\|709205_710366_+\|CRISPR-associated-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.	1.38438e-33
NC_011978.1\|WP_144399088.1\|713059_713344_+\|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.	1.40083e-27
NC_011978.1\|WP_015919205.1\|708420_709203_+\|type-I-B-CRISPR-associated-protein-Cas5	gnl\|CDD\|273860	TIGR01895, conserved_hypothetical_protein, CRISPR-associated protein Cas5, subtype I-B/TNEAP. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family is represented by TM1800 from Thermotoga maritima. It is related to TIGR01868 (CRISPR-associated protein, CT1976 family).	2.68051e-92

>NC_011978.1|WP_144399088.1|713059_713344_+|CRISPR-associated-endonuclease-Cas2
MVKVILVYDISTETKEGVKRLNKVRKIARRYLDHIQKSVFEGELTEGEVEKLKFELSCVIDKNEDFVIIYKMPPSIMMERDFLTNTEDPSSNFI
>NC_011978.1|WP_038067041.1|712076_713057_+|type-I-B-CRISPR-associated-endonuclease-Cas1
MGKNYYVFSSGRVKRHENTILIEYQKAGMQQRKFIPVENIDQIFFLGEVDLNSKFLDFAAKNNIVLHFFNYYGYYTGSFYPREKFISGELLVRQVEHYLDSEKRLTLARKFVEGAVHNFKRNIEKRGFDITDKISEYLERTKYAKTIPELMSCEAHARKLYYSTWEEITGWPFEERSMQPPLNELNALISFGNSLTYSIVLKELYFTHLNPTISYLHEPGTKRFSLALDIAEIFKPIFVDRIIFKLINLKKIDREKHFLQEARGVFLNEEGRRLFIEEFENMLQQTILHRKLKRKIKYQSLIRLEAYKIIKHLLGEDEYRPLKVWW
>NC_011978.1|WP_015919208.1|711548_712067_+|CRISPR-associated-protein-Cas4
MEELDILNISGTMVSYYFTCKRKLWLFAKNIDMEQSQPTTDLIIGKLLNFKSFKQEKHKEIEIEDCVIDFITFRGEIIIHETKKSRKFEEAHVWQTKYYMFVLRKYGLDITHGVIHYPKLMRKEEINFEKDDEEKIRNALLEIKRITHEKIPPPVLNKSFCKRCSYYELCYV
>NC_011978.1|WP_015919207.1|710352_711546_+|CRISPR-associated-helicase-Cas3'
MVIDEIQAYSPEAAAIIVKTVEDVNTLGGKFLIMTATLPGFIKDEIIKRTDLDEGVKDVYDSIPQGRLRRNVLKFKDSSDPTEEAVKLYEEGWKVLVVRNTVKKAIETYQKLVEKIGKERVLLVHSRMTLEDRKEVERILENYRPGMNGESIVLVSTQVVEASMDIDFDILLTDVAPADSLVQRMGRIFRKREWTENNPNTFIYIGKSKKEFDSLIKGVYSKDIVENTLKALSEVILGLGEEKIDVLFKNLPKQQPFSLNESQKRTWVEKTYEKLELEKGYMERFRKTLDVLDSGYSSEKKHEAHRIFRRISSMSIVPENLKEDLVEELKGASNYFEFKQITSRYLVDVPLYDMDGSLLEPLKVEAQDEKVLRWTSSLYVLKGSKYEKGIGIFLKEK
>NC_011978.1|WP_015919206.1|709205_710366_+|CRISPR-associated-endonuclease-Cas3''
MPILAKSNGISLREHVEDVLKVLNNFSIEPDLKEFLRKAVFYHDLGKVSYEFQKKVGGNVPEDGIPEVPHSFLSIAFVPENTLEEMGEDLSKVFLSAILYHHWRETYLDYLFGSKQGNVREAFKRLLEVGNNLIRMIKEEMKDFLEYDVELNRSLCEYLSQNSILDSGLILPPHLISLLPSIVLKELNLKDDVYRCYILTLGTLMRADRFASCAEGVGKKDLLERADIEFKEDTFEVIESDLKRRYEKVWQSDVVKEIRGKNVVLVAPTGAGKTEFALMWSKGKTVFTLPLQSATNMMYERVKKYFGEENVGLLHSDAAIHLFLTSLYRKDFEDREGEILEIAEQSRFFSYPFVVATGDQVFPATLKYPGYEMIYSVMANSFLGDR
>NC_011978.1|WP_015919205.1|708420_709203_+|type-I-B-CRISPR-associated-protein-Cas5
MKLLRIEIKASTGHFAIPFLIFERKTFPIPMYSTMIGFVCNILADEAKISRFLSSNFSMAVVGDHDGVVEEYTWFRNLSKESHTKKFICSFNREANNEIEHPGGQSPVKIQTLINPKINLFLKAEEWILEMVKESFENPQCISRPHLGRSEDVVDDIKVELIDCEKKQVFDTNGYTWMPSPEFVDDVSDSYEELYKRISGSVYRVSSVYIIQNNRRIFEFVHAKLHRGAIPMVGFKVPEVLSWNGTPIFLARIRFPDKGG
>NC_011978.1|WP_015919204.1|707407_708424_+|type-I-B-CRISPR-associated-protein-Cas7/Cst2/DevR
MSNPKAITATIVFESSAVNRDENIANNIQSLKKLRREDGVYTFFSRASMRHHVFNALVRKHGWKPARVAKDGDVIQFDVLEESILTSEELDFFGYMRTFESASLSRKAPVGMTKAVSLEKWEGDMAFYANHDLVQRAREIGESADPNPFSKEEHLSLYKYSVVVDLENIGKEKVIINEKQCEKLNRLFGIDLKELKEKESIANDKGTISLESVGEKSYRILVTLNDPEKQKRLKQFFDIIINGFEIHSSTESWCVSPVFIVIATTRLPVTLFNPYIKLDDGKIDVDLVAKIAEENTNVIDYRIWGVPFILKGEVDKLCKGPKDLNDWVTGVIGGKENS
>NC_011978.1|WP_144399156.1|706200_707415_+|type-I-B-CRISPR-associated-protein-Cas8b1/Cst1
MLDELYLIDNFDNLSLPRLFVFILEETARIEGDIRKAYNYFKGNVGYYENYVAQVKEKQFMENLSKIVHYIFRKPSLEGTDRCFFCGNSLKTDEDRSILQRKQFSRILFKDFSSSEGKFPNSFWNMSNEFYLCDVCSQMALFRHFVFPKSGESIFVNVPSFKAIWYLNEAIKAYRDLSLELSVSRAISEVHLKLQRLLGIWERQNVEVIYYNSKSYRIYYMPQRVINLLLNTRISSILNSLNSIKIFEAVIYQERLNEILECEYLLLKYLFDVSSSGRSHLAENVKQYVGDVKRNAGYYMNTLPDLFQEVRSVMGVKQMVPVWRMRELGKEASQLFERTRYRLLELIRLAKKDEVYHLILKTYMANNKPFPEDLNRVFSAKDEDFKNLMFAYVSGMISGGEENE
>NC_011978.1|WP_038067033.1|705328_706057_+|CRISPR-associated-endoribonuclease-Cas6
MRIFVKIQPESGSEGKFPADYRRIFMSLLKQVYKRTPFEEIVNSHDRIPKPYVFSVGFNKIKDISGDSIIFESPIFFNFSSSIPQMVGYLYNYIVSQDSIMNGLKVAGVDLPVPKIITSKTVTFKIMGSAVLTRAEKDRYYVLPEDNDFEEALNHSIQVRLNLSRELFETFGVRIPNFKPVKVVNKNLRKVPAKHYGGYIEAFSGTITLDGDPDVLSFLHENGLGVRTGQGFGMLKVVREWH
>NC_011978.1|WP_038067006.1|703840_704182_-|J-domain-containing-protein
MNPYEVLGVEPGASKEEIERAYRELVKKYHPDRYKDHPLRDLAEEKMKQINEAYQMLMNEEPEKNYSEEDSRFFSYSMGYRNNECRDILACLGCAWCTDTCCEACGGDCIPCM
>NC_011978.1|WP_015919213.1|715624_716464_+|GGDEF-domain-containing-protein
MKNGRFEFLKRVLGSIQSIRGFVLFESVGGELSVKTSVGKVPLFFKEGFSFTTDEIFELLKFQCDTAVVSVMKDREWSKMLVLFLEKPLEKETLSLIQSLMSVSECEDLFFDMKELEYMAYHDPLTGLPNRRYFFELGGKYLDIAKREDKKVFILFLDLSGFKKINDTYGHPFGDEVLKTVSKRILDRIRKSDVISRFGGDEFTLLLYDMKEDYLDSFLKRLFSAFKMPVKIGNTEISVSANVGVARFPEDGTNLEELLKMADSRMYEAKKMKIPYVFV
>NC_011978.1|WP_144399089.1|716472_716940_-|DUF192-domain-containing-protein
MNLRRLLLLALIAAGISVIIVVSNRENRVKFPEGEIVITDGERSLKLRVEIANTPFFRSIGLMYRKSIPDDFGMLFVFEEDTRSGFWMKNTYVPLEIAFIDRNGIVFSIQEMEPCEKEPCKVYYAPKPFRYALEVKRGFFERHGFGVGSRVLIEK
>NC_011978.1|WP_015919215.1|716957_718292_-|xylose-isomerase
MAEFFPEIPKVQFEGKESTNPLAFKFYDPEEIIDGKPLKDHLKFSVAFWHTFVNEGRDPFGDPTADRPWNRYTDPMDKAFARVDALFEFCEKLNIEYFCFHDRDIAPEGKTLRETNKILDKVVERIKERMKDSNVKLLWGTANLFSHPRYMHGAATTCSADVFAYAAAQVKKALEITKELGGEGYVFWGGREGYETLLNTDLGFELENLARFLRMAVDYAKRIGFTGQFLIEPKPKEPTKHQYDFDVATAYAFLKSHGLDEYFKFNIEANHATLAGHTFQHELRMARILGKLGSIDANQGDLLLGWDTDQFPTNVYDTTLAMYEVIKAGGFTKGGLNFDAKVRRASYKVEDLFIGHIAGMDTFALGFKVAYKLVKDGVLDKFIEEKYRSFREGIGRDIVEGKVDFEKLEEYIIDKETIELPSGKQEYLESLINSYIVKTILELR
>NC_011978.1|WP_038067045.1|718399_719590_+|M20-family-metallo-hydrolase
MEITRKIEELKDEMVDSLKRFISINSVNPVFGGPGEKEKADWLEELLKKMGYTVERHDTKDQNGIWRSNLLAIIPGRDRSKTLWIVTHIDTVPPGDLSLWETDPFIPVVKDDRVYGRGAEDNGGSMIASIYAGKALMELDVVPEYNFGLALVADEEAGSEYGIQYLIEKGVFRPDDMFLVPDAGNKKGDFIEIAEKSILWFKVTVNGKQGHASRPKTTENALRKGAQIITELDETLHRKFSEKDELFDEPLSTFEPTRSEKTVDNVNTVPGRFVFYFDCRVLPRYDLEDVLSTVKSVLDGRGAELEVVVKQPAPDPTPADSDLVVKLSSVLKSLRNLEVRVGGIGGGTCAAFFRKKGWPAVVWSTIEETAHQPNEYRKISHMVEDAKVFALLGVER
>NC_011978.1|WP_038067049.1|719594_720143_+|ATP-binding-protein
MLRTIADHLMDIAQNSVKAGARNIKITIEETDEWFTFTVEDDGPGIENPEKVFDPFFTTRDPRLRKVGLGLPFLKQAAEQSGGKVSLWTQPGKGTVVKASFNLKSVDCQPIGDLAGTLASLILSDPNVNWYVLRKKDGRGYEIDTSKLKEAGLWDPENPRFASFLFETLENLEEDLKRGEEK
>NC_011978.1|WP_015919218.1|720139_720775_+|class-I-SAM-dependent-methyltransferase
MSEKKFEHYYTVEPTSKLKVREAKLVLKNGHEYVFKTPSGVYSYGKIDKATKVLLENMKVHGKKVLDLGCGYGVIGIVLKKEYPDLEVYMSDINKRAVEFAKINAKDHNVEVEVRWGNLYEPWEGMKFDMIVCNPPIVAGKEVWMEIVRRAPEFLEDGGSLQLVAYHNKGGRRIREYMREIFGNVEELCKSGGIRVYRSVKGLKEDEDIVE
>NC_011978.1|WP_015919219.1|720755_721520_+|ABC-transporter-ATP-binding-protein
MKISLNDVSFGYNGRHVLKNVNMEFETGKIYIVVGKNGSGKTTLLKVVSGLLEAEGTILIDGEPADPLMLRRNVGYVFQNPSSQIIGATVEEDVAFSLEILGIDRDEMQRRIKRVLELVGLSGLEKEDPLNLSGGQKQRLAIASMLARDTHFLAMDEPLSMLDPPSQREISKVIEDLKREGKGIIIATHELEYLEDFDVVLHMRDGTIDFCGSWEAFMDKGFEDVEVPFKWKLWKKFGKESKWEVEDADTFDER
>NC_011978.1|WP_015919220.1|721494_722250_+|5'/3'-nucleotidase-SurE
MRILLTNDDGINSKGIILLAEYLSKEHEVFVVAPDKERSATGHSITIHVPLWMKKVFISEDVVAYSTTGTPADCVKLGYNVIMEKRVDLVVSGINRGPNMGMDILYSGTVSGAMEGAMMNIPSIAISSASYESPDFEGAARFLISFLKEFDLSLLDPFTMLNINVPVGEIKGWKLTRQSRRRWNDYFEERISPFGEKYYWMMGEVIEDDDREDVDYRVVQQGYVSVTPIHPFLTNEGCLRKLREVYESCTE
>NC_011978.1|WP_015919221.1|722237_722732_+|peptide-deformylase
MYRVRVFGDPVLRKRAKPVTKFDEALKRTIERMIETMYHYDGVGLAAPQVGISQRFFVMDVGNGPVAVINPEILEASPETEIAEEGCLSFPEIFVEIERSKRVKVRYQNVRGEFVEEELEGYPARVFQHEFDHLNGVLIIDRIKPAKRLLLRKRLMDIAKSARG
>NC_011978.1|WP_015919222.1|722745_723717_+|M23-family-metallopeptidase
MKKWLLILALVLLFSVVFSFSPPVDSPRVSASFGEYRGSGNRGPHFHMGMDFSTGLKEGVPIYASERGWLVRLEIDRDDIYGYTVVLEHENGYRTLYAHLSGFAKKLEVIVESLKEEFGDVRIVVEFPEKEIWFEKGEVVGYSGTTGEAPIPHAHFEIRDKKEEVSYDPSNFLNLQKPVDEDIFLENLKIGDNVYDFVENRTYPFTGNFPVLSIKAYSRGFNNTLGLKKISLLMEGEEIYQISFEQIPWSEFTNVWGVYDRKSVSAAYRFELWYKLFPETFSSLVKVNKFPEIGKFPDFAKYTIVLEDIWGMKKEFSFYLQRR

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Crispr_ID: NC_011978_6

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011978_6

739743-739910

Orphan

III-A

Consensus_repeat	Method
CGGGTTTCAATACTTCCTTAGAGGTATGGAAAC	CRISPRCasFinder

2 spacers

The CRISPR arrays of NC_011978_6

>merge|NC_011978|6|739743-739910|CRISPRCasFinder
CGGGTTTCAATACTTCCTTAGAGGTATGGAAACAGGTCTGTGTCTTTGACCGTCGCCAGGAACTGCTCGGGTTTCAATACTTCCTTAGAGGTATGGAAACGAGTGTTCTGGCAGGCGAAAGAACTTTTTGATGAGAAAGTTTCAATATTTCCTTATAGGTACAAACCC

>NC_011978|6|6|739743-739910|CRISPRCasFinder
CGGGTTTCAATACTTCCTTAGAGGTATGGAAAC	AGGTCTGTGTCTTTGACCGTCGCCAGGAACTGCT
CGGGTTTCAATACTTCCTTAGAGGTATGGAAAC	GAGTGTTCTGGCAGGCGAAAGAACTTTTTGATGAG
AAAGTTTCAATATTTCCTTATAGGTACAAACCC

Protein	Signature genes	Signature genes Name	Protein_function
NC_011978.1\|WP_015919233.1\|734683_734965_+\|DUF503-family-protein	unknown	unknown	gnl\|CDD\|224467
NC_011978.1\|WP_041437575.1\|744670_746176_+\|glutamine-hydrolyzing-GMP-synthase	unknown	unknown	gnl\|CDD\|234614
NC_011978.1\|WP_038067065.1\|736650_737472_-\|carboxylating-nicotinate-nucleotide-diphosphorylase	unknown	unknown	gnl\|CDD\|272894
NC_011978.1\|WP_038067062.1\|735548_736205_+\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_038067096.1\|744054_744570_-\|chromate-transporter	unknown	unknown	gnl\|CDD\|224970
NC_011978.1\|WP_004082369.1\|747738_748590_+\|protease-modulator-HflC	unknown	unknown	gnl\|CDD\|259803
NC_011978.1\|WP_015919243.1\|740523_740892_+\|NifB/NifX-family-molybdenum-iron-cluster-binding-protein	unknown	unknown	gnl\|CDD\|224350
NC_011978.1\|WP_038067093.1\|740921_743519_-\|valine--tRNA-ligase	unknown	unknown	gnl\|CDD\|235582
NC_011978.1\|WP_038067070.1\|738385_739114_-\|aspartate-dehydrogenase	unknown	unknown	gnl\|CDD\|163567
NC_011978.1\|WP_015919245.1\|743550_744051_-\|chromate-transporter	unknown	unknown	gnl\|CDD\|224970
NC_011978.1\|WP_015919236.1\|736201_736660_+\|YaaR-family-protein	unknown	unknown	gnl\|CDD\|224642
NC_011978.1\|WP_015919249.1\|748602_749412_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|279798
NC_011978.1\|WP_015919234.1\|734968_735565_+\|bis(5'-nucleosyl)-tetraphosphatase-(symmetrical)-YqeK	unknown	unknown	gnl\|CDD\|224627
NC_011978.1\|WP_015919239.1\|737476_738373_-\|quinolinate-synthase-NadA	unknown	unknown	gnl\|CDD\|236489
NC_011978.1\|WP_038067091.1\|740093_740510_+\|ferredoxin-family-protein	unknown	unknown	gnl\|CDD\|224069
NC_011978.1\|WP_015919232.1\|733400_734669_+\|alpha-amylase	unknown	unknown	gnl\|CDD\|200452
NC_011978.1\|WP_015919248.1\|746815_747742_+\|FtsH-protease-activity-modulator-HflK	unknown	unknown	gnl\|CDD\|259802
NC_011978.1\|WP_004082367.1\|746180_746804_+\|N-glycosylase/DNA-lyase	unknown	unknown	gnl\|CDD\|234924
NC_011978.1\|WP_015919230.1\|729686_731348_+\|phosphodiester-glycosidase-family-protein	unknown	unknown	gnl\|CDD\|378342
NC_011978.1\|WP_038067078.1\|731347_733399_+\|elongation-factor-G	unknown	unknown	gnl\|CDD\|237186

Protein	Function_ID	Function_description	E-value
NC_011978.1\|WP_015919233.1\|734683_734965_+\|DUF503-family-protein	gnl\|CDD\|224467	COG1550, COG1550, Uncharacterized protein conserved in bacteria [Function unknown].	5.47688e-37
NC_011978.1\|WP_015919249.1\|748602_749412_-\|hypothetical-protein	gnl\|CDD\|279798	pfam01501, Glyco_transf_8, Glycosyl transferase family 8. This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, and glycogenin glucosyltransferase.	0.000259826
NC_011978.1\|WP_038067065.1\|736650_737472_-\|carboxylating-nicotinate-nucleotide-diphosphorylase	gnl\|CDD\|272894	TIGR00078, Probable_nicotinate-nucleotide_pyrophosphorylase, nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating) [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides].	4.95578e-110
NC_011978.1\|WP_015919234.1\|734968_735565_+\|bis(5'-nucleosyl)-tetraphosphatase-(symmetrical)-YqeK	gnl\|CDD\|224627	COG1713, COG1713, Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism].	6.49253e-64
NC_011978.1\|WP_038067096.1\|744054_744570_-\|chromate-transporter	gnl\|CDD\|224970	COG2059, ChrA, Chromate transport protein ChrA [Inorganic ion transport and metabolism].	4.7245e-34
NC_011978.1\|WP_004082369.1\|747738_748590_+\|protease-modulator-HflC	gnl\|CDD\|259803	cd03405, SPFH_HflC, High frequency of lysogenization C (HflC) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model characterizes proteins similar to prokaryotic HflC (High frequency of lysogenization C). Although many members of the SPFH (or band 7) superfamily are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this SPFH domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflC is an integral membrane protein which may localize to the plasma membrane. HflC associates with another SPFH superfamily member (HflK) to form an HflKC complex. HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins. HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection.	2.4416e-118
NC_011978.1\|WP_015919243.1\|740523_740892_+\|NifB/NifX-family-molybdenum-iron-cluster-binding-protein	gnl\|CDD\|224350	COG1433, COG1433, Uncharacterized conserved protein [Function unknown].	2.34814e-34
NC_011978.1\|WP_038067093.1\|740921_743519_-\|valine--tRNA-ligase	gnl\|CDD\|235582	PRK05729, valS, valyl-tRNA synthetase; Reviewed.	0
NC_011978.1\|WP_038067070.1\|738385_739114_-\|aspartate-dehydrogenase	gnl\|CDD\|163567	TIGR03855, NAD_NadX, aspartate dehydrogenase. Members of this protein family are L-aspartate dehydrogenase, as shown for the NADP-dependent enzyme TM_1643 of Thermotoga maritima. Members lack homology to NadB, the aspartate oxidase (EC 1.4.3.16) of most mesophilic bacteria (described by TIGR00551), which this enzyme replaces in the generation of oxaloacetate from aspartate for the NAD biosynthetic pathway. All members of the seed alignment are found adjacent to other genes of NAD biosynthesis, although other uses of L-aspartate dehydrogenase may occur.	4.19224e-111
NC_011978.1\|WP_015919245.1\|743550_744051_-\|chromate-transporter	gnl\|CDD\|224970	COG2059, ChrA, Chromate transport protein ChrA [Inorganic ion transport and metabolism].	3.92128e-30
NC_011978.1\|WP_015919236.1\|736201_736660_+\|YaaR-family-protein	gnl\|CDD\|224642	COG1728, COG1728, Uncharacterized protein conserved in bacteria [Function unknown].	1.31229e-47
NC_011978.1\|WP_041437575.1\|744670_746176_+\|glutamine-hydrolyzing-GMP-synthase	gnl\|CDD\|234614	PRK00074, guaA, GMP synthase; Reviewed.	0
NC_011978.1\|WP_015919239.1\|737476_738373_-\|quinolinate-synthase-NadA	gnl\|CDD\|236489	PRK09375, PRK09375, quinolinate synthase NadA.	6.56195e-160
NC_011978.1\|WP_038067091.1\|740093_740510_+\|ferredoxin-family-protein	gnl\|CDD\|224069	COG1146, COG1146, Ferredoxin [Energy production and conversion].	1.6016e-11
NC_011978.1\|WP_015919232.1\|733400_734669_+\|alpha-amylase	gnl\|CDD\|200452	cd11313, AmyAc_arch_bac_AmyA, Alpha amylase catalytic domain found in archaeal and bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes firmicutes, bacteroidetes, and proteobacteria. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.	1.26709e-156
NC_011978.1\|WP_015919248.1\|746815_747742_+\|FtsH-protease-activity-modulator-HflK	gnl\|CDD\|259802	cd03404, SPFH_HflK, High frequency of lysogenization K (HflK) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model characterizes proteins similar to prokaryotic HflK (High frequency of lysogenization K). Although many members of the SPFH (or band 7) superfamily are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this SPFH domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflK is an integral membrane protein which may localize to the plasma membrane. HflK associates with another SPFH superfamily member (HflC) to form an HflKC complex. HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins. HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection.	3.17243e-128
NC_011978.1\|WP_004082367.1\|746180_746804_+\|N-glycosylase/DNA-lyase	gnl\|CDD\|234924	PRK01229, PRK01229, N-glycosylase/DNA lyase; Provisional.	9.73323e-110
NC_011978.1\|WP_015919230.1\|729686_731348_+\|phosphodiester-glycosidase-family-protein	gnl\|CDD\|378342	pfam09992, NAGPA, Phosphodiester glycosidase. This is a family conserved from bacteria to humans. The structure of a member from Bacteroides has been crystallized and modelled onto the luminal region of the human member of the family, the transmembrane glycoprotein N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase. There is some conservation of potentially functional residues, implying that in the bacterial members this family acts in some way as a phosphodiester glycosidase. The human protein is also present, so the eukaryotic members are likely to be catalyzing the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides.	2.03255e-19
NC_011978.1\|WP_038067078.1\|731347_733399_+\|elongation-factor-G	gnl\|CDD\|237186	PRK12740, PRK12740, elongation factor G-like protein EF-G2.	0

>NC_011978.1|WP_038067070.1|738385_739114_-|aspartate-dehydrogenase
MRVLIIGVGNIGKQILKMTHFEKVYAFDKFRKDHIPDIHWLEEFHVPEDVDTVIECASPEAVKEYSSQILKSPVNYLIISTSAFADRVFRESFFEELKVSPAKVFFPSGAIGGLDLLAAVRKNIHRVIIETRKHPKSLGINIEGETTVFEGSVEEAAKLFPRNINIASTVGLIAGFEKVKVIIKADSSLSNNVHIISVISDVGKYEFRIENLPSPENPKTSMVTVYSILKTIESLNSKIVFG
>NC_011978.1|WP_015919239.1|737476_738373_-|quinolinate-synthase-NadA
MIDKILKLKKEKGYVILAHNYQIPELQDIADFVGDSLQLARKAMDLEEKKILFLGVDFMAELVKILNPEKKVIVPDRSATCPMANRLTPETIEEYKRKYPNAPVVLYVNSTAECKTLADVICTSANAVEVVRKIESDVILFGPDRNLAEYVAEKTGKKIFAMPEDGHCPVHQFSENSVDIAKKKHPDARVVVHPECPKPVRDKADYVGSTGQMEKIPEKDTAKTFVIGTEVGMIHKLKKKFPDRNFIPLESAICVNMKKNTLENTLLALETESFEVTLPEDIIEKARRPILKMFEIMG
>NC_011978.1|WP_038067065.1|736650_737472_-|carboxylating-nicotinate-nucleotide-diphosphorylase
MEKLLEILSSHVREDEGNLDIASFPLRNTTSRATVFLKTENVVASGIELAQRFLEKYHLKSIFHVKDGEFIPKKGAIGEIEGNTYSLLLIERTLLNTLSLMFSTATVTRRFARKLKHAKIAATRKTIPGFSLFQKLAVMHGGGDTHRFNLGDCVMIKDNHLKLYGSVEKAIQEVKKISSFTRKIEIEVENMEDALKAVEMGADIVMLDNMSPEMVEKVSKKIKEMNPNVVVEVSGGITEENVSDYDIETVDVISTSRLTLSEVFVDLSLEIQR
>NC_011978.1|WP_015919236.1|736201_736660_+|YaaR-family-protein
MRIDPLGGESLKNQEVKGKKSKRTSRTGEVDKKEFFDIMKDISVEQFEKLLKEALEEVIESGNELVRSPTPSNLKRYKNAIKEFLKLVEKKLYKLSGSFDMTSGKAKLHVVVEEVNEKLMDLAEKIMKNEWQTINLAARIEEINGLILNLYR
>NC_011978.1|WP_038067062.1|735548_736205_+|hypothetical-protein
MKRSSKILLIVVFVVVAVIAVGFLYYRSFLSSPDYRAKEIHYLFRVEGESYFVRIDDTKRMVYIVSFPKESYDPERKESLFSERPLSDLEKIENLLKVKAERVFYSVMSKEEFLKLSQNLLGKQVESFTDFVKELSKRKVKLFDFLFVGSWVKNFGFNNLNRFSLYKFLEKVSSYAIDIFEAPTITKAPVIVKVQGKEYRRLYLDPEKLEVITEEMKR
>NC_011978.1|WP_015919234.1|734968_735565_+|bis(5'-nucleosyl)-tetraphosphatase-(symmetrical)-YqeK
MTLVIDELEAILNRVLSKKRIVHVKSVVDFSKRLGEIYNVDLNRLELAALSHDMFRDVPPRKLLKMSRAYGLKISDLEKAHPVLLHGKVAAEFLKRRFGVDDEEVLIAVAYHTSGHVGFREIGKILFIADSLEFTRDFPGVDALRKIAFRNLEEGFFQVLKNKIFYAVGRDLLLIPETVELWNSILMSRGGHVDEEVE
>NC_011978.1|WP_015919233.1|734683_734965_+|DUF503-family-protein
MNIGVVNLRVRLFGVRSLKEKRGILRRLMNDLRKKYNISISEVGAHDSKNFFEIGIAMVNTDKAFIEKVFDAIIDYLELYPGMEVEEAEREVW
>NC_011978.1|WP_015919232.1|733400_734669_+|alpha-amylase
MNLKNLIIYEAFARAYPGEKGKKFLSLEKDLERLKGMGINTVWLMPIHPTGVEGRKGTLGSPYAIRDYYEIDLLIGTKGDFKKFVKRAHELNMYVLMDMVLNHAAVDNVLVKKHPEWFLRDENGNPTRKVPDWSDVVDFDYSNGELREYMINMMRYWVEEFDVDGFRCDVAGLVPLDFWLQARKNLDPVKRLIWISETHDPYMYQAFDITYDYDGYYRFRDFIEGKNSLREYIDFLRMQDHMYPRGYIKMRFLENHDQPRVAKFLSRESLMHWIAFLFTVKGVPLVHNGQEYALKEDLDIFNEYTLPIPGEENEIFSLHRKLAHYRYKTNVFSNGEMIFIRNDQPERVISYLWRHGNRFILCVLNPLLENTSVTLDFSGIWENICIHSKNVFNDDIVRVSVKNSRAKIKVGREPLILSFVLY
>NC_011978.1|WP_038067078.1|731347_733399_+|elongation-factor-G
MGDIRNVRTAALIGHNGSGKSLLLARILYKLNMIDKPETKYVDYDPVEEEKGASFSSHVASFEWKGKRMFLIDTPGFADFISEVINAIFVAENVVSVVNAVAGVEIQTERTWNLAEEMKKPIMVFVNQMDKERANFDNVVAELKERFSRKILPLVVPIGAAENFEGVVDLLKKKAYRYNGEEPVEEDMPSEFDELRSEILEDIVEQDEELMMRYLDGEEIGYDELVKVLKESYRKGELVPVIAGSALSGIGVDVLLDYLENIGVSPAEASPYRATMEDGKEVEIPFSEEEPFCAYIFKSVVDQFVGRITFAKVIAGTLKSGDTIVNVQKDTSEKVGHVYLPVLKQQKEVESVGPGEIVVLLKLKEGAVGETLAHRDRRVKIIAPSFPEPMFSRSVHPKSKSDIDKISGGLSRLSDSDPTFVWEYDPETGETVISGLGAMHLDVMVERLKKIFGVDVEVGRPKIAYRETITATAIAEHKHKKQTGGHGQYGHVKIQLEPLPRGQGYEFVDKIVGGVIPRNFIPSVDKGVREAMKRGVLAGYPVTDVRVILFDGSYHEVDSSDISFQIAAIQAFKKGMEAAKPVILEPIMEVEVFVPEENAGDVMGEISSRRGRPLGMEPSGKGMVKVKAEVPLAEMLDFSNKLSSITSGRGYFTMRFQRYEIVPPNIQEKIIEERRREMQEQEK
>NC_011978.1|WP_015919230.1|729686_731348_+|phosphodiester-glycosidase-family-protein
MKQLMFIFLLLACLSFASYVISGKEAFPVRSVFRDGVYYVYVEDLSPVGVGYIHANGYHYVVYDDHVLFVKEKETVLDFVKKLSPPLFLEGKLLLPIDAVKELMEGFQVYTKGENVLIYNSLPILLSATKEKDRIVISYTGVLVPDMVEVEKSMGRVVLKISPVVENIPVVSEGIEVKPGKNEITIITSIGNFYPDVRLTFEKNRLVCQLALIEGFFGKLEIADGVVFERKIEEFGKGEKTVVNYLIMDPEKVEVKPVIAEKGFGSLEKLDDMVKRVGGVAGINGNYFDPVTKFPIGLVVIDGKPYSTMFSGRPIFAITEEGDVFIGRVLVDVTLTVNDVLFLVKGINTLGEGEVLVYTKEFSGTIPKKDDKLYFVVEGNTVKYLGYKEKAEGSESVIAVSRKYETYLSNLKIGDRAYLSIQPNLPIRIRQAVEGGPLLIQNGAPIPDAQEEKARYGGGIAYAKAPRTVVATKNGKLWFIVFEGYNHITRGLNYDELVDFLLSRGFEDAMCVDGGSSSVMAVGGNLFGKAENSTAAIPVGIVVWEKKSTEVGE
>NC_011978.1|WP_038067091.1|740093_740510_+|ferredoxin-family-protein
MESKNTPVIGKDALGREIRDLSKIPWWGVDRKAIEWYPVINYDKCATCGICFVTCGRRVFDFDRKEGKVIVARPYNCMVACQTCMNLCPTGAISFPDVSYIKKLVAQNKIVKKTFEIIKPLLPDEHLSIKETETDPEP
>NC_011978.1|WP_015919243.1|740523_740892_+|NifB/NifX-family-molybdenum-iron-cluster-binding-protein
MIIAIPVSENKGKDSPISEHFGRAPYFAFVKVENDKVLDISVEENPLAQDHIAGAVPNFVKEKGAELVIVRGIGKRAFSIFETLGIKVIRGASGTVEEVVNRYLAGQLRDLDYEVREKFHHH
>NC_011978.1|WP_038067093.1|740921_743519_-|valine--tRNA-ligase
MAELSTRYNPAEIETKWYRYWEEKGYFTPKGVGEKFSIVIPPPNITGRIHMGHALNITLQDIVVRYKRMKGYDVLWVPGEDHAGIATQNAVEKFLLQTQGKTREEIGREKFLEITWEWANKYRREIREQIKALGASVDWTRERFTLDEGLSRAVRKVFVELYKKGLIYRGKYIVNWCPRCKTVLSDEEVEHKEHQSKLYYVKYPVKDSDEYIVVATTRPETMLGDTAVAVHPEDERYKDFVGKTLILPLVGREIPVVADKYVDPKFGTGAVKVTPAHDPNDYLIAQRHNLPMVEIFDDNARINENGGKYRGLDRYEAREKIVKDLEEQGFLVKIEDYTHSVGHCYRCDTVIEPKLSDQWFVATKPLAKRGIEAVEKGEIKFFPERWTKIYLNWMYEIRDWCISRQLWWGHRIPVWYCQDCGHINVSEEDVEKCEKCGSTNLKQDEDVLDTWFSSALWPFSTLGWPEETEDLKRYYPTDLLVTGFDIIFFWVARMIMMGYEFMNEKPFSHVYIHQLVRDKYGRKMSKSLGNGIDPLEVIDEYGADPMRFTLAILAAQGRDIKLDPRYFDAYKKFANKIWNATRFVLMNLEDYKEVPLENLKTVDKWILTRLNKTVKEVTSALENYDFNIAARTIYNFFWDEFCDWYIEASKPRLKTEERHLVQTLLVKTLDTSLRLLHPFMPFLTEELWQKLPVDGESITIAKWPEVEEENIDEAAEKEFTRLMNMIRGVRNVRAEMNLPQSQRVRIFVKGLEITDEMKLLLKTLGNIEEIAIVNEKPQKTATAYVEESVEVYVDLGGLIDFEKEKERLKQNMEKIKKEIDRLEKKLSNKDFLEKAPEEVVEETKERLESNRERLERLESILKDLE
>NC_011978.1|WP_015919245.1|743550_744051_-|chromate-transporter
MWNLAFVFLKVGFLSFGGGWAIVGVLKEELVSRGFLTLEEFSQAISIAQMTPGPVAINLATYTGYKFFGLTGAVLNTLAFLGAPILVLSFAIFLGRFLKLQRKRLMKALEGVTTTLMIVTLFSLMGSIRSPIMIIFSVVAFLCSFTKVHPLVIIFGCGLVGALLRF
>NC_011978.1|WP_038067096.1|744054_744570_-|chromate-transporter
MVVRLFFLFLRISTLTIGGGYAMIPVMKWELEKSGLLTEKEFFRIVSTAQVIPGPIAFNTAILVGRKLSGLPGAVASGVAVVLPPFFAIVAVTEIIRSFSGVSYVRSFLRGAYVAIVGLVGSVLFRLVKNQRWDLYRFSLVGISALLLIFQSFLVIPMIVLLAFLLYLKEE
>NC_011978.1|WP_041437575.1|744670_746176_+|glutamine-hydrolyzing-GMP-synthase
MVLVVDYGSQYSRLITRRIRENEVYSEVVFPDDPVDLSKVDAVVLSGGPKSVYEEGAPGLPEWFREYRGPVLAICYGMQLIVKEFGGEVKRGRGEYGRTLVELSEDPLFEGIPDRIHVWMSHGDEVVKLPEGFHPIAVSETGVIAAATDGKRFWLLQFHPEVHHTEYGDRMISNFLFNVCKLEKNWKIGDLVEEKIRHIKETIGNKKAILALSGGVDSSVAAVLVHRAIGKNLVCVFVDHGLLRKNEREEVERVFKEHFDMNLVVVDARKRFLEKLRGVTDPEKKRKIIGEEFIRVFEEEAKKHDVEFLVQGTIYSDVIESAASGKTTAKIKSHHNVGGLPEKMNLKLVEPLRDLFKDEVRKVGKYLGIPDRIINRHPFPGPGLAVRVLGEVTEEKLEILREADYIFIETLRKHDYYDKVWQAFAVLLPIKSVGVKGDARAYEYVVALRAVNSVEGMTADWSRIPHDILDEASRRITREVKGVGRVVYDITSKPPATIEWE
>NC_011978.1|WP_004082367.1|746180_746804_+|N-glycosylase/DNA-lyase
MEELLKELERIREEAKPLVEQRFEEFKRLGEEGTEEDLFCELSFCVLTANWSAEGGIRAQKEIGKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGESPGKFDLYLWYLVKGKVDK
>NC_011978.1|WP_015919248.1|746815_747742_+|FtsH-protease-activity-modulator-HflK
MRKYVWIVVFIVLGIYFLTGVYQVGPSEVALLKTFGRFTSVVPSGIHYHLPYPIQSHVTVDVTTVRKIEIGFRSIQRGERISYQSVPQEAIMITGDNNLVSVEAVVQYRVKDPVAFAFNITEADSIVRFTTESVLREKVAMRSIDDVLTTGRDEIGFETARMLQQILDSYNCGVKVENVYLQEVVPPDPVVDAFDDVNNARQDKERLINEARKYANDVVPKAQGQAQEILRQAEAYAQEVYLKALGEAKRFEEVLEEYSKAPDITRKRMLLDALQSLLEKSENKVFFVGNGDSLNILNISDLLKGMGK
>NC_011978.1|WP_004082369.1|747738_748590_+|protease-modulator-HflC
MKIWMISLLIILIVVGAILLFSSFYVLDQTQQAVVLRFGKIVAVETEPGLHFKQPFVDNVVRFDKRILLYDIEPEKIIAADKKTLVIDTYVLWRIKDAEAFIKSLKSVKLALPRIDDVVYSHVRNIFAKANFDEIISEKREDLLREVTALSREDLKDFGIEVVDVRVKHADLPAENEKAVYERMKAERYSIAAQIRAEGEKEARKIRAEADKTAKVLIAEAQSKAEQIKGTGEASAVKIYAEVFSKDKDFYEFWRTMEVYRSIEKGILIIGDELDALKYLKTK
>NC_011978.1|WP_015919249.1|748602_749412_-|hypothetical-protein
MNLIATAGNEKIQDFLVNDWYRSLKENVDLSKTDVLVINYGLTGLPKEVINFPAVERSGLINNTRFINLAIFLENHPEYDQILFCDGGDIIFQSDISHLFEEHRDAFRAVVEQLSPPIDLVVKEEDLVNGKEIKSFLSNKKLFNVGVIIAPREGFLELARTMERRLKNINVWGGDTVIGNYVIYKNPHVELPSKYNFIPSTAREKFYVKDSKFYLENGELIPIVHNAGRYRFLRPVKDFGYGPGKNRVNKFNIWMFRMLFSVSNFLKMK

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Crispr_ID: NC_011978_7

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011978_7

961160-961393

Orphan

III-A

Consensus_repeat	Method
TTGGTTTCCATACCTCTAAGGAAGTATTGAAACC	CRT
GGTTTCCATACCTCTAAGGAAGTATTGAAACC	PILER-CR
GTTTCCATACCTCTAAGGAAGTATTGAAAC	CRISPRCasFinder

3 spacers

The CRISPR arrays of NC_011978_7

>merge|NC_011978|7|961160-961393|CRT,PILER-CR,CRISPRCasFinder
TTTGTTTCCATACCTCTAAGGAAGTATTGAAACCTTTATCAGATGATCAAAAGGCTTGAAAAGGAGGATGGTTTCCATACCTCTAAGGAAGTATTGAAACAGTCCAGAGCCAGAGCCATCCACGTTCTGGAGTTTTGGTTTCCATACCTCTAAGGAAGTATTGAAACCCGCATAGTCCAGGTCAGAAAACGGCCCTCCGATGGGTTTCCATACCTCAAAGGAAGTATTGAAACC

>NC_011978|7|6|961160-961393|CRT
TTTGTTTCCATACCTCTAAGGAAGTATTGAAACC	TTTATCAGATGATCAAAAGGCTTGAAAAGGAGG
ATGGTTTCCATACCTCTAAGGAAGTATTGAAACA	GTCCAGAGCCAGAGCCATCCACGTTCTGGAGTT
TTGGTTTCCATACCTCTAAGGAAGTATTGAAACC	CGCATAGTCCAGGTCAGAAAACGGCCCTCCGA
TGGGTTTCCATACCTCAAAGGAAGTATTGAAACC

>NC_011978|7|6|961163-961393|PILER-CR
GTTTCCATACCTCTAAGGAAGTATTGAAACCT	TTATCAGATGATCAAAAGGCTTGAAAAGGAGGATG
GTTTCCATACCTCTAAGGAAGTATTGAAACAG	TCCAGAGCCAGAGCCATCCACGTTCTGGAGTTTTG
GTTTCCATACCTCTAAGGAAGTATTGAAACCC	GCATAGTCCAGGTCAGAAAACGGCCCTCCGATGG
GTTTCCATACCTCAAAGGAAGTATTGAAACC

>NC_011978|7|7|961163-961392|CRISPRCasFinder
GTTTCCATACCTCTAAGGAAGTATTGAAAC	CTTTATCAGATGATCAAAAGGCTTGAAAAGGAGGATG
GTTTCCATACCTCTAAGGAAGTATTGAAAC	AGTCCAGAGCCAGAGCCATCCACGTTCTGGAGTTTTG
GTTTCCATACCTCTAAGGAAGTATTGAAAC	CCGCATAGTCCAGGTCAGAAAACGGCCCTCCGATGG
GTTTCCATACCTCAAAGGAAGTATTGAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_011978.1\|WP_015919461.1\|960436_960889_-\|ribosome-maturation-factor-RimP	unknown	unknown	gnl\|CDD\|184777
NC_011978.1\|WP_015919458.1\|957822_958995_+\|ComEC/Rec2-family-competence-protein	unknown	unknown	gnl\|CDD\|377126
NC_011978.1\|WP_041437852.1\|969687_970098_+\|transcriptional-repressor	unknown	unknown	gnl\|CDD\|223806
NC_011978.1\|WP_015919460.1\|959389_960424_-\|transcription-termination-factor-NusA	unknown	unknown	gnl\|CDD\|236410
NC_011978.1\|WP_015919455.1\|953418_955005_+\|DAK2-domain-containing-protein	unknown	unknown	gnl\|CDD\|224378
NC_011978.1\|WP_038067406.1\|967435_968596_+\|diaminopimelate-decarboxylase	unknown	unknown	gnl\|CDD\|273415
NC_011978.1\|WP_015919463.1\|962253_963231_+\|aspartate-semialdehyde-dehydrogenase	unknown	unknown	gnl\|CDD\|237845
NC_011978.1\|WP_015919454.1\|953072_953402_+\|Asp23/Gls24-family-envelope-stress-response-protein	unknown	unknown	gnl\|CDD\|377129
NC_011978.1\|WP_041437623.1\|951249_953076_+\|1-deoxy-D-xylulose-5-phosphate-synthase	unknown	unknown	gnl\|CDD\|235470
NC_011978.1\|WP_015919466.1\|964814_965465_+\|4-hydroxy-tetrahydrodipicolinate-reductase	unknown	unknown	gnl\|CDD\|223366
NC_011978.1\|WP_015919457.1\|956620_957826_+\|2,3-bisphosphoglycerate-independent-phosphoglycerate-mutase	unknown	unknown	gnl\|CDD\|179745
NC_011978.1\|WP_038067541.1\|963271_963949_+\|diaminopimelate-epimerase	unknown	unknown	gnl\|CDD\|223331
NC_011978.1\|WP_015919470.1\|968596_969673_+\|amidohydrolase	unknown	unknown	gnl\|CDD\|349882
NC_011978.1\|WP_015919465.1\|963933_964818_+\|4-hydroxy-tetrahydrodipicolinate-synthase	unknown	unknown	gnl\|CDD\|235107
NC_011978.1\|WP_038067410.1\|970094_970487_+\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_015919452.1\|951059_951284_+\|exodeoxyribonuclease-VII-small-subunit	unknown	unknown	gnl\|CDD\|184486
NC_011978.1\|WP_015919459.1\|958885_959368_-\|transcriptional-repressor	unknown	unknown	gnl\|CDD\|223806
NC_011978.1\|WP_081434637.1\|965466_966168_+\|2,3,4,5-tetrahydropyridine-2,6-dicarboxylate-N-acetyltransferase	unknown	unknown	gnl\|CDD\|132571
NC_011978.1\|WP_015919456.1\|955001_956618_+\|tetratricopeptide-repeat-protein	unknown	unknown	gnl\|CDD\|276809
NC_011978.1\|WP_038067403.1\|966182_967394_+\|aspartate-kinase	unknown	unknown	gnl\|CDD\|235843

Protein	Function_ID	Function_description	E-value
NC_011978.1\|WP_015919461.1\|960436_960889_-\|ribosome-maturation-factor-RimP	gnl\|CDD\|184777	PRK14638, PRK14638, ribosome maturation factor RimP.	2.3087e-89
NC_011978.1\|WP_015919458.1\|957822_958995_+\|ComEC/Rec2-family-competence-protein	gnl\|CDD\|377126	pfam03772, Competence, Competence protein. Members of this family are integral membrane proteins with 6 predicted transmembrane helices. Some members of this family have been shown to be essential for bacterial competence in uptake of extracellular DNA. These proteins may transport DNA across the cell membrane. These proteins contain a highly conserved motif in the amino terminal transmembrane region that has two histidines that may form a metal binding site.	5.01016e-12
NC_011978.1\|WP_041437852.1\|969687_970098_+\|transcriptional-repressor	gnl\|CDD\|223806	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism].	6.93872e-34
NC_011978.1\|WP_015919460.1\|959389_960424_-\|transcription-termination-factor-NusA	gnl\|CDD\|236410	PRK09202, nusA, transcription elongation factor NusA; Validated.	7.77647e-167
NC_011978.1\|WP_015919455.1\|953418_955005_+\|DAK2-domain-containing-protein	gnl\|CDD\|224378	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only].	0
NC_011978.1\|WP_038067406.1\|967435_968596_+\|diaminopimelate-decarboxylase	gnl\|CDD\|273415	TIGR01048, Diaminopimelate_decarboxylase, diaminopimelate decarboxylase. This family consists of diaminopimelate decarboxylase, an enzyme which catalyzes the conversion of diaminopimelic acid into lysine during the last step of lysine biosynthesis. [Amino acid biosynthesis, Aspartate family].	2.08352e-170
NC_011978.1\|WP_015919463.1\|962253_963231_+\|aspartate-semialdehyde-dehydrogenase	gnl\|CDD\|237845	PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase; Provisional.	7.49536e-151
NC_011978.1\|WP_015919454.1\|953072_953402_+\|Asp23/Gls24-family-envelope-stress-response-protein	gnl\|CDD\|377129	pfam03780, Asp23, Asp23 family, cell envelope-related function. The alkaline shock protein Asp23 was identified as an alkaline shock protein that was expressed in a sigmaB-dependent manner in Staphylococcus aureus. Following an alkaline shock Asp23 accumulates in the soluble protein fraction of the S. aureus cell. Asp23 is one of the most abundant proteins in the cytosolic protein fraction of stationary S. aureus cells, with a copy-number of >25000 per cell. A second Asp23-family protein, AmaP, which is encoded within the asp23-operon, is required to localize Asp23 to the cell membrane. The overall function for the family is thus a cell envelope-related one in Gram-positive bacteria.	1.22375e-26
NC_011978.1\|WP_041437623.1\|951249_953076_+\|1-deoxy-D-xylulose-5-phosphate-synthase	gnl\|CDD\|235470	PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional.	0
NC_011978.1\|WP_015919466.1\|964814_965465_+\|4-hydroxy-tetrahydrodipicolinate-reductase	gnl\|CDD\|223366	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism].	1.34193e-86
NC_011978.1\|WP_015919457.1\|956620_957826_+\|2,3-bisphosphoglycerate-independent-phosphoglycerate-mutase	gnl\|CDD\|179745	PRK04135, PRK04135, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase.	0
NC_011978.1\|WP_038067541.1\|963271_963949_+\|diaminopimelate-epimerase	gnl\|CDD\|223331	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism].	4.33652e-55
NC_011978.1\|WP_015919470.1\|968596_969673_+\|amidohydrolase	gnl\|CDD\|349882	cd03886, M20_Acy1, M20 Peptidase Aminoacylase 1 family. Peptidase M20 family, Aminoacylase 1 (ACY1; hippuricase; acylase I; amido acid deacylase; IAA-amino acid hydrolase; dehydropeptidase II; N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14) subfamily. ACY1 is the most abundant of the aminoacylases, a class of zinc binding homodimeric enzymes involved in the hydrolysis of N-acetylated proteins. It is encoded by the aminoacylase 1 gene (Acy1) on chromosome 3p21 that comprises 15 exons. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity; substrates include indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). ACY1 appears to physically interact with Sphingosine kinase type 1 (SphK1) and may influence its physiological functions; SphK1 and its product sphingosine-1-phosphate have been shown to promote cell growth and inhibit apoptosis of tumor cells. Strong expression of the human gene and its mouse ortholog Acy1 in brain, liver, and kidney, suggest a role of the enzyme in amino acid metabolism of these organs. Defects in ACY1 are the cause of aminoacylase-1 deficiency (ACY1D), resulting in a metabolic disorder manifesting encephalopathy and psychomotor delay.	4.80719e-122
NC_011978.1\|WP_015919465.1\|963933_964818_+\|4-hydroxy-tetrahydrodipicolinate-synthase	gnl\|CDD\|235107	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional.	1.57335e-166
NC_011978.1\|WP_015919452.1\|951059_951284_+\|exodeoxyribonuclease-VII-small-subunit	gnl\|CDD\|184486	PRK14070, PRK14070, exodeoxyribonuclease VII small subunit; Provisional.	1.80141e-18
NC_011978.1\|WP_015919459.1\|958885_959368_-\|transcriptional-repressor	gnl\|CDD\|223806	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism].	2.25886e-48
NC_011978.1\|WP_081434637.1\|965466_966168_+\|2,3,4,5-tetrahydropyridine-2,6-dicarboxylate-N-acetyltransferase	gnl\|CDD\|132571	TIGR03532, DapD_Ac, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase. This enzyme is part of the diaminopimelate pathway of lysine biosynthesis. Alternate name: tetrahydrodipicolinate N-acetyltransferase. Note that IUBMB lists this alternate name as the accepted name. Unfortunately, the related succinyl transferase acting on the same substrate (EC:2.3.1.117, TIGR00695) uses the opposite standard. We have decided to give these two enzymes names which more clearly indicated that they act on the same substrate.	1.76859e-116
NC_011978.1\|WP_015919456.1\|955001_956618_+\|tetratricopeptide-repeat-protein	gnl\|CDD\|276809	sd00006, TPR, Tetratricopeptide repeat. The Tetratricopeptide repeat (TPR) typically contains 34 amino acids and is found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans. It is present in a variety of proteins including those involved in chaperone, cell-cycle, transcription, and protein transport complexes. The number of TPR motifs varies among proteins. Those containing 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accommodate an alpha-helix of a target protein. It has been proposed that TPR proteins preferentially interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes.	1.7156e-18
NC_011978.1\|WP_038067403.1\|966182_967394_+\|aspartate-kinase	gnl\|CDD\|235843	PRK06635, PRK06635, aspartate kinase; Reviewed.	0

>NC_011978.1|WP_015919461.1|960436_960889_-|ribosome-maturation-factor-RimP
MFEEMIVEKVRKEAERIAEKQGLEIFDIQYRRESRGWVLRVVIDNPVGYVSVRDCELFSRELERFLDREDLIEHSYTLEVSSPGLDRPLRGPKDYQRFTGKLAKIITKDGKTFIGRIESFVDGIVTISDEKGKHEIDIEDVRKANLEIEF
>NC_011978.1|WP_015919460.1|959389_960424_-|transcription-termination-factor-NusA
MNIGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGSSKNVEVVIDRNTGNIKVYQLLEVVENVEDSTTQISLEEAKKLDPTAEIGSIIKKELDVKNFGRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVTSDWADIRIGKLETRLPKKEWIPGEEIKPGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEIENGIVEIKAIAREPGVRTKVAVTSNNPNVDPIGACIGEGGSRIAAILRELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKENRAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIMNL
>NC_011978.1|WP_015919459.1|958885_959368_-|transcriptional-repressor
MYEELRNELKKRKYRITAQREMILKIFLESKGRHLGVDEVYRELLNRNVRVSKATVYRAVELLVELGFLRKLNFGEGLYRYELIDRSTRESHQHVICQKCGKIVEINSEQVKKIVSDISEKTGYVIKWHDLKFYGLCPECQKEESKAPESGQRTEISEEG
>NC_011978.1|WP_015919458.1|957822_958995_+|ComEC/Rec2-family-competence-protein
MILIFFSLCLGALLGALFRFPWYVFFPAAIPLWRKNKEISIAVLFILSGAFLYSLGTLPPGNYELVGLVEGSRVTRVKVFQGEWKKVRPIRIRTSKDGFIYAVGYYDGSIFHPSYLKELEKPSLRRLREEFSKEVRGTAFSLLFGEKDNAVYRSGLGHFFAVSGLHVGIAFSLYTTLISFFTWRRMYQELVALLLLIPYVLSVNTPSVLRAYLTILLWKVLRTLGFKTTPSYITATVGSLMIVLDPTVLFTPSFLLSFFVTLSILNSKNIFELVVKAYLASLPFLCLFFGETNVSALLFSIPMSFAVIPVTWVSHLSFLLFLLGLKTPSMVAADVANIVSFPVDVLVRLSNMMPIIPLPKFLFFVLIPVPLILLFDIRGIIRRTSGRAIL
>NC_011978.1|WP_015919457.1|956620_957826_+|2,3-bisphosphoglycerate-independent-phosphoglycerate-mutase
MLDKQKFVSKLVTTNDTKIVLLVMDGLGDIPVNGKTPLQAASTPNLDSLAKESDLGQTVPVLPGITPGSGPGHLSLFGYDPIKYQIGRGILEALGIGVEVGEKDVVARANFATWDGNVVLDRRAGRPATEESAKVVQLLSEKIKKIEDVEITFYPGKEHRFVVKFTGEGLGDRVTDADPQKEGHPMVWAEGLDEPSKKTARIANELIRKIAEVLKDNPKINFALIRGFSKYPDLPKFPEIYKLRAGAIATYPMYRGLAKLVGMEIIETGQTVEDEINTLKEKWNDFDFFYVHVKKTDSYGEDGKFDEKVKVIEEVDRVIPEILALKPDVLVITGDHSTPVPLKAHSWHPVPLLIWSRYTRRGLSQAFNEFECARGTLGTIHASDVMTLALAYAGRLEKFGA
>NC_011978.1|WP_015919456.1|955001_956618_+|tetratricopeptide-repeat-protein
MRGENIKAIVYLPLDPDKAKQNNLPVKLPVLAEDLPRIVEEDRIPLDVVLRGLEAQYEVSKDEYYRSYYVFFLYEKFKELLREQRFDEAEKILEKAREVQYDYRYHFYRGLLLKHRGNLGEAEVEMRIATSMKEDFAPAYFELANILKEKGEIEDSLLFYEKAHETNRDFLLPLLKKGDLLLEEGRFEEALEEYKRILEKDPNFTEVYERLGVIYNQLQRFKEAEKFFRKALEAERKDHVEFNLSYTLIKLGRLFEALGILKRLYEKTPDDPMLANEYGLLLKTLGLYEEALEVFEEAYSRHRDEEIVKYNYATILLHFDREKAISVLSEITGELKERAEHMIALAESKVKIPTFEEFEWLRDYFDEEGVIDVVSLAEDLASSNEEVQKRIDALREGQFPFYDTTIDTSEMIETMMGIIFESPDIFKMEENVVKFTSAFFGSSIMIASSLVLVRIVQHLLVFKDLLMDDLLREIVAETQDINWRFALRIARFRHADKFDFEKLSDLVVALLQSLEQGVPVADDDRLKYVMEKLRIKEG
>NC_011978.1|WP_015919455.1|953418_955005_+|DAK2-domain-containing-protein
MKKITGRFLKTIIKKATENLLKHKDEINALNVFPVPDGDTGSNMCSTMLEACKYIDNLKSDDLSEVWKAIKEGALMGARGNSGVILSQILRGLADASPENYITPGDFIKMISNARKVAYSAVMRPVEGTMLTVVRELDEKLKGRSFETFEELFDQIVEMIKDTVNRTPSMLSKLREAGVVDAGAKGLYYLFEGMRDAIKGDIEVNLEQVEQASVEDLKRMALEEITNQYCTEVAVRRKRVFEKSELESFLNEIGDSVVLVEQDDIFRLHVHTNHPGQVLEKVLDFGEIIKVKVDNMKLQHEHIISAQVEKEIGVVAVSPGKGISEILKSLGVDEIVPGGQTMNPSFADLKAAVDKTHAKVVFLFPNNANVLLTAKQVAESVDDKRVIVVQTSHVQECVAAMVEYDPDEDPEELKRRFEEAINQCVPISITRAVRDSRYGKRRIRKGEYLVFVRKELLAHGFNLVKALKDVLEKENAREKEILTVFLGDNYRKAELEKIQNLIGEEFPNLDLEIHEGGQPHYPFLMLLQ
>NC_011978.1|WP_015919454.1|953072_953402_+|Asp23/Gls24-family-envelope-stress-response-protein
MKIMLEHGELEITVEALKKIVYLATVESYGTVGIGESRSFFERIFGGDKGIKIEELEDSSLNVDVYIEVEYGVNIKEVARNIADNVAHKLKTLAGCENLNITVHVVGIK
>NC_011978.1|WP_041437623.1|951249_953076_+|1-deoxy-D-xylulose-5-phosphate-synthase
MMLDEIRKMSHEELKSLAEEIRQRIVEVVLKNGGHLASNLGTVELTLALYRVFDPREDAVIWDTGHQTYTHKILTGRDEQFHTIRTFGGLSGFVTRRESPLDWFGTGHAGTSIAAALGFEKAFEFLKEKRHVVVVIGDGALTSGMALEALNQLKNLNSKIKIILNDNGMSISQNVGGLAYHLSRLRTNPIYLKGKKALKKVLEKTEIGFELEEEMRYLRDGLKGLIQGTNFFEALGLKYFGPFDGHDVELLERVLKRVKEYDYPSVVHVVTRKGRGFKAAEEDPTTYHSASPVGKPKRLSYSELLGYTLSKIAESDEKIVAITAAMADGTGLSIFQKNHPERFFDLGITEQSCVTFGAALGLQGMKPVVAIYSTFLQRAFDQIVHDVALQNAPVLFAIDRSGVVGEDGPTHHGLFDINYLLPIPNMKIVSPSSPQEFVNVLYTVLANLDGPVAVRYPKESFEADLNSLFENMREIDLGWKVVREGKDAAVIVTGTLLKEVLRIPLDVTVINALTVKPLDTHVLREVAQNHRLIFTVEEAMKIGGFGSYVAQKLWEMGWKGRVVNIGVNDHFVTHGSRKELLEMLGLDSKGLSKTMLTYIKVRSEEGKA
>NC_011978.1|WP_015919452.1|951059_951284_+|exodeoxyribonuclease-VII-small-subunit
MDFEEMMKELEEIVNRLESEDLSLEESIELFQRGVELYKKCREILQKEQLKIIDVLKELEGDEDDAGRNQEDES
>NC_011978.1|WP_015919463.1|962253_963231_+|aspartate-semialdehyde-dehydrogenase
MKVGVVGATGEVGRAMVKVLEEFNVPVTELRLFASERSVGKEIEFRGEKVKVELLTEEAMKWDCDYFLFSAGASVSRKFAPIAAENGVTVIDNSSAFRMEKDIPLVVPEVNAHLLKGYTGIIANPNCSTIQMILSIYKLHEVYGIEEIFVATYQSVSGAGHKGIEELLSQERGENVVRVFPKPIHRNVIPLIGDVQDNLFTQEEMKMINETRKILNDYSIRVYPTTVRVPVLYGHSEAVMVRLKRPFESLEKVKEIIASGEDVVVTDDLVTAVDVAGKNETYVCRLRKGDERSILFWNVADNIRVGAVTNAVRILLKHAKMNGRM
>NC_011978.1|WP_038067541.1|963271_963949_+|diaminopimelate-epimerase
MVDNTEKKISENEKPDFVRNHVGDLDGVIFVEKVGEKFFMDYYNRDGSMATFCGNGARAFSQYLIDRGWVKQRKFTFLSRAGEIKVFLDDGIWVRMPAVSEVKELEVDGYRGHFVVVGVPHFILEVKNVDEVDVEKLGRLLRHKTNANVDFYEVAQGFLKVRTYERGVERETKACGTGVTAVFFVHHSRTGSKEMKVLVPGGTLFLREENGEIYLKGDVRRCSEE
>NC_011978.1|WP_015919465.1|963933_964818_+|4-hydroxy-tetrahydrodipicolinate-synthase
MFRGVGTAIVTPFKNGELDLEAYERLVRYQLDGGVSALIVLGTTGEAPTVNDDERERLVSKTLEIVDGKIPVIVGAGTNSTEKTLKLVKQAEKLGADGVLIVTPYYNKPTQEGLYQHYKYISERTDLKIIVYNVPGRTGVNVLPETAARIASDLKNVVGIKEANGDIDQIDRTVTLTKSARSDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMSDLCAEFFSGNIEKAREIHRKLRPLMKALFVETNPIPVKAALSLMGYVENELRLPLVPASEKTVELLKGVLRESGLL
>NC_011978.1|WP_015919466.1|964814_965465_+|4-hydroxy-tetrahydrodipicolinate-reductase
MKYGIVGYSGRMGQEIQKVFSEKGHELVLKVDVNGKEIKDSPDVIVDFSSADALPETVDLCRKYKSALVLGTTALKEEHFEMLRELSKEVPVVQSYNFSIGINVLKRFLSELSKVLSDWDVEIVEAHHRFKKDAPSGTAILLKNALGKEVPIHSLRIGGIPGDHVIVFGNVGETIEIKHRAISRTVFAIGALKAAEFLVGREPGFYSFEEIVFGGE
>NC_011978.1|WP_081434637.1|965466_966168_+|2,3,4,5-tetrahydropyridine-2,6-dicarboxylate-N-acetyltransferase
MDAREIIEMIAKSKKKTPIVAYIKGKLDGIDFSKFKFFGNDQFGVLFGEYEDFRELLEKYGEKIEDYHLEVKARNSALPLADITKYRARIEPGAIIRDMVEIGEGAVIMMGAVINVGAVIGEGTMIDMNAVVGGRAIIGKKCHIGAGAVIAGVIEPPSAKPVVIEDEVVVGANAVILEGVTVGKGSVVAAGAVVTKDVPPYTVVAGVPARVIKQIDEKTKEKTRIVDELRNLE
>NC_011978.1|WP_038067403.1|966182_967394_+|aspartate-kinase
MKLVVQKYGGSSVATPERIKNVAMRIKKKVEEGFKVVVVVSAMGKTTDELIKLAKEVSPKPDARELDMLLATGEQVSAALLSMALKDLGVKAKSLNAFQVRIKTTPHHTSARIMDIDDSVIMENLKEHDALVVTGFQGVNERGDLTTLGRGGSDTSAVALAAKLRVPCEIYSDVDGIYTCDPRLIPGAKKLKYITYDEALELTALGAKVLHSRSVEIAKKYRIPVYCASSFVEEEGTMVVERLPEWLEEPVVTGATISHGQIKVSISFLPKEAEYITAIFEEVGKRSLNVDMISLVPSNGKVFLSFTILEDHKDDLDEALRNALKNVEGWKSSYEEGFAKLSIVGVGMRTSPGVAARFFSALKRVGVTPELVTTSEIKISCLVPEKDAEKALKAVVDEFDLAE
>NC_011978.1|WP_038067406.1|967435_968596_+|diaminopimelate-decarboxylase
MEALKKAAEIHGTPLYVYFEETIRERARRVKEVFHGINLLPTFAVKANNNPNLLAILKEEGFGMDVVTKGELFAARLAGVDPFLIVWNGNGKSKEEMLHFLKEGVRTINVDSFEEMEMWESLSPEDVNFFVRVNPEVDARTHPHISTGLKKHKFGIPLNMLDSFMKRFKGMNIKGLHVHIGSQITKVDPFLEAYEKVVEASRRYGFEEINIGGGWGIDYQGEELNVQEYREKVVPLLDGFKRVFVEIGRYIIAPAGFLVLKVILVKRGENKVFVVVDGGMNTLIRPALYSAHHRIFVYGKEGSDFKADVVGPLCESGDVIAYDRNLPAVEPGDFLFVENAGAYGYTMANNYNSTSKPAEVLVKKDGELVLIRRRENIMDIFKDVVM
>NC_011978.1|WP_015919470.1|968596_969673_+|amidohydrolase
MDEIELRHLLHMNPEPSFKEFKTQEILKSAIQKIGYGKIMEVAGTGLVVEKKETEGPYVVLRAEMDALPIKEETGWEFASRNDYMHACGHDFHMSALFGAMKRLKTVRKNFLFVFQPAEETGGGAKEVVEFLRKNYTIKAAVGFHVTDEYDVGTVVSRAGVLFASATEFDVYFKGVPAHIAFAEKGKDALKVAVSFLHWLYGRKWDALVGVGKIVGGRVRNVVPSEVKIEGTIRAKSLKIAEEILSEMKNQLLSLKDSSGVDFSLEKGSVYPEVKVNADLLEILKKTCERLNLRFIECEMKKTGEDFGYFTQVFPSLSFWFGVGEGEKRVGLHHPCFLPKDEYIPLASELLAFLAEAI
>NC_011978.1|WP_041437852.1|969687_970098_+|transcriptional-repressor
MNLEEIVEQLKAKKIKLTTQRMEIIKFVSKMEKGHFEAKELFSVLSKKIPSLSIATLYSTLYLLVDLGVIYSFSDGQKTIFDFNPAPHGHFVCRICGKIEDIEIKKLDLEKIRGKREKIEIVIRGVCEDCLKRVKD
>NC_011978.1|WP_038067410.1|970094_970487_+|hypothetical-protein
MRFFTQLLSILLIVVGTIGFIGWVAFYFLEPYISTFLGVSVPKNFLAVLLSLFLPFLFSGISLNYYTSSGKKWLAVLGFLLLFPSLVAQLYGLYVFGNLVSRLIGVYVLFLLFTVVLLAFFLTVIRRDES

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Crispr_ID: NC_011978_8

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_011978_8

1152061-1152421

Orphan

III-A

Consensus_repeat	Method
GTTTCCATACCTCAAAGGAAGTATTGAAAC	PILER-CR
GTTTCAATACTTCCTTTGAGGTATGGAAAC	CRISPRCasFinder
GTTTCAATACTTCCTTTGAGGTATGGAAAC	CRT

5 spacers

The CRISPR arrays of NC_011978_8

>merge|NC_011978|8|1152061-1152421|PILER-CR,CRISPRCasFinder,CRT
GTTTCAATACTTCCTTTGAGGTATGGAAACGAGAATCAGATATACCCTGTGAAGGCATATGTGAGCGTTTCAATACTTCCTTTGAGGTATGGAAACCTCCTATTCTTGAGGCAAACCTGAGCCTTGCATCTACGTTTCAATACTTCCTTTGAGGTATGGAAACTATGAGCCCGATTATGACATCTCGGGCATAACGTAAGTTTCAATACTTCCTTTGAGGTATGGAAACTTTCGATCCCGGTCAATCTTGTCAACAGCTCCGCCGGTTTCAATACTTCCTTTGAGGTATGGAAACCGGGAGACAAGGAGCACAAGAAAATCTCGTATCTTGGTTTCAATACTTCCTTAGAGGTATGGAAAC

>NC_011978|8|7|1152061-1152421|PILER-CR
GTTTCAATACTTCCTTTGAGGTATGGAAAC	GAGAATCAGATATACCCTGTGAAGGCATATGTGAGC
GTTTCAATACTTCCTTTGAGGTATGGAAAC	CTCCTATTCTTGAGGCAAACCTGAGCCTTGCATCTAC
GTTTCAATACTTCCTTTGAGGTATGGAAAC	TATGAGCCCGATTATGACATCTCGGGCATAACGTAA
GTTTCAATACTTCCTTTGAGGTATGGAAAC	TTTCGATCCCGGTCAATCTTGTCAACAGCTCCGCCG
GTTTCAATACTTCCTTTGAGGTATGGAAAC	CGGGAGACAAGGAGCACAAGAAAATCTCGTATCTTG
GTTTCAATACTTCCTTAGAGGTATGGAAAC

>NC_011978|8|8|1152061-1152421|CRISPRCasFinder
GTTTCAATACTTCCTTTGAGGTATGGAAAC	GAGAATCAGATATACCCTGTGAAGGCATATGTGAGC
GTTTCAATACTTCCTTTGAGGTATGGAAAC	CTCCTATTCTTGAGGCAAACCTGAGCCTTGCATCTAC
GTTTCAATACTTCCTTTGAGGTATGGAAAC	TATGAGCCCGATTATGACATCTCGGGCATAACGTAA
GTTTCAATACTTCCTTTGAGGTATGGAAAC	TTTCGATCCCGGTCAATCTTGTCAACAGCTCCGCCG
GTTTCAATACTTCCTTTGAGGTATGGAAAC	CGGGAGACAAGGAGCACAAGAAAATCTCGTATCTTG
GTTTCAATACTTCCTTAGAGGTATGGAAAC

>NC_011978|8|7|1152061-1152421|CRT
GTTTCAATACTTCCTTTGAGGTATGGAAAC	GAGAATCAGATATACCCTGTGAAGGCATATGTGAGC
GTTTCAATACTTCCTTTGAGGTATGGAAAC	CTCCTATTCTTGAGGCAAACCTGAGCCTTGCATCTAC
GTTTCAATACTTCCTTTGAGGTATGGAAAC	TATGAGCCCGATTATGACATCTCGGGCATAACGTAA
GTTTCAATACTTCCTTTGAGGTATGGAAAC	TTTCGATCCCGGTCAATCTTGTCAACAGCTCCGCCG
GTTTCAATACTTCCTTTGAGGTATGGAAAC	CGGGAGACAAGGAGCACAAGAAAATCTCGTATCTTG
GTTTCAATACTTCCTTAGAGGTATGGAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_011978.1\|WP_015919684.1\|1157363_1158065_+\|isoprenyl-transferase	unknown	unknown	gnl\|CDD\|173302
NC_011978.1\|WP_015919678.1\|1152493_1153264_-\|ABC-transporter-permease	unknown	unknown	gnl\|CDD\|130314
NC_011978.1\|WP_015919671.1\|1145832_1146681_-\|acetylglutamate-kinase	unknown	unknown	gnl\|CDD\|234869
NC_011978.1\|WP_015919673.1\|1147887_1148907_-\|N-acetyl-gamma-glutamyl-phosphate-reductase	unknown	unknown	gnl\|CDD\|273832
NC_011978.1\|WP_015919674.1\|1148903_1150100_-\|argininosuccinate-lyase	unknown	unknown	gnl\|CDD\|223243
NC_011978.1\|WP_015919683.1\|1156809_1157367_+\|ribosome-recycling-factor	unknown	unknown	gnl\|CDD\|178850
NC_011978.1\|WP_015919665.1\|1141047_1141593_-\|YkgJ-family-cysteine-cluster-protein	unknown	unknown	gnl\|CDD\|308985
NC_011978.1\|WP_015919682.1\|1155446_1156601_-\|alanine--glyoxylate-aminotransferase-family-protein	unknown	unknown	gnl\|CDD\|223153
NC_011978.1\|WP_015919675.1\|1150096_1151326_-\|argininosuccinate-synthase	unknown	unknown	gnl\|CDD\|234785
NC_011978.1\|WP_038067645.1\|1144475_1144655_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|238698
NC_011978.1\|WP_038067659.1\|1158057_1158870_+\|phosphatidate-cytidylyltransferase	unknown	unknown	gnl\|CDD\|366491
NC_011978.1\|WP_015919679.1\|1153268_1154246_-\|ATP-binding-cassette-domain-containing-protein	unknown	unknown	gnl\|CDD\|213232
NC_011978.1\|WP_015919667.1\|1143564_1144389_+\|DMT-family-transporter	unknown	unknown	gnl\|CDD\|273359
NC_011978.1\|WP_015919686.1\|1158866_1161461_+\|alanine--tRNA-ligase	unknown	unknown	gnl\|CDD\|234701
NC_011978.1\|WP_015919666.1\|1141711_1143172_-\|tetratricopeptide-repeat-protein	unknown	unknown	gnl\|CDD\|276808
NC_011978.1\|WP_015919681.1\|1154520_1155441_-\|D-2-hydroxyacid-dehydrogenase	unknown	unknown	gnl\|CDD\|240628
NC_011978.1\|WP_162828739.1\|1154396_1154540_+\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_015919687.1\|1161467_1162520_+\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_161595589.1\|1140257_1140509_-\|hypothetical-protein	unknown	unknown	unknown
NC_011978.1\|WP_015919672.1\|1146677_1147871_-\|bifunctional-glutamate-N-acetyltransferase/amino-acid-acetyltransferase-ArgJ	unknown	unknown	gnl\|CDD\|376687

Protein	Function_ID	Function_description	E-value
NC_011978.1\|WP_015919684.1\|1157363_1158065_+\|isoprenyl-transferase	gnl\|CDD\|173302	PRK14841, PRK14841, undecaprenyl pyrophosphate synthase; Provisional.	1.02748e-159
NC_011978.1\|WP_015919678.1\|1152493_1153264_-\|ABC-transporter-permease	gnl\|CDD\|130314	TIGR01247, drrB, daunorubicin resistance ABC transporter membrane protein. This model describes daunorubicin resistance ABC transporter, membrane associated protein in bacteria and archaea. The protein associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc. [Transport and binding proteins, Other].	2.49104e-88
NC_011978.1\|WP_015919671.1\|1145832_1146681_-\|acetylglutamate-kinase	gnl\|CDD\|234869	PRK00942, PRK00942, acetylglutamate kinase; Provisional.	1.87574e-161
NC_011978.1\|WP_015919673.1\|1147887_1148907_-\|N-acetyl-gamma-glutamyl-phosphate-reductase	gnl\|CDD\|273832	TIGR01850, N-acetyl-gamma-glutamyl-phosphate_reductase, N-acetyl-gamma-glutamyl-phosphate reductase, common form. This model represents the more common of two related families of N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme catalyzing the third step or Arg biosynthesis from Glu. The two families differ by phylogeny, similarity clustering, and the gap architecture in a multiple sequence alignment. Bacterial members of this family tend to be found within Arg biosynthesis operons. [Amino acid biosynthesis, Glutamate family].	0
NC_011978.1\|WP_015919674.1\|1148903_1150100_-\|argininosuccinate-lyase	gnl\|CDD\|223243	COG0165, ArgH, Argininosuccinate lyase [Amino acid transport and metabolism].	4.67175e-165
NC_011978.1\|WP_015919683.1\|1156809_1157367_+\|ribosome-recycling-factor	gnl\|CDD\|178850	PRK00083, frr, ribosome recycling factor; Reviewed.	3.92456e-92
NC_011978.1\|WP_015919665.1\|1141047_1141593_-\|YkgJ-family-cysteine-cluster-protein	gnl\|CDD\|308985	pfam03692, CxxCxxCC, Putative zinc- or iron-chelating domain. This family of proteins contains 8 conserved cysteines. It has in the past been annotated as being one of the complex of proteins of the flagellar Fli complex. However this was due to a mis-annotation of the original Salmonella LT2 Genbank entry of 'fliB'. With all its conserved cysteines it is possibly a domain that chelates iron or zinc ions.	7.43856e-05
NC_011978.1\|WP_015919682.1\|1155446_1156601_-\|alanine--glyoxylate-aminotransferase-family-protein	gnl\|CDD\|223153	COG0075, COG0075, Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism].	1.28172e-178
NC_011978.1\|WP_015919675.1\|1150096_1151326_-\|argininosuccinate-synthase	gnl\|CDD\|234785	PRK00509, PRK00509, argininosuccinate synthase; Provisional.	0
NC_011978.1\|WP_038067645.1\|1144475_1144655_+\|hypothetical-protein	gnl\|CDD\|238698	cd01407, SIR2-fam, SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.	0.000441948
NC_011978.1\|WP_038067659.1\|1158057_1158870_+\|phosphatidate-cytidylyltransferase	gnl\|CDD\|366491	pfam01148, CTP_transf_1, Cytidylyltransferase family. The members of this family are integral membrane protein cytidylyltransferases. The family includes phosphatidate cytidylyltransferase EC:2.7.7.41 as well as Sec59 from yeast. Sec59 is a dolichol kinase EC:2.7.1.108.	1.62463e-59
NC_011978.1\|WP_015919679.1\|1153268_1154246_-\|ATP-binding-cassette-domain-containing-protein	gnl\|CDD\|213232	cd03265, ABC_DrrA, Daunorubicin/doxorubicin resistance ATP-binding protein. DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin. In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.	4.94629e-150
NC_011978.1\|WP_015919667.1\|1143564_1144389_+\|DMT-family-transporter	gnl\|CDD\|273359	TIGR00950, Uncharacterized_inner_membrane_transporter_YicL, Carboxylate/Amino Acid/Amine Transporter. [Transport and binding proteins, Amino acids, peptides and amines].	6.69774e-08
NC_011978.1\|WP_015919686.1\|1158866_1161461_+\|alanine--tRNA-ligase	gnl\|CDD\|234701	PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.	0
NC_011978.1\|WP_015919666.1\|1141711_1143172_-\|tetratricopeptide-repeat-protein	gnl\|CDD\|276808	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs. The Tetratricopeptide repeat (TPR) typically contains 34 amino acids and is found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans. It is present in a variety of proteins including those involved in chaperone, cell-cycle, transcription, and protein transport complexes. YbbN is a thioredoxin-like protein containing two tandem TPR repeats at the C-terminus, separated by two alpha helices. Its N-terminal thioredoxin-like domain is not a functional oxidoreductase. It functions in heat stress response and DNA synthesis as a chaperone or co-chaperone.	4.96161e-05
NC_011978.1\|WP_015919681.1\|1154520_1155441_-\|D-2-hydroxyacid-dehydrogenase	gnl\|CDD\|240628	cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains. Phosphoglycerate dehydrogenase (PGDH) catalyzes the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDH comes in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence.	3.70763e-155
NC_011978.1\|WP_015919672.1\|1146677_1147871_-\|bifunctional-glutamate-N-acetyltransferase/amino-acid-acetyltransferase-ArgJ	gnl\|CDD\|376687	pfam01960, ArgJ, ArgJ family. Members of the ArgJ family catalyze the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in arginine biosynthesis.	0

>NC_011978.1|WP_015919675.1|1150096_1151326_-|argininosuccinate-synthase
MKEKVVLAYSGGLDTSVILKWLCEKGFEVIAYVANVGQKDDFEAIKEKALKTGASKVYIEDLRREFVTDYIFTALLGNALYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGKGNDQVRFELTYAALNPNLKVISPWKDPEFLSRFKGRTDLINYAREKGIPVKVSKKRPYSEDENLMHISHEAGKLEDPMYIPDEDVFTWTVSPKEAPDEETLLEIHFEKGVPVKVVNLKDGTEKTDPLELFEYLNEIGAKNGVGRLDMVENRFIGIKSRGVYETPGATILWIAHRDLEGITMDKEVMHLRDMLAPKFSELIYNGFWFSPEMEFLLAAFKKSQENVTGKVIVSVYKGNVMPVARYSPCSLYNPELSSMDVEGGFDATDSKGFINIHALRLKVYRLTKKGYEK
>NC_011978.1|WP_015919674.1|1148903_1150100_-|argininosuccinate-lyase
MSEKLWEKGYTVDEEVEKFTVGDDYIVDMRIIKYDIKASIVHSKMLQRTGLLTQEEQKKIEEALNELLHLVEEGKFQIKPEDEDCHTAIENFLVKKLGETGKKIHTARSRNDQVLTALRLMYKDELKKIKDLVVELQKSLDGFIERFGQIKFAGFTHTRKAMPTDFATWAGALRDALQDDLKLLETVYDIIDQSPLGTGAGYGVPIEVDREFTAKELGFSRVQWNPIYTQNSRGKFEYLLLHVLSQISYDLNRFASDIIFFSLPEIGFLKLPKELCTGSSIMPHKINPDPLELVRAYHHFVVSRMVMAVSLPSNLILGYHRDLQLLKKPVIESIDVVKNILRIMKIIFDRIEVDREKSEDSITEEVLATHRVYELVKKGIPFRDAYRMVAEKYGREKD
>NC_011978.1|WP_015919673.1|1147887_1148907_-|N-acetyl-gamma-glutamyl-phosphate-reductase
MIRVGIVGATGYTGIELFRLLKKHPSAKIVYMSSRTYAGKKMMEVYPSTLEEAVLEDFDSRKISESCDVVFTALPAGVSYRLAMELQNVKIIDLGADFRFDDPNTYAEWYGNKLEDYNSTERVYGLPELYRDSIKNARIVGNPGCYPTSVILALTPALKSGIVEVDTIVVDSKSGVSGAGRKETLDYTFSEVNENLRPYNVAKHRHVPEMEQELKKIAGKDVKVIFTPHLVPMTRGILSTIYVKTNASLEKIHRIYQEFYAGEPFVHVLPLGVFPSTKWCYGSNHVFIGMQLEERTGTLILMSAIDNLVKGASGQAIQNMNIMFDLKETEGLESLPIYP
>NC_011978.1|WP_015919672.1|1146677_1147871_-|bifunctional-glutamate-N-acetyltransferase/amino-acid-acetyltransferase-ArgJ
MFVPRGFSYAGVHCRIKRKRKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGIRAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESGIEEAVKNLSKDPVPFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATMLSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETDGFWKLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKTAIYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDTAKKILSEKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT
>NC_011978.1|WP_015919671.1|1145832_1146681_-|acetylglutamate-kinase
MRIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKEEKAKKAFIQDIILLKYTGIKPVIVHGGGPAISQMMKELGIEPVFKNGHRVTDERTMEIVEMVLVGKINKEIVMNINLHGGRAVGICGKDSKLIVAEKETKYGDLGFVGKVKQVNPEILHALIENDYIPVIAPVGIGEDGHSYNINADTAAAEIAKSLMAEKLILLTDVDGVLKDGKLLSTLTPEEAENLIKDGVVTGGMIPKVECAISAVREGVGAVHIINGGLEHAILLEIFSRKGIGTMIKESEG
>NC_011978.1|WP_038067645.1|1144475_1144655_+|hypothetical-protein
MPYIYRCTKCGAIYYSATSIEYQLNKNCEKCGGELEQLGEEGELMKKEEEEKEKEDRKK
>NC_011978.1|WP_015919667.1|1143564_1144389_+|DMT-family-transporter
MRPAFYLLLSVLIASFSGVLVKISTLSPQTIAFYRVFIASFLFLLIVKKTRFLPLQDEMLSALAGFFLAMHFRFWIEAFDYTTVAGAVIPLMLQPVVTGFLSYLLYKERPTPQQFVTGSIVVIGVLISALGNEKFSDATRGDWLAITGTLFLCGYLVLGKKLNQRMGSLAFSLRTHAVASIVLFALSFSSFEIVSLREWFILIALGAGCSFLGYLFINLSLKNFPSSVVSVALVGETSLSMLWAYLLLGEVLGVFQVAGFLISSAGLVLFLLNA
>NC_011978.1|WP_015919666.1|1141711_1143172_-|tetratricopeptide-repeat-protein
MYFKRVLPVLLSGLALMIFLFSCAGPITFGPGETSEEEISNLLEDALDSLESGDTDGAKDAFEDALAEDPENPTANAGMSIILLYELFRDYSDEIGQFTGIFRMVPVRFKSFREITRSFSLMKYFMNMKQFPPPLPPEPPVPPPPFLPEENPIETWNQLYENLYIMFSELWPRLKELETCLEYAVTGNASLTIHPNNFDWDGDSVLESETPLELSDGTNTYSVVDLLYDSASPEGTLVVVQSGGDAWFDFETISGQNPEEIVFDENDYLILDKGAFSALLVVVKAVLSISDLLLTWDLTLSTNLPNPADYEDTEEWIQAVLLQLAGDDYIISNNGDGGEWNELDPFLRFRENGSDYLEDLVDSVVKGLEAILWLNEDIVEDDPGDEHDFTSRYYFEEPLLDEDTENTLQDIVETKQVELPEGEQFTYKHTETETLTATIVGIDFGILAENPDNFENLKAFFPTLDLQNEYYEFPDPAFGGLLVLEE
>NC_011978.1|WP_015919665.1|1141047_1141593_-|YkgJ-family-cysteine-cluster-protein
MKRLEELAIKVMELYRELENIQRGLPSCNGCRECCDTPSINIEATILEFLPLAIHLLKEGSIERWLKILETTGESDRCVLFDPRSEQGGCSYHSFRPLVCRLFSGSYILRKGRPEVWACRYLKPQLTSLYESLPECQKVHLRLLSIDFFLAQERYPINIAFKKALEYTCVSLFPELRYKGA
>NC_011978.1|WP_161595589.1|1140257_1140509_-|hypothetical-protein
MIVENQNGSTFTGLFGGVELSSGIQFFLPMTGTITSGGNIVITVTLTDPTTGQTVTATSQGVYASGRITIIGENQTIDLVKVQ
>NC_011978.1|WP_015919678.1|1152493_1153264_-|ABC-transporter-permease
MAAFVTMVYRQLIRFVRSRSRVIGMIINPLIWLVFFGLGWSKVFDNPWARMMFGGVDYLTYLAPGIFAMTIFNMSFISGVSLIWDKQFGFFKEVLVAPSSRRLSVMGRIIGDGLVTVLQGFIILFFTYFLAENLKISGLIPALIVGFLMSVTIASFGIALALKMESTEGFQMIMMTLMMPLIFLSGAMYPIDSMPNWMKAIAYINPLTYAVDASRGYLVGSHVMKFSFGMDWGILSILMVVGLLLATESFERARIS
>NC_011978.1|WP_015919679.1|1153268_1154246_-|ATP-binding-cassette-domain-containing-protein
MEDVIVVENLVKKFGDFEAVKGISFSVKKGEIFAFLGPNGAGKTTTIHILTTLLKPTDGKAWVAGHDVLKEPREVRKKIGIVFQDQSIDRELTAYENMYIHGRIYGYGGEKLKKRILELLEFVELLEFKDKPVKTFSGGMTRRLEIARSLIHEPEILFLDEPTIGLDPHTRAHIWEYISKMKKEHNMTIFLTTHYMDEAEQLADRVAIIDHGKIIALGSPDELKQMVGKEIIYVKFSDPVDCLDGEFIKSCKKLSDGRLELNVENSSRAIPKIFELAQQKGLKIEEITYHKPTLNDVFLHLTGRELREEGPENFFKAVARMRMRR
>NC_011978.1|WP_162828739.1|1154396_1154540_+|hypothetical-protein
MERIRDFFILIFCVVLFLYEITSLSMKVIFKRKKSRETAPGLRSQAL
>NC_011978.1|WP_015919681.1|1154520_1155441_-|D-2-hydroxyacid-dehydrogenase
MAKYRVHVNDPLDEEATKLLMEKEELTVTSRHLEKEELLKTISEVDVLVVRSATKVTSDIIEAGKNLKIIARAGIGLDNIDVQKAKEKGIKILNTPGASAPSVAELAIGLMLACARHIAKATISLKEGKWEKKILKGKELLGKTLGLIGFGNIGQEVARRALGFGMRVIAYDPARPKTDLPVEYVDLDTLLKESDFISLHVPLIESTKHMINKDTISKMKDGVIIVNTSRGGTIDEEALYEALVSGKVYAAGLDVFEVEPPSDELRRKLLSLDNVVATPHIGASTAEAQKRVGKELVEKIFRELGI
>NC_011978.1|WP_015919682.1|1155446_1156601_-|alanine--glyoxylate-aminotransferase-family-protein
MGKFLKKHYIMAPGPTPVPNDILTEGAKETIHHRTPQFVSIMEETLEDAKYLFQTKNNVYAFASTGTGAMEAAVANLVSPGDKVIVVVAGKFGERWKELCQSYGANIVEISLEWGEAVTPEQIEDALNRNPDAKVVFTTYSETSTGTVIDLEGIARVTREKNVVLVTDAVSALGAEPLKMDEWGVDVVVTGSQKGLMLPPGLALISLNDKAWELVEKSKSPRYYFDLRAYRKSYPDNPYTPAVNMIYMLRKSLKMIKEEGIENVWERHRVLGEATRSAVKALGLELLSKRPGNVVTAVKVPAGIDGKQIPKIMRDKYGVTIAGGQAKLKGKIFRIAHLGYMSPFDTITAIAALEFTLKELGYDLELGAGVKAAETIFAKEFIGE
>NC_011978.1|WP_015919683.1|1156809_1157367_+|ribosome-recycling-factor
MVNPLIKEAKEKMKKTLEKIEDELKKMRTGKPSPAILEEIKVDYYGVPTPVNQLATISVSEERTLVIKPWDRSVLSLIEKAINASDLGLNPVNDGNVIRLVFPTPTTEQREKWVKKAKEIVEEGKIAIRNIRREIMKKIKEDQKEGNIPEDDARRLENEVQKLTDEFIEKLDEVFEIKKKEIMEF
>NC_011978.1|WP_015919684.1|1157363_1158065_+|isoprenyl-transferase
MRIPQHVAIIMDGNGRWAKKRGLPRIKGHERGAHVLHNTVKWSLELGIKYLTAYSFSTENWKRPKEEVEFLMNLFVQMIDREMDLLRREKVRVRILGRKEGLPESVLRKWNEVEEKTNSFDRMTLVIAFNYGGRREILDAVERILRDVEKEKKIVLNEETFKSYLYLPDVPDPDLIIRTSGELRLSNFLIWQSAYSELYFTRKLWPDFTKRDFLRAIESYSRRERRFGGLGDG
>NC_011978.1|WP_038067659.1|1158057_1158870_+|phosphatidate-cytidylyltransferase
MDDLKTRVITASVVAPFVVLCFVSYESLVGLVSAIVILAGYELITLELKERDARFFYVILLAVYPVLYGVAFKEPVQPLSLVFIIGVVFSLATDKDPSQVFRTVSVFSIALVYVSFFLSFFLPIYSEFGAANALLVLTSTWVFDSFAYFTGLKFGKTRISPHYSPRKSLEGVIGGFLGVLIYTFLYRLIVSNILSVNVIDYRTFLPFASVVAVMDTFGDIFESALKRHYRVKDSGKTLPGHGGMLDRIDGLLFVTPVSYIVFKIFEGVVR
>NC_011978.1|WP_015919686.1|1158866_1161461_+|alanine--tRNA-ligase
MRYMTSEEIREAFLRFFEKKGHKILPSASLIPDDPQLLFTVAGMVPFKPIFWGKVEPVYTRIATCQKCLRTVDIENVGKTPRHHTFFEMLGNFSFGDYFKEEAIEWAWEFLTQVLGVPEEKLWVSVYEEDEEAFRIWNEKIGLPEKKILRLGKEDNFWGPAGPTGPCGPDTEIFYDTGYSKGCPEGEECTPANSEGRFVEIWNLVFTEYYQDEEGKLHPLPRKNIDTGAGLERFCAMMQGVYSNFDTDLFQPIIKAIEELTGVSYKTDEEKDISIRVIADHIRAITFLISEGVFPSNEGRGYVLRRIIRRAMRHGILLGMNEPFLYKVVDAVVEKMGKVYPEIVRGKDMVKEVLSSEENRFLKTLEQGMRIFDELVEKKGKIDSQDAFRLYDTYGLPLELTLEIAKEKGVEIDVKDFDRYMKEQQRKSREAMGKVEFAKRYEYLESLPEGFKTEFTGYERLEDEAETVLIAKENRPLEEAKEKDTVEVVFSRTPFYAEKGGQVSDVGTVEWESGEGRVEYVFEALEGVIVHRIRVLKGILRRGQKVFLKVDRKRRKDTMRNHTATHLLHAALRKVLGEHVRQAGSLVAPERLRFDFTHYRALSAEEIKKVEDMVNEWIMQAIPVEVRYTSYEEAIRSGVIALFTEKYGDVVRVVEVPGVSKELCGGTHVKNTGQIGLFKIVSEESVSSGVRRVEAVTGFYTLELIRRYEDVMTRLKELLGAGENEIINRVESLREKVRELERRLSQGRVSEERISEKKLNDGTKLFYGVFEGVESKHLGGIADNVLNREKSGVVVLFSRFEDKVSLVVKVSNDLIEKYDASSIARNIAKELGGSGGGRKNFAQAGGRHPERLDEVLNRLEEFLG
>NC_011978.1|WP_015919687.1|1161467_1162520_+|hypothetical-protein
MELLVDSRELKEWLFLLDKLVGTVEPSARFVDFFFRDGLWLRASDNCASVEVFLGKIPRFEGSRRVSLDLLKFFLSDVKVKEVHVTISQDHLVLKAGNEVLDVRCRVGGVPPEDGKEEFLCTLSKREFESSINFASSNLDEGEFLVLLFEEKDVLMFGPSSEIVTLSQISAVPTTSFSLKIPYVTVRHVFKALQRLNVQTLDFYEKSGKLVVKYPYLVMEVCGDRVSVEEREALKRVLSEKVVERLESKKEVLAKLVRKAAVISRGSYATLSRRGNVMRVVVKKKNLSYTAELFVEPGRDFLVVFPSKKLRSALARMEGEKVVLELTERFLKISNLSGTRTVFLELEEFS

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Click the colored protein region to show detailed information

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_011978_6	6.1\|739776\|34\|NC_011978\|CRISPRCasFinder	739776-739809	34	NZ_CP015867	Streptomyces parvulus strain 2297 plasmid pSPA1, complete sequence	162741-162774	9	0.735
NC_011978_4	4.10\|705115\|35\|NC_011978\|CRISPRCasFinder	705115-705149	35	NZ_CP015733	Arthrobacter sp. U41 plasmid unnamed1, complete sequence	168499-168533	10	0.714

1. spacer 6.1|739776|34|NC_011978|CRISPRCasFinder matches to NZ_CP015867 (Streptomyces parvulus strain 2297 plasmid pSPA1, complete sequence) position: , mismatch: 9, identity: 0.735

aggtctgtgtctttgaccgtcgccaggaactgct	CRISPR spacer
ccgtagatctcgttgaccgtcgccacgaactgcg	Protospacer
  **  .* ** ************* *******

2. spacer 4.10|705115|35|NC_011978|CRISPRCasFinder matches to NZ_CP015733 (Arthrobacter sp. U41 plasmid unnamed1, complete sequence) position: , mismatch: 10, identity: 0.714

tttttctttgcgtgaagtaagcgtttgggaattct	CRISPR spacer
ggattgtttgcgggaagtaagcgtttggatgtcat	Protospacer
   ** ****** ***************. .*. *

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

720755 : 728381

Bacillus_phage(33.33%)

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

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_015919219.1\|720755_721520_+	ABC transporter ATP-binding protein	G3M9Y6	Bacillus_virus	9.4e-25	34.3
WP_015919220.1\|721494_722250_+	5'/3'-nucleotidase SurE	NA	NA	NA	NA
WP_015919221.1\|722237_722732_+	peptide deformylase	A0A067XQZ3	Caulobacter_phage	9.7e-23	49.2
WP_015919222.1\|722745_723717_+	M23 family metallopeptidase	D7RWE0	Brochothrix_phage	3.0e-07	30.8
WP_038067053.1\|723721_724048_+	hypothetical protein	NA	NA	NA	NA
WP_015919224.1\|724121_725309_+	methionine adenosyltransferase	A0A2H4PQS6	Staphylococcus_phage	2.0e-138	65.3
WP_015919225.1\|725324_725624_+	30S ribosomal protein S20	NA	NA	NA	NA
WP_015919226.1\|725697_726360_+	hypothetical protein	NA	NA	NA	NA
WP_038067057.1\|726419_727139_+	response regulator transcription factor	W8CYM9	Bacillus_phage	3.2e-43	43.6
WP_015919228.1\|727142_728381_+	PAS domain-containing protein	W8CYF6	Bacillus_phage	2.3e-36	36.1

DBSCAN-SWA_2

1273075 : 1290957

Bacillus_phage(25.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_012311192.1\|1273075_1273831_+	phosphate ABC transporter ATP-binding protein	W6JKT0	Anomala_cuprea_entomopoxvirus	9.3e-17	29.4
WP_015919783.1\|1273844_1274543_+	phosphate signaling complex protein PhoU	NA	NA	NA	NA
WP_015919784.1\|1274517_1275198_+	response regulator transcription factor	W8CYM9	Bacillus_phage	3.6e-28	33.0
WP_015919785.1\|1275178_1276138_+	HAMP domain-containing histidine kinase	W8CYF6	Bacillus_phage	3.2e-14	28.3
WP_038067760.1\|1276130_1277939_-	ATP-binding protein	A0A139ZPI2	Marinitoga_camini_virus	5.5e-31	25.2
WP_015919788.1\|1277940_1279674_-	ABC transporter ATP-binding protein	W8CYL7	Bacillus_phage	2.9e-45	27.5
WP_015919789.1\|1279648_1280782_-	pyridoxal phosphate-dependent aminotransferase	NA	NA	NA	NA
WP_038067763.1\|1280878_1281529_+	HAD family phosphatase	A0A1D8KNV9	Synechococcus_phage	6.6e-11	26.3
WP_038067766.1\|1281512_1283243_-	NAD+ synthase	A0A2L0UZF5	Agrobacterium_phage	1.0e-87	34.5
WP_015919792.1\|1283193_1283787_-	hypothetical protein	NA	NA	NA	NA
WP_015919793.1\|1283779_1284724_-	phosphoribosylformylglycinamidine cyclo-ligase	A0A0E3F114	Synechococcus_phage	1.0e-36	34.9
WP_038067768.1\|1284720_1285914_-	phosphoribosylamine--glycine ligase	NA	NA	NA	NA
WP_015919795.1\|1285926_1287285_-	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosine monophosphate cyclohydrolase	Q58MG4	Prochlorococcus_phage	8.0e-43	38.3
WP_038067771.1\|1287265_1287883_-	phosphoribosylglycinamide formyltransferase	M4QRX9	Synechococcus_phage	2.6e-25	36.7
WP_015919797.1\|1287843_1289139_-	amidophosphoribosyltransferase	A0A0M3SGR2	Mollivirus	1.6e-48	32.5
WP_145971578.1\|1289145_1290957_-	phosphoribosylformylglycinamidine synthase subunit PurL	A6N228	Microbacterium_phage	1.6e-91	37.6

DBSCAN-SWA_3

1431788 : 1440507

Powai_lake_megavirus(16.67%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_015919930.1\|1431788_1432511_-	ribonuclease III	A0A167RGU4	Powai_lake_megavirus	7.3e-19	26.0
WP_038067848.1\|1432503_1433061_-	phosphodiesterase	NA	NA	NA	NA
WP_081434645.1\|1433063_1434233_-	ABC transporter permease	NA	NA	NA	NA
WP_038067850.1\|1434156_1434750_-	dTMP kinase	M1PSC7	Streptococcus_phage	1.2e-32	42.6
WP_015919935.1\|1435333_1436275_-	ornithine carbamoyltransferase	M1I6M4	Paramecium_bursaria_Chlorella_virus	2.9e-23	30.7
WP_015919936.1\|1436278_1437472_-	adenylosuccinate synthase	L7Y4J5	Megavirus	9.5e-48	31.9
WP_038067853.1\|1437477_1438773_-	adenylosuccinate lyase	A0A1B3B081	Gordonia_phage	2.0e-19	30.1
WP_015919939.1\|1439187_1440507_-	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	A0A2K5B251	Erysipelothrix_phage	1.6e-48	28.2

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_011978

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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