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_018939	Helicobacter pylori 26695, complete genome	4 crisprs	cas2,cas14j,DEDDh	1	1	1	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_018939_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018939_1

350475-350601

Unclear

Consensus_repeat	Method
CTCTCTAGCGTTACTGAAGAGATTATTTCAAAAAAAC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_018939_1

>merge|NC_018939|1|350475-350601|CRISPRCasFinder
CTCTCTAGCGTTACTGAAGAGATTATTTCAAAAAAACAAGAAGAATTACAGAGCAAAGAAACCCCAGAAGGCAAGCATGATGGAGAGAGACTCTCTAGCGTTACCGAAGAGATTATTTCAAAAAAAC

>NC_018939|1|1|350475-350601|CRISPRCasFinder
CTCTCTAGCGTTACTGAAGAGATTATTTCAAAAAAAC	AAGAAGAATTACAGAGCAAAGAAACCCCAGAAGGCAAGCATGATGGAGAGAGA
CTCTCTAGCGTTACCGAAGAGATTATTTCAAAAAAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_018939.1\|WP_001207734.1\|345558_346551_+\|ketol-acid-reductoisomerase	unknown	unknown	gnl\|CDD\|235491
NC_018939.1\|WP_001201399.1\|341567_343121_+\|bifunctional-UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose-hydrolase/pseudaminic-acid-cytidylyltransferase	unknown	unknown	gnl\|CDD\|226488
NC_018939.1\|WP_000599146.1\|348420_348825_+\|Holliday-junction-resolvase-RuvX	unknown	unknown	gnl\|CDD\|234639
NC_018939.1\|WP_001019069.1\|346575_347382_+\|septum-site-determining-protein-MinD	unknown	unknown	gnl\|CDD\|225447
NC_018939.1\|WP_001076175.1\|347611_348424_+\|DNA-protecting-protein-DprA	unknown	unknown	gnl\|CDD\|273238
NC_018939.1\|WP_001117124.1\|353999_354896_-\|RNA-pseudouridine-synthase	unknown	unknown	gnl\|CDD\|223638
NC_018939.1\|WP_010875465.1\|350696_351047_+\|lysozyme	unknown	unknown	gnl\|CDD\|381597
NC_018939.1\|WP_000833936.1\|343592_344531_-\|tetraacyldisaccharide-4'-kinase	unknown	unknown	gnl\|CDD\|224577
NC_018939.1\|WP_010875469.1\|353223_354006_+\|hypothetical-protein	unknown	unknown	unknown
NC_018939.1\|WP_000051415.1\|347378_347612_+\|cell-division-topological-specificity-factor-MinE	unknown	unknown	gnl\|CDD\|188120
NC_018939.1\|WP_000373222.1\|356454_358071_-\|CTP-synthase-(glutamine-hydrolyzing)	unknown	unknown	gnl\|CDD\|235437
NC_018939.1\|WP_000699933.1\|349783_350089_+\|hypothetical-protein	unknown	unknown	unknown
NC_018939.1\|WP_000810700.1\|354895_356446_-\|single-stranded-DNA-specific-exonuclease-RecJ	unknown	unknown	gnl\|CDD\|273193
NC_018939.1\|WP_010875466.1\|351600_351993_+\|DUF1294-domain-containing-protein	unknown	unknown	gnl\|CDD\|225863
NC_018939.1\|WP_000829924.1\|358331_359000_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|239486
NC_018939.1\|WP_001862999.1\|352768_353104_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|226894
NC_018939.1\|WP_001862993.1\|351034_351301_+\|hypothetical-protein	unknown	unknown	unknown
NC_018939.1\|WP_001168317.1\|344527_345310_-\|NAD+-synthase	unknown	unknown	gnl\|CDD\|184435
NC_018939.1\|WP_000916576.1\|351312_351408_+\|hypothetical-protein	unknown	unknown	unknown
NC_018939.1\|WP_000742697.1\|343117_343660_+\|UDP-4-amino-4,-6-dideoxy-N-acetyl-beta-L-altrosamine-N-acetyltransferase	unknown	unknown	gnl\|CDD\|274661

Protein	Function_ID	Function_description	E-value
NC_018939.1\|WP_001207734.1\|345558_346551_+\|ketol-acid-reductoisomerase	gnl\|CDD\|235491	PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.	1.62341e-179
NC_018939.1\|WP_001201399.1\|341567_343121_+\|bifunctional-UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose-hydrolase/pseudaminic-acid-cytidylyltransferase	gnl\|CDD\|226488	COG3980, spsG, Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane].	3.7254e-112
NC_018939.1\|WP_000599146.1\|348420_348825_+\|Holliday-junction-resolvase-RuvX	gnl\|CDD\|234639	PRK00109, PRK00109, Holliday junction resolvase RuvX.	1.29686e-35
NC_018939.1\|WP_001019069.1\|346575_347382_+\|septum-site-determining-protein-MinD	gnl\|CDD\|225447	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning].	3.38301e-150
NC_018939.1\|WP_001076175.1\|347611_348424_+\|DNA-protecting-protein-DprA	gnl\|CDD\|273238	TIGR00732, Protein_smf, DNA protecting protein DprA. Disruption of this gene in both Haemophilus influenzae and Helicobacter pylori drastically reduces the efficiency of transformation with exogenous DNA, but with different levels of effect on chromosomal (linear) and plasmid (circular) DNA. This difference suggests the DprA is not active in recombination, and it has been shown not to affect DNA binding, leaving the intermediate step in natural transformation, DNA processing. In Strep. pneumoniae, inactivation of dprA had no effect on the uptake of DNA. All of these data indicated that DprA is required at a later stage in transformation. Subsequently DprA and RecA were both shown in S. pneumoniae to be required to protect incoming ssDNA from immediate degradation. Role of DprA in non-transformable species is not known. The gene symbol smf was assigned in E. coli, but without assignment of function. [Cellular processes, DNA transformation].	1.76728e-100
NC_018939.1\|WP_001117124.1\|353999_354896_-\|RNA-pseudouridine-synthase	gnl\|CDD\|223638	COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis].	1.08076e-66
NC_018939.1\|WP_010875465.1\|350696_351047_+\|lysozyme	gnl\|CDD\|381597	cd00735, T4-like_lys, bacteriophage T4-like lysozymes. Bacteriophage T4-like lysozymes hydrolyze the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan heteropolymers of prokaryotic cell walls. Members include a variety of bacteriophages (T4, RB49, RB69, Aeh1), as well as Dictyostelium.	2.23312e-16
NC_018939.1\|WP_010875466.1\|351600_351993_+\|DUF1294-domain-containing-protein	gnl\|CDD\|225863	COG3326, COG3326, Predicted membrane protein [Function unknown].	2.33177e-31
NC_018939.1\|WP_000051415.1\|347378_347612_+\|cell-division-topological-specificity-factor-MinE	gnl\|CDD\|188120	TIGR01215, Cell_division_topological_specificity_factor, cell division topological specificity factor MinE. This protein is involved in the process of cell division. This protein prevents the proteins MinC and MinD to inhibit cell division at internal sites, but allows inhibiton at polar sites. This allows for correct cell division at the proper sites. [Cellular processes, Cell division].	3.3313e-26
NC_018939.1\|WP_001168317.1\|344527_345310_-\|NAD+-synthase	gnl\|CDD\|184435	PRK13980, PRK13980, NAD synthetase; Provisional.	3.80738e-126
NC_018939.1\|WP_000373222.1\|356454_358071_-\|CTP-synthase-(glutamine-hydrolyzing)	gnl\|CDD\|235437	PRK05380, pyrG, CTP synthetase; Validated.	0
NC_018939.1\|WP_000810700.1\|354895_356446_-\|single-stranded-DNA-specific-exonuclease-RecJ	gnl\|CDD\|273193	TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ. All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. [DNA metabolism, DNA replication, recombination, and repair].	0
NC_018939.1\|WP_000829924.1\|358331_359000_+\|hypothetical-protein	gnl\|CDD\|239486	cd03392, PAP2_like_2, PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase.	5.56786e-13
NC_018939.1\|WP_001862999.1\|352768_353104_+\|hypothetical-protein	gnl\|CDD\|226894	COG4499, COG4499, Predicted membrane protein [Function unknown].	0.00242841
NC_018939.1\|WP_000833936.1\|343592_344531_-\|tetraacyldisaccharide-4'-kinase	gnl\|CDD\|224577	COG1663, LpxK, Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane].	3.46263e-96
NC_018939.1\|WP_000742697.1\|343117_343660_+\|UDP-4-amino-4,-6-dideoxy-N-acetyl-beta-L-altrosamine-N-acetyltransferase	gnl\|CDD\|274661	TIGR03585, PseH, UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase. Sequences in this family are members of the pfam00583 (GNAT) superfamily of acetyltransferases and are proposed to perform a N-acetylation step in the process of pseudaminic acid biosynthesis in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci. Significantly, many genomes containing other components of this pathway lack this gene, indicating that some other N-acetyl transferases may be incolved and/or the step is optional, resulting in a non-acetylated pseudaminic acid variant sugar.	1.02691e-59

>NC_018939.1|WP_000699933.1|349783_350089_+|hypothetical-protein
MKIMHQVRDFLDSCKQTIQKNSSEVFQKTKRAFFKEESQKIREQAVKIVEKRLKKEGMKLSDFNEEELKIMFEAEEKRLLEQIQTKHFKEVWEKGDNEQGK
>NC_018939.1|WP_000599146.1|348420_348825_+|Holliday-junction-resolvase-RuvX
MILACDVGLKRIGIAALLNGVILPLEAILRHNRNQASRDLSDLLREKNIQVLVVGKPHESYADTNARIEHFIKLVDFKGEIVFINEDRSSIEAYENLEHLGKKNKRLAIKDGRLDSLSACRILERYCQKVLKNH
>NC_018939.1|WP_001076175.1|347611_348424_+|DNA-protecting-protein-DprA
MNQRMKSHFQYSTLENIPKAFDILKDPPKKLYCVGDTKLLDTPLKVAIIGTRRPTPYSKQHTITLARELAKNGAVIVSGGALGVDIIAQENALPKTIMLSPCSLDFIYPTNNHKVIQEIAQNGLILSEYEKDFMPIKGSFLARNRLVIALSDVVIIPQADLKSGSMSSARLAQKYQKPLFVLPQRLNESDGTNELLEKGQAQGIFNIQNFINTLLKDYHLKEMPEMEDEFLEYCAKNPSYEEAYLKFGDKLLEYELLGKIKRINHIVVLA
>NC_018939.1|WP_000051415.1|347378_347612_+|cell-division-topological-specificity-factor-MinE
MSLFDFFKNKGSAATATDRLKLILAKERTLNLPYMEEMRKEIIAVIQKYTKSSDIHFKTLDSNQSVETIEVEIILPR
>NC_018939.1|WP_001019069.1|346575_347382_+|septum-site-determining-protein-MinD
MAIVVTITSGKGGVGKSTTTANLAIGLAESGKKVVAVDFDIGLRNLDMILGLENRIVYDVVDVMEKNCNLSQALITDKKTKNLSFLAASQSKDKNILDKEKVAILINALRADFDYILIDSPAGIESGFEHAILHADMALVVVTPEVSSLRDSDRVVGIIDAKSNRAKKGMEVHKHLIINRLKPELVANGEMISIEEVLKILCLPLIGIIPEDHHIISATNKGEPVIRTDCESAKAYQRITRRILGEEVEYVEFKAKRGFFSALKGIFS
>NC_018939.1|WP_001207734.1|345558_346551_+|ketol-acid-reductoisomerase
MALPVYYDKDIDLGVIQSLQVGIIGYGAQGEAQALNLRDSKVKARIGLYQGSLSVSKAKKEGFEVLEVKELVQNSDVIMALLPDELHKEVLEKEVIPFLKEGQIVGFAHGFSVHFNQVVLPKGVGAILVAPKGPGSALREEYLKNRGLYHLIAIEQESSIHNAKAVALSYAKAMGGGRMGVLETSFKEECESDLFGEQAVLCGGLEAIVRMGFETLIKAGYPEELAYFECVHEVKLVADLLHYKGVEGLRKHISNTAEFGAIKAREPMGKLLKKRMQKILKKIQNGSFAKDFLLEKSLNYPRLNTERKALKETKIEQIGEILRAPFNHKK
>NC_018939.1|WP_001168317.1|344527_345310_-|NAD+-synthase
MQKDYQKLIVYLCDFLEKEVQKRGFKKVVYGLSGGLDSAVVGVLCQKVFKENAHALLMPSSVSMPENKTDALNLCEKFSIPYTEYSIAPYDAIFSSHFKDASLTRKGNFCARLRMAFLYDYSLKSDSLVIGTSNKSERMLGYGTLFGDLACAINPIGELFKTEVYELARRLNIPKKILNKPPSADLFVGQSDEKDLGYPYSVIDPLLKDIEALFQTKPIDTETLAQLGYDEILVKNITSRIQKNAFKLELPAIAKRFNPE
>NC_018939.1|WP_000833936.1|343592_344531_-|tetraacyldisaccharide-4'-kinase
MKSDKPFLERYFYDPTLLQKGLIFALYPFSLIYQGIATLKRKTAKKHDFKIPIISIGNLIAGGSGKTPFILEIAPRYQEVAVVSRGYQRDSKGLVVVSVKGNILVSQKTAGDEAYLLALNLKQASVIVSEKRELGVLKALELGAKIVFLDDGFRFNFNQFNLLLKPKVPPYYPFCLPSGLYRESIKSYEEAHLVVTEDKDYQRITSISRPTKRMLLVTAIANPSRLDAFLPKEVVKKLYFKDHAPFNLELLEKEFYQNNATSLLVTSKDLVKLQDCNLPLSVLNLKLEICPKVLEEIDHYILSYPYNTKERL
>NC_018939.1|WP_000742697.1|343117_343660_+|UDP-4-amino-4,-6-dideoxy-N-acetyl-beta-L-altrosamine-N-acetyltransferase
MKKNYSYKNIQAIDFTNLNDGEKLLVLEFRNHPNTALWMYSTFISLKTHLQFIEDLKNSPNHRYFLFKEEGVYLGVGSITKINFFHKHGYLGIYKNPFLKNGGETILKALEFIAFEEFQLHSLHLEVMENNFKAIAFYEKNHYELEGRLKGFISKDKEFIDVLLYYKDKKGYNDQSLLKL
>NC_018939.1|WP_001201399.1|341567_343121_+|bifunctional-UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose-hydrolase/pseudaminic-acid-cytidylyltransferase
MRAIAIVLARSSSKRIKNKNIIDFFNKPMLAYPIEVALNSKLFEKVFISSDSMEYVNLAKNYGASFLNLRPKILADDRATTLEVMAYHMEELELKDEDIACCLYGASALLQEKHLKNAFETLNKNQNTDYVFTCSPFSASPYRSFSLENGVQMAFKEHSNTRTQDLKTLYHDAGLLYMGKAQAFKEMRPIFSQNSIALELSPLEVQDIAHFRRFRISQAQIQPFEKRMPVKILCDCFLTSGLGHVRRCEKILSFIEKLGVEASLYLHKQNNISAFLEGVGGNDFLITDSYCLNSKDFYLLKEKAKSLMVIEDTEHAKGFYPKNTKILNFTLNALKHYHHLSKDYQYYLGVGFYPVDARFIYDRPINTENKEVLITLGGSEQKTLKEIVKILENKNVNLHIISPYTPKNPPKNTHYYSPLNPLEFSSLMKSCACAISAAGQTLYELALSQTPSLILPIASNQIIQSKEFESLGIFKQTSLKTLAKDFENLQIQKNQAWAKNLVFGDKLEGALREFLEI
>NC_018939.1|WP_010875465.1|350696_351047_+|lysozyme
MDSEGFSPSIYTDKTGHPTIGYGYNLSVYSYEGKRITKTYGLLTDILSYGWYKNLDAMRRMVILDLSYNLGLNGLLKFKQFIKAIEDKNYALAVERLQKSPYFNQVKKERQGIWKF
>NC_018939.1|WP_001862993.1|351034_351301_+|hypothetical-protein
MEILKLEGCEKHCKKKYAIEKVIKEVGLELKSKSVMPYFFNEYDLTKNANRKEPERLRSQIISILMKTPKGREILKEYLNEGCILLGE
>NC_018939.1|WP_000916576.1|351312_351408_+|hypothetical-protein
MLKNFKKAFFRALCLGALCLLGEWCSNLGRL
>NC_018939.1|WP_010875466.1|351600_351993_+|DUF1294-domain-containing-protein
MSVEFASIVWLLIVNILIFILMLVDKNSADQKMWRIPEKALWVLSLLGGSVGFLVAMVVSHHKILKPEFKYGVSLIYLIESTILYFVSKDLSWIVALTIFSLSLILVAFKIFLLKDNPNKRFKNNKRDKK
>NC_018939.1|WP_001862999.1|352768_353104_+|hypothetical-protein
MENDVKEDLEQARPKLEPEKQKQEPEEQKQEKQDKQEQKPKQEKEESKSKEQEENKKQKRSSYIFWGCIIGLCIVVIIAKIIAFGGSSEEAKADKPKNSLSMLKNFYLPIL
>NC_018939.1|WP_010875469.1|353223_354006_+|hypothetical-protein
MDKFLDWHYSVKGDYSELALFVAKKIGLSAEDAVANVLQEKLLGKDYKQRLDAITKKLSKTYGSLLNQHEKFVSETALKGVDTDLSQNAKILDTLGDEVARKLKANFTGAIGATAGVSGLAIAAKLTPKLMAKIGAKLGAKVGGKFLAKIGTALSGSWTCGPFVPACTIGLWFGSDAAFNYIDEWLHRDDFKKEILNNINEVKENLKNSYKQQFNDSFVKISQEFQKSFKNAPVVEKKTIKEHIGDLNQTPEEDNQKINQ
>NC_018939.1|WP_001117124.1|353999_354896_-|RNA-pseudouridine-synthase
MPFVEEEFEILKPTKALFFVRDVLKCSLKEAQRHLDKQRLKQNQQAVRKSQIIQGVVRLIHFKPNEKTQALVFETKDFGVFDKPHQVYTHPKGYFYHESLLDCIQSHFGKNAHPAHRLDYETSGLVLAGKTLQSVKDLKALFMQKKVKKTYLALAHGLVEKSMKIDKPILTPQNIQKDLHIRSKISPLGKQSITLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVDHRIVGEGLYGVADENAREYLQLKRENNAPLLMLHAASLEFEFKGAIYKIASPMPERFMPFLKDLSFFY
>NC_018939.1|WP_000810700.1|354895_356446_-|single-stranded-DNA-specific-exonuclease-RecJ
MKQKLKAQIKERMASIAYNEKGFPSPFLFKDLKKAALKIIEAMRTNTEILVVGDYDADGVISSAIMAKFFESLNYKHVRIAIPNRFMDGYGISKKFLEKHHAPLIITVDNGINAFEAARFCKEKNYTLIITDHHCLHHDEVPDAYAVINPKQPDCDFIQKEVCGALVAFYLCYGIHQLLGKEKSHSSELLCLAGVATIADMMPLTFFNRFLVSKALYFLQKESLGAMGFLRQREVFRKRSLKASDISFNIAPLINSAGRMQDAKMALDFLSANNSQDGYSLYERLKACNLKRKMIQQQVFEEAFKHAMVGEKIIVAFKDNWHEGVLGIVASKLVEATQKPSLVFTFKEGVYKGSARSSSNIDLIDALNGVSSLLLGYGGHRQACGLSVEKNNIISLFETLENFDFKVLPFCKTEPPLTLKLKDIDRELLEIIEMGEPYGQENPEPLFQAKNLEVIEEKIIKESHQVLRFKDKECVKEAIYFSAERFLKAGEKVSVLFSVELDECSNEPKMFVKSLL
>NC_018939.1|WP_000373222.1|356454_358071_-|CTP-synthase-(glutamine-hydrolyzing)
MDRAKFIFVTGGVLSSLGKGISSSSIATLLQHCNYQVSILKIDPYINIDPGTMSPLEHGEVFVTSDGAETDLDIGHYERFLNRNLTRLNNFTTGQIFSSVIENERKGEYLGKTIQIVPHVTDEIKRRIKSAAKGLDFLIVEVGGTVGDMEGMFYLEAIRQLKLELGNEKVINVHVTLIPYIQTTNELKTKPTQHSVQELRRLGVTPQIILARSPKPLDKELKNKIALSCDVEQDSVIVATDTKSIYACPILFLQEGILTPIARRFNLNKLHPKMAAWNTLVEKIIAPKHKVKIGFVGKYLSLKESYKSLIEALIHAGAHLDTQVNIEWLDSENFNEKTDLEGVDAILVPGGFGERGIEGKICAIQRARLEKLPFLGICLGMQLAIVEFCRNVLGLKGANSTEFNQRCEYPVVYLIGDFMDQNHQKQVRTYNSPLGGTMRLGEYECEIMPNSLLEKAYKKPSIKERHRHRYEINPKYRQEWENKGLKVVGFGSNHLIEAIELEDHPFFVGVQFHPEFTSRLQSPNPIILDFIKSALSKS
>NC_018939.1|WP_000829924.1|358331_359000_+|hypothetical-protein
MAENSFKNVSTQPKVFFLLPAKTLFLLGGVFSAFFILIAGLVFFDYAHLMDNAIFNFARSTPFNSSPILTLILQNIANLGSSQFVLPLSLLVGVFLSLYRRNLVLGVWFVLSVILFEALLESLKHLFAYSIQWLSRSANFPNATALSLVLFYGLLILLIPHLITHQTLKNVLFYSLFGLIFLIGLALIVLGVSFSSVLGGFCLGALGACFSIGIYLSVFQKI

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Crispr_ID: NC_018939_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018939_2

556183-556470

Orphan

Consensus_repeat	Method
CTTCCTCTAAAAGTTTTCTCGCTTCAGGCGTGAGTAATTTCTCGCATTCTTTTTTCTCTTTTT	PILER-CR

2 spacers

The CRISPR arrays of NC_018939_2

>merge|NC_018939|2|556183-556470|PILER-CR
CTAAAAATTTTCTCGCTTCAGGCGTGAGTAATTTCTCGCATTCTTTTTTCTCTTTTTCATTCCTAGCTCTTGATACGCAGTCCAAATAAGCCTTAATGCTTTTCTTAACTTCTTGCTCTAAGAGTTTTCTCGCTTCAGGCGTGAGTAGTTTCTCGCAAGCTCTCCTTTCTTCTTCATTTCTAGCTTGAGAGAGGCAGTCTTTATAAGCTTTAAGACTCTCTTTGGCTTCTTCTAAAAGTTTTTTCGCTTCAGGGGTGAGCAATTTCTCGCATTCTTTTTTCTCTTTTT

>NC_018939|2|1|556183-556470|PILER-CR
CTAAAAATTTTCTCGCTTCAGGCGTGAGTAATTTCTCGCATTCTTTTTTCTCTTTTTCATTCC	TAGCTCTTGATACGCAGTCCAAATAAGCCTTAATGCTTTTCTTAACTTCTTGCT
CTAAGAGTTTTCTCGCTTCAGGCGTGAGTAGTTTCTCGCAAGCTCTCCTTTCTTCTTCATTTC	TAGCTTGAGAGAGGCAGTCTTTATAAGCTTTAAGACTCTCTTTGGCTTCTTCTAAAAGTTTTTTCGCT
TCAGGGGTGAGCAATTTCTCGCATTCTTTTTTCTCTTTTT

Protein	Signature genes	Signature genes Name	Protein_function
NC_018939.1\|WP_015056047.1\|565082_565754_+\|cag-pathogenicity-island-protein-T	unknown	unknown	gnl\|CDD\|372486
NC_018939.1\|WP_001863356.1\|567964_568309_-\|cag-pathogenicity-island-protein-CagP	unknown	unknown	unknown
NC_018939.1\|WP_000040764.1\|543017_544349_+\|HslU--HslV-peptidase-ATPase-subunit	unknown	unknown	gnl\|CDD\|235364
NC_018939.1\|WP_000529349.1\|560013_561582_-\|type-IV-secretion-system-apparatus-protein-CagX	unknown	unknown	gnl\|CDD\|226035
NC_018939.1\|WP_000418809.1\|553478_554078_-\|cag-pathogenicity-island-translocation-protein-CagZ	unknown	unknown	gnl\|CDD\|72471
NC_018939.1\|WP_000879904.1\|568732_569863_+\|type-IV-secretion-system-apparatus-protein-CagM	unknown	unknown	unknown
NC_018939.1\|WP_000900785.1\|563246_564005_-\|cag-pathogenicity-island-type-IV-secretion-system-protein-CagV	unknown	unknown	gnl\|CDD\|226259
NC_018939.1\|WP_000389328.1\|550226_552473_-\|cag-pathogenicity-island-type-IV-secretion-system-protein-Cag5	unknown	unknown	gnl\|CDD\|226036
NC_018939.1\|WP_000462193.1\|549598_550108_+\|cag-pathogenicity-island-peptidoglycan-hydrolase-Cag4	unknown	unknown	gnl\|CDD\|374577
NC_018939.1\|WP_000757130.1\|545250_546243_+\|flagellin-deglycosylation-protein	unknown	unknown	gnl\|CDD\|225577
NC_018939.1\|WP_000481884.1\|561634_563242_-\|cag-pathogenicity-island-translocation-protein-CagW	unknown	unknown	unknown
NC_018939.1\|WP_000133885.1\|552481_553474_-\|cag-pathogenicity-island-type-IV-secretion-system-ATPase	unknown	unknown	gnl\|CDD\|274301
NC_018939.1\|WP_000978372.1\|544345_545254_+\|GTPase-Era	unknown	unknown	gnl\|CDD\|224081
NC_018939.1\|WP_000471692.1\|546331_547162_-\|HP0519-family-Sel1-like-repeat-protein	unknown	unknown	gnl\|CDD\|223861
NC_018939.1\|WP_154079849.1\|565775_565925_+\|hypothetical-protein	unknown	unknown	unknown
NC_018939.1\|WP_000785752.1\|547337_547685_+\|cag-pathogenicity-island-protein-Cag1	unknown	unknown	unknown
NC_018939.1\|WP_000938081.1\|567151_567532_-\|cag-pathogenicity-island-type-IV-secretion-system-protein-CagQ	unknown	unknown	unknown
NC_018939.1\|WP_000488766.1\|548143_549589_+\|type-IV-secretion-system-apparatus-protein-Cag3	unknown	unknown	unknown
NC_018939.1\|WP_000069596.1\|566135_566726_-\|cag-pathogenicity-island-protein-CagS	unknown	unknown	gnl\|CDD\|374741
NC_018939.1\|WP_001000423.1\|564390_565047_+\|cag-pathogenicity-island-translocation-protein-CagU	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NC_018939.1\|WP_000040764.1\|543017_544349_+\|HslU--HslV-peptidase-ATPase-subunit	gnl\|CDD\|235364	PRK05201, hslU, ATP-dependent protease ATPase subunit HslU.	0
NC_018939.1\|WP_000529349.1\|560013_561582_-\|type-IV-secretion-system-apparatus-protein-CagX	gnl\|CDD\|226035	COG3504, VirB9, Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion].	8.26684e-63
NC_018939.1\|WP_000418809.1\|553478_554078_-\|cag-pathogenicity-island-translocation-protein-CagZ	gnl\|CDD\|72471	pfam09053, CagZ, CagZ. CagZ is a 23 kDa protein consisting of a single compact L-shaped domain, composed of seven alpha-helices that run antiparallel to each other. 70% of the residues are in alpha-helix conformation and no beta-sheet is present. CagZ is essential for the translocation of the pathogenic protein CagA into host cells.	2.69445e-123
NC_018939.1\|WP_000389328.1\|550226_552473_-\|cag-pathogenicity-island-type-IV-secretion-system-protein-Cag5	gnl\|CDD\|226036	COG3505, VirD4, Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion].	0
NC_018939.1\|WP_000462193.1\|549598_550108_+\|cag-pathogenicity-island-peptidoglycan-hydrolase-Cag4	gnl\|CDD\|374577	pfam16494, Na_Ca_ex_C, C-terminal extension of sodium/calcium exchanger domain. Na_Ca_ex_C is a region of the higher eukaryote sodium/calcium exchanger domain that extends toward the C-terminal, and is cytoplasmic.	0.00432887
NC_018939.1\|WP_000757130.1\|545250_546243_+\|flagellin-deglycosylation-protein	gnl\|CDD\|225577	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown].	3.97147e-110
NC_018939.1\|WP_000900785.1\|563246_564005_-\|cag-pathogenicity-island-type-IV-secretion-system-protein-CagV	gnl\|CDD\|226259	COG3736, VirB8, Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion].	1.18232e-71
NC_018939.1\|WP_000133885.1\|552481_553474_-\|cag-pathogenicity-island-type-IV-secretion-system-ATPase	gnl\|CDD\|274301	TIGR02788, conjugal_transfer_protein, P-type DNA transfer ATPase VirB11. The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.	2.07028e-143
NC_018939.1\|WP_015056047.1\|565082_565754_+\|cag-pathogenicity-island-protein-T	gnl\|CDD\|372486	pfam13117, Cag12, Cag pathogenicity island protein Cag12. This is a Proteobacterial family of Cag pathogenicity island proteins.	2.03741e-27
NC_018939.1\|WP_000471692.1\|546331_547162_-\|HP0519-family-Sel1-like-repeat-protein	gnl\|CDD\|223861	COG0790, COG0790, FOG: TPR repeat, SEL1 subfamily [General function prediction only].	2.80522e-23
NC_018939.1\|WP_000978372.1\|544345_545254_+\|GTPase-Era	gnl\|CDD\|224081	COG1159, Era, GTPase [General function prediction only].	4.50752e-124
NC_018939.1\|WP_000069596.1\|566135_566726_-\|cag-pathogenicity-island-protein-CagS	gnl\|CDD\|374741	pfam16707, CagS, Cag pathogenicity island protein S of Helicobacter pylori. CagS is a family of proteins from the pathogenicity island of Helicobacter pylori. The gene lies just downstream of the cluster whose protein-products resemble those of the Vibrio proteins that form the structural core of T4SS. The exact function of CagS is not known.	2.63479e-111

>NC_018939.1|WP_000418809.1|553478_554078_-|cag-pathogenicity-island-translocation-protein-CagZ
MELGFNEAERQKILDSNSSLMGNANEVRDKFIQNYASSLKDSNDPQDFLRRVQELRINMQKNFISFDVYYNYLNNLVLASYNRCKQEKTFAESTIKNELTLGEFVAEISDNFNNFMCDEVARISDLVASYLPREYLPPFIDGNMMGVAFQILGIDDFGRKLNEIVQDIGTKYIILSKNKTYLTSLERAKLITQLKLNLE
>NC_018939.1|WP_000133885.1|552481_553474_-|cag-pathogenicity-island-type-IV-secretion-system-ATPase
MTEDRLSAEDKKFLEVERALKEAALNPLRHATEELFGDFLKMENITEICYNGNKVVWVLKNNGEWQPFDVRDRKAFSLSRLMHFARCCASFKKKTIDNYENPILSSNLANGERVQIVLSPVTVNDETISISIRIPSKTTYPHSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELRSSEAYDFYNVLCSGHKGTLTTLHAGSSEEAFIRLANMSSSNSAARNIKFESLIEGFKDLIDMIVHINHHKQCDEFYIKHR
>NC_018939.1|WP_000389328.1|550226_552473_-|cag-pathogenicity-island-type-IV-secretion-system-protein-Cag5
MEDFLYNTLYFIEDYKLVVIFSFIGLIALFFLYKFIKAQKKAFKDKANQPQKKKSFKEIIIDGLKERVKTFGFWLQAILLLSYSFITSGLFFLILLGNFYDDNRSPESDDDLFDIWIYAIQDFPNYYFKALGFSSLKIYGFNISLVVYGSILCSYIFITFFVWFLKYLTRTRDIGANKKVDDLFGSASWETEEKMIKAKLITPNNKKRAFDKREVIVGRRGLGDFIAYAGQAFIGLIAPTRSGKGVGFIMPNMINYPQNIVVFDPKADTMETCGKIREKRFNQKVFIYEPFSLKTHRFNPFAYVDFGNDVVLTEDILSQIDTRLKGHGMVASGGDFSTQIFGLAKLVFPERPNEKDPFFSNQARNLFVINCNIYRDLMWTKKGLEFVKRKKIIMPETPTMFFIGSMASGINLIDEDTNMEKVVSLMEFFGGEEDKSGDNLRVLSPATRNMWNSFKTMGGARETYSSVQGVYTSAFAPYNNAMIRNFTSANDFDFRRLRIDEVSIGVIANPKESTIVGPILELFFNVMIYSNLILPIHDPQCKRSCLMLMDEFTLCGYLETFVKAVGIMAEYNMRPAFVFQSKAQLENDPPLGYGRNGAKTILDNLSLNMYYGINNDNYYEHFEKLSKVLGKYTRQDVSRSIDDNTGKTNTSISNKERFLMTPDELMTMGDELIILENTLKPIKCHKALYYDDPFFTDELIKVSPSLSKKYKLGKVPNQATFYDDLQAAKTRGELSYDKSLVPVGSSEL
>NC_018939.1|WP_000462193.1|549598_550108_+|cag-pathogenicity-island-peptidoglycan-hydrolase-Cag4
MFEKWIGLTLLLNSLAYPCQKVTISFKQYENLLHIHQKGCDNEVMCRTLISIALLESSLGLNNRREKSLKDTSYSMFHITLNTAKKFYPTYSKTLLKFKLLNDVGFAIQLAKQILKENFDYYKQKHPNKSVYQLVEMAIGAYNGGMKHNPNGAYVKKFRCIYSQVRYNE
>NC_018939.1|WP_000488766.1|548143_549589_+|type-IV-secretion-system-apparatus-protein-Cag3
MFRKLATAVSLIGLLTSNTLYAKEISEADKVIKATKETKETKKEAKRLKKEAKQRQQIPDHKKPQYVSVDDTKTQALFDIYDTLNVNDKSFGDWFGNSALKDKTYLYAMDLLDYNNYLSIENPIIKTRAMGTYADLIIITGSLEQVNGYYNILKALNKRNAKFVLKINENMPYAQATFLRVPKRSDPNAHTLDKGASIDENKLFEQQKKMYFNYANDVICRPDDEVCSPLRDEMVAMPTSDSVTQKPNIIAPYSLYRLKETNNANEAQPSPYATQTAPENSKEKLIEELIANSQLVANEEEREKKLLAEKEKQEAELAKYKLKDLENQKKLKALEAELKKKNAKKPRVVEVPVSPQTSNSDETMRVVKEKENYNGLLVDKETTIKRSYEGTLISENSYSKKTPLNPNDLRSLEEEIKSYYIKSNGLCYTNGINLYVKIKNDPYKEGMLCGYESVQNLLSPLKDKLKYDKQKLQKALLKDSK
>NC_018939.1|WP_000785752.1|547337_547685_+|cag-pathogenicity-island-protein-Cag1
MADTINTTEATHETKKPNAFVNFFKNNLTDKRYDSLGLIGAGVLCCVLSGAMGIVGIIFVAIGIFLSFSNINLVKLVEKLSKKQSKVPTTVNNETQKSQATSVTNEPTEAKETKD
>NC_018939.1|WP_000471692.1|546331_547162_-|HP0519-family-Sel1-like-repeat-protein
MFKDFYRTTLSFLKPLLLLLVLLLPFSLCIADEYISISDDWDEIVRNHKTYYFENGLDHFNQGQYQQAFKDFRLAQEYSIGLGSVYLAKMYLEGKGVKVDYKKAQFYAENAIKGYGSGLLGGALILGRMQAEGLGMKKDLKQALKTYRHVVRMFSNKSTNFANNFRLPNLAEFTSMLIGSRFIDLSGLSANPIKFGKKFGILVKKSTQIKDKTLLWEDIAEISSNITLLKQQMGEILYRIGIAYKEGLGTRKKKDRAKKFLQKSAEFGYEKAMEAL
>NC_018939.1|WP_000757130.1|545250_546243_+|flagellin-deglycosylation-protein
MKKVLPALLMGFVGLNASDRLLEIMRLYQKQGLEMVGQKLDSYLADKSFWAEELQNKDTDFGYYQNKQFLFVANKSKPSLEFYEIENNMLKKINSSKALVGSKKGDKTLEGDLATPIGVYRITQKLERLDQYYGVLAFVTNYPNLYDTLKKRTGHGIWVHGMPLNGDRNELNTKGCIAIENPLLSSYDKVLKGEKAFLITYEDKFFPSTKEELSMILSSLFQWKEAWARGDFERYMRFYNPNFTRYDGMKFNAFKEYKKRVFAKNEKKNIAFSSINVIPYPNSQNKRLFYVVFDQDYKAYQHNKLSYSSNSQKELYIEIENNQVSIIMEK
>NC_018939.1|WP_000978372.1|544345_545254_+|GTPase-Era
MMKTKAGFVALIGKPNAGKSTLLNTLLNAHLALVSHKANATRKLMKCIVPFKDKEWYESQIIFLDTPGLHHQEKLLNQCMLSQALKAMGDAELCVFLASVHDDLKGYEEFLSLCQKPHILALSKIDTATHKQVLQKLQEYQQYDSQFLALVPLSAKKSQNLNALLECISQHLSPSAWLFEKDLMSDEKMRDIYKEIIRESLFDFLSDEIPYESDVMIDKFIEEERIDKVYARIIVEKESQKKIVIGKNGVNIKRIGTNARLKMQEVGEKKVFLNLQVIAQKSWSKEEKSLQKLGYIHRRNRD
>NC_018939.1|WP_000040764.1|543017_544349_+|HslU--HslV-peptidase-ATPase-subunit
MSKLNMTPREIVAYLDEYIIGQKEAKKSIAIAFRNRYRRLQLEKSLQEEITPKNILMIGSTGVGKTEIARRIAKIMELPFVKVEASKYTEVGFVGRDVESMVRDLVNNSVLLVENEHKEKLKDKIEEAVIEKIAKKLLPPLPNGVSEEKKQEYANSLLKMQQRIAQGELDSREIEIEVRKKSIEIDSNVPPEILRVQENLIKVFHKEQDKVKKTLSVKEAKEALKAEISDTLLDSEAIKMEGLKRAESSGVIFIDEIDKIAVSSKEGSRQDPSKEGVQRDLLPIVEGSVVNTKYGSIKTEHILFIAAGAFHLSKPSDLIPELQGRFPLRVELENLTEEIMYMILTQTKTSIIKQYQALLKVEGVEIAFEDDAIKELAKLSYNANQKSEDIGARRLHTTIEKVLEDISFEAEDYSGQNVTITKELVQSKLEDLVADENLVKYIL
>NC_018939.1|WP_000529349.1|560013_561582_-|type-IV-secretion-system-apparatus-protein-CagX
MGQAFFKKIVGCFCLGYLFLSSAIEAAALDIKNFNRGRVKVVNKKIAYLGDEKPITIWTSLDNVTVIQLEKDETISYITTGFNKGWSIVPNSNHIFIQPKSVKSNLMFEKEAVNFALMTRDYQEFLKTKKLIVDAPDPKELEEQKKALEKEKEAKEQAQKAQKDKREKRKEERAKNRANLENLTNAMSNPQNLSNNKNLSEFIKQQRENELDQMERLEDMQEQAQANALKQIEELNKKQAEETIKQRAKDKINIKTDKPQKSPEDNSIELSPSDSAWRTNLVVRTNKALYQFILRIAQKDNFASAYLTVKLEYPQRHEVSSVIEEELKKREEAKRQKELIKQENLNTTAYINRVMMASNEQIINKEKIREEKQKIILDQAKALETQYVHNALKRNPVPRNYNYYQAPEKRSKHIMPSEIFDDGTFTYFGFKNITLQPAIFVVQPDGKLSMTDAAIDPNMTNSGLRWYRVNEIAEKFKLIKDKALVTVINKGYGKNPLTKNYNIKNYGELERVIKKLPLVRDK
>NC_018939.1|WP_000481884.1|561634_563242_-|cag-pathogenicity-island-translocation-protein-CagW
MFNIKRNFLITIISFFLIVPNWLKAIDLPIVSNLKIYQTVYCMLIPSYVLTNKSFADILTGYTSIGASGSGKSSGQGVIEALSTPLATSLAASNLVKYLNTLGPLWGSAWASVATAIQGFALTPSSGCNFGWNALINKNIDVSMDSVLDNLSNKIQNFTKGGVEDNVKGNILLQIIGSITAQASTNITADGLIWLIGKEFTANKLQNNTTAMLAFAALESVVKGADAAVLPAYGVVNLPDIIIGQGSYLDFVSYLIYIVFGIFVFISFMKLRDISSNIQINIGFEYMRFVGGTLFKMAMVSFIAYAGFGYLYKISYSIYFGLAGAFGLNQVLFWALDLVLNYTVNSILPAVRAVFSNVGNNAPSLLQGLQVAGISLFAIFMQVTIIMRISTVVVKPLIAGAFSGIVFPIAVSLIVLDWFKDSMKNILIWFINNLFILVLAIPILLFGVLALLAFNLTITPSVAIQNINQGGLGIDSTIASLITLFILKGFIETIIESVNAIVNTIFSSVSMDGSRMDRERDALMVGRVGGSMFKG
>NC_018939.1|WP_000900785.1|563246_564005_-|cag-pathogenicity-island-type-IV-secretion-system-protein-CagV
MLGKKNEEVLIDENLVGGVIALDRLAKLNKANRTFKRAFYLSMALNVAAVTSIVMMMPLKKTDIFVYGIDRYTGEFKIVKRSDARQIVNSEAVVDSATSKFVSLLFGYSKNSLRDRKDQLMQYCDVSFQTQAMRMFNENIRQFVDKVRAEAIISSNIQREKVKNSPLTRLTFFITIKITPDTMENYEYITKKQVTIYYDFARGNSSQENLIINPFGFKVFDIQITDLQNEQTVSEILRKIREVESKNKALNK
>NC_018939.1|WP_001000423.1|564390_565047_+|cag-pathogenicity-island-translocation-protein-CagU
MNDTTEHHGPNPLNAPPPSNSQSNDLLNLLDSLYPKGSLGEQRFHEALKNQEELKNILIEIEKLPQEKRYELLMQIGQAKQRIMEAYAHSFLGYIGGLEHLLGLCMGGIFVLFAIYFVFLRTSKNMELVESLKTKLKLQYFYYAFGVGAVLFFGLETIRSIYELYILGIGSTNDKVLFVLKNICFIGMGYLIYKVIKVIGIKNFINGLFTSKKQGGAE
>NC_018939.1|WP_015056047.1|565082_565754_+|cag-pathogenicity-island-protein-T
MKLRASVLIGATILCLILSACSNYAKKVVKQKNHVYTPVYNELIEKYSEIPLNDKLKDTPFMVQVKLPNYKDYLLDNKQVVLTFKLVHHSKKITLIGDANKILQYKNYFQANGARSDIDFYLQPTLNQKGVVMIASNYNDNPNSKEKPQTFDVLQGSQPMLGANTKNLHGYDVSGANNKQVINEVAREKAQLEKINQYYKTLLQDKEQEYTTRKNNQREILET
>NC_018939.1|WP_154079849.1|565775_565925_+|hypothetical-protein
MRQNVISSEIFKNGNLNMQAKEEEVREKLQEERENEYLRNQIRSLLSGK
>NC_018939.1|WP_000069596.1|566135_566726_-|cag-pathogenicity-island-protein-CagS
MSNNMRKLFSMIADSKDKKEKLIESLQENELLSTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIMFKMSIREMDSQIELYGTKLPLLKLFVMTDEEMNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKGV
>NC_018939.1|WP_000938081.1|567151_567532_-|cag-pathogenicity-island-type-IV-secretion-system-protein-CagQ
MLPTKTRIRDPNKQELTQPKIKGLIMGKILASLLGGGTNLFTGLSSDLFSMILNFLFFLMLMMGLNEILGKKFNLPMDNIKNFMAEVLKNGFDSIKNMGSALVGNGFGSNKSDKTTNKMSVSQVRL
>NC_018939.1|WP_001863356.1|567964_568309_-|cag-pathogenicity-island-protein-CagP
MKRPISKLKQNFLQFKHSFNKHLDKYSLYYRLFNISSIVIGFLVALFSYGAGVILVYPILFLFALIIKPSFFYYTTYLLLLVSLSIISKYYLLSHANFTMKLIILMTQWQNWFL
>NC_018939.1|WP_000879904.1|568732_569863_+|type-IV-secretion-system-apparatus-protein-CagM
MLAKIVFSSLVAFGVLSANVEQFGSFFNEIKKEQEEVAAKEDALKARKKLLNNTHDFLEDLIFRKQKIKELMDHRAKVLSDLENKYKKEKEALEKETRGKILTAKSKAYGDLEQALKDNPLYRKLLPNPYAYVLNQETFTKEDRERLSYYYPQVKTSSIFKKTTATTKDKAQALLQMGVFSLDEEQNKKASRLALSYKQAIEEYSNNVSNLLSRKELDNIDYYLQLERNKFDSKAKDIAQKATNTLIFNSERLAFSMAIDKINEKYLRGYEAFSNLLKNVKDDVELNTLTKNFTNQKLSFAQKQKLCLLVLDSFNFDTQSKKSILKKTNEYNIFVDSDPMMSDKTTMQKEHYKIFNFFKTVVSAYRNNVAKNNPFE

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Crispr_ID: NC_018939_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018939_3

980289-980430

Orphan

I-B

Consensus_repeat	Method
TTCAATCAAGGGACTTATAACTTTAATAGCA	PILER-CR

2 spacers

The CRISPR arrays of NC_018939_3

>merge|NC_018939|3|980289-980430|PILER-CR
TTCAATCAAGGGACTTATAACTTTAATAGCACTCAATCTGCTTTTAATAACAGCGCTTTCAATCAAGGGACTTATCATTTCAATGGCAACGCCAGCTTTGATAACGACACCTTCAATCAAGGCACTTATAGCTTTAATACCA

>NC_018939|3|2|980289-980430|PILER-CR
TTCAATCAAGGGACTTATAACTTTAATAGCA	CTCAATCTGCTTTTAATAACAGCGCT
TTCAATCAAGGGACTTATCATTTCAATGGCA	ACGCCAGCTTTGATAACGACACC
TTCAATCAAGGCACTTATAGCTTTAATACCA

Protein	Signature genes	Signature genes Name	Protein_function
NC_018939.1\|WP_001863228.1\|971041_972730_-\|TonB-dependent-receptor	unknown	unknown	gnl\|CDD\|366183
NC_018939.1\|WP_000722451.1\|992726_993530_+\|5'/3'-nucleotidase-SurE	unknown	unknown	gnl\|CDD\|234732
NC_018939.1\|WP_000592437.1\|965190_966738_+\|Hop-family-adhesin-AlpA	unknown	unknown	gnl\|CDD\|280099
NC_018939.1\|WP_000812546.1\|966759_968349_+\|Hop-family-adhesin-AlpB	unknown	unknown	gnl\|CDD\|280099
NC_018939.1\|WP_001240277.1\|977530_978223_-\|Bax-inhibitor-1/YccA-family-protein	unknown	unknown	gnl\|CDD\|198414
NC_018939.1\|WP_001248496.1\|969251_970796_-\|outer-membrane-beta-barrel-protein-HofG	unknown	unknown	gnl\|CDD\|334957
NC_018939.1\|WP_000098051.1\|991818_992730_+\|polyprenyl-synthetase-family-protein	unknown	unknown	gnl\|CDD\|223220
NC_018939.1\|WP_000427004.1\|991260_991803_+\|GTP-cyclohydrolase-I-FolE	unknown	unknown	gnl\|CDD\|129173
NC_018939.1\|WP_001052415.1\|989195_990341_+\|tRNA-pseudouridine(13)-synthase-TruD	unknown	unknown	gnl\|CDD\|272903
NC_018939.1\|WP_001126584.1\|974174_977432_-\|carbamoyl-phosphate-synthase-large-subunit	unknown	unknown	gnl\|CDD\|235393
NC_018939.1\|WP_000688567.1\|978366_979365_+\|type-I-glyceraldehyde-3-phosphate-dehydrogenase	unknown	unknown	gnl\|CDD\|273675
NC_018939.1\|WP_001863226.1\|972729_973479_-\|TonB-dependent-receptor-plug-domain-containing-protein	unknown	unknown	gnl\|CDD\|273808
NC_018939.1\|WP_000894570.1\|962644_964672_+\|ATP-dependent-helicase	unknown	unknown	gnl\|CDD\|223288
NC_018939.1\|WP_000775643.1\|994791_995547_+\|7-carboxy-7-deazaguanine-synthase-QueE	unknown	unknown	gnl\|CDD\|223675
NC_018939.1\|WP_000236875.1\|994186_994789_+\|6-carboxy-5,6,7,8-tetrahydropterin-synthase	unknown	unknown	gnl\|CDD\|223792
NC_018939.1\|WP_001229996.1\|973738_974170_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|376519
NC_018939.1\|WP_001115881.1\|988255_988462_-\|4-oxalocrotonate-tautomerase-family-protein	unknown	unknown	gnl\|CDD\|129125
NC_018939.1\|WP_010875563.1\|990279_991260_+\|zinc-metalloprotease-HtpX	unknown	unknown	gnl\|CDD\|235081
NC_018939.1\|WP_001099619.1\|988617_989199_+\|recombination-protein-RecR	unknown	unknown	gnl\|CDD\|273176
NC_018939.1\|WP_001160353.1\|987086_988196_+\|Hop-family-outer-membrane-protein-HopJ/HopK	unknown	unknown	gnl\|CDD\|280099

Protein	Function_ID	Function_description	E-value
NC_018939.1\|WP_001863228.1\|971041_972730_-\|TonB-dependent-receptor	gnl\|CDD\|366183	pfam00593, TonB_dep_Rec, TonB dependent receptor. This model now only covers the conserved part of the barrel structure.	1.01149e-24
NC_018939.1\|WP_000722451.1\|992726_993530_+\|5'/3'-nucleotidase-SurE	gnl\|CDD\|234732	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional.	2.33034e-125
NC_018939.1\|WP_000592437.1\|965190_966738_+\|Hop-family-adhesin-AlpA	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	1.25518e-54
NC_018939.1\|WP_000812546.1\|966759_968349_+\|Hop-family-adhesin-AlpB	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	2.08243e-53
NC_018939.1\|WP_001240277.1\|977530_978223_-\|Bax-inhibitor-1/YccA-family-protein	gnl\|CDD\|198414	cd10432, BI-1-like_bacterial, Bacterial BAX inhibitor (BI)-1/YccA-like proteins. This family is comprised of bacterial relatives of the mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. In plants, BI-1 like proteins play a role in pathogen resistance. A characterized prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes.	3.70513e-52
NC_018939.1\|WP_001248496.1\|969251_970796_-\|outer-membrane-beta-barrel-protein-HofG	gnl\|CDD\|334957	pfam02521, HP_OMP_2, Putative outer membrane protein. This family consists of putative outer membrane proteins from Helicobacter pylori (campylobacter pylori).	2.48666e-179
NC_018939.1\|WP_000098051.1\|991818_992730_+\|polyprenyl-synthetase-family-protein	gnl\|CDD\|223220	COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism].	1.02024e-75
NC_018939.1\|WP_000427004.1\|991260_991803_+\|GTP-cyclohydrolase-I-FolE	gnl\|CDD\|129173	TIGR00063, GTP_cyclohydrolase_1, GTP cyclohydrolase I. alternate names: Punch (Drosophila),GTP cyclohydrolase I (EC 3.5.4.16) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid].	2.83851e-108
NC_018939.1\|WP_001052415.1\|989195_990341_+\|tRNA-pseudouridine(13)-synthase-TruD	gnl\|CDD\|272903	TIGR00094, tRNA_pseudouridine_synthase_D, tRNA pseudouridine synthase, TruD family. an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. [Protein synthesis, tRNA and rRNA base modification].	3.64837e-148
NC_018939.1\|WP_001126584.1\|974174_977432_-\|carbamoyl-phosphate-synthase-large-subunit	gnl\|CDD\|235393	PRK05294, carB, carbamoyl-phosphate synthase large subunit.	0
NC_018939.1\|WP_000688567.1\|978366_979365_+\|type-I-glyceraldehyde-3-phosphate-dehydrogenase	gnl\|CDD\|273675	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I. This model represents glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In some species, NAD- and NADP- utilizing forms exist, generally being responsible for reactions in the anabolic and catabolic directions respectively. Two Pfam models cover the two functional domains of this protein; pfam00044 represents the N-terminal NAD(P)-binding domain and pfam02800 represents the C-terminal catalytic domain. An additional form of gap gene is found in gamma proteobacteria and is responsible for the conversion of erythrose-4-phosphate (E4P) to 4-phospho-erythronate in the biosynthesis of pyridoxine. This pathway of pyridoxine biosynthesis appears to be limited, however, to a relatively small number of bacterial species although it is prevalent among the gamma-proteobacteria. This enzyme is described by TIGR001532. These sequences generally score between trusted and noise to this GAPDH model due to the close evolutionary relationship. There exists the possiblity that some forms of GAPDH may be bifunctional and act on E4P in species which make pyridoxine and via hydroxythreonine and lack a separate E4PDH enzyme (for instance, the GAPDH from Bacillus stearothermophilus has been shown to posess a limited E4PD activity as well as a robust GAPDH activity). There are a great number of sequences in the databases which score between trusted and noise to this model, nearly all of them due to fragmentary sequences. It seems that study of this gene has been carried out in many species utilizing PCR probes which exclude the extreme ends of the consenses used to define this model. The noise level is set relative not to E4PD, but the next closest outliers, the class II GAPDH's (found in archaea, TIGR01546) and aspartate semialdehyde dehydrogenase (ASADH, TIGR01296) both of which have highest-scoring hits around -225 to the prior model. [Energy metabolism, Glycolysis/gluconeogenesis].	2.18883e-164
NC_018939.1\|WP_001863226.1\|972729_973479_-\|TonB-dependent-receptor-plug-domain-containing-protein	gnl\|CDD\|273808	TIGR01786, hemoglobin-haptoglobin-binding_protein, TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein. This model represents a family of TonB-dependent outer membrane receptor/transporters acting on iron-containing proteins such as hemoglobin, transferrin and lactoferrin. Two subfamily models with a narrower scope are contained within this model, the heme/hemoglobin receptor family protein model (TIGR01785) and the transferrin/lactoferrin receptor family model (TIGR01776). Accessions which score above trusted to this model while not scoring above trusted to the more specific models are most likely to be hemoglobin transporters. Nearly all of the species containing trusted hits to this model have access to hemoglobin, transferrin or lactoferrin or related proteins in their biological niche. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins].	9.11385e-28
NC_018939.1\|WP_000894570.1\|962644_964672_+\|ATP-dependent-helicase	gnl\|CDD\|223288	COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair].	5.599e-138
NC_018939.1\|WP_000775643.1\|994791_995547_+\|7-carboxy-7-deazaguanine-synthase-QueE	gnl\|CDD\|223675	COG0602, NrdG, Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones].	3.72098e-47
NC_018939.1\|WP_000236875.1\|994186_994789_+\|6-carboxy-5,6,7,8-tetrahydropterin-synthase	gnl\|CDD\|223792	COG0720, COG0720, 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism].	3.80774e-22
NC_018939.1\|WP_001229996.1\|973738_974170_-\|hypothetical-protein	gnl\|CDD\|376519	pfam01300, Sua5_yciO_yrdC, Telomere recombination. This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast.	9.94839e-05
NC_018939.1\|WP_001115881.1\|988255_988462_-\|4-oxalocrotonate-tautomerase-family-protein	gnl\|CDD\|129125	TIGR00013, Probable_tautomerase_K2, 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function. [Energy metabolism, Other].	2.46126e-26
NC_018939.1\|WP_010875563.1\|990279_991260_+\|zinc-metalloprotease-HtpX	gnl\|CDD\|235081	PRK02870, PRK02870, heat shock protein HtpX; Provisional.	0
NC_018939.1\|WP_001099619.1\|988617_989199_+\|recombination-protein-RecR	gnl\|CDD\|273176	TIGR00615, Recombination_protein_RecR, recombination protein RecR. All proteins in this family for which functions are known are involved in the initiation of recombination and recombinational repair. RecF is also required. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair].	1.88416e-98
NC_018939.1\|WP_001160353.1\|987086_988196_+\|Hop-family-outer-membrane-protein-HopJ/HopK	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	9.56908e-49

>NC_018939.1|WP_000688567.1|978366_979365_+|type-I-glyceraldehyde-3-phosphate-dehydrogenase
MKIFINGFGRIGRCVLRAILERNDTNPKLEVIGINDPANWEILAYLLEHDSVHGLLPKEVRYSNYKLIIGSLEIPVFNSIKDLKGVDVIIECSGKFLEPKTLENYLLLGAKKVLLSAPFMGEYDEKQYPTLVYGVNHFCYQNQAIVSNASCTTNAIAPICAILDKAFKIKEGMLTTIHSYTSDQKLIDLAHPLDKRRSRAAASNIIPTTTKAALALHKVLPNLKNKMHGHSVRVPSLDVSMIDLSLFLEKKAPKDPINDLLIEASKGVLKGVLEIDLKERVSSDFISNPHSVIIAPDLTFTLENMVKIMGWYDNEWGYSNRLVDMAQFMYHY
>NC_018939.1|WP_001240277.1|977530_978223_-|Bax-inhibitor-1/YccA-family-protein
MALYDRANSRNAYAEDSLLRESELVSFVKTTYKFFAGSLLLATIGALLGLMNFQAVVQYKWVFFIAEIAAFFGLMFSKSKPGLNLFMLFAFTSLSGVTLVPLLGMVIAKAGLGAIWQALGMTTIVFGLMSVYALKTKNDLANMGKMLFIALIVVVVCSLINLFLGSPMFQVVIAGASAILFSLYIAYDTQNIVKGMYDSPIDAAVSLYLDFLNVFISILQIIGIFSDRDT
>NC_018939.1|WP_001126584.1|974174_977432_-|carbamoyl-phosphate-synthase-large-subunit
MPKRTDISNILLIGSGPIVIGQACEFDYSGTQSCKTLKSLGYRVILINSNPATVMTDPEFSHQTYIQPITPENIATIIEKEKIDAILPTMGGQTALNAVMQMHQKGMLEGVELLGAKIEAIKKGEDRQAFKEAMLKIGMDLPKGRYAYTELEALEAINEIGFPAIIRASFTLAGGGSGVAYNIEEFQELAKNALDASPINEILIEESLLGWKEYEMEVIRDSKDNCIIVCCIENIDPMGVHTGDSITIAPSLTLTDKEYQRMRDASFAILREIGVDTGGSNVQFAIHPETLRMVVIEMNPRVSRSSALASKATGFPIAKVATMLAVGFSLDEIQNDITNTPASFEPSLDYIVVKIPRFAFEKFAGVSSTLGTSMKSIGEVMAIGGNFLEALQKALCSLENNWLGFESLSKDLEAIKKEIRRPNPKRLLYIADAFRLGVCVDEVFELCQIDRWFLSQIQKLVEVEESINSSVLTDAKKLRGLKNLGFSDARIAAKIKENENLEVSPFEVELARSNLQIVPNFEEVDTCAAEFLSLTPYLYSTYAPNPLPPIENKQEKKEKKILIIGSGPNRIGQGIEFDYCCVHASLALKDLNIKSVMFNCNPETVSTDYDTSDTLYFEPIHFECVKSIIQRERVDGIIVHFGGQTPLKLAKDLAKMQAPIIGTPFKVIDIAEDREKFSLFLKELDIKQPKNGMAKSVDEAYSIANVIGFPIIVRPSYVLGGQHMQILENIEELRHYLESVTHALEISPKNPLLIDKFLEKAVELDVDAICDKKEVYIAGILQHIEEAGIHSGDSACFIPSTLSPEILDEIERVSAKIALHLGVVGLLNIQFAVHQNSLYLIEVNPRASRTVPFLSKALGVPLAKVATRVMVLEDLKEALKFYDKKNIVGYSKGVYKPKMPHFVALKEAVFPFNKLYGSDLILGPEMKSTGEVMGIARSLGLAFFKAQTACFNPIKNKGLIFVSIKDKDKEEACVLMKRLVQLGFELCATEGTHKALEKAGVKSLKVLKISEGRPNIMDLMMNGEISMAINTSDHKSQDDAKLIRASVLKNHVSYFTTLSTIEVLLLALEESSKEDELLALQDYLK
>NC_018939.1|WP_001229996.1|973738_974170_-|hypothetical-protein
MALVYLVQSDTTIGLLSKDSEKLNALKGRPKNQSVLIESADFSTLKSLVRAPNAFKNLIRRSAKTTFIYPNSKAVRVIRGRHGDFLNRFKTLYSTSANLTQCAYDKEIASNLADVIVSDERGLFESSSSKIFRLYKDKKVRIR
>NC_018939.1|WP_001863226.1|972729_973479_-|TonB-dependent-receptor-plug-domain-containing-protein
MNDKRFRKYCSFSIFLSLLGTFELEAKEEEEKEERKTERKKEKNAQHTLGKVTTQAAKIFNYNNQTTISSKELERRQANQISDMFRRNPNINVGGGAVIAQKIYVRGIEDRLARVTVDGAAQMGASYGHQGNTIIDPGMLKSVVVTKGAAQASAGPMALIGAIKMETKSASDFIPKGKDYAISGAATFLTNFGDRETVMGAYRHNHFDALLYYTHQNIFYYRDGDNATKDLFRPKAENKVTEVLASKTM
>NC_018939.1|WP_001863228.1|971041_972730_-|TonB-dependent-receptor
MAKINGYLSERDILTLSYNMTRDNANRPLRANFTGTFLPYSCGDFNAFPNEKNPSDCLFENDASLFKTYSVNLVHNVSLNYEREGGSRFGDPKLKINGYTSIRNVQIDPLFKPNDIAASIPFTPNPKLGEENECVAQGGIYDALKQTCSITFKSLGGGSVVANKNLFIINSGFNANVIHTIDHKNDNLLEYGLNYQNLTTFDKAIPNSELVKPGDAPDACLRVTSPNDPNMNGRCQRNGATANVIGVYAQANYTLHPMVTLGAGTRYDVYTLVDKDWQLHITQGFSPSAALNVSPLENLNFRLSYAYVTRGPMPGGLVWMRQDNLRYNRNLKPEIGQNVEFNTEYSSQYFDFRAAGFVQLISNYINQFSSTLFVTNLPAQDIIYVPGYEVSGTAKYKGFSLGLSVARSWPSLKGRLIADVYELAATTGNVFILTASYKIPRTGLSITWLSRFVTDLSYCSYSPYRNGPTDIDRRPSNCPKTPGIFHVHKPGYGVSSFFVTYKPTYKKLKGLSLNAVFNNVFNQQYIDQASPVMSPDEPNQDKYARGMAEPGFNARFEISYKF
>NC_018939.1|WP_001248496.1|969251_970796_-|outer-membrane-beta-barrel-protein-HofG
MRQEKYFLTSSLSLLSFLLCPAEAFDYRFSGRVENFSKIGFNNSQINTKKGIYPTESFIDIVTLAQVKVNLLPKGTENHRLSVSLGGAIAAIPYDKTKYDINQANGKIFGSIVENFIGGYHGYFFNKYLGPAYAGTSQSASYHARPYVVDTAFLRYDYKDVFGFKAGRYEANIDFMSGSNQGWEVYYQPYKTETQRLRFWWWSSFGRGLAFNSWIYEFFATVPYLKKGGNPNNSNDFINYGWHGITTTYSYKGLDAQFFYYFAPKTYNAPGFKLVYDTNRNFQNVGFRSQSMIMTTFPLYYRGWYNPETNTYSLEDSTPHGSLLGRNGVTLNIRQVFWWDNFNWSIGFYNTFGNSDAFLGSHTMPRGNNTSYIGSEISITTRHAGMIGYDFWDNTAYDGLADAITNANTFTFYTSVGGIHKRFAWHVFGRVSHANKNALGQVGRANEYSLQFNASYAFTESILLNFRITYYGARINKGYQAGYFGAPKFNNPDGDFSANYQDRSYMMTNLTLKF
>NC_018939.1|WP_000812546.1|966759_968349_+|Hop-family-adhesin-AlpB
MKQNLKPFKMIKENLMTQSQKVRFLAPLSLALSLSFNPVGAEEDGGFMTFGYELGQVVQQVKNPGKIKAEELAGLLNSNTTNNTNTNIAGTGGNVAGTLGNLFMNQLGNLIDLYPILNTKNIHQCGTTNNGSSSATTAAATTNNGLCFQGNLDLYNEMVGSIKTLSQNISKNIFQGNNNTTSQNLSNQLSELNTASVYLTYMNSFLNANNQAGGIFQNNTNQAYGNGVTAQQIAYILKQASITMGPSGDSGAAAAFLDAALAQHVFNSANAGNDLSAKEFTSLVQNIVNNSQNALTLANNANISNSTGYQVSYGGHIDQARSTQLLNNTTNTLAKVTALNNELKANPWLGNFAAGNSSQVNAFNGFITKIGYKQFFGENKNVGLRYYGFFSYNGAGVGNGPTYNQVNLLTYGVGTDVLYNVFSRSFGSRSLNAGFFGGIQLAGDTYISTLRNSPQLANRPTATKFQFLFDVGLRMNFGILKKDLKSHNQHSIEIGVQIPTIYNTYYKAGGAEVKYFRPYSVYWVYGYAF
>NC_018939.1|WP_000592437.1|965190_966738_+|Hop-family-adhesin-AlpA
MIKKNRTLFLSLALCASISYAEDDGGFFTVGYQLGQVMQDVQNPGGAKSDELARELNADVTNNILNNNTGGNVAGALSNAFSQYLYSLLGAYPTKLNGNDVSANALLSGAVGSGTCAAAGTAGGSTLNTQSACTAAGYYWLPSLTDRILSTIGSQTNYGTNTNFPNMQQQLTYLNAGNVFFNAMNKALEAKNGSSGASGATGSDGQTYSTQAIQYLQRQQNILNNAANLLKQDELLLEAFNSAVAANIGNKEFNSAAFTGLVQGIIDQSQLVYNELTKNTISGSAVNGAEINSNQANAVQGRASQLPNALYNAQVTLDKINALNNQVRSMPYLPQFRAGNSRSTNILNGFYTKIGYKQFFGKKRNIGLRYYGFFSYNGASVGFRSTQNNVGLYTYGVGTDVLYNIFSRSYQNRSVDMGFFSGIQLAGETFQSTLRDDPNVKLHGKINNTHFQFLFDFGMRMNFGKLDGKSNRHNQHTVEFGVVVPTIYNTYYKSAGTTVKYFRPYSVYWSYGYSF
>NC_018939.1|WP_000894570.1|962644_964672_+|ATP-dependent-helicase
MLETLQLNPEQLKAAKALQGHNLIIASAGTGKTSTIVGRILYLLDNGIKPEEILLLTFTNKASNEMIARVAKYFKSSSKIEAGTFHAVAYRYLKEHYPNLSLKQPKELRKLLESIVDTKNAIDDDKKPYTSQHLYALYSLYTNALKQEDFSAWLSNKNPEHTPYAALYENILEEFENTKKKHNYIDYNDLLLLFKKAMLERPSPYKEVLCDEFQDTNPLQESILDAINPPSLFCVGDYDQSIYAFNGADISIISNFTQKYKNAQVFTLTKNYRSSKEILDLANQVIQHNERIYPKNLEVVKSGKFNKPTLLNYNDNIAQCQDIAKRIVMRKDFKEVAVIFRNNASADQLEAALRSYNVPSKRKGSASFFESKEVALALDICVLIFNPKDIMAAIHILSYISDIGSNTAKDIHEALMLLGNGDLKLALIQPNKEAKIYTKKKEITSMGLFEEIFALENSSRFNSVIDKAFHSHPVLMHPKISLNGAKTLSDFFTLYTKAPTHSPSALIKHILESAFFQTFKTRLLKERSKNKDGSYNEFKKLQAQKRFNEKMDLLSSLAKNYQNLGRFLNGTLIGSNEATQGCGVNLLSVHASKGLEFKDVYIIDLMEGRFPNHKLMNTGGGIEEERRLFYVAITRAKENLWLSYAKNELRENAKPKEHKPSVFLYEAGLLKPDSK
>NC_018939.1|WP_001160353.1|987086_988196_+|Hop-family-outer-membrane-protein-HopJ/HopK
MQFQKALLHSSFFLPLFLSFCIAEENGAYASVGFEYSISHAVEHNNPFLNQERIQIISNAQNKIYKLHQVKNEITSMPKTFAYINNALKNNSKLTPTEMQAEQYYLQSTFQNIEKIVMLSGGVSSNPQLVQALEKMQEPITNPLEFEENLRNLEVQFAQSQNRMLSSLSSQIAAISNSLNALDPNSYSKNISSMYGVSLSVGYKHFFTKKKNQGLRYYLFYDYGYTNFGFVGNGFDGLGKMNNHLYGLGIDYLYNFIDNAKKHSSVGFYLGFALAGSSWVGSGLSMWVSQTDFINNYLTGYQAKMHTSFFQIPLNFGVRVNVNRHNGFEMGLKIPLAMNSFYETHGKGLNTSLFFKRLVMFNVSYVYSF
>NC_018939.1|WP_001115881.1|988255_988462_-|4-oxalocrotonate-tautomerase-family-protein
MPFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQKN
>NC_018939.1|WP_001099619.1|988617_989199_+|recombination-protein-RecR
MNTYKNSLNHFLNLVDCLEKIPNVGKKSAFKMAYHLGLENPYLALKITHALENALENLKTCSSCNALSESEVCEICSDESRQNSQLCMVLHPRDVFILEDLKDFLGRYYVLNSIEEVDFNALEKRLIEENIKEIIFAFPPTLANDSLMLYIEDKLQHFHLTFTKIAQGVPTGVNFENIDSVSLSRAFNSRIKA
>NC_018939.1|WP_001052415.1|989195_990341_+|tRNA-pseudouridine(13)-synthase-TruD
MNLNFMPLLHAYNHASIDFHFNSSARDFCVHEVPLYEFSNTGEHAVIQVRKSGLSTLEMLQIFSQILGVRIAELGYAGLKDKNALTTQFISLPKKYAPLLEKNTSNFQEKNLKILSLNYHHNKIKLGHLKGNRFFMRFKKMTPLNAQKTKQVLEQIAQFGMPNYFGSQRFGKFNDNHQEGLKILQNQTKFAHQKLNAFLISSYQSYLFNALLSKRLEISKIISAFSVKENLEFFKQKNLSVDSDTLKTLKNQAHPFKILEGDVMCHYPYGKFFDALELEKEGERFLKKEVAPTGLLDGKKALYAKNLSLEIEKEFQHNLLSSHAKTLGSRRFFWVFVENVTSQYVKEKAQFELGFYLPKGSYASALLKEIKHEKGENNDEF
>NC_018939.1|WP_010875563.1|990279_991260_+|zinc-metalloprotease-HtpX
MRARCSKKSSMRKEKIMTNFEKIIAQNRIKTNAVLATYCVIFAFIGLLVDVIRINANDLGIALFKLMTFQIFPTITMIMFLVAFVVIVVCIQNFSSIMLSGDGYKLIDTSKVLSSKENQIHRLLLELLEEANLHFEPKLYIINAPYMNAFASGWNESNSLIALTSALIERLDRDELKAVIAHELSHIRHNDIRLTMCVGILSNIMLLVANFSVYFFMGNRKNSGANLARMILWVLQIILPFLTLLLQMYLSRTREYMADSGAAFLMHDNKPMIRALQKISNDYTNNDYKEIDKNSTRSAAYLFNAEMFSTHPSIKNRIQSLRKRVI
>NC_018939.1|WP_000427004.1|991260_991803_+|GTP-cyclohydrolase-I-FolE
MENFFNQFFESIGEDKNREGLKETPKRVQELWKFLYKGYKEDPRVALKSAYFQGVCDEMIVAQNIEFYSTCEHHLLPFLGNISVGYIPKEKIVGISAIAKLIEIYSRRLQIQERLTIQIAETFDEIIEPRGVIVVCEAKHLCMSMQGVQKQNAIIKTSVLRGLFKKDSKTRAEFMQLLKS
>NC_018939.1|WP_000098051.1|991818_992730_+|polyprenyl-synthetase-family-protein
MSSPNLSFYYNECERFESFLKNHHLHLESFHPYLEKAFFEMVLNGGKRFRPKLFLAVLCALVGQKDYSNQQTEYFKIALSIECLHTYSLIHDDLPCMDNAALRRNHPTLHAKYDETTAVLIGDALNTYSFELLSNALLESHIIVELIKILSANGGIKGMILGQALDCYFENTPLNLEQLTFLHEHKTAKLISASLIMGLVASGIKDEELFKWLQAFGLKMGLCFQVLDDIIDVTQDEEESGKTTHLDSAKNSFVNLLGLERANNYAQTLKTEVLNDLDALKPAYPLLQENLNALLNTLFKGKT
>NC_018939.1|WP_000722451.1|992726_993530_+|5'/3'-nucleotidase-SurE
MKKILLTNDDGYHAKGIKALEQALEEMAEIYVVAPKHEKSACSQCITITAPLRAEKIKGKEGRHYRIDDGTPSDCVYLAINELFKHVCFDLVISGINLGSNMGEDTIYSGTVAGAIEGTIQGVPSIAISQILSNKNKNTPLSFDLAQKIIQDLVQNIFTKGYPLKGRKLLNVNVPNCSLQEYQGERITPKGYRLYKKEVHKRTDPKNESYFWLGLHPLEWQKRENEDRLSDFDAIASNHASITPLNLDLTSYDDLKSLESWHEGMLK
>NC_018939.1|WP_000236875.1|994186_994789_+|6-carboxy-5,6,7,8-tetrahydropterin-synthase
MVIRRLYQFCASHVVRNCSSLKCAQNIHGHNYEVEVFIETNRLDNANMALDFGLMQQEMQVFIESFDHAHHFWDKESLEFQRFIENHCVRYVKCSFNLSAESYALMFLYYLTKILQKSVFSNDEGELKVSSVRVHETKNGYAESFLKDLENPHFKSLVHDHCVSFSQGIQNLWHDKDFFNKIISDEKQCFFHAKPLHQIP
>NC_018939.1|WP_000775643.1|994791_995547_+|7-carboxy-7-deazaguanine-synthase-QueE
MKLPVVESFFSLQGEGKRIGKPSLFLRLGGCNLSCKGFNCKTLLNDEILTGCDSLYAVHPKFKTSWDYYNEPKPLIERLEDLAPNYKDFDFILTGGEPSLYFNNPILISVLEHFYRQKIPLCVESNGSIFFEFSPILKELHFTLSVKLSFSLEEESKRIHLKALQNILNNAKSAHFKFVLESQNAAQSIIEIQSLLKQLSLKNNEIFLMPLGTNNNELDKNLKTLAPLAIKHGFRLSDRLHIRLWDNQKGF

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Crispr_ID: NC_018939_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_018939_4

1166569-1166657

TypeV

Consensus_repeat	Method
CATGCGAGAAGTAGTGGTTCAAGAACATT	CRISPRCasFinder

1 spacers

cas14j

The CRISPR arrays of NC_018939_4

>merge|NC_018939|4|1166569-1166657|CRISPRCasFinder
CATGCGAGAAGTAGTGGTTCAAGAACATTTCAAGGGAGTTTTCTTTGATCTCTGCATGGGCATGCGAGAAGTAGTGGTTCAAGAACATT

>NC_018939|4|2|1166569-1166657|CRISPRCasFinder
CATGCGAGAAGTAGTGGTTCAAGAACATT	TCAAGGGAGTTTTCTTTGATCTCTGCATGGG
CATGCGAGAAGTAGTGGTTCAAGAACATT

Protein	Signature genes	Signature genes Name	Protein_function
NC_018939.1\|WP_000883625.1\|1162213_1163491_+\|glucose-6-phosphate-dehydrogenase	unknown	unknown	gnl\|CDD\|223441
NC_018939.1\|WP_001863208.1\|1169201_1169864_-\|outer-membrane-protein	unknown	unknown	gnl\|CDD\|280099
NC_018939.1\|WP_001126886.1\|1164171_1165182_+\|glucokinase	unknown	unknown	gnl\|CDD\|129832
NC_018939.1\|WP_000892717.1\|1158734_1159607_-\|Sel1-like-repeat-protein-HcpC	unknown	unknown	gnl\|CDD\|223861
NC_018939.1\|WP_000576584.1\|1167887_1169195_+\|hypothetical-protein	unknown	unknown	unknown
NC_018939.1\|WP_000542222.1\|1163501_1164185_+\|6-phosphogluconolactonase	unknown	unknown	gnl\|CDD\|273494
NC_018939.1\|WP_000486467.1\|1170153_1170714_+\|pyruvate-flavodoxin-oxidoreductase-subunit-gamma	unknown	unknown	gnl\|CDD\|180284
NC_018939.1\|WP_001127890.1\|1175653_1177630_-\|excinuclease-ABC-subunit-B	unknown	unknown	gnl\|CDD\|235395
NC_018939.1\|WP_001152804.1\|1159676_1160303_-\|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase	unknown	unknown	gnl\|CDD\|273490
NC_018939.1\|WP_000238135.1\|1172367_1173312_+\|pyruvate-ferredoxin-oxidoreductase-subunit-beta	unknown	unknown	gnl\|CDD\|239471
NC_018939.1\|WP_000656174.1\|1170729_1171122_+\|4Fe-4S-dicluster-domain-containing-protein	unknown	unknown	gnl\|CDD\|236596
NC_018939.1\|WP_001129867.1\|1171131_1172355_+\|2-oxoacid:ferredoxin-oxidoreductase-subunit-alpha	unknown	unknown	gnl\|CDD\|181999
NC_018939.1\|WP_010875593.1\|1177699_1178386_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|139585
NC_018939.1\|WP_000930565.1\|1156739_1158023_-\|IS200/IS605-family-element-transposase-accessory-protein-TnpB	cas14j	-	gnl\|CDD\|223747
NC_018939.1\|WP_001265981.1\|1165343_1166390_+\|NAD(P)-dependent-alcohol-dehydrogenase	unknown	unknown	gnl\|CDD\|176186
NC_018939.1\|WP_001124018.1\|1160321_1162148_-\|phosphogluconate-dehydratase	unknown	unknown	gnl\|CDD\|130264
NC_018939.1\|WP_000893828.1\|1173421_1174744_+\|adenylosuccinate-lyase	unknown	unknown	gnl\|CDD\|181437
NC_018939.1\|WP_000816949.1\|1174809_1175643_+\|outer-membrane-protein	unknown	unknown	gnl\|CDD\|280099
NC_018939.1\|WP_001185550.1\|1158618_1158714_-\|hypothetical-protein	unknown	unknown	unknown
NC_018939.1\|WP_010875484.1\|1158092_1158521_+\|IS200/IS605-family-transposase	unknown	unknown	gnl\|CDD\|376616

Protein	Function_ID	Function_description	E-value
NC_018939.1\|WP_000883625.1\|1162213_1163491_+\|glucose-6-phosphate-dehydrogenase	gnl\|CDD\|223441	COG0364, Zwf, Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism].	0
NC_018939.1\|WP_001863208.1\|1169201_1169864_-\|outer-membrane-protein	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	2.117e-36
NC_018939.1\|WP_001126886.1\|1164171_1165182_+\|glucokinase	gnl\|CDD\|129832	TIGR00749, Glucokinase_Glucose_kinase., glucokinase, proteobacterial type. This model represents glucokinase of E. coli and close homologs, mostly from other proteobacteria, presumed to have equivalent function. This glucokinase is more closely related to a number of uncharacterized paralogs than to the glucokinase glcK (fromerly yqgR) of Bacillus subtilis and its closest homologs, so the two sets are represented by separate models. [Energy metabolism, Glycolysis/gluconeogenesis].	0
NC_018939.1\|WP_000892717.1\|1158734_1159607_-\|Sel1-like-repeat-protein-HcpC	gnl\|CDD\|223861	COG0790, COG0790, FOG: TPR repeat, SEL1 subfamily [General function prediction only].	4.68547e-48
NC_018939.1\|WP_000542222.1\|1163501_1164185_+\|6-phosphogluconolactonase	gnl\|CDD\|273494	TIGR01198, 6-phosphogluconolactonase_6PGL., 6-phosphogluconolactonase. This enzyme of the pentose phosphate pathway is often found as a part of a multifunctional protein with [Energy metabolism, Pentose phosphate pathway].	3.41385e-98
NC_018939.1\|WP_000486467.1\|1170153_1170714_+\|pyruvate-flavodoxin-oxidoreductase-subunit-gamma	gnl\|CDD\|180284	PRK05844, PRK05844, pyruvate flavodoxin oxidoreductase subunit gamma; Validated.	4.6316e-128
NC_018939.1\|WP_001127890.1\|1175653_1177630_-\|excinuclease-ABC-subunit-B	gnl\|CDD\|235395	PRK05298, PRK05298, excinuclease ABC subunit UvrB.	0
NC_018939.1\|WP_001152804.1\|1159676_1160303_-\|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase	gnl\|CDD\|273490	TIGR01182, KHG/KDPG_aldolase_., Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida [Amino acid biosynthesis, Glutamate family, Energy metabolism, Entner-Doudoroff].	9.71254e-113
NC_018939.1\|WP_000816949.1\|1174809_1175643_+\|outer-membrane-protein	gnl\|CDD\|280099	pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.	3.34961e-36
NC_018939.1\|WP_000656174.1\|1170729_1171122_+\|4Fe-4S-dicluster-domain-containing-protein	gnl\|CDD\|236596	PRK09625, porD, pyruvate flavodoxin oxidoreductase subunit delta; Reviewed.	5.72644e-84
NC_018939.1\|WP_001129867.1\|1171131_1172355_+\|2-oxoacid:ferredoxin-oxidoreductase-subunit-alpha	gnl\|CDD\|181999	PRK09622, porA, 2-oxoacid:ferredoxin oxidoreductase subunit alpha.	0
NC_018939.1\|WP_010875593.1\|1177699_1178386_-\|hypothetical-protein	gnl\|CDD\|139585	PRK13460, PRK13460, F0F1 ATP synthase subunit B; Provisional.	0.001592
NC_018939.1\|WP_000930565.1\|1156739_1158023_-\|IS200/IS605-family-element-transposase-accessory-protein-TnpB	gnl\|CDD\|223747	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair].	1.16023e-62
NC_018939.1\|WP_001265981.1\|1165343_1166390_+\|NAD(P)-dependent-alcohol-dehydrogenase	gnl\|CDD\|176186	cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.	2.28765e-163
NC_018939.1\|WP_001124018.1\|1160321_1162148_-\|phosphogluconate-dehydratase	gnl\|CDD\|130264	TIGR01196, Phosphogluconate_dehydratase, 6-phosphogluconate dehydratase. A close homolog, designated MocB (mannityl opine catabolism), is found in a mannopine catabolism region of a plasmid of Agrobacterium tumefaciens. However, it is not essential for mannopine catabolism, branches within the cluster of 6-phosphogluconate dehydratases (with a short branch length) in a tree rooted by the presence of other dehydyatases. It may represent an authentic 6-phosphogluconate dehydratase, redundant with the chromosomal copy shown to exist in plasmid-cured strains. This model includes mocB above the trusted cutoff, although the designation is somewhat tenuous. [Energy metabolism, Entner-Doudoroff].	0
NC_018939.1\|WP_000893828.1\|1173421_1174744_+\|adenylosuccinate-lyase	gnl\|CDD\|181437	PRK08470, PRK08470, adenylosuccinate lyase; Provisional.	0
NC_018939.1\|WP_000238135.1\|1172367_1173312_+\|pyruvate-ferredoxin-oxidoreductase-subunit-beta	gnl\|CDD\|239471	cd03376, TPP_PFOR_porB_like, Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea and some hyperthermophilic bacteria. PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The 36-kDa porB subunit contains the binding sites for the cofactors, TPP and a divalent metal cation, which are required for activity.	6.58599e-136
NC_018939.1\|WP_010875484.1\|1158092_1158521_+\|IS200/IS605-family-transposase	gnl\|CDD\|376616	pfam01797, Y1_Tnp, Transposase IS200 like. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS200 from E. coli.	6.85779e-41

>NC_018939.1|WP_001265981.1|1165343_1166390_+|NAD(P)-dependent-alcohol-dehydrogenase
MRVQSKGFAIFSKDGHFKPHDFSRHAVGPKDVLIDILYAGICHSDIHSAYSEWKEGIYPMVPGHEIAGAIKEVGKEVKKFKVGDVVGVGCFVNSCKACKPCKEHQEQFCAKVVFTYDCLDYFHDNEPHMGGYSNNIVVDENYVISVDKNAPLEKVAPLLCAGITTYSPLKFSKVTKGTKVGVAGFGGLGSMAVKYAVAMGAEVSVFARNEHKKQDALSMGVKHFYTDPKQCKEELDFIISTIPTHYDLKDYLKLLTYNGDLALVGLPPVEIAPALSVFDFIHLGNRKVYGSLIGGIKETQEMMDFSIKHNIYPEIDLILGKDIDTAYHNLTHGKAKFRYVIDMKKSFD
>NC_018939.1|WP_001126886.1|1164171_1165182_+|glucokinase
MPKTETYPRLLADIGGTNARFGLEVAPRQIECIEVLRCEDFESLSDAVRFYLSKCKESLKLHPIYGSFAVATPIMGDFVQMTNNHWTFSIETTRQCLTLKKLLVINDFVAQAYAISAMQENDLAQIGGIKCEINAPKAILGPGTGLGVSTLIQNSDGSLKVLPGEGGHVSFAPFDDLEILVWQYARSKFNHVSAERFLSGSGLVLIYEALSKRKGLEKVAKLSKAELTPQIISECALNGDYPICRLTLDTFCSMLGTLAADVALTLGARGGVYLCGGIIPRFIDYFKTSPFRARFETKGRMGAFLASIPVHVVLKKTPGLDGAGIALENYLLHDKI
>NC_018939.1|WP_000542222.1|1163501_1164185_+|6-phosphogluconolactonase
MGYQLFEFENLKDCHKALTERFKEFFNTALKKHHQISIAFSGGRSPISLLQKLSVLNLKWHECLISLVDERIIDTSHDDSNTKLLHDYLLQNNALKASFIPLLPEKISSDTNALFNFANQHFKQPHLAILGMGTDGHTASLFPETSAFLNEEKENIVLTKPINAPYERLSMSVNALENCEKLFLSISGVEKRGVLEKALKENAPYSLPIARILHSQKVTTEVFYAKN
>NC_018939.1|WP_000883625.1|1162213_1163491_+|glucose-6-phosphate-dehydrogenase
MLDFDLVLFGATGDLAMRKLFVSLYEIYTHYGFKNDSRIIASGRKELSNEEFLTLLCEKTQLHSREKGREFLAHISYLCVRLDNPKDFEELSKIATKNKPLIFYFSISPSFFATTAQHLAKNALNHANTRLILEKPLGHDLKTCKEIFQSISVFFKEEQIFRIDHYLGKKGVQNILELRLNNPILNILWDQISAVEICVYETLGVEERGEFYDKIGALRDMVQNHLLQVLSLIATDLPNNLKDLRKEKIKVLKTLQPPKDFKKQVIRAQYQGYRDENKVHKESQTETFVAIKAFLDTPKFKGVPFYLKHAKKMPHNQASVKIHFNAVNTLEFFLSQDKITLTLKDHQNPLILETHNKQEFLRPYAKLLYDAIQNNHNNFAHQLELEASWVFIDTLIEGFMNNATPLYSYESHHLNESEFLKPLYQ
>NC_018939.1|WP_001124018.1|1160321_1162148_-|phosphogluconate-dehydratase
MPKHSLEQIKEKITERSKKTRELYLENIFNPKNQPKIESLGCANIAHVTASMPEHLKMPLGSHKRKHFAIITAYNDMLSAHQPFKNYPDLIKKELQEHNAYASVASGVPAMCDGITQGYDGMELSLFSRDVIALSTAVGLSHNVFDGAFFLGVCDKIVPGLLIGALSFGNLASVFVPSGPMVSGIENYKKAKARQDFAMGKINREELLKVEMQSYHDVGTCTFYGTANSNQMMMEFMGLHVANSSFINPNNPLRKVLVEESAKRLASGKVLPLAKLIDEKSILNALIGLMATGGSTNHTLHLIAIARSCGVILNWDDFDAVSNLIPLLAKVYPNGSADVNAFEACGGLVFVIKELLKEGLLFEDTHTIMDTETQKGMQNYTKTPFLENNQLVYKDAINHSLNTDILRPVSDPFAANGGLKILKGNLGRAVIKISAIKDEHRKVKARAIVFKTQSEFLERFKNKELERDFVAVLPFQGPKSNGMPELHKLTTNLGALQDMGYKVALVTDGRMSGASGKVPSAIHLSPEGALNGAIIKIKDGDLIELDAPNNALNVLEKDFEKRGINPLFLETLENLEKPSFGLGRELFTSLRLNVNTAEEGGMSFGIKV
>NC_018939.1|WP_001152804.1|1159676_1160303_-|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase
MQDKIIEVLQISPIVPVVVIENIKDAVPLAQSLIEGGIPIIEVTLRSSCALEAIELIAKNMPKMRVGAGTILNPTQLEQAQNRGAEFLISPGLTIKLLEHAKKKDMPLIPGVSSSSEVMQALELGYSALKFFPAEYCGGVKLLNAFNGPFKGVKFCPTGGISADNMRSYLNLENVLCVGGSWLTPKNLIQNKEWDKITEICKRALALR
>NC_018939.1|WP_000892717.1|1158734_1159607_-|Sel1-like-repeat-protein-HcpC
MLENVKKSFFRVLCLGALCLGGLMAEQDPKELVGLGAKSYKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAKGACDILKQLKIKV
>NC_018939.1|WP_001185550.1|1158618_1158714_-|hypothetical-protein
MALKSALLGVRRILGEVLGENNFKILPIPLR
>NC_018939.1|WP_010875484.1|1158092_1158521_+|IS200/IS605-family-transposase
MRKNHYPLRGYISTNRSKHNLKAHLILVCKYRKKLLQGDLNNFIKSVIDEIATQSNFIIIAMESDIDHLHLMVQYIPRMSISSIISRIKQITTYRVWRDKRFIPLLQKHFWKEKTFWTDGFFVCSIGEANPETIKAYIENQG
>NC_018939.1|WP_000930565.1|1156739_1158023_-|IS200/IS605-family-element-transposase-accessory-protein-TnpB
MLNAIKFRIYPNAQQKELISKHFGCSRVVYNYFLDYRQKQYAKGIKETYFTMQKVLTQIKRQEKYHYLNECNSQSLQMALRQLVSAYDNFFSKRARYPKFKSKKNAKQSFAIPQNIETKTETQTIALPKFKEGIKAKLHRDLPKDSVIKQAFISCIADQYFCSLSYETKEPIPKPTIIKKAVGLDMGLRTLIVTSDKIGYPHIRFYQKLEKKLTKAQRRLSKKVKDSNNRKKQAKKVSRLHLACSNTRDDYLHKISNEITNQYDLIGVETLNVKALMRTYHSKSLANASWGKFLTMLEYKAQRKGKTLLSIDRFFPSSQLCSYCGVNTGKKHESITKFTCPHCQTTHHRDYNASVNIRNYALGMLDDRHKVKTDKARVGIIRSDYTHHTNECVKACGASSNGVSSKYGNILDLASYGAMKQEKAQSL
>NC_018939.1|WP_000576584.1|1167887_1169195_+|hypothetical-protein
MIFLKKSLYALLFSGFLTPPLMKAASFVYDLKFMSFNFNLVAPANNPYWNSLTKMQGRLMPQIGVQLDKRQALMFGAWFIQNLHTHYSYFPYSWGVTMYYQYIGKNLRFFLGIVPRSYQIGHYPLSAFKKLFWFIDPTFRGGAFQFKPAYDPNRWWNGWFEGVVDWYGGRNWNNQPKKKNYDFDQFLYFVSSEFQFLKGYLGLGGQLVVFHNASHHSMGDNYPYGGNSYLKPGDVTPQWPNGYPYFSQKNNPQGGEIGKYSNPTILDRVYYHAYLKADFKNLMPYMDNIFMTFGTQSSQTHYCVRYASECKNARFYNSFGGEFYAQAQYKGFGIFNRYYFSNKPQMHFYATYGQSLYTGLPWYRAPNFDMIGLYYVYKNKWVSVRADAFFNFLGGGDGYHLYGKGGKWITTYQQFLTLTIDTRELIDFVKSKTSK
>NC_018939.1|WP_001863208.1|1169201_1169864_-|outer-membrane-protein
MNKTTVKILMGMALLSSLQAAEAELDEKSKKPKFADRNTFYLGVGYQLSAINTSFSTESVDKSYFMTGNGFGVVLGGKFVAKTQAVEHVGFRYGLFYDQTFSSHKSYISTYGLEFSGLWDAFNSPKMFLGLEFGLGIAGATYMPGGAMHGIIAQNLGKENSLFQLLVKVGFRFGFLHNEITFGLKFPVIPNKRTEIIDGLSTTTLWHRLPVAYFNYIYNF
>NC_018939.1|WP_000486467.1|1170153_1170714_+|pyruvate-flavodoxin-oxidoreductase-subunit-gamma
MFQIRWHARAGQGAITGAKGLADVISKTGKEVQAFASYGSAKRGAAMMAYNRVDDEPILNHERFMQPDYVLVIDPGLVFIENIFANEKEDTTYIITSYLNKEELFEKKPELKTRKVFLVDCLKISMETLKRPIPNTPMLGALMKVSGMLEIGAFKEAFKKVLGKKLTQEVIDANMLAIQRAYEEVQ
>NC_018939.1|WP_000656174.1|1170729_1171122_+|4Fe-4S-dicluster-domain-containing-protein
MKDWNEFEMGAVLFPFEKNAQSEMEKHNDERHYTEQSYFTTSVAHWRVAKPVHNNNICINCFNCWVYCPDAAILSREGKLKGVDYSHCKGCGVCVDVCPTNPKSLWMFEEQIEPATALTQWPQKQEKKKS
>NC_018939.1|WP_001129867.1|1171131_1172355_+|2-oxoacid:ferredoxin-oxidoreductase-subunit-alpha
MAKSIELQEIEVWDGNTASSNALRQAQIDVIAAYPITPSTPIVQNYGSFKDNGYVDGEFVLVESEHAAMSACVGAAAAGGRVSTATSSQGLALMVEVLYQASGMRLPIVLNLVNRALAAPLNIHGDHSDMYLSRDSGWISLCTCNPQEAYDFTLMAFRIAEHQKVRVPTIVNQDGFLCSHTVQNVRPLSDAVAYQFVGEYQTKHSLLDFDKPVSYGAQAEEEWHYEHKAQLHHAIMSASSVIEEVFNDFAKLTGRQYHLTKTFQLEDAEIAIFALGTTYESAIVAAKEMRKKGIKAGVATIHSLRPFPYERLGQDLKNLKALAILDKSSPAGTMGAMFNEVTSAVYQTQGTKHPVVSNYIYGLGERDMTIAHLCEIFEEINEDALKGTLTHPTQQFVGLHGPKMSFF
>NC_018939.1|WP_000238135.1|1172367_1173312_+|pyruvate-ferredoxin-oxidoreductase-subunit-beta
MVKEVKTLKGFSQSAEKFQGSHLLCPGCGHGIIVREVLNAVDGPIVLGNSTGCLEVCSAVYPHTSWDVPWIHIGFENGSTAISGVEAMYKALTNKGRYQGQKPKFVAFGGDGASYDIGLQFISGCMERGHDMTYICLDNENYANTGGQRSGSTPLGASTSTTPAGSVSFGKKEKKKDIVNIMASHGVPYVAQLSPNKWKDMNKKIKTALDTEGPCFINALSPCTTEWKFESNKTIELADMAVDSLMFPLFEIFNGRELKITYRPRNIIPVRDYLGAQKRFKHLFKKENEHIIEELQKDVNERWEYLQRREEAKV
>NC_018939.1|WP_000893828.1|1173421_1174744_+|adenylosuccinate-lyase
MLERYANEEMKALWNEQTKFETYLEVEKAVVRAWNKLGQIQDSDCEKICAKAAFNLERIKEIEKTTKHDLIAFTTCVAESLGEESRFFHYGITSSDCIDTAMALLMTKSLKLIQKGVKNLYETLKNRALEHKDTLMVGRSHGVFGEPITFGLVLALFADEIKRHLKALDLTMEFISVGAISGAMGNFAHAPLELEELACEFLGLKTANISNQVIQRDRYARLACDLALLASSCEKIAVNIRHLQRSEVYEVEEAFSTGQKGSSAMPHKRNPILSENITGLCRVIRSFTTPMLENVALWHERDMSHSSVERFALPDLFITSDFMLSRLNSVIKNLVVYPKNMLKNLALSGGLVFSQRVLLELPKKGLSREESYSIVQENAMKIWEVLQQGAFKNTDENLFLNALLNDERLKKYLSEDEIKACFDYNYYTKNVGAIFKRVFE
>NC_018939.1|WP_000816949.1|1174809_1175643_+|outer-membrane-protein
MKRALYLILGLFYTLNAESFKDVLTKVDYTFFNKKVVSPIKRYADRSAFYLGLGYQLGSIQHNSSNLNLSQQFNKSQIIFSDSLSPVFKNSYVSNGLGVQVGYKWVGKHEETKWFGFRWGLFYDLSASLYGQKESQSVIISTYGTYMDLLLNAYNGDKFFAGFNLGIAFAGVYDKVSDALLYQALLLDTFGGKVDPNGFQFLVNLGVRLGNKHNQFGFGIKIPTYYFNHYYSMNNISNNSEDVLKVLRFLEYGINSLLYQVDFRRNYSVYFNYTYIF
>NC_018939.1|WP_001127890.1|1175653_1177630_-|excinuclease-ABC-subunit-B
MPLFDLKSPYPPAGDQPQAIEALTKSLKNNNHYQTLVGVTGSGKTYTMANIIAQTNKPALIMSHNKTLCAQLYSEFKAFFPHNRVEYFISHFDYYQPESYIPRRDLFIEKDSSINDDLERLRLSATTSLLGYDDVIVIASVSANYGLGNPEEYLKVMEKIKVGEKRAYKSFLLKLVEMGYSRNEVVFDRGSFRATGECVDIFPAYNDAEFIRIEFFGDEIERIAVFDALEKNEIKRLDSVMLYAASQFAVGSERLNLAIKSIEDELALRLKFFKEQDKMLEYNRLKQRTEHDLEMISATGVCKGIENYARHFTGKAPNETPFCLFDYLGIFEREFLVIVDESHVSLPQFGGMYAGDMSRKSVLVEYGFRLPSALDNRPLKFDEFIHKNCQFLFVSATPNKLELELSKKNVAEQIIRPTGLLDPKFEVRDSDKQVQDLFDEIKLVVARGERVLITTLTKKMAEELCKYYAEWGLKARYMHSEIDAIERNHIIRSLRLKEFDILIGINLLREGLDLPEVSLVAIMDADKEGFLRSETSLIQTMGRAARNANGKVLLYAKKITQSMQKAFEITSYRRAKQEEFNKIHNITPKTVTRALEEELKLRDDEIRIAKALKKDKMPKSEREKIIKELDKKMRECTKNLDFEEAMRLRDEIAQLRTL
>NC_018939.1|WP_010875593.1|1177699_1178386_-|hypothetical-protein
MINYPNLPNSALEITEQPEVKEITNELLKQLQNALNSNSLFSEQVELSLKGIVRILEVLLSLDFFKNANEIDSSLRNSIEWLNNAGESLKTKMKEYEGFFSDFNTSMRTNEQEVSATLNANTENIKSEIKKLENQLIETTTRLLTSYQIFLNNARDSANNQITANKTESLEALNQAKTSANNEITANQTQALTNINEAKENANNQITENKTQAITNINEAKNQSLSKH

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
NC_018939_2	2.1\|556246\|54\|NC_018939\|PILER-CR	556246-556299	54	NC_018939.1	555916-555969	1	0.981

1. spacer 2.1|556246|54|NC_018939|PILER-CR matches to position: 555916-555969, mismatch: 1, identity: 0.981

cattcctagctcttgatacgcagtccaaataagccttaatgcttttcttaactt	CRISPR spacer
cattcctagctcttgatacgcagtccaaataagccttaacgcttttcttaactt	Protospacer
***************************************.**************

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_018939_3	3.2\|980377\|23\|NC_018939\|PILER-CR	980377-980399	23	NZ_CP010123	Escherichia coli strain C5 plasmid A, complete genome	183244-183266	3	0.87

1. spacer 3.2|980377|23|NC_018939|PILER-CR matches to NZ_CP010123 (Escherichia coli strain C5 plasmid A, complete genome) position: , mismatch: 3, identity: 0.87

acgccagctttgataacgacacc	CRISPR spacer
gcgccagctttgatatcgacacg	Protospacer
.************** ******

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1018476 : 1070401

Helicobacter_phage(50.0%)

tRNA,integrase,transposase

attL 1028984:1029003|attR 1080324:1080343

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_001150920.1\|1018476_1019388_-\|tRNA	glycine--tRNA ligase subunit alpha	NA	NA	NA	NA
WP_000401714.1\|1019401_1020340_-	NAD(P)H-dependent glycerol-3-phosphate dehydrogenase	NA	NA	NA	NA
WP_001862971.1\|1020471_1020933_-	acyl carrier protein	M4QDG5	Prochlorococcus_phage	1.3e-05	47.1
WP_001862974.1\|1020925_1022269_-	dynamin-like GTPase family protein	NA	NA	NA	NA
WP_010875568.1\|1022265_1023357_-	hypothetical protein	NA	NA	NA	NA
WP_010875569.1\|1023266_1024598_-	dynamin-like GTPase family protein	NA	NA	NA	NA
WP_010875570.1\|1024594_1026244_-	GTPase	NA	NA	NA	NA
WP_000271456.1\|1026464_1026752_-	endoribonuclease VapD	NA	NA	NA	NA
WP_000978968.1\|1027119_1030182_-	CusA/CzcA family heavy metal efflux RND transporter	S5VTK5	Leptospira_phage	2.8e-83	25.7
1028984:1029003	attL	NA	NA	NA	NA
WP_000816822.1\|1030178_1031258_-	sodium:proton antiporter	NA	NA	NA	NA
WP_010875571.1\|1031254_1032496_-	membrane protein	NA	NA	NA	NA
WP_000555186.1\|1032545_1034651_-\|tRNA	glycine--tRNA ligase subunit beta	NA	NA	NA	NA
WP_000682021.1\|1034762_1035824_+	hypothetical protein	A0A2D1GN01	Pseudoalteromonas_phage	2.0e-09	30.1
WP_000057737.1\|1035836_1037312_+	2,3-bisphosphoglycerate-independent phosphoglycerate mutase	NA	NA	NA	NA
WP_001165207.1\|1037326_1037608_+\|tRNA	Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC	NA	NA	NA	NA
WP_001010809.1\|1037727_1039038_-	adenosylmethionine--8-amino-7-oxononanoate transaminase	NA	NA	NA	NA
WP_000574070.1\|1039166_1040630_+	peptidylprolyl isomerase	NA	NA	NA	NA
WP_000400290.1\|1040645_1042124_+	cell division protein FtsA	NA	NA	NA	NA
WP_000233600.1\|1042254_1043412_+	cell division protein FtsZ	NA	NA	NA	NA
WP_001863015.1\|1044569_1044872_+	hypothetical protein	NA	NA	NA	NA
WP_049794234.1\|1044882_1045155_+	exonuclease VII large subunit	NA	NA	NA	NA
WP_010875573.1\|1045526_1046222_+	hypothetical protein	NA	NA	NA	NA
WP_001169565.1\|1046222_1046513_+	hypothetical protein	NA	NA	NA	NA
WP_000343415.1\|1047071_1047896_+	mechanosensitive ion channel family protein	NA	NA	NA	NA
WP_010875574.1\|1048105_1048429_-	hypothetical protein	NA	NA	NA	NA
WP_010875575.1\|1048731_1049445_-	DUF1887 family protein	NA	NA	NA	NA
WP_000886948.1\|1050828_1051062_+	hypothetical protein	NA	NA	NA	NA
WP_010875484.1\|1051068_1051497_-\|transposase	IS200/IS605 family transposase	A0A1S5RG71	Helicobacter_phage	8.6e-76	97.9
WP_000930564.1\|1051566_1052850_+\|transposase	IS200/IS605 family element transposase accessory protein TnpB	A0A1S5REX3	Helicobacter_phage	1.2e-200	85.2
WP_080012132.1\|1052898_1053612_+	hypothetical protein	NA	NA	NA	NA
WP_010875576.1\|1053616_1054246_-	hypothetical protein	NA	NA	NA	NA
WP_000006537.1\|1054831_1055083_+	hypothetical protein	NA	NA	NA	NA
WP_000009099.1\|1055054_1055858_+	nucleotidyl transferase AbiEii/AbiGii toxin family protein	NA	NA	NA	NA
WP_001120382.1\|1056174_1057242_-\|integrase	tyrosine-type recombinase/integrase	S5W9T9	Leptospira_phage	1.7e-08	26.7
WP_010875578.1\|1058390_1060193_-	relaxase/mobilization nuclease domain-containing protein	NA	NA	NA	NA
WP_000930565.1\|1060341_1061625_-\|transposase	IS200/IS605 family element transposase accessory protein TnpB	A0A1S5REX3	Helicobacter_phage	2.6e-200	85.0
WP_010875484.1\|1061694_1062123_+\|transposase	IS200/IS605 family transposase	A0A1S5RG71	Helicobacter_phage	8.6e-76	97.9
WP_000587397.1\|1062704_1063361_+	ParA family protein	A2I303	Vibrio_virus	7.1e-05	23.4
WP_000394638.1\|1063445_1063730_+	hypothetical protein	NA	NA	NA	NA
WP_000665511.1\|1063773_1064958_+	hypothetical protein	NA	NA	NA	NA
WP_000065304.1\|1067173_1067488_+	hypothetical protein	NA	NA	NA	NA
WP_000254056.1\|1068038_1068572_-	type IV secretory system conjugative DNA transfer family protein	NA	NA	NA	NA
WP_001862466.1\|1069984_1070401_+\|transposase	IS200/IS605 family transposase	A0A1S5RHE3	Helicobacter_phage	4.6e-74	96.4
1080324:1080343	attR	NA	NA	NA	NA

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NC_018939

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection