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_009655	Actinobacillus succinogenes 130Z, complete genome	2 crisprs	cas9,cas1,cas2,cas3,DEDDh,DinG,cas5,cas8c,cas7,cas4,csa3	0	5	2	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NC_009655_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_009655_1

436472-436903

TypeII

Consensus_repeat	Method
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	PILER-CR
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	CRISPRCasFinder
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	CRT

6 spacers

cas2,cas1,cas9

The CRISPR arrays of NC_009655_1

>merge|NC_009655|1|436472-436903|PILER-CR,CRISPRCasFinder,CRT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAACGATGGATTAGTTCCGTCGGGGCTTTTTATTATTATAGCACTGCGAAATGAAAAAGGGAGCTACAACGCTAGAAAGCTCGACATCCTTAAAAAGCCTATTATAGCACTGCGAAATGAAAAAGGGAGCTACAACTCGTTCTGTTATTCAGGCGTTCGCTAACGGATTATAGCACTGCGAAATGAAAAAGGGAGCTACAACGATTAAGGATGGGCTTAATCGCACCGTGCAATTATAGCACTGCGAAATGAAAAAGGGAGCTACAACAAACAACTGTACCAGTTGAATTACGTTGAGATTATAGCACTGCGAAATGAAAAAGGGAGCTACAACTCCATATTGCTCCTTATTTATGCAACCATTATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC

>NC_009655|1|1|436472-436903|PILER-CR
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GATGGATTAGTTCCGTCGGGGCTTTTTATT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GCTAGAAAGCTCGACATCCTTAAAAAGCCT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	TCGTTCTGTTATTCAGGCGTTCGCTAACGG
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GATTAAGGATGGGCTTAATCGCACCGTGCA
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	AAACAACTGTACCAGTTGAATTACGTTGAG
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	TCCATATTGCTCCTTATTTATGCAACCATT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC

>NC_009655|1|1|436472-436903|CRISPRCasFinder
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GATGGATTAGTTCCGTCGGGGCTTTTTATT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GCTAGAAAGCTCGACATCCTTAAAAAGCCT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	TCGTTCTGTTATTCAGGCGTTCGCTAACGG
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GATTAAGGATGGGCTTAATCGCACCGTGCA
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	AAACAACTGTACCAGTTGAATTACGTTGAG
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	TCCATATTGCTCCTTATTTATGCAACCATT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC

>NC_009655|1|1|436472-436903|CRT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GATGGATTAGTTCCGTCGGGGCTTTTTATT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GCTAGAAAGCTCGACATCCTTAAAAAGCCT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	TCGTTCTGTTATTCAGGCGTTCGCTAACGG
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	GATTAAGGATGGGCTTAATCGCACCGTGCA
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	AAACAACTGTACCAGTTGAATTACGTTGAG
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC	TCCATATTGCTCCTTATTTATGCAACCATT
ATTATAGCACTGCGAAATGAAAAAGGGAGCTACAAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_009655.1\|WP_011979024.1\|425915_427517_+\|mannitol-dehydrogenase-family-protein	unknown	unknown	gnl\|CDD\|223324
NC_009655.1\|WP_011979023.1\|424842_425916_+\|mannonate-dehydratase	unknown	unknown	gnl\|CDD\|235172
NC_009655.1\|WP_011979035.1\|440059_440770_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|283861
NC_009655.1\|WP_011979030.1\|436080_436407_+\|CRISPR-associated-endonuclease-Cas2	cas2	COG3512_cas2_CAS-II-A:CAS-II-B:CAS-II-C	gnl\|CDD\|226043
NC_009655.1\|WP_012072148.1\|441667_442675_-\|NAD(P)H-dependent-glycerol-3-phosphate-dehydrogenase	unknown	unknown	gnl\|CDD\|234629
NC_009655.1\|WP_041834594.1\|431918_435116_+\|type-II-CRISPR-RNA-guided-endonuclease-Cas9	cas9	COG3513_cas9_CAS-II-A:CAS-II-B:CAS-II-C	gnl\|CDD\|226044
NC_009655.1\|WP_011979022.1\|423792_424812_+\|zinc-binding-alcohol-dehydrogenase-family-protein	unknown	unknown	gnl\|CDD\|176222
NC_009655.1\|WP_011979031.1\|436994_437462_-\|thioredoxin-dependent-thiol-peroxidase	unknown	unknown	gnl\|CDD\|181857
NC_009655.1\|WP_011979032.1\|437558_438134_+\|Der-GTPase-activating-protein-YihI	unknown	unknown	gnl\|CDD\|367878
NC_009655.1\|WP_011979026.1\|428207_429146_+\|sugar-kinase	unknown	unknown	gnl\|CDD\|238571
NC_009655.1\|WP_011979036.1\|440860_441658_-\|serine-O-acetyltransferase	unknown	unknown	gnl\|CDD\|182987
NC_009655.1\|WP_011979033.1\|438137_438569_+\|DUF2489-domain-containing-protein	unknown	unknown	gnl\|CDD\|378470
NC_009655.1\|WP_012072150.1\|443245_443683_-\|rhodanese-like-domain-containing-protein	unknown	unknown	gnl\|CDD\|238089
NC_009655.1\|WP_011979025.1\|427526_428207_+\|GntR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|224715
NC_009655.1\|WP_011979029.1\|435170_436088_+\|type-II-CRISPR-associated-endonuclease-Cas1	cas1	cd09720_cas1_CAS-II-A:CAS-II-B:CAS-II-C	gnl\|CDD\|274694
NC_009655.1\|WP_012072149.1\|442734_443235_-\|protein-export-chaperone-SecB	unknown	unknown	gnl\|CDD\|180234
NC_009655.1\|WP_011978808.1\|429175_429814_+\|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase	unknown	unknown	gnl\|CDD\|235577
NC_009655.1\|WP_011979027.1\|430007_431357_-\|NADP-specific-glutamate-dehydrogenase	unknown	unknown	gnl\|CDD\|181834
NC_009655.1\|WP_011979034.1\|438622_439990_+\|oxygen-independent-coproporphyrinogen-III-oxidase	unknown	unknown	gnl\|CDD\|236430
NC_009655.1\|WP_012072151.1\|443803_444730_-\|cell-division-protein-FtsX	unknown	unknown	gnl\|CDD\|182910

Protein	Function_ID	Function_description	E-value
NC_009655.1\|WP_011979024.1\|425915_427517_+\|mannitol-dehydrogenase-family-protein	gnl\|CDD\|223324	COG0246, MtlD, Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism].	1.03528e-113
NC_009655.1\|WP_011979023.1\|424842_425916_+\|mannonate-dehydratase	gnl\|CDD\|235172	PRK03906, PRK03906, mannonate dehydratase; Provisional.	0
NC_009655.1\|WP_011979035.1\|440059_440770_-\|hypothetical-protein	gnl\|CDD\|283861	pfam06293, Kdo, Lipopolysaccharide kinase (Kdo/WaaP) family. These lipopolysaccharide kinases are related to protein kinases pfam00069. This family includes waaP (rfaP) gene product is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that WaaP is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of S. enterica.	0.00139478
NC_009655.1\|WP_011979030.1\|436080_436407_+\|CRISPR-associated-endonuclease-Cas2	gnl\|CDD\|226043	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms].	9.75542e-53
NC_009655.1\|WP_012072148.1\|441667_442675_-\|NAD(P)H-dependent-glycerol-3-phosphate-dehydrogenase	gnl\|CDD\|234629	PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate dehydrogenase.	0
NC_009655.1\|WP_041834594.1\|431918_435116_+\|type-II-CRISPR-RNA-guided-endonuclease-Cas9	gnl\|CDD\|226044	COG3513, COG3513, Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms].	0
NC_009655.1\|WP_011979022.1\|423792_424812_+\|zinc-binding-alcohol-dehydrogenase-family-protein	gnl\|CDD\|176222	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family. 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 includes various 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.	5.70326e-157
NC_009655.1\|WP_011979031.1\|436994_437462_-\|thioredoxin-dependent-thiol-peroxidase	gnl\|CDD\|181857	PRK09437, bcp, thioredoxin-dependent thiol peroxidase; Reviewed.	7.39322e-118
NC_009655.1\|WP_011979032.1\|437558_438134_+\|Der-GTPase-activating-protein-YihI	gnl\|CDD\|367878	pfam04220, YihI, Der GTPase activator (YihI). YihI activates the GTPase activity of Der, a 50S ribosomal subunit stability factor. The stimulation is specific to Der as YihI does not stimulate the GTPase activity of Era or ObgE. The interaction of YihI with Der requires only the C-terminal 78 amino acids of YihI. A yihI deletion mutant is viable and shows a shorter lag period, but the same post-lag growth rate as a wild-type strain. yihI is expressed during the lag period. Overexpression of yihI inhibits cell growth and biogenesis of the 50S ribosomal subunit. YihI is an unusual, highly hydrophilic protein with an uneven distribution of charged residues, resulting in an N-terminal region with high pI and a C-terminal region with low pI.	3.33036e-64
NC_009655.1\|WP_011979026.1\|428207_429146_+\|sugar-kinase	gnl\|CDD\|238571	cd01166, KdgK, 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the glycolysis and therefore use polymers, like pectin and xylan as carbon sources.	8.74084e-101
NC_009655.1\|WP_011979036.1\|440860_441658_-\|serine-O-acetyltransferase	gnl\|CDD\|182987	PRK11132, cysE, serine acetyltransferase; Provisional.	0
NC_009655.1\|WP_011979033.1\|438137_438569_+\|DUF2489-domain-containing-protein	gnl\|CDD\|378470	pfam10675, DUF2489, Protein of unknown function (DUF2489). This is a bacterial family of uncharacterized proteins.	1.10575e-47
NC_009655.1\|WP_012072150.1\|443245_443683_-\|rhodanese-like-domain-containing-protein	gnl\|CDD\|238089	cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.	3.91446e-25
NC_009655.1\|WP_011979025.1\|427526_428207_+\|GntR-family-transcriptional-regulator	gnl\|CDD\|224715	COG1802, GntR, Transcriptional regulators [Transcription].	5.80132e-45
NC_009655.1\|WP_011979029.1\|435170_436088_+\|type-II-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|274694	TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype II/NMENI. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is a prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 variant of the NMENI subtype of CRISPR/Cas system.	1.17512e-125
NC_009655.1\|WP_012072149.1\|442734_443235_-\|protein-export-chaperone-SecB	gnl\|CDD\|180234	PRK05751, PRK05751, preprotein translocase subunit SecB; Validated.	1.85354e-76
NC_009655.1\|WP_011978808.1\|429175_429814_+\|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase	gnl\|CDD\|235577	PRK05718, PRK05718, keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional.	1.37829e-123
NC_009655.1\|WP_011979027.1\|430007_431357_-\|NADP-specific-glutamate-dehydrogenase	gnl\|CDD\|181834	PRK09414, PRK09414, NADP-specific glutamate dehydrogenase.	0
NC_009655.1\|WP_011979034.1\|438622_439990_+\|oxygen-independent-coproporphyrinogen-III-oxidase	gnl\|CDD\|236430	PRK09249, PRK09249, coproporphyrinogen dehydrogenase.	0
NC_009655.1\|WP_012072151.1\|443803_444730_-\|cell-division-protein-FtsX	gnl\|CDD\|182910	PRK11026, ftsX, cell division ABC transporter subunit FtsX; Provisional.	0

>NC_009655.1|WP_011979030.1|436080_436407_+|CRISPR-associated-endonuclease-Cas2
MSENVFMRMIVLFDLPVTTKAKMRAANQFRQFLLKDGYQMLQLSIYSRIIRGRDSMEKHHKRLVEHLPEEGSIRCISITEKQFANMEILVGEKKLQEKKVNANQLLLF
>NC_009655.1|WP_011979029.1|435170_436088_+|type-II-CRISPR-associated-endonuclease-Cas1
MTWRSILMSKGGKLSLQQNQMLIQQEGNEFTVPLEDIAIVVVESRETVITIPLLSAFGLHGVTFLTCDEQFLPCGQWLPFNQYHRQLKTLKLQLEASLPQKKQLWQAIVQQKIRNQAGVLKICKFQAESDRLLKMAEKVKSGDKENLEAQSAVIYFQTLFGKGFKRSEDESAVNSALNYGYTVMRSAVARALVLYGWLPQIGLFHRSELNAFNLADDFIEPFRPLVDLLVVQLENEDKLSANLSPILKQRLIKVLNYQLLFKQEKVNALTAIERSVGSFQTALSQRNADLLKLPEIIPLAEHQYE
>NC_009655.1|WP_041834594.1|431918_435116_+|type-II-CRISPR-RNA-guided-endonuclease-Cas9
MNNMNLNYILGLDLGIASVGWAVVEIDEQENPQRLIDVGVRTFDRAEVLKTGESLALARRLARSSRRLVKRRAERIKKAKRLLKAENLLLSADEILPNEAWQLRVKGLDQKLERQEWAAVLLHLLKHRGYLSQRKNESKSENKELGALLSGVAINHQILQSAEYRTPAEIAVNKFQAEEGHIRNQRGAYTHTFSRLDLLAEMELLFQRQATLGNPHTSTKLLENLTALLMWQKPALAGEAILKMLGKCTFEPTEYKAAKNSYSAERFVWLTKLNNLRILEQGAERALTDNERFALLDQPYEKAKLTYAQVRTLLGLSDEAIFKGLRYQGEDKKAVETKTTLMEVKAYHQIRKALEGLDLKAEWNELKNNPALLDEIGTAFSLYKTDDDIHRYLDGKLSESVLNALLENLNFDKFIQLSLKALQQILPLMLQGQRYDEAVSAIYGDHYGKKSDEIDRLLPNIPTDEIRNPVVLRTLTQARKVINAVVRLYGSPARIHIETGREVGKSYQDRKKLEKQQEENRKQRENAVKKFKEYFPNFVGEPKGKDILKMRLYELQQAKCLYSGKSLELYRLLEKGYVEVDHALPFSRTWDDSFNNKVLVLANENQNKGNATPYEWLDGKNNSEGWQHFVARVQTSGFSYAKKQRVLIQELDEKSFIERNLNDTRYVARFLCNHIADNMLLTGKGKRKVFASNGQITALLRGCWGLQKVRENNDRHHALDAVVVACSTKSMQDKITKFVKYKEGRLFKDKKDGVYKGERINRETGEIISLHFPTPWKFFKENVEIRIFSENPKLELENRLPDYPQYNHEFVQPLFVSRMPTRKMTGQGHMETVKSAKRLDKGLSVLKVPLTQLKLSDLERMVNREREMALYEALKECLEQFGNDPAKAFAEPFYKKGGALVKAVRVEQTQKSGVLVRNGNGVADNATGSIVRVDVFTKGGKYFLVPIYTWQVAKGILPNKAVIQGKDESEWEEMDENAVFQFSMHKNDLIKVKTKKGEIFGYFNGLDRATGSIEIEEHDLEKSKGKNGSHRGLGVKTAFFLEKYQVDELGKNIRPCRPTKRQHVR
>NC_009655.1|WP_011979027.1|430007_431357_-|NADP-specific-glutamate-dehydrogenase
MSNSVASLEEFLALVAKRDGNQPEFLQAVREVFTSIWPFLEKNPQYRSQALLERLVEPERAIQFRVAWTDDKGQTQVNRAFRVQFNSAIGPFKGGMRFHPSVNLSILKFLGFEQIFKNALTTLPMGGGKGGSDFDPKGKSDGEVMRFCQALISELYRHVGPDTDVPAGDIGVGGREVGYLAGYMKKLSNQAACVFTGRGLSFGGSLIRPEATGYGLVYFAQAMLAEKGQSFDGKTVLVSGSGNVAQYAIEKALQLGAKVVTCSDSSGYVYDEAGFTAEKLAALLEIKNVQRGRVKDYAEKFGLKYVAGEKPWTVKADIALPCATQNELDLDAAKTLIANGVQLVAEGANMPTTIEATEALQQAGVLFGPGKAANAGGVATSGLEMAQGSQREYWTAEVVDQKLHNIMLDIHANCKKYGTDEQGNINYVAGANIAGFVKVADAMLAQGVY
>NC_009655.1|WP_011978808.1|429175_429814_+|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase
MAYSTEQIIEKLSRLKVVPVIAVDEAKDIIPLVQTLSDNGLPVAEITFRSAAGEEAIRLTRQHFPDVLIAAGTVLTPAQAVAAKNAGADCIVTPGFNPNIVRLCQALDLPVTPGVNNPMAIEAALELGVKAVKFFPAEASGGVNMIKALLGPYANLQIMPTGGISPSNIKDYLAVPNVVACGGSWFVDKALIKSQNWDEIGRLVREAVELVS
>NC_009655.1|WP_011979026.1|428207_429146_+|sugar-kinase
MKKLALIGECMIELNGEPFGTMRQTYGGDTLNTATYVARVSSPERIQVCYVSALGTDKLSQGMIDRWQGDGIQTDWVLRDENRSAGLYLIQLDKQGERTFLYWRNQSAARYLLQHPDYPQVLSALKSADMIYLSGISLAILPENDRTLLIAQLRELKKAGVEIAFDSNFRPKLWDSLAQAQACYRALLPLVDVALVTFDDEEMLWSDTDEQATITRLSAFDIPKIIVKQGSLGATICENGTQTFVPTIPVENVTDTTSAGDSFNAGFLAGYLQGKPLTVCCEQGNRLAGIVIQHKGAIIDPAATEALRAAFN
>NC_009655.1|WP_011979025.1|427526_428207_+|GntR-family-transcriptional-regulator
MIEPKLRESSRDYAYRVIREMIVNMELVPGSKVSEIELANLLGISRTPVREALIDLARNGAVTIQPQKGTFISLIDSDLVEEARFLRKTLEKEVIALLCEDSYQKDLHILDESLSLQEFYLKQGNYEKFLELDNEFHQLFFKITHKDRIYALMKGLNIHFDRARTSIFKKKPSIKTLEEHKILLKAIHNQDKDTATQCIERHLYQYELDKDSFEKEYSHYFNKSGN
>NC_009655.1|WP_011979024.1|425915_427517_+|mannitol-dehydrogenase-family-protein
MKLSYDALNSKEWQEKGYQLPRFGISDVVSNTKQQPVWLHLGAGNIFRAFLANLQQRLLNQGDAQQGIIVAEGFDYEIIEKAYQPFDNLCVFAKLKNDHSVDKIVVASIVESLRMDPAFTQDFSRLKAIFQSPSLQMVSLTITEKGYLIKGLDGEYYPAVKADFEEGPAKPQSYIGKIIALLHERFAVGALPLAVVSMDNMSKNGEKLQKVILEFAEQWKKCGHLSQDFLDYLNSDKISFPWSMIDKITPRPDTEVQQQLQNDGIENLAPVVTSKNTYVAPFVNAEELEYLAVEDDFPNGRPALEKVGVIFADRDTVNKIETMKVTTCLNPLHTGLAIFGCLLGFTKISTEVQDADLSALIRKLGYQEGLPVVIDPQLINPKQFLDEVINIRFSNDFIPDTPQRIATDTSQKLAIRFGETIKSYVKAGKSTDSLVAIPLIFAGWLRYLLGIDDEGQPFENSPDPRLTELKAKLANITLGSVVSSATLKPILSDKSIFGVDLYEVGLAGRVEQYFNELLVGVGAVRTSLHKYVN
>NC_009655.1|WP_011979023.1|424842_425916_+|mannonate-dehydratase
MKTTFRWYGLGNDTIPLAHIKQIPSMTGVVWALHDIPAGEIWPEERIAEVKSQVEPYGLSIDVVESVNVHESIKLGASDRDVYIENYKTTLRSLGKYGVKVVCYNFMPVFDWIRTDLFKEADDGSTALFYEHARIDGIDPKVLVKQFEENSKDLTLPGWEPERLKHLDKLFDLYKGMTEDKLRENLKYFLEQIIPVAEEAGIRMAIHPDDPPFSVFGLPRIVKCHEDFQKIVDMVDSPANGITLCSGALGPNLKNNLPEMIRTFHKRIPFAHIRNIKVFENGDFYETSHLTRDGSLDIAEIVKAYHEVGFDGYWRPDHGRHIWDEKCRPGYGLYDRALGIMYVEGLWDAYEKEKGRK
>NC_009655.1|WP_011979022.1|423792_424812_+|zinc-binding-alcohol-dehydrogenase-family-protein
MKAITVSQPFELTVADVPAPTVTKDDDVIIKVAFGGICGSDIGIYTGGNSLAKYPAIIGHEFVGTVVETGKAVTHVKVGDYVVSDIVNSCGHCYACRTGHHNVCKNLQVTGVHSQGGFAEYAKTRADNVYLVDTNKIPHKTACLIEPYAVGVEINTRASIAAGDKVVVFGSGPAGLAVMQVARARGAEVLITDIFEERLQLAREMGATKAINVKDIDMRQAVNEFTDDEGAHVVVDAVCSPQSILDALDIVAPSGRLVVLGTGAAPSEIPQVAFTKKGINVFGTRLNNKRFPEVIRLFEEHKVTPEKMITHTYKFEDIEKAFDVIKNEKNTVCKVLLEW
>NC_009655.1|WP_011979031.1|436994_437462_-|thioredoxin-dependent-thiol-peroxidase
MNTLKPGENAPHFTLPNQHNEPVSLTDFQGKKVLIYFYPKALTPGCTIQACGLRDAKAELDKSGVIILGISPDSPKKLAQFEEKQALNFTLLSDEDHQVAEQFGVWGEKKFMGKVYDGIHRISFLIDENGKIEQVFTKFKTGEHHQVVLNYLTEK
>NC_009655.1|WP_011979032.1|437558_438134_+|Der-GTPase-activating-protein-YihI
MSRQKKSRRLTDVMPTRKADKKTEIGAVKARPGKKLTRYELDARAREEKRKRKHKGLDSGSRHSASSDSGKNQQTEVKDPRIGSRKKVPLVVEFVNKPEKGQFIQPIKTEKKPTALDPATELEQLENNECLNDLLDQLDAGKVLSKEDQVFVDECLARIAQLMDELGISDDEEGEDDLLRTFEKIDINQFR
>NC_009655.1|WP_011979033.1|438137_438569_+|DUF2489-domain-containing-protein
MMTTVLFVIGVAVMLAMAAYSVYLLAQLHKQQRLYQQARQARVARLKESIRIIARAMQSGECNHSEGVIRLKMLLDPLGQKTLTEYAAMWRLYETVRDMPTHDERRALKKNERMRLDLEREAKEIELEAAIKAEAKLLLSELP
>NC_009655.1|WP_011979034.1|438622_439990_+|oxygen-independent-coproporphyrinogen-III-oxidase
MTDITFDLALIQKYNQSGPRYTSYPTALEFNENYSENDFETAAARYPDRPLSLYVHIPFCHKLCYFCGCNKVITRHQHKADIYLDFLEKEITNRAPLFKNRTATQIHWGGGTPTYLSEAQSARLMDMLKSNFNIAENAEISIEMDPREIELSMLEHLRNIGFNRISMGVQDFNKEVQKAVNREQDEDFIRALLVRARELGFQSTNLDLIYGLPFQTVESFMFTLQKVIELNPDRLSVFNYAHLPSRFAGQVKIKDKDLPSPETKLSILQNTIETLAAAGYKFIGMDHFAKPDDELAIAQQNGVLHRNFQGYTTQEECDLLGLGVSAISLLGDSYAQNQKELKQYYADVDEKGIALHKGLTLTEEDCLRRDVIKALICNFKLDYAAIEQQYHIDFNTHFAEDLALLKPLAEDGLADIRPNGITVSSKGRLLIRNICLCFDTYSRQQARRQQFSRII
>NC_009655.1|WP_011979035.1|440059_440770_-|hypothetical-protein
MTLADYVETLQAEHRMERVYSFQFEGKSYWLKQPEHPKGIQRLLKPFSRAAFKREIQRIKLLIFQKAPIPPVKIINSRCLVMEDAGRTVRSWLESDITDEQKQRILDDCAKTLANLHARNIVHGRPLLKDILWQNGKASFIDFEVASRSRKLAQQKTRDALLFIYGVCRERTTPAQIQRTINTFIHYEDSRVWHYALSLVKKHRILYYVLLPFKSLAKTDLLGFYVLFETLLTKFL
>NC_009655.1|WP_011979036.1|440860_441658_-|serine-O-acetyltransferase
MAIKVWKQIRKEAQCLVNKEPMLASFFHSTILKHKHLGGALSYILANKLATTTMPAITLREIIEDAYAAKPSIIESAACDITAVRQRDPAVDLWSTPLLYLKGFHALQSYRITHYLWQENRRSLAIYLQNQISVAFDVDIHPAARIGCGIMFDHATGIVVGETAVIENDVSILQGVTLGGTGKECGDRHPKIREGVMIGAGAKILGNIEVGKYAKIGANSVVLQPVPEHATAAGVPARIIGKDHDSKPAFEMNQYFIDDAAMLNI
>NC_009655.1|WP_012072148.1|441667_442675_-|NAD(P)H-dependent-glycerol-3-phosphate-dehydrogenase
MVNQSPITILGAGSYGTALAICFSRNGYPTTLWGHNREECQHLQQERQNRRFLPDIAFPDSLTIEADLASAVKKSKDLLIVVPSHAFGEVIHRIKPFLRPDSRIAWATKGLERNSGRLLQSVVEDELGKAYPLAVLSGPTFAKELAAGMPTAIALAANDERFAREFQTRIHCSKHFRVYLNRDMIGVQLGGAIKNVIAIAAGMSDGLGFGANARTALITRGLAEISRLGVSLGANLKTFTGMSGLGDLVLTCTDNQSRNRRFGMMLGQGVSAQAAMEQIGQIVEGFYNTKETMALAQRQGVEMPITEQIYAALFHGKNPQEMATALLQRERKDEY
>NC_009655.1|WP_012072149.1|442734_443235_-|protein-export-chaperone-SecB
MTDENQAAPAEQAQEPVLQIQRIYVKDVSFEAPNLPDIFQQEWKPNLNFDLGTEAKQLGENLFEVTLNVSVETTLEDSGDAAFICEVKQAGVFTIGGLTDIQLTHALTSQCPNMLFPYARELVASLVNRGTFPPLNLAPVNFDALFLEHMRRVEEESAPEEQPTLN
>NC_009655.1|WP_012072150.1|443245_443683_-|rhodanese-like-domain-containing-protein
MEEFLTLATPFIKNHTLMVVGWVAIFIAFIYVNFKAITSKVKLVSNAEAVALINNQNAVVIDLRTIEEFKRGHIVNSKEFVPSDIKNHNLGKLEQHKDVPVILVCASGITARSSGEILAKQGFNHVYVLQEGIAGWNAENLPLVK
>NC_009655.1|WP_012072151.1|443803_444730_-|cell-division-protein-FtsX
MSSTQKAPFWVQMKYVLAYVRADLIKKKYGTLLTVLVIAVSLTIPTVSFLLWKNTHNAITRFSPDSELTVYLHKNLNEDDANGVVEKVRSQEGVESLNYVSRQESLKDFRAWSGFGEELDILDDNPLPAVVMIKPTEEFKASEKRQELRENLAKIKGVEEVRMDNDWLEKLTAITWLIAHVAIFCAVLMTLAVFLVIGNSIRSDVYSSQADIQVMKLLGATDQFILRPFLYTGIIYGFFGAFFACFFSALLIGYFTSAVKYVTDIFAVSFNLGGLDFGEMLFLLVICSIVGYASAWISATRHIRLLDK

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Crispr_ID: NC_009655_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_009655_2

1440909-1441676

TypeI

Consensus_repeat	Method
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	PILER-CR
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	CRISPRCasFinder
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	CRT

11 spacers

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

The CRISPR arrays of NC_009655_2

>merge|NC_009655|2|1440909-1441676|PILER-CR,CRISPRCasFinder,CRT
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACGCCGTTTTCGGCGATCAATTAGCCGCGCTCTATGCGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACAGCGTTGTGTTGAACAAGCAGTTGAGCAAATAAGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACTGATGCATCACGCGTAGTCCCAACCGCAGCCGAAAAGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACCAATTCACCATCGTACCGAAATCCGAGGGTTTCGGCAGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACCCGCCGGGATGGTGATGCCGGCGGCCTCTTTGGCGGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACGTTAAAGCGCAGTTTAACACTGCAACAACATTAAAGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACGCGAAATCAACCATGCTTAAAAAATTGTATTTGGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACGCGTTATCGGTTTCCGCCGGCAAAGCAAGGGTAAGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACAGCGCGTTAGCATGATTTGCTTGTTTAGTTTTTAGGCAGCCGCCTTCGGGCGGCTGTGTGTTGAAACGCAAGTATAGTTTACGCCGGGAAAAACGAGGAGGTGCAGCCGCCTTCAGGCGGCTGTGTGTTGAAACATCAAGCGTTGAAGGTGCGGATATTAATAGCGGTATGCAGCCGCCTTCGGGCGGCTGTGTTGCTTACT

>NC_009655|2|2|1440909-1441608|PILER-CR
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCCGTTTTCGGCGATCAATTAGCCGCGCTCTATGC
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	AGCGTTGTGTTGAACAAGCAGTTGAGCAAATAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	TGATGCATCACGCGTAGTCCCAACCGCAGCCGAAAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	CAATTCACCATCGTACCGAAATCCGAGGGTTTCGGCA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	CCGCCGGGATGGTGATGCCGGCGGCCTCTTTGGCG
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GTTAAAGCGCAGTTTAACACTGCAACAACATTAAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCGAAATCAACCATGCTTAAAAAATTGTATTTG
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCGTTATCGGTTTCCGCCGGCAAAGCAAGGGTAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	AGCGCGTTAGCATGATTTGCTTGTTTAGTTTTTAG
GCAGCCGCCTTCGGGCGGCTGTGTGTTGAAAC	GCAAGTATAGTTTACGCCGGGAAAAACGAGGAGGT
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC

>NC_009655|2|2|1440909-1441676|CRISPRCasFinder
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCCGTTTTCGGCGATCAATTAGCCGCGCTCTATGC
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	AGCGTTGTGTTGAACAAGCAGTTGAGCAAATAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	TGATGCATCACGCGTAGTCCCAACCGCAGCCGAAAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	CAATTCACCATCGTACCGAAATCCGAGGGTTTCGGCA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	CCGCCGGGATGGTGATGCCGGCGGCCTCTTTGGCG
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GTTAAAGCGCAGTTTAACACTGCAACAACATTAAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCGAAATCAACCATGCTTAAAAAATTGTATTTG
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCGTTATCGGTTTCCGCCGGCAAAGCAAGGGTAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	AGCGCGTTAGCATGATTTGCTTGTTTAGTTTTTAG
GCAGCCGCCTTCGGGCGGCTGTGTGTTGAAAC	GCAAGTATAGTTTACGCCGGGAAAAACGAGGAGGT
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	ATCAAGCGTTGAAGGTGCGGATATTAATAGCGGTAT
GCAGCCGCCTTCGGGCGGCTGTGTTGCTTACT

>NC_009655|2|2|1440909-1441676|CRT
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCCGTTTTCGGCGATCAATTAGCCGCGCTCTATGC
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	AGCGTTGTGTTGAACAAGCAGTTGAGCAAATAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	TGATGCATCACGCGTAGTCCCAACCGCAGCCGAAAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	CAATTCACCATCGTACCGAAATCCGAGGGTTTCGGCA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	CCGCCGGGATGGTGATGCCGGCGGCCTCTTTGGCG
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GTTAAAGCGCAGTTTAACACTGCAACAACATTAAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCGAAATCAACCATGCTTAAAAAATTGTATTTG
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	GCGTTATCGGTTTCCGCCGGCAAAGCAAGGGTAA
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	AGCGCGTTAGCATGATTTGCTTGTTTAGTTTTTAG
GCAGCCGCCTTCGGGCGGCTGTGTGTTGAAAC	GCAAGTATAGTTTACGCCGGGAAAAACGAGGAGGT
GCAGCCGCCTTCAGGCGGCTGTGTGTTGAAAC	ATCAAGCGTTGAAGGTGCGGATATTAATAGCGGTAT
GCAGCCGCCTTCGGGCGGCTGTGTTGCTTACT

Protein	Signature genes	Signature genes Name	Protein_function
NC_009655.1\|WP_012073032.1\|1443395_1444049_+\|GTP-cyclohydrolase-I-FolE	unknown	unknown	gnl\|CDD\|129173
NC_009655.1\|WP_012073030.1\|1440423_1440717_+\|CRISPR-associated-endonuclease-Cas2	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|187856
NC_009655.1\|WP_012073037.1\|1447177_1448386_-\|ATP-binding-protein	unknown	unknown	gnl\|CDD\|224292
NC_009655.1\|WP_012073028.1\|1438454_1439357_+\|hypothetical-protein	unknown	unknown	unknown
NC_009655.1\|WP_012073035.1\|1445757_1446120_-\|RidA-family-protein	unknown	unknown	gnl\|CDD\|100004
NC_009655.1\|WP_012073022.1\|1432938_1433682_+\|type-I-C-CRISPR-associated-protein-Cas5	cas5	cd09752_cas5_CAS-I-C	gnl\|CDD\|187782
NC_009655.1\|WP_012073025.1\|1436603_1437278_+\|CRISPR-associated-protein-Cas4	cas4	cd09637_cas4_CAS-I:CAS-II:CAS-V	gnl\|CDD\|273040
NC_009655.1\|WP_012073036.1\|1446119_1446743_-\|transcriptional-regulator	unknown	unknown	gnl\|CDD\|377981
NC_009655.1\|WP_012073029.1\|1439370_1440384_+\|type-I-C-CRISPR-associated-endonuclease-Cas1	cas1	cd09721_cas1_CAS-I-C	gnl\|CDD\|188360
NC_009655.1\|WP_012073024.1\|1435763_1436603_+\|type-I-C-CRISPR-associated-protein-Cas7/Csd2	cas7	cd09689_cas7_CAS-I-C	gnl\|CDD\|187820
NC_009655.1\|WP_049752185.1\|1437882_1438266_+\|transcriptional-regulator	unknown	unknown	gnl\|CDD\|334619
NC_009655.1\|WP_012073039.1\|1449219_1449933_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|225917
NC_009655.1\|WP_083757705.1\|1437318_1437726_-\|carboxymuconolactone-decarboxylase-family-protein	unknown	unknown	gnl\|CDD\|223672
NC_009655.1\|WP_012073031.1\|1441745_1443149_-\|asparagine--tRNA-ligase	unknown	unknown	gnl\|CDD\|235176
NC_009655.1\|WP_012073023.1\|1433678_1435742_+\|type-I-C-CRISPR-associated-protein-Cas8c/Csd1	cas8c	pfam09709_cas8c_CAS-I-C	gnl\|CDD\|187887
NC_009655.1\|WP_012073034.1\|1444652_1445747_-\|pyridoxal-phosphate-dependent-enzyme	unknown	unknown	gnl\|CDD\|107206
NC_009655.1\|WP_012073040.1\|1450173_1451502_-\|TRAP-transporter-large-permease-subunit	unknown	unknown	gnl\|CDD\|225407
NC_009655.1\|WP_012073038.1\|1448774_1449134_+\|rhodanese-like-domain-containing-protein	unknown	unknown	gnl\|CDD\|238089
NC_009655.1\|WP_012073021.1\|1430488_1432924_+\|CRISPR-associated-helicase/endonuclease-Cas3	cas3	COG1203_cas3_CAS-I	gnl\|CDD\|224124
NC_009655.1\|WP_012073033.1\|1444151_1444643_-\|YbaK/prolyl-tRNA-synthetase-associated-domain-containing-protein	unknown	unknown	gnl\|CDD\|239828

Protein	Function_ID	Function_description	E-value
NC_009655.1\|WP_012073032.1\|1443395_1444049_+\|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].	2.69931e-97
NC_009655.1\|WP_012073030.1\|1440423_1440717_+\|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.	1.48025e-33
NC_009655.1\|WP_012073037.1\|1447177_1448386_-\|ATP-binding-protein	gnl\|CDD\|224292	COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only].	3.73729e-60
NC_009655.1\|WP_012073035.1\|1445757_1446120_-\|RidA-family-protein	gnl\|CDD\|100004	cd00448, YjgF_YER057c_UK114_family, YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.	3.99784e-40
NC_009655.1\|WP_012073022.1\|1432938_1433682_+\|type-I-C-CRISPR-associated-protein-Cas5	gnl\|CDD\|187782	cd09651, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family.	3.48893e-93
NC_009655.1\|WP_012073025.1\|1436603_1437278_+\|CRISPR-associated-protein-Cas4	gnl\|CDD\|273040	TIGR00372, conserved_hypothetical_protein, CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.	8.51511e-44
NC_009655.1\|WP_012073036.1\|1446119_1446743_-\|transcriptional-regulator	gnl\|CDD\|377981	pfam08348, PAS_6, YheO-like PAS domain. This family contains various hypothetical bacterial proteins that are similar to the E. coli protein YheO. Their function is unknown, but are likely to be involved in signalling based on the presence of this PAS domain.	1.74118e-41
NC_009655.1\|WP_012073029.1\|1439370_1440384_+\|type-I-C-CRISPR-associated-endonuclease-Cas1	gnl\|CDD\|188360	TIGR03640, cas1_DVULG, CRISPR-associated endonuclease Cas1, subtype I-C/DVULG. 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 the Cas1 protein particular to the DVULG subtype of CRISPR/Cas system.	0
NC_009655.1\|WP_012073024.1\|1435763_1436603_+\|type-I-C-CRISPR-associated-protein-Cas7/Csd2	gnl\|CDD\|187820	cd09689, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas7. 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; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as Csd2 family.	3.2183e-111
NC_009655.1\|WP_049752185.1\|1437882_1438266_+\|transcriptional-regulator	gnl\|CDD\|334619	pfam01638, HxlR, HxlR-like helix-turn-helix. HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.	3.30007e-36
NC_009655.1\|WP_012073039.1\|1449219_1449933_-\|hypothetical-protein	gnl\|CDD\|225917	COG3382, COG3382, Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only].	6.10556e-44
NC_009655.1\|WP_083757705.1\|1437318_1437726_-\|carboxymuconolactone-decarboxylase-family-protein	gnl\|CDD\|223672	COG0599, COG0599, Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown].	2.34095e-23
NC_009655.1\|WP_012073031.1\|1441745_1443149_-\|asparagine--tRNA-ligase	gnl\|CDD\|235176	PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.	0
NC_009655.1\|WP_012073023.1\|1433678_1435742_+\|type-I-C-CRISPR-associated-protein-Cas8c/Csd1	gnl\|CDD\|187887	cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c. 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; Zn-finger domain containing protein, distant homologs of Cas8 proteins; signature gene for I-C subtype; also known as Csd1 family.	0
NC_009655.1\|WP_012073034.1\|1444652_1445747_-\|pyridoxal-phosphate-dependent-enzyme	gnl\|CDD\|107206	cd01563, Thr-synth_1, Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants, OPH is an intermediate between the methionine and threonine/isoleucine pathways. Thus threonine synthase competes for OPH with cystathionine-gamma-synthase, the first enzyme in the methionine pathway. These enzymes are in general dimers. Members of this CD, Thr-synth_1, are widely distributed in bacteria, archaea and higher plants.	3.28437e-130
NC_009655.1\|WP_012073040.1\|1450173_1451502_-\|TRAP-transporter-large-permease-subunit	gnl\|CDD\|225407	COG2851, CitM, H+/citrate symporter [Energy production and conversion].	2.83788e-121
NC_009655.1\|WP_012073038.1\|1448774_1449134_+\|rhodanese-like-domain-containing-protein	gnl\|CDD\|238089	cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.	2.07515e-29
NC_009655.1\|WP_012073021.1\|1430488_1432924_+\|CRISPR-associated-helicase/endonuclease-Cas3	gnl\|CDD\|224124	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms].	3.34925e-52
NC_009655.1\|WP_012073033.1\|1444151_1444643_-\|YbaK/prolyl-tRNA-synthetase-associated-domain-containing-protein	gnl\|CDD\|239828	cd04336, YeaK, YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, and ProX. The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation. Organisms whose ProRS lacks the INS domain express a single-domain INS homolog such as YbaK, ProX, or PrdX which supplies the function of INS in trans.	1.71215e-67

>NC_009655.1|WP_012073030.1|1440423_1440717_+|CRISPR-associated-endonuclease-Cas2
MLMLITYDISFDDPGGQKRLRRIAKHCLDYGVRTQYSVFECDVTPDQWVRLKAKLLETYDPECDSLRFYHLGSKWRRKVEHHGAKPAVDIFKDTLIL
>NC_009655.1|WP_012073029.1|1439370_1440384_+|type-I-C-CRISPR-associated-endonuclease-Cas1
MRKLQNTLYITTQGSYLHKERETLVVEQDRKKVAQLPVHSIGHIFCFGNVLVSPFLMGFCGENNVNLAFFTENGRFLGRLQGRQSGNVLLRRAQYQRSESNPVSIARNIIAAKIQASKRVLQRQIRNHGDNAEIQTAVSALNSSLMQLKKAENLELIRGIEGDAASRYFGVFGQLLKAESGFVFDGRNRRPPRDGVNALLSFLYSILGKDISGALQGVGLDPQVGFLHADRPGRDSLAQDILEEFRAWWVDRMVLSLINRGQIKPDDFTQEAGGAVNIKPDVRKLIFQTLQAKKQEKITHPFLGEEVEIGLLPYIQSMLLARHLRGDLAEYPPFLMR
>NC_009655.1|WP_012073028.1|1438454_1439357_+|hypothetical-protein
MMSLQQAYSLDLGKKVNAKEADIAYQAGLISSQKNFRCPHQLCGIAVTCANLERPKHKRKVEPYFKSVEYHKPNCPFAEEERCIKLQGTDQRSLYENVASGEILVNLAEPSPKKQNILGASEVKKGSFSRTTQSSDSKKEKVSINHTKTLSVLISSFLNNENFQITLPKPYQETIFLKDVFIKIDEQNLSDLEQNCWRIFYGKAWINKGANGDYRIVFNNKLYDSSLEKGEVRPSFFIPKQWIDNSAYQKFSSEKMDELVTKKWPRTVFILADTPALNHSQKYINFMLEGLPYLEMRYLK
>NC_009655.1|WP_049752185.1|1437882_1438266_+|transcriptional-regulator
MKKISAIDLAMKLVGGKWKCLILYHLYCGDKRPRDLLQLLEGISQKVLTEQLRQLEGDGLIARRVYSEVPPRVEYRLTDEGAGLEPALRMLCDWSRDYDSRHGNRVEICFAKNEQDTSSLSLQGNVD
>NC_009655.1|WP_083757705.1|1437318_1437726_-|carboxymuconolactone-decarboxylase-family-protein
MIALTLFGCITAAHAQRNEQNTTDRLAAQAPTQVTIGRERLGKFAPKFAEINDDLVYGQIWSRTNELPLRERAMITIAAMIAAGDFDQLEFQMQRAKEYGVTKQEMSELITHLAFYSGGPKAWSAFQRAIKVYGE
>NC_009655.1|WP_012073025.1|1436603_1437278_+|CRISPR-associated-protein-Cas4
MTENLQNFPQKPPLAGRNGVGESRPIPLSALQHYAFCPRQCALIHNEQAWAENFLTAQGRVLHERVDGGEPETRKGVRFERSMHLSAQRLGISGIADMVERDLATGRLKPVEYKRGKPKPTAMDEIQLCAQALCLEEMTGQTIEEGALWYMQTRRRIPVAFSDELRAQTLAVIEQVRALLESGRTPPPRYGKHCKACSLVEICQPKLLEKDKSGRYVKGLFGEY
>NC_009655.1|WP_012073024.1|1435763_1436603_+|type-I-C-CRISPR-associated-protein-Cas7/Csd2
MSLTKKIDFALILKVTNANPNGDPLNGNRPRTDFAGIGEMTDVCLKRKIRDRLQSNGESIFVQSDEKKTDGMTSLANRAKDKDVGLGAEAFGKKANKDETAKAACAKWLDVRSFGQVFAFGKSDDGAGVSIAVRGPVTIQSAFSVEPVNITSTQITKSVSGEGDGTKRGSDTMGMKHRVDSGIYVAFGAMSPQLAERTGFSDEDADKIKAVLTKLFEGDASSARPEGSMQVLKLIWWEHNCKSGQYSSAKVHGSLKVNTDGSYQLDNLDGLKPEEIDGF
>NC_009655.1|WP_012073023.1|1433678_1435742_+|type-I-C-CRISPR-associated-protein-Cas8c/Csd1
MSWMQKLYRTYNEVEMRSDLSDTDKEALAPLWHSPQTAHIQITLDGAGNFISAKVLVDKPIIMLPVTESSEGRTSGLAPHALADSLQYVAKDLGLTYQKEVITEIEGKNDKKKKTKIKQEDLIFNLYVEQLDKWCAKTDNKKILAIQKYVHKGTVLADLIKVKVVPTNEQGTLLDNWIEKDNKERSKPELFTVLAKEQGKFEIRKALVVWAVEIPGDESSATWKDKEVQQNWGIYYQSTLDSQFCMMTGEERQIRESHPAKLTYTGDKAKLISANDKDGYTFRGRFETSNQASSISAEVSHKAHAVLRWLIARQGIRNGDQVTVAWAISGKEIPSPMKDTFDEIDWDNLDTSAVENNEEIKMPSENENNGIDWSANIGRQAAAIIKKKWRGYQAELKEYEQISLLMLDSATPGRMALTYYQEFLPADYFDNLDAWVDDFAWYQRRSIEKKNGKKNDKQTLWPELPPSPFDIGHAVYGKALSDTLKKQLYARLLPVIAGGRQVPIPYDLVQKSFQTACNPHGFENWEWQRNIGVACALYKGWRARHHDLSQRRTYLMSLDKENRSRDYLFGRLLAVADNIESYALYLAGEKRAPTAERYMQQFAERPFSTWRNIELALKPYQERLRNNGKDTGSQAISEIMELFAWEEFVDDGKLSGEFLLGYHCQKMAIAREISERVAAKTKTTETH
>NC_009655.1|WP_012073022.1|1432938_1433682_+|type-I-C-CRISPR-associated-protein-Cas5
MNNKNTFRSKPFCFRVWGRQALFTDPVTKIGGEKFSYQVPTYEALKGILKSIYWKPTLIWHIDRVRVMKPIRTQSKSTKPLDWNGGNTLAIYTFLQDVEYQVEAHFTWNENWEELKGDRNEGKHTAIAERMLHRGGRQDIFLGTRDCQGYVEPCEFGSGKGFYDEIDNLDFGLMFHSFGYPEETGKHELISRFWNAGMQRGKIEFPSVNDVSGSLKTRFIRKMKPEKPFKRGENVKPVEDEAKELGL
>NC_009655.1|WP_012073021.1|1430488_1432924_+|CRISPR-associated-helicase/endonuclease-Cas3
MNESFIAHIREVDKQRQSVQVHLLETAVIASMFAVKLDLSEAGELLGLMHDFGKYSTAFQEYIRAVTGQDPDADNDYVLPNGKKIDHSTAGAQWVYRRLKKFGLQNGIGELVGQILGLCIASHHGEGLIDCLNMNGEAVWQKRFDKEDELTHLSECEQRADKAVKIRAEELAGENLVKSLLKLLAAIFKNPDSNDKIKEFYLGCLTRFLFSCLIDADRINSADFEREEQKDLRRLNQSPDWQQAIDKLETHLANFEIRYPIDEIRREISSTCLKRANDPQGIYTLTVPTGGGKTLASLRYALHHAHKHNLDRIIYIIPYTSIIDQNASAVREILGEDWVLEHHSNLEPEQQNWQDKLLSENWDKPIVFTTMVQFLDAWFGGGTRGVRHIHPMTKSVLIFDEIQTLPVKCVHLFCNVLNWLTQFGKSSAVLCTATQPLLDNLPKSEFGELKLAENSEIMGQNKTLNQLFDDLSRVEIHYKPKAGGWSADEAGAFLLEQFQTASSCLFIVNTKKWAQELYQYCQRQDVPPEALFHLSTNQCSVHRKAIFDEIKGRLKNKQPVICISTQLIEAGVDISMSCVIRALGGLDSIAQAAGRCNRHGEKVGKGQVYVLNLQEPNLARVLPDIDQGQQNAERVLREFAEQDILQPAAMRQYFEYYFYNRSNDMSYTVKGSTSGSLLDWLSDNRLNVYAAKNDKRRPKLPLLMQSFKSAGRAFQAIDAPTRAVIVPYSKGKDLIAELCGVWNPKEMYRILSKVQRYSVNVFPNVWEKLEKEQAVQEVQAGLGIYYLKERYYSDEYGLSVDEVGAMTFYEL
>NC_009655.1|WP_012073031.1|1441745_1443149_-|asparagine--tRNA-ligase
MTKIASIADVLQGEIAVGEKVTVRGWVRTRRDSKAGLSFLTVYDGSCFNPIQAIINNDIVNYESEVLRLTAGCSVIVTGTVVESPAQGQAVELQTETVEVVGWVEDPDTYPMAAKRHSIEYLREVAHLRPRTNIIGAVARVRHCLAQAIHRFFHEQGFYWVATPLITASDTEGAGEMFRVSTLDLENLPRTQAGTVDFNQDFFGKEAFLTVSGQLNGETYACALSKIYTFGPTFRAENSNTTRHLAEFWMVEPEIAFATLADNAKLAEDMLKYVFNAVLTERRDDLEFFSKHVDKDVITRLEHFVNSPFAQIDYTDAIDVLVKSGKKFEFPVSWGIDLSSEHERYLAEEHFKSPVVVKNYPKGIKAFYMRLNDDGKTVAAMDVLAPGIGEIIGGSQREERLDVLDKRMVEMGLKPEDYWWYRDLRKYGTVPHSGFGLGFERLIVYVTGVQNIRDVIPFPRSPRNANF
>NC_009655.1|WP_012073032.1|1443395_1444049_+|GTP-cyclohydrolase-I-FolE
MTISAEAKKVRNALIEKGIETPMVEFQQNKNERRTAIQQKMREVMELIGLDLRDDSLEETPVRLAKMYVDEIFSGLDYANFPKITNIENRMKVSEMVLVNDVTLTSTCEHHFVTIDGLVSVAYYPKKWVIGLSKINRVVQFFAQRPQVQERLTEQVLLAFQTILETDDVAVYMKATHFCVKCRGIKDSNSYTVTSAFGGVFLEDRETRKEFLSLVNK
>NC_009655.1|WP_012073033.1|1444151_1444643_-|YbaK/prolyl-tRNA-synthetase-associated-domain-containing-protein
MSEKTFEKLTALLDRQHARYRVVEHSSAGKSKEVAKLRGTELGQGAKALVCKIKGNGVKQAVLAVLPADKQAELTKIAEYLGGAKASLASPKEVSELTDCVFGAIPPFSFHPDLRLIADPSLLERYDELAFNAGTLERSLILNTQDYARITAPEWVRFAKPDE
>NC_009655.1|WP_012073034.1|1444652_1445747_-|pyridoxal-phosphate-dependent-enzyme
MKFICNQCHQTAPVSTRQAKCQCGGLWTLDYHPPKFDLNDIDRHEWSLFRYRKFIALQDESWRGISLGEGMTPIVRFDDNVLLKMDYFMPTLSFKDRGAAVLISHCKAIGVDSVVQDSSGNAGNSVAAYCAKAGIQCEIFVPEGTSPKKINMIEAHGAKANVIAGSRDHCADVCRAKVENEGIYYANHVYNPFFYEGTKTYIYETFEQLGRIPKHIVVPVGNGTLFIGVIKGLEHLLASGAINEMPTIIALQSEHCDPLLQAVEKGQKFAENVEVKPTIAEGIAIGQPMRAAEILTYAEKYPVRFVHAPEDKILAARDILAKKGVYCEHTTAANYAAYLRYCELYGTAEDCLITMCGAGLKSDH
>NC_009655.1|WP_012073035.1|1445757_1446120_-|RidA-family-protein
MEMILPDQSKGHYSPAVKSNGMLYVSGQLPFNAEGKIVGDVAAQTKQALANLAQVLSAAGLSKNDVVQCRVYIPDVAYWDTVNQVYADFFGSHKPTRTIVPCGNLHYNALIEIEATAEFA
>NC_009655.1|WP_012073036.1|1446119_1446743_-|transcriptional-regulator
MNPILTPYISMADMLVETFGKSCEVVLHDLNDPEHSVVYVAGEVTHRKLGQNFEHLVKEVMLSDKLNNDYVANYYFEAKGKLIRSSTQLIFDQNHQLVGALCINIDTTPITDQIAYLNALLPNLNPPKQAEQTAELPLSEMVENLMEKILNGRSAEAMTRDEKIEKVRFMEQKGLFLMKGSIEKAAEKLGVNKVTIYSYLDEVRGKR
>NC_009655.1|WP_012073037.1|1447177_1448386_-|ATP-binding-protein
MKKDLIYRKRYLERVRPFIGKSLIKVFTGQRRVGKSYLLFQIMQEIQAGDSQANIIYINKEDLAFSHLKTAQDLAEFVLGEKKSGQKNYVFIDEIQEISEFDTALRSLLLDDDLDLYCTGSNAHLLSRDIAGSLSGRAIEINVHSLSYFEFLEFMRLEDGDKAMSQFLKYGGLPYLKDLPLQDNIVFEYLRNIYSTIAIRDIVNRYALRNVQFLEQLTQFFASNIGNLFSAKKISDFLKSQKINANTVQVQNYAEYLANAFLIHKVPRYDIEGKRLFEIGEKYYFEDLGLRNALIGYQVQDRGKLLENTIFNHLQIAGYDVKIGGLGTQEIDFIAEKDGERIYVQATLTINEEKTLEREFGNLLKIQDNYPKYVVTMDEFEGNTFEGVECLSLKGFLSILNK
>NC_009655.1|WP_012073038.1|1448774_1449134_+|rhodanese-like-domain-containing-protein
MKKLTLTLLAALVWASPMISVAAETERAVERSEQARAIWIDVRTPEEFAEGHIEGAVNLPFDQIGARIHEVTADKNAPIHLYCRSGRRSGLALETLKAQGYTNLVNRGGYRDLLVQNIR
>NC_009655.1|WP_012073039.1|1449219_1449933_-|hypothetical-protein
MKFKIAAEIFEKLPHFCAGVVVVKGFDNRKHYPEIDALLEQAVAAAEQRFADVKVKESPLITPYRNAFQALDINPNKFQCSAEALFTRIAKGKGLPHINPLVDLNNAVSLTYTLPMGTHDLGISPQDIEMRPAKDSDRFIPFGATESENVPTGEVVYAVDNQVRTRRWTWRQSEVGKIGADTHYVFFPIDGFIGVNDDSVRQAASALAEMLEKLGAGKVKTGFVDKANPEMDLSLDE
>NC_009655.1|WP_012073040.1|1450173_1451502_-|TRAP-transporter-large-permease-subunit
MFLGVVGMLMIVVIVWALIQSKTHPVPIFVIVPIIAALICGFTPVEIFGFIKDGVSKTWSTAVLFIFSIVYFSLMGDVGLFDPMVNWLAKKAGNNIMLVTIATSLISVVAHLDGALASTLLITIPAMLPVYKKLHIRPVVLLCIIGASMSIMNLVPWGGPVARTGVVLSADVNELWKELIPLQIVGLIILVIFAGYMGLIEKRRGAGINPTGKAAELDETLVPTDSGTSKADLEAMKRPKLLWFNALLTLVVIGLLCFTKIPLYGAFMFGLAVALIVNFPGSKAQAKAIKVHADTALTMPMILLASGIFLGVLSGTKMMENMAMLLISVIPNAIGGHLQDVFGILGLPIGMLLGTDSYFFGLMPLAIGVGEQFGVSGQDMAMAMLISKNYGVLVTPHAATTFLACGLAGVEIKDMLKFCAPRLWVLSLISLACGAALGLFAL

You can click texts colored in the table to view more detailed information

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_009655_1	1.5\|436772\|30\|NC_009655\|PILER-CR,CRISPRCasFinder,CRT	436772-436801	30	MK552327	Pseudomonas phage Psa21, complete genome	195841-195870	6	0.8
NC_009655_1	1.2\|436574\|30\|NC_009655\|PILER-CR,CRISPRCasFinder,CRT	436574-436603	30	NZ_CP045414	Roseovarius sp. THAF8 plasmid pTHAF8_d, complete sequence	49497-49526	8	0.733
NC_009655_2	2.2\|1441008\|33\|NC_009655\|PILER-CR,CRISPRCasFinder,CRT	1441008-1441040	33	MN657118	Psychrobacter sp. strain ANT_P53 plasmid pA53P4, complete sequence	957-989	8	0.758
NC_009655_2	2.2\|1441008\|33\|NC_009655\|PILER-CR,CRISPRCasFinder,CRT	1441008-1441040	33	NZ_MK422609	Psychrobacter sp. DAB_AL32B plasmid pP32BP2, complete sequence	1136-1168	8	0.758
NC_009655_2	2.5\|1441210\|35\|NC_009655\|PILER-CR,CRISPRCasFinder,CRT	1441210-1441244	35	NZ_AP022593	Mycolicibacterium arabiense strain JCM 18538 plasmid pJCM18538, complete sequence	1055902-1055936	8	0.771
NC_009655_2	2.7\|1441344\|33\|NC_009655\|PILER-CR,CRISPRCasFinder,CRT	1441344-1441376	33	MN855609	Siphoviridae sp. isolate 454, complete genome	3631-3663	9	0.727
NC_009655_2	2.7\|1441344\|33\|NC_009655\|PILER-CR,CRISPRCasFinder,CRT	1441344-1441376	33	MN855739	Bacteriophage sp. isolate 86, complete genome	1005-1037	9	0.727
NC_009655_2	2.5\|1441210\|35\|NC_009655\|PILER-CR,CRISPRCasFinder,CRT	1441210-1441244	35	NZ_CP032928	Agrobacterium tumefaciens strain 1D1460 plasmid pAt1D1460, complete sequence	15907-15941	10	0.714

1. spacer 1.5|436772|30|NC_009655|PILER-CR,CRISPRCasFinder,CRT matches to MK552327 (Pseudomonas phage Psa21, complete genome) position: , mismatch: 6, identity: 0.8

aaacaactgtaccagttgaattacgttgag	CRISPR spacer
agacaactgtaacaggtgaattacgttatc	Protospacer
*.********* *** ***********.

2. spacer 1.2|436574|30|NC_009655|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP045414 (Roseovarius sp. THAF8 plasmid pTHAF8_d, complete sequence) position: , mismatch: 8, identity: 0.733

gctagaaagctcgacatccttaaaaagcct	CRISPR spacer
cctgcccgtctcgacatccttaaatagcct	Protospacer
 **.   . *************** *****

3. spacer 2.2|1441008|33|NC_009655|PILER-CR,CRISPRCasFinder,CRT matches to MN657118 (Psychrobacter sp. strain ANT_P53 plasmid pA53P4, complete sequence) position: , mismatch: 8, identity: 0.758

agcgttgtgttgaacaagcagttgagcaaataa	CRISPR spacer
agtcagttattgaaaaagccgttgagcaaataa	Protospacer
**.    *.***** **** *************

4. spacer 2.2|1441008|33|NC_009655|PILER-CR,CRISPRCasFinder,CRT matches to NZ_MK422609 (Psychrobacter sp. DAB_AL32B plasmid pP32BP2, complete sequence) position: , mismatch: 8, identity: 0.758

agcgttgtgttgaacaagcagttgagcaaataa	CRISPR spacer
agtcagttattgaaaaagcagtcgagcaaataa	Protospacer
**.    *.***** *******.**********

5. spacer 2.5|1441210|35|NC_009655|PILER-CR,CRISPRCasFinder,CRT matches to NZ_AP022593 (Mycolicibacterium arabiense strain JCM 18538 plasmid pJCM18538, complete sequence) position: , mismatch: 8, identity: 0.771

ccgccgggatggtgatgccggcggcctctttggcg	CRISPR spacer
ccgccgggatggtgctgacggcggctgcgaggccg	Protospacer
************** ** *******. *   * **

6. spacer 2.7|1441344|33|NC_009655|PILER-CR,CRISPRCasFinder,CRT matches to MN855609 (Siphoviridae sp. isolate 454, complete genome) position: , mismatch: 9, identity: 0.727

gcgaaatcaaccatgcttaaaaaattgtatttg	CRISPR spacer
aagaaatcaacattgcttaaaaaattgaacgca	Protospacer
. *********  ************** *. ..

7. spacer 2.7|1441344|33|NC_009655|PILER-CR,CRISPRCasFinder,CRT matches to MN855739 (Bacteriophage sp. isolate 86, complete genome) position: , mismatch: 9, identity: 0.727

gcgaaatcaaccatgcttaaaaaattgtatttg	CRISPR spacer
aagaaatcaacattgcttaaaaaattgaacgcc	Protospacer
. *********  ************** *. .

8. spacer 2.5|1441210|35|NC_009655|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP032928 (Agrobacterium tumefaciens strain 1D1460 plasmid pAt1D1460, complete sequence) position: , mismatch: 10, identity: 0.714

ccgccgggatggtgatgccggcggcctctttggcg	CRISPR spacer
ccgccgggacggtgatgctggcggctcgcgagacc	Protospacer
*********.********.******.. .  *.*

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

888142 : 895999

Enterobacteria_phage(42.86%)

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

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_012072574.1\|888142_889204_+	dTDP-glucose 4,6-dehydratase	I7HTA3	Enterobacteria_phage	3.4e-105	55.2
WP_012072575.1\|889222_889669_+	hypothetical protein	NA	NA	NA	NA
WP_012072576.1\|889661_889955_+	nucleotidyltransferase domain-containing protein	NA	NA	NA	NA
WP_012072577.1\|889969_890845_+	glucose-1-phosphate thymidylyltransferase RfbA	I7I009	Enterobacteria_phage	5.4e-109	64.9
WP_012072578.1\|890927_891803_+	dTDP-4-dehydrorhamnose reductase	A0A291LA50	Escherichia_phage	6.7e-43	37.3
WP_012072579.1\|891814_892381_+	GTP pyrophosphokinase	NA	NA	NA	NA
WP_012072580.1\|892382_892925_+	dTDP-4-dehydrorhamnose 3,5-epimerase	I7HJC4	Enterobacteria_phage	6.9e-54	53.6
WP_041834734.1\|893004_894297_+	aminopeptidase PepB	Q6GYZ8	Mycoplasma_phage	1.0e-31	31.6
WP_012072582.1\|894298_894724_+	nucleoside-diphosphate kinase	A0A167REB2	Powai_lake_megavirus	2.5e-19	41.7
WP_012072583.1\|894847_895999_+	methionine adenosyltransferase	A0A2H4PQS6	Staphylococcus_phage	4.0e-128	63.0

DBSCAN-SWA_2

1360850 : 1444643

Mannheimia_phage(21.43%)

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

attL 1361612:1361633|attR 1402661:1402682

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_012072945.1\|1360850_1361567_+\|tRNA	tRNA pseudouridine(65) synthase TruC	NA	NA	NA	NA
1361612:1361633	attL	NA	NA	NA	NA
WP_012072946.1\|1361709_1361895_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_041834629.1\|1362236_1362473_-	hypothetical protein	NA	NA	NA	NA
WP_012072947.1\|1362485_1362980_-	methyltransferase	A0A0M3LQH0	Mannheimia_phage	2.5e-58	63.3
WP_012072948.1\|1363211_1363880_-	DUF1071 domain-containing protein	O48509	Lactococcus_phage	6.8e-19	33.3
WP_041834766.1\|1363876_1364527_-	ribonuclease H	NA	NA	NA	NA
WP_041834631.1\|1365626_1366094_-	hypothetical protein	NA	NA	NA	NA
WP_012072950.1\|1366600_1366918_+	type II toxin-antitoxin system RelE/ParE family toxin	NA	NA	NA	NA
WP_012072951.1\|1366910_1367201_+	putative addiction module antidote protein	A4JWV1	Burkholderia_virus	2.2e-14	48.8
WP_041834632.1\|1367283_1368363_-	HigA family addiction module antidote protein	NA	NA	NA	NA
WP_012072953.1\|1368375_1368717_-	killer suppression protein	NA	NA	NA	NA
WP_012072954.1\|1368949_1369636_-	helix-turn-helix domain-containing protein	E7C9R0	Salmonella_phage	1.0e-30	35.8
WP_012072955.1\|1369761_1369965_+	helix-turn-helix domain-containing protein	Q76H55	Enterobacteria_phage	1.5e-09	51.6
WP_012072956.1\|1370013_1370457_+	hypothetical protein	NA	NA	NA	NA
WP_041834633.1\|1370533_1370791_+	hypothetical protein	A0A088FAW9	Sulfitobacter_phage	2.7e-08	47.7
WP_049752184.1\|1370787_1371309_+	hypothetical protein	A0A0P0IKQ2	Acinetobacter_phage	1.1e-11	36.4
WP_083757689.1\|1371305_1371632_+	hypothetical protein	A0A0M5M7Y1	Salmonella_phage	1.1e-25	56.6
WP_012072958.1\|1371631_1372288_+	replication P family protein	A0A0M3LS65	Mannheimia_phage	2.0e-31	41.0
WP_012072959.1\|1372297_1372813_+	DNA N-6-adenine-methyltransferase	D0UIL3	Aggregatibacter_phage	4.2e-69	73.9
WP_012072960.1\|1372779_1373415_+	DUF1367 family protein	K7PKS6	Enterobacteria_phage	7.1e-18	28.1
WP_012072961.1\|1373539_1373830_+	DUF1364 domain-containing protein	A0A0M3LQ97	Mannheimia_phage	8.5e-43	84.8
WP_012072962.1\|1373826_1374192_+	RusA family crossover junction endodeoxyribonuclease	A0A0M3LPZ2	Mannheimia_phage	2.2e-32	54.1
WP_012072963.1\|1374206_1374557_+	hypothetical protein	NA	NA	NA	NA
WP_041834634.1\|1374720_1375089_+	hypothetical protein	NA	NA	NA	NA
WP_041834635.1\|1375103_1376603_+	DUF4041 domain-containing protein	X5JAC1	Clostridium_phage	2.0e-42	43.7
WP_012072965.1\|1376898_1377819_+	antirepressor protein	A0A2H4FRZ6	Salmonella_phage	1.2e-61	45.2
WP_012072966.1\|1377974_1378553_-	hypothetical protein	A0A0M3LS77	Mannheimia_phage	3.5e-56	55.2
WP_012072967.1\|1378790_1379180_+\|holin	phage holin, lambda family	A0A2D1GNJ3	Pseudomonas_phage	2.3e-11	43.0
WP_143228885.1\|1379142_1379748_+	peptidoglycan-binding protein LysM	A0A223VZY5	Agrobacterium_phage	1.2e-14	32.4
WP_041834636.1\|1379842_1380190_+	DUF2570 domain-containing protein	NA	NA	NA	NA
WP_012072970.1\|1380386_1380635_+	hypothetical protein	NA	NA	NA	NA
WP_012072971.1\|1380615_1380966_+	HNH endonuclease	A0A1P8DTD1	Proteus_phage	8.9e-39	62.6
WP_012072972.1\|1381081_1381576_+\|terminase	phage terminase small subunit P27 family	Q8W6V0	Burkholderia_virus	4.1e-21	40.6
WP_012072973.1\|1381563_1383267_+\|terminase	terminase large subunit	Q8HAD6	Salmonella_phage	3.0e-244	71.7
WP_012072975.1\|1383412_1384633_+\|portal	phage portal protein	A0A1W6JP33	Morganella_phage	6.1e-143	61.5
WP_012072976.1\|1384625_1385228_+\|head,protease	HK97 family phage prohead protease	A0A1W6JP53	Morganella_phage	2.9e-77	70.3
WP_012072977.1\|1385292_1386519_+\|capsid	phage major capsid protein	Q8SBH8	Shigella_phage	2.2e-148	67.0
WP_012072978.1\|1386567_1386888_+\|head,tail	phage gp6-like head-tail connector protein	A0A1W6JNZ5	Morganella_phage	1.5e-11	34.9
WP_012072979.1\|1386884_1387202_+\|head	phage head closure protein	A0A286S2A2	Klebsiella_phage	4.8e-15	45.7
WP_012072980.1\|1387201_1387684_+	HK97 gp10 family phage protein	A0A220NRP5	Escherichia_phage	1.1e-13	33.3
WP_012072981.1\|1387685_1388030_+	DUF3168 domain-containing protein	NA	NA	NA	NA
WP_012072982.1\|1388033_1388690_+	hypothetical protein	NA	NA	NA	NA
WP_012072983.1\|1388750_1389158_+	hypothetical protein	NA	NA	NA	NA
WP_083757704.1\|1389232_1389433_+	DUF4035 domain-containing protein	NA	NA	NA	NA
WP_012072985.1\|1389477_1389735_+	hypothetical protein	NA	NA	NA	NA
WP_012072986.1\|1389791_1393088_+	tape measure protein	A0A0E3JQ03	Enterobacteria_phage	1.6e-65	27.9
WP_012072987.1\|1393097_1393433_+\|tail	phage tail protein	D6PGG4	uncultured_phage	2.1e-05	27.6
WP_012072988.1\|1393432_1394170_+\|tail	phage minor tail protein L	A0A0M3LPR8	Mannheimia_phage	6.9e-65	50.8
WP_012072989.1\|1394171_1394951_+	C40 family peptidase	A0A0M3LP75	Mannheimia_phage	6.2e-64	50.6
WP_041834638.1\|1394968_1395493_+\|tail	tail assembly protein	A0A0M3LQC4	Mannheimia_phage	1.6e-31	48.5
WP_012072991.1\|1395563_1399535_+\|tail	phage tail protein	A0A0M3LR06	Mannheimia_phage	1.1e-10	56.5
WP_012072992.1\|1399531_1399813_+	hypothetical protein	NA	NA	NA	NA
WP_041834639.1\|1399814_1400810_+	hypothetical protein	NA	NA	NA	NA
WP_012072994.1\|1400822_1401161_+	hypothetical protein	NA	NA	NA	NA
WP_041834640.1\|1401198_1402518_-\|integrase	integrase arm-type DNA-binding domain-containing protein	A0A1B5FPC6	Escherichia_phage	1.7e-42	30.6
WP_012072996.1\|1403088_1403412_-	YciU family protein	NA	NA	NA	NA
1402661:1402682	attR	NA	NA	NA	NA
WP_012072997.1\|1403421_1404237_-	pyridoxal phosphatase	NA	NA	NA	NA
WP_012072998.1\|1404351_1405251_-	formate dehydrogenase accessory protein FdhE	NA	NA	NA	NA
WP_012072999.1\|1405481_1406168_-	formate dehydrogenase subunit gamma	NA	NA	NA	NA
WP_012073000.1\|1406160_1407105_-	formate dehydrogenase subunit beta	NA	NA	NA	NA
WP_083757690.1\|1407104_1410167_-	formate dehydrogenase-N subunit alpha	NA	NA	NA	NA
WP_012073003.1\|1410470_1411289_+	formate dehydrogenase accessory sulfurtransferase FdhD	NA	NA	NA	NA
WP_012073004.1\|1411389_1412439_-	ABC transporter substrate-binding protein	NA	NA	NA	NA
WP_012073005.1\|1412697_1414893_+	DNA helicase II	A7KV33	Bacillus_phage	1.1e-118	37.1
WP_012073006.1\|1414962_1416405_-	bifunctional indole-3-glycerol-phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF	A0A0P0IR83	Acinetobacter_phage	3.6e-33	39.8
WP_012073007.1\|1416427_1417429_-	anthranilate phosphoribosyltransferase	A0A0N7IRD9	Acinetobacter_phage	2.4e-52	38.6
WP_012073008.1\|1417479_1418067_-	aminodeoxychorismate/anthranilate synthase component II	A0A0P0IKJ1	Acinetobacter_phage	2.0e-35	39.6
WP_012073009.1\|1418077_1419619_-	anthranilate synthase component I	NA	NA	NA	NA
WP_012073010.1\|1419850_1420777_+	ABC transporter ATP-binding protein	A0A2R8FG22	Brazilian_cedratvirus	3.5e-13	31.2
WP_012073011.1\|1420773_1421541_+	ABC transporter permease	NA	NA	NA	NA
WP_012073012.1\|1421619_1422681_+\|protease	protease SohB	A0A219YA27	Aeromonas_phage	9.4e-07	25.2
WP_012073013.1\|1422812_1423661_+	OmpA family protein	NA	NA	NA	NA
WP_012073014.1\|1423899_1425045_+	hydrogenase 2 small subunit	NA	NA	NA	NA
WP_012073015.1\|1425064_1426057_+	hydrogenase 2 operon protein HybA	NA	NA	NA	NA
WP_012073016.1\|1426049_1427261_+	Ni/Fe-hydrogenase cytochrome b subunit	NA	NA	NA	NA
WP_012073017.1\|1427276_1428986_+	hydrogenase 2 large subunit	NA	NA	NA	NA
WP_012073018.1\|1428985_1429474_+	HyaD/HybD family hydrogenase maturation endopeptidase	NA	NA	NA	NA
WP_012073019.1\|1429482_1429989_+	hydrogenase-2 assembly chaperone	NA	NA	NA	NA
WP_012073020.1\|1430014_1430287_+	hydrogenase maturation factor HybG	NA	NA	NA	NA
WP_012073021.1\|1430488_1432924_+	CRISPR-associated helicase/endonuclease Cas3	NA	NA	NA	NA
WP_012073022.1\|1432938_1433682_+	type I-C CRISPR-associated protein Cas5	NA	NA	NA	NA
WP_012073023.1\|1433678_1435742_+	type I-C CRISPR-associated protein Cas8c/Csd1	NA	NA	NA	NA
WP_012073024.1\|1435763_1436603_+	type I-C CRISPR-associated protein Cas7/Csd2	NA	NA	NA	NA
WP_012073025.1\|1436603_1437278_+	CRISPR-associated protein Cas4	NA	NA	NA	NA
WP_083757705.1\|1437318_1437726_-	carboxymuconolactone decarboxylase family protein	NA	NA	NA	NA
WP_049752185.1\|1437882_1438266_+	transcriptional regulator	NA	NA	NA	NA
WP_012073028.1\|1438454_1439357_+	hypothetical protein	NA	NA	NA	NA
WP_012073029.1\|1439370_1440384_+	type I-C CRISPR-associated endonuclease Cas1	NA	NA	NA	NA
WP_012073030.1\|1440423_1440717_+	CRISPR-associated endonuclease Cas2	NA	NA	NA	NA
WP_012073031.1\|1441745_1443149_-\|tRNA	asparagine--tRNA ligase	A0A1V0SDB6	Indivirus	7.4e-84	38.3
WP_012073032.1\|1443395_1444049_+	GTP cyclohydrolase I FolE	I6XC45	Vibriophage	3.5e-52	50.2
WP_012073033.1\|1444151_1444643_-\|tRNA	YbaK/prolyl-tRNA synthetase associated domain-containing protein	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_009655

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

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection