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
LR134516	Neisseria animaloris strain NCTC12227 genome assembly, chromosome: 1	3 crisprs	DEDDh,cas9,cas1,cas2,csa3,cas3,cas4,cas7,cas8c,cas5,DinG	1	1	3	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: LR134516_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR134516_1

1231419-1231850

TypeII

Consensus_repeat	Method
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	PILER-CR
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	CRISPRCasFinder
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	CRT

6 spacers

cas2,cas1,cas9

The CRISPR arrays of LR134516_1

>merge|LR134516|1|1231419-1231850|PILER-CR,CRISPRCasFinder,CRT
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAACATAATAAATACGGATGGCGCATTTATGTAGATTGTAGCACTACGAGATGAGAGAGGAAGCTACAACCAACTCCCCCGGCACGAAACGCAGCTTACGATTGTAGCACTACGAGATGAGAGAGGAAGCTACAACACTATATGGGGCAGTTTGGGTAACGACCGCATTGTAGCACTACGAGATGAGAGAGGAAGCTACAACAAGATCATCCTGCAATTCTTGAGAGAGAAAATTGTAGCACTACGAGATGAGAGAGGAAGCTACAACGGAATCAGTATTTATGGCGTAGTTATTTTTATTGTAGCACTACGAGATGAGAGAGGAAGCTACAACGTCAGCATTACGCTCAATATCCTGCAATTGATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC

>LR134516|1|1|1231419-1231850|PILER-CR
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	ATAATAAATACGGATGGCGCATTTATGTAG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	CAACTCCCCCGGCACGAAACGCAGCTTACG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	ACTATATGGGGCAGTTTGGGTAACGACCGC
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	AAGATCATCCTGCAATTCTTGAGAGAGAAA
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	GGAATCAGTATTTATGGCGTAGTTATTTTT
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	GTCAGCATTACGCTCAATATCCTGCAATTG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC

>LR134516|1|1|1231419-1231850|CRISPRCasFinder
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	ATAATAAATACGGATGGCGCATTTATGTAG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	CAACTCCCCCGGCACGAAACGCAGCTTACG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	ACTATATGGGGCAGTTTGGGTAACGACCGC
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	AAGATCATCCTGCAATTCTTGAGAGAGAAA
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	GGAATCAGTATTTATGGCGTAGTTATTTTT
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	GTCAGCATTACGCTCAATATCCTGCAATTG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC

>LR134516|1|1|1231419-1231850|CRT
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	ATAATAAATACGGATGGCGCATTTATGTAG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	CAACTCCCCCGGCACGAAACGCAGCTTACG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	ACTATATGGGGCAGTTTGGGTAACGACCGC
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	AAGATCATCCTGCAATTCTTGAGAGAGAAA
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	GGAATCAGTATTTATGGCGTAGTTATTTTT
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC	GTCAGCATTACGCTCAATATCCTGCAATTG
ATTGTAGCACTACGAGATGAGAGAGGAAGCTACAAC

Protein	Signature genes	Signature genes Name	Protein_function
LR134516.1\|VEJ21401.1\|1221372_1221792_-\|membrane-protein	unknown	unknown	gnl\|CDD\|378909
LR134516.1\|VEJ21409.1\|1231046_1231355_+\|CRISPR-associated-endoribonuclease-Cas2	cas2	COG3512_cas2_CAS-II-A:CAS-II-B:CAS-II-C	gnl\|CDD\|226043
LR134516.1\|VEJ21419.1\|1243097_1243454_+\|Uncharacterised-protein	unknown	unknown	gnl\|CDD\|379548
LR134516.1\|VEJ21415.1\|1239843_1240095_+\|Uncharacterised-protein	unknown	unknown	unknown
LR134516.1\|VEJ21402.1\|1221956_1222958_-\|DNA-polymerase-III-subunit-delta	unknown	unknown	gnl\|CDD\|235511
LR134516.1\|VEJ21418.1\|1242595_1243024_+\|MerR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|133384
LR134516.1\|VEJ21403.1\|1222957_1223524_-\|Rare-lipoprotein-B,-putative	unknown	unknown	gnl\|CDD\|225527
LR134516.1\|VEJ21413.1\|1237254_1238424_-\|Uncharacterised-protein	unknown	unknown	gnl\|CDD\|379536
LR134516.1\|VEJ21417.1\|1241566_1242433_-\|Molecular-chaperone-Hsp31-and-glyoxalase-3	unknown	unknown	gnl\|CDD\|235228
LR134516.1\|VEJ21414.1\|1238522_1239368_-\|Uncharacterised-protein	unknown	unknown	gnl\|CDD\|376806
LR134516.1\|VEJ21400.1\|1220757_1221270_-\|oligoketide-cyclase/lipid-transport-protein	unknown	unknown	gnl\|CDD\|225422
LR134516.1\|VEJ21406.1\|1225984_1226329_-\|Glyoxalase-like-domain	unknown	unknown	gnl\|CDD\|319898
LR134516.1\|VEJ21407.1\|1226809_1230046_+\|putative-CRISPR-associated-protein	cas9	COG3513_cas9_CAS-II-A:CAS-II-B:CAS-II-C	gnl\|CDD\|226044
LR134516.1\|VEJ21404.1\|1223603_1225061_-\|outer-membrane-efflux-protein	unknown	unknown	gnl\|CDD\|224455
LR134516.1\|VEJ21412.1\|1233954_1237089_-\|ABC-transporter-ATP-binding-protein	unknown	unknown	gnl\|CDD\|224054
LR134516.1\|VEJ21411.1\|1232803_1233925_-\|Inner-membrane-transport-permease-yhhJ	unknown	unknown	gnl\|CDD\|378925
LR134516.1\|VEJ21405.1\|1225331_1225895_+\|Inner-membrane-protein-yagU	unknown	unknown	gnl\|CDD\|226008
LR134516.1\|VEJ21408.1\|1230124_1231036_+\|putative-DNA-repair-protein	cas1	cd09720_cas1_CAS-II-A:CAS-II-B:CAS-II-C	gnl\|CDD\|274694
LR134516.1\|VEJ21410.1\|1232014_1232767_-\|methylated-DNA--protein-cysteine-methyltransferase	unknown	unknown	gnl\|CDD\|223427
LR134516.1\|VEJ21416.1\|1240192_1241335_-\|FMN-oxidoreductase-CC3083	unknown	unknown	gnl\|CDD\|240086

Protein	Function_ID	Function_description	E-value
LR134516.1\|VEJ21401.1\|1221372_1221792_-\|membrane-protein	gnl\|CDD\|378909	pfam12670, DUF3792, Protein of unknown function (DUF3792). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. These proteins are integral membrane proteins.	0.0016362
LR134516.1\|VEJ21409.1\|1231046_1231355_+\|CRISPR-associated-endoribonuclease-Cas2	gnl\|CDD\|226043	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms].	1.23569e-47
LR134516.1\|VEJ21419.1\|1243097_1243454_+\|Uncharacterised-protein	gnl\|CDD\|379548	pfam14302, DUF4377, Domain of unknown function (DUF4377). This domain family is found in bacteria and archaea, and is approximately 80 amino acids in length.	1.28546e-26
LR134516.1\|VEJ21417.1\|1241566_1242433_-\|Molecular-chaperone-Hsp31-and-glyoxalase-3	gnl\|CDD\|235228	PRK04155, PRK04155, protein deglycase HchA.	8.83817e-175
LR134516.1\|VEJ21402.1\|1221956_1222958_-\|DNA-polymerase-III-subunit-delta	gnl\|CDD\|235511	PRK05574, holA, DNA polymerase III subunit delta; Reviewed.	7.22351e-118
LR134516.1\|VEJ21418.1\|1242595_1243024_+\|MerR-family-transcriptional-regulator	gnl\|CDD\|133384	cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.	1.57284e-41
LR134516.1\|VEJ21403.1\|1222957_1223524_-\|Rare-lipoprotein-B,-putative	gnl\|CDD\|225527	COG2980, RlpB, Rare lipoprotein B [Cell envelope biogenesis, outer membrane].	1.93767e-35
LR134516.1\|VEJ21413.1\|1237254_1238424_-\|Uncharacterised-protein	gnl\|CDD\|379536	pfam14281, PDDEXK_4, PD-(D/E)XK nuclease superfamily. Members of this family belong to the PD-(D/E)XK nuclease superfamily.	1.87463e-08
LR134516.1\|VEJ21414.1\|1238522_1239368_-\|Uncharacterised-protein	gnl\|CDD\|376806	pfam02517, Abi, CAAX protease self-immunity. Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide being removed by one of the CAAX prenyl proteases). The family contains the CAAX prenyl protease. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding. While they are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin. Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity.	0.000105632
LR134516.1\|VEJ21400.1\|1220757_1221270_-\|oligoketide-cyclase/lipid-transport-protein	gnl\|CDD\|225422	COG2867, COG2867, Oligoketide cyclase/lipid transport protein [Lipid metabolism].	1.93893e-63
LR134516.1\|VEJ21406.1\|1225984_1226329_-\|Glyoxalase-like-domain	gnl\|CDD\|319898	cd06587, VOC, vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases.	5.03455e-05
LR134516.1\|VEJ21407.1\|1226809_1230046_+\|putative-CRISPR-associated-protein	gnl\|CDD\|226044	COG3513, COG3513, Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms].	0
LR134516.1\|VEJ21404.1\|1223603_1225061_-\|outer-membrane-efflux-protein	gnl\|CDD\|224455	COG1538, TolC, Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion].	1.42979e-55
LR134516.1\|VEJ21412.1\|1233954_1237089_-\|ABC-transporter-ATP-binding-protein	gnl\|CDD\|224054	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms].	3.00653e-90
LR134516.1\|VEJ21411.1\|1232803_1233925_-\|Inner-membrane-transport-permease-yhhJ	gnl\|CDD\|378925	pfam12698, ABC2_membrane_3, ABC-2 family transporter protein. This family is related to the ABC-2 membrane transporter family pfam01061.	3.13208e-29
LR134516.1\|VEJ21405.1\|1225331_1225895_+\|Inner-membrane-protein-yagU	gnl\|CDD\|226008	COG3477, COG3477, Predicted periplasmic/secreted protein [Function unknown].	1.51654e-49
LR134516.1\|VEJ21408.1\|1230124_1231036_+\|putative-DNA-repair-protein	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.	1.5138e-124
LR134516.1\|VEJ21410.1\|1232014_1232767_-\|methylated-DNA--protein-cysteine-methyltransferase	gnl\|CDD\|223427	COG0350, Ada, Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair].	4.58317e-61
LR134516.1\|VEJ21416.1\|1240192_1241335_-\|FMN-oxidoreductase-CC3083	gnl\|CDD\|240086	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.	4.54909e-169

>LR134516.1|VEJ21409.1|1231046_1231355_+|CRISPR-associated-endoribonuclease-Cas2
MRLIVFFDLPVTTAAKRKAASQFRKFLQKDGYHMLQLSVYSRIVKGRDALQKHHKRLMLHLPEEGQVRYLEVTEKQYTSMVMLIGEPKPREKKVNADQLLLF
>LR134516.1|VEJ21408.1|1230124_1231036_+|putative-DNA-repair-protein
MTWRSILISRPSRLSLQQNHLLIQQDEAIPIPLEDIAVIVVEAREVILTAPLLSALAQYGITLLTCDEQFLPCGQWLPFAQYHRSLKVLKQQINMTEPQKKQLWQQIVKQKIRNQAWLLDYSGHDIAASRLNALADSVKSGDKNFAESQAAALHFRVLFGEQFTRSYENSVNAHLNYGYSILRSAIARALVQYGFLPALGLHHRSELNPFNLADDLIEPYRPIADLWVYDKMLSNSLPDELTPASKQQLISLLCCQAALDGYKYSVLAAIDRTIQSFQTAVSQNKPKLLKLPQMLRLKVHDYE
>LR134516.1|VEJ21407.1|1226809_1230046_+|putative-CRISPR-associated-protein
MKQQPQRYILGLDLGIASVGWALILVDEEGNPIGLLDCGVRTFERAEVPKTGDSLALARRQARSVRRLIRRRAHRLLRLRRLLKREGVLSATDFNSDGLPNLPIDTWQLRVAGLERKLTNQEWAAVLLHLVKHRGYLSQRKSETQTENKELGHLLAGVAKNSKLLSENANQYRTPAELAVKLFAEQSRHLRNKGGNYTHTFNRLDLQKELHLLFEQQRAFGNPFASAELQNKVDELLMMQRSALQGEAVLKMLGKCTFEPSEYKAAKHTYSAERFIWLTKLNNLRILENGTERALNEAERKLLLDEPYKKAKLTYAQARKLLDMSHDATFKGLRYGKDSDGLKAENGALMEMKAYHKIRTVLDKAGLKGEWENRIRNPEILDKIGTAFSLYKTDEDIQAALADLKLPENVLDALLAGLNFDKFIQLSLKALGNILPLMERGMRYDEACKEVYGDHRALAESKNQMLLPPIPANEIRNPVVLRTLTQARKVINAIIRRYGSPQRVHIETARELGKSFKDRKEIEKRQEENRKERERAAEHFKELFPHFAGEPKGGDILKLRLYEQQQGKCLYSGIPIDLGRLNEKGYVEIDHALPFSRTWDDSFNNKVLVLGSENQKKRNQTPYEYLDGASNSQRWREFQARLQGCRFSYAKKQRIQTAKLDSKTEQGFLERNLNDTRYIARFLCGFIEENLHLQSEGKRRVFASNGQITALLRGLWGLKKVREENDRHHALDAIVVACSTVSMQQKITKAMQRRETLETVDSETGEVKTRIPQPWDFFRQEVMIRVFSDTPREELAEKLSSRPEALHDFVSPLFVSRAPNRKMTGQGHLETVKSAKRLSENISVVRKPLTALKLKDIENIVGYPDREPALYQALRERLLTHKDDPVKAFAERFYKPAKNGGQGSLVKAVRVKDVQKTGVMVRKDRGGMARGIADNATMVRVDVFGKKGKHYLVPVYAWQVAKGILPNRAVVAYADEADWDEMDDSYEFKFTLYPNDLVEIISKKGRIFGYYSGLNRATGAIDIKEHDLSKEKAKNGIHQSVGVKTVLSFQKYQVDPLGKEICLCKVEKHPELNSKKKK
>LR134516.1|VEJ21406.1|1225984_1226329_-|Glyoxalase-like-domain
MKLFKTSSLVSVINASDFQTSLAWYRTWLGEPDVVPMENMAEWRIADNAWLQLTDSGTIAEAEVIIGVDDIAACRKALLGAGIEAGDINDWEVVLTCGITDPDNHKIFFAQAVG
>LR134516.1|VEJ21405.1|1225331_1225895_+|Inner-membrane-protein-yagU
MARTLCSSEVNRKVILWTTLIGGFFSSLVKWGSEVNMPPRMPGEISPPGANIDAWLGWLGFNQHSLDYMYQGNSVLGAVTLYHWLFSFVFAFVYVWVSAYWPKIRLWYGAFYGIIITVVMHWLLIPMFGFRNPAYADGATGWAWNLNAAEHISEILGHVYWSVSIEVCMIAVLAYYARPIKGDWVER
>LR134516.1|VEJ21404.1|1223603_1225061_-|outer-membrane-efflux-protein
MNISLKHFYVSMASALMLAACKSTVVPLDSKINIPQAFSQAEAARGSAEIGRWWQHWNDPVLSRLIEQGLQQNHDIRIARSRLNEARAIERLADADKGPTVGAGAEASRLNARIGNPLSDEERALLGRIPQAADLAGERFTLKGNSLTGGFSASWEPDIFGQKRSDADAAAYAALGRQEEVYGTQVLIGGEIAEHYLQARAAQARLKSVNRNIATVERLAKYVQGRFKAGHVTAYEVDEVATQLTALRAKHSTIESEYAAHVRSIAVLTGQTPQTFSLPESSVNILSAQPAAPSGQTPQGLLERRPDIRAHAAQVNAYAAKLASAKADLLPRFNIEFLGRGTISIGSDSDLKGWGSLIKAGIQVPIFTNGRIKANIAAADARLQTALLQYDQNILKALGEVDSAYQAHSALTRQNALLITAHKQAAKQAGDAEKLFKYGQKTLDNALTARLNEEAMQENLIQSQLARARMLIGLYKALGGGWVGG
>LR134516.1|VEJ21403.1|1222957_1223524_-|Rare-lipoprotein-B,-putative
MSGRLNRLSDGLTNPLPLGYNPSLFILRRKPYMNKILLPAAALLLAACGFHLKGMGGISGSLPYQEWHVAGGQMQQPLENALRRADGKPATQAPVSVTVTNIETRRDIYTITRAADISEFLLILRVEAQAAKNGQPWGEPMVVLVQRKMDYADSEVLGKQEEEATVWAEMRADAADQIVRRLTFLKAD
>LR134516.1|VEJ21402.1|1221956_1222958_-|DNA-polymerase-III-subunit-delta
MPVISIEQLSPDLALKPLYVIHGEEDLLRVEALDTLRAAAKQQGYLNREVYTADNSFDWNELLQSAGSMGLFADLKLLEIHIPNGKPGKNGGDALQSLAENLLEDTVIIVMLPKLERAQTQAKWFGALAAYGVVLEAKAVSGAALPQWIRGRLNALNLNIEPDALALFAERVEGNLLAAKQEIDKLALLHPAGHLVNMADAEAAVANVARFDVFQLAGAWMSGDGLRVARLLEGLEAEGEEPVLLLWAVAEDIRTLIRLTAALKQGQSIQAVRNSLRLWGDKQTLAPMAVKRISISRLLAALQDCARIDRIIKGAEDGNAWAEFKHLVTGLAL
>LR134516.1|VEJ21401.1|1221372_1221792_-|membrane-protein
MDNKTKLRLGGLALLATAVLSLILVLFTDSWPVAILLAISIMSGVIGGLIWSSRRQQRQFLERLKKFDIDPEKGRVNEANLRRMYHSGGQAQKDVITIICMSQNCSVDEAHEMMKKRPTRQQMNQMAQQQMKGQRRPHR
>LR134516.1|VEJ21400.1|1220757_1221270_-|oligoketide-cyclase/lipid-transport-protein
MQAARQTRLQAAGVSFIMLAFPPAPKIMKTVEKNVLVLHSAEQMFELVDKVEDYPKFLPWYSKTEIIERTGNELKARLFMDYMKVQQSFATHNHNVPGREIRMDLLEGPFKSLQGTWTFIPLGDDCCKIEFRLQYDFSSSLLSALISPVFSHLSGTLVDAFIKEADRRYG
>LR134516.1|VEJ21410.1|1232014_1232767_-|methylated-DNA--protein-cysteine-methyltransferase
MDIRHLPDPQTQLPARWQVYAAWLAARGNPSKSYRDHPFESPDELAALKKDFERYVGMSLGQYIRLKRIMHLLAKRNNKHGNELMVSVSATPLGQMLAVFSTQGLCLLEFPERKMLESELLAVQKAFQADFVWRDTAHSQTLQQELNLYFEGRLKNFATPLDPVGTPFQQQVWRKLQSIPYGETRSYKQQAERIGKPQAVRAVAAANGQNKISILIPCHRVIGNNGDLTGYGGGLARKKALLELEGAIPV
>LR134516.1|VEJ21411.1|1232803_1233925_-|Inner-membrane-transport-permease-yhhJ
MRSIKNIFYLAQKELRSLFSDLVLMVLIVFMFTVTIFSAAQIDPGVKNAAVAVVDGDRSALSYRLRDAVREPFFQPPQEVEAEVVNQAMDKGEYIFALEIPPNFERDVLMGRSPELLLQVDATAMSQAGLGAAYLTRILERETAEFARQQPAEKWLPVKPVIRSHFNANAEGSYYGPPMELGNMVLVLALILVGAAVIREREHGTIEHLLVMPVNAAEIMLAKVLANSAMILLVSILAMWVVVKGILGVPIHGSIMLYGFGVAVYLFSIAALAVMLATIAPSMAQFGLLMIPLYMVLLLFSGVASPRNNMPEAAQWISEYWPSTQFIRFAQSVLFRDAGFSIVWPQLLAMALTGLLFLVFALMRFRKMLEQQG
>LR134516.1|VEJ21412.1|1233954_1237089_-|ABC-transporter-ATP-binding-protein
MINNPAVSLRSVSHRYGKTTLALDDVSLTIPRGVTVGLIGPDGVGKSTLLSLIAGVKIIQSGTVEVFGCDMADKAARQALSHRIAFMPQGLGRNLYPTLSVYENVDFHARLFGLNAAERKARISRLLEATGLAPFPDRAAGKLSGGMKQKLSLCCALVHSPDLLILDEPTTGVDPLSRRQFWALVDELQAESAGMTVIVATAYIEEAERFGHLLAMDDGKLLVNKPTREVMRDSGAATLEAAYVQMLPSEKQQGSGGLEMVPFAPDPASPPAIEAHGLTKRFGSFTAVDHVSFTIQKGEIFGFLGSNGCGKSTTMKMLTGLLEASEGKAELLGQPVEAGNIRTRMRVGYMSQAFSLYEELSVRDNLMLHARLYQMGAAGKQAVADALIQFELAEAADMKPAALPLGIRQRLQLAAACLHKPEVLILDEPTSGVDPAARDMFWRHLLKLSREDKITIFVSTHFMNEAERCDRISFMHKGRVLAVGTPAELTARQAAPNLEEAFVRYLLDDEAREGLSERPSETAVSVQANAQTNNAAVPPQQTADDSERPSETASVAQLAARIVWADQDLDVRAGIRPSENVRSDSGLASSQAEEEQTVVSPEAPISSTPAESYSETGKITEREQAADVSDKLPETESVVQAAARSVQENQDSDAQAGNRPSENTPPTDTLKYWLASVRTFALRETKELLRDKVRLFFALAGPVILMVALSWSVSFDVKDLTFTVLDRDQTTESRRLTEYFSGSRYFQQQPPLSSSSDIDTALQSAQTRLVIEIPEGFGRDMLAGRRPEAAFYVDGAMPFNASNIQGYIGGIFALYGQDLARETGLTLPPPAAKIEQRFMYNQDFESIFAIAPGVLMLVLMLIPAMMSVVGVVREREIGSISNFYTSPATVPQFLLGKQLPYIAVGMVNYVVLTAMMVFGFGVPVKGSLLVLTAGTLILLFVSTALGLLASTIVCSQVAAISLTAIVIMIPTFNYSGFLHPLSSMEGGAYWMGKLMPASWYLNISIGSFTKGLGWHDLSREMLVLLAFYVVYFTSACWILKKQEK
>LR134516.1|VEJ21413.1|1237254_1238424_-|Uncharacterised-protein
MNIEKFENLVNDFKKLDLKTIKEKPTYLEIIGKRHLEDVSSRALAFFFDTSKEHGLGDICLQALLAVYNTKLDKNDRYEEDVLRTLSVKREVSISLINDRQVKQAKQSERGRIDLLIETPTKIILIENKINHSNNNPFEAYWKYINLEEFCSKEKLCILLVKDKTESPHKNFKVITHFEWVKELKKRLPEIWQQADNKYLIFLMDYVYAIDSLNPEKERNKMDKQILKLFKKHHQILIDLEDQKDNVCEFYQNDLENFIKNEDLQKFRWKDPELNNNNYKYLGAYVYTYPYTYSVKRNIEYQISFWLGWNLSSFMLGIELTKGNGRSKKHDEMLDLLQKAGIEHKLIENNGEIYLEVFSLGEKGDIPLDSFAKKTASKLNEVIKKLNLK
>LR134516.1|VEJ21414.1|1238522_1239368_-|Uncharacterised-protein
MRPTQHTVNPAVYRPVFFFAWSLLLPWAAWLAAAYLSHQPDGGHKGLLTALLLAGLLAPVCLAAGLLWRQPSLREDALSRLRLSGAPKRYLLAAVLLPPLSLVLAQGVSLLFGYPAYQFHISGSPSFTSALISPWLALVLGAVLEELAWHSYGTDALLSRFSLFAASLVFTVYWALWHVPLGLVKGYYHSELVAQGWLYSANFVASMVVFVLLMNWLYLKSGRSIMVALLFHLAANLGNEIFQTHPDSKVIQTGILLLLTVWVLWKERTLFFRRPQFKQAG
>LR134516.1|VEJ21415.1|1239843_1240095_+|Uncharacterised-protein
MRRMHIGSIIILICGLSAVIPGLMVLFGLGGWVHDLLDQPIGAIALLVIGGSCVLAAFFPLVATYLTRKEQGKPPFEDDEAEE
>LR134516.1|VEJ21416.1|1240192_1241335_-|FMN-oxidoreductase-CC3083
MNPKYTPLFQPYTLNNGTVIKNRLAVAPMTHWASLPDGNISPEERLFLSNRFKGFGLFISAATLVSPEGKAFAGQPEAVGTEHLPSLKEVAQIAHEQGAKAVLQLHHGGIQASADLLNGADKIAPSDDEASGSRALIEPEIRALIDAFARAAELALEAGFDGAEIHGANGYLIQQFVSAQSNRRSDEWGGSLANRLRFPLAVVEAVDAVRRKHNRSDFIVGYRFSPEEGGDNGLTMQDTFALIDALVQKPLQYLHVSLWDFYKKARRGANTDLTRIEQIHQRIGGKLPLIGVGNLFTAEQILAAYQTGWAEFIALGKTVLLNPDLVELIESGREAEVVCELDPDKADRYRIPERLWQQCQMGLAYLPPLKGRADWQPVDI
>LR134516.1|VEJ21417.1|1241566_1242433_-|Molecular-chaperone-Hsp31-and-glyoxalase-3
MSDLSKTPVPDHAEYNAFFPSEYSLSQYTAPKTDFSGVKFNEPYTGGKYRVLMIATDERYLQMQNGKLFSTGNHPVETLLPMLHIHEAGFEIDVATLSGNAAKFEMWAMPKEDEAVKSIFETYLPKLQKPLKLADIIDRATAPDSPYIAVLIPGGHGAFTAIPHSKEVARLLNWAVGQNRFIVTLCHGPAALNAAAEHGTFPFAGYKLAVFPDVLDEGANIDIGYMPGRLPWLVAERLEQLGMIVVNQGISGEVCRDRQLLTGDSPLAANNLGILAADVLLDAVKNLD
>LR134516.1|VEJ21418.1|1242595_1243024_+|MerR-family-transcriptional-regulator
MKDYLTIGEAASKYGISPHTLRYYDKAGLLPPQIRSGGNRLFGTADLEWLELILGLKQTGMSLKDIQAFVATMHESDGIARRLAILRQQRKKVDEQIAALKRADKLLEQKCAIYETALKTGEIPANSVCRAFLRDKEPKQAT
>LR134516.1|VEJ21419.1|1243097_1243454_+|Uncharacterised-protein
MNIFHKLTCLLTVAAGACTVSPASSDIYWVSGTKAECSAGAGKMMCLRVSKHPDLQQADWQYFYAPIKGFVFEEGILKKIEVRKTELVPETVPADASSIRYTLVRELEKRPDNPELYR

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Crispr_ID: LR134516_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR134516_2

1889321-1889554

TypeI

Consensus_repeat	Method
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	PILER-CR
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	CRISPRCasFinder
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	CRT

3 spacers

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

The CRISPR arrays of LR134516_2

>merge|LR134516|2|1889321-1889554|PILER-CR,CRISPRCasFinder,CRT
GTTTCAACACACAGCCGCCCGAAGGCGGCTGATGGCGGTTAAAGCCCCCATTAAAGACGGAACCTTCGTTTCAACACACAGCCGCCCGAAGGCGGCTGATAAAACAGAGAGCCAATGTGTACCCGCCCGGGTTTGTTTCAACACACAGCCGCCCGAAGGCGGCTGAGTGGCGTATGAAATTGTAACGGGAGTGCCTCCACGGGTTTCAACACACAGCCGCCCGAAGGCGGCTGA

>LR134516|2|2|1889321-1889554|PILER-CR
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	TGGCGGTTAAAGCCCCCATTAAAGACGGAACCTTC
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	TAAAACAGAGAGCCAATGTGTACCCGCCCGGGTTT
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	GTGGCGTATGAAATTGTAACGGGAGTGCCTCCACGG
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA

>LR134516|2|2|1889321-1889554|CRISPRCasFinder
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	TGGCGGTTAAAGCCCCCATTAAAGACGGAACCTTC
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	TAAAACAGAGAGCCAATGTGTACCCGCCCGGGTTT
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	GTGGCGTATGAAATTGTAACGGGAGTGCCTCCACGG
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA

>LR134516|2|2|1889321-1889554|CRT
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	TGGCGGTTAAAGCCCCCATTAAAGACGGAACCTTC
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	TAAAACAGAGAGCCAATGTGTACCCGCCCGGGTTT
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA	GTGGCGTATGAAATTGTAACGGGAGTGCCTCCACGG
GTTTCAACACACAGCCGCCCGAAGGCGGCTGA

Protein	Signature genes	Signature genes Name	Protein_function
LR134516.1\|VEJ21991.1\|1889745_1890039_-\|CRISPR-associated-endoribonuclease-Cas2	cas2	cd09725_cas2_CAS-I:CAS-II:CAS-III:CAS-V	gnl\|CDD\|187856
LR134516.1\|VEJ21986.1\|1879215_1879677_-\|membrane-protein	unknown	unknown	gnl\|CDD\|225168
LR134516.1\|VEJ21981.1\|1875944_1876520_-\|RNA-polymerase-sigma-factor	unknown	unknown	gnl\|CDD\|274359
LR134516.1\|VEJ21987.1\|1880259_1880553_-\|ComE1	unknown	unknown	gnl\|CDD\|213597
LR134516.1\|VEJ21990.1\|1887805_1889176_+\|signal-recognition-particle-protein	unknown	unknown	gnl\|CDD\|236780
LR134516.1\|VEJ21997.1\|1894251_1896039_-\|phage-associated-protein	cas8c	cd09757_cas8c_CAS-I-C	gnl\|CDD\|187887
LR134516.1\|VEJ21993.1\|1891555_1891819_-\|Uncharacterised-protein	unknown	unknown	unknown
LR134516.1\|VEJ21998.1\|1896035_1896707_-\|CRISPR-associated-protein-Cas5,-subtype-I-C/DVULG	cas5	cd09752_cas5_CAS-I-C	gnl\|CDD\|187534
LR134516.1\|VEJ21996.1\|1893385_1894249_-\|phage-associated-protein	cas7	cd09689_cas7_CAS-I-C	gnl\|CDD\|377458
LR134516.1\|VEJ21988.1\|1886881_1887406_-\|CcsA-like-protein	unknown	unknown	gnl\|CDD\|226621
LR134516.1\|VEJ22000.1\|1898684_1900997_-\|Superfamily-II-helicase	cas3	COG1203_cas3_CAS-I	gnl\|CDD\|224124
LR134516.1\|VEJ21989.1\|1887420_1887663_-\|CcsA-like-protein	unknown	unknown	gnl\|CDD\|226621
LR134516.1\|VEJ21999.1\|1896773_1898621_-\|Predicted-ATP-binding-protein-involved-in-virulence	unknown	unknown	gnl\|CDD\|226121
LR134516.1\|VEJ21992.1\|1890116_1891130_-\|CRISPR-associated-endonuclease-Cas1,-subtype-I-C/DVULG	cas1	cd09721_cas1_CAS-I-C	gnl\|CDD\|188360
LR134516.1\|VEJ21982.1\|1876618_1877356_-\|Uncharacterized-protein-conserved-in-bacteria	unknown	unknown	gnl\|CDD\|225760
LR134516.1\|VEJ21995.1\|1892647_1893271_-\|Uncharacterised-protein	unknown	unknown	unknown
LR134516.1\|VEJ21994.1\|1891965_1892571_-\|recombinase-B	cas4	cd09637_cas4_CAS-I:CAS-II:CAS-V	gnl\|CDD\|187768
LR134516.1\|VEJ21983.1\|1877342_1878194_-\|Protein-of-uncharacterised-function-(DUF692)	unknown	unknown	gnl\|CDD\|235447
LR134516.1\|VEJ21985.1\|1878841_1879117_-\|Periplasmic-protein	unknown	unknown	unknown
LR134516.1\|VEJ21984.1\|1878366_1878729_-\|Uncharacterized-low-complexity-protein	unknown	unknown	gnl\|CDD\|140324

Protein	Function_ID	Function_description	E-value
LR134516.1\|VEJ21991.1\|1889745_1890039_-\|CRISPR-associated-endoribonuclease-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.	1.66282e-31
LR134516.1\|VEJ21986.1\|1879215_1879677_-\|membrane-protein	gnl\|CDD\|225168	COG2259, COG2259, Predicted membrane protein [Function unknown].	7.80149e-23
LR134516.1\|VEJ21981.1\|1875944_1876520_-\|RNA-polymerase-sigma-factor	gnl\|CDD\|274359	TIGR02943, RNA_polymerase_sigma-24_subunit_RpoE, RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.	9.87992e-60
LR134516.1\|VEJ21987.1\|1880259_1880553_-\|ComE1	gnl\|CDD\|213597	TIGR01259, ComE_operon_protein_1, comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation. [Cellular processes, DNA transformation].	2.96063e-24
LR134516.1\|VEJ21990.1\|1887805_1889176_+\|signal-recognition-particle-protein	gnl\|CDD\|236780	PRK10867, PRK10867, signal recognition particle protein; Provisional.	0
LR134516.1\|VEJ21998.1\|1896035_1896707_-\|CRISPR-associated-protein-Cas5,-subtype-I-C/DVULG	gnl\|CDD\|187534	cd09752, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family.	3.07785e-110
LR134516.1\|VEJ21996.1\|1893385_1894249_-\|phage-associated-protein	gnl\|CDD\|377458	pfam05107, Cas_Cas7, CRISPR-associated protein Cas7. CRISPR-associated protein Cas7 is one of the components of the type I-B cascade-like antiviral defense complex. In Haloferax volcanii, Cas5, Cas6 and Cas7 form a small complex that aids the stability of CRISPR-derived RNA.	2.10073e-151
LR134516.1\|VEJ21988.1\|1886881_1887406_-\|CcsA-like-protein	gnl\|CDD\|226621	COG4137, COG4137, ABC-type uncharacterized transport system, permease component [General function prediction only].	3.64742e-58
LR134516.1\|VEJ22000.1\|1898684_1900997_-\|Superfamily-II-helicase	gnl\|CDD\|224124	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms].	1.54899e-58
LR134516.1\|VEJ21989.1\|1887420_1887663_-\|CcsA-like-protein	gnl\|CDD\|226621	COG4137, COG4137, ABC-type uncharacterized transport system, permease component [General function prediction only].	4.23147e-07
LR134516.1\|VEJ21999.1\|1896773_1898621_-\|Predicted-ATP-binding-protein-involved-in-virulence	gnl\|CDD\|226121	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair].	2.74844e-15
LR134516.1\|VEJ21992.1\|1890116_1891130_-\|CRISPR-associated-endonuclease-Cas1,-subtype-I-C/DVULG	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
LR134516.1\|VEJ21982.1\|1876618_1877356_-\|Uncharacterized-protein-conserved-in-bacteria	gnl\|CDD\|225760	COG3219, COG3219, Uncharacterized protein conserved in bacteria [Function unknown].	2.4425e-42
LR134516.1\|VEJ21997.1\|1894251_1896039_-\|phage-associated-protein	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
LR134516.1\|VEJ21994.1\|1891965_1892571_-\|recombinase-B	gnl\|CDD\|187768	cd09637, Cas4_I-A_I-B_I-C_I-D_II-B, CRISPR/Cas system-associated protein Cas4. 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; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster.	5.95078e-42
LR134516.1\|VEJ21983.1\|1877342_1878194_-\|Protein-of-uncharacterised-function-(DUF692)	gnl\|CDD\|235447	PRK05409, PRK05409, hypothetical protein; Provisional.	2.94031e-140
LR134516.1\|VEJ21984.1\|1878366_1878729_-\|Uncharacterized-low-complexity-protein	gnl\|CDD\|140324	PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.	0.00135312

>LR134516.1|VEJ21990.1|1887805_1889176_+|signal-recognition-particle-protein
MLDNLTNRFSNVLKNIRGQAKLTEDNIKDALREVRLALLEADVALPVVKEFINNVKEKALGQEIAGSLTPDQAFIGVVNNALIELMGKENSTLNLAVSPPAVILMAGLQGAGKTTTVGKLSRLLKNNQKKKILVVSADVYRPAAIEQLKLLAEQVGVDFFPSNTGQQPVEIAKAAVDHAKRHFYDVLMVDTAGRLAIDEEMMNEIKALHAAVNPVETLFVVDAMLGQDAVNTAQAFNEALPLTGVILTKMDGDSRGGAALSVRQVTGKSIKFIGVGEKISGLEPFYPDRIASRILGMGDVLSLIEDVQKGIDEEAAAKMAKKLNKGKGFDLNDFKEQIQQMRNMGGLENLMSKMPGELGQLSKQIPEGTAEKAMGHVEAIINSMTPKERANPTLIKASRKRRIAEGSGTSVQEVNKMLKQFEQSQQMMKMFSGKGMAKLMRMAKGMKGMKGMFPGL
>LR134516.1|VEJ21989.1|1887420_1887663_-|CcsA-like-protein
MLVYAGLAGFVWLHHKKRNDKPYPLKTELGILMPALVTHGAVLSLPVLQDQVLIMGFGYSISLIVWLMLMMYWMGSFFTV
>LR134516.1|VEJ21988.1|1886881_1887406_-|CcsA-like-protein
MLYPCATLSLLLGLVFPGKFIGYQISDWPFMLHISTSLLAYGLFGIVTLLAVLILLLNHDLHKKRFSPLVSFLPPLLSLEKLMFQGMWAGFILLTYSVVSGTFFAEAVFGRPVSFTHKTVFGVLSWLIYGGLLLNHSMTAWRGKKAAVWTIVGFISLLLAYIGSKFILEVVLHK
>LR134516.1|VEJ21987.1|1880259_1880553_-|ComE1
MKRYVLALVGMLVSAWSLAAVNINTATAEELKALPGIGPSKAAAIVEYRTQNGKFKSVDELKNVKGIGEGILSKLKAEAVVSGHGSAKGKAQPVLKK
>LR134516.1|VEJ21986.1|1879215_1879677_-|membrane-protein
MIKAACLSRFSDTWGKDIALLGLRLFVAYEFWEAGFEKWNGENWFASIQDSFPFPFNLFSADFNWVLAMGTELVVPILLILGLAGRWGALALMGVTIVAWVAVHGENGYNVCSNGYKMALIYLVALLPLVMQGMGRLSLDHVIFRRVDKKNSL
>LR134516.1|VEJ21985.1|1878841_1879117_-|Periplasmic-protein
MKTTSSLIALAGFLALAGCQGQSNGSAESTPAASVSAPKAEEGKCGEGKCGASHAGEKAGEGKCGEGKCGASHAGEKAGEGKCGEGKCGSH
>LR134516.1|VEJ21984.1|1878366_1878729_-|Uncharacterized-low-complexity-protein
MKKSSSLIALAGALALLGSQAAFAESKHASSNIVKTAAKKAHEGACGEGKCGAHGKKKSAKAGEGKCGEGKCGEGKCGAHGKKSSKAGEGKCGEGKCGAHGKKKSTKAGEGKCGEGKCGG
>LR134516.1|VEJ21983.1|1877342_1878194_-|Protein-of-uncharacterised-function-(DUF692)
MKTLHGAGLGYKRSMADDFLNLNLETSAIQFIEIAPENWLRMGGAARKKFDAVAERFPIACHGLSLSLGGQDPLQIDFLRQVKAFLQQYDIEFFSEHLSYCSHHGHVYDLLPLPFTEESVHHTAARIRLVQDILEQRIAIENTSYYAHSPIAEMDEVDFLNAVVREADCNIHLDVNNVYVNAVNHGIVQPNDYINRTDLNRVCYMHMAGHDEESENLLIDTHGQPVCADVWDLFAYTCHKLPHNVPTLLERDSNFPPFAELEAEVSRIAAIQQQAEEARHAAA
>LR134516.1|VEJ21982.1|1876618_1877356_-|Uncharacterized-protein-conserved-in-bacteria
MQQRSVLTTPISSADFQSVLADHVRDPSLPAPEGIASERLAVYTRLVRNNLRSFLDLCFSDSSEFADAALWQELQNRFLIEARPESPFFNDIPTQFLEYARTREGLQRLPDNVLEMMDFETALLHAETMVQPASDGRWEDNTVLSWAPAAQIRHYNYNFVDSHLESIEEEPSIVLTWRNLDNEVYYRSVEDADLFLLEHFRKQSDTFINVLNNLKEMLDGQDIEAWLRENIDGWVEAGVLLPTHM
>LR134516.1|VEJ21981.1|1875944_1876520_-|RNA-polymerase-sigma-factor
MENFKKLLTSIQPDILRFARIQLRDDHLAEDIVQETLAAAIDKYSQFRGDAGLKTWVMTILKNKITDYFRSKKNIVSIEGLQEENAAIDDAYNECFDETGHWFASASPQQWREAPEEFTRQQDFFRTLENCMQGLPEDTAQIFYLREIMGLEITEICSRFDISKDNCYVILHRARNGLRNCLQHRWFDLNE
>LR134516.1|VEJ21991.1|1889745_1890039_-|CRISPR-associated-endoribonuclease-Cas2
MLMLITYDISLEDTEGQARLRRIAKHCLDYGVRVQYSVFECDVTPDQWVKLKAKLLDTYQPETDSLRFYHLGSKWRRKVEHHGAKAAVDVFQDTLIV
>LR134516.1|VEJ21992.1|1890116_1891130_-|CRISPR-associated-endonuclease-Cas1,-subtype-I-C/DVULG
MRKLQNTLYITTQGSYLHKERETLVVEQERKKVAQLPVHAIGHIFCFGNVLVSPFLMGFCGENNVNLAFFTENGRFLGCLQGRQSGNVLLRRAQYRLSEQNPVPIARHMIAAKIQSAKRVLQRRLRNHGEHAEVLAAVTALNFSLQQLKRVECLDKIRGIEGDAAARYFGVFRHLLAEKSGFDFDGRNRRPPRDGVNALLSFLYAVLGKDISGALQGVGLDPQVGFLHADRPGRDSLAQDILEEFRAWWVDRLVLSLINRGQIKPQDFVHEASGAVNIKPEARKLVFQALQAKKQEKIIHPFLQEEVEIGLLPYIQAMLLARHLRGDLVEYPPFLMR
>LR134516.1|VEJ21993.1|1891555_1891819_-|Uncharacterised-protein
MLNHMYRAKEKKMAYVLHAEFGYTKQAIAQLMKISPQQMGQWIKEVSYELRIHKMGQEIEELKKELISLGYSPQKQLGHDVIEYLEG
>LR134516.1|VEJ21994.1|1891965_1892571_-|recombinase-B
MISIPLSALQHYAFCPRQCALIHNEQAWAENYLTAQGRALHERVDGGEPETRKGVRFERSVHVSAEKLGVHGVLDMVERDIQTGRLKPVEYKRGKPKPEPFDEIQLCAQALCLEEMTGQTVAEGALWYMQTRHRVPVAFSGSLRAQTLQVIGEVRGLLESGVTPPPEYVKRCKACSLIEVCQPKLMERDRSVGYVAGLFGE
>LR134516.1|VEJ21995.1|1892647_1893271_-|Uncharacterised-protein
MKNFIQSLENEFVEKNQEKTTFSIRLSVKEDLILQEIAESFDLSRQELLHRLITEQIIVPWKKRFEEQANEELEEVDAEQSTQYFLLNTNKVNDIDDHDFMLEKQVAAAFEDGYKEKIAKFKKGDWVFLYESGQGIVAFGQASGKLEKAPHYGREDKTYYQRLEGFTRLSKAIKASEVKRILNRSFPFAQTLARIADGEKLLSEVKK
>LR134516.1|VEJ21996.1|1893385_1894249_-|phage-associated-protein
MSIQNRYEFVFFFDVSNGNPNGDPDAGNMPRLDPESSKGLVTDVCLKRKIRNFVELANENQAGYEIYVKEKSVLNLQNKRAYEALGIESEAKKLPKDEAKARDITAWMCKNFFDIRTFGAVMTTEVNSGQVRGPVQLAFAQSIDPIVPLEVSITRMAVTNEKDLEKERTMGRKYIVPYALYRVHGFVSASLAAKTGFSDEDLQQLWNALKLMFEHDRSAARGEMAARKLIVFKHDSALGNEPAHKLFEAVKVERIHGESGTPAAAFSDYRISVDSDGLKDVEVMEIL
>LR134516.1|VEJ21997.1|1894251_1896039_-|phage-associated-protein
MILTSLARYYRRLAAENDVAGNPKVPPYGFSEEKIGWVLVLDSDGLLVDVVPHLTDDKKPQPRLMSVPRPEKRTSGVKPNFLWDKTAYALGVEANKDKATAKEQPFRPSEKTFAAFRELHLEALKDTQDEGLLALRRFLERWQPEQFAHPPCRPDMLDANVVFRLDGTRGYIHQREAAQALWAGRLKNDEAEQGLCLISGESAPIARLHPAIKGVFGGQSSGGSIISFNKESFTSFGKEQGANAPVSEVSAFAYTTALNYLLRRDNGHCLTIGDASTVFWAEADTPEQAAAAEACFVDMLDPPDDEQENQKIFNILAQVAKGRPLREIDPNLDDQTRFYILGLAPNASRISIRFWLDTTFGKLAEHLAQHWRDLALEPRAWKTPPSIWRLLVQTAPLGKSENISPVLAGEMTRAVIGGTPYPMSLLLQLIARIRADGDANGLRVAMIKAVLQRRFRKSLIKEEIPMSLDTESRNTAYLLGRLFAVLERIQNQALGDLNAGIADRYYGSASAVPFSVFPRLLSGAKHHLSRLRKDKAGMAVNLDKDLGGIIAGLPETFPRHLSIEEQGRFAIGYYHQKQSYFAKKDPAETQSHEGE
>LR134516.1|VEJ21998.1|1896035_1896707_-|CRISPR-associated-protein-Cas5,-subtype-I-C/DVULG
MNRVRLHIWGDYACFTRPEMKVERVSYDVITPSAARGILAAVHWKPAIRWVIDRIHVLKPIRFESVRRNELGSKISASKVSGAMRRKSVEDLYALIEDDRQQRAATVLKDVGYVIEAHAVLTARAGAGETVAKHIEMFKRRAAKGQCFQQPCMGVREFPAHFAWVDEDSLPESELPENERDRDLGWMLHDIDFDGSNLPHFFRAEMKSGVVEVPPFFAEEVKK
>LR134516.1|VEJ21999.1|1896773_1898621_-|Predicted-ATP-binding-protein-involved-in-virulence
MSKSHLVRMHIKNLGCIGNEGLTIELDDIVCLVGANNSGKTTVLRAYELAVNQEKLRADDFHKEANGNPATVELWVHIPENAGNIDDKWKEKTTDGLLLVRSKWEWNGLDKPKRTTWNPELQEYSEDEKASGLDAVFSSRLPKPFRIGSLDNPEDEHKKLLSLALEPILKEYKFLIEDEASDFSKKLLELKESAREPINKLNRQIESTQEKINSSYRKIFSSSEVKLTVSIGDLGFNLQKALTDNSRIDVSERNSLSRWDMQGTGAQRALFWSILQVRSELNREYEAEKLRGKLKIDLEKLQSKSKKTTADERKIQTLIEQLSEGNDDSDVFLPGYMLLIDEPETALHPSAIRAAKEHLYSLASEAGWQVMLSTHNPIFIDPLADHTTIVRLHRTEESFSPNTYRTEAIEFSDSEKDNLKALMLFDTNLSEMFFGNKVLIVEGDTEFAAFSEIMRRDPEKYPINKRPLIVRARGKATIAILVKMLAHFKINFSVLHDIDSPRNKEGKSNPAYSINKNIAEVIRNAKSKGLKIIHRCSCPNFEEHHQMKLPNKDKPFESWKAVKENSEICLSVESMLDQLIDESTDIQEKDGSNYEEILKDWIGDNGNEDIRYKFS
>LR134516.1|VEJ22000.1|1898684_1900997_-|Superfamily-II-helicase
MSVKNQTIQTYYAHSVENQPYEYWQTMRSHAHNVGDTAAGFAAFFGAQEMARYTGQLHDLGKYTPQFNRRLHGGPSVDHATAGAKIAFERWSVLGKLMAFCIAGHHAGLANGDGEGDNRRTLTQRLAVPFGTGTHDIPEPDEVWRQEIQLPQKLAMPGVKFGVADSADQYAKSFSVAFFTRMLYSCLVDADYLDTEAFYAGLEDKTVQRGGHPDLLQLQQRFNRFIGDFRRHIAEKPQHTEEEKRNAALNRLRSDILDHAVSQAEQAPGLFTLTVPTGGGKTFTSMAFALEHAKQHGMRRVIYVIPFTSIIEQNAAEFRKAFGDLGEAAVLEHHSTFDDSNLEDQHSKDKLRQASENWDMPVVVTTAVQFFESLFADRSSRCRKLHNISGSVIILDEAQMLPLKLLLPIMQAVKELARNYHCSVVMCTATQPAIQAEHGFYRGLENTRELAPNPLELFDKLRRTTVQHIGLQTDADLLEKLTQHKQILIIVNNRRHARSLYDSAKQLEGVFHLTTLMCAKHRSQVLETIRGRLKNSEPCRVIATSLIEAGVDVDFPLVMRAEAGLDSIAQAAGRCNREGKRPSENSFVWVFKPEEQWKAPPELGLLSAAMREVVCHHADDLLSPQAIRRYFQRVYEEKGKELDSKGILEMHKKAGNSLNFPFQTIAQKFRMIESHMQPLIIPFDQDAERLIDSLRHADQIGGLLRKLQPYTVQVPESALQALFKAGRIETVNEKRFGKQFYSLIGLDLYDEVAGLWWEDVGFLRGEGLIM

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Crispr_ID: LR134516_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR134516_3

2068961-2069125

Orphan

Consensus_repeat	Method
GTTTCAACACACAGCCACCCGAAGGTGGCTGA	CRISPRCasFinder

2 spacers

The CRISPR arrays of LR134516_3

>merge|LR134516|3|2068961-2069125|CRISPRCasFinder
GGTTTAATACACAACCACTCGAAGGTGGCTGAGTTTCTTTGGCCCAAGGCTCAAAGCCTATACATCCGTTTCAACACACAGCCACCCGAAGGTGGCTGAGCAGGAACTTGGGCTTACCCGACGCGGTTACGAAGTTTCAACACACAGCCACCCGAAGGTGGCTGA

>LR134516|3|3|2068961-2069125|CRISPRCasFinder
GGTTTAATACACAACCACTCGAAGGTGGCTGA	GTTTCTTTGGCCCAAGGCTCAAAGCCTATACATCC
GTTTCAACACACAGCCACCCGAAGGTGGCTGA	GCAGGAACTTGGGCTTACCCGACGCGGTTACGAA
GTTTCAACACACAGCCACCCGAAGGTGGCTGA

Protein	Signature genes	Signature genes Name	Protein_function
LR134516.1\|VEJ22174.1\|2075407_2076307_+\|ABC-transporter-ATP-binding-protein,-iron-related	unknown	unknown	gnl\|CDD\|224054
LR134516.1\|VEJ22178.1\|2081915_2082209_-\|ComE1	unknown	unknown	gnl\|CDD\|213597
LR134516.1\|VEJ22175.1\|2076406_2078560_-\|integral-membrane-protein	unknown	unknown	gnl\|CDD\|130727
LR134516.1\|VEJ22166.1\|2065776_2066493_-\|septum-formation-inhibitor	unknown	unknown	gnl\|CDD\|179856
LR134516.1\|VEJ22168.1\|2067524_2068895_+\|adenylosuccinate-lyase	unknown	unknown	gnl\|CDD\|236452
LR134516.1\|VEJ22165.1\|2064931_2065744_-\|protein-MinD	unknown	unknown	gnl\|CDD\|225447
LR134516.1\|VEJ22170.1\|2070756_2071080_-\|Putative-periplasmic-protein	unknown	unknown	unknown
LR134516.1\|VEJ22160.1\|2060841_2061309_+\|lipoprotein	unknown	unknown	unknown
LR134516.1\|VEJ22176.1\|2078784_2080239_-\|outer-membrane-protein-OmpU	unknown	unknown	gnl\|CDD\|368004
LR134516.1\|VEJ22169.1\|2069365_2070670_-\|Peptidase-M16-inactive-domain	unknown	unknown	gnl\|CDD\|223685
LR134516.1\|VEJ22161.1\|2061407_2062046_+\|5-formyltetrahydrofolate-cyclo-ligase	unknown	unknown	gnl\|CDD\|223290
LR134516.1\|VEJ22162.1\|2062208_2063630_+\|amino-acid-transport-protein	unknown	unknown	gnl\|CDD\|224040
LR134516.1\|VEJ22164.1\|2064658_2064928_-\|cell-division-topological-specificity-factor-MinE	unknown	unknown	gnl\|CDD\|184442
LR134516.1\|VEJ22159.1\|2058303_2060664_-\|ATP-dependent-DNA-helicase	unknown	unknown	gnl\|CDD\|273594
LR134516.1\|VEJ22167.1\|2066560_2067415_+\|Uncharacterized-conserved-protein	unknown	unknown	gnl\|CDD\|378484
LR134516.1\|VEJ22172.1\|2072285_2073041_-\|Inner-membrane-transport-permease-yadH	unknown	unknown	gnl\|CDD\|237896
LR134516.1\|VEJ22171.1\|2071597_2072155_+\|outer-membrane-protein-X	unknown	unknown	gnl\|CDD\|379226
LR134516.1\|VEJ22177.1\|2080581_2081076_+\|integral-membrane-protein	unknown	unknown	unknown
LR134516.1\|VEJ22163.1\|2063732_2064662_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176103
LR134516.1\|VEJ22173.1\|2073125_2075210_-\|methionyl-tRNA-synthetase	unknown	unknown	gnl\|CDD\|234655

Protein	Function_ID	Function_description	E-value
LR134516.1\|VEJ22174.1\|2075407_2076307_+\|ABC-transporter-ATP-binding-protein,-iron-related	gnl\|CDD\|224054	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms].	2.7955e-97
LR134516.1\|VEJ22178.1\|2081915_2082209_-\|ComE1	gnl\|CDD\|213597	TIGR01259, ComE_operon_protein_1, comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation. [Cellular processes, DNA transformation].	2.96063e-24
LR134516.1\|VEJ22175.1\|2076406_2078560_-\|integral-membrane-protein	gnl\|CDD\|130727	TIGR01666, Uncharacterized_protein_HI_1680, TIGR01666 family membrane protein. This model represents a clade of sequences from gamma and beta proteobacteria. These proteins are >700 amino acids long and many have been annotated as putative membrane proteins. The gene from Salmonella has been annotated as a putative efflux transporter. The gene from E. coli has the name yccS. [Cell envelope, Other].	0
LR134516.1\|VEJ22166.1\|2065776_2066493_-\|septum-formation-inhibitor	gnl\|CDD\|179856	PRK04516, minC, septum site-determining protein MinC.	1.31514e-97
LR134516.1\|VEJ22168.1\|2067524_2068895_+\|adenylosuccinate-lyase	gnl\|CDD\|236452	PRK09285, PRK09285, adenylosuccinate lyase; Provisional.	0
LR134516.1\|VEJ22165.1\|2064931_2065744_-\|protein-MinD	gnl\|CDD\|225447	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning].	2.44498e-173
LR134516.1\|VEJ22176.1\|2078784_2080239_-\|outer-membrane-protein-OmpU	gnl\|CDD\|368004	pfam04575, DUF560, Protein of unknown function (DUF560). Family of hypothetical bacterial proteins.	1.91705e-98
LR134516.1\|VEJ22169.1\|2069365_2070670_-\|Peptidase-M16-inactive-domain	gnl\|CDD\|223685	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only].	5.40896e-76
LR134516.1\|VEJ22161.1\|2061407_2062046_+\|5-formyltetrahydrofolate-cyclo-ligase	gnl\|CDD\|223290	COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism].	1.48482e-44
LR134516.1\|VEJ22162.1\|2062208_2063630_+\|amino-acid-transport-protein	gnl\|CDD\|224040	COG1115, AlsT, Na+/alanine symporter [Amino acid transport and metabolism].	0
LR134516.1\|VEJ22164.1\|2064658_2064928_-\|cell-division-topological-specificity-factor-MinE	gnl\|CDD\|184442	PRK13989, PRK13989, cell division topological specificity factor MinE; Provisional.	2.10168e-33
LR134516.1\|VEJ22159.1\|2058303_2060664_-\|ATP-dependent-DNA-helicase	gnl\|CDD\|273594	TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ. [DNA metabolism, DNA replication, recombination, and repair].	0
LR134516.1\|VEJ22167.1\|2066560_2067415_+\|Uncharacterized-conserved-protein	gnl\|CDD\|378484	pfam10728, DUF2520, Domain of unknown function (DUF2520). This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases.	4.81318e-35
LR134516.1\|VEJ22172.1\|2072285_2073041_-\|Inner-membrane-transport-permease-yadH	gnl\|CDD\|237896	PRK15066, PRK15066, inner membrane transport permease; Provisional.	1.6775e-65
LR134516.1\|VEJ22171.1\|2071597_2072155_+\|outer-membrane-protein-X	gnl\|CDD\|379226	pfam13505, OMP_b-brl, Outer membrane protein beta-barrel domain. This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold.	3.75858e-14
LR134516.1\|VEJ22163.1\|2063732_2064662_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|176103	cd08411, PBP2_OxyR, The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.	4.64098e-76
LR134516.1\|VEJ22173.1\|2073125_2075210_-\|methionyl-tRNA-synthetase	gnl\|CDD\|234655	PRK00133, metG, methionyl-tRNA synthetase; Reviewed.	0

>LR134516.1|VEJ22168.1|2067524_2068895_+|adenylosuccinate-lyase
MINPISALSPLDGRYAQSVEALRPIFSEYGLMKARVKVELNWLKALAAEPKITEVPAFSDFTVAEIDRVIAEFSLEDAAAVKAIEATTNHDVKAIEYWLKERFSGVPEVAAAGEFIHFACTSEDINNLSHALMLADAREAVLLPKLAEITAKLTEMAHDLAAVPMMSRTHGQPATPSTLGKEIANVVYRLQRQIKQLAAQEFLGKINGAVGNYNAHMVAYPDVDWEAHCQTFVEQALGLTFNPYTIQIEPHDYMAEFFQTLSRINTILIDFNRDVWGYISLGYFKQKVKAGEVGSSTMPHKVNPIDFENSEGNLGMANAVLGFLSEKLPVSRWQRDLTDSTVLRNMGVGAGYTVLGLAAHLRGLNKLEANPAALAADLDATWELLAEPIQTVMRRYGVANPYEKLKDLTRGKDGITPEVLKVFVESLDIPADAKQLLLALTPALYVGKAEALAKRI
>LR134516.1|VEJ22167.1|2066560_2067415_+|Uncharacterized-conserved-protein
MKKTFHIIGAGRVGQTFATVLPKNGRWQLANVVSRSSTVAMADCISKAIVPRISYLPEADTVFICTPDNIIEETAAAVACLPWLNTGTLVLHMSGAKTVAVLDAAARSGAMTGSLHPVFAFADIEKSVAELAGNLCALEAGSEAAMTVLHELADAAGLRAFEIPSEHKARYHAALSAASNFSVTLAAFAQDLLHPLHLPEQLSRELVCNLMQQSVNNLARLTPLQALTGPIVRGDDSTVAAHLACMNVQEQKNYRLWAQATLELARARLSEESARQMENLLERL
>LR134516.1|VEJ22166.1|2065776_2066493_-|septum-formation-inhibitor
MTEQKMKPAFDVKSARLDVLSVQLHTADLGELEEFLQQRVSQHKELDSMLFLLDVQEFNNPGELNIGGIVSLFARYGLQIVGLRHENEAWAAHAAAYHLSFSQNEKAPETQTQPAAAKPVKATVISKPTVLVSTPIRTGQQVYAENADLIVTDIVNEGAEIIADGNIHVYGTMRGRALAGATGNREARIFIYSMQAELVSVAGIYRNFEQSLPAHLHKKPVQISLQDNRLVISPIGEE
>LR134516.1|VEJ22165.1|2064931_2065744_-|protein-MinD
MAKIIVVTSGKGGVGKTTTSASIASGLALRGHKTAVIDFDVGLRNLDLIMGCERRVVYDLINVIQGEATLNQALIKDKHCDNLYILPASQTRDKDALSRDGVEKVLQDLAGEMGFEFVICDSPAGIEQGALMALYFADEAIVTTNPEVSSVRDSDRILGILQSKSRKAEKGETVKEHLLITRYSPERVNKGEMLSVQDICDILRIPLIGVIPESQSVLQASNSGSPVIHQNDAVAAEAYKDVVARLLGENREMRFLEAEKKGFFKRLFGG
>LR134516.1|VEJ22164.1|2064658_2064928_-|cell-division-topological-specificity-factor-MinE
MSLIDLIFGRRNKTAEVARDRLQIIIAQERAKDQAPDYLPTLQKELLEVLSKYVHVSLDDIRITQEKQNGMDVLELNITLPEQQKKAEE
>LR134516.1|VEJ22163.1|2063732_2064662_-|LysR-family-transcriptional-regulator
MTLTELRYIVAVAQERHFGRAARRCFVSQPTLSIAIKKLEEELSVSLFDRSSNDIITTEAGERIIAQARRVLEEAELIRHLANAEQNELEGALKLGLIFTVAPYLLPKLIVALRKIAPNMPLMLDENYTHILTEALKRGDLDAIVVAEPYHEPGIITEPLYDEPFFVIVPKGHHFEDLDAVTPELLAEEQVLLLSEGNCMRDQVLTSCSELASKQKIQGLTNTLQGSSINTIRHMVASGLSISVMPATALTENDHMLFSIIPFEGVIPHRRVVLAYRRNFVRPKALAALRNAVLSSQLSGVTFVGNQAV
>LR134516.1|VEJ22162.1|2062208_2063630_+|amino-acid-transport-protein
MVETIHTFVNKLNGPLWQLLVFLLLGVGLFFTFRTGFVQIRLFARSVKEMLSGRQEGDDPHGITPFQAFVTGLASRVGVGNIAGVAIAVSMGGPGAVFWMWLTALLGMSSAFAESSLAQLFKVRDYDSHHFRGGPAYYITQGLKQRWLGILFALSLILAFGFVFNAVQANSIVAATQTAWGWKPELVGMALVIMTAPIIFGGIRRVSKISEGVVPVMAILYLLMAVYVILTNLSAVPAVFALIFEKAFDFQAAAGGFFGGMAAQAMMLGIKRGLFSNEAGMGSAPNAAAAAEVKHPVSQGMIQMLGVFVDTVVVCSCTAFILLLSHVTQNPGEMTGVQLTQTAIESHVGAWGKDFLAVLLFMFAYSSIIGNYAYAESNVQFIKSSRLSLAIFRSIVLGFVYFGAVNSVPVVWDMADLSMGIMALINLIAIIALSPLVFLLLRDYTAKLKMGKDPEFKLSEHPGLKRRIKSDIW
>LR134516.1|VEJ22161.1|2061407_2062046_+|5-formyltetrahydrofolate-cyclo-ligase
MWFPALNERPSEMPRTADKASLRRQFRRARAKLGKSERRQATRKINNLLKRYIRRNSRIGVYWPIGSELRLDGLIEAVLKRGAKPYLPYIEPHSLRLWFTPYSGNRKAAERQRGNGKLYIPQFAGEKIRAHRLNLLLVPVVGIDRQGCRLGQGGGYYDVSLAACRHRLQPHTLGVGFACQLCDELPREIHDTTLNGFVCELGEMRFKMPKCF
>LR134516.1|VEJ22160.1|2060841_2061309_+|lipoprotein
MNISLILRRTAAAALVSSIAACTAMDDMGDMGGKGPNVSGHWDKIGTTSNGNIKAFIDRNSIQKNGNLVTFRDKKTVQKPNEERYVNTPRYKTAIGTWEMHCVNKTYRLTELQLIDEKGMLLVNETYTAAGLRPLSVMSGSITEKQFEAVCDKKL
>LR134516.1|VEJ22159.1|2058303_2060664_-|ATP-dependent-DNA-helicase
MTKPPAAQILHDVFGYPEFRGSQAEIVDTLAGGNSLLVLMPTGGGKSLCYQIPALMREGVAVVVSPLIALMNDQVAALHTAGVAAACVHSGTTPDEARQIADDIQSGRLKLLYVAPERLVSERFLRFLDQHTISLFAIDEAHCVSQWGHDFRPEYQQLGLLADRYPHVPRIALTATADAATRADIKHHLRLEDAAEFVASFDRLNIYYQVIEKNNGKKQLLQFIQKQMMGQSGIVYCLSRKKVEDVTAFLCENGLDAIPYHAGLSMDVREANQRRFTREDNVIVVATVAFGMGIDKPDVRFVAHLDMPQSVEHFYQESGRAGRDGLPAASWLCYGLNDWVLLRERIQTGNSDDMQKQIELQKLDAMLSVCETADCRRVLLLKHFGEDSQPCGHCDNCLHPPVRFDGTVLVQKLLSCVYRVGQQFAAGYVINVLRGKSDDWIARNRHHELSTFGIGDNLSDKEWRAVIRQCISAGYLTVNPLMHQALQLTPAAKTVLKGGTPVWLRPLKRDKAATQKPKEEWLRTEREERIWQALRAWRLKRAQAEEVPAYVIFGDKTLRDIVEKLPATPAELHDIYGLGEAKINSFGEDIIEVCQTAAASSRPSESELGELRPNPSGAVSDSLSDGLETERDRRLWQALNTWRSRTAQAEGVTPHTVCPDDSLLDLVRNTPEEAADLNGIYGLGAVRIGKFGSSILAVCKPFSDGLSNEAKHKRRLMRALMQWCAATAETEGEPEHTVFSKITLRAIAAKQPQTLAELGGIHGVGADKIEKYGEAVLEVCRRLSRP
>LR134516.1|VEJ22169.1|2069365_2070670_-|Peptidase-M16-inactive-domain
MFPHKTLAALLFLPLAAQAAVGIQRWHTPEGTQILLVERHENPIVDIQISFKGAGSAFNPQDKGEVSEFTAGLLTDGTRQLDEEAFKERTNDLAVSLSSGSSSEGASITLRSLSKPKNLNAAVTLLNHSLTQPRFDAAVFDRQQKQSITALKQNETDPGFIADRAFTRLSYGNHPYGRSAQTSVESIRRVTLDDIRAFHRTRYGKNNAIVAVVGDLNRHQTEALVKKALDGLPERSKESGSIPAVPVRGAMRQNIPFAGEQAQIIMGMPLIKRHDPDYYALVVGNYVLGAGGFDSRLMKVLRDQYGYTYGAYSSLSPSTEAGPLSIAFSTQKANTAQALAAARKVLADFIAEGPTEAELAQAKANLTGSFPLRFDTNAKLLGYLSLIGFHNLPDDYLEAYPKAVSAVTAEQIKSAWQRRVKAEQMNIVVVGADK
>LR134516.1|VEJ22170.1|2070756_2071080_-|Putative-periplasmic-protein
MKKLIVLTLLAVSPLAFADNAADELLSAQAAYRDALKAQSTGGNRIATLQSELSAAQSRLKQAQADVVGLQEKLHKETAAQAQADNVFQAASKRLDAAWKAARTTSN
>LR134516.1|VEJ22171.1|2071597_2072155_+|outer-membrane-protein-X
MKKALLTVLILGSTAIASAESFSDTFTGPAVEVGVGVSKTDVKHRSLNEKHKADVSVRGNYNVEYGNNWIGGAEVALKPLNRKISNHGNGKVKQKYDASVSYLQGYRFAQDAMVYGKVGYHYGKFDNVIAGTNRHMNGLGYGAGLKYAVTPNVEVGGEWEQTRYKRSDNKATNNSYMATIGYRFK
>LR134516.1|VEJ22172.1|2072285_2073041_-|Inner-membrane-transport-permease-yadH
MIGFYTLFKKEILRFWKVGLQTIAAPMLTALLYQLIFSHAIGRHVEALPDVAYNAFLIPGLAMMSMTQNAFANSSSSLIQSRLAGNLVFILLPPLSTAAFFSAYVGAAVVRGLLVGAGVIAVTAPFGLPMPHNIGWILAFSLLGCTIMGMLGLLAGIVAEKFDQLAMFQNFLIMPLTFLSGVFYSINSLPAFWRGVSGLNPVFYMIDGFRYGFFGVGDVSPWLSFAVVGGFSLVLGAGVLAILKSGWKLRN
>LR134516.1|VEJ22173.1|2073125_2075210_-|methionyl-tRNA-synthetase
MTQRKILVTSALPYANGSIHLGHMVEHIQTDIWVRFQKLRGHQCHYCCADDTHGTPVMLAAQKQGMKPEDMIAKVREEHLADFTGFHIGYDNYYSTHSPENKQLSEQIYLALKANGKIESRVIEQLFDPEKNMFLPDRFVKGECPKCHAKDQYGDNCESCGTTYSPTELINPYSAVSGATPVLKESEHFFFKLGECADYLKEWTSGSTTLSDGRIQPHLQAEALNKMNEWLGGGENGETTLSDWDISRDAPYFGFEIPGAPGKYFYVWLDAPVGYMASFKNLCDRTGLNYDEYFQAGSQTEMYHFIGKDILYFHALFWPAMLKFSGHRAPTGVFAHGFLTVDGQKMSKSRGTFITAKSYLDGGLNPEWMRYYIAAKLNSKIEDIDLNLNDFIARVNSDLVGKYVNIAARASGFIAKRFEGRLKDVSGSKLVQKLAAERDNIAADFEHREYAKALREIMALADAVNEYVDANKPWELAKQEGQDARLHEVCSELINAFKILTIYLAPVLPKVAERAAAFLNLDGLRWSDAATVLPEGHTINQYSHLMQRVEQKQVDDLIEANKQSIQTASTEAVPAEKSPYAPVAEQAGFDDFMKIDMRVAKVLNCEAVEGSTKLLKFDLDFGFEKRIIFSGIAASYPNPAELNGRMVIAVANFAPRKMAKFGVSEGMILSAATADGKLKLLDVDAGAQPGDKVG
>LR134516.1|VEJ22174.1|2075407_2076307_+|ABC-transporter-ATP-binding-protein,-iron-related
MSAAIHIQNAVKTYKNGFTALKDVSFNVEQGEFFGLLGPNGAGKTTLISAMAGLSRLTSGNISVMGHDVVADAYAARMSLGVVPQELVFDPFFTVREALQFQSGYFGIKNNDAWIDEIIDNLGLTDKAGTNTRNLSGGMKRRLMVAQALVHRPPVIVLDEPTAGVDVELRQNLWTFISGLNRQGHTIILTTHYLEEAQSMCTRIAMLKHGELVALDKTEHLLRNEKGLRVELLLGGALPENLQQWQVPQENDAVLLKLEDYDQLAFVLQTLKYADVEVKHLSLPKTDLEDVFVQMMRAK
>LR134516.1|VEJ22175.1|2076406_2078560_-|integral-membrane-protein
MRTPPVNPKVIATLPIFVSVFIAASLVWYFNVPKLTTPFVLGVIAGGLVDLDNRLTGRLKNIVITLVLFSVSSLGAQMTHGTGLPFILMMTVFTFLFTLTGAVGLRYRTFAFGTLAVATYTTLSYTPEIPWFVSPLMILCGTLLYSMMTLLLHVVFPHRPVQESVADAYAALGSYFDAKAAFFDPDEADWLESRQIDLAMKNTGVIDAFNQCRIALFYRMRGQHRHPRTNRMLRYYFAAQDIHERISSAHVDYRELADRLKNTDLIFRINRLLELQGQACRDVAESLRSGKPYQYGKRLERAIQGCRQSLKIYAENHNGAEVHTLQRLLENLFSVDYQLSHLEKDEHNAAEMHSDKSGIAAMERGGLRHVWNTVRSQMNFESAVFRHAVRLSIVVFAACAIVEVFHLDLGYWILMTALFVCQPNYSATKSRVVQRIAGTILGVVVGSLVPYFTPSVETKLWIVIASTTLFFFFRTNKYSFSTFFITVQALTSLSLAGIDVSAALWPRFTDTVIGTGIAWAAVSYLWPDWRYLTLSRTAGQSVSQNGRYLRHILGQLQNGSVDDMAYRSVRRQAHERAAALSSTLSDMSGEPKKYGSQLQDGFNLLKTSYALIGYISALGAYRNRMVKDCALDFTEGFFQTAYQIADILENIAVEPPEAFQTALNEVKDSLENLHERVADDRQSSILWHQLCLIARQLQPCYTALHGAQEEADQVQAV
>LR134516.1|VEJ22176.1|2078784_2080239_-|outer-membrane-protein-OmpU
MLKYLFIISSIGVVAPAFANEPPPQVLPTVETPFFDDPLKIEAKPKPKKPEVAPAVDALPEKQTESVELNEDDLRQNPELAAQLIERAMRSQNWPLLADLLSLYRTIPEHDVILYDYASGALLRSQKKHAQAIAAYRRIISAHPELSYVRLDLAGMLYENKQYQAAKDQFERVKADNIDANARMLADAYLERIQKQAGWQFNAGVQYERNDNVNNASSVKYIEIGGRRFVRDEDSLPKRANGLQYNFSVERDWNLTGNHYATTEASVDGTWYWDNKDYSEESVRVSAGYKNQNIRRWASFKPFVGYNRLGGESYSRNFGATAEYGGWVNDNWQLIGSAVHMQRHYARDYHAKRYNGHLNSASFTAAWLPTAGLMIYGGVDYSREHTVEKIESSDRKGGRVGVIKEWNNGLSTRANLRYALRDFDEPSIRRDKEYQANVALWHRSVHLYGITPKLNFRYLKIDSNIPVFYSRQNRQWFITLEKTF
>LR134516.1|VEJ22177.1|2080581_2081076_+|integral-membrane-protein
MKRILTSLPIWIVLTDMAYGFFLNISQSLNLHQQARPVKDSLPVSPDIAFSGLQVLTNGGMTLIIGFGLMVLLQLNRSVLQKQILPIGIFRTLGLLAVLAFSLPSLWEWFWAAINFAKGQYTIAFDNPRYLITAICLPLISCLCIVRLTGWYRLHKNLSQENNL
>LR134516.1|VEJ22178.1|2081915_2082209_-|ComE1
MKRYVLALVGMLVSAWSLAAVNINTATAEELKALPGIGPSKAAAIVEYRTQNGKFKSVDELKNVKGIGEGILSKLKAEAVVSGHGSAKGKAQPVLKK

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
LR134516_1	1.5\|1231719\|30\|LR134516\|PILER-CR,CRISPRCasFinder,CRT	1231719-1231748	30	LR134516.1	345525-345554	0	1.0

1. spacer 1.5|1231719|30|LR134516|PILER-CR,CRISPRCasFinder,CRT matches to position: 345525-345554, mismatch: 0, identity: 1.0

ggaatcagtatttatggcgtagttattttt	CRISPR spacer
ggaatcagtatttatggcgtagttattttt	Protospacer
******************************

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
LR134516_1	1.5\|1231719\|30\|LR134516\|PILER-CR,CRISPRCasFinder,CRT	1231719-1231748	30	AP012539	Stx2-converting phage Stx2a_WGPS6 proviral DNA, complete genome	19069-19098	6	0.8
LR134516_1	1.5\|1231719\|30\|LR134516\|PILER-CR,CRISPRCasFinder,CRT	1231719-1231748	30	AJ304858	Bacteriophage CP-1639 and chromosomal integration site	18025-18054	6	0.8

1. spacer 1.5|1231719|30|LR134516|PILER-CR,CRISPRCasFinder,CRT matches to AP012539 (Stx2-converting phage Stx2a_WGPS6 proviral DNA, complete genome) position: , mismatch: 6, identity: 0.8

ggaatcagtatttatggcgtagttattttt	CRISPR spacer
gcgctcagcatttctggcgtagttattttg	Protospacer
* . ****.**** ***************

2. spacer 1.5|1231719|30|LR134516|PILER-CR,CRISPRCasFinder,CRT matches to AJ304858 (Bacteriophage CP-1639 and chromosomal integration site) position: , mismatch: 6, identity: 0.8

ggaatcagtatttatggcgtagttattttt	CRISPR spacer
gcgctcagcatttctggcgtagttattttg	Protospacer
* . ****.**** ***************

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

1355756 : 1363149

Streptococcus_phage(16.67%)

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
VEJ21515.1\|1355756_1356734_-	DNA polymerase III subunit delta'	M1NSC1	Streptococcus_phage	8.7e-15	31.3
VEJ21516.1\|1356925_1357606_+	Uncharacterized BCR, COG1636	NA	NA	NA	NA
VEJ21517.1\|1357802_1359437_-	molecular chaperone GroEL	A0A2I7SAK5	Vibrio_phage	4.9e-172	62.8
VEJ21518.1\|1359527_1359815_-	co-chaperonin GroES	A0A221S322	uncultured_virus	2.1e-14	39.4
VEJ21519.1\|1360389_1361289_+	recombination associated protein	L7TP07	Pseudomonas_virus	9.7e-45	34.8
VEJ21520.1\|1361402_1361969_+	deoxycytidine triphosphate deaminase	S5VM63	Pseudomonas_phage	3.1e-73	71.0
VEJ21521.1\|1362024_1362225_-	Uncharacterised protein	NA	NA	NA	NA
VEJ21522.1\|1362456_1363149_-	membrane peptidase	I3PV79	Clostridium_phage	7.0e-11	35.4

DBSCAN-SWA_2

1367452 : 1373756

Escherichia_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VEJ21528.1\|1367452_1367779_-	Uncharacterised BCR, YnfA/UPF0060 family	A0A218MNG8	uncultured_virus	3.4e-24	54.9
VEJ21529.1\|1367845_1368436_-	LemA family	NA	NA	NA	NA
VEJ21530.1\|1368700_1369774_+	dTDP-glucose 4,6-dehydratase	I7HTA3	Enterobacteria_phage	4.2e-95	51.5
VEJ21531.1\|1369814_1370681_+	glucose-1-phosphate thymidylyltransferase	K7QKA7	Escherichia_phage	1.3e-107	66.2
VEJ21532.1\|1370828_1371365_+	dTDP-4-dehydrorhamnose 3,5-epimerase (dTDP-4-keto-6-deoxyglucose 3,5-epimerase; dTDP-L-rhamnose synthetase)	A0A291LA62	Escherichia_phage	3.5e-58	56.6
VEJ21533.1\|1371361_1372228_+	dTDP-4-dehydrorhamnose reductase	A0A291LA50	Escherichia_phage	7.4e-42	36.5
VEJ21534.1\|1372631_1373756_+	ABC transporter ATP-binding protein, polyamine	G3M9Y6	Bacillus_virus	4.6e-28	35.3

DBSCAN-SWA_3

1482090 : 1491109

Acinetobacter_phage(16.67%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
VEJ21640.1\|1482090_1483167_-	peptide chain release factor 1	G0YKC3	Acinetobacter_phage	5.3e-05	45.5
VEJ21641.1\|1483428_1483761_-	Uncharacterised protein	NA	NA	NA	NA
VEJ21642.1\|1483744_1484047_-	integration host factor subunit alpha	A0A0H3UZA0	Geobacillus_virus	6.8e-11	38.5
VEJ21643.1\|1484121_1486485_-\|tRNA	phenylalanyl-tRNA synthetase subunit beta	A0A1L3IZU3	BeAn_58058_virus	5.5e-07	30.0
VEJ21644.1\|1486600_1487587_-\|tRNA	phenylalanyl-tRNA synthetase subunit alpha	A0A2I2L4E3	Orpheovirus	5.1e-31	34.0
VEJ21645.1\|1487943_1488300_-	50S ribosomal protein L20	NA	NA	NA	NA
VEJ21646.1\|1488311_1488509_-	putative 50S ribosomal protein L35	NA	NA	NA	NA
VEJ21647.1\|1488656_1489061_-	translation initiation factor IF-3	A0A2L0UZ54	Agrobacterium_phage	3.8e-09	32.1
VEJ21648.1\|1489195_1491109_-\|tRNA	threonyl-tRNA synthetase	A0A2K9L297	Tupanvirus	1.1e-125	36.8

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. LR134516

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CRISPR-Cas detection and classification

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Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection