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_016913	Rickettsia rickettsii str. Brazil, complete genome	1 crisprs	cas3,PD-DExK	0	1	0	0

Cas Category Instructions

Results visualization

1. NC_016913

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CRISPR-Cas detection and classification

Crispr_ID: NC_016913_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NC_016913_1

10004-10102

Orphan

Consensus_repeat	Method
AGTTAATATTGAGATATTAATATGCTAGAAACAC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NC_016913_1

>merge|NC_016913|1|10004-10102|CRISPRCasFinder
AGTTAATATTGAGATATTAATATGCTAGAAACACTTTTAAAAACCTTATAAACATAATATATTACAGTTAATATTGAGATATTAATATGCTAGAAACAC

>NC_016913|1|1|10004-10102|CRISPRCasFinder
AGTTAATATTGAGATATTAATATGCTAGAAACAC	TTTTAAAAACCTTATAAACATAATATATTAC
AGTTAATATTGAGATATTAATATGCTAGAAACAC

Protein	Signature genes	Signature genes Name	Protein_function
NC_016913.1\|WP_012151373.1\|9004_9922_+\|tyrosine-recombinase-XerC	unknown	unknown	gnl\|CDD\|234698
NC_016913.1\|WP_012151375.1\|7894_8497_+\|phospholipase-D-family-protein	unknown	unknown	gnl\|CDD\|197267
NC_016913.1\|WP_010977828.1\|11313_11529_-\|translation-initiation-factor-IF-1	unknown	unknown	gnl\|CDD\|178954
NC_016913.1\|WP_012151365.1\|17253_17445_-\|hypothetical-protein	unknown	unknown	unknown
NC_016913.1\|WP_050987956.1\|14575_14791_+\|hypothetical-protein	unknown	unknown	unknown
NC_016913.1\|WP_041472367.1\|15045_15408_+\|hypothetical-protein	unknown	unknown	unknown
NC_016913.1\|WP_012151368.1\|15383_15668_+\|hypothetical-protein	unknown	unknown	unknown
NC_016913.1\|WP_012151371.1\|10654_11302_-\|septum-formation-inhibitor-Maf	unknown	unknown	gnl\|CDD\|234957
NC_016913.1\|WP_041472556.1\|14774_15086_+\|hypothetical-protein	unknown	unknown	unknown
NC_016913.1\|WP_012151374.1\|8544_8694_-\|phasin-family-protein	unknown	unknown	unknown
NC_016913.1\|WP_012151370.1\|12244_12487_+\|hypothetical-protein	unknown	unknown	unknown
NC_016913.1\|WP_012151377.1\|5697_7176_+\|UbiD-family-decarboxylase	unknown	unknown	gnl\|CDD\|223121
NC_016913.1\|WP_012151378.1\|3976_5551_+\|peptidylprolyl-isomerase	unknown	unknown	gnl\|CDD\|182731
NC_016913.1\|WP_012151364.1\|17658_17844_-\|hypothetical-protein	unknown	unknown	unknown
NC_016913.1\|WP_012262613.1\|7296_7425_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|225783
NC_016913.1\|WP_012151369.1\|13007_13250_+\|hypothetical-protein	unknown	unknown	unknown

Protein	Function_ID	Function_description	E-value
NC_016913.1\|WP_012151373.1\|9004_9922_+\|tyrosine-recombinase-XerC	gnl\|CDD\|234698	PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed.	1.14085e-128
NC_016913.1\|WP_010977828.1\|11313_11529_-\|translation-initiation-factor-IF-1	gnl\|CDD\|178954	PRK00276, infA, translation initiation factor IF-1; Validated.	1.11247e-43
NC_016913.1\|WP_012151375.1\|7894_8497_+\|phospholipase-D-family-protein	gnl\|CDD\|197267	cd09170, PLDc_Nuc, Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Catalytic domain of an EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Nuc is an endonuclease cleaving both single- and double-stranded DNA. It is the smallest known member of the phospholipase D (PLD, EC 3.1.4.4) superfamily that includes a diverse group of proteins with various catalytic functions. Most members of this superfamily have two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain and both are required for catalytic activity. However, Nuc only has one copy of the HKD motif per subunit but form a functionally active homodimer (it is most likely also active in solution as a multimeric protein), which has a single active site at the dimer interface containing the HKD motifs from both subunits. Due to the lack of a distinct domain for DNA binding, Nuc cuts DNA non-specifically. It utilizes a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit.	5.66231e-65
NC_016913.1\|WP_012151377.1\|5697_7176_+\|UbiD-family-decarboxylase	gnl\|CDD\|223121	COG0043, UbiD, 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism].	0
NC_016913.1\|WP_012151378.1\|3976_5551_+\|peptidylprolyl-isomerase	gnl\|CDD\|182731	PRK10788, PRK10788, periplasmic folding chaperone; Provisional.	9.27554e-18
NC_016913.1\|WP_012262613.1\|7296_7425_+\|hypothetical-protein	gnl\|CDD\|225783	COG3243, PhaC, Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism].	5.60153e-12
NC_016913.1\|WP_012151371.1\|10654_11302_-\|septum-formation-inhibitor-Maf	gnl\|CDD\|234957	PRK01526, PRK01526, Maf-like protein; Reviewed.	2.0307e-145

>NC_016913.1|WP_012151373.1|9004_9922_+|tyrosine-recombinase-XerC
MLDTSIQALINKWQKYLVLQRNYSNHTVISYNNDLKHFLEFMNYYNSELVTINHIKTADIRLIRSWLAKRNCDNFAASSISRGLSAVKNFYRFLEKTTQLNSHIIFSIKSPKKTKLLPKALSEDDVVISLEHIEEYGNIKWVELRNKALLVLIYASGLRISEALSITKLHLQNLEFIRIIGKGSKERIIPWLPIAKNLITQYLEILPYKLGDNEPIFRGKQGKKLQPPVFNRELIKLKHFYGLPQHLTAHSFRHSFASHLLEHGADLRSLQALLGHKSLSTTQNYTKTSIKHLEAVYTTAYPIKK
>NC_016913.1|WP_012151374.1|8544_8694_-|phasin-family-protein
MLSLLKKNSEIIQNNVNTILNTTKEAATSKDFKQASECHQKCLKSIYIF
>NC_016913.1|WP_012151375.1|7894_8497_+|phospholipase-D-family-protein
MKRKNNKFIEISIAFILGIALGIYGQNPDYFTNLISKKSLALSALQIKHYNISELSRSKVSTCFTPPAGCTKFIANQIDKAEESIYMQAYGMSDALITTALINAQARGVKVRILLDRSNLKQKFSKLYELQRAKIDVYIDKVPGIAHNKVIIIDKKKVITGSFNFTAAADKRNAENVIIIEDQELAESYLQNWLNRKASN
>NC_016913.1|WP_012262613.1|7296_7425_+|hypothetical-protein
MPFDLLYWNADSTNLLAKVYEEYLQNTYCNNLLKESNNLEVL
>NC_016913.1|WP_012151377.1|5697_7176_+|UbiD-family-decarboxylase
MSFKDLPEFLKFLEKNGELKRIALEVKTDLEITEISRRVLAQGGPALLFENVIKVDGIKSDIPVLTNLYASINRICMGLKLKSPKELRELGVLLAFLKQPQPPASFKETLSMLPLAKRIFAMSPKTVSKAACHEIVIDKPNINILPIQRCWPDDISPLITWGIVFTKGPTKDKIDNYNLGIYRMQVISENKLLMRWLKLRGGAEHHKRWKEAKKEPFPTAIVIGANPAVTLAAVMPIPENISEYNFAGLLGNKKVELVQCKTIDLKVPAHSEIVLEGYVSLEEYLPEGPFGDHTGYYNDVEEFPVFTVTAITMKKNPVYLSTYTGEPPDEPSILGEALNEIFIPILQQQFPEIVDFWLPPEGCSYRVAVVSIKKSYPGHAKRIMLGIWSYLRHFMYSKFIIVVDDDIDVRNWQEVIWAIATRSDPRRDTSFIDNSPIDYLDFASPESGLGSKMGIDATDKIYPETNRKWGKKIEMSQEVIDKVNSMWNRLKI
>NC_016913.1|WP_012151378.1|3976_5551_+|peptidylprolyl-isomerase
MLNNIRKTADSFIMRVLFAMIAFAFVGFGIKDVLNGRRSGDIVTFSHVKNISQEDFLRAKSLEINAISKQTGTSLTDEEIAQLNIDNRILKRLVYDNVLDYLVSYYDLDLSDDTVKILVKESPVFKNEQGVFNIKIFKTYFRNSYMDEEKYLLNFKEKALKNIFVGTFIESFYVPKAMTDNIVDYMAEKREVELIQIDLQNKPKDLQIPTPTGQQLKDFYQDNKTAFEVPEKRSFSYIKANIKDLKVSVTQDELLEFYNENKDEFGDQSFEAVQKQLHDLLKAQKIDILNMEFAKKLEDETAAGSSLVEIAEKYKLPIQNVNYISYAELIEDKIIAESADNIFELSEGELSYPIETEDKSYLILVELKSIQPAKIPEFDAIKEQVNKAWIKRNIADVNLKIIKDLAKEYNSDQENIKELKATGIKISKKSYIRSEMENDLTLTPEILLSIFNTTIGSNTPVFQVGDEVYFAHIKSSSIDELTAKNIHVNSEKNIIYNIKNSVIDELINYTIIQNDMQVKANFSK
>NC_016913.1|WP_012151371.1|10654_11302_-|septum-formation-inhibitor-Maf
MKQNRKNLPIILASSSPARIELLNRIKIIPSQIIPADIDETPNLRELPAPLAIRLAYEKAIKIASQIEESAIIIAADTVAAVGRRILPKATTYEEVKNCIKMLSGRRHRVYTGLCIIKKENDQLTVRQKIVQTIVKFKKLSDEEINFYCSLDEGIDKAGGCKISGYAEAFISFISGSYSNVMGLPLFETVNALTSLGFRCSSIMPAKMNYCHSAT
>NC_016913.1|WP_010977828.1|11313_11529_-|translation-initiation-factor-IF-1
MSKDDLIQFTGTVLELLPNATFRVKLENDHVIIAHTSGRMRKNRIRILLGDKVMVEMTPYDLTKGRVIHRH
>NC_016913.1|WP_012151370.1|12244_12487_+|hypothetical-protein
MLALVSALGTANRIVTVGGGAVADGSAFGGGAYVPGSFVTLGEVNNFTVDVPAIPSIYLDTFNNATMTVPNNIFWTGYTC
>NC_016913.1|WP_012151369.1|13007_13250_+|hypothetical-protein
MASFNLVPANDVDGQLRVQVASGSREIALNAGSGNGTGGTIRLNKFLTDWDRSSSKSHSSYNYRNHLCLNYSDREPVSAY
>NC_016913.1|WP_050987956.1|14575_14791_+|hypothetical-protein
MINTAVLNIAVGGVFADASLTSAKIIKINIGEVNAGPAVYALDALNGDFPLDAPGVTFVSRICFKVNDYRS
>NC_016913.1|WP_041472556.1|14774_15086_+|hypothetical-protein
MTTVASGKNSTIELTGNIEPVVPNTGVVEINARNANTKLTIDGMANKYAIGTKANPVSKVQLTGHGTLVITALNTPNIDVSVAKVAIGSKFGSNFFLHSFRSY
>NC_016913.1|WP_041472367.1|15045_15408_+|hypothetical-protein
MDQIFFSTPSGPINSEFGAVKIDGNMNFQNNVGTVAIFASDIANNITLAITGNITSTGGTNGTIGTVDGNGNSTNTITNLAMLKAGVDNSTVTINAGGNMSIAEIQGTGTGNKCLLKQLI
>NC_016913.1|WP_012151368.1|15383_15668_+|hypothetical-protein
MFTQATNLTSGINITGGKVVDLMFTGPSSVSGAIGSSTSKVGDITISGDILNCTGGINAGYIILINVGDIKFKETTNSLDISEGSSFSPFVFKS
>NC_016913.1|WP_012151365.1|17253_17445_-|hypothetical-protein
MPPTLAGPLGPKPPVPTDGLPPPVPILSPVVPPVPGPLGPNSPVPVTGVVGVLYPAGLLGVTS
>NC_016913.1|WP_012151364.1|17658_17844_-|hypothetical-protein
MPLLLLAGETPVALGLQLLPYGLLPLLVTPPLVVPPKLELFPCAEELPLLAGAIPVAAGLL

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
NC_016913_1	1.1\|10038\|31\|NC_016913\|CRISPRCasFinder	10038-10068	31	JQ680349	Unidentified phage clone 1013_scaffold24 genomic sequence	5427-5457	5	0.839
NC_016913_1	1.1\|10038\|31\|NC_016913\|CRISPRCasFinder	10038-10068	31	MT028491	Ochrobactrum phage vB_OspM_OC, complete genome	49025-49055	5	0.839
NC_016913_1	1.1\|10038\|31\|NC_016913\|CRISPRCasFinder	10038-10068	31	NC_018689	Bacillus thuringiensis MC28 plasmid pMC429, complete sequence	231736-231766	7	0.774
NC_016913_1	1.1\|10038\|31\|NC_016913\|CRISPRCasFinder	10038-10068	31	NZ_CP020434	Bacillus sp. FDAARGOS_235 plasmid 1, complete sequence	101693-101723	8	0.742
NC_016913_1	1.1\|10038\|31\|NC_016913\|CRISPRCasFinder	10038-10068	31	NZ_CP018062	Enterococcus mundtii strain DSM 4838 plasmid pLDW-8, complete sequence	11780-11810	9	0.71
NC_016913_1	1.1\|10038\|31\|NC_016913\|CRISPRCasFinder	10038-10068	31	NZ_CP018062	Enterococcus mundtii strain DSM 4838 plasmid pLDW-8, complete sequence	135812-135842	9	0.71
NC_016913_1	1.1\|10038\|31\|NC_016913\|CRISPRCasFinder	10038-10068	31	NC_021832	Spiroplasma taiwanense CT-1 plasmid unnamed, complete sequence	2889-2919	9	0.71

1. spacer 1.1|10038|31|NC_016913|CRISPRCasFinder matches to JQ680349 (Unidentified phage clone 1013_scaffold24 genomic sequence) position: , mismatch: 5, identity: 0.839

ttttaaaaaccttataaacataat--atattac	CRISPR spacer
gtttaaaaaccttctatacataattaatatt--	Protospacer
 ************ ** *******  *****

2. spacer 1.1|10038|31|NC_016913|CRISPRCasFinder matches to MT028491 (Ochrobactrum phage vB_OspM_OC, complete genome) position: , mismatch: 5, identity: 0.839

ttttaaaaaccttataaacataatatattac-	CRISPR spacer
ttttataaaccttataatcataa-agattatt	Protospacer
***** *********** ***** * ****.

3. spacer 1.1|10038|31|NC_016913|CRISPRCasFinder matches to NC_018689 (Bacillus thuringiensis MC28 plasmid pMC429, complete sequence) position: , mismatch: 7, identity: 0.774

ttttaaaaaccttataaacataatatattac	CRISPR spacer
tctatataaccatataaatataatatattaa	Protospacer
*.*  * **** ******.***********

4. spacer 1.1|10038|31|NC_016913|CRISPRCasFinder matches to NZ_CP020434 (Bacillus sp. FDAARGOS_235 plasmid 1, complete sequence) position: , mismatch: 8, identity: 0.742

ttttaaaaaccttataaacataatatattac	CRISPR spacer
cctatataaccatataaatataatatattaa	Protospacer
..*  * **** ******.***********

5. spacer 1.1|10038|31|NC_016913|CRISPRCasFinder matches to NZ_CP018062 (Enterococcus mundtii strain DSM 4838 plasmid pLDW-8, complete sequence) position: , mismatch: 9, identity: 0.71

ttttaaaaaccttataaacataatatattac	CRISPR spacer
aactgcaaacattagaaacataatatatttg	Protospacer
  .*. **** *** **************

6. spacer 1.1|10038|31|NC_016913|CRISPRCasFinder matches to NZ_CP018062 (Enterococcus mundtii strain DSM 4838 plasmid pLDW-8, complete sequence) position: , mismatch: 9, identity: 0.71

ttttaaaaaccttataaacataatatattac	CRISPR spacer
aactgcaaacattagaaacataatatatttg	Protospacer
  .*. **** *** **************

7. spacer 1.1|10038|31|NC_016913|CRISPRCasFinder matches to NC_021832 (Spiroplasma taiwanense CT-1 plasmid unnamed, complete sequence) position: , mismatch: 9, identity: 0.71

ttttaaaaaccttataaacataatatattac	CRISPR spacer
acgaattaaccttataaatataatacattat	Protospacer
 .  *  ***********.******.****.

Prophage detection

Region	Region Position	Protein_number	Hit_taxonomy	Key_proteins	Att_site	Prophage annotation

Anti-CRISPR protein detection

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