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
NZ_AP021898	Akkermansia muciniphila strain JCM 30893	0 crisprs	csa3,DinG,cas3,cas4	0	0	0	0
NZ_AP021899	Akkermansia muciniphila strain JCM 30893 plasmid pJ30893, complete sequence	1 crisprs	NA	0	1	1	0

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NZ_AP021899_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_AP021899_1

3379-3459

Orphan

Consensus_repeat	Method
TTTCTTTATAGGTGGTTCACCACC	CRISPRCasFinder

1 spacers

The CRISPR arrays of NZ_AP021899_1

>merge|NZ_AP021899|1|3379-3459|CRISPRCasFinder
TTTCTTTATAGGTGGTTCACCACCTATAGGTAAAAAAACTCCCTTCTTTTTGATTCTCTTTTTTATAGGTGGTTCACCACC

>NZ_AP021899|1|1|3379-3459|CRISPRCasFinder
TTTCTTTATAGGTGGTTCACCACC	TATAGGTAAAAAAACTCCCTTCTTTTTGATTCT
CTTTTTTATAGGTGGTTCACCACC

Protein	Signature genes	Signature genes Name	Protein_function
NZ_AP021899.1\|WP_155844645.1\|1325_1631_-\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_155844652.1\|6864_7620_-\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_162378861.1\|1921_2206_-\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_155844650.1\|3547_3979_-\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_162378862.1\|2878_3346_+\|hypothetical-protein	unknown	unknown	gnl\|CDD\|379492
NZ_AP021899.1\|WP_155844648.1\|2573_2789_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|378935
NZ_AP021899.1\|WP_102748993.1\|4898_5228_+\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_155844656.1\|12565_12844_-\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_102749031.1\|7576_7822_-\|YgiT-type-zinc-finger-protein	unknown	unknown	gnl\|CDD\|240606
NZ_AP021899.1\|WP_155844653.1\|7818_9975_-\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_102748994.1\|4417_4894_+\|DUF4065-domain-containing-protein	unknown	unknown	gnl\|CDD\|226128
NZ_AP021899.1\|WP_155844655.1\|10657_12544_-\|hypothetical-protein	unknown	unknown	gnl\|CDD\|274008
NZ_AP021899.1\|WP_155844646.1\|1764_1932_-\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_155844644.1\|933_1329_-\|hypothetical-protein	unknown	unknown	unknown
NZ_AP021899.1\|WP_155844651.1\|5644_6832_+\|tyrosine-type-recombinase/integrase	unknown	unknown	gnl\|CDD\|271184
NZ_AP021899.1\|WP_155844654.1\|10026_10611_-\|DUF4339-domain-containing-protein	unknown	unknown	gnl\|CDD\|379517

Protein	Function_ID	Function_description	E-value
NZ_AP021899.1\|WP_155844648.1\|2573_2789_-\|hypothetical-protein	gnl\|CDD\|378935	pfam12728, HTH_17, Helix-turn-helix domain. This domain is a DNA-binding helix-turn-helix domain.	0.000375239
NZ_AP021899.1\|WP_155844655.1\|10657_12544_-\|hypothetical-protein	gnl\|CDD\|274008	TIGR02168, Chromosome_partition_protein_Smc, chromosome segregation protein SMC, common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins].	4.70991e-05
NZ_AP021899.1\|WP_102748994.1\|4417_4894_+\|DUF4065-domain-containing-protein	gnl\|CDD\|226128	COG3600, GepA, Uncharacterized phage-associated protein [Function unknown].	2.44716e-27
NZ_AP021899.1\|WP_162378862.1\|2878_3346_+\|hypothetical-protein	gnl\|CDD\|379492	pfam14163, SieB, Super-infection exclusion protein B. This family includes superinfection exclusion proteins. These proteins prevent the growth of superinfecting phage which are insensitive to repression. It aborts lytic development of superinfecting phage.	5.11355e-15
NZ_AP021899.1\|WP_102749031.1\|7576_7822_-\|YgiT-type-zinc-finger-protein	gnl\|CDD\|240606	cd12870, MqsA, antitoxin MqsA for MqsR toxin. This family includes domains similar to the antitoxin MqsA that binds motility quorum-sensing regulator MqsR, a toxin that is highly upregulated in persisters (dormant cells found in biofilms that are a source of antibiotic resistance), thus forming a unique toxin:antitoxin (TA) pair. MqsA neutralizes MsqR toxicity. It binds its own promoter as well as those of genes important for E. coli physiology, such as mcbR and spy. It also binds zinc and has been shown to coordinate DNA via its C-terminal domain. This family also includes the B. subtilis YokU protein, which is functionally uncharacterized.	0.000411391
NZ_AP021899.1\|WP_155844651.1\|5644_6832_+\|tyrosine-type-recombinase/integrase	gnl\|CDD\|271184	cd01184, INT_C_like_1, Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain. Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.	1.5745e-13
NZ_AP021899.1\|WP_155844654.1\|10026_10611_-\|DUF4339-domain-containing-protein	gnl\|CDD\|379517	pfam14237, DUF4339, Domain of unknown function (DUF4339). This domain is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. There are two completely conserved residues (G and W) that may be functionally important.	1.15392e-07

>NZ_AP021899.1|WP_162378862.1|2878_3346_+|hypothetical-protein
MAELLKFACNYAGIIFSATGVYLFAPQSVLEALHISYADHDYRNIAGYVFLFSGCALLERVWNIIKSSYAEAKSRKKVIKRLHALTPKEKDVLLRYIFFDTRTQRFDDRDGIVNGLIAAGILIRLSFYGSIVTGFDVNITDVAWEYLKKNPHLLS
>NZ_AP021899.1|WP_155844648.1|2573_2789_-|hypothetical-protein
MKTIYLTSKELRKALKISPGTLVQYNKEGCPRVYFGTVVGGSGTHVRYKLDDVTAWLEKRTQEFLKKGGKK
>NZ_AP021899.1|WP_162378861.1|1921_2206_-|hypothetical-protein
MKVIMDKDKSIVDLLIELDKVLKVETHKDASPYYLSSDSEDKIFRAKYAGHIYIARRLLGLSLECKPGALLPSEPVDEFSDLVNKSKSSGNNDH
>NZ_AP021899.1|WP_155844646.1|1764_1932_-|hypothetical-protein
MIIEYDNDNKCIRVNGEYLPIREAEGIKDELELAIDQWEVDHAEQCDNPDGHYDD
>NZ_AP021899.1|WP_155844645.1|1325_1631_-|hypothetical-protein
MSENKTTMTTLATTLETLAGVLREMATTPAKPESSSVSRSKAIGKKYAKSSTLAPYYDVSTRQMDYILARAGKKIRRLEGVGRGTLYNTEDVEKHINNNRK
>NZ_AP021899.1|WP_155844644.1|933_1329_-|hypothetical-protein
MTTYQHLIDRGPYKGMVETLTDNPHPSKTTRCYMCAEPLKASTSWMSLVGDHQNGVFCARFLCPLCARERLNGIPDDAERSWNYTQEAKPKAFWIERLFEKFMAFFVWSLIVLAGGFILFVFFLLIRTFFN
>NZ_AP021899.1|WP_155844650.1|3547_3979_-|hypothetical-protein
MNSSISSFPRSAIKDSLGVHINVDVSTYLHYALNSNDEKKLGRRSGMMLYEKNVKKMKNSVDWWLTTDYVERMPSQRKIDKKQISVWIPIVLFRKFQKRAKELNMTMTEIITAYLVQQTQNVILTPEDYENIAREIREKANNN
>NZ_AP021899.1|WP_102748994.1|4417_4894_+|DUF4065-domain-containing-protein
MCKIEYKSYSIEAIANQILTEAWQQGLSVTNMKIQKLAYFVQGFALKQLEHPLFTEEIQAWTYGPVIPELYKKLKHLGDTPITGFLASPDAITDDEDAKNVIKNVVDKLGKLSAPQLVELSHQPNSPWAAAWEKKKYSRIPLWQMAIYFDRMLTPSAS
>NZ_AP021899.1|WP_102748993.1|4898_5228_+|hypothetical-protein
MTTKLDDQIKALVNSDKAPPVPTIEKIEEETKRDEVALEKEKKHTVHQAWKWVLVTAVICCIVALATLTLNYVLPEKWCWIVEEKRYIMTTGFLSTLVGYMVKSVQKYV
>NZ_AP021899.1|WP_155844651.1|5644_6832_+|tyrosine-type-recombinase/integrase
MAGIIKRNNKWVAVFRSLDGKELRKTTGIDVVPKALLPGANKKSVMSQNEARARLVAQEMEKEARYGVFDLDKVKAIAGDQAGVLKATMNGMTVSRFLFDWLDGRKNKKRAYERDGMAVRRLLAYLGDRRNMPLAALNKGMAKDFVETELERVSAGTVIRYVSTLSTAFNVAVDREILSRNPFRGVMPSRSDHQAEKQLRGAFTMEEVNTIIECFPDEWPDLVRVCLYTGGQRLGDLATLKWEQIDLKNSFLFMTTQKSRRRMNKPIIQPLKEVLERRLLNRVNDYVFPLAALRHAHAGGRSDKLSTEFTTLLKMYGIIREMPGEVRGDRHRLSEKSFHSLRATAVTVLRLAGVSPDLCRFIVGHDSEEIERVYFRPDSADVQAAMSKIAVGVAR
>NZ_AP021899.1|WP_155844652.1|6864_7620_-|hypothetical-protein
MIRIYLFTYAGDADEALVCVRCAAAALPEAVITVVDDESTPIAERARTALVEAGARYCQTSWPRNGNLRGPDCVRGIISTLAGEAEDDDVIVKIDSDTLLLSGDWIRDMQRHGLALHASGYQVPSHPSERFAYGPCYAISGRAARLAEEELEQADLPPLAPEDLIICRAVQNHFPAERIRLDEPWTPFYREGKWTAWNWFSIAVTPQKYADFWMVTFGNPRPTNIPKSERARAMDALFRYRFPQNADGSSC
>NZ_AP021899.1|WP_102749031.1|7576_7822_-|YgiT-type-zinc-finger-protein
MSQSINLPCHECQEGYYENTFLSLKYTLPDGSTLIVPKVPAQHCNRCGDVSISYKTVLWIQKYIEQHHDQNLPIHLCRRRR
>NZ_AP021899.1|WP_155844653.1|7818_9975_-|hypothetical-protein
MLALKPSSLTHDQQSFSASTITAVYPVRTLGEVLPFHQFETVTISQNGNTILSGLVSSIEKTYSGSSRAWKIVFSDPWYYLDNCFALDSEWKPVFSMWQSTGGGNEIIPKISISSALSRVLNLAKHHPADYELRISDDKMLIPWNASCDTLGSLLQSIRHWSPRMVTYYDYSGARPKLIITDYDVLTPISLPLQPSNDVKAMDVSLVPRADLVPPCVAIVAETTGSNGYRVSYLSKYPEDGDPTLPHSIVYRTSVDFYYSKYNSTGEPVEDPQPVQGTKAGSLSYQRMKVTGTRINQNDMINSFWKNHFPWMKDVDALAAYDQEPVITGKPWDGTEEDKPKGYNTTATGYELTDGQIHTKSIRPQWCNATIKQRLAIPESAPAKWREKFKNIGTLEGKPCFWEEFSVDLVTMDRPFASYPIDGIYNGEQPSNGPEEGESPEPSEGVPYGDIAKTVWESMQELPWDGSISFVALGEAQTRQYMGRRVSLLGGNPAWQNINTMIQTVNRDLQTNVITLSYGAPEQLGIEEWVELKRVNATSRRSSTLENMQGAPESTEYAFDPKPESPTISQHITKSTGEATPAPEYGFQVRVQKDTEGAITGAQIKPGALYLNGHLLGKYPQGGSSGSSWVQLTQTSGEVWLNVHFDKEAQLTGVDVSGIPGPVYPIPLLDYTPGPHPDVNFDYTFLIADIEDDQVTQYALGMIQIPVFGGTFYPYGPA
>NZ_AP021899.1|WP_155844654.1|10026_10611_-|DUF4339-domain-containing-protein
MANYYVAFDSNHADGPYSFEELEALYKEGKILSETLVCPEGGQEWLSFGRIYHLTKNTNRKSEEKETEWQPKKRFVDILLDKSEKRREERLLKEKVPKGNLIESKKESILEKDPSWKESQEWDEQEPLKITVEGIFRFVGIIALIAGFILFCNNVEEKQTEIGFIYLVSGAFSCLGCFWCAKVLTLLQKIADKK
>NZ_AP021899.1|WP_155844655.1|10657_12544_-|hypothetical-protein
MATKKEIEIKLKSTLDGKGVEEAKQKIDSLNKSTEQLDKDSQQATRSVKNMGQGALQAAYFFDDLQYGIRGIMNNIPGLVMEFGGGAGLAGAMSLAVLAGAKLYEWMGKTEDKSADLAKKMKEHSKEIAEASRQAIRASYQALQEFNQQERTKTVNEEYQNYVKGITREFEYQTEELEKQIRLRREEAARQKGIDTRQAELDRVNLEVGYQEGRITKRQRDYGLMMVDQNLDQKIRQRDLGVEQANYMDIGKQLAEAVKARDAAEAHAFDMQFKQGNLPSLQNVLGLLQQQERSQRSIDSLESQLPDLRGEIWEKNKEYNKVLKRNGGYETTYSSLVKKEIDDLVAKQDRLVELIKTAREEANQANDQLKSFQDVLGEGGVNLELDYSQGTDVNSRFKQVSDAVEEFKKNTDAAKKQFDKLTEKAGSLGDAMASTEASIKNMEQIDAIQNQIDAGKVKSFNMQRDREEAEEARRNEEKIKKARERAEREAQKQTAERQQAMIRGITLEGVPEHPTAQQRARIAAAREALNAGKKRLSESISDKDTEIDPSELQEVFDVMKNSLIESGQYTKKLMDFLKTIATAQTANVNAIQADTKKYVDAKFEEILKIVQKGNGRLQTGINRLAGGF
>NZ_AP021899.1|WP_155844656.1|12565_12844_-|hypothetical-protein
MNEPQNGIERLFVEFAEECGKNPNLNQAVQELKESVFAASQAAGVDPSHAFGVIIRDMMILESLQKRVEESRNALTAGKLPAFVIEEVSAQR

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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
NZ_AP021899_1	1.1\|3403\|33\|NZ_AP021899\|CRISPRCasFinder	3403-3435	33	NZ_AP021899	Akkermansia muciniphila strain JCM 30893 plasmid pJ30893, complete sequence	3403-3435	0	1.0
NZ_AP021899_1	1.1\|3403\|33\|NZ_AP021899\|CRISPRCasFinder	3403-3435	33	MN693842	Marine virus AFVG_250M286, complete genome	7956-7988	10	0.697

1. spacer 1.1|3403|33|NZ_AP021899|CRISPRCasFinder matches to NZ_AP021899 (Akkermansia muciniphila strain JCM 30893 plasmid pJ30893, complete sequence) position: , mismatch: 0, identity: 1.0

tataggtaaaaaaactcccttctttttgattct	CRISPR spacer
tataggtaaaaaaactcccttctttttgattct	Protospacer
*********************************

2. spacer 1.1|3403|33|NZ_AP021899|CRISPRCasFinder matches to MN693842 (Marine virus AFVG_250M286, complete genome) position: , mismatch: 10, identity: 0.697

tataggtaaaaaaactcccttctttttgattct	CRISPR spacer
ctctttgaaaaaaatttccttctttttgatttt	Protospacer
. .    *******.*.**************.*

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

26104 : 32742

uncultured_Mediterranean_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
WP_155844667.1\|26104_27412_-	hypothetical protein	A0A1B1IPD6	uncultured_Mediterranean_phage	2.5e-57	35.0
WP_155844668.1\|27484_27892_-	hypothetical protein	Q775B8	Bordetella_phage	7.0e-11	32.8
WP_155844669.1\|28066_29077_-	hypothetical protein	NA	NA	NA	NA
WP_155844670.1\|29081_29606_-	hypothetical protein	G9L6B3	Escherichia_phage	1.5e-18	49.6
WP_155844488.1\|29619_30090_-	class I SAM-dependent methyltransferase	A8ATY8	Listeria_phage	1.5e-57	65.5
WP_155844671.1\|30553_30940_-	hypothetical protein	NA	NA	NA	NA
WP_155844672.1\|30920_31202_-	hypothetical protein	NA	NA	NA	NA
WP_155844673.1\|31208_31544_-	hypothetical protein	NA	NA	NA	NA
WP_155844674.1\|31540_32053_-	hypothetical protein	K7R6I2	Vibrio_phage	1.9e-13	32.1
WP_155844675.1\|32052_32742_-	hypothetical protein	A0A0M3LPU0	Mannheimia_phage	1.8e-19	38.7

Anti-CRISPR protein detection

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