CRISPRimmunity

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Overview of predicted results

Overview of the results

Contig_ID	Contig_def	CRISPR array number	Contig Signature genes	Prophage number
NZ_CP028145	Vibrio parahaemolyticus strain R14 plasmid pVpR14_74Kb, complete sequence	0 crisprs	NA	0
NZ_CP028142	Vibrio parahaemolyticus strain R14 chromosome 2, complete sequence	1 crisprs	WYL,csa3,DEDDh,cas3	0
NZ_CP028144	Vibrio parahaemolyticus strain R14 plasmid pVpR14_56Kb, complete sequence	0 crisprs	NA	0
NZ_CP028143	Vibrio parahaemolyticus strain R14 plasmid pVpR14_20Kb, complete sequence	0 crisprs	NA	0
NZ_CP028141	Vibrio parahaemolyticus strain R14 chromosome 1, complete sequence	0 crisprs	DEDDh,DinG,cas3,csx1,csa3	3

Results visualization

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CRISPR-Cas detection and classification

Crispr_ID: NZ_CP028142_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

NZ_CP028142_1

1109724-1109821

Orphan

Consensus_repeat	Method
TTTTTGAAAAGGCGTTTTAAAAATA	CRISPRCasFinder

1 spacers

DEDDh

The CRISPR arrays of NZ_CP028142_1

>merge|NZ_CP028142|1|1109724-1109821|CRISPRCasFinder
TTTTTGAAAAGGCGTTTTAAAAATATTGATTGCGATCTTGTTTTTCTGGATTCTTTAATTGCGCGGTTTCAAATTTTTGAAAAGGCATTTTAAAAATA

>NZ_CP028142|1|1|1109724-1109821|CRISPRCasFinder
TTTTTGAAAAGGCGTTTTAAAAATA	TTGATTGCGATCTTGTTTTTCTGGATTCTTTAATTGCGCGGTTTCAAA
TTTTTGAAAAGGCATTTTAAAAATA

Protein	Signature genes	Signature genes Name	Protein_function
NZ_CP028142.1\|WP_005482916.1\|1108862_1109624_-\|2-dehydro-3-deoxy-D-gluconate-5-dehydrogenase-KduD	unknown	unknown	gnl\|CDD\|181605
NZ_CP028142.1\|WP_005460834.1\|1104663_1105287_-\|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase	unknown	unknown	gnl\|CDD\|235577
NZ_CP028142.1\|WP_057619727.1\|1116587_1117427_+\|S-formylglutathione-hydrolase	unknown	unknown	gnl\|CDD\|178061
NZ_CP028142.1\|WP_046264956.1\|1109879_1110662_+\|DNA-binding-transcriptional-regulator-KdgR	unknown	unknown	gnl\|CDD\|185046
NZ_CP028142.1\|WP_005482884.1\|1105298_1106228_-\|sugar-kinase	unknown	unknown	gnl\|CDD\|238571
NZ_CP028142.1\|WP_005464959.1\|1118333_1119425_+\|GGDEF-domain-containing-protein	unknown	unknown	gnl\|CDD\|143635
NZ_CP028142.1\|WP_005497706.1\|1108319_1108844_-\|YgjV-family-protein	unknown	unknown	gnl\|CDD\|378474
NZ_CP028142.1\|WP_108745363.1\|1106326_1107238_-\|alpha/beta-hydrolase	unknown	unknown	gnl\|CDD\|223730
NZ_CP028142.1\|WP_108745364.1\|1110745_1112614_+\|CBS-domain-containing-protein	unknown	unknown	gnl\|CDD\|225457
NZ_CP028142.1\|WP_005464962.1\|1115377_1116526_+\|S-(hydroxymethyl)glutathione-dehydrogenase/class-III-alcohol-dehydrogenase	unknown	unknown	gnl\|CDD\|176260
NZ_CP028142.1\|WP_005482833.1\|1117872_1118334_+\|oxidoreductase	unknown	unknown	gnl\|CDD\|226429
NZ_CP028142.1\|WP_005460779.1\|1107315_1107951_-\|RpiB/LacA/LacB-family-sugar-phosphate-isomerase	unknown	unknown	gnl\|CDD\|181746
NZ_CP028142.1\|WP_108745362.1\|1102739_1104479_+\|transporter	unknown	unknown	gnl\|CDD\|271371
NZ_CP028142.1\|WP_062867082.1\|1112616_1113327_+\|DNA-polymerase-III-subunit-epsilon	DEDDh	cd06127_DEDDh_CAS-I	gnl\|CDD\|236392
NZ_CP028142.1\|WP_005482845.1\|1101932_1102610_-\|porin	unknown	unknown	gnl\|CDD\|368776
NZ_CP028142.1\|WP_005467181.1\|1107991_1108312_-\|cupin-domain-containing-protein	unknown	unknown	gnl\|CDD\|380366
NZ_CP028142.1\|WP_006740949.1\|1114277_1115084_-\|arylamine-N-acetyltransferase	unknown	unknown	gnl\|CDD\|366312
NZ_CP028142.1\|WP_031831553.1\|1119434_1119839_+\|hypothetical-protein	unknown	unknown	unknown
NZ_CP028142.1\|WP_108745361.1\|1099688_1101917_-\|exopolygalacturonate-lyase	unknown	unknown	unknown
NZ_CP028142.1\|WP_025553232.1\|1113327_1114197_-\|LysR-family-transcriptional-regulator	unknown	unknown	gnl\|CDD\|176159

Protein	Function_ID	Function_description	E-value
NZ_CP028142.1\|WP_005482916.1\|1108862_1109624_-\|2-dehydro-3-deoxy-D-gluconate-5-dehydrogenase-KduD	gnl\|CDD\|181605	PRK08993, PRK08993, 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD.	0
NZ_CP028142.1\|WP_005460834.1\|1104663_1105287_-\|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.	4.28455e-121
NZ_CP028142.1\|WP_057619727.1\|1116587_1117427_+\|S-formylglutathione-hydrolase	gnl\|CDD\|178061	PLN02442, PLN02442, S-formylglutathione hydrolase.	1.19274e-142
NZ_CP028142.1\|WP_046264956.1\|1109879_1110662_+\|DNA-binding-transcriptional-regulator-KdgR	gnl\|CDD\|185046	PRK15090, PRK15090, DNA-binding transcriptional regulator KdgR; Provisional.	0
NZ_CP028142.1\|WP_005482884.1\|1105298_1106228_-\|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.	1.15929e-102
NZ_CP028142.1\|WP_005497706.1\|1108319_1108844_-\|YgjV-family-protein	gnl\|CDD\|378474	pfam10688, Imp-YgjV, Bacterial inner membrane protein. This is a family of inner membrane proteins. Many of the members are YgjV protein.	9.00507e-50
NZ_CP028142.1\|WP_108745363.1\|1106326_1107238_-\|alpha/beta-hydrolase	gnl\|CDD\|223730	COG0657, Aes, Esterase/lipase [Lipid metabolism].	7.53471e-18
NZ_CP028142.1\|WP_108745364.1\|1110745_1112614_+\|CBS-domain-containing-protein	gnl\|CDD\|225457	COG2905, COG2905, Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms].	1.3724e-138
NZ_CP028142.1\|WP_005464962.1\|1115377_1116526_+\|S-(hydroxymethyl)glutathione-dehydrogenase/class-III-alcohol-dehydrogenase	gnl\|CDD\|176260	cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding.	0
NZ_CP028142.1\|WP_005482833.1\|1117872_1118334_+\|oxidoreductase	gnl\|CDD\|226429	COG3915, COG3915, Uncharacterized protein conserved in bacteria [Function unknown].	3.9997e-40
NZ_CP028142.1\|WP_005460779.1\|1107315_1107951_-\|RpiB/LacA/LacB-family-sugar-phosphate-isomerase	gnl\|CDD\|181746	PRK09273, PRK09273, hypothetical protein; Provisional.	2.15977e-144
NZ_CP028142.1\|WP_108745362.1\|1102739_1104479_+\|transporter	gnl\|CDD\|271371	cd11477, SLC5sbd_u1, Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain. SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate (PutF) cotransporters. One member of the SLC5 family, human SGLT3, has been characterized as a glucose sensor and not a transporter. This subfamily belongs to the solute carrier 5 (SLC5) transporter family.	6.89387e-108
NZ_CP028142.1\|WP_062867082.1\|1112616_1113327_+\|DNA-polymerase-III-subunit-epsilon	gnl\|CDD\|236392	PRK09146, PRK09146, DNA polymerase III subunit epsilon; Validated.	1.43568e-38
NZ_CP028142.1\|WP_005482845.1\|1101932_1102610_-\|porin	gnl\|CDD\|368776	pfam06178, KdgM, Oligogalacturonate-specific porin protein (KdgM). This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM from Erwinia chrysanthemi. The phytopathogenic Gram-negative bacteria Erwinia chrysanthemi secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. KdgM is a major outer membrane protein, whose synthesis is strongly induced in the presence of pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. In contrast to most porins, KdgM seems to be monomeric.	3.08357e-24
NZ_CP028142.1\|WP_005467181.1\|1107991_1108312_-\|cupin-domain-containing-protein	gnl\|CDD\|380366	cd02238, cupin_KdgF, pectin degradation protein KdgF and related proteins, cupin domain. This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.	1.13072e-54
NZ_CP028142.1\|WP_006740949.1\|1114277_1115084_-\|arylamine-N-acetyltransferase	gnl\|CDD\|366312	pfam00797, Acetyltransf_2, N-acetyltransferase. Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30kDa. It facilitates the transfer of an acetyl group from Acetyl Coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (M. tuberculosis, M. smegmatis etc) to man. It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat Tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid.	1.88138e-97
NZ_CP028142.1\|WP_005464959.1\|1118333_1119425_+\|GGDEF-domain-containing-protein	gnl\|CDD\|143635	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain. Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.	5.06677e-44
NZ_CP028142.1\|WP_025553232.1\|1113327_1114197_-\|LysR-family-transcriptional-regulator	gnl\|CDD\|176159	cd08470, PBP2_CrgA_like_1, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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.	8.18471e-109

>NZ_CP028142.1|WP_005482916.1|1108862_1109624_-|2-dehydro-3-deoxy-D-gluconate-5-dehydrogenase-KduD
MILDSFNLEGKVAIVTGCDTGLGQGMALGLAKAGCDIVGVNISEPTETIEKVEAEGRKFVDIRANLMKLDDIPTIVDRAVTELGRIDILVNNAGIIRRNDAIEFSEQDWDDVMNINVKSVFFMSQAVAKQFIAQGEGGKIINIASMLSFQGGIRVPSYTASKSGVMGVTRLMANEWASHGINVNAIAPGYMATNNTAALRADEQRNKEIVDRIPAARWGTPEDLAGPCVFLASKAADYINGYTIAVDGGWLAR
>NZ_CP028142.1|WP_005497706.1|1108319_1108844_-|YgjV-family-protein
MVDTTILAQALGFISFGLGFSVFYQKNDRHLKILMLIFNLNHLLHFLLLGSMVSALSALLSALRTTTAIFVSSKRVAAVFIVISLVSGFWVAEQWRDLWPIIGTVIGTYSVFCLSGIRMRIGFLLGASCWLTNNILVGSIGGTLLEMTVIVMNLLTIYRLHRQQSESMINQSSY
>NZ_CP028142.1|WP_005467181.1|1107991_1108312_-|cupin-domain-containing-protein
MFVFNQDIPMEDLGEGISRKVLAHSDNMMSVEVHFEEGAIGAMHSHPHEQLTYVLSGEFEFTIGDEKKIVKTGDTMYKEPNIEHGCVCLKAGVLIDTFTPMRKDFV
>NZ_CP028142.1|WP_005460779.1|1107315_1107951_-|RpiB/LacA/LacB-family-sugar-phosphate-isomerase
MKIALMMENSQAAKNAMVAGELNSVAGGLGHDVFNVGMTDENDHHLTYIHLGIMASILLNSKAVDFVVTGCGTGQGALMSCNLHPGVVCGYCLEPSDAFLFNQINNGNAISLAFAKGFGWAGELNVRYIFEKAFTGKRGEGYPIERAAPQQANAAILNNVKSAVAKDVVEGLRAIDQELVKTAVGSTQFQECFFAHCQVPEIAEYVKSLLD
>NZ_CP028142.1|WP_108745363.1|1106326_1107238_-|alpha/beta-hydrolase
MHVAPITSLQTWFPEHPVLPLWSEPQIPSHLVQSYQERNPNELLPDRAVFEITHPEIVVFEPEQSNGIGILLMPGGGYQRVSVDKEGADSARVLNQAGFTVFVMTYRMPNEGHEFGSWTPLADAQRAMRLVRQLPLASHLSSIGVLGFSAGGHVAASLATSHALDIYPLQDEADRVSAKPDFCALMYPVISMNTDIAHMGSRAELLANLERESDLLRFSLEKQVTSDMPPCFLLHASDDTAVRVENSLVFWQALRQHEIATEMHLFEQGKHGFGIRDAQGLPVAAWPQLLSAWLQNLTEKARR
>NZ_CP028142.1|WP_005482884.1|1105298_1106228_-|sugar-kinase
MNPISRVAIIGECMVELKKHDGVLQQGFGGDTLNTAVYLSRLTKQHGVETSYVTGLGHDPFSREMLTAWREEGINTDMVYLSEDKLPGIYAIETAEDGERSFFYWRNDAAAKYWLRERALLSLVKDLCQHQMIYLSGISLAIISDDCRQMLIELLTMCRKEGVKIAFDNNFRPKLWPNIEQARDFYSKILSVTDMAFLTFDDEVMLWGDKHEDEAISRTKNFGVKEIIVKRGADDCFVVTQDQQHTVAALKVDAVVDTTAAGDSFSAGYLAKRILGGDVAESALAGHKVAGTVIQHRGAIIPSQAMPTI
>NZ_CP028142.1|WP_005460834.1|1104663_1105287_-|bifunctional-4-hydroxy-2-oxoglutarate-aldolase/2-dehydro-3-deoxy-phosphogluconate-aldolase
MKDLNQQLSEIKVVPVIAIKDAGKAVKLAQVLIENGLPCAEVTFRTEDAALAIKNMREAYPEMLIGAGTVLTSAQVDEAIDAGVDFIVSPGFNPTTVKYCQQRNVTIVPGVNNPSLVEQAMEMGLRTLKFFPAEPSGGVAMLKALSAVYPVKFMPTGGVSPSNVKDYLSISSVLACGGTWMVPGDLIDNEQWDELAKLVREVAGIIE
>NZ_CP028142.1|WP_108745362.1|1102739_1104479_+|transporter
MTLLDSMIVMIYLLFIGIAAWLFRRFSTSSNDFLQGGGTMMWWMAGATAFMTQFSAWTFTGAAAKAYEDGISVMFIFWGNALGFFVAAAFFARRYRRLRVETAMEVIRVRFGHTSEQLFTWLSFPLTLIACAIWMNGLASFFSAVFAIEMSTTILAMGVVVTLIAVSGGAWTVSVTNVIQLILLIAITLVIGYTALQRFDSPSEVFAHATPIYGEQIRMPSLFVMWAITMLLQQTMSNNHTLSCYRFLTTANDKDATKAAFVAGVLFVFAPVLWFMPAWFVAAQNIDLLAIYPALEQSANNAAYLYYIQHYMPQGLLGLVMVALVAATIAPLSSAHNRNAGIVVKSLYQVWFNPNATSRQQLMVGKIATIVSGVLATVTALLLASVESYSLFDMMIVFAAFIQMPINIPSLLALVSLKTPNWSGWATVMVGCAVSLFMMFIFDVQWLSSLPLTPRESKDLSVVATLAVHLLVTGGFFLFTRVFYAKESPSIQQSRTALAIQLATPISDEELSPINHKQGLYVGSITALAGMLLILAGVVLVGSSQSIFVVIGCIVLLFSLFLLQPTQHSKRAWQKQKTK
>NZ_CP028142.1|WP_005482845.1|1101932_1102610_-|porin
MKVRYLTSALLLAMTSGLAAAASVDIRHEYVPDRDGDEHRDRIYVSHRFDNQIGFSVEAKWNYKDGHMGNAGHETGVSYRWKATDNFSLTPGINIDASPSGASVFKYNLTGAYKINDEWDVAARIRHGYKNTDDSRYNQLNLYANRKFEWGKLGVEAEYKDIHGGEGGWKDKGHDQLIDFKGEYTKLESGVIPFFAIAAITHKGDGSEFKDEYVPRFRVGLKYNF
>NZ_CP028142.1|WP_108745361.1|1099688_1101917_-|exopolygalacturonate-lyase
MKKHTLALCLAAILAPAAHAAEIKVEDLTWKAITFGQSTDMNFGSTILPEKVGVNQVTVNGEAVAAGKLASTFTIESRGGKLANSHEGLTFYYTELPTDVNFTLSADVVLEQLGPETGATPNRQEGAGLMVRDILGAERLVPQPEGHEEFPSASNMVMNLMRSHTRTNDGMTNINASFREGVYQPWGTPGNRLSRVDYVEGVPYGTAETYRMTLTRTNDGFKVSYRNGEKFIEQAVKGANANIVEMQNSDSQYVGFFASRNAKMTVSNVDLQLAAADTVDAPKYAAKQGELVFQIASSPRSATKEYPVQARANYSGEFEVLHNGKVVAKQTVTAGELFSQWLTLDSGANQMEVRFTAIDGPNKETQAHRYSVDVVSLPDPMTLYVAPNGSDKGNGSQAQPLDLATAVELLPAGGTIILKDGDYQGMEIPLTASGSADKLKHLRAEGDNVRFVSELRHEANYWHYQGIEVAGAQFIVHGSHNTFEKMVTHGAPDTGFVITSPENIGRALWASYNQVIESESYNNMDPSQINADGFAAKMRIGDGNTFIRCLSHHNIDDGWDLFNKVEDGANGAVTILDSISFSNGRTLDVANKGGTIGNGFKLGGEGIPVPHVVKNSLSFNNNMDGFTDNFNPGALVLSDNVSIDNKRFNYLFRKSPYSGEIEQGTFTNNRSYRFHVSSKYDDVINSAKSTGNALVENGTTYTSDGKAVDSKTLAPLKQASVIDTQQAIPGKQEAMQLKQLIH
>NZ_CP028142.1|WP_046264956.1|1109879_1110662_+|DNA-binding-transcriptional-regulator-KdgR
MEKSTQPEAVSSVLKVFHILQALGEQKAIGVSELSQRLMMSKATTYRFLQTMKSLGYVSQEGEADKYSLTLKLFELGAKSLEYVDLIELADKEMRHISEQTNEALHLGALDDNAIIYIHKIDSGYNLRMQSRIGRRNPLYSTAIGKVLLSERDESFVRDVLSDVEFIKHTEKTLENTDQVLEELAKVRDFHYAEDNEEQEPGLRCIAAPIYDRFGQIIAGLSISFPTIRFDEERMEYYVGLLHQAGKNISEQLGYHDYPA
>NZ_CP028142.1|WP_108745364.1|1110745_1112614_+|CBS-domain-containing-protein
MGTSVTPNIFDFLIKIDPFDKLPEPVVESIANSVKVKYLVRGETIGFSALCDQRYLYIIRTGAIEQRTPNGELRARLGQDDQFGFTFLDPLENAEDGYQAEAIEDSLLYLIPHSELKLVSEEHPEFADYFAAQANVRLSSAVKYVCRKEEKGLFFRTVGEIASENIAIVDVNDSIRSVAQTMCGKQRSSCAVVMKEGEIIGLVTDRDMTKSVVAQDMDTNQPIADVMTPSPVLIEDDAKVIQAISLMLQYNIRCLPVVHGKQVKGLLTTTHLVHNHRTQSLFLIEKIKYASSLNALAALKEERQTIFQALVESGVSAEIQGRVMSMIMDAFTRRIIQLNEELLGPPPCDYAWLVAGSHARNEVHMLSDQDSAIVLSDDATEEHKLYFTHLAMRVCNGLAACGYPLCDGKYMAASPKWCQPIRRWKEYYQKWVASPEYNKLLSISVFLEVRAIHGNREFVDQIQQHLHDCIQKSPSFIPALVRDAIDTQPPLGIFNNLVLEKGGENSNTLNIKKYALNLIIDLARIFSLAAGGSLTGTEERFRYAAQHGTLSKDSVENIIGAYRFITQVRFRHQLNAILAGTTPDNHIAPDDFSSFERKHLKDAFKIISELQDVAKLKFVKGA
>NZ_CP028142.1|WP_062867082.1|1112616_1113327_+|DNA-polymerase-III-subunit-epsilon
MIKRWFKRWETPLSPEQKRQAIHVIDDWPIVLKDYLQRPLVDDSTTLKDLSFVALDFETTGVDAQGDKILSIGVVDLTLDGIDIASSKEWYICHGQFIKPETAQINGLTPQDLAKGLPLDEGMNRLLERITGKVVLAHGCCIEKAFIHAYFSSRYQVEDFPAYFIDTLQIEKQFSYAGKSGAHSSYQLDDLRRYYHLPGYLSHSAASDALACAELFLVQSKKLTALPDVTLRQLMR
>NZ_CP028142.1|WP_025553232.1|1113327_1114197_-|LysR-family-transcriptional-regulator
MANWEGVSEFVAVAETNSFTGAAAKLKTSVAQISRRVSALEERLAVKLLHRTTRKVSLSEAGQLYYQQCKHLVEGLELAELAVTQMQTEPRGLLRVTAPVTYGEMNLAPLLHQFLEKYPRVDLDLVLTNQKLDLIEQGVDVAIRLGRLQDSSMIAKRLSSRQTYVCASPMYLERFGEPHTLSELGRHQCLVGSVDYWHFKENKRDKSLRVSGRIKCNSGFALVDAAKRGLGLVQLPDYYVQEALDSGELVEVLTDYRDDREGIWALYPQSRNLSPKVRLLIDFLAQELT
>NZ_CP028142.1|WP_006740949.1|1114277_1115084_-|arylamine-N-acetyltransferase
MNKTDLNAYLTKLGLPSELPADLESLHKIHVAQHRCLPFENFDISLQRGISVEIEDIIQKTVYHSRGGYCFELNGLMLDVLKTLGFEARSLLGRVHVMGTPTGRSHQITLVTLDEQAWIVDVGFGSNTPRAPLPFILNQVIQTDLQTFRFVEDAQFGYFLQVLSTDGTDTWNNLYSFDLEFVFAGDIACGNFFTSTSPHSRFTSARVAAKATESGLVTLLNYTLKYTSQGEQTELELEPGQAYLDALKEYFGIELDAQYGDLRPLPDA
>NZ_CP028142.1|WP_005464962.1|1115377_1116526_+|S-(hydroxymethyl)glutathione-dehydrogenase/class-III-alcohol-dehydrogenase
MTLEIKPGQTHIKSKAMVAWAAGEPLKMEEVDVQLPKAGEVLVRIVATGVCHTDAFTLSGDDPEGIFPSILGHEGGGIVEMVGEGVTSVEVGDHVIPLYTAECGECKFCKSGKTNLCQAVRETQGKGLMPDGTSRFSINGETIFHYMGCSTFSEYTVLPEISLAKVNKQAPLEEVCLLGCGVTTGMGAVLNTAKVEKGDTVAIFGLGGIGLSAIIGARMAGASRIIGIDINESKFDLAKQLGATDVINPQKFDKPIQEVIVEMTDGGVDYSFECIGNVNVMRQALECCHKGWGESVIIGVAGAGQEISTRPFQLVTGRVWRGSAFGGVKGRSELPEIVNRYMAGEFGLQEFITHTMGLEDVNKAFDLMHEGKSIRTVIHMDK
>NZ_CP028142.1|WP_057619727.1|1116587_1117427_+|S-formylglutathione-hydrolase
MTIENVSQTKVFGGWHKQYTHDSKALNCTMRFAIFLPPNATKSNPVPALYWLSGLTCTDENFMQKAGAFRMAAELGIAIIAPDTSPRGEGVADDASYDLGQGAGFYLNATQAPWSLHYHMYDYVTQELPAIIEANFPVSDVKSISGHSMGGHGALTIGLKNPTIYRSISAFSPIGNPMQCPWGQKAFTAYLGTDIESWKQYDASELLKKEKSPLPILVDQGDADGFLSEQLKPEVLLAAAKQHGSELNLRMQSGYDHSYYFISSFIDNHLNFHAKYLFA
>NZ_CP028142.1|WP_005482833.1|1117872_1118334_+|oxidoreductase
MKKIVSLSLLLFAPFLSANSITFSSPQQPSVTLKLEELQSLPTTSYTTDLPWIQQSSEFLGVKLSTLLTHVYGSIPEQVDIGSLNNYHSTLSRKDIVRYQPILAYQQDHHYIKVRNKGPYWVIYPLSQYPELDHNEYHAQMVWQVNEMKIKQK
>NZ_CP028142.1|WP_005464959.1|1118333_1119425_+|GGDEF-domain-containing-protein
MKLSEAYPIKQKNYSTTSKMLLLVFATSLLLANVILLQQTRVLAQSFTDEQKQATWFLFQLSKELSELVSEARRLDENVLKIEGAELQYELAWSRFDLLINSKDVYTFFSRNHIQQYFLQLFNEFKELEPLLVEAKTGDSQAAAQFYRATQTLYLNLVEFVNQNFRLTSQVYETQKDESQRLMKAQYMLFATFVLSILSLTYFFYRESHFHRKLALSDPLTGLGNRNALFVTLRNNTRNRTAFSLCLLDLNGFKNVNDTYGHQAGDTVLCEIAKRLKDMNIDSFSTYRMGGDEFAVVIESSDVDAEEAKKHIHSVFDTPVLNANNVSSLSTSIGVAHYPSDSDNVDFLISIADKRMYKMKFQR
>NZ_CP028142.1|WP_031831553.1|1119434_1119839_+|hypothetical-protein
MMRKFMQVLLLLAVIAAGVLAWVFIPSHETIGQKTLEQALNDDYSLVGHRIYSTDPDAGNRFGYFVLATGQSIEEQEPFLVTSDQFIRMEQTGDNTLSVTVNGRIYQYHNDLWVPKSDGKLQHFLVSATAKYVR

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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

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

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

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

Prophage detection

Region

Region Position

Protein_number

Hit_taxonomy

Key_proteins

Att_site

Prophage annotation

DBSCAN-SWA_1

231642 : 319707

uncultured_Mediterranean_phage(20.0%)

transposase,integrase,tRNA,protease

attL 257174:257190|attR 284695:284711

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_005477377.1\|231642_232623_+\|tRNA	tRNA dihydrouridine(20/20a) synthase DusA	NA	NA	NA	NA
WP_005496590.1\|232786_233002_+	envelope stress response protein PspG	NA	NA	NA	NA
WP_005455819.1\|233103_233763_+	TIGR04219 family outer membrane beta-barrel protein	NA	NA	NA	NA
WP_005455817.1\|233914_234145_+	hypothetical protein	NA	NA	NA	NA
WP_029864061.1\|234262_236134_+	assimilatory sulfite reductase (NADPH) flavoprotein subunit	NA	NA	NA	NA
WP_015297344.1\|236133_237870_+	assimilatory sulfite reductase (NADPH) hemoprotein subunit	NA	NA	NA	NA
WP_005477371.1\|237862_238642_+	phosphoadenylyl-sulfate reductase	NA	NA	NA	NA
WP_079399815.1\|250067_250220_-\|transposase	transposase	NA	NA	NA	NA
WP_101945907.1\|250440_250584_-	winged helix-turn-helix domain-containing protein	NA	NA	NA	NA
WP_011106084.1\|250929_252264_-	sodium:proton antiporter	A0A2H4J178	uncultured_Caudovirales_phage	2.8e-40	38.1
WP_057619617.1\|252455_256136_+	methionine synthase	A0A140XBC7	Dickeya_phage	5.2e-20	74.6
WP_005480997.1\|256259_257612_-	lysine-sensitive aspartokinase 3	NA	NA	NA	NA
257174:257190	attL	NA	NA	NA	NA
WP_057619616.1\|258219_259341_+	alanine--glyoxylate aminotransferase family protein	NA	NA	NA	NA
WP_053302082.1\|259474_261253_-	O-antigen ligase C-terminal domain-containing protein	NA	NA	NA	NA
WP_108745155.1\|261320_264143_-	excinuclease ABC subunit UvrA	A0A1B1IVR3	uncultured_Mediterranean_phage	0.0e+00	57.4
WP_005466627.1\|264280_265153_-	UTP--glucose-1-phosphate uridylyltransferase GalU	A0A127AW70	Bacillus_phage	3.8e-62	46.4
WP_108744711.1\|265410_266055_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA
WP_005466625.1\|266333_266864_+	single-stranded DNA-binding protein	A0A2I7RHA9	Vibrio_phage	5.9e-58	89.2
WP_108744712.1\|267049_268366_+\|integrase	site-specific integrase	NA	NA	NA	NA
WP_108744713.1\|268378_269932_+\|integrase	site-specific integrase	NA	NA	NA	NA
WP_108744714.1\|269924_272306_+\|integrase	integrase	NA	NA	NA	NA
WP_108744715.1\|272308_272725_+	hypothetical protein	NA	NA	NA	NA
WP_108744716.1\|272735_273221_+	hypothetical protein	NA	NA	NA	NA
WP_108744717.1\|273217_275413_+	AAA family ATPase	A0A0K2FLP8	Brevibacillus_phage	3.7e-37	26.5
WP_108744718.1\|275829_277476_+	DUF262 domain-containing protein	NA	NA	NA	NA
WP_162597335.1\|277495_277660_-	DUF3265 domain-containing protein	NA	NA	NA	NA
WP_108744720.1\|277641_277887_-	hypothetical protein	NA	NA	NA	NA
WP_011106082.1\|279480_281490_+	RNase E specificity factor CsrD	NA	NA	NA	NA
WP_025547506.1\|281501_282947_+	MSHA biogenesis protein MshI	NA	NA	NA	NA
WP_005497276.1\|282943_283594_+	type II secretion system protein M	NA	NA	NA	NA
WP_005481006.1\|283586_283916_+	MSHA biogenesis protein MshK	NA	NA	NA	NA
WP_005456314.1\|283936_285580_+	pilus (MSHA type) biogenesis protein MshL	NA	NA	NA	NA
284695:284711	attR	NA	NA	NA	NA
WP_108744721.1\|285623_286469_+	ExeA family protein	NA	NA	NA	NA
WP_025558463.1\|286465_287542_+	MSHA biogenesis protein MshN	NA	NA	NA	NA
WP_015297335.1\|287538_289263_+	type II/IV secretion system protein	NA	NA	NA	NA
WP_021484749.1\|289271_290495_+	type II secretion system F family protein	NA	NA	NA	NA
WP_005456302.1\|290498_290960_+	MSHA biogenesis protein MshF	NA	NA	NA	NA
WP_005381181.1\|291254_291722_+	type II secretion system protein	NA	NA	NA	NA
WP_054395004.1\|291793_292027_+	MSHA biogenesis protein MshA	NA	NA	NA	NA
WP_021453808.1\|292142_292628_+	type II secretion system protein	NA	NA	NA	NA
WP_054395011.1\|292624_293191_+	type II secretion system protein	NA	NA	NA	NA
WP_108744722.1\|293191_293905_+	prepilin-type N-terminal cleavage/methylation domain-containing protein	NA	NA	NA	NA
WP_054395003.1\|293894_294338_+	hypothetical protein	NA	NA	NA	NA
WP_054395002.1\|294337_298348_+	hypothetical protein	NA	NA	NA	NA
WP_005381144.1\|298499_299543_+	rod shape-determining protein	F2Y0P3	Organic_Lake_phycodnavirus	2.7e-06	20.3
WP_005461822.1\|299680_300577_+	rod shape-determining protein MreC	NA	NA	NA	NA
WP_005461823.1\|300566_301055_+	rod shape-determining protein MreD	NA	NA	NA	NA
WP_005461824.1\|301059_301629_+	septum formation inhibitor Maf	NA	NA	NA	NA
WP_005461826.1\|301647_303117_+	ribonuclease G	NA	NA	NA	NA
WP_025545974.1\|303128_307007_+	TIGR02099 family protein	NA	NA	NA	NA
WP_025517838.1\|307041_307863_+	carbon-nitrogen hydrolase family protein	NA	NA	NA	NA
WP_020835343.1\|307874_309320_+\|protease	metalloprotease TldD	NA	NA	NA	NA
WP_005461836.1\|309390_310767_-	PhoH family protein	A0A2I7SAD7	Vibrio_phage	1.3e-104	44.4
WP_025545975.1\|311329_314239_+	RNA polymerase-associated protein RapA	A0A1B1IUI1	uncultured_Mediterranean_phage	4.9e-21	36.1
WP_025545977.1\|314308_315574_-	Nramp family divalent metal transporter	NA	NA	NA	NA
WP_021484738.1\|315903_316656_+\|tRNA	bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA	NA	NA	NA
WP_025545978.1\|316690_317653_+	D-2-hydroxyacid dehydrogenase	M1HMI7	Paramecium_bursaria_Chlorella_virus	1.1e-27	29.9
WP_005457057.1\|317725_318253_-	ribosome-associated protein	NA	NA	NA	NA
WP_005459755.1\|318363_319707_+\|protease	metalloprotease PmbA	NA	NA	NA	NA

DBSCAN-SWA_2

447926 : 462597

uncultured_Mediterranean_phage(20.0%)

tRNA

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_005455581.1\|447926_449567_+	CTP synthase	A0A1J0FA14	Only_Syngen_Nebraska_virus	4.2e-155	52.4
WP_005455579.1\|449645_450947_+	phosphopyruvate hydratase	A0A1X9I5Z8	Streptococcus_phage	4.2e-134	59.2
WP_005455577.1\|451360_451642_+	cell division protein FtsB	NA	NA	NA	NA
WP_025546668.1\|451643_452348_+	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	A0A2H4UTB4	Bodo_saltans_virus	4.5e-05	24.3
WP_005380896.1\|452365_452842_+	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	NA	NA	NA	NA
WP_024702352.1\|452888_453932_+\|tRNA	tRNA pseudouridine(13) synthase TruD	NA	NA	NA	NA
WP_005478553.1\|453931_454708_+	5'/3'-nucleotidase SurE	A0A1B1ITZ2	uncultured_Mediterranean_phage	5.0e-66	52.4
WP_005455562.1\|454707_455334_+	protein-L-isoaspartate(D-aspartate) O-methyltransferase	A0A1B1IU40	uncultured_Mediterranean_phage	1.3e-35	52.1
WP_025546666.1\|455348_456272_+	peptidoglycan DD-metalloendopeptidase family protein	D7RWE0	Brochothrix_phage	4.1e-06	35.2
WP_162597300.1\|456352_457342_+	RNA polymerase sigma factor RpoS	F4YCU2	Synechococcus_phage	6.9e-36	35.2
WP_025546664.1\|457420_459982_-	DNA mismatch repair protein MutS	A0A1V0SC35	Catovirus	1.3e-33	23.7
WP_021450025.1\|460066_460549_+	nicotinamide-nucleotide amidase	B5TK85	Pseudomonas_phage	2.9e-27	48.7
WP_108744746.1\|461550_462597_+	recombinase RecA	A0A2D1GPX2	Mycobacterium_phage	4.8e-112	60.3

DBSCAN-SWA_3

2478592 : 2485294

Staphylococcus_phage(50.0%)

Protein_ID	Protein_Def	Hit_ID	Hit_Def	E-value	Identity
WP_005440184.1\|2478592_2479063_-	6,7-dimethyl-8-ribityllumazine synthase	A0A2H4PQS3	Staphylococcus_phage	1.7e-32	49.3
WP_057619201.1\|2479232_2480342_-	bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	A0A2H4PQS2	Staphylococcus_phage	8.8e-64	39.6
WP_005483039.1\|2480511_2481165_-	riboflavin synthase	A0A2H4PQS5	Staphylococcus_phage	1.6e-33	37.5
WP_025548687.1\|2481177_2482302_-	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	A0A1V0SE20	Indivirus	2.4e-48	36.0
WP_005482986.1\|2482309_2482759_-	transcriptional regulator NrdR	NA	NA	NA	NA
WP_017448803.1\|2482886_2484137_-	glutamate-5-semialdehyde dehydrogenase	A0A1X9I5D4	Streptococcus_phage	2.1e-98	47.9
WP_005483011.1\|2484154_2485294_-	glutamate 5-kinase	A0A1X9I5D0	Streptococcus_phage	1.3e-62	41.7

Anti-CRISPR protein detection

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

Overview of predicted results

Overview of the results

Cas Category Instructions

Results visualization

1. NZ_CP028142

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CRISPR-Cas detection and classification

Click the colored protein region to show detailed information

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection

2. NZ_CP028141

Click the left colored region to show detailed information

CRISPR-Cas detection and classification

Self-targeting detection

MGE targeting detection<

Prophage detection

Anti-CRISPR protein detection