Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200363
• Name: oriT_ICEPca4
• Organism: Pectobacterium atrosepticum strain 36A
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP024956 (24409..24539 [-], 131 nt)
• oriT length: 131 nt
• IRs (inverted repeats): _
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 131 nt

>oriT_ICEPca4
GGCGCGACCAACCCCTTTAAAGGTCAGCTTCCCTTTTATTCACGCTGCGAGGAACGAGCAAAGGGAATAAAAAGGCAAAAGCGACCGTCTTAAAGGGGTTGGTCGCGCGTAGCGGGCGACGGTGTGCCGCC

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_CVS35_08370_ICEPca4

• ID: 16892
• GenBank: ATY93021
• Name: t4cp2_CVS35_08370_ICEPca4
• UniProt ID: _
• Length: 623 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 623 a.a.
• Molecular weight: 70037.98 Da
• Isoelectric Point: 5.5998

>ATY93021.1 MFS transporter [Pectobacterium atrosepticum]
MILNKLAVSLSPIVNGALSFMAFMQQHQLMLALLSGLTMPFFASMKSDERQKAPLWQKLIIAFSLLCFLS
GTMAPIVIWIFQWLYQGRVVDSIPVLAWPVLITFTVTGFIFHILLRRVLTPELDKIKKRLVRKTALEREL
RSDVRTVKSLLPETLHYDPLDYIDLNKGLFIGIDRDIQPMYLPLKDWQRQHADIIGTTGAGKGVATGILL
YQSILAGEGVFVMDPKDDEWAPHLYRKACEDAGKTFALIDLRKPQYQLNLIEEITADELEELFVAGFSLA
EKGQESDFYRIDDRKAARIAAQFVNQHATATIRDVYNGDYVQGIADKIKAFFGKIEELALLNAINAPTGF
SLNTIFEEGGCCYVIGSMRNSKIITAQRMLLVRLYQLAERRERVKDVPRPIAIYLSELKYHLSRPALEGL
GAARDKGVHIIMDHQSIADLKDCPADLKGDAVVGAVVENAKFKLVYRVMDPDTAEWVARMSGTILVDDEV
RKAKTDAVLTETIDDERTIRQAERFFTDSNMILNLPDFVSFIFTTRTLPSASLISPIRVKKRELEISAVS
PAITATAATVNITLDFSEEETYPGPASKTDITTTRPDLFFDTDEKNTTTPNTNKEENPSLLDF

Protein domains

No domain identified.

Protein structure

No available structure.

t4cp2_CVS35_08420_ICEPca4

• ID: 16893
• GenBank: ATY90376
• Name: t4cp2_CVS35_08420_ICEPca4
• UniProt ID: _
• Length: 915 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 915 a.a.
• Molecular weight: 104053.40 Da
• Isoelectric Point: 8.3080

>ATY90376.1 ATPase [Pectobacterium atrosepticum]
MTTLNKALTRPAAIMGIPLVPFVIVSGAIVLLSVYISYYLALLLIPAWLEMKAKARTDIHYFGLLWLAFK
TRGRFATDRHFGARAVLASHYDAVDVSEFTDKMKLNERITLDKYIPYSSHIHPHIIRNRSSDLVATWELG
GTVFECEDEHHLTLLASHLNNLIRSYEGLPITFYIHRIREQYQDGFDASSGIPFSDEVTERYYQPIKEKP
LWRHRLFFTVCYAPFSTLEKKVMKTQTAGKRKAALDDALKGMLEHQDAINTALSRYMATPLGIYEEKGRV
FSSQLAFYHRLITGKWQNVAVTRTPFYHVLSTPDVFFTTDTAECQAVGGSRFFRSLEIKDYSPETYTGLL
DALLYAESEYVLTQSFTCMARDEAQNHIRLAEKRLNSTDDDAISQREELIVLRDLLQSGHVSCGKYHFSL
LVSSVSAAQVVKETNALAQPFNDLGIMTSLSTLSLPAAYLAQLPGVYALRPRLVVVSSQNYADMGSLHNF
HSHKRNGNPWGEAIAILKSPSGGGYYLNLHDSQAGRNDFNEKTPGNTAIIGKTGSGKTLLMTMMKQLMQK
YRNPATFSASATIKLLTTVYFDKDRAAEMSIRQMGGRYFRIRTGIPTGFNPFSLAPTRRNISFIKRLIRM
LCRRDGKPLDPRDEERISTAVDTIMLDYPPEYRRYGITRLLEVLPEPPTKEVRTNGLRIRLKQWAQGGEF
GWVFDNEEDTFNISNIDNFGIDGTEFLDDDDIRGPITFYLLYRVTSLLDGRRLVMFMDEFWKWLADVEFS
KFSLNMLKVIRKLNGIFIPATQSPDEIVRHPIAPAIIEQCSTQIFLANPKASHTDYVEKMKVPESVYDMV
RNLDPSEHYMVVLKTPLRAGETRPFVAMARMNLSGLGNITKILSGNEDNLKIFDVIYQEGMSPQDWKETF
LNQAI

Protein domains

Predicted by InterproScan.

• Type IV secretory pathway, VirB3-like protein (VirB3) (3-81)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (271-472)

• TraG P-loop domain (P-loop_TraG) (535-820)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1888251..1898004

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CVS35_08360	1884162..1884446	-	285	ATY90366	hypothetical protein	-
CVS35_08365	1884545..1885291	-	747	ATY90367	molybdopterin-guanine dinucleotide biosynthesis protein MobC	-
CVS35_08370	1885302..1887173	-	1872	ATY93021	MFS transporter	-
CVS35_08375	1887308..1887877	-	570	Protein_1626	hypothetical protein	-
CVS35_08380	1887902..1888204	-	303	ATY90368	conjugal transfer protein	-
CVS35_08385	1888251..1889264	-	1014	ATY90369	P-type DNA transfer ATPase VirB11	virB11
CVS35_08390	1889254..1890486	-	1233	ATY90370	hypothetical protein	virB10
CVS35_08395	1890483..1891373	-	891	ATY90371	P-type conjugative transfer protein VirB9	virB9
CVS35_08400	1891373..1892056	-	684	ATY90372	type IV secretion system protein	virB8
CVS35_08405	1892277..1893317	-	1041	ATY90373	conjugal transfer protein TrbL	virB6
CVS35_08410	1893329..1893553	-	225	ATY90374	Eex protein	-
CVS35_08415	1893564..1894280	-	717	ATY90375	type IV secretion system protein VirB5	-
CVS35_08420	1894304..1897051	-	2748	ATY90376	ATPase	virb4
CVS35_08425	1897061..1897342	-	282	ATY90377	conjugal transfer protein	virB2
CVS35_08430	1897339..1898004	-	666	ATY90378	transglycosylase	virB1
CVS35_08435	1898084..1898305	-	222	ATY90379	hypothetical protein	-
CVS35_08440	1898816..1900384	+	1569	ATY90380	hypothetical protein	-
CVS35_08445	1900774..1900983	-	210	ATY90381	conjugal transfer protein TraR	-
CVS35_08450	1900973..1901557	-	585	ATY90382	DUF2857 domain-containing protein	-
CVS35_08455	1901574..1901768	-	195	ATY90383	AlpA family transcriptional regulator	-
CVS35_08460	1901922..1902834	-	913	Protein_1643	hypothetical protein	-

Host bacterium

• ID: 320
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEPca4
• GenBank: CP024956
• Element size: 4965575 bp
• Coordinate of oriT [Strand]: 24409..24539 [-]
• Host bacterium: Pectobacterium atrosepticum strain 36A
• Coordinate of element: 1863011..1908923

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -