Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200232
• Name: oriT_ICEKpnKp_Goe_822579-1
• Organism: Klebsiella pneumoniae strain Kp_Goe_822579
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP018140 (46142..46265 [+], 124 nt)
• oriT length: 124 nt
• IRs (inverted repeats): 40..47, 59..66 (ATTTTTTC..GAAAAAAT)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 124 nt

>oriT_ICEKpnKp_Goe_822579-1
CCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCCATTTTTTCGAGCTTGCGAAGAAAAAATAGGCTAAACGCGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGGGCGACGGTGTGCTGCC

oriT secondary structure

Predicted by RNAfold.

T4CP

virB4_BB744_01796_ICEKpnKp_Goe_822579-1

• ID: 16718
• GenBank: APD43759
• Name: virB4_BB744_01796_ICEKpnKp_Goe_822579-1
• UniProt ID: _
• Length: 912 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 912 a.a.
• Molecular weight: 103030.97 Da
• Isoelectric Point: 7.2895

>APD43759.1 Type IV secretion system protein virB4 [Klebsiella pneumoniae]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGNAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPCKGELSSQNFVELAALHNFYP
GKRDKAPWGDAMALLRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYG
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYYRVISGESTGWNPFSLPATKRNINFIKQLMKILC
TRNGSTISPRDERRLSDAVNAVMNDEPQYRVYGITRMLENLPEPATKEAQENGLSIRLSQWAQGGEFGWV
FDNESDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWKWLRDPVFKDFA
YNKLKTIRKLNGMLVVGTQSPAEIIKDDIAPAVIEQCGTQILAANPNADRAHYVDGMKFEPEVFDVVKGL
DPQARQYVVVKNQFKRGDTKRFAARVTLDLSGIGRYTKVMSGDAPNLEIFESIYREGMQPHEWLDTYLAK
AL

Protein domains

Predicted by InterproScan.

• Type IV secretory pathway, VirB3-like protein (VirB3) (3-79)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (269-468)

• TraG P-loop domain (P-loop_TraG) (535-813)

Protein structure

No available structure.

t4cp2_BB744_01807_ICEKpnKp_Goe_822579-1

• ID: 16719
• GenBank: APD43770
• Name: t4cp2_BB744_01807_ICEKpnKp_Goe_822579-1
• UniProt ID: _
• Length: 619 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 619 a.a.
• Molecular weight: 69752.68 Da
• Isoelectric Point: 5.7361

>APD43770.1 conjugative coupling factor TraD, SXT/TOL subfamily [Klebsiella pneumoniae]
MILNKLTASLSPIVNGMLALLAFVQQQQLILALLAGLTMPFFTSMKSDERQKAPLWKKLIIAFSLLCFIS
GTMAPIVIGSFQWLYKIRLTSDNTVLAWAVRITFTVTGIIFHIMLRRVFTPELDRIKKRLVKKTTLEREL
RTDVRTVKSLLPETLHYNPLDYIDLNKGIFTGMDSEKEPLYLPLKDWQKQHADIIGTTGAGKGVAAGILL
YQSILAGEGVFVMDPKDDEWAPHLYRKACEDAGKPFALIDLRKQQYQLNLIEDITPDELEELFVAGFSLA
EKGQESDFYRIDDRKAARMAAQFVSDNPSATLRDVYNGDYVQSIAEKIKAFFGKIEELALLNAINSPEGF
SLQQMFDEGGCCYVIGSMRNSKIITTQRMLLVRLYQLAERRDRVTNVPRSIAIYLSELKYHLSRPALEGL
GAARDKGVHIIMDHQSIADLKDCPADLKGDAVVGAVVENAKFKLVYRVMDPDTAEWVARMSGTILVDDEL
RKAKTDNMLTETIDSERTIRQAERYFIDSNMILNLHDFVSFIFTTKTLPSASLISPIKIRKRQLKIFSVS
PDIAASAAPVKIALDFDEDDKPSIQDVMTTHPDLFFNESEVQPAEPQPDEGEHLSPLDF

Protein domains

Predicted by InterproScan.

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (291-541)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1863956..1873881

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
BB744_01789	1860490..1861416	+	927	APD43752	hypothetical protein	-
BB744_01790	1861556..1861741	+	186	APD43753	putative transcriptional regulator	-
BB744_01791	1861763..1861945	+	183	APD43754	hypothetical protein	-
BB744_01792	1861930..1862511	+	582	APD43755	hypothetical protein	-
BB744_01793	1863650..1863883	+	234	APD43756	hypothetical protein	-
BB744_01794	1863956..1864666	+	711	APD43757	Type IV secretion system protein virB1	virB1
BB744_01795	1864666..1864959	+	294	APD43758	Pertussis toxin liberation protein A	virB2
BB744_01796	1864972..1867710	+	2739	APD43759	Type IV secretion system protein virB4	virb4
BB744_01797	1867728..1868435	+	708	APD43760	P-type DNA transfer protein VirB5	-
BB744_01798	1868443..1868685	+	243	APD43761	hypothetical protein	-
BB744_01799	1868689..1869762	+	1074	APD43762	TrbL/VirB6 plasmid conjugal transfer protein	virB6
BB744_01800	1869854..1869991	+	138	APD43763	hypothetical protein	-
BB744_01801	1869984..1870667	+	684	APD43764	Pertussis toxin liberation protein E	virB8
BB744_01802	1870667..1871572	+	906	APD43765	Type IV secretion system protein virB9 precursor	virB9
BB744_01803	1871616..1872866	+	1251	APD43766	Type IV secretion system protein virB10	virB10
BB744_01804	1872856..1873881	+	1026	APD43767	Type IV secretion system protein VirB11	virB11
BB744_01805	1874312..1874617	+	306	APD43768	hypothetical protein	-
BB744_01806	1874651..1874956	+	306	APD43769	hypothetical protein	-
BB744_01807	1875666..1877525	+	1860	APD43770	conjugative coupling factor TraD, SXT/TOL subfamily	-
BB744_01808	1877535..1878281	+	747	APD43771	hypothetical protein	-

Host bacterium

• ID: 214
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEKpnKp_Goe_822579-1
• GenBank: CP018140
• Element size: 5381436 bp
• Coordinate of oriT [Strand]: 46142..46265 [+]
• Host bacterium: Klebsiella pneumoniae strain Kp_Goe_822579
• Coordinate of element: 1829156..1892707

Cargo genes

• Drug resistance gene: -
• Virulence gene: ybtS, ybtX, ybtQ, ybtP, ybtA, irp2, irp1, ybtU, ybtT, ybtE, fyuA
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -