Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200278
• Name: oriT_ICEKpnRJF293-1
• Organism: Klebsiella pneumoniae subsp. pneumoniae strain RJF293
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP014008 (46132..46255 [+], 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_ICEKpnRJF293-1
CCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCCATTTTTTCGAGCTTGCGAAGAAAAAATAGGCTAAACGCGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGTGCGACGGTGTGCCGCC

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_RJF2_16770_ICEKpnRJF293-1

• ID: 16800
• GenBank: AMA25930
• Name: t4cp2_RJF2_16770_ICEKpnRJF293-1
• UniProt ID: _
• Length: 912 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 912 a.a.
• Molecular weight: 103068.02 Da
• Isoelectric Point: 7.4625

>AMA25930.1 ATPase [Klebsiella pneumoniae subsp. pneumoniae]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGNAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFAEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
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) (269-470)

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

Protein structure

No available structure.

t4cp2_RJF2_16810_ICEKpnRJF293-1

• ID: 16801
• GenBank: AMA25937
• Name: t4cp2_RJF2_16810_ICEKpnRJF293-1
• UniProt ID: _
• Length: 619 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 619 a.a.
• Molecular weight: 69574.86 Da
• Isoelectric Point: 6.6673

>AMA25937.1 molybdopterin-guanine dinucleotide biosynthesis protein MobB [Klebsiella pneumoniae subsp. pneumoniae]
MILNKLTASLSPIVNGMLAVLAFVQQKQLVLALLAGLTMPFFASMKSDERQKAPLWKKLIIAFSLLCFLS
GTLAPVVIGSFQWLYKIRPTSDNTVLAWSVRIAFTVTGIIFHIMLRRIFTPELDKIKKRLVKKTTLEREL
RTDVRTVKSLLPETLHYNPLDYIDLNKGIFTGMGRENEPMYLPLKDWQKQHADIIGTTGAGKGVAAGILL
YQSILAGEGVFVMDPKDDEWAPHLYRKACEDAGKPFALIDLRKQQYQLNLIEDITPDELEELFVAGFSLA
EKGQESDFYRIDDRKAARIAAQFVSDNPSTTIRDVYNGDYVQSIAEKIKAFFGKIEELALLNAINSPEGF
SLKHIFDEGGCCYVVGSMRNSKIITAQRMLLVRLYQLAEKRDRVIDVPRPIAVYLSELKYHLSRSALEGL
GAARDKGVHIIMDHQSIADLKDCPADLKGDAVVGAVVENAKFKLVYRVMDPDTAEWVARMSGTILVDDEL
RKAKTDNMLTETIDSERTIRQAERFFIDSNMILNLPDFVSFIFTTKTLPSASLISPIKVRKRQLKTFSVS
PDIAATVAPVKIMLDFCEDDKPAMSDVMTTHPALFFDESEVKPVKPKPDDEEHLSPLDF

Protein domains

Predicted by InterproScan.

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (418-542)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3415602..3425519

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
RJF2_16735	3412137..3413062	+	926	Protein_3266	hypothetical protein	-
RJF2_16740	3413202..3413387	+	186	AMA25924	DNA-binding protein	-
RJF2_16745	3413576..3414157	+	582	AMA25925	hypothetical protein	-
RJF2_16750	3414599..3414727	+	129	AMA25926	transcriptional regulator	-
RJF2_16755	3415296..3415529	+	234	AMA25927	ATP-binding protein	-
RJF2_16760	3415602..3416312	+	711	AMA25928	type VI secretion protein	virB1
RJF2_16765	3416312..3416605	+	294	AMA25929	TriB protein	virB2
RJF2_16770	3416618..3419356	+	2739	AMA25930	ATPase	virb4
RJF2_16775	3419374..3420081	+	708	AMA25931	type IV secretion system protein VirB5	-
RJF2_16780	3420335..3421408	+	1074	AMA25932	conjugal transfer protein TrbL	virB6
RJF2_16785	3421630..3422313	+	684	AMA25933	hypothetical protein	virB8
RJF2_16790	3422313..3423218	+	906	AMA27723	type VI secretion protein	virB9
RJF2_16795	3423254..3424504	+	1251	AMA25934	type VI secretion protein	virB10
RJF2_16800	3424494..3425519	+	1026	AMA25935	P-type DNA transfer ATPase VirB11	virB11
RJF2_16805	3426289..3426594	+	306	AMA25936	dpoa decarboxylase	-
RJF2_16810	3427304..3429163	+	1860	AMA25937	molybdopterin-guanine dinucleotide biosynthesis protein MobB	-
RJF2_16815	3429173..3429919	+	747	AMA25938	molybdopterin-guanine dinucleotide biosynthesis protein MobC	-

Host bacterium

• ID: 255
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEKpnRJF293-1
• GenBank: CP014008
• Element size: 5226330 bp
• Coordinate of oriT [Strand]: 46132..46255 [+]
• Host bacterium: Klebsiella pneumoniae subsp. pneumoniae strain RJF293
• Coordinate of element: 3380804..3439778

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: -