Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200269
• Name: oriT_ICEKpnNH54-1
• Organism: Klebsiella pneumoniae strain NH54
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP024916 (46131..46254 [+], 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_ICEKpnNH54-1
CCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCCATTTTTTCGAGCTTGCGAAGAAAAAATAGGCTAAACGCGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGTGCGACGGTGTGCCGCC

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_CU643_17675_ICEKpnNH54-1

• ID: 16782
• GenBank: AVT95357
• Name: t4cp2_CU643_17675_ICEKpnNH54-1
• 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

>AVT95357.1 ATPase [Klebsiella 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_CU643_17740_ICEKpnNH54-1

• ID: 16783
• GenBank: AVT95369
• Name: t4cp2_CU643_17740_ICEKpnNH54-1
• 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

>AVT95369.1 MFS transporter [Klebsiella 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: 3496025..3505960

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CU643_17630	3492520..3493503	+	984	AVT95348	hypothetical protein	-
CU643_17635	3493643..3493828	+	186	AVT95349	AlpA family transcriptional regulator	-
CU643_17640	3493847..3494032	+	186	AVT95350	hypothetical protein	-
CU643_17645	3494017..3494598	+	582	AVT95351	DUF2857 domain-containing protein	-
CU643_17650	3494588..3494797	+	210	AVT95352	conjugal transfer protein TraR	-
CU643_17655	3495001..3495168	+	168	AVT95353	transcriptional regulator	-
CU643_17660	3495737..3495970	+	234	AVT95354	hypothetical protein	-
CU643_17665	3496025..3496753	+	729	AVT95355	type VI secretion protein	virB1
CU643_17670	3496753..3497046	+	294	AVT95356	TriB protein	virB2
CU643_17675	3497059..3499797	+	2739	AVT95357	ATPase	virb4
CU643_17680	3499815..3500522	+	708	AVT95358	type IV secretion system protein VirB5	-
CU643_17685	3500530..3500772	+	243	AVT95359	hypothetical protein	-
CU643_17690	3500776..3501849	+	1074	AVT95360	conjugal transfer protein TrbL	virB6
CU643_17695	3502071..3502754	+	684	AVT95361	type IV secretion system protein	virB8
CU643_17700	3502751..3503659	+	909	AVT95362	P-type conjugative transfer protein VirB9	virB9
CU643_17705	3503689..3504945	+	1257	AVT95363	type VI secretion protein	virB10
CU643_17710	3504935..3505960	+	1026	AVT95364	P-type DNA transfer ATPase VirB11	virB11
CU643_17715	3505957..3506355	+	399	AVT95365	Cag pathogenicity island protein Cag12	-
CU643_17720	3506391..3506696	+	306	AVT95366	conjugal transfer protein	-
CU643_17725	3506730..3507035	+	306	AVT95367	dpoa decarboxylase	-
CU643_17730	3507056..3507447	+	392	Protein_3461	hypothetical protein	-
CU643_17735	3507466..3507744	+	279	AVT95368	hypothetical protein	-
CU643_17740	3507744..3509603	+	1860	AVT95369	MFS transporter	-
CU643_17745	3509613..3510359	+	747	AVT95370	molybdopterin-guanine dinucleotide biosynthesis protein MobC	-

Host bacterium

• ID: 246
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEKpnNH54-1
• GenBank: CP024916
• Element size: 5399501 bp
• Coordinate of oriT [Strand]: 46131..46254 [+]
• Host bacterium: Klebsiella pneumoniae strain NH54
• Coordinate of element: 3461245..3519441

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: -