oriTDB

The information of the oriT region

oriTDB accession number	100017
Name	oriT_R64
Sequence Completeness	intact
oriT length	92 nt
oriT sequence	GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTA TTACAATTGCACATCCTGTCCCGTTTTTCGGG
IR (inverted repeat)	8-bp: [6-13] [17-24] nt (GTCGGGGC..GCCCTGAC) 17-bp: [31-47] [54-70] nt (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC)
Location of nic site	[78-79] nt
Conserved sequence flanking the nic site	CATCCTG\|T
Note	minimal oriT sequence
	L:6-13;R:17-24;L:31-47;R:54-70;D:78-79

Visualization of oriT structure (The oriT was characterized experimentally)

1...5....10....15....20....25....30....35....40....45....50....55....60

1

GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTA

61

TTACAATTGCACATCCTGTCCCGTTTTTCGGG

Reference

[1] Furuya N et al (1991) Determination of the nick site at oriT of IncI1 plasmid R64: global similarity of oriT structures of IncI1 and IncP plasmids. J Bacteriol. 173(20):6612-7. [PMID:1917882]

[2] Komano T et al (1990) Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. J Bacteriol. 172(5):2230-5. [PMID:1970558]

I. Information of Relaxase

ID	16
Name	NikB_R64
GenBank accession number	NP_863436
Family	MOB_P
Length	899 aa
UniProt ID	Q79VV7
PDB ID	_
Pfam	Relaxase [PF03432.13], Evalue: 9.20E-64, Aligned region: 47..315
Note	to recognize the conserved nick region sequence
Protein sequence [Download]	MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRL RNESFVALVDVMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHY ILSWQSHESPRPEQIYDSVRHTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYL NRLSWSQEKLSRACRELELKHGFAPDNGCWVHAPGNRIVRKTAVERDRQNAWTRGKKQTF REYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGKFLVMDGWDRNREGVQLDSFG PSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETESLQQYACRHL GERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKREL FSDKESLWGYSISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHE QTPVKASSIHPDLTLGRAEPQAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDP MLRRQRREARAEARADLRARYLAWREQWRKPDLRYGERCREIHQACRLRKSHIRAQYDDP ALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPPSYRQWVEIQAAQGDRAAVS QLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSVRFRDRRTGE FVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

Reference

[1] Furuya N et al (1991) Determination of the nick site at oriT of IncI1 plasmid R64: global similarity of oriT structures of IncI1 and IncP plasmids. J Bacteriol. 173(20):6612-7. [PMID:1917882]

II. Auxiliary DNA-binding protein(s) of the relaxosome

#	ID	Name	GenBank	Length	Note
1	26	NikA_R64	NP_863435	110 aa	an oriT-binding protein (to recognize the 17-bp repeat A sequence)

Information of T4CP

ID	16
Name	TrbC_R64
SecReT4 accesion number	_
GenBank accession number	NP_863437
Family	VirD4/TraG
Length	763
UniProt ID	Q79VV6
PDB ID	_
Pfam
Note	NP_863437 hypothetical protein R64_p082 (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
Protein sequence [Download]	MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITML VFSLQRWRCPLRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQR VRDIGRELWLSMDDLTRHIMFFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTAR TIWYLARRFGREDDVEVINFMNGGKSRSEIILSGEKTRPQSNTWNPFCYSTEAFTAETMQ SMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSLQMLREHMTLEGMAKLYCRGL DDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSETFSTFTEAFG DIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQ TTATNTATLMQNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDS PQISILMESKINVQELIELHPGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISV DAPRLDRLRRLVPRTTQRRIPSPENVSAIIGVLTAKPSRKRRKIRTEPHTIVDTFQQRIA GRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERRIRYITLNRPELPETKEENQI SVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

Reference

[1] Ding Z et al (2003) Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. Trends Microbiol. 11(11):527-35. [PMID:14607070]

Information of plasmid

ID	16
Plasmid name	R64
GenBank accession number	NC_005014.1
Incompatibility group	IncI1
Genome size	120826 bp
Coordinate of oriT [Strand]	66951..67033 [-]
Drug resistance	resistance to streptomycin and tetracycline
Heavy-metal resistance	resistance to arsenic
Virulence factor	_
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Salmonella enterica serovar Typhimurium [90371]

Reference

[1] Kaur S et al (2009) Diversity of arsenate reductase genes (arsC Genes) from arsenic-resistant environmental isolates of E. coli. Curr Microbiol. 59(3):288-94. [PMID:19484295]

[2] Komano T et al (1990) Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. J Bacteriol. 172(5):2230-5. [PMID:1970558]