oriTDB

The information of the oriT region

oriTDB accession number	100052
Name	oriT_pIFM3804
Sequence Completeness	intact
oriT length	110 nt
oriT sequence	CCTGAAAAACGGGACAGGATGTGCAATTGTAATACCGTCACACGCGACGCTATTACAATT GCCATCTGGTCAGGGCTTCGCCCCGACACCCCGTAAGGAGCCTGAAGTGA
IR (inverted repeat)	8-bp: [24-31] [35-42] nt (GTCGGGGC..GCCCTGAC) 17-bp: [49-65] [72-88] nt (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC)
Location of nic site	[96-97] nt
Conserved sequence flanking the nic site	CATCCTG\|T
Note	similar to oriT of plasmid R64
	L:24-31;R:35-42;L:49-65;R:72-88;D:96-97

Visualization of oriT structure

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

1

CCTGAAAAACGGGACAGGATGTGCAATTGTAATACCGTCACACGCGACGCTATTACAATT

61

GCCATCTGGTCAGGGCTTCGCCCCGACACCCCGTAAGGAGCCTGAAGTGA

Reference

[1] Freire Martín I et al (2014) Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:i:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm. J Antimicrob Chemother. 69(8):2098-101. [PMID:24729584]

I. Information of Relaxase

ID	50
Name	NikB_pIFM3804
GenBank accession number	YP_008998777
Family	MOB_P
Length	899 aa
UniProt ID	E9LLN1
PDB ID	_
Pfam	Relaxase [PF03432.13], Evalue: 9.20E-64, Aligned region: 47..315
Note	Relaxase/Mobilisation nuclease
Protein sequence [Download]	MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRL RNESFVALVDVMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHY ILSWQSHESPRPEQIYDSVRHTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYL NRLSWSQEKLSRACRELELKHGFAPDNGCWVHAPGNRIVRKTAVERDRQNAWTRGKKQTF REYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGKFLVMDGWDRNREGVQLDSFG PSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETESLQQYACRHL GERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKREL FSDKESLWGYSISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHE QTPVKASSIHPDLTLGRAEPQAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDP MLRRQRREARAEARADLRARYLAWREQWRKPDLRYGERCREIHQACRLRKSHIRAQYDDP ALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPPSYRQWVEIQAAQGDRAAVS QLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSVRFRDRRTGE FVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

Reference

[1] Freire Martín I et al (2014) Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:i:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm. J Antimicrob Chemother. 69(8):2098-101. [PMID:24729584]

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

#	ID	Name	GenBank	Length	Note
1	81	NikA_pIFM3804	YP_008998776	110 aa	_

Information of T4CP

ID	50
Name	TrbC_pIFM3804
SecReT4 accesion number	_
GenBank accession number	YP_008998778
Family	VirD4/TraG
Length	763
UniProt ID	E9LLN2
PDB ID	_
Pfam
Note	nucleotide-binding protein
Protein sequence [Download]	MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITML VFSLQRWRCPLRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQR VRDIGRELWLSMDDLTRHIMFFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTAR TIWYLARRFGREDDVEVINFMNGGKSRSEIILSGEKTRPQSNTWNPFCYSTEAFTAETMQ SMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSLQMLREHMTLEGMAKLYCRGL DDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSETFSTFTEAFG DIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQ TTATNTATLMQNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDS PQISILMESKINVQELIELHPGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISV DAPRLDRLRRLVPRTTQRRIPSPENVSAIIGVLTAKPSRKRRKIRTEPHTIVDTFQQRIA GRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERRIRYITLNRPELPETKEENQI SVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

Reference
N/A

Information of plasmid

ID	50
Plasmid name	pIFM3804
GenBank accession number	NC_023329.1
Incompatibility group	IncI1
Genome size	104399 bp
Coordinate of oriT [Strand]	47883..47992 [-]
Drug resistance	bla_CTX-M-1 gene
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Escherichia coli B3804 [562]

Reference

[1] Freire Martín I et al (2014) Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:i:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm. J Antimicrob Chemother. 69(8):2098-101. [PMID:24729584]