oriTDB

The information of the oriT region

oriTDB accession number	100082
Name	oriT_ColIb-P9
Sequence Completeness	intact
oriT length	110 nt
oriT sequence	TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATA GCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
IR (inverted repeat)	IR1: [24-31] [35-42] nt (GTCGGGGC..GCCCTGAC) IR2: [49-65] [72-88] nt (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC)
Location of nic site	[96-97] nt
Conserved sequence flanking the nic site	CATCCTG\|T
Note	possible oriT region deduced from sequence homology with 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

TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATA

61

GCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG

Reference

[1] Wilkins BM et al (2000) DNA-independent transport of plasmid primase protein between bacteria by the I1 conjugation system. Mol Microbiol . 38(3):650-7. [PMID:11069687]

I. Information of Relaxase

ID	77
Name	NikB_ColIb-P9
GenBank accession number	NP_052501
Family	MOB_P
Length	899 aa
UniProt ID	Q9R2J7
PDB ID	_
Pfam	Relaxase [PF03432.13], Evalue: 1.30E-64, Aligned region: 47..315
Note	relaxase
Protein sequence [Download]	MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRL RNESFVALVDVMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHY ILSWQSHESPRPEQIYDSVRHTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYL NRLSWSQEKLSRACRELELKHGFAPDNGCWVHAPGNRIVRKTAVERDRQNAWTRGKKQTF REYIAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGKFLVMDGWDRNREGVQLDSFG PSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETESLQQYACRHL GERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKREL FSDKESLWGYSISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHE QTPVKASSIHPDLTLGRAEPQAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDP MLRRQRREARAEARADLRARYLAWREQWRKPDLRYGERCREIHQACRLRKSHIRAQYDDP ALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPPSYRQWVEIQAAQGDRAAVS QLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSVRFRDRRTGE FVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

Reference

[1] Wilkins BM et al (2000) DNA-independent transport of plasmid primase protein between bacteria by the I1 conjugation system. Mol Microbiol . 38(3):650-7. [PMID:11069687]

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

#	ID	Name	GenBank	Length	Note
1	111	NikA_ColIb-P9	NP_052500	110 aa	relaxosome component

Information of T4CP

ID	77
Name	TrbC_ColIb-P9
SecReT4 accesion number	_
GenBank accession number	NP_052502
Family	VirD4/TraG
Length	763
UniProt ID	Q7DJX5
PDB ID	_
Pfam
Note	Type IV Secretion System Coupling Protein
Protein sequence [Download]	MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITML VFSLQRWRCPLRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQR VRDIGRELWLSMDDLTRHIMFFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTAR TIWYLARRFGREDDVEVINFMNGGKSRSEIILSGEKTRPQSNTWNPFCYSTEAFTAETMQ SMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSLQMLREHMTLEGMAKLYCRGL DDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSETFSTFTEAFG DIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQ TTATNTATLMQNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDS PQISILMESKINVQELIELHPGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISV DAPRLDRLRRLVPRTTQRRIPSPENVSAIIGVLTAKPSRKRRKIRTEPHTIVDTFQQRIA GRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERRIRYITLNRPELPETKEENQI SVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

Reference

[1] Ding Z et al (2003) DNA-independent transport of plasmid primase protein between bacteria by the I1 conjugation system. Trends Microbiol. 11(11):527-35. [PMID:14607070]

Information of plasmid

ID	77
Plasmid name	ColIb-P9
GenBank accession number	NC_002122.1
Incompatibility group	IncI1
Genome size	93399 bp
Coordinate of oriT [Strand]	39622..39731 [-]
Drug resistance	_
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Shigella sonnei [624]

Reference
N/A