oriTDB

The information of the oriT region

oriTDB accession number	100209
Name	oriT_R1
Sequence Completeness	core
oriT length	71 nt
oriT sequence	AGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCAC CAACCTGTTGA
IR (inverted repeat)	[10-17] [20-27] nt (GCAAAAAC..GTTTTTGC)
Location of nic site	[36-37] nt
Conserved sequence flanking the nic site	GTGGGGTGT\|GG
Note	_
	L:10-17;R:20-27;D:36-37

Visualization of oriT structure (The oriT was characterized experimentally)

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

1

AGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCAC

61

CAACCTGTTGA

Reference

[1] Csitkovits VC et al (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]

I. Information of Relaxase

ID	202
Name	TraI_R1
GenBank accession number	AAQ98619
Family	MOB_F
Length	1756 aa
UniProt ID	Q6TDU5
PDB ID	4L0J
Pfam	TrwC [PF08751.10], Evalue: 2.10E-75, Aligned region: 10..284 TraI [PF07057.10], Evalue: 1.70E-56, Aligned region: 1434..1556 AAA_30 [PF13604.5], Evalue: 1.80E-33, Aligned region: 968..1159 AAA_19 [PF13245.5], Evalue: 1.10E-08, Aligned region: 973..1108
Note	TraI; relaxase; oriT nicking and unwinding
Protein sequence [Download]	MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRL PDGADLSRMQDGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEAL ASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKV GKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQA IREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQTLKETGFDIRAYRDAADQRTE IRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPENGVIERARAG IDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDE RLSGELITGRRQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQR TGTGSALMAMKDAGVNTYRWQGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQ VSGVREQAILTQAIRSELKTQGVLGHPEVTMTALSPVWLDSRSRYLRDMYRPGMVMEQWN PETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRV TGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKLENGWVETPGH SVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTG FTELGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMER VPGELMETLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRV VGLGPTHRAVGEMRSAGVDAQTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNTEM ARAYALIAAGGGRAVASGDTDQLQAIAPGQSFRLQQTRSAADVVIMKEIVRQTPELREAV YSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEAQQKAMLKGEA FPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLIS PREAVAEGVTLYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQT RVIRPGQERAEQHIDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMK QHVQVYTDNRQGWTDAINNAVQKGTAHDVLEPKPDREVMNAQRLFSTARELRDVAAGRAV LRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAGIWLNPLTTDDGNGLRGFSGE GRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGEGRPWNPGAIT GGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQME RDMVRDLQKEKTLGGD

Reference

[1] Csitkovits VC et al (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]

[2] Schwab M et al (1991) The TraM protein of plasmid R1 is a DNA-binding protein. Mol Microbiol. 5(2):439-46. [PMID:2041477]

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

#	ID	Name	GenBank	Length	Note
1	283	TraM_R1	P07294	127 aa	TraM mediates signalling between transferosome and relaxosome; cd14804
2	284	TraY_R1	CAA31972	75 aa	conjugal transfer protein TraY

Information of T4CP

ID	202
Name	TraD_R1
SecReT4 accesion number	_
GenBank accession number	AAT85682
Family	TrwB/TraD
Length	735
UniProt ID	Q6B3Y6
PDB ID	_
Pfam	TrwB_AAD_bind [PF10412.8], Evalue: 2.20E-119, Aligned region: 171..561 TraD_N [PF12615.7], Evalue: 1.10E-29, Aligned region: 31..128 TraG-D_C [PF12696.6], Evalue: 4.60E-18, Aligned region: 419..542 T4SS-DNA_transf [PF02534.13], Evalue: 2.20E-07, Aligned region: 198..500
Note	Type IV Secretion System Coupling Protein
Protein sequence [Download]	MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIY WWCTTLEGMRDLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVAL VICLITFFVVSWILGRQGKQQSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPII RDSEIQNFCLHGTVSTGKSEVIRRLANYARKRGDMVVIYDRSCEFVKSYYDPSIDKILNP LDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQGSGRTIFAEAAYLMRNDPNRS YSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKAIRYLQGIEHN GEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRA FFRSPSHQIAEFAAGEIGEKEHLKASLQYSYGADPVRDGISTGKEMERQTLVSYSDIQSL PDLTCYVTLPGPYPAVKLSLKYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMA SLFEPDVPEVVSGEDVTQAEQPQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNIP AGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVNIN VHRERGEDVEPGDDF

Reference

[1] Csitkovits VC et al (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]

Information of plasmid

ID	202
Plasmid name	R1
GenBank accession number	X00783.1
Genome size	_
Coordinate of oriT [Strand]	299..369 [+]
Drug resistance	resistance to chloramphenicol, kanamycin, ampicillin, streptomycin and spectinomycinand sulphonamides
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Escherichia coli [562]

Reference

[1] Dionisio F et al (2005) The evolution of a conjugative plasmid and its ability to increase bacterial fitness. Biol Lett. 1(2):250-2. [PMID:17148179]