oriTDB
The information of the oriT region
oriTDB accession number 100207
Name oriT_pAD1  experimental
Sequence Completeness incomplete
oriT length 13 nt
oriT sequence GAAAATGGTCAGG
IR (inverted repeat)_
Location of nic site [6-7] nt
Conserved sequence flanking the
  nic site 		_
Note CloDF13 familiy
D:6-7
Visualization of oriT structure (The oriT was characterized experimentally)
Reference
[1] Francia MV et al (2001) Completion of the nucleotide sequence of the Enterococcus faecalis conjugative virulence plasmid pAD1 and identification of a second transfer origin. Plasmid. 46(2):117-27. [PMID:11591137]
[2] Francia MV et al (2004) A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev. 28(1):79-100. [PMID:14975531]
[3] Francia MV et al (2002) Transfer origins in the conjugative Enterococcus faecalis plasmids pAD1 and pAM373: identification of the pAD1 nic site, a specific relaxase and a possible TraG-like protein. Mol Microbiol. 45(2):375-95. [PMID:12123451]
I. Information of Relaxase
ID 200
Name Orf57_pAD1 insolico
GenBank accession number AAL59457
Family MOBC
Length 216 aa
UniProt ID Q8VT37
PDB ID _
Pfam Replic_Relax [PF13814.5], Evalue: 4.50E-08, Aligned region: 1..160
Note Replication-relaxation; pfam13814
Protein sequence [Download] MAKKSSVYGNLKKLKEKNLVECSQIGSTKFYYLTKEGHNYIGGYYTLPKVPEYNLQHHLQ
INDYLIKMLELCNNHPHLKAVVSERRKVYEVKDEKKNQKGVKYFVPDFIFMFLDSIGREV
EWQFEIELTLKTKRRYSQGVFPKYIKHLKNYEDARLIYVTPSSIIKEELDMFKEYFIDKE
GDEYKEVFDRLHVFSAEEFESELKRLLEKDKFINWE
Reference
[1] Francia MV et al (2001) Completion of the nucleotide sequence of the Enterococcus faecalis conjugative virulence plasmid pAD1 and identification of a second transfer origin. Plasmid. 46(2):117-27. [PMID:11591137]
[2] Francia MV et al (2004) A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev. 28(1):79-100. [PMID:14975531]
[3] Francia MV et al (2002) Transfer origins in the conjugative Enterococcus faecalis plasmids pAD1 and pAM373: identification of the pAD1 nic site, a specific relaxase and a possible TraG-like protein. Mol Microbiol. 45(2):375-95. [PMID:12123451]


II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 281 _ insolico
Information of T4CP
ID 200
Name Orf53_pAD1 insolico
SecReT4 accesion number _
GenBank accession number AAL59453
Family VirD4/TraG
Length 747
UniProt ID Q8VT41
PDB ID _
Pfam TraG-D_C [PF12696.6], Evalue: 2.50E-10, Aligned region: 586..712
TrwB_AAD_bind [PF10412.8], Evalue: 3.00E-05, Aligned region: 480..725
DUF87 [PF01935.16], Evalue: 2.90E-09, Aligned region: 208..460
Note conjugative coupling factor TraD, SXT/TOL subfamily; TIGR03743
Protein sequence [Download] MFNNGLLQPKKPPIGQEQQKMTRYHQLRLVFGLVGVLLYPFAILGSIPLLIGLAVDKRDK
AANVFDMDYESFLKRNSIVFLSFSAVLFVINAFAFILWIPRGYLSAYLLFPLNLLHTALR
FNWETIVALLIGSSGMGAIFLAFSSFVAKRKVISKEDERKKITESKAYKDREKNKFKESQ
RFTDEQEEAYEEAVETVDIDKYKELSNQLLLGTSEFGLPYIINFSEFNQHVLVPATTGSG
KTTLLQLLVQHAVKFNFPVILIDGKGARDTLESMREIAKFYDKEVHAFTDDGDMRYNPVE
HGNDISIRDKLVSLAETESVFYSGAAKALLQVTIQLLDEFKGAKVTLSGDTRTTETVERS
LPFVQRFLLPRNVLHLFADAILQNNPKLFEIEVEKKIQQPKKKSAKERSEILPDSDLDKE
EKEEDSQIRNSKFRNISQLGIAQKETETVVLNPETLDLDSYYLLLKRNLRYLPTDKETGE
NIKQKLFERLFVRYEHKDSPFYLYATSEALQTNINMLLDSELGKLFDTKNAKNVLDVQEI
VNQRKLVYVSFNGLIYKEYIRTLAQMLVGDVNYFASEMYRKNVKREVLVIFDEPASYLNE
TFIDMVNKGRGAGVYGIFTPQTMADIAKLGDKLMEQLVGNVNTLFIGKTNEKGEAEYWSE
TMGTYQDIDVTSVTEQEDGYSDVGKSDWSGDRGTKRNVDRFKISPNKIKELRTGEFIIYR
TAENVNLPPQKVYVRNALEWLQKSNSK

Reference
[1] Francia MV et al (2004) Transfer origins in the conjugative Enterococcus faecalis plasmids pAD1 and pAM373: identification of the pAD1 nic site, a specific relaxase and a possible TraG-like protein. FEMS Microbiol Rev. 28(1):79-100. [PMID:14975531]
[2] Francia MV et al (2002) Transfer origins in the conjugative Enterococcus faecalis plasmids pAD1 and pAM373: identification of the pAD1 nic site, a specific relaxase and a possible TraG-like protein. Mol Microbiol. 45(2):375-95. [PMID:12123451]
Information of plasmid
ID 200
Plasmid name pAD1
GenBank accession number AH011360.2
Genome size 59.3 kb
Coordinate of oriT  [Strand] _
Drug resistance _
Heavy-metal resistance _
Virulence factor experimental The plasmid encodes a lantibiotic cytolysin which is able to lyse bacteria as well as red blood cells and contributes to virulence in animal models.
Xenobiotic degradation _
Host bacterium [NCBI Taxonomy ID] Enterococcus faecalis OG1X [1351]
Reference
[1] Francia MV et al (2001) Completion of the nucleotide sequence of the Enterococcus faecalis conjugative virulence plasmid pAD1 and identification of a second transfer origin. Plasmid. 46(2):117-27. [PMID:11591137]

Microbial Bioinformatics Group in MML, SJTU