oriTDB

The information of the oriT region

oriTDB accession number	100220
Name	oriT_pADP-1
Sequence Completeness	core
oriT length	60 nt
oriT sequence	AGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGC
IR (inverted repeat)	[8-26] [29-47] nt (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site	[55-56] nt
Conserved sequence flanking the nic site	CATCCTG\|C
Note	_
	L:8-26;R:29-47;D:55-56

Visualization of oriT structure

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

1

AGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGC

Reference

[1] Pachulec E et al (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]

I. Information of Relaxase

ID	213
Name	TraI_pADP-1
GenBank accession number	NP_862458
Family	MOB_P
Length	746 aa
UniProt ID	Q937B9
PDB ID	_
Pfam	Relaxase [PF03432.13], Evalue: 5.60E-63, Aligned region: 12..252
Note	DNA relaxase
Protein sequence [Download]	MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTN TRAKGDKTYHLIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIA INKIHPTRHTMHEPYYPHRALAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVE SLVGWVKRECLDEIKGAQSWQELHQVMRDNGMELRVRANGLVFEAGDGTMVKASTVARDL SKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTVELYAKYKAEQQNLTTARAQA LERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSEIQAINKQFQQ ERTALYAEHRRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEF KAQMIRAAVDSQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPA ADQHATGAAAVARAGDGRPAAGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRAL SELGVVRIAGGSEVLLPRDVPRHVEQQGTQPDHALRRGISRPGTGVGQTPPGVAAADKYI AEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALALLKRGDEVMVMPIDQATARR LTRIAVGDAVSITAKGSIKTSKGRSR

Reference

[1] Pachulec E et al (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]

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

#	ID	Name	GenBank	Length	Note
1	299	TraH_pADP-1	NP_862459	130 aa	relaxosome stabilization protein
2	300	TraJ_pADP-1	NP_862457	124 aa	conjugal transfer relaxosome component TraJ
3	301	TraK_pADP-1	NP_862456	132 aa	TraK protein; oriT binding protein

Information of T4CP

ID	213
Name	TraG_pADP-1
SecReT4 accesion number	32455808
GenBank accession number	NP_862460
Family	VirD4/TraG
Length	637
UniProt ID	Q937B8
PDB ID	_
Pfam	T4SS-DNA_transf [PF02534.13], Evalue: 2.70E-162, Aligned region: 121..624 TraG-D_C [PF12696.6], Evalue: 5.50E-32, Aligned region: 444..569 TrwB_AAD_bind [PF10412.8], Evalue: 5.10E-22, Aligned region: 187..586
Note	conjugal transfer coupling protein TraG
Protein sequence [Download]	MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHV YAPWSILHWTYKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSA RWAEKKDIQAAGLLPRERNVLEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLT YAPTRSGKGVGLVVPTLLSWGASSVITDLKGELWALTAGWRQKHAKNKVLRFEPASTSGG VCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQKTAFALLVGVILHALYKAKD DGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMMDRPEEEAGSV LSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQ DINQLKSRETGYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRT AAMLGQVSRTYQEVQRPLLTPDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPL YFKDPVFSARAAIPAPKVSDRLRAVAQAETEGEGITI

Reference

[1] Pachulec E et al (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]

Information of plasmid

ID	213
Plasmid name	pADP-1
GenBank accession number	NC_004956.1
Incompatibility group	IncP1
Genome size	108845 bp
Coordinate of oriT [Strand]	11993..12052 [-]
Drug resistance	_
Heavy-metal resistance	mercury resistance
Virulence factor	_
Xenobiotic degradation	degradation of herbicide atrazine
Host bacterium [NCBI Taxonomy ID]	Pseudomonas sp. ADP [47660]

Reference

[1] Martinez B et al (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol. 183(19):5684-97. [PMID:11544232]