oriTDB

The information of the oriT region

oriTDB accession number	100045
Name	oriT_pJP4
Sequence Completeness	intact
oriT length	92 nt
oriT sequence	GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTG CCCGCCTTACGGCGTTAATAACACCAAGGAAA
IR (inverted repeat)	[13-31] [34-52] nt (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site	[60-61] nt
Conserved sequence flanking the nic site	CATCCTG\|C
Note	_
	L:13-31;R:34-52;D:60-61

Visualization of oriT structure

Reference
N/A

I. Information of Relaxase

ID	43
Name	TraI_pJP4
GenBank accession number	AAR31100
Family	MOB_P
Length	746 aa
UniProt ID	Q6UP38
PDB ID	_
Pfam	Relaxase [PF03432.13], Evalue: 9.90E-64, Aligned region: 12..252
Note	conjugal transfer relaxase TraI; Provisional
Protein sequence [Download]	MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTN TRAKGDKTYHLIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIA INKIHPTRHTMHEPYYPHRALAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVE SLVGWIKRECLDEIKGAQSWQELHQVMRDNGMELRVRANGLVFEAGDGTMVKASTVARDL SKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTVELYAKYKAEQQSLTTARAQA LERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSELQAINKQFQQ ERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEF KAQMIRAAVDSQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPA ADQHATGAAAVARAGDGRPAAGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRAL SELGVVRIAGGSEVLLPRDVPRHVEQQGTQPDHALRRGISRPGTGVGQTPPGVAAADKYI AEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALALLKRGDEVMVMPIDQATARR LTRIAVGDAVSITAKGSIKTSKGRSR

Reference

[1] Trefault N et al (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol. 6(7):655-68. [PMID:15186344]

[2] Shintani M et al (2010) The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms. Microbes Environ. 25(4):253-65. [PMID:21576880]

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

#	ID	Name	GenBank	Length	Note
1	71	TraH_pJP4	AAR31099	130 aa	_
2	72	TraJ_pJP4	AAR31101	105 aa	conjugal transfer relaxosome component TraJ
3	73	TraK_pJP4	AAR31102	132 aa	oriT binding protein

Information of T4CP

ID	43
Name	TraG_pJP4
SecReT4 accesion number	49176943
GenBank accession number	AAR31098
Family	VirD4/TraG
Length	637
UniProt ID	Q6UP39
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] Trefault N et al (2004) . Environ Microbiol. 6(7):655-68. [PMID:15186344]

Information of plasmid

ID	43
Plasmid name	pJP4
GenBank accession number	AY365053.1
Incompatibility group	IncP1
Genome size	87688 bp
Coordinate of oriT [Strand]	85790..85881 [+]
Drug resistance	_
Heavy-metal resistance	mercury resistance
Virulence factor	_
Xenobiotic degradation	degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) and 3-chlorobenzoic acid (3-CB)
Host bacterium [NCBI Taxonomy ID]	Ralstonia eutropha JMP134 [264198]

Reference

[1] Trefault N et al (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol. 6(7):655-68. [PMID:15186344]