oriTDB

The information of the oriT region

oriTDB accession number	100002
Name	oriT_RK2
Sequence Completeness	intact
oriT length	112 nt
oriT sequence	CCGGCCAGCCTCGCAGAGCAGGATTCCCGTTGAGCACCGCCAGGTGCGAATAAGGGACAG TGAAGAAGGAACACCCGCTCGCGGGTGGGCCTACTTCACCTATCCTGCCCGG
IR (inverted repeat)	[60-78] [81-99] nt (GTGAAGAAGGAACACCCGC..GCGGGTGGGCCTACTTCAC)
Location of nic site	[107-108] nt
Conserved sequence flanking the nic site	TATCCTG\|C
Note	_
	L:60-78;R:81-99;D:107-108

Visualization of oriT structure (The oriT was characterized experimentally)

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

1

CCGGCCAGCCTCGCAGAGCAGGATTCCCGTTGAGCACCGCCAGGTGCGAATAAGGGACAG

61

TGAAGAAGGAACACCCGCTCGCGGGTGGGCCTACTTCACCTATCCTGCCCGG

Reference

[1] Guiney DG et al (1983) Location and nucleotide sequence of the transfer origin of the broad host range plasmid RK2. Proc Natl Acad Sci U S A. 80(12):3595-8. [PMID:6304722]

[2] Cook DM et al (1992) The oriT region of the Agrobacterium tumefaciens Ti plasmid pTiC58 shares DNA sequence identity with the transfer origins of RSF1010 and RK2/RP4 and with T-region borders. J Bacteriol. 174(19):6238-46. [PMID:1400174]

[3] Schmidhauser TJ et al (1985) Regions of broad-host-range plasmid RK2 involved in replication and stable maintenance in nine species of gram-negative bacteria. J Bacteriol. 164(1):446-55. [PMID:4044529]

[4] Dam B et al (2009) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Appl Environ Microbiol. 75(13):4362-73. [PMID:19411426]

[5] Waters VL et al (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]

I. Information of Relaxase

ID	2
Name	TraI_RK2
GenBank accession number	CAJ85725
Family	MOB_P
Length	732 aa
UniProt ID	A6H977
PDB ID	_
Pfam	Relaxase [PF03432.13], Evalue: 7.90E-67, Aligned region: 12..252
Note	TraI DNA relaxase
Protein sequence [Download]	MIAKHVPMRSIKKSDFAELVKYITDEQGKTERLGHVRVTNCEANTLPAVMAEVMATQHGN TRSEADKTYHLLVSFRAGEKPDAETLRAIEDRICAGLGFAEHQRVSAVHHDTDNLHIHIA INKIHPTRNTIHEPYRAYRALADLCATLERDYGLERDNHETRQRVSENRANDMERHAGVE SLVGWIKRECLPELQAAQSWEDLHRVLRENGLKLRERGNGFIFEAGDGTTVKASTVSRDL SKPKLEARFGAFTPAEGGEAPRRREYRAKPLKTRIDTTELYARYQSERQEMGAVRKGELD TLRRRRDRLIEAAMRSNRLRRAAIKLLGEGRIAKRLMYAQAHKALRADLDKINREYRQGR QAVQERTQRRAWADWLKAEAMKGDDKALAALRAREGRSDLKGNTIQGSGEAKPGHAAVTD NITKKGTIIYRVGSSAVRDDGDRLQVSREATTDGLDAALRLAMERFGDRITVNGTAEFKE RIAQAAAAGRLAITFDDAALERRRQELLTKEQAHEQPERNDGRRDRGGDGGIRPAAARTT LNATGGDGDRRDARAVSAGGTVALRKPNVGRIGRKPPPQSQNRLRALSQLGVVRIAGGAE MLLPRDVPGHVEQQGAEPAHALRRGVSGPGRGLKPEQIAAAEKYVAEREQKRLNGFDIPK HARYTDYVGALSYAGTRNVEDQALALLRKENDEILVLPVDKATVQRMKRLAIGDPVTVTP RGSLKTTRGRSR

Reference

[1] Zatyka M et al (1994) Location and nucleotide sequence of the transfer origin of the broad host range plasmid RK2. Microbiology. 140 ( Pt 11):2981-90. [PMID:7812437]

[2] Waters VL et al (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]

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

#	ID	Name	GenBank	Length	Note
1	4	TraH_RK2	CAJ85726	119 aa	relaxosome stabilisation
2	5	TraJ_RK2	CAJ85728	123 aa	TraJ oriT recognising protein
3	6	TraK_RK2	CAJ85729	134 aa	TraK oriT binding protein

Information of T4CP

ID	2
Name	TraG_RK2
SecReT4 accesion number	_
GenBank accession number	CAJ85724
Family	VirD4/TraG
Length	635
UniProt ID	A6H976
PDB ID	_
Pfam	T4SS-DNA_transf [PF02534.13], Evalue: 2.20E-174, Aligned region: 120..624 TraG-D_C [PF12696.6], Evalue: 2.70E-31, Aligned region: 443..568 TrwB_AAD_bind [PF10412.8], Evalue: 1.80E-23, Aligned region: 175..575
Note	Type IV Secretion System Coupling Protein
Protein sequence [Download]	MKNRNNAVGPQIRAKKPKASKTVPILAGLSLGAGLQTATQYFAHSFQYQAGLGWNINHVY TPWSILQWAGKWYGQYPDDFMRAASMGMVVSTVGLLGTAVTQMVKANTGKANDYLHGSAR WADKKDIQAAGLLPRPRTVVELVSGKHPPTSSGVYVGGWQDKDGKFHYLRHNGPEHVLTY APTRSGKGVGLVVPTLLSWAHSAVITDLKGELWALTAGWRKKHARNKVVRFEPASAQGSA CWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLESHWQKTSQALLVGVILHALYKAKNE GTPATLPSVDGMLADPNRDVGELWMEMTTYGHVDGQNHPAVGSAARDMMDRPEEESGSVL STAKSYLALYRDPVVARNVSKSDFRIKQLMHHDDPVSLFIVTQPNDKARLRPLVRVMVNM IVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQD INQLKSRETGYGHDESITSNCHVQNAYPPNRVETAEHLSKLTGTTTIVKEQITTSGRRTS ALLGNVSRTFQEVQRPLLTPDECLRMPGPKKSADGSIEEAGDMVVYVAGYPAIYGKQPLY FKDPIFQARAAVPAPKVSDKLIQTATVEEGEGITI

Reference

[1] Zatyka M et al (1994) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Microbiology. 140 ( Pt 11):2981-90. [PMID:7812437]

[2] Waters VL et al (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]

Information of plasmid

ID	2
Plasmid name	RK2
GenBank accession number	BN000925.1
Incompatibility group	IncP1
Genome size	60096 bp
Coordinate of oriT [Strand]	51129..51240 [+]
Drug resistance	resistance to kanamycin, ampicillin and tetracycline
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	degradation of biphenyl and 4-chlorobiphenyl
Host bacterium [NCBI Taxonomy ID]	Klebsiella aerogenes K8841 [548]

Reference

[1] Zatyka M et al (1994) Location and nucleotide sequence of the transfer origin of the broad host range plasmid RK2. Microbiology. 140 ( Pt 11):2981-90. [PMID:7812437]

[2] Ditta G et al (1980) Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc Natl Acad Sci U S A. 77(12):7347-51. [PMID:7012838]

[3] Toussaint A et al (2003) The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol. 69(8):4837-45. [PMID:12902278]