 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 | _ |
Visualization of oriT structure (The oriT was characterized experimentally) 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] |
| ID | 2 |
| Name | TraI_RK2 |
| GenBank accession number | CAJ85725 |
| Family | MOBP |
| 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] |
| # | 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 |
| 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] |
| 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] |