Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100002
Name   oriT_RK2 experimental
Organism   Klebsiella aerogenes K8841
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   BN000925 (51129..51240 [+], 112 nt)
oriT length   112 nt
IRs (inverted repeats)      60..78, 81..99  (GTGAAGAAGGAACACCCGC..GCGGGTGGGCCTACTTCAC)
Location of nic site      107..108
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   _

  oriT sequence  


Download         Length: 112 nt

>oriT_RK2
CCGGCCAGCCTCGCAGAGCAGGATTCCCGTTGAGCACCGCCAGGTGCGAATAAGGGACAGTGAAGAAGGAACACCCGCTCGCGGGTGGGCCTACTTCACCTATCCTGCCCGG

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] 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]
[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] 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]
[4] 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]
[5] 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]


Relaxosome

This oriT is a component of a relaxosome.

Relaxosome name   RelaxosomeRK2 in_silico
oriT   oriT_RK2 experimental
Relaxase   TraI_RK2 experimental (MOBP)
Auxiliary protein   TraH_RK2 experimental, TraJ_RK2 experimental, TraK_RK2 experimental

  Reference


[1] 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]
[2] 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]
[3] 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]
[4] 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]
[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]
[6] 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]
[7] 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]


Relaxase

ID   2 GenBank   CAJ85725
Name   TraI_RK2 experimental UniProt ID   A6H977
Length   732 a.a. PDB ID   
Note   TraI DNA relaxase

  Relaxase protein sequence


Download         Length: 732 a.a.        Molecular weight: 81563.20 Da        Isoelectric Point: 10.5791

>CAJ85725.1 TPA: TraI DNA relaxase (plasmid) [Birmingham IncP-alpha plasmid]
MIAKHVPMRSIKKSDFAELVKYITDEQGKTERLGHVRVTNCEANTLPAVMAEVMATQHGNTRSEADKTYH
LLVSFRAGEKPDAETLRAIEDRICAGLGFAEHQRVSAVHHDTDNLHIHIAINKIHPTRNTIHEPYRAYRA
LADLCATLERDYGLERDNHETRQRVSENRANDMERHAGVESLVGWIKRECLPELQAAQSWEDLHRVLREN
GLKLRERGNGFIFEAGDGTTVKASTVSRDLSKPKLEARFGAFTPAEGGEAPRRREYRAKPLKTRIDTTEL
YARYQSERQEMGAVRKGELDTLRRRRDRLIEAAMRSNRLRRAAIKLLGEGRIAKRLMYAQAHKALRADLD
KINREYRQGRQAVQERTQRRAWADWLKAEAMKGDDKALAALRAREGRSDLKGNTIQGSGEAKPGHAAVTD
NITKKGTIIYRVGSSAVRDDGDRLQVSREATTDGLDAALRLAMERFGDRITVNGTAEFKERIAQAAAAGR
LAITFDDAALERRRQELLTKEQAHEQPERNDGRRDRGGDGGIRPAAARTTLNATGGDGDRRDARAVSAGG
TVALRKPNVGRIGRKPPPQSQNRLRALSQLGVVRIAGGAEMLLPRDVPGHVEQQGAEPAHALRRGVSGPG
RGLKPEQIAAAEKYVAEREQKRLNGFDIPKHARYTDYVGALSYAGTRNVEDQALALLRKENDEILVLPVD
KATVQRMKRLAIGDPVTVTPRGSLKTTRGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(417-507)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)


  Protein structure


Source ID Structure
AlphaFold DB A6H977

  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]


Auxiliary protein

ID   4 GenBank   CAJ85726
Name   TraH_RK2 experimental UniProt ID   A6H978
Length   119 a.a. PDB ID   _
Note   relaxosome stabilisation

  Auxiliary protein sequence


Download         Length: 119 a.a.        Molecular weight: 12869.28 Da        Isoelectric Point: 4.1047

>CAJ85726.1 TPA: TraH protein (plasmid) [Birmingham IncP-alpha plasmid]
MSNPNEMTDEEIAAAMEAFDLPQPEPPSTPQAATATDGTLAPSAPAEPSHSASPTLDALDESRRPKAKTV
CERCPNSVWFASPAELKCYCRVMFLVTWSSKEPNQLTHCDGEFLGQEEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A6H978

  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   5 GenBank   CAJ85728
Name   TraJ_RK2 experimental UniProt ID   A6H980
Length   123 a.a. PDB ID   _
Note   TraJ oriT recognising protein

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13463.65 Da        Isoelectric Point: 7.9867

>CAJ85728.1 TPA: TraJ oriT recognising protein (plasmid) [Birmingham IncP-alpha plasmid]
MADETKPTRKGSPPIKVYCLPDERRAIEEKAAAAGMSLSAYLLAVGQGYKITGVVDYEHVRELARINGDL
GRLGGLLKLWLTDDPRTARFGDATILALLAKIEEKQDELGKVMMGVVRPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A6H980

  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   6 GenBank   CAJ85729
Name   TraK_RK2 experimental UniProt ID   A6H981
Length   134 a.a. PDB ID   _
Note   TraK oriT binding protein

  Auxiliary protein sequence


Download         Length: 134 a.a.        Molecular weight: 14716.82 Da        Isoelectric Point: 10.5082

>CAJ85729.1 TPA: TraK oriT binding protein (plasmid) [Birmingham IncP-alpha plasmid]
MPKSYTDELAEWVESRAAKKRRRDEAAVAFLAVRADVEAALASGYALVTIWEHMRETGKVKFSYETFRSH
ARRHIKAKPADVPAPQAKAAEPAPAPKTPEPRRPKQGGKAEKPAPAAAPTGFTFNPTPDKKDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB A6H981

  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]


T4CP

ID   2 GenBank   CAJ85724
Name   TraG_RK2 experimental UniProt ID   A6H976
Length   635 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 635 a.a.        Molecular weight: 69857.88 Da        Isoelectric Point: 9.1256

>CAJ85724.1 TPA: TraG protein (plasmid) [Birmingham IncP-alpha plasmid]
MKNRNNAVGPQIRAKKPKASKTVPILAGLSLGAGLQTATQYFAHSFQYQAGLGWNINHVYTPWSILQWAG
KWYGQYPDDFMRAASMGMVVSTVGLLGTAVTQMVKANTGKANDYLHGSARWADKKDIQAAGLLPRPRTVV
ELVSGKHPPTSSGVYVGGWQDKDGKFHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWAHSAVITDLKG
ELWALTAGWRKKHARNKVVRFEPASAQGSACWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLESHWQK
TSQALLVGVILHALYKAKNEGTPATLPSVDGMLADPNRDVGELWMEMTTYGHVDGQNHPAVGSAARDMMD
RPEEESGSVLSTAKSYLALYRDPVVARNVSKSDFRIKQLMHHDDPVSLFIVTQPNDKARLRPLVRVMVNM
IVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSRETG
YGHDESITSNCHVQNAYPPNRVETAEHLSKLTGTTTIVKEQITTSGRRTSALLGNVSRTFQEVQRPLLTP
DECLRMPGPKKSADGSIEEAGDMVVYVAGYPAIYGKQPLYFKDPIFQARAAVPAPKVSDKLIQTATVEEG
EGITI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(120-621)

  Protein structure


Source ID Structure
AlphaFold DB A6H976

  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]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 18825..29252

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_17 14050..15249 + 1200 CAJ85682 tetracycline exporter protein -
Locus_18 15881..16546 - 666 CAJ85683 hypothetical protein -
Locus_19 16521..17669 - 1149 CAJ85684 TrfA replication protein -
Locus_20 16521..17378 - 858 CAJ85685 TrfA replication protein -
Locus_21 17718..18068 - 351 CAJ85686 single stranded DNA binding protein -
Locus_22 18189..18554 + 366 CAJ85687 TrbA repressor protein -
Locus_23 18825..19784 + 960 CAJ85688 TrbB protein virB11
Locus_24 19797..20234 + 438 CAJ85689 TrbC protein virB2
Locus_25 20237..20548 + 312 CAJ85690 TrbD protein virB3
Locus_26 20545..23103 + 2559 CAJ85691 TrbE protein virb4
Locus_27 23100..23858 + 759 CAJ85692 TrbF protein virB8
Locus_28 23870..24763 + 894 CAJ85693 TrbG protein virB9
Locus_29 24767..25249 + 483 CAJ85694 TrbH protein -
Locus_30 25254..26645 + 1392 CAJ85695 TrbI protein virB10
Locus_31 26662..27438 + 777 CAJ85696 TrbJ protein virB5
Locus_32 27450..27659 + 210 CAJ85697 TrbK entry exclusion protein -
Locus_33 27666..29252 + 1587 CAJ85698 TrbL protein virB6
Locus_34 29276..29875 + 600 CAJ85699 TrbM protein -
Locus_35 29891..30595 + 705 CAJ85700 TrbN protein -
Locus_36 30626..30889 + 264 CAJ85701 TrbO protein -
Locus_37 30926..31660 + 735 CAJ85702 TrbP protein -
Locus_38 31677..32096 + 420 CAJ85703 hypothetical protein -
Locus_39 32111..32806 + 696 CAJ85704 FiwA -
Locus_40 32842..33504 + 663 CAJ85705 Upf32.8 protein -
Locus_41 33528..34187 - 660 CAJ85706 ParA -
Locus_42 33528..34151 - 624 CAJ85707 ParA -

Host bacterium

ID   2 GenBank   BN000925
Plasmid name   RK2 Incompatibility group   IncP1
Plasmid size   60096 bp Coordinate of oriT [Strand]   51129..51240 [+]
Host baterium   Klebsiella aerogenes K8841

Cargo genes

Drug resistance gene   resistance to kanamycin, ampicillin and tetracycline
Virulence gene   _
Metal resistance gene   klaC/telB, klaB/telA/kilB
Degradation gene   degradation of biphenyl and 4-chlorobiphenyl
Symbiosis gene   -
Anti-CRISPR   AcrIIA9