Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100180
Name   oriT_pTiC58 experimental
Organism   Agrobacterium fabrum str. C58
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_004972 (_)
oriT length   61 nt
IRs (inverted repeats)      19..27, 32..40  (ATACGTCGC..GCGACGCCT)
Location of nic site      11..12
Conserved sequence flanking the
  nic site    		  _
Note   Ti plasmid

  oriT sequence  


Download         Length: 61 nt

>oriT_pTiC58
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCTTGCGTAGGGGGCCAAACAGGG

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Wetzel ME et al. (2015) The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups. Genome Biol Evol. 7(12):3337-57. [PMID:26590210]
[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]


Relaxase

ID   173 GenBank   AAC17212
Name   TraA_pTiC58 insolico UniProt ID   Q44349
Length   1101 a.a. PDB ID   
Note   similar to conjugal endonucleases MobA of RSF1010 and MobL of pTF1; contains domains similar to the TraI helicase of the F plasmid; 123 kDa protein

  Relaxase protein sequence


Download         Length: 1101 a.a.        Molecular weight: 123590.57 Da        Isoelectric Point: 9.8136

>AAC17212.1 TraA (plasmid) [Agrobacterium fabrum str. C58]
MAIAHFSASIVSRGDGRSVVLSAAYQHCAKMEYEREARTIDYTRKQGLVHQEFILPADAPKWVRALIADC
SVAGASEAFWNKVEAFEKRSDAQLARDLTIALPRELTSEQNIALVRDFVEKHILGKGMVADWVYHDNPGN
PHIHLMTTLRPLTEDGFGAKKVAVIGEDGQLVRTKSGKILYELWAGSTDDFNVVRDGWFERLNHHLTLGG
IDLKIDGRSYEKQGIDLEPTIHLGVGAKAISRKAEQQGVRPELERIELNEERRSENTRRILKNPAIVLDL
IMREKSVFDERDVAKVLHRYVDDPAVFQQLMLRIILNPEVLRLQRDTIEFATGEKVPARYSTRAMIRLEA
TMARQAMWLSDKETHAVSTAVLLAATFGRHGRLSEEQKAAIECIAGPARIAAVVGRAGAGKTTMMKAARE
AWELAGYRVVGGALAGKASEGLDKEAGIESRTLSSWELRWNRGRDVLDNKTVFVMDEAGMVASKQMAGFV
DAVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALALY
NANARIVGERLKAEAVERLIADWNRDYDQTKTTLILAHLRRDVRMLNVMAREKLVERGIVGEGHVFRTAD
GERRFHAGDQIVFLKNETLLGVKNGMIGHVVEAVPNRIVAVVGDRDHRRHVVVEQRFYSNLDHGYATTIH
KSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGCRSFAFNGGLAKVLSRKNAKETTLDYERGKL
YREALRFAENRGLHIMQVARTMLRDRLDWTLRQKTKVSDLVHRLRALGERLGLDQSPKTQTMKEAAPMVT
GIKTFSGSVADTVGDKLGADPTLKQQWEEVSARFRYVFADPETAFRAVNFDTVLADKEAAKAVLQKLEAE
PASIGALKGKTGILASKTEREARRVAEVNVPALKRDLEQYLRMRETATLRIVTEEQALRQRVSIDIPALS
PAARVVLERVRDAIDRNDLPAALGYALSNRETKLEIDGFNQAVTERFGERTLLSNVAREPSGKLYEKLSD
GMRPEQKEQLKQAWPIMRTAQQLAAHERTVQSLKQAEELRQTLRQAPVLKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(383-567)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(693-737)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(856-952)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure


Source ID Structure
AlphaFold DB Q44349

  Reference


[1] 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]


T4CP

ID   173 GenBank   YP_009075421
Name   TraG_pTiC58 experimental UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 71106.43 Da        Isoelectric Point: 9.2101

>YP_009075421.1 TraG (plasmid) [Agrobacterium fabrum str. C58]
MTMNRLLLLILPAIIMLAAMFATSGMEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGIIGLFAANGSA
NIKAAGLSVLAGSGVVITIATLREVIRLNSIASSVPAEQSVLAYADPVTMIGASIAFISGMFALRVAIKG
NAAFATTAPKRIGGKRAVHGEADWMKIQEAAKLFPERGGIIIGERYRVDRDSVAAMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVCEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTET
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVKGRTLFLLDEVARLGY
LRILETARDAGRKYGIMLTMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLHMRSDEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
ENRFHRTGTGTDTHTEHAPPWQKEGTRP

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



  Reference


[1] Hamilton CM et al. (2000) TraG from RP4 and TraG and VirD4 from Ti plasmids confer relaxosome specificity to the conjugal transfer system of pTiC58. J Bacteriol. 182(6):1541-8. [PMID:10692358]
[2] Cabezón E et al. (1994) Requirements for mobilization of plasmids RSF1010 and ColE1 by the IncW plasmid R388: trwB and RP4 traG are interchangeable. J Bacteriol. 176(14):4455-8. [PMID:8021231]


Host bacterium

ID   173 GenBank   NC_004972
Plasmid name   pTiC58 Incompatibility group   -
Plasmid size   8288 bp Coordinate of oriT [Strand]   
Host baterium   Agrobacterium fabrum str. C58

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   virulence-tumorigenic
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -