Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121738
Name   oriT_pAt2 in_silico
Organism   Agrobacterium tumefaciens strain Yub002
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048468 (103400..103440 [+], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pAt2
TCCAAGGGCGCAATTATACGTCGCTGATGCGACGTGCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13718 GenBank   WP_173995559
Name   traA_FY157_RS27560_pAt2 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123269.13 Da        Isoelectric Point: 9.9132

>WP_173995559.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium/Agrobacterium group]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLVHEEFMLPADAPKWVRAMIADR
SVAGASEAFWNKVEAFEKRADAQLARDLTIALPLELPAEQNIALVRDFVEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLTGDGFGTKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLEPTIHLGVGAKAIERKAKEQGIRPELERIELNEDRRSENARRILRRPEIVLDL
ITREKSVFDERDVAKVLHRYVDDPALFQQLMLRIILNPEVLRLQRDTIEFATGEKVPARYSTRAMIRLEA
TMARQAMWLSDKETHAVSTAVLAATFGRHGRLSEEQKAAIECIAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIHSRTLASWELRWNRGRDVLDRKTVFVMDEAGMVASKQMARFVD
TAVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNHDYDQTKTTLILAHLRRDVRMLNVMAREKFVERGVVGEGHVFKTADG
IRQFDAGDQIVFLKNETSLGVKNGMIAHVVEAAPNRIVAVVGEGDKRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDVQLYYGRRSFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAEGRGLNIVQVARTLVRDRLDWTLRQKMKLVELGQRLAVFAEHLGLHHPLKTQTMKEAAPMVAG
IKTFSGSVADTLSDRLGADPALKQQWEEVSARFAYVFADPETAFRAMNFDAVLADKDSARQALQKLEAEP
TSIGALTGKTGILASKTEREARRIAELNVPALKRDLEQYLRMRETASQRLQADEQALRQRVSIDIPALSP
AACVVLERVRDAIDRNDLPAALGYALSNRETKLEIDGFNKAVTERFGERTLLTNAARQPSGTLFDKLSNG
MQPAQKEQLREAWPVMRTAQQIAAHERTTQTLKQAEELRLTQRQSPVMKQ

  Protein domains


Predicted by InterproScan.

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

(855-951)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-567)


  Protein structure



No available structure.




T4CP

ID   16030 GenBank   WP_173995561
Name   traG_FY157_RS27545_pAt2 insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 71160.44 Da        Isoelectric Point: 9.0431

>WP_173995561.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MTMNRLLLLILPAIIMLAAMFATSGMEQRLAAFGTSPRAKLMLGHAGLALPYIAAVAIGIIGLFAANGSA
NIKAAGLSVLAGNGVVITTATLREVIRLNSIASRVPAEQSVLAYADPVTMIGVGIAFISGMFALRVAIKG
NAAFSTTAPKRIGGKRAVHGEADWMKIQETAKLFPEPGGIVIGERYRVDRDSVAAMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVCEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEA
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVEGRTLFLLDEVARLGY
LRILETARDAGRKYGIMLTMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMKGSSRSRSKQLSRRPLILPHEVLRMRSDEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
ENRFHRTGTGTDTHTEHAPPWQKEGTRP

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   16031 GenBank   WP_173995645
Name   t4cp2_FY157_RS27870_pAt2 insolico UniProt ID   _
Length   822 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 822 a.a.        Molecular weight: 92049.83 Da        Isoelectric Point: 5.5826

>WP_173995645.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALKLFRHSGPSFADLVPYAGLVDSGIILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINLILSRLG
SGWMIQVEALRVPTIDYPAGDICHFPDPVTRAIDTERRSHFERESGHFESRHALILTWRPPEPRRSGLTR
YVYSDTASRSATYADTALDTFRTSIREVEQYLANVLSIRRMVTRETEERGGFRVARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLVTAELQHGLTPTVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFVF
LDEQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMMMVAETEDAIAEASSQLVAYGYYTPVIVL
FDEQQERLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLVNTRNLADLIPLNSVWS
GSPVAPCPFYPPGSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLSLIAAQFRRYADAQIFA
FDKGRSMLPLTLAIGGDHYEIGGDAAEGGEGDSPRLAFCPLAELASDGDRAWAAEWIETLVALQGVTVTP
DYRNAISRQLALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLALGAFQCFEVEEL
MNLGERNLVPVLLYMFRRVEKRLTGAPSLIILDEAWLMLGHPTFRNKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVASPEGRRLFDM
SLGPVALSFVGASGKEDLKRIRALHFEHGADWPKHWLQQRGIAHAETLFQAA

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(188-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 164461..174133

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FY157_RS27810 (FY157_27620) 159745..160470 - 726 WP_173995637 nopaline ABC transporter permease NocM -
FY157_RS27815 (FY157_27625) 160472..161182 - 711 WP_173995654 nopaline ABC transporter permease NocQ -
FY157_RS27820 (FY157_27630) 161256..162107 - 852 WP_173995638 nopaline ABC transporter substrate-binding protein NocT -
FY157_RS27825 (FY157_27635) 162172..162945 - 774 WP_173995639 nopaline ABC transporter ATP-binding protein NocP -
FY157_RS27830 (FY157_27640) 163199..164101 + 903 WP_045023359 LysR family transcriptional regulator -
FY157_RS27835 (FY157_27645) 164461..165768 - 1308 WP_174168418 IncP-type conjugal transfer protein TrbI virB10
FY157_RS27840 (FY157_27650) 165783..166259 - 477 WP_045025162 conjugal transfer protein TrbH -
FY157_RS27845 (FY157_27655) 166259..167113 - 855 WP_173995641 P-type conjugative transfer protein TrbG virB9
FY157_RS27850 (FY157_27660) 167131..167793 - 663 WP_060716494 conjugal transfer protein TrbF virB8
FY157_RS27855 (FY157_27665) 167808..169004 - 1197 WP_173995642 P-type conjugative transfer protein TrbL virB6
FY157_RS27860 (FY157_27670) 168998..169216 - 219 WP_173995643 entry exclusion protein TrbK -
FY157_RS27865 (FY157_27675) 169213..170022 - 810 WP_173995644 P-type conjugative transfer protein TrbJ virB5
FY157_RS27870 (FY157_27680) 169994..172462 - 2469 WP_173995645 conjugal transfer protein TrbE virb4
FY157_RS27875 (FY157_27685) 172473..172772 - 300 WP_173995646 conjugal transfer protein TrbD virB3
FY157_RS27880 (FY157_27690) 172765..173172 - 408 WP_173995647 conjugal transfer pilin TrbC virB2
FY157_RS27885 (FY157_27695) 173162..174133 - 972 WP_173995648 P-type conjugative transfer ATPase TrbB virB11
FY157_RS27890 (FY157_27700) 174130..174765 - 636 WP_173995649 acyl-homoserine-lactone synthase -

Host bacterium

ID   22165 GenBank   NZ_CP048468
Plasmid name   pAt2 Incompatibility group   -
Plasmid size   175130 bp Coordinate of oriT [Strand]   103400..103440 [+]
Host baterium   Agrobacterium tumefaciens strain Yub002

Cargo genes

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