Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120995
Name   oriT_pW2_73_2 in_silico
Organism   Agrobacterium rubi strain W2/73
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP049209 (98495..98537 [-], 43 nt)
oriT length   43 nt
IRs (inverted repeats)      22..27, 32..37  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 43 nt

>oriT_pW2_73_2
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13245 GenBank   WP_065699131
Name   traA_G6M88_RS24275_pW2_73_2 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: 123869.00 Da        Isoelectric Point: 10.0632

>WP_065699131.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium rubi]
MAIAHFSASIVSRGRGASVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPADAPKWVRAMIADR
SVSGASEAFWNKVEAFEKRSDAQLARDLTIALPLELTPEQNIALVRDFVEKHIHAKGMVADWVYHDNPGN
PHIHLMTTLRPLTEEGFGSKKVAVIGEDRQPVRTKSGKILYQLWAGSTDDFSVLRDGWFERLNHHLALGG
IDLKIDGRSYEKQGIELEPTIHLGVGTKAIERKAQEQGVRPELERIELNEELRSENTRRILRNPAIVLDL
ITREKSVFDERDIAKVLHRYVDDPAVFLQLMARIIQNPEALRLQRDTIKFATGEKVPARYSTIAMIRLEA
TMVRQALWLSHRNSRAVSEAALAATFRRHERLSEEQRTAIERIAGPARIAAVVGRAGAGKTTMMKAAREV
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVLDDKTVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRTIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
VNTRIKGTRLKAEAVERLIGDWNNDYDQTKTTLILAHLRRDVRMLNVMAREKLVERGIVGEGYVFKTADG
VRRFDVGDQIVFLKNETSLGVKNGMIAHVIEAAPNKIVAVVGEGDQRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFSGGLAKVLSRRQAKETTLDYERGKLY
REALRFAESRGLNIVQVARTLIRDQLDWTLRQKMKLVDLGQRLAVFAERLGLHQPPMTQTMKEAAPMVAG
IKTFSGSVADTVEHKLDTDPALRQQWEEVSTRFAYVFADPETAFRAMNFDAVLAHKETAKLALQTLTTAP
ASIGPLRGKTGILASKVEREARRIAEINAPALKRDLEQYLQMREAATKRLQADEQALRQRVSIDIPALSP
AARVVLERVRDAIDRNDVPAAMAYALSNRETKLEIDGFNKAITERFGERTLLTNAAREPSGKLFDKLSDG
MQPQQKERLKEAWPIMRTSQQLAAHERTIQTLRQAEDLRLAQRQTPVMKQ

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(18-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

AAA domain (AAA_30)

(382-567)

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

(855-951)


  Protein structure



No available structure.




T4CP

ID   15526 GenBank   WP_065699101
Name   t4cp2_G6M88_RS24080_pW2_73_2 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: 92138.01 Da        Isoelectric Point: 5.8903

>WP_065699101.1 conjugal transfer protein TrbE [Agrobacterium rubi]
MVALKSFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVETIRVATGDYPTETEAHFPDPVTRAIDEERRMHFQKEKGHFESRHALILTWRPPEPRRSRLTR
YIYSDAASRSATYADKALTSFLTSIREVEQYLANVVSIRRMVTRETSERGGYRVARYDELFQFIRFCVTG
ENHPVRLPDIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNTLDRMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAISEASSQLVAYGYYTPVIVI
FEEDPTRLQEKSEAIRRLVQAEGFGARIETLNATDAFLGSLPGISYANIREPLINTRNLADLIPLNSVWS
GSPNAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADAQVFA
FDKGSSMLPLTLGLNGDHYQIGGDIGSSASGEVRALSFCPLAELSSDGDRAWAAEWIEMLVALQGVTITP
DYRNAISRQVALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGPFQCFEIEEL
MNMGERNLVPVLTYLFRRIEKRLTGDPSLIILDEAWLMLGHPVFRDKIRDWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNEQQIEIVATAIPKREYYVVSPEGRRLFDM
ALGPVALSFVGATGKKDLKRIRILHSEHGDAWPLHWLQQRGIAHAETLFPTF

  Protein domains


Predicted by InterproScan.

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

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 50992..60684

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G6M88_RS26210 46132..46287 - 156 WP_234791161 hypothetical protein -
G6M88_RS24045 (G6M88_24070) 46347..47561 - 1215 WP_065699094 plasmid replication protein RepC -
G6M88_RS24050 (G6M88_24075) 47735..48694 - 960 WP_065699095 plasmid partitioning protein RepB -
G6M88_RS24055 (G6M88_24080) 48797..49993 - 1197 WP_065699096 plasmid partitioning protein RepA -
G6M88_RS24060 (G6M88_24085) 50360..50995 + 636 WP_065699097 acyl-homoserine-lactone synthase TraI -
G6M88_RS24065 (G6M88_24090) 50992..51963 + 972 WP_065699098 P-type conjugative transfer ATPase TrbB virB11
G6M88_RS24070 (G6M88_24095) 51953..52357 + 405 WP_065699099 conjugal transfer pilin TrbC virB2
G6M88_RS24075 (G6M88_24100) 52350..52649 + 300 WP_065699100 conjugal transfer protein TrbD virB3
G6M88_RS24080 (G6M88_24105) 52659..55127 + 2469 WP_065699101 conjugal transfer protein TrbE virb4
G6M88_RS24085 (G6M88_24110) 55099..55908 + 810 WP_065699102 P-type conjugative transfer protein TrbJ virB5
G6M88_RS24090 (G6M88_24115) 55905..56129 + 225 WP_065699103 entry exclusion protein TrbK -
G6M88_RS24095 (G6M88_24120) 56123..57313 + 1191 WP_065699104 P-type conjugative transfer protein TrbL virB6
G6M88_RS24100 (G6M88_24125) 57331..58008 + 678 WP_065699105 conjugal transfer protein TrbF virB8
G6M88_RS24105 (G6M88_24130) 58026..58877 + 852 WP_045232178 P-type conjugative transfer protein TrbG virB9
G6M88_RS24110 (G6M88_24135) 58877..59353 + 477 WP_065699106 conjugal transfer protein TrbH -
G6M88_RS24115 (G6M88_24140) 59365..60684 + 1320 WP_065699107 IncP-type conjugal transfer protein TrbI virB10
G6M88_RS24120 (G6M88_24145) 60944..63439 - 2496 WP_234791162 HAMP domain-containing methyl-accepting chemotaxis protein -
G6M88_RS24125 (G6M88_24150) 64358..65560 - 1203 WP_065699109 GTP-binding protein -

Host bacterium

ID   21424 GenBank   NZ_CP049209
Plasmid name   pW2_73_2 Incompatibility group   -
Plasmid size   179725 bp Coordinate of oriT [Strand]   98495..98537 [-]
Host baterium   Agrobacterium rubi strain W2/73

Cargo genes

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