Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120994
Name   oriT_pW2_73_1 in_silico
Organism   Agrobacterium rubi strain W2/73
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP049208 (44043..44076 [-], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_pW2_73_1
TCCAAGGGCGCAATTATACGTCGCAGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13244 GenBank   WP_065700853
Name   traA_G6M88_RS22705_pW2_73_1 insolico UniProt ID   _
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 123249.06 Da        Isoelectric Point: 9.7724

>WP_065700853.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium rubi]
MAVPHFSVSIVARSSGRSAVLSAAYRHCARMEFEREARTIDYTRKQGLLHEAFVIPDDAPEWVRSMMADR
SVAGASEAFWNKVEDFEKRSDAQLAKDVTIALPLELTAEQNIELMRDFVTSHITSKGMVADWVYHDAPGN
PHVHLMATLRPLTEDGFGSKKVAVTGPEGKPIRNDAGKIVYELWAGSAEDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELEPTIHLGVGTKAIARKAEETNRKQQRPASKLERIEIQEQRRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRVLQSPEALRLERERINFATGIRSPAKYTTREM
IRLEAEMAHRAIWLSGSPSHGVPEAVLQATFARHSRLSEEQRTAISHVAAPARIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGSLAGKAAEGLDKDAGIVSRTLSSWELRWSQGRNQLDDKTVFVLDEAGMVSSRQM
ALLVETVTKAGAKLVLVGDPQQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVGQA
VDAYRAHGYMRGSDLKAQAVDKLITDWDRDFDPSRTSLILAHLRRDVRKLNDMARARLVDRGVLEDGFAF
KTEDGSRMFATGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEVGDGEHRRQVTVEQRFYNTLDHGYA
TTIHKAQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFSKAGGLTQILSRQNAKETSLDYE
QSTLYRHALRFAEARGLHLMNVARTIAQDRLQWAVRQKHKLADLGTRLAAIGTALGLALGSNKHAITDTI
NEARPMVSGITIFPKSLDQAVEDKLAADPGLKMQWDDVSTRFHFVYANPQAAFKAIDVDTMLKDPSVAQF
TLAKIAHQPESFGTLKGKTGLLASRGDRQDREKAIANVPALARNLERYLRERAEAEIKHETEERAVRQKV
SVDIPALSPSAKQTLERVRDAIDRNDLSAGLEYALADKMVKAELEGFARAVSERFGERTFLPLAAKDTGG
KTFETVTSGMTVGQKAEVQSAWNSMRTVQQLGAHERTTEAFRQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(693-740)

AAA domain (AAA_30)

(387-572)


  Protein structure



No available structure.




T4CP

ID   15524 GenBank   WP_065700841
Name   t4cp2_G6M88_RS22630_pW2_73_1 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91867.65 Da        Isoelectric Point: 5.6923

>WP_065700841.1 MULTISPECIES: conjugal transfer protein TrbE [Agrobacterium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLELNELSRQINAVLSRLG
SGWMIQVEAIRVPTVDYPSEDRCHFPDPVTRAIDAERRAHFEHEQGHFESKHAIVLTYRPLASKRTSLSK
YIYSDEESRKKSYADTVLFVFKSAIREVEQYFANTLSIRRMETRETIERGGERIARYDELLQFAKFCITG
ESHPVRLPDVPMYLDWIATAEFEHGLTPKVENRFLGIVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEAAIAQASSKLVAYGYYTPVVVL
FDSDHEALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPVSPSPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLATGGDHYELGGDIAEEGRDLAFCPLSELQTDADRAWATEWIEMLVGLQGITITPDHRN
AISRQVGLMAKASGRSLSDFVSGVQLREVKDALHHYTVDGPMGQLLDAEEDGLTLGTFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARETGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGATGKEDLKRVRILKSEHGREWPIRWLETRGVHDAASLLKYE

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.



ID   15525 GenBank   WP_065700856
Name   traG_G6M88_RS22720_pW2_73_1 insolico UniProt ID   _
Length   646 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 646 a.a.        Molecular weight: 69454.52 Da        Isoelectric Point: 9.1262

>WP_065700856.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Agrobacterium]
MAINRIALAVVPGTLMIVVVIAMTGIEQWLSGFGKTGSARLAWGRAGIALPYVSSAAIGILFLFASAGSI
NIRQAGCGVLAGCSGAILVAAARETMRLAAFTETLDADMSVLAYLDPATAIGAGVALMCACFALRVVLMG
NAAFASAEPKRIQGKRALHGKADWMKLTEAANLFPDAGGIVIGERYRVDKDSVGARAFRAGSAETWGVGG
KSPLLCFDGAFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGRAGRDVFVLD
PNTPDVGFNALDWVGRFGGTKEEDIASVASWIMSDSSGARGVRDDFFRASALQLLTALIADVCLSGHTDE
KNQTLRQVRMNLSEPEPTLRKRLQNIYDNSDSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGSSDVFININLKTLEAHSGLARVIIGSFLNAIYNRDGQMKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAGINDPETADYISRRCGVTT
VEIDQISLSWQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGHAPLRCGRAIWFRRDDMRACVD
GNRFHSNPSVPPTKTK

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 25197..38902

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G6M88_RS22595 (G6M88_22605) 20506..21750 - 1245 WP_065700834 plasmid replication protein RepC -
G6M88_RS22600 (G6M88_22610) 21906..22901 - 996 WP_065700835 plasmid partitioning protein RepB -
G6M88_RS22605 (G6M88_22615) 22986..24176 - 1191 WP_065700836 plasmid partitioning protein RepA -
G6M88_RS22610 (G6M88_22620) 24562..25200 + 639 WP_065700837 acyl-homoserine-lactone synthase -
G6M88_RS22615 (G6M88_22625) 25197..26174 + 978 WP_065700838 P-type conjugative transfer ATPase TrbB virB11
G6M88_RS22620 (G6M88_22630) 26164..26547 + 384 WP_065700839 TrbC/VirB2 family protein virB2
G6M88_RS22625 (G6M88_22635) 26540..26839 + 300 WP_065700840 conjugal transfer protein TrbD virB3
G6M88_RS22630 (G6M88_22640) 26850..29306 + 2457 WP_065700841 conjugal transfer protein TrbE virb4
G6M88_RS22635 (G6M88_22645) 29278..30084 + 807 WP_065700842 P-type conjugative transfer protein TrbJ virB5
G6M88_RS22640 (G6M88_22650) 30078..30254 + 177 WP_065700843 entry exclusion protein TrbK -
G6M88_RS22645 (G6M88_22655) 30298..31446 + 1149 Protein_33 P-type conjugative transfer protein TrbL -
G6M88_RS22650 (G6M88_22660) 31467..32129 + 663 WP_065701003 conjugal transfer protein TrbF virB8
G6M88_RS22655 (G6M88_22665) 32147..32959 + 813 WP_065700844 P-type conjugative transfer protein TrbG virB9
G6M88_RS22660 (G6M88_22670) 32962..33402 + 441 WP_065700845 conjugal transfer protein TrbH -
G6M88_RS22665 (G6M88_22675) 33415..34710 + 1296 WP_065700846 IncP-type conjugal transfer protein TrbI virB10
G6M88_RS22670 (G6M88_22680) 34974..35678 + 705 WP_065700847 autoinducer binding domain-containing protein -
G6M88_RS22675 (G6M88_22685) 35681..36004 - 324 WP_065700848 transcriptional repressor TraM -
G6M88_RS22680 (G6M88_22690) 36213..36419 + 207 WP_062653296 helix-turn-helix domain-containing protein -
G6M88_RS22685 (G6M88_22695) 36499..38064 - 1566 WP_065700849 Fic family protein -
G6M88_RS22690 (G6M88_22700) 38288..38902 - 615 WP_065700850 TraH family protein virB1
G6M88_RS22695 (G6M88_22705) 38919..40085 - 1167 WP_065700851 conjugal transfer protein TraB -
G6M88_RS22700 (G6M88_22710) 40075..40572 - 498 WP_234791255 conjugative transfer signal peptidase TraF -

Host bacterium

ID   21423 GenBank   NZ_CP049208
Plasmid name   pW2_73_1 Incompatibility group   -
Plasmid size   289141 bp Coordinate of oriT [Strand]   44043..44076 [-]
Host baterium   Agrobacterium rubi strain W2/73

Cargo genes

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