Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100093
Name   oriT_pRiA4b in_silico
Organism   Agrobacterium tumefaciens
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   AB050904 (9988..10025 [-], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      15..23, 28..36  (ATACGTCGC..GCGACGTGT)
Location of nic site      7..8
Conserved sequence flanking the
  nic site    		  AGGG|CGCA
Note   Ri plasmid

  oriT sequence  


Download         Length: 38 nt

>oriT_pRiA4b
CCAAGGGCGCAATTATACGTCGCTGGCGCGACGTGTTG

Visualization of oriT structure

  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]


Relaxase

ID   88 GenBank   BAB47249
Name   TraA_pRiA4b insolico UniProt ID   Q93UY4
Length   1108 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 123366.63 Da        Isoelectric Point: 9.5978

>BAB47249.1 traA (plasmid) [Agrobacterium tumefaciens]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPIELTAEQNIALMRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYDLWAGSTEEFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLELITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPVALRLERERIDFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLEATFARHVRLSDEQRTAIEHVADGERIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNQLDDKTIIVLDEAGMVSSRQM
ALLVETVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNEMARAKLVERGIVANGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVLEAALGRIVAEIGEGEHRRKVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGDLVPILSRRNAKETTLDYE
KASFYGQALRFADTRGLHLMDVARTVARDRLEWTIRQSSRLVDLGVRLAAIATKLGFVGSFKNSPIQNPI
KEAKPMVSGITTFPKSLEQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGVLASRADRQDREKAIANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPSAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETATAGMTAGQKAEVQSAWNSMRTVQQLAAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

AAA domain (AAA_30)

(387-570)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-740)


  Protein structure


Source ID Structure
AlphaFold DB Q93UY4

  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]


Auxiliary protein

ID   127 GenBank   BAB47248
Name   TraC_pRiA4b insolico UniProt ID   Q93UY5
Length   97 a.a. PDB ID   _
Note   conjugal transfer protein TraC

  Auxiliary protein sequence


Download         Length: 97 a.a.        Molecular weight: 10078.31 Da        Isoelectric Point: 8.6578

>BAB47248.1 traC (plasmid) [Agrobacterium tumefaciens]
MKKPSSKIRDEIAKLQEQLKIAETREAERIGRIALKAGLGDIEVEEGELQAAFEEVAKRFRGGKGASNGK
ERGGPGAVTQQTAPISSGAGAGSTGEA

  Protein domains


Predicted by InterproScan.

TraC-like protein (TraC)

(2-96)


  Protein structure


Source ID Structure
AlphaFold DB Q93UY5

ID   128 GenBank   BAB47247
Name   TraD_pRiA4b insolico UniProt ID   Q93UY6
Length   71 a.a. PDB ID   _
Note   conjugal transfer protein TraD

  Auxiliary protein sequence


Download         Length: 71 a.a.        Molecular weight: 7833.03 Da        Isoelectric Point: 10.3460

>BAB47247.1 traD (plasmid) [Agrobacterium tumefaciens]
MARTMTFDARKKDTREKIELGGLIVKAGLRYQKRALLLGALIDVARRINADDGERSRLTAIGVEAFGNDG
E

  Protein domains


Predicted by InterproScan.

Conjugal transfer protein TraD (TraD)

(8-66)


  Protein structure


Source ID Structure
AlphaFold DB Q93UY6


T4CP

ID   88 GenBank   BAB47246
Name   TraG_pRiA4b insolico UniProt ID   Q93UY7
Length   652 a.a. PDB ID   _
Note   conjugal transfer coupling protein TraG

  T4CP protein sequence


Download         Length: 652 a.a.        Molecular weight: 70250.40 Da        Isoelectric Point: 9.4783

>BAB47246.1 traG (plasmid) [Agrobacterium tumefaciens]
MTVSRIALVAGPAALMILVVIGMTGIEQWLSDFGKTGAARLTWGRVGIALPYVVSSAIGILFLFASAGSI
NIKQAGWGALTGCTATILIAAIRETTRLGAFMKVLPADKTILAYLDPATSIGASAALLCACFALRVALIG
NAAFASAKPKRIHGKRALHGEADWMKLTEAATLFSDAGGIVIGERYRVDKDNVAAQAFRADNAETWGAGG
KSPLLCFNGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGSTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PKKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
TEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGRKFSTSDIAGGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGQLEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDASSKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQVSRSSQARGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAMWFRREAMKACVG
KNRFHGTRDPDATAQKAATRRL

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure


Source ID Structure
AlphaFold DB Q93UY7


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15155..28928

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_6 13422..13985 + 564 BAB47250 - -
Locus_7 13975..15138 + 1164 BAB47251 - -
Locus_8 15155..15769 + 615 BAB47252 - virB1
Locus_9 15975..17555 + 1581 BAB47253 - -
Locus_10 17601..17813 - 213 BAB47254 - -
Locus_11 18045..18368 + 324 BAB47255 - -
Locus_12 18371..19180 - 810 BAB47256 LuxR family quorum-sensing transcription factor -
Locus_13 19405..20703 - 1299 BAB47257 - virB10
Locus_14 20715..21155 - 441 BAB47258 - -
Locus_15 21159..21971 - 813 BAB47259 - virB9
Locus_16 21989..22651 - 663 BAB47260 - virB8
Locus_17 22672..23853 - 1182 BAB47261 - virB6
Locus_18 23847..24050 - 204 BAB47262 - -
Locus_19 24044..24847 - 804 BAB47263 - virB5
Locus_20 24819..27275 - 2457 BAB47264 - virb4
Locus_21 27286..27585 - 300 BAB47265 - virB3
Locus_22 27578..27961 - 384 BAB47266 - virB2
Locus_23 27951..28928 - 978 BAB47267 protein similar to VirB11 virB11
Locus_24 28939..29562 - 624 BAB47268 - -
Locus_25 29561..29791 + 231 BAB47269 - -
Locus_26 29951..30000 + 50 BAB47270 - -

Host bacterium

ID   88 GenBank   AB050904
Plasmid name   pRiA4b Incompatibility group   -
Plasmid size   30000 bp Coordinate of oriT [Strand]   9988..10025 [-]
Host baterium   Agrobacterium tumefaciens

Cargo genes

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