Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105819
Name   oriT_pRvVAR031b in_silico
Organism   Agrobacterium vitis strain VAR03-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP023271 (40164..40207 [-], 44 nt)
oriT length   44 nt
IRs (inverted repeats)      21..27, 32..38  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 44 nt

>oriT_pRvVAR031b
GGATCCAAGGGCGCAATTATACGTCGCTGATGCGACGTGCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3929 GenBank   WP_180642278
Name   traA_RvVAT039_RS24250_pRvVAR031b 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: 123485.17 Da        Isoelectric Point: 10.0423

>WP_180642278.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium vitis]
MAIAHFSASIVSRGGGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPADAPKWVRALIADR
SVSGAVEAFWNKVEAFEKRSDAQLARDLTIALPLELTPEQNIALVRDFVEKHIHAKGMVADWVYHDNPGN
PHIHLMTTLRPLTEEGFGSKKVAVTAKGGQPVRTKSGKILYELWAGSTGDFNVLRDGWFERLNHHLALGG
IDLKIDGRSYEKQGIDLEPTIHLGVGAKAIERKAQQQGVRPELERIELNEQRRSENARRILNNPAIVLDV
ITREKSVFDERDVAKVLHRYVDDPAVFQQLMLRIILNPEVLRLQRDTIEFATGEKLPARYSTRAMIRLEA
TMVRQTLWLSNRDGHSVSEAALDATFRRHERLSQEQKAAIERITGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVLDHKTVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLIGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREGWMRKASLDLARGNVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNNDYDQSKTTLILAHLRRDVRTLNIRAREKLVERGIVGEGHVFKTADG
VRQFDAGDQIVFLKNEGLLGVKNGMIAHVIEAAPSRIVAVIGEGDQRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGHQSFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAESRGLNIVQVARTLVRDRLDWTLRQKTRLVDLGQRLAVFAERLGLHHPLKTQTKKEAAPMVAG
IKTFPGSVADTVENKLDTDPALRQQWEEVSTRFAYVFADPETAFRAMNFDTVPADKEKAKLALQTLTTAP
ASIGPLKGKTGILASKTEREDRRVADLNVPALKRDLEQYLRMRETAVQRLQADEQVLRQRVSIDIPALSP
AAHVVLERVRDAIDRNDLPAAMAYALSNRETKLEIDGFNQAVTERFGERTMLTNAAREPSGKLFDKLSDG
MQPEQKERLKEAWPIMRTSQQLAAHERTVQTLRQAEDLRLAQRQTPVMKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

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

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)


  Protein structure



No available structure.




T4CP

ID   3945 GenBank   WP_180642233
Name   t4cp2_RvVAT039_RS24095_pRvVAR031b 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: 91702.50 Da        Isoelectric Point: 5.4869

>WP_180642233.1 conjugal transfer protein TrbE [Agrobacterium vitis]
MVALKSLRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNDVSRQINAILSRLG
SGWMIQVEAVRVPTGDYPTEAESHFPDPVTRAIDDERRTHFQTERGHYESRHALILTWRPPEPRRSGLTR
YVYSDTTSRSATYADTMLQSFLTSIREVEQYLANVVSIRRMMTRETPERGGFRVARYDELFQFIRFCVTG
ENHPVRLPDISMYLDWLVTAELQHGLTPMVENRFLGVVAIDGLPAESWPGILNTLDRMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVI
FEEDPTRLQEKCEAIRKLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPTAPCPFFPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADAQVFA
FDKGGSMLPLTLGLNGDHYQIGGDIGPSAGGEVKALAFCPLAELSTDGDRAWASEWIEMLVALQGVTISP
DYRNAISRQLALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFEIEDL
MNMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKREYYVVSPEGRRLFNM
ALGPVALSFVGATGKEDLKQIRSLHSEHGAAWPCPWLQQRGIAHAETLFSAE

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.



ID   3946 GenBank   WP_071207755
Name   traG_RvVAT039_RS24265_pRvVAR031b insolico UniProt ID   _
Length   656 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 656 a.a.        Molecular weight: 70396.46 Da        Isoelectric Point: 9.3253

>WP_071207755.1 Ti-type conjugative transfer system protein TraG [Agrobacterium vitis]
MTVGKLLLAVIPATAMIVVVVFMPGIEHWLAAFGKTAQTKLMLGRIGLALPYATAAAIGTICLFAANGAA
GIKRAGWGVVGGNGVAILIALLREGVRLAGIAGDIPEGQSVLGYVDPPTTLGASTTFLAGVFALRVAMNG
NAAFAKAAPRRIGGKRAVHGEADWMKVQEAAKLFPNSGGIVVGERYRVGRDSVAAVSFRADDPSTWGAGG
KNPLLCFDGSFGSSHGIVFAGSGGFKTTSVTVPTALKWGGGLVVLDPSSEVAPMVSEHRRKAGRKVIILD
PSASGVGFNALDWIGRHGSTKEEDIVSVATWIMTDNPRSASARDDFFRASAMQLLTALIADVCLSGHTDE
EDQTLRRVRKNLSEPEPQLRARLTKIYEQSESDFVKENVSVFVNMTPETFCGVYANAVKETHWLSYPNYA
ALVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGDVKGRALFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSRQLSRRPLILPHEVLRMRADEQIVFTSGNPPLRCGRAIWFRRKDMSASVG
ENRFHKPITEGVKSYKAAPTTDTEAT

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 4264..13956

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RvVAT039_RS24065 (RvVAR031_pl05490) 984..1979 - 996 WP_180642225 plasmid partitioning protein RepB -
RvVAT039_RS24070 (RvVAR031_pl05500) 2064..3254 - 1191 WP_180642227 plasmid partitioning protein RepA -
RvVAT039_RS24075 (RvVAR031_pl05510) 3632..4267 + 636 WP_180642228 acyl-homoserine-lactone synthase -
RvVAT039_RS24080 (RvVAR031_pl05520) 4264..5235 + 972 WP_180642230 P-type conjugative transfer ATPase TrbB virB11
RvVAT039_RS24085 (RvVAR031_pl05530) 5225..5629 + 405 WP_180642232 conjugal transfer pilin TrbC virB2
RvVAT039_RS24090 (RvVAR031_pl05540) 5622..5921 + 300 WP_020046779 conjugal transfer protein TrbD virB3
RvVAT039_RS24095 (RvVAR031_pl05550) 5931..8399 + 2469 WP_180642233 conjugal transfer protein TrbE virb4
RvVAT039_RS24100 (RvVAR031_pl05560) 8371..9180 + 810 WP_180642235 P-type conjugative transfer protein TrbJ virB5
RvVAT039_RS24105 (RvVAR031_pl05570) 9177..9404 + 228 WP_180642237 entry exclusion protein TrbK -
RvVAT039_RS24110 (RvVAR031_pl05580) 9398..10585 + 1188 WP_180642239 P-type conjugative transfer protein TrbL virB6
RvVAT039_RS24115 (RvVAR031_pl05590) 10603..11280 + 678 WP_180642241 conjugal transfer protein TrbF virB8
RvVAT039_RS24120 (RvVAR031_pl05600) 11355..12149 + 795 WP_234616830 P-type conjugative transfer protein TrbG virB9
RvVAT039_RS24125 (RvVAR031_pl05610) 12149..12625 + 477 WP_180642245 conjugal transfer protein TrbH -
RvVAT039_RS24130 (RvVAR031_pl05620) 12637..13956 + 1320 WP_180642248 IncP-type conjugal transfer protein TrbI virB10
RvVAT039_RS24135 (RvVAR031_pl05630) 14093..14995 - 903 WP_156551308 LysR family transcriptional regulator -
RvVAT039_RS24140 (RvVAR031_pl05640) 15248..16021 + 774 WP_156551382 nopaline ABC transporter ATP-binding protein NocP -
RvVAT039_RS24145 (RvVAR031_pl05650) 16087..16938 + 852 WP_156551309 nopaline ABC transporter substrate-binding protein NocT -
RvVAT039_RS24150 (RvVAR031_pl05660) 17011..17721 + 711 WP_045025159 nopaline ABC transporter permease NocQ -
RvVAT039_RS24155 (RvVAR031_pl05670) 17723..18448 + 726 WP_080868320 nopaline ABC transporter permease NocM -

Host bacterium

ID   6256 GenBank   NZ_AP023271
Plasmid name   pRvVAR031b Incompatibility group   -
Plasmid size   161351 bp Coordinate of oriT [Strand]   40164..40207 [-]
Host baterium   Agrobacterium vitis strain VAR03-1

Cargo genes

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