Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118328
Name   oriT_pAvCG678b in_silico
Organism   Agrobacterium vitis strain CG678
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056045 (284429..284465 [-], 37 nt)
oriT length   37 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: 37 nt

>oriT_pAvCG678b
GGCTCCAAGGGCGCAATTATACGTCGCTGATGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11639 GenBank   WP_071205421
Name   traA_AVCG678_RS25530_pAvCG678b 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: 123909.64 Da        Isoelectric Point: 9.9753

>WP_071205421.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium/Agrobacterium group]
MAIAHFSASIISRGDGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHQEFVLPADAPNWVRSLIADR
SVSGAVEAFWNKVEAFEKRSDAQLARDLTIALPLELTAEQNIALVRDFVEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLSEDGFGAKKVAVIGEDGQPVRTKSGKIVYELWAGSTEDFNALRDGWFERLNHHLALRG
FDLRVDGRSYEKQGIDLEPTIHLGVGTKAIERKAKSKALRPELERIELNEQLRRDNARRILRKPGIVLDM
ITRERSVFDERDVAKVLHRYVDDPAVFQQLMLRIIQNPEVLRLQRDTIEFATGEKVPARYSTRAMIRLEA
TMVRQALWLSNRYGHDVSDAALNATFRRHERLSDEQKTAIELIARPSRIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVLDDRTVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRALVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNHDYDQTKTTLILAHLRRDVRMLNVMAREKLVERGIVGEGHVFKTADG
VRQFDVGDQIVFLKNETSLGVKNGMIAQVIEAAPNRIVAIIGEGDERRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAESRGLNIVQVARTLVRDQLDWTLRQKTKLVDLGQRLASFAERLGLHHPPKTQTIKEAAPMVAG
IKTFSGSVADTVEHKLDTDPALRQQWEEVSTRFSYVFADPETAFRAMNFDAVLADKETAKLALQTLTTAP
VSIGPLRGKTGILASKADREHRRVAELNVPALKRDLEHYLRMRETAVQRLKADEQVLRQRISIDIPALSP
AAHVVLERVRYAIDRNDLPAAMANALSNRETKLEIDGFNQAVTQRFGERTLLTNAAREPSGKIFDTLSNG
MEPEQKERLKQAWPVMRAAQQLAAHERTVQSLKQSEELRLIQSQTSVLKQ

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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   13618 GenBank   WP_071585024
Name   traG_AVCG678_RS25545_pAvCG678b insolico UniProt ID   _
Length   655 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 655 a.a.        Molecular weight: 70556.77 Da        Isoelectric Point: 9.1709

>WP_071585024.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium/Agrobacterium group]
MTANRLLLFVLLAAIMLAALVMTSGMEHRLAEFGSSTQAKLMLGRTGLALPYIAVAAIGAIALFAANGSA
DIKTVGVSVLAANSAAIVIAMIRETIRLTGIASSVPAGQSVLTYADPATAVGAGVAFISAMFALRVTIKG
NAAFAQTGPKRIGGKRAVHGEADWMKLQEAAKLFPEPGGIVIGERYRVDKDSVATMPFRADEPQSWGAGG
KSQLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVVDHRRKAGRKVIVLD
PTLQGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNARTASVRDDFFRASAMQLLTALIADVCLSGHTDA
KNQTLRRVRANLSEPEPKLRGRLTEIYEQSESDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPHYA
GLVSGDSFSTDDLANGGTDIFIALDLKVLEAHPGLARVVIGALLNAIYNRNGDVKGRTLFLLDEVARLGY
LRILETARDAGRKYGITLTLIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSKQLSRRPLILPHELLRMRSDEQIVFTAGNAPLRCGRAIWFRREDMKACVG
ENRFHHPHTTTTAITAPKVTKSDED

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   13619 GenBank   WP_071204871
Name   t4cp2_AVCG678_RS25930_pAvCG678b 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: 91967.89 Da        Isoelectric Point: 5.8031

>WP_071204871.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALKSFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAIRVPTGDYPTEAESHFSDPVTRAIDDERRAHFQKERGHFESRHALILTWRPPEPRRSGLTR
YIYSDAASRSATYADKALESFLTSIREVEQYLANVVSIRRMMTRETPERGGFRIARYDELFQFIRFCVTG
ENHPVRLPDIPMYLDWLVTAELQHGLTPMVENRFLGVVAIDGLPAESWPGILNTLDRMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMMMVAETEDAIAEASSQLVAYGYYTPVIVI
FEEDATRLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPVAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADAQVFA
FDKGGSMLPLTLGLDGDHYQIGGDIGASTVEEGKVLAFCPLAELSTDGDRAWASEWIEMLVALQGVTITP
DYRNAISRQLALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLSLGAFQCFEIEEL
MNMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKREYYVVSPEGRRLFNM
ALGPVALSFVGATGKEDLKRIRSSHSQHGAAWPLHWLQQRGIAYAEKLFSAE

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 360113..369811

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AVCG678_RS25870 (AVCG678_25835) 356191..356685 + 495 WP_071205479 hypothetical protein -
AVCG678_RS25875 (AVCG678_25840) 356798..356956 + 159 WP_156582886 hypothetical protein -
AVCG678_RS25880 (AVCG678_25845) 357242..358063 + 822 WP_071205480 LON peptidase substrate-binding domain-containing protein -
AVCG678_RS25885 (AVCG678_25850) 358360..359058 - 699 WP_071205481 SMC-Scp complex subunit ScpB -
AVCG678_RS25890 (AVCG678_25855) 359061..360014 - 954 WP_071205482 DUF1403 family protein -
AVCG678_RS25895 (AVCG678_25860) 360113..361435 - 1323 WP_071204877 IncP-type conjugal transfer protein TrbI virB10
AVCG678_RS25900 (AVCG678_25865) 361447..361923 - 477 WP_071204876 conjugal transfer protein TrbH -
AVCG678_RS25905 (AVCG678_25870) 361923..362717 - 795 WP_234618193 P-type conjugative transfer protein TrbG virB9
AVCG678_RS25910 (AVCG678_25875) 362792..363469 - 678 WP_071204875 conjugal transfer protein TrbF virB8
AVCG678_RS25915 (AVCG678_25880) 363487..364677 - 1191 WP_071585038 P-type conjugative transfer protein TrbL virB6
AVCG678_RS25920 (AVCG678_25885) 364671..364898 - 228 WP_071204873 entry exclusion protein TrbK -
AVCG678_RS25925 (AVCG678_25890) 364895..365662 - 768 WP_234618192 P-type conjugative transfer protein TrbJ virB5
AVCG678_RS25930 (AVCG678_25895) 365676..368144 - 2469 WP_071204871 conjugal transfer protein TrbE virb4
AVCG678_RS25935 (AVCG678_25900) 368166..368453 - 288 WP_071204870 conjugal transfer protein TrbD virB3
AVCG678_RS25940 (AVCG678_25905) 368446..368850 - 405 WP_071204869 conjugal transfer pilin TrbC virB2
AVCG678_RS25945 (AVCG678_25910) 368840..369811 - 972 WP_071204868 P-type conjugative transfer ATPase TrbB virB11
AVCG678_RS25950 (AVCG678_25915) 369808..370446 - 639 WP_071585036 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   18761 GenBank   NZ_CP056045
Plasmid name   pAvCG678b Incompatibility group   -
Plasmid size   370902 bp Coordinate of oriT [Strand]   284429..284465 [-]
Host baterium   Agrobacterium vitis strain CG678

Cargo genes

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