Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118331
Name   oriT_pAvCG78b in_silico
Organism   Agrobacterium vitis strain CG78
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056050 (284430..284466 [-], 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_pAvCG78b
GGCTCCAAGGGCGCAATTATACGTCGCTGATGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11641 GenBank   WP_071205421
Name   traA_AVCG78_RS25525_pAvCG78b 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   13622 GenBank   WP_071585024
Name   traG_AVCG78_RS25540_pAvCG78b 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   13623 GenBank   WP_071204871
Name   t4cp2_AVCG78_RS25925_pAvCG78b 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: 360114..369812

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AVCG78_RS25865 (AVCG78_25840) 356192..356686 + 495 WP_071205479 hypothetical protein -
AVCG78_RS25870 (AVCG78_25845) 356799..356957 + 159 WP_156582886 hypothetical protein -
AVCG78_RS25875 (AVCG78_25850) 357243..358064 + 822 WP_071205480 LON peptidase substrate-binding domain-containing protein -
AVCG78_RS25880 (AVCG78_25855) 358361..359059 - 699 WP_071205481 SMC-Scp complex subunit ScpB -
AVCG78_RS25885 (AVCG78_25860) 359062..360015 - 954 WP_071205482 DUF1403 family protein -
AVCG78_RS25890 (AVCG78_25865) 360114..361436 - 1323 WP_071204877 IncP-type conjugal transfer protein TrbI virB10
AVCG78_RS25895 (AVCG78_25870) 361448..361924 - 477 WP_071204876 conjugal transfer protein TrbH -
AVCG78_RS25900 (AVCG78_25875) 361924..362718 - 795 WP_234618193 P-type conjugative transfer protein TrbG virB9
AVCG78_RS25905 (AVCG78_25880) 362793..363470 - 678 WP_071204875 conjugal transfer protein TrbF virB8
AVCG78_RS25910 (AVCG78_25885) 363488..364678 - 1191 WP_071585038 P-type conjugative transfer protein TrbL virB6
AVCG78_RS25915 (AVCG78_25890) 364672..364899 - 228 WP_071204873 entry exclusion protein TrbK -
AVCG78_RS25920 (AVCG78_25895) 364896..365663 - 768 WP_234618192 P-type conjugative transfer protein TrbJ virB5
AVCG78_RS25925 (AVCG78_25900) 365677..368145 - 2469 WP_071204871 conjugal transfer protein TrbE virb4
AVCG78_RS25930 (AVCG78_25905) 368167..368454 - 288 WP_071204870 conjugal transfer protein TrbD virB3
AVCG78_RS25935 (AVCG78_25910) 368447..368851 - 405 WP_071204869 conjugal transfer pilin TrbC virB2
AVCG78_RS25940 (AVCG78_25915) 368841..369812 - 972 WP_071204868 P-type conjugative transfer ATPase TrbB virB11
AVCG78_RS25945 (AVCG78_25920) 369809..370447 - 639 WP_071585036 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   18764 GenBank   NZ_CP056050
Plasmid name   pAvCG78b Incompatibility group   -
Plasmid size   370903 bp Coordinate of oriT [Strand]   284430..284466 [-]
Host baterium   Agrobacterium vitis strain CG78

Cargo genes

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