Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118445
Name   oriT_pRvVAT039b in_silico
Organism   Agrobacterium vitis strain VAT03-9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP023282 (304906..304942 [+], 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_pRvVAT039b
GGCTCCAAGGGCGCAATTATACGTCGCTGATGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11719 GenBank   WP_071205421
Name   traA_H1Z14_RS26115_pRvVAT039b 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   13723 GenBank   WP_071204871
Name   t4cp2_H1Z14_RS25680_pRvVAT039b 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.



ID   13724 GenBank   WP_071585024
Name   traG_H1Z14_RS26100_pRvVAT039b 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 207517..217215

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H1Z14_RS25615 (RvVAT039_pl07390) 202623..203576 + 954 WP_071204882 AAA family ATPase -
H1Z14_RS25620 (RvVAT039_pl07400) 203573..204304 + 732 WP_071204881 DUF6602 domain-containing protein -
H1Z14_RS25625 (RvVAT039_pl07410) 204362..204838 + 477 WP_071204880 hypothetical protein -
H1Z14_RS25635 205764..206462 - 699 Protein_184 SMC-Scp complex subunit ScpB -
H1Z14_RS25640 (RvVAT039_pl07440) 206465..207418 - 954 WP_071204878 DUF1403 family protein -
H1Z14_RS25645 (RvVAT039_pl07450) 207517..208839 - 1323 WP_071204877 IncP-type conjugal transfer protein TrbI virB10
H1Z14_RS25650 (RvVAT039_pl07460) 208851..209327 - 477 WP_071204876 conjugal transfer protein TrbH -
H1Z14_RS25655 (RvVAT039_pl07470) 209327..210121 - 795 WP_234618193 P-type conjugative transfer protein TrbG virB9
H1Z14_RS25660 (RvVAT039_pl07480) 210196..210873 - 678 WP_071204875 conjugal transfer protein TrbF virB8
H1Z14_RS25665 (RvVAT039_pl07490) 210891..212081 - 1191 WP_071585038 P-type conjugative transfer protein TrbL virB6
H1Z14_RS25670 (RvVAT039_pl07500) 212075..212302 - 228 WP_071204873 entry exclusion protein TrbK -
H1Z14_RS25675 (RvVAT039_pl07510) 212299..213066 - 768 WP_234618192 P-type conjugative transfer protein TrbJ virB5
H1Z14_RS25680 (RvVAT039_pl07520) 213080..215548 - 2469 WP_071204871 conjugal transfer protein TrbE virb4
H1Z14_RS25685 (RvVAT039_pl07530) 215570..215857 - 288 WP_071204870 conjugal transfer protein TrbD virB3
H1Z14_RS25690 (RvVAT039_pl07540) 215850..216254 - 405 WP_071204869 conjugal transfer pilin TrbC virB2
H1Z14_RS25695 (RvVAT039_pl07550) 216244..217215 - 972 WP_071204868 P-type conjugative transfer ATPase TrbB virB11
H1Z14_RS25700 (RvVAT039_pl07560) 217212..217850 - 639 WP_071585036 acyl-homoserine-lactone synthase TraI -
H1Z14_RS25705 (RvVAT039_pl07570) 218217..219404 + 1188 WP_071204866 plasmid partitioning protein RepA -
H1Z14_RS25710 (RvVAT039_pl07580) 219479..220465 + 987 WP_071204865 plasmid partitioning protein RepB -
H1Z14_RS25715 (RvVAT039_pl07590) 220620..221834 + 1215 WP_071204864 plasmid replication protein RepC -

Host bacterium

ID   18878 GenBank   NZ_AP023282
Plasmid name   pRvVAT039b Incompatibility group   -
Plasmid size   371025 bp Coordinate of oriT [Strand]   304906..304942 [+]
Host baterium   Agrobacterium vitis strain VAT03-9

Cargo genes

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