Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118444
Name   oriT_pRvVAR0630b in_silico
Organism   Agrobacterium vitis strain VAR06-30
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP023275 (274412..274448 [+], 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_pRvVAR0630b
GGCTCCAAGGGCGCAATTATACGTCGCTGATGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11718 GenBank   WP_180575622
Name   traA_H1Y61_RS25365_pRvVAR0630b 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: 123490.61 Da        Isoelectric Point: 9.6338

>WP_180575622.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium vitis]
MAIAHFSASIISRGDGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHQEFVLPADAPNWVRSLIADR
SVSGAVEAFWNKVEAFEKRSDAQLARDLTIALPLELTAEQNIALVRDFVEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLTENGFGAKKVAVIGEDGQPVRTKSGKIVYELWAGSTEDFNKLRDGWFERQNHHLALSG
IDLRVDGRSYEKQGIDLEPTIHLGVGAKAIERKAESQGVRPELERIELNEKRRSENTRRILRRPEIVLDL
ITHEKSVFDEGDISKVLHRYIDDPGMFQQLMARIIQSPDVLRLKRDTIDFATGDKVPARYSTRAMIRLEA
RMATQAIWLSNREGRAVSPTILDETFRRHVRLSDEQRIAIERIAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWGRGRDMLNERTVFVMDEAGMVASKQMADFVD
AVVRTGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRHASLDFARGNVARALSAYQ
SEGKVLGSTLKAEAADHLISDWYRDYDPAKSTLILAHLRRDVGMLNGMARDKLVESGIIGEGHAFRTADG
IRQFDVGDQIVFLKNEGSLGVKNGMIGHVIEAAPNRIVAVVGEGDQRRQVTVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGTRSFAFNGGLTKVLSRRNAKETTLDYERGNLY
RGALRYAENRGLNIVQVARTLLRDQLDWTLRQKTRLADLAQRLRAIGERFGLQQSPKTQAMKETAPMVAG
IKTFSGSVADTVEQKLDSDPALKKQWEEVSTRFVYVYADPETAFRAMNFDAVLADKDSARQVLQTLEAEP
AFIGPLRGKTGILASKADREDRRVAELNVPVLKRDLEHYLRMRETAVQRLQADEQVLRQRISIDIPALSP
AAHVVLERVRDAIDRNDLPAAMAYALSNRETKTEIDGFNQALAQRFGERTLLTNAAREPSGKLFDTLSEG
MQPEQKERLKQAWPVMRAAQQLAAHERTVQSLKQSEELRLIQSQTSVLKQ

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(691-736)

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

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-565)


  Protein structure



No available structure.




T4CP

ID   13720 GenBank   WP_180575524
Name   t4cp2_H1Y61_RS24830_pRvVAR0630b 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: 91776.74 Da        Isoelectric Point: 5.5838

>WP_180575524.1 conjugal transfer protein TrbE [Agrobacterium vitis]
MVAPKSFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDGERNEVSRQINAILSRLG
SGWMIQVDAVRVPTGDYPDEAESHFPDPVTRAIDDERRAHFQKERGHFESRHALILTWRPPEPRRSGLAR
YVYSDAASRSATYADTMLQSFLTSIREIEQYLANVLSIRRMMTREISERGGFRVARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNTLDLMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVI
FEEDAIRLQEKCEAIRRLIQAEGFGARIEALNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPTAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADAQLFA
FDKGGSMLPLTLGLNGDHYQIGGDITPSAGAEVRMLAFCPLAELSTDGDRAWASEWIETLVALQGVTITP
DYRNAISRQIALMADSRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLSLGAFQCFEIEEL
MNMGERNLVPVLLYLFRRIEKRLTGAPSLIILDEAWLMLGHSVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKREYYVVSPEGRRLFNM
ALGPVALSFVGATGKEDLKRIRTLHSEHGAAWPCPWLQQRGIAHAEALFPTS

  Protein domains


Predicted by InterproScan.

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

(186-400)

  Protein structure



No available structure.



ID   13721 GenBank   WP_180575534
Name   traG_H1Y61_RS25035_pRvVAR0630b insolico UniProt ID   _
Length   640 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 640 a.a.        Molecular weight: 68915.68 Da        Isoelectric Point: 8.9882

>WP_180575534.1 Ti-type conjugative transfer system protein TraG [Agrobacterium vitis]
MLAALVMTSGMEHRLAEFGSSTQAKLMLGRTGLALPYIAVAAIGAIALFAANGSADIKTVGVSVLAANSA
AIVIAMIRETIRLTGIASSVPAGQSVLTYADPATAVGAGVAFISAMFALRVTIKGNAAFAQTGPKRIGGK
RAVHGEADWMKLQEAAKLFPEPGGIVIGERYRVDKDSVATMPFRADEPQSWGAGGKSQLLCFDGSFGSSH
GIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVVDHRRKAGRKVIVLDPTLQGVGFNALDWIG
RHGNTKEEDIVAVATWIMTDNARTASVRDDFFRASAMQLLTALIADVCLSGHTDAKNQTLRRVRANLSEP
EPKLRGRLTEIYEQSESDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPHYAGLVSGDSFSTDDLAN
GGTDIFIALDLKVLEAHPGLARVVIGALLNAIYNRNGDVKGRTLFLLDEVARLGYLRILETARDAGRKYG
ITLTLIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTTVEVDQTNRSSGMKGS
SRSRSKQLSRRPLILPHELLRMRSDEQIVFTAGNAPLRCGRAIWFRREDMKACVGENRFHHPHTTTTAIT
APKVTKSDED

  Protein domains


Predicted by InterproScan.

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

(148-620)

  Protein structure



No available structure.



ID   13722 GenBank   WP_180575579
Name   traG_H1Y61_RS25350_pRvVAR0630b 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: 70542.70 Da        Isoelectric Point: 9.1713

>WP_180575579.1 Ti-type conjugative transfer system protein TraG [Agrobacterium vitis]
MTANRLLLFVLLAAIMLAALVMTSGMEHRLAEFGSSTQAKLMLGRTGLALPYIAVAAIGAIALFAANGSA
DIKTVGVSVLAANSAAIVIAMIRETIRLTGIASSVPAGQSVLTYADPATAVGAGVAFISAMFALRVTIKG
NAAFAQTGPKRIGGKRAVHGEADWMKLQEAAKLFPEPGGIVIGERYRVDKDSVATMPFRADEPQSWGAGG
KSQLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVVDHRRKAGRKVIVLD
PTLQGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNARTASVRDDFFRASAMQLLTALIADVCLSGHTDA
KNQTLRRVRANLSEPEPKLRGRLTEIYEQSESDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPHYA
GLVSGDSFSTDDLANGGTDIFIALDLKVLEAHPGLARVVIGALLNAIYNRNGDVKGRTLFLLDEVARLGY
LRILETARDAGRKYGITLTLIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSKQLSRRPLILPHEVLRMRSDEQIVFTAGNAPLRCGRAIWFRREDMKACVG
ENRFHHHHTTTTAIAASKVTKSDED

  Protein domains


Predicted by InterproScan.

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

(163-637)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 164653..182713

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H1Y61_RS24795 (RvVAR0630_pl05470) 159972..161216 - 1245 WP_180575517 plasmid replication protein RepC -
H1Y61_RS24800 (RvVAR0630_pl05480) 161373..162368 - 996 WP_180575518 plasmid partitioning protein RepB -
H1Y61_RS24805 (RvVAR0630_pl05490) 162453..163643 - 1191 WP_180575519 plasmid partitioning protein RepA -
H1Y61_RS24810 (RvVAR0630_pl05500) 164018..164656 + 639 WP_180575520 acyl-homoserine-lactone synthase TraI -
H1Y61_RS24815 (RvVAR0630_pl05510) 164653..165624 + 972 WP_180575521 P-type conjugative transfer ATPase TrbB virB11
H1Y61_RS24820 (RvVAR0630_pl05520) 165614..166018 + 405 WP_180575522 conjugal transfer pilin TrbC virB2
H1Y61_RS24825 (RvVAR0630_pl05530) 166011..166310 + 300 WP_180575523 conjugal transfer protein TrbD virB3
H1Y61_RS24830 (RvVAR0630_pl05540) 166321..168789 + 2469 WP_180575524 conjugal transfer protein TrbE virb4
H1Y61_RS24835 (RvVAR0630_pl05550) 168761..169570 + 810 WP_180575525 P-type conjugative transfer protein TrbJ virB5
H1Y61_RS24840 169567..169794 + 228 WP_180575526 entry exclusion protein TrbK -
H1Y61_RS24845 (RvVAR0630_pl05560) 169788..170978 + 1191 WP_180575527 P-type conjugative transfer protein TrbL virB6
H1Y61_RS24850 (RvVAR0630_pl05570) 170996..171658 + 663 WP_180575528 conjugal transfer protein TrbF virB8
H1Y61_RS24855 (RvVAR0630_pl05580) 171736..172530 + 795 WP_234644437 P-type conjugative transfer protein TrbG virB9
H1Y61_RS24860 (RvVAR0630_pl05590) 172530..173006 + 477 WP_156556228 conjugal transfer protein TrbH -
H1Y61_RS24865 (RvVAR0630_pl05600) 173018..174340 + 1323 WP_180575529 IncP-type conjugal transfer protein TrbI virB10
H1Y61_RS24870 174439..174735 + 297 Protein_167 DUF1403 family protein -
H1Y61_RS24875 (RvVAR0630_pl05610) 174851..175567 - 717 WP_156619943 IS6 family transposase -
H1Y61_RS24880 (RvVAR0630_pl05620) 175791..176294 + 504 Protein_169 OB-fold nucleic acid binding domain-containing protein -
H1Y61_RS24885 (RvVAR0630_pl05630) 176305..176970 + 666 WP_180575530 SOS response-associated peptidase family protein -
H1Y61_RS24890 (RvVAR0630_pl05640) 177000..177644 + 645 WP_174113416 SOS response-associated peptidase -
H1Y61_RS24895 177652..177964 - 313 Protein_172 hypothetical protein -
H1Y61_RS24900 (RvVAR0630_pl05670) 177968..178204 - 237 WP_235681004 hypothetical protein -
H1Y61_RS24905 (RvVAR0630_pl05680) 178315..178485 + 171 WP_156556177 hypothetical protein -
H1Y61_RS24910 (RvVAR0630_pl05690) 178482..179288 + 807 WP_174113417 exodeoxyribonuclease III -
H1Y61_RS24915 (RvVAR0630_pl05700) 179278..179496 + 219 WP_156556175 hypothetical protein -
H1Y61_RS24920 (RvVAR0630_pl05710) 179657..180568 - 912 WP_234644357 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
H1Y61_RS24925 (RvVAR0630_pl05720) 180558..180956 - 399 WP_234625163 DUF6088 family protein -
H1Y61_RS24930 (RvVAR0630_pl05730) 181421..181600 + 180 WP_180575531 hypothetical protein -
H1Y61_RS24935 (RvVAR0630_pl05740) 181778..182713 + 936 WP_156556169 DUF3991 and toprim domain-containing protein traP
H1Y61_RS24940 (RvVAR0630_pl05750) 182846..183451 + 606 WP_156556168 DUF1419 domain-containing protein -

Host bacterium

ID   18877 GenBank   NZ_AP023275
Plasmid name   pRvVAR0630b Incompatibility group   -
Plasmid size   309504 bp Coordinate of oriT [Strand]   274412..274448 [+]
Host baterium   Agrobacterium vitis strain VAR06-30

Cargo genes

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