Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118332
Name   oriT_pAvF25b in_silico
Organism   Agrobacterium vitis strain F2/5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055271 (158752..158788 [-], 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_pAvF25b
GGCTCCAAGGGCGCAATTATACGTCGCTGATGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11642 GenBank   WP_174113424
Name   traA_AVF2S5_RS24460_pAvF25b 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: 123939.67 Da        Isoelectric Point: 9.9753

>WP_174113424.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium vitis]
MAIAHFSASIISRGDGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHQEFVLPADAPNWVRSLIADR
SVSGAVEAFWNKVEAFEKRSDAQLARDLTIALPLELTAEQNIALVRDFVEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLSEDGFGAKKVAVIGEEGQPVRTKSGKIVYELWAGSTEDFNALRDGWFERLNHHLALRG
FDLRVDGRSYEKQGIDLEPTIHLGVGTKAIERKAKSKALRPELERIELNEQLRRDNARRILRKPGIVLDM
ITRERSVFDERDVAKVLHRYVDDPAVFQQLMLRIIQNPEVLRLQRDTIEFATGEKVPARYSTRAMIRLEA
TMVRQALWLSNRYGHDVSDSALNATFRRHERLSDEQKTAIELIARPSRIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVLDDRTVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRALVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNHDYDQTKTTLILAHLRRDVRMLNVMAREKLVERGIVGEGHVFKTADG
VRQFDVGDQIVFLKNETSLGVKNGMIAQVIEAAPNRIVAIIGEGDERRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAESRGLNIVQVARTLVRDQLDWTLRQKTKLVDLGQRLASFAERLGLHHPPKTQTIKEAAPMVAG
IKTFSGSVADTVEHKLDTDPALRQQWEEVSTRFSYVFADPETAFRAMNFDAVLADKETAKLALQTLTTAP
VSIGPLRGKTGILASKADREHRRVAELNVPALKRDLEHYLRMRETAVQRLKADEQVLRQRISIDIPALSP
AAHVVLERVRYAIDRNDLPAAMANALSNRETKLEIDGFNQAVTQRFGERTLLTNAAREPSGKIFDTLSNG
MEPEQKERLKQAWPVMRAAQQLAAHERTVQSLKQSEELRLIQSQTSVLKQ

  Protein domains


Predicted by InterproScan.

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

(855-951)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-567)


  Protein structure



No available structure.




T4CP

ID   13624 GenBank   WP_071585024
Name   traG_AVF2S5_RS24475_pAvF25b 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   13625 GenBank   WP_174113412
Name   t4cp2_AVF2S5_RS24695_pAvF25b 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: 91739.69 Da        Isoelectric Point: 5.3930

>WP_174113412.1 conjugal transfer protein TrbE [Agrobacterium vitis]
MVALKSFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDGERNEVSRQINAILSRLD
SGWMIQVDAVRVPTGDYPDEAESHFPDPVTRAIDDERRAHFQKERGHFESCHALILTWRPPEPRRSGLTR
YVYSDAASRSATYADTMLQSFLTSIREVEQYLANVVSIRRMMTRETTERGGFRIARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLVTAELQHGLTPLVENRVLGVVAIDGLPAESWPGILNTLDLMPLTYRWSSRFIF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVI
FDEDAIQLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPTAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYSDAQIFA
FDKGGSMLPLTLGLGGDHYQIGGDITPSAGAEVRMLAFCPLAELSTDGDRAWASEWIETLVALQSVTITP
DYRNAISRQIALMADSRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFEIEEL
MNMGERNLVPVLLYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKREYYVVSPEGRRLFNM
ALGPVALSFVGATGKEDLKQIRSLHSKHGAAWPCPWLQQRGIAHAETLFPTS

  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: 185532..203525

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AVF2S5_RS24585 (AVF2S5_24530) 184794..185399 - 606 WP_156556168 DUF1419 domain-containing protein -
AVF2S5_RS24590 (AVF2S5_24535) 185532..186467 - 936 WP_156556169 DUF3991 and toprim domain-containing protein traP
AVF2S5_RS24595 (AVF2S5_24540) 186645..186824 - 180 WP_156556171 hypothetical protein -
AVF2S5_RS24600 (AVF2S5_24545) 187289..187687 + 399 WP_234625163 DUF6088 family protein -
AVF2S5_RS24605 (AVF2S5_24550) 187677..188588 + 912 WP_234644357 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
AVF2S5_RS24610 (AVF2S5_24555) 188749..188967 - 219 WP_156556175 hypothetical protein -
AVF2S5_RS24615 (AVF2S5_24560) 188957..189763 - 807 WP_174113417 exodeoxyribonuclease III -
AVF2S5_RS24620 (AVF2S5_24565) 189760..189930 - 171 WP_156556177 hypothetical protein -
AVF2S5_RS24625 (AVF2S5_24570) 190041..190277 + 237 WP_235681004 hypothetical protein -
AVF2S5_RS24630 (AVF2S5_24575) 190281..190593 + 313 Protein_180 hypothetical protein -
AVF2S5_RS24635 (AVF2S5_24580) 190601..191245 - 645 WP_174113416 SOS response-associated peptidase -
AVF2S5_RS24640 (AVF2S5_24585) 191275..191873 - 599 Protein_182 DUF159 family protein -
AVF2S5_RS24645 (AVF2S5_24590) 191884..192387 - 504 Protein_183 OB-fold nucleic acid binding domain-containing protein -
AVF2S5_RS24650 (AVF2S5_24595) 192611..193327 + 717 WP_156619943 IS6 family transposase -
AVF2S5_RS24655 (AVF2S5_24600) 193395..193835 - 441 Protein_185 DUF1403 family protein -
AVF2S5_RS24660 (AVF2S5_24605) 193838..195160 - 1323 WP_156556200 IncP-type conjugal transfer protein TrbI virB10
AVF2S5_RS24665 (AVF2S5_24610) 195172..195648 - 477 WP_156556228 conjugal transfer protein TrbH -
AVF2S5_RS24670 (AVF2S5_24615) 195648..196514 - 867 WP_267966963 P-type conjugative transfer protein TrbG virB9
AVF2S5_RS24675 (AVF2S5_24620) 196520..197182 - 663 WP_156556196 conjugal transfer protein TrbF virB8
AVF2S5_RS24680 (AVF2S5_24625) 197200..198390 - 1191 WP_174113415 P-type conjugative transfer protein TrbL virB6
AVF2S5_RS24685 (AVF2S5_24630) 198384..198611 - 228 WP_174113414 entry exclusion protein TrbK -
AVF2S5_RS24690 (AVF2S5_24635) 198608..199417 - 810 WP_174113413 P-type conjugative transfer protein TrbJ virB5
AVF2S5_RS24695 (AVF2S5_24640) 199389..201857 - 2469 WP_174113412 conjugal transfer protein TrbE virb4
AVF2S5_RS24700 (AVF2S5_24645) 201868..202167 - 300 WP_174113411 conjugal transfer protein TrbD virB3
AVF2S5_RS24705 (AVF2S5_24650) 202160..202564 - 405 WP_174113410 conjugal transfer pilin TrbC virB2
AVF2S5_RS24710 (AVF2S5_24655) 202554..203525 - 972 WP_174113409 P-type conjugative transfer ATPase TrbB virB11
AVF2S5_RS24715 (AVF2S5_24660) 203522..204160 - 639 WP_174113408 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   18765 GenBank   NZ_CP055271
Plasmid name   pAvF25b Incompatibility group   -
Plasmid size   204451 bp Coordinate of oriT [Strand]   158752..158788 [-]
Host baterium   Agrobacterium vitis strain F2/5

Cargo genes

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