Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118333
Name   oriT_pAvF25c in_silico
Organism   Agrobacterium vitis strain F2/5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055272 (80897..80936 [+], 40 nt)
oriT length   40 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 40 nt

>oriT_pAvF25c
TCCAAGGGCGCAATTATACGTCGCTGACACGACGCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11643 GenBank   WP_174113225
Name   traA_AVF2S5_RS25095_pAvF25c 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: 123770.52 Da        Isoelectric Point: 9.9361

>WP_174113225.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Agrobacterium]
MAIAHFSASIVSRGGGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPIDAPKWARAMIADR
SVSGAVEAFWNKVEDFEKRSDAQLARDLTIALPLELTPEQNIALVRDFVEKHIHAKGMVADWVYHNNPGN
PHIHLMTTLRPLTEDGFGAKKVAVTAKDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLEPAIHLGVGAKAIERKAQEQGFRPELERLELNEERRGENARRILRRPEIVLDL
IMREKSVFDERDVAKVLHRYIDDPAVFQQLMLRIILNPEVLRLQRDTIDFSTGEKVPARYSTRAMIRLEA
TMVRQATWLSGKDTHAVSAAVLDATLRRHERLSEEQKTAIERIAGPARIAAVVGRAGAGKTTMMKAVREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVLDSKTIFVMDEAGMVASKQMAGFVD
TVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANVRITGTRLKAEAVERLIGDWNHDYDHTKTTLILAHLRRDVRMLNQMAREKLVERGIVGEGHVFKTADG
IRQFDAGDQIVFLKNEGSLGVKNGMIAHIIEAAPNRIVAVIGEGDQRRRVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFNGGLSKVLSRKNAKETTLDYERGSLY
REALRYAENRGLNIVQVARTLLRDQLDWTLRQKTRLDELGQRLAVFAERLGLHHPPKTQTMKEAAPMVAG
IKTFPGSVADTVGDRLGTDPALKRQWEEVSTRFAYVFADPETAFRAMNFDAVLADKDSALQVLQKLEAEP
ASIGPLKGKTGILASKTDREDRRIAELNVPALKRDLEQYLRMRENAAQRLQTDEQALRQRVSIDIPALSP
AARVVLERVRDAIDRNDLPAALGYVLSNRETKLEIDGFSKAVTERFGERTLLTNAARQPSGPLFDKLSNG
MRPAQKEQLKEAWPVMRTAQQIAAHERTTQTLKQAEELRLTQRQSPVMKQ

  Protein domains


Predicted by InterproScan.

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

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

AAA domain (AAA_30)

(382-567)


  Protein structure



No available structure.




T4CP

ID   13626 GenBank   WP_153517022
Name   traG_AVF2S5_RS25080_pAvF25c insolico UniProt ID   _
Length   641 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 641 a.a.        Molecular weight: 69244.33 Da        Isoelectric Point: 9.4596

>WP_153517022.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Agrobacterium]
MTVNRLLLLILPAIIMLAAMFATSGTEQRLAAFGTSPQAKLMLGRAGLALPYIAAVAIGLIGLFAANGSA
NIKAAGLSVLAGNGVVITIATLREVIRLNSITSRVPAEQSVLAYADPVTMIGVGIAFISGMFALRVAIKG
NAAFATTAPKRIGGKRAVHGEADWMKIQEAAKLFPEPGGIVIGERYRVDRDSVATMPFRADDRQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVYEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGSTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEA
EDQTLRRVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGDVKGRTLFLLDEVARLGY
LRILETARDAGRKYGTTLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSRQLSRRPLILPHEVLRMRADEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
TNRFHREEKAP

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   13627 GenBank   WP_060716498
Name   t4cp2_AVF2S5_RS25625_pAvF25c 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: 92090.79 Da        Isoelectric Point: 5.4919

>WP_060716498.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALNLFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINMIMSRLG
SGWMIQVEALRVPTIDYPADDACHFADPVTRAIDTERRTHFERESGHFESRHALILTWRPPEPRRSGLAR
YVYSDTASRSATYADTALESFRTSIREVEQYLANVVSIRRMVTRETEERGGFRIARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLVTAELQHGLTPTVESRFLGVVAIDGLAAESWPGILNSLDLMPLTYRWSSRFVF
LDEQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMMMVAETEDAIAEASSQLVAYGYYTPVIVL
FDEQQERLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLVNTRNLADLIPLNSVWS
GSPVAPCPFYPPGSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLSLIAAQFRRYADAQIFA
FDKGRSMLPLTLAIGGDHYEIGGDAAEGGERDSPRLAFCPLAELASDGDRAWAAEWIETLVALQGVTVTP
DYRNAISRQLALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLALGAFQCFEVEEL
MNLGERNLVPVLLYMFRRVEKRLTGAPSLIILDEAWLMLGHPTFRNKIREWLKVVRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVASPEGRRLFDM
SLGPVALSFVGASGKEDLKRIRALHFEHGADWPKHWLQQRGIAHAETLFQAA

  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: 190069..199745

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AVF2S5_RS25575 (AVF2S5_25515) 185706..186491 + 786 WP_060716474 amino acid ABC transporter ATP-binding protein -
AVF2S5_RS25580 (AVF2S5_25520) 186637..187974 + 1338 WP_202037108 MmgE/PrpD family protein -
AVF2S5_RS25585 (AVF2S5_25525) 188150..190015 + 1866 WP_060716476 LysR family transcriptional regulator -
AVF2S5_RS25590 (AVF2S5_25530) 190069..191379 - 1311 WP_153517050 IncP-type conjugal transfer protein TrbI virB10
AVF2S5_RS25595 (AVF2S5_25535) 191392..191871 - 480 WP_071208209 conjugal transfer protein TrbH -
AVF2S5_RS25600 (AVF2S5_25540) 191871..192725 - 855 WP_071208371 P-type conjugative transfer protein TrbG virB9
AVF2S5_RS25605 (AVF2S5_25545) 192743..193405 - 663 WP_153517051 conjugal transfer protein TrbF virB8
AVF2S5_RS25610 (AVF2S5_25550) 193420..194616 - 1197 WP_153517052 P-type conjugative transfer protein TrbL virB6
AVF2S5_RS25615 (AVF2S5_25555) 194610..194828 - 219 WP_060716496 entry exclusion protein TrbK -
AVF2S5_RS25620 (AVF2S5_25560) 194825..195634 - 810 WP_153517054 P-type conjugative transfer protein TrbJ virB5
AVF2S5_RS25625 (AVF2S5_25565) 195606..198074 - 2469 WP_060716498 conjugal transfer protein TrbE virb4
AVF2S5_RS25630 (AVF2S5_25570) 198085..198384 - 300 WP_045023373 conjugal transfer protein TrbD virB3
AVF2S5_RS25635 (AVF2S5_25575) 198377..198784 - 408 WP_060716499 conjugal transfer pilin TrbC virB2
AVF2S5_RS25640 (AVF2S5_25580) 198774..199745 - 972 WP_060716500 P-type conjugative transfer ATPase TrbB virB11
AVF2S5_RS25645 (AVF2S5_25585) 199742..200377 - 636 WP_060716501 acyl-homoserine-lactone synthase -

Host bacterium

ID   18766 GenBank   NZ_CP055272
Plasmid name   pAvF25c Incompatibility group   -
Plasmid size   200741 bp Coordinate of oriT [Strand]   80897..80936 [+]
Host baterium   Agrobacterium vitis strain F2/5

Cargo genes

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