Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106338
Name   oriT_pB19.1.4a in_silico
Organism   Agrobacterium vaccinii strain B19.1.4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP054148 (152920..152962 [+], 43 nt)
oriT length   43 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: 43 nt

>oriT_pB19.1.4a
GGATCCAAGGGCGCAATTATACGTCGCTGATGCGACGCCCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4239 GenBank   WP_233137999
Name   traA_HRS00_RS23165_pB19.1.4a 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: 123520.22 Da        Isoelectric Point: 10.0736

>WP_233137999.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium vaccinii]
MAIAHFSASIISRGGGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPADAPKWVRAMIADR
SVAGASEAFWNKVEVFEKRSDAQLARDLTIALPLELSSEQNIALVRDFAEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLTEDGFGSKKVAVIGEDGQPVRTKSGKILYQLWAGSTDDFNSLRDGWFERLNHHLALGG
NDLKIDGRSYEKQGIDLQPTIHLGVGAKAIVRKAQEQGVRPELERLELNEQRRSENTRRILNNPAIVLDL
ITREKSVFDERDVAKVLHRYVDDPTVFQKLMLRIILNPQVLRLQRDTIDFSTGEKVPARYSTRAMIRLEA
TMVRQAVWLSNRDGHAVSKAALDATFRRHERLSQEQKAAIERIAGPARIAGVVGRAGAGKTTMMKAAREV
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVPDDKTVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
VNTRITGTRLKAEAVERLIGDWNHDYDHTKTTLILAHLRRDVRMLNVMAREKLVERGIVGEGHVFKTADG
VRQFDAGDQIVFLKNEGSLGVKNGMIAHVIEAAPNRIVAVIGENDQRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGHRPFAFNGGLAKVLSRKNAKETTLDYERGKLY
REALRFAESRGLNIVQVARTIARDRLDWTLRQKTKLVELGQRLAVFAQRLGLHHPLKTQTMKEAAPMVAG
IKTFSGSVADTVENKLDTDSALRQQWEEVSTRFAYVFADPETAFRAMNFNAVLADKETAKLALQTLTTAP
ASIGPLKGKTGILASKDERESRRIAEINVPALKRDLEQYLRMREAAIKRLSTDEQVQRQRVSIDIPALSP
AAHVVLERVRDAIDRNDLPAAMAYALSNRETKLEIDGFNQAVTERFAERTLLTNAAREPSGTLFDKLSDG
MQPEQKERLKEVWPIMRTSQQLAAHERTVQTLRQAADLRLAQRQTPVMKQ

  Protein domains


Predicted by InterproScan.

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

(855-951)

AAA domain (AAA_30)

(382-567)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)


  Protein structure



No available structure.




T4CP

ID   4261 GenBank   WP_233137869
Name   traG_HRS00_RS23150_pB19.1.4a insolico UniProt ID   _
Length   656 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 656 a.a.        Molecular weight: 70630.75 Da        Isoelectric Point: 9.4261

>WP_233137869.1 Ti-type conjugative transfer system protein TraG [Agrobacterium vaccinii]
MTVSKVFLAVIPATTMIVVVVFMPGIEHWLAALGKTAQAKLMLGRIGLALPYATAAAIGTIFLFAANGAV
AIKAAGWGVVSGDGVAILIALLREGGRLAGIAGDIPKGQSVLGYVDPASLLGASTTFLSGVFALRVAMMG
NAAFAKAAPRRIGGKRAVHGEADWMKVQEAAKLFPDPGGIVVGERYRVDRDSVAAVSFRADDPSTWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTVPTALKWGGGLVVLDPSSEVAPMVSEHRRKAGRKVIILD
PSTSGVGFNALDWIGRHGSTKEEDIVAVATWIMTDNPRSASARDDFFRASAMQLLTALIADVCLSGHTDE
EDQTLRRVRRNLSEPEPQLRARLTKIYEQSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNLKGRALFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSRQISRRPLILPHEVLRMRSDEQIVFTSGNPPLRCGRAIWFRRKDMSASVG
ENRFHKQITDGVKSYKAAPMTHTEET

  Protein domains


Predicted by InterproScan.

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

(163-637)

  Protein structure



No available structure.



ID   4262 GenBank   WP_233137925
Name   t4cp2_HRS00_RS23455_pB19.1.4a 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: 91909.81 Da        Isoelectric Point: 5.9706

>WP_233137925.1 conjugal transfer protein TrbE [Agrobacterium vaccinii]
MVTLKSFRHSGPSFADLAPYAGLVDNGVILLKDCSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAIRVPTGDYPNEGESHFPDPVTRAIDDERRTHFQKERGHFESRHALILTWRPPEPRRSGLTR
YIYSDAASRSATYADKALESFLTSIREVEQYLANVVSIRRMMTRETSERGGYRVARYDELFQFIRFCVTG
ENHPVRLPDIPMYLDWLVTAELQHGLTPMVENRFLGVVAIDGLPAESWPGILKTLDRMPLTYRWSSRFVF
LDSEEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVI
FEEDAVRLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPVAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADAQVFA
FDKGGSMLPLTLGLDGDHYQIGGGIGPSAGGEVKALAFCPLAELSTDSDRAWASEWIEMLVALQGVTITP
DYRNAISRQLSLMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFEIEEL
MNMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGGAREPGTREFYERIGFNERQIEIVATAIPKREYYVVSPEGRRLFNM
ALGRVALSFVGATGKEDLKQIHSLHSEHGAAWPLHWLQQRGIAHAETLFPTT

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 208205..217911

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HRS00_RS23400 (HRS00_23335) 203783..205180 - 1398 WP_233137915 amidase -
HRS00_RS23405 (HRS00_23340) 205198..205398 - 201 WP_233137916 hypothetical protein -
HRS00_RS23410 (HRS00_23345) 205395..206831 - 1437 WP_233137917 MmgE/PrpD family protein -
HRS00_RS23415 (HRS00_23350) 206828..207865 - 1038 WP_233137918 ABC transporter substrate-binding protein -
HRS00_RS23420 (HRS00_23355) 208205..209533 - 1329 WP_233137919 IncP-type conjugal transfer protein TrbI virB10
HRS00_RS23425 (HRS00_23360) 209545..210021 - 477 WP_233137920 conjugal transfer protein TrbH -
HRS00_RS23430 (HRS00_23365) 210021..210872 - 852 WP_233137921 P-type conjugative transfer protein TrbG virB9
HRS00_RS23435 (HRS00_23370) 210890..211567 - 678 WP_233137922 conjugal transfer protein TrbF virB8
HRS00_RS23440 (HRS00_23375) 211585..212775 - 1191 WP_233137923 P-type conjugative transfer protein TrbL virB6
HRS00_RS23445 (HRS00_23380) 212769..212996 - 228 WP_233137924 entry exclusion protein TrbK -
HRS00_RS23450 (HRS00_23385) 212993..213763 - 771 WP_233138002 P-type conjugative transfer protein TrbJ virB5
HRS00_RS23455 (HRS00_23390) 213774..216242 - 2469 WP_233137925 conjugal transfer protein TrbE virb4
HRS00_RS23460 (HRS00_23395) 216254..216553 - 300 WP_065657872 conjugal transfer protein TrbD virB3
HRS00_RS23465 (HRS00_23400) 216546..216950 - 405 WP_065657873 conjugal transfer pilin TrbC virB2
HRS00_RS23470 (HRS00_23405) 216940..217911 - 972 WP_233137926 P-type conjugative transfer ATPase TrbB virB11
HRS00_RS23475 (HRS00_23410) 217908..218543 - 636 WP_233137927 acyl-homoserine-lactone synthase -

Host bacterium

ID   6775 GenBank   NZ_CP054148
Plasmid name   pB19.1.4a Incompatibility group   -
Plasmid size   218909 bp Coordinate of oriT [Strand]   152920..152962 [+]
Host baterium   Agrobacterium vaccinii strain B19.1.4

Cargo genes

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