Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119214
Name   oriT_pRgalR602b in_silico
Organism   Rhizobium gallicum bv. gallicum R602sp strain R602 voucher MSDJ1109
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP006879 (484280..484321 [+], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      20..25, 30..35  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pRgalR602b
ATCCAAGGGCGCAATTATACGTCGCTGATGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12158 GenBank   WP_040114402
Name   traA_RGR602_RS23280_pRgalR602b insolico UniProt ID   A0A0B4XBP6
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122379.56 Da        Isoelectric Point: 9.9596

>WP_040114402.1 Ti-type conjugative transfer relaxase TraA [Rhizobium gallicum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLAHEEFVIPADAPDWLRTIIADR
SVSGASEAFWNKVEAFEKRSDAQLAKDVTIALPVELTYEQNIALVREFVERHIIATGMVADWVYHDAPGN
PHVHLMTTLRPLTDDGFGGKKVAVLGPDGNPMRNESGKIVYELWAGSTDDFNALRDGWFACQNRHLALAG
LDICIDGRSFDKQGIELTPTIHLGVGTKAIERKSEAATKPLTLERIELQEDRRAENARRVQRRPEIVLDL
ITREKSVFDERDVAKVLHRYIDDADLFQSLLVRTLQSPETLQLERERIEFATGVRVSAKYTTREVIQLEA
EMANRAIWLSHRSSHGVREAVLEATFSRHSRLSEEQKIAIAHVAGGERIAAVIGRAGAGKTTMMKAAREA
WQAAGYRVVGAALAGKAAEGLQKEAGIRSRTLSSWVLRWNAGRNQLDDKTVFVLDEAGMVSSRQMALFVE
AATKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRKQWMRDASLDLARGKVGKAVDAYR
AYGHFKGSELKAQAVENLIADWNGDYDPVKTTLILAHLRRDVRMLNEMARAKLVERGILAEGFVFKTEDG
NRKFAAGDHIVFLKNEGSLSVKNGMLAKVVEALPGRIVAEIGEGEHRRQVTVEQRFYNHVDHGYATTIHK
SQGATIDRVYILASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYEKGAFY
KQALRFAEARGLHLVNVARTLVRDRLEWTVRQKQKLADLAARLAAIGGQFGLSTGAKKSPIQNIIKEAKP
MVSGIATFAKSLEQAVEDKVAADPGLKKQWEEVSSRFHLVYAQPETAFKAVNVDAILKDEAAAKSTIARI
GTQPDSFGALKGKTGILASRADKQGRERALNNAPALARNLERYLRQRADAERKHEIEERAVRLKVSVDIP
ALSPAAKRTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFARAVSERFGERTFLPLAAKDTSGQAFQT
VTTGMSAGQKAEVQSAWNSMRTVQQFAAHERTTEALKQVETLRQTKAQGLSLK

  Protein domains


Predicted by InterproScan.

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

(859-955)

AAA domain (AAA_30)

(382-566)

MobA/MobL family (MobA_MobL)

(17-243)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(692-735)


  Protein structure


Source ID Structure
AlphaFold DB A0A0B4XBP6


T4CP

ID   14240 GenBank   WP_040114399
Name   traG_RGR602_RS23265_pRgalR602b insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 68887.05 Da        Isoelectric Point: 9.7297

>WP_040114399.1 Ti-type conjugative transfer system protein TraG [Rhizobium gallicum]
MNRVLLAITPVMLMVGVAILASGMAPSLAGFGKTEAAKLMLGRAGIALPYVLAAAIGVVFLFAAVGAIRI
HFAGWGVVAGSASAISIAALREATRLAAFSGQLPAGRSIFAYLDPPTMIGAAAALMAGCFALRVALLGNA
GFARSEPTRIRGKRALHGEADWMKLNEAEKLLPDAGGIVIGERYRVDKDSTAALSFRADSPETWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVCKRREDAGRRIRILDPR
NPQTGFNALDWIGQFGGTKEEDIAAVASWIMSDSGRTSGVRDDFFRASGLQLLTAIIADVCLSGHTEKER
QTLRQVRANLSEPEPKLRQRLQEIYDNSESDFVRENVAAFVNMTPETFSGVYANAIKETHWLSYPNYAAL
VSGSTFLTEDIASGKTDVFINIDLKTLETHAGLARVIIGSLVNAIYNRDGVMNGRALFLLDEVARLGHMR
ILETARDAGRKYGITLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRQDMRTCVAKN
RFKSPST

  Protein domains


Predicted by InterproScan.

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

(161-634)

  Protein structure



No available structure.



ID   14241 GenBank   WP_040114416
Name   t4cp2_RGR602_RS23360_pRgalR602b insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91600.37 Da        Isoelectric Point: 5.8201

>WP_040114416.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVGLKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDIERNEVSRQMNAVLSRLG
SGWMIQAEAIRIPTVDYPSEDRCYFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKIALSK
YIYADGESRRTSYADTVLFVFKNAIREIEQYFANTLSIRRMETRETVERGGERIVRYDELLQFVRFCITG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRYLSVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARAKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVIL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYSNIREPLINTSNLADLIPLNAVWS
GNPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYQNAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSGLGTDADRAWATDWIEMLVGLQGVSITPDHRN
AISRQVGLMTSAAGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLSLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGFPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARQPGTREFYERIGFNERQIEIVSGSIPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLQTRGVRDAVSLLNFE

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 489438..502579

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RGR602_RS23285 (RGR602_PB00495) 487762..488268 + 507 WP_052451721 conjugative transfer signal peptidase TraF -
RGR602_RS23290 (RGR602_PB00496) 488258..489421 + 1164 WP_040114404 conjugal transfer protein TraB -
RGR602_RS23295 (RGR602_PB00497) 489438..490052 + 615 WP_040114405 TraH family protein virB1
RGR602_RS23300 (RGR602_PB00498) 490074..490451 - 378 WP_040114406 DUF5615 family PIN-like protein -
RGR602_RS23305 (RGR602_PB00499) 490448..491080 - 633 WP_040114407 DUF433 domain-containing protein -
RGR602_RS23310 (RGR602_PB00500) 491241..491456 - 216 WP_040114408 helix-turn-helix domain-containing protein -
RGR602_RS23315 (RGR602_PB00501) 491674..491997 + 324 WP_040114409 transcriptional repressor TraM -
RGR602_RS23320 (RGR602_PB00502) 492001..492705 - 705 WP_040114495 autoinducer binding domain-containing protein -
RGR602_RS23325 (RGR602_PB00503) 493022..494359 - 1338 WP_052451722 IncP-type conjugal transfer protein TrbI virB10
RGR602_RS23330 (RGR602_PB00504) 494371..494808 - 438 WP_040114410 conjugal transfer protein TrbH -
RGR602_RS23335 (RGR602_PB00505) 494812..495624 - 813 WP_040114411 P-type conjugative transfer protein TrbG virB9
RGR602_RS23340 (RGR602_PB00506) 495642..496304 - 663 WP_040114412 conjugal transfer protein TrbF virB8
RGR602_RS23345 (RGR602_PB00507) 496323..497504 - 1182 WP_040114413 P-type conjugative transfer protein TrbL virB6
RGR602_RS23350 (RGR602_PB00508) 497498..497698 - 201 WP_040114414 entry exclusion protein TrbK -
RGR602_RS23355 (RGR602_PB00509) 497695..498498 - 804 WP_040114415 P-type conjugative transfer protein TrbJ virB5
RGR602_RS23360 (RGR602_PB00510) 498470..500926 - 2457 WP_040114416 conjugal transfer protein TrbE virb4
RGR602_RS23365 (RGR602_PB00511) 500937..501236 - 300 WP_040114417 conjugal transfer protein TrbD virB3
RGR602_RS23370 (RGR602_PB00512) 501229..501612 - 384 WP_040114418 TrbC/VirB2 family protein virB2
RGR602_RS23375 (RGR602_PB00513) 501602..502579 - 978 WP_040114419 P-type conjugative transfer ATPase TrbB virB11
RGR602_RS23380 (RGR602_PB00514) 502590..503213 - 624 WP_040114420 acyl-homoserine-lactone synthase TraI -
RGR602_RS23385 (RGR602_PB00516) 503535..504818 + 1284 WP_040114421 plasmid partitioning protein RepA -
RGR602_RS23390 (RGR602_PB00517) 504815..505846 + 1032 WP_040114422 plasmid partitioning protein RepB -
RGR602_RS23395 (RGR602_PB00518) 506041..507243 + 1203 WP_040114423 plasmid replication protein RepC -

Host bacterium

ID   19644 GenBank   NZ_CP006879
Plasmid name   pRgalR602b Incompatibility group   -
Plasmid size   507254 bp Coordinate of oriT [Strand]   484280..484321 [+]
Host baterium   Rhizobium gallicum bv. gallicum R602sp strain R602 voucher MSDJ1109

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   hupE
Degradation gene   LinG, dxnH, linJ
Symbiosis gene   nodD, nodA, nodF, nodE, nodM, fixN, fixO, fixQ, fixS, nodB, nodC, nodS, nodU, nodI, nodJ, nodH, nifT, nifZ, nifB, nifA, fixX, fixC, fixB, fixA, nifW, nifS, nifH, nifD, nifE, nifN, nifX, mLTONO_5203
Anti-CRISPR   AcrIIC1