Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107441
Name   oriT_pRCCGE531b in_silico
Organism   Rhizobium sp. CCGE531
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032687 (555923..555958 [+], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      21..26, 31..36  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_pRCCGE531b
ATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4977 GenBank   WP_065091806
Name   traA_CCGE531_RS32575_pRCCGE531b insolico UniProt ID   A0A387HA03
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122065.88 Da        Isoelectric Point: 10.0272

>WP_065091806.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADAPSWLRTMIADR
SVSGASEAFWNSVEIFEKRVDAQLAKDVTVALPMELSSEQNIELVRDFIERHITSKGMIADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKVAVTGPGGKPVRNDAGKIVYELWAGSLDDFNAFRDGWFACQNRHLARAG
LDLRVDGHSFEKQGINLTPTIHLGVGAKAIERKSAEAERAPSLERLELQEERRAENARRIQRRPELVLDL
ITREKSVFDERDVAKILHRYIDDAGLFQSLMARILQSPETLRLERERIEFSGGLRVPTKYTTRDLVRLEA
EMANRAIWLAQRSSHGVADAVREATFARHLRLADEQKTAIAHVTGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGILSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQMALFVE
AATKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYGELENIYRQREQWMREASLDLARGNIGRAVEAYR
AQGRVSGADLKADAVQALIADWNRDYDPQRSSLILAHLRRDVRMLNGMARAKLVERGLVADGFAFRTEDG
HRKFAAGDQIVFLKNEGSLGVKNGMLAKVVDATPGRIVAEVGDGEHRRQVTVEQRFYANLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDFGLYHGRRSFAKAGGLIPILSRRQAKETTLDYASGRFY
AQALRFADARGLHLVNVARTVVRDRIEWTVRQKSKLAALGARLAAIARRLGLSAGAAKTSQSHSMQEAKP
MVSGITTFPKSLEQVVEDLLAADPGLKKQWEEVSARFHLVYAQPEDAFKAVNVDAMLRNEAAAKSTITKI
GSEPETFGALKGKTGILAGRADKQAHERAVTNAPALARNLERYLRQRTEAEHKYDAEERAVRMKISLDIP
ALSPAAKQTLERVRDAIDRNDLPAGLENALADKMVKAELEGFARAVSERFGERTFLPLAAKDMTGQTFQS
VTSSMSAGQKAEVQSAWSTMRTVQQLSAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

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

(860-955)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-568)


  Protein structure


Source ID Structure
AlphaFold DB A0A387HA03


T4CP

ID   5179 GenBank   WP_004119814
Name   traG_CCGE531_RS32560_pRCCGE531b insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 71115.08 Da        Isoelectric Point: 9.0145

>WP_004119814.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTRILLFVAPCALMMLMAIGMTGTELWLSHFGKSDAARQMLGRAGIALPYVAASVVGIIFLFASAGSARI
RTAGWGVVTGATATLVLAVLREASRLSAYLEQVPAGKTVFNYLDPATAIGAAAVLMSALFGMRVAIAGNA
TFARAEPKRIVGKRALHGEADWMKLSQAEKLFAESGGIVIGERYRVDRDSIAAPSFRADSAASWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVLKHRGDANRDVFVLDPK
HSEIGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTTEND
QTLRQVRKNLSEPEPQLRQRLHEIYDDSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGTSFSTSDLADGKTDVFINIDLKTLETHAGLARVIIGAFLNAIYNRNGEMQGRALFLLDEVARLGYMR
ILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKGCVGAR
AFSKAANPAENSPDRPARSAASKADREQ

  Protein domains


Predicted by InterproScan.

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

(161-633)

  Protein structure



No available structure.



ID   5180 GenBank   WP_065091804
Name   t4cp2_CCGE531_RS32640_pRCCGE531b 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: 91755.65 Da        Isoelectric Point: 6.3779

>WP_065091804.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRAPDPSFADLVPYAGLVDNGVLLLKDGSLMAAWYFAGPDSESATALDRNELSRHINTILSRLG
SGWMIQVEAVRIPTFDYPSDNRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEVSRKKTYADTVLFIFKNAVREIEQYFANTLSIRRMETREALERGGARVARYDELLQFVRFCITG
DNHPIRLPDAPMYLDWIATAELEHGLTSKVESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMNMVAETEEAIAQASSQLVAYGYYTPVIVL
FDHDREGLQEKAESIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLATGGDHYEIGGDAQEEAKALAFCPLSDLSSDSDRAWAAEWIEMLIALQGVTITPDHRN
AVSRQIGLMASAAGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEKDGLLLGSFQTFEIEELMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAASEPGTREFYERIGFNERQIEIVSNAIPKREYYVATSEGRRLFDMSLGP
VALSFVGASGKEDLKRIRTLSSKHGRDWPIHWLRTRGVQDAAALLNLE

  Protein domains


Predicted by InterproScan.

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

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 561081..572952

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CCGE531_RS32580 (CCGE531_32595) 559346..559912 + 567 WP_120670997 conjugative transfer signal peptidase TraF -
CCGE531_RS32585 (CCGE531_32600) 559902..561065 + 1164 WP_004119833 conjugal transfer protein TraB -
CCGE531_RS32590 (CCGE531_32605) 561081..561689 + 609 WP_004119835 TraH family protein virB1
CCGE531_RS32595 (CCGE531_32610) 561953..562189 - 237 WP_004119837 helix-turn-helix transcriptional regulator -
CCGE531_RS32600 (CCGE531_32615) 562439..562753 + 315 WP_065091805 transcriptional repressor TraM -
CCGE531_RS32605 (CCGE531_32620) 562757..563461 - 705 WP_004119842 autoinducer binding domain-containing protein -
CCGE531_RS32610 (CCGE531_32625) 563620..564921 - 1302 WP_004119844 IncP-type conjugal transfer protein TrbI virB10
CCGE531_RS32615 (CCGE531_32630) 564932..565366 - 435 WP_004119847 conjugal transfer protein TrbH -
CCGE531_RS32620 (CCGE531_32635) 565370..566182 - 813 WP_004119849 P-type conjugative transfer protein TrbG virB9
CCGE531_RS32625 (CCGE531_32640) 566199..566861 - 663 WP_004119850 conjugal transfer protein TrbF virB8
CCGE531_RS32630 (CCGE531_32645) 566886..568064 - 1179 WP_004119851 P-type conjugative transfer protein TrbL virB6
CCGE531_RS32635 (CCGE531_32650) 568069..568872 - 804 WP_004119852 P-type conjugative transfer protein TrbJ virB5
CCGE531_RS32640 (CCGE531_32655) 568844..571300 - 2457 WP_065091804 conjugal transfer protein TrbE virb4
CCGE531_RS32645 (CCGE531_32660) 571310..571609 - 300 WP_004119854 conjugal transfer protein TrbD virB3
CCGE531_RS32650 (CCGE531_32665) 571602..571985 - 384 WP_004119857 TrbC/VirB2 family protein virB2
CCGE531_RS32655 (CCGE531_32670) 571975..572952 - 978 WP_004119858 P-type conjugative transfer ATPase TrbB virB11
CCGE531_RS32660 (CCGE531_32675) 572949..573587 - 639 WP_004119859 acyl-homoserine-lactone synthase TraI -
CCGE531_RS32665 (CCGE531_32680) 573966..575186 + 1221 WP_028755142 plasmid partitioning protein RepA -
CCGE531_RS32670 (CCGE531_32685) 575246..576220 + 975 WP_004119861 plasmid partitioning protein RepB -
CCGE531_RS32675 (CCGE531_32690) 576382..577596 + 1215 WP_120670998 plasmid replication protein RepC -

Host bacterium

ID   7876 GenBank   NZ_CP032687
Plasmid name   pRCCGE531b Incompatibility group   -
Plasmid size   577596 bp Coordinate of oriT [Strand]   555923..555958 [+]
Host baterium   Rhizobium sp. CCGE531

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   LinG, dxnH, linJ
Symbiosis gene   nodD, nodA, nodE, fixN, fixO, fixQ, fixG, nodB, nodC, nodS, nodU, nodI, nodJ, nodH, nifT, nifZ, nifB, nifA, fixX, fixC, fixB, fixA, nifW, nifS, nifH, nifD, nifK, nifE, nifN, nifX, mLTONO_5203, nodM
Anti-CRISPR   AcrIIA7