Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107440
Name   oriT_pRCCGE532b in_silico
Organism   Rhizobium sp. CCGE532
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032692 (484487..484522 [+], 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_pRCCGE532b
ATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4976 GenBank   WP_065091806
Name   traA_CCGE532_RS31740_pRCCGE532b 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   5177 GenBank   WP_004119814
Name   traG_CCGE532_RS31725_pRCCGE532b 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   5178 GenBank   WP_065091804
Name   t4cp2_CCGE532_RS31805_pRCCGE532b 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: 489645..501516

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CCGE532_RS31745 (CCGE532_31750) 487910..488476 + 567 WP_004119831 conjugative transfer signal peptidase TraF -
CCGE532_RS31750 (CCGE532_31755) 488466..489629 + 1164 WP_004119833 conjugal transfer protein TraB -
CCGE532_RS31755 (CCGE532_31760) 489645..490253 + 609 WP_004119835 TraH family protein virB1
CCGE532_RS31760 (CCGE532_31765) 490517..490753 - 237 WP_004119837 helix-turn-helix transcriptional regulator -
CCGE532_RS31765 (CCGE532_31770) 491003..491317 + 315 WP_004119838 transcriptional repressor TraM -
CCGE532_RS31770 (CCGE532_31775) 491321..492025 - 705 WP_004119842 autoinducer binding domain-containing protein -
CCGE532_RS31775 (CCGE532_31780) 492184..493485 - 1302 WP_004119844 IncP-type conjugal transfer protein TrbI virB10
CCGE532_RS31780 (CCGE532_31785) 493496..493930 - 435 WP_004119847 conjugal transfer protein TrbH -
CCGE532_RS31785 (CCGE532_31790) 493934..494746 - 813 WP_004119849 P-type conjugative transfer protein TrbG virB9
CCGE532_RS31790 (CCGE532_31795) 494763..495425 - 663 WP_004119850 conjugal transfer protein TrbF virB8
CCGE532_RS31795 (CCGE532_31800) 495450..496628 - 1179 WP_004119851 P-type conjugative transfer protein TrbL virB6
CCGE532_RS31800 (CCGE532_31805) 496633..497436 - 804 WP_004119852 P-type conjugative transfer protein TrbJ virB5
CCGE532_RS31805 (CCGE532_31810) 497408..499864 - 2457 WP_065091804 conjugal transfer protein TrbE virb4
CCGE532_RS31810 (CCGE532_31815) 499874..500173 - 300 WP_004119854 conjugal transfer protein TrbD virB3
CCGE532_RS31815 (CCGE532_31820) 500166..500549 - 384 WP_004119857 TrbC/VirB2 family protein virB2
CCGE532_RS31820 (CCGE532_31825) 500539..501516 - 978 WP_004119858 P-type conjugative transfer ATPase TrbB virB11
CCGE532_RS31825 (CCGE532_31830) 501513..502151 - 639 WP_004119859 acyl-homoserine-lactone synthase TraI -
CCGE532_RS31830 (CCGE532_31835) 502530..503750 + 1221 WP_028755142 plasmid partitioning protein RepA -
CCGE532_RS31835 (CCGE532_31840) 503810..504784 + 975 WP_004119861 plasmid partitioning protein RepB -
CCGE532_RS31840 (CCGE532_31845) 504946..506160 + 1215 WP_120764334 plasmid replication protein RepC -

Host bacterium

ID   7875 GenBank   NZ_CP032692
Plasmid name   pRCCGE532b Incompatibility group   -
Plasmid size   506160 bp Coordinate of oriT [Strand]   484487..484522 [+]
Host baterium   Rhizobium sp. CCGE532

Cargo genes

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