Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120380
Name   oriT_pRlX2 in_silico
Organism   Rhizobium johnstonii strain TP5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140821 (96260..96297 [+], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 38 nt

>oriT_pRlX2
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12825 GenBank   WP_130790745
Name   traA_U8P72_RS26620_pRlX2 insolico UniProt ID   _
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 123282.59 Da        Isoelectric Point: 10.0651

>WP_130790745.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCANMEFEREARTIDYTRKQGLLHEEFVVPADAPEWLRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKSIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
RDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRRENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLAGRTSHGVREAMLRATFARHVRLSDEQRTAIEHIARATRIAAVIGRAGAGKTTMLK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIGSRTLSSWELRWNQGRNKFDHKTVFVLDEAGMVSSRQM
ALFVEAVSRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VEAYTVHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRKLNDMARAKLVERGVIADGSAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRVVAELGEGEHRRLVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYE
KRALYRQALRFAEARGLHLMDVARTVAHDRLQWAVRQSSRLADLGARLAAIGAALGLVRGGNKQSIPNTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPKAAFKAINVDSMLKDQSVAQS
TLARIAGEPESFGALKGKTGLFASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTADQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-740)


  Protein structure



No available structure.




T4CP

ID   15070 GenBank   WP_130790746
Name   traG_U8P72_RS26605_pRlX2 insolico UniProt ID   _
Length   644 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 644 a.a.        Molecular weight: 69472.74 Da        Isoelectric Point: 9.2484

>WP_130790746.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVIVPAALMIPVVIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYLASAAVGILFLFATAGAI
SIKQAGWGVVAGCSGTILIAALRETIRLSAFMKTVPADKTVLAFLDPATSIGANAALLCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSGHRGGAGRDVFLLD
PRKPDIGFNVLDWVGRFGGTKEEDIASIASWIMSDSGGVRGVRDDFFRASALQLLTALIADVCLSGHTDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPRPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   15071 GenBank   WP_130790739
Name   t4cp2_U8P72_RS26705_pRlX2 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: 91814.32 Da        Isoelectric Point: 5.5010

>WP_130790739.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNEQSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLIPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPSNSPPLVQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRVLAFCPLSDLNSDVDRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEELMNMG
ERNLVPVLTYLFRRIERRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLRFE

  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: 93684..115727

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8P72_RS26570 (U8P72_26585) 89556..89732 - 177 WP_018482051 hypothetical protein -
U8P72_RS26575 (U8P72_26590) 90183..90494 + 312 WP_127431460 DUF736 domain-containing protein -
U8P72_RS26580 (U8P72_26595) 90795..90956 + 162 WP_018516739 hypothetical protein -
U8P72_RS26585 (U8P72_26600) 91177..91320 - 144 WP_245488070 hypothetical protein -
U8P72_RS26590 (U8P72_26605) 91489..91797 - 309 WP_130790747 WGR domain-containing protein -
U8P72_RS26595 (U8P72_26610) 92241..92555 + 315 WP_064251367 hypothetical protein -
U8P72_RS26600 (U8P72_26615) 92798..93246 - 449 Protein_89 thermonuclease family protein -
U8P72_RS26605 (U8P72_26620) 93684..95618 - 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
U8P72_RS26610 (U8P72_26625) 95605..95820 - 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
U8P72_RS26615 (U8P72_26630) 95825..96121 - 297 WP_063473650 conjugal transfer protein TraC -
U8P72_RS26620 (U8P72_26635) 96376..99702 + 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
U8P72_RS26625 (U8P72_26640) 99699..100262 + 564 WP_130790744 conjugative transfer signal peptidase TraF -
U8P72_RS26630 (U8P72_26645) 100252..101418 + 1167 WP_130790743 conjugal transfer protein TraB -
U8P72_RS26635 (U8P72_26650) 101436..102056 + 621 WP_130790742 TraH family protein virB1
U8P72_RS26640 (U8P72_26655) 102201..102923 - 723 Protein_97 Crp/Fnr family transcriptional regulator -
U8P72_RS26645 (U8P72_26660) 103280..103654 - 375 WP_130790741 DUF5615 family PIN-like protein -
U8P72_RS26650 (U8P72_26665) 103651..104283 - 633 WP_128408809 DUF433 domain-containing protein -
U8P72_RS26655 (U8P72_26670) 104397..104639 - 243 WP_128408808 helix-turn-helix domain-containing protein -
U8P72_RS26660 (U8P72_26675) 104865..105206 + 342 WP_128408807 transcriptional repressor TraM -
U8P72_RS26665 (U8P72_26680) 105191..105895 - 705 WP_128408806 autoinducer binding domain-containing protein -
U8P72_RS26670 (U8P72_26685) 106204..107502 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
U8P72_RS26675 (U8P72_26690) 107514..107954 - 441 WP_130692284 conjugal transfer protein TrbH -
U8P72_RS26680 (U8P72_26695) 107958..108770 - 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
U8P72_RS26685 (U8P72_26700) 108788..109450 - 663 WP_130692280 conjugal transfer protein TrbF virB8
U8P72_RS26690 (U8P72_26705) 109471..110652 - 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
U8P72_RS26695 (U8P72_26710) 110646..110846 - 201 WP_130759154 entry exclusion protein TrbK -
U8P72_RS26700 (U8P72_26715) 110843..111646 - 804 WP_130790740 P-type conjugative transfer protein TrbJ virB5
U8P72_RS26705 (U8P72_26720) 111618..114074 - 2457 WP_130790739 conjugal transfer protein TrbE virb4
U8P72_RS26710 (U8P72_26725) 114085..114384 - 300 WP_027681723 conjugal transfer protein TrbD virB3
U8P72_RS26715 (U8P72_26730) 114377..114760 - 384 WP_063473648 TrbC/VirB2 family protein virB2
U8P72_RS26720 (U8P72_26735) 114750..115727 - 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
U8P72_RS26725 (U8P72_26740) 115724..116362 - 639 WP_063473646 acyl-homoserine-lactone synthase -
U8P72_RS26730 (U8P72_26745) 116840..117052 + 213 WP_326912969 hypothetical protein -
U8P72_RS26735 (U8P72_26750) 117152..119263 - 2112 WP_130790737 recombinase family protein -
U8P72_RS26740 (U8P72_26755) 119556..120017 - 462 WP_024323550 helix-turn-helix domain-containing protein -

Host bacterium

ID   20809 GenBank   NZ_CP140821
Plasmid name   pRlX2 Incompatibility group   -
Plasmid size   266623 bp Coordinate of oriT [Strand]   96260..96297 [+]
Host baterium   Rhizobium johnstonii strain TP5

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixN, fixO, fixQ, fixG, nodD, nodM, nodE, nodF, nodA, nodC, nodI, nodJ, nifT, nifA, fixX, fixC, fixB, fixA, nifD, nifE, nifN
Anti-CRISPR   AcrVIB