Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120824
Name   oriT_pRlX1 in_silico
Organism   Rhizobium beringeri strain TP24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140852 (183925..183962 [-], 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_pRlX1
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13134 GenBank   WP_128401822
Name   traA_U8P69_RS24910_pRlX1 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: 123009.21 Da        Isoelectric Point: 9.7914

>WP_128401822.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVVPADAPEWLRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTVEQNIALMRDFVERHITAQGMIADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDDKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRVDGRSFEKQGIELEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVPEAVLQATFARHSRLSDEQRTAIEHIAGTTRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDRCVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMLGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLAYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYE
KSALYRQALRFAEARGLHLMNVARTIAHDRLQWAVRQSSRLADLGARLAAIGKALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDAMLKDQSVAQS
TLARIAGKPESFGALKGNTGLLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPSAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDAGG
KTFETVTTGMTPGQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-569)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-740)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   15413 GenBank   WP_128411486
Name   t4cp2_U8P69_RS24770_pRlX1 insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 91617.41 Da        Isoelectric Point: 6.1236

>WP_128411486.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVSLRLFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDFERNEMSRQINAIMSRLG
SGWMIQVEAVRLATVDYATAGKSHFPDRVTRAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSRLSK
YLYSDEGSRRRSYADTVLFLFRNAIRELEQYLANIVSIRRMLTREIAERGGARVARYDELLQFIRFCVTG
ENHPVRLPDIAMYLDWVATAELQHGLSPRVESRFLGVVAIDGLPSESWPGILNGLDAMPLSYRWSSRFIF
LDAEEAKVRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEEAIAEASSQLVAYGYYTPVVVL
FENDPELLNEKVEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNTVWS
GNPQAPCPFYPPGSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLAAGGDYYDVGGDEDTSLSFCPLAELSSDADRAWASEWIESLVAMQGITITPDHRNAIS
RQIGLMAVAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAETDGLALGLFQAFEIEQVMSMGERN
LVPVLTYLFRRIEKRLTGAPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAREPGTREFYERIGFNQRQIQIVASAIPKREYYVASPDGRRLFDMALGPLTL
SFVGASSKDDLKRIRALHEEHGPEWPLHWLQQRGIKDAASLLNDT

  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.



ID   15414 GenBank   WP_245461678
Name   traG_U8P69_RS24925_pRlX1 insolico UniProt ID   _
Length   667 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 667 a.a.        Molecular weight: 71799.22 Da        Isoelectric Point: 9.1969

>WP_245461678.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVGPAALMILAVIGMTGIEQWLSGIGKTEAARLAWGRARIALPYAASAAIGVLFLFACAGSI
NIKRAGWGVLAGCIGTMLIAAVRETLRLSALMKTLPAGKTVLAYLDPATSIGASAALLCAGFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDIVGSQAFRADSAENWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSDHTDE
KDQTLRRVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQLNGRALFLLDEVARLGY
MRILETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETAEYISKRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIIFTAGNAPLRCARAIWFRRADMRACVG
ENRFYSMGGGEREGSNSTPAVNPYETKPTVTSAGEEG

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 151583..161052

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8P69_RS24735 (U8P69_24725) 146829..148094 - 1266 WP_327206240 plasmid replication protein RepC -
U8P69_RS24740 (U8P69_24730) 148333..149373 - 1041 WP_128411487 plasmid partitioning protein RepB -
U8P69_RS24745 (U8P69_24735) 149358..150575 - 1218 WP_128401849 plasmid partitioning protein RepA -
U8P69_RS24750 (U8P69_24740) 150939..151568 + 630 WP_128401848 acyl-homoserine-lactone synthase TraI -
U8P69_RS24755 (U8P69_24745) 151583..152548 + 966 WP_327206241 P-type conjugative transfer ATPase TrbB virB11
U8P69_RS24760 (U8P69_24750) 152538..152912 + 375 WP_128401846 TrbC/VirB2 family protein virB2
U8P69_RS24765 (U8P69_24755) 152909..153208 + 300 WP_128401845 conjugal transfer protein TrbD virB3
U8P69_RS24770 (U8P69_24760) 153218..155665 + 2448 WP_128411486 conjugal transfer protein TrbE virb4
U8P69_RS24775 (U8P69_24765) 155637..156437 + 801 WP_128401843 P-type conjugative transfer protein TrbJ virB5
U8P69_RS24780 (U8P69_24770) 156625..157800 + 1176 WP_128401842 P-type conjugative transfer protein TrbL virB6
U8P69_RS24785 (U8P69_24775) 157820..158482 + 663 WP_128401841 conjugal transfer protein TrbF virB8
U8P69_RS24790 (U8P69_24780) 158497..159321 + 825 WP_128401840 P-type conjugative transfer protein TrbG virB9
U8P69_RS24795 (U8P69_24785) 159353..159751 + 399 WP_327206242 conjugal transfer protein TrbH -
U8P69_RS24800 (U8P69_24790) 159763..161052 + 1290 WP_128401838 IncP-type conjugal transfer protein TrbI virB10
U8P69_RS24805 (U8P69_24795) 161637..162431 - 795 WP_245461681 autoinducer binding domain-containing protein -
U8P69_RS24810 (U8P69_24800) 162713..163444 - 732 WP_128401837 response regulator transcription factor -
U8P69_RS24815 (U8P69_24805) 164480..164776 + 297 WP_245462682 winged helix-turn-helix domain-containing protein -

Host bacterium

ID   21253 GenBank   NZ_CP140852
Plasmid name   pRlX1 Incompatibility group   -
Plasmid size   655862 bp Coordinate of oriT [Strand]   183925..183962 [-]
Host baterium   Rhizobium beringeri strain TP24

Cargo genes

Drug resistance gene   -
Virulence gene   gmd
Metal resistance gene   hupE2
Degradation gene   -
Symbiosis gene   noeL
Anti-CRISPR   AcrIIA7