Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119113
Name   oriT_pSM51_Rh08 in_silico
Organism   Rhizobium beringeri strain SM51
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SILG01000005 (181238..181275 [+], 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_pSM51_Rh08
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12072 GenBank   WP_130806924
Name   traA_ELH03_RS33635_pSM51_Rh08 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: 122919.18 Da        Isoelectric Point: 9.8379

>WP_130806924.1 Ti-type conjugative transfer relaxase TraA [Rhizobium beringeri]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLIEDGFGSKKVAILGPDGKPIRNDAGKIVYELWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPTKYTTREM
IRIEAEMANHAIWLSARASHGVREAVLHATFARHSRLSDEQRTAIEHVAGATRIAAIIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNRLDDKTVIVLDEAGMVSSRQM
ALLVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLARVLEAASGRIVAEIGDGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYQ
KSALYRQALRFAEARGLQLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSIRDTI
KEAKPMVSGITTFPKSLDQAVEGKLAADPSLKKQWEDVSTRFHLVYAQPEAAFKAINVDAMLTDQSVAQS
TLARIAGEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   14136 GenBank   WP_130806922
Name   traG_ELH03_RS33620_pSM51_Rh08 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: 69446.66 Da        Isoelectric Point: 9.3616

>WP_130806922.1 Ti-type conjugative transfer system protein TraG [Rhizobium beringeri]
MTINRIALVIVPAALMIPVVIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYGASAAIGILFLFASAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTKALNADKSVLAYLDPATAIGAGVALMCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLLPDAGGIVIGERYRVDKDNVGSQAFRADSAETWGASG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTEE
QEQTLRRVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGQMKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIRPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPKPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   14137 GenBank   WP_130806925
Name   t4cp2_ELH03_RS33720_pSM51_Rh08 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91431.16 Da        Isoelectric Point: 5.7018

>WP_130806925.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKPFRVTGPSFADLVPYAGLIDDGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSKDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANSLSIRRMETRETFERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLESTRKKWQQKVRPFFEQIFQTQSRSVDQDAMTMVVETQDAIAQASSRLVAYGYYTPVVVL
FDIDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATATPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSENGHDWPIHWLETRGVHDAAPLLK

  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: 186411..200547

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH03_RS33640 (ELH03_33640) 184678..185241 + 564 WP_130714114 conjugative transfer signal peptidase TraF -
ELH03_RS33645 (ELH03_33645) 185231..186394 + 1164 WP_130729903 conjugal transfer protein TraB -
ELH03_RS33650 (ELH03_33650) 186411..187028 + 618 WP_130654292 TraH family protein virB1
ELH03_RS33655 (ELH03_33655) 187131..187997 - 867 Protein_174 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELH03_RS33660 (ELH03_33660) 187990..188607 - 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELH03_RS38280 (ELH03_33665) 188698..189129 - 432 Protein_176 hypothetical protein -
ELH03_RS33670 (ELH03_33670) 189232..189474 - 243 WP_130654290 helix-turn-helix domain-containing protein -
ELH03_RS33675 (ELH03_33675) 189697..190020 + 324 WP_130654289 transcriptional repressor TraM -
ELH03_RS33680 (ELH03_33680) 190024..190728 - 705 WP_130654288 autoinducer binding domain-containing protein -
ELH03_RS33685 (ELH03_33685) 191040..192338 - 1299 WP_130654287 IncP-type conjugal transfer protein TrbI virB10
ELH03_RS33690 (ELH03_33690) 192350..192790 - 441 WP_130654286 conjugal transfer protein TrbH -
ELH03_RS33695 (ELH03_33695) 192794..193606 - 813 WP_130654285 P-type conjugative transfer protein TrbG virB9
ELH03_RS33700 (ELH03_33700) 193624..194286 - 663 WP_130654284 conjugal transfer protein TrbF virB8
ELH03_RS33705 (ELH03_33705) 194307..195494 - 1188 WP_130654283 P-type conjugative transfer protein TrbL virB6
ELH03_RS33710 (ELH03_33710) 195499..195675 - 177 WP_130654282 entry exclusion protein TrbK -
ELH03_RS33715 (ELH03_33715) 195669..196466 - 798 WP_130654281 P-type conjugative transfer protein TrbJ virB5
ELH03_RS33720 (ELH03_33720) 196444..198894 - 2451 WP_130806925 conjugal transfer protein TrbE virb4
ELH03_RS33725 (ELH03_33725) 198905..199204 - 300 WP_130654279 conjugal transfer protein TrbD virB3
ELH03_RS33730 (ELH03_33730) 199197..199580 - 384 WP_065276633 TrbC/VirB2 family protein virB2
ELH03_RS33735 (ELH03_33735) 199570..200547 - 978 WP_130654278 P-type conjugative transfer ATPase TrbB virB11
ELH03_RS33740 (ELH03_33740) 200544..201182 - 639 WP_130654277 acyl-homoserine-lactone synthase -
ELH03_RS33745 (ELH03_33745) 201559..202782 + 1224 WP_065276670 plasmid partitioning protein RepA -
ELH03_RS33750 (ELH03_33750) 202779..203816 + 1038 WP_130657451 plasmid partitioning protein RepB -
ELH03_RS33755 (ELH03_33755) 204006..205220 + 1215 WP_130806927 plasmid replication protein RepC -

Host bacterium

ID   19545 GenBank   NZ_SILG01000005
Plasmid name   pSM51_Rh08 Incompatibility group   -
Plasmid size   283601 bp Coordinate of oriT [Strand]   181238..181275 [+]
Host baterium   Rhizobium beringeri strain SM51

Cargo genes

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