Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102569
Name   oriT_pSM35_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM35
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKQ01000005 (79714..79751 [+], 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_pSM35_Rh07
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1918 GenBank   WP_130790745
Name   traA_ELG87_RS34625_pSM35_Rh07 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   1538 GenBank   WP_130790746
Name   traG_ELG87_RS34610_pSM35_Rh07 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   1539 GenBank   WP_130790739
Name   t4cp2_ELG87_RS34710_pSM35_Rh07 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: 77138..99181

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG87_RS37140 73010..73186 - 177 WP_018482051 hypothetical protein -
ELG87_RS34585 (ELG87_34590) 73637..73948 + 312 WP_127431460 DUF736 domain-containing protein -
ELG87_RS37145 74249..74410 + 162 WP_018516739 hypothetical protein -
ELG87_RS37705 74631..74774 - 144 WP_245488070 hypothetical protein -
ELG87_RS38015 (ELG87_34600) 74943..75251 - 309 WP_130790747 WGR domain-containing protein -
ELG87_RS34600 (ELG87_34605) 75695..76009 + 315 WP_064251367 hypothetical protein -
ELG87_RS34605 (ELG87_34610) 76252..76700 - 449 Protein_77 thermonuclease family protein -
ELG87_RS34610 (ELG87_34615) 77138..79072 - 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
ELG87_RS34615 (ELG87_34620) 79059..79274 - 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
ELG87_RS34620 (ELG87_34625) 79279..79575 - 297 WP_063473650 conjugal transfer protein TraC -
ELG87_RS34625 (ELG87_34630) 79830..83156 + 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
ELG87_RS34630 (ELG87_34635) 83204..83716 + 513 WP_245505007 conjugative transfer signal peptidase TraF -
ELG87_RS34635 (ELG87_34640) 83706..84872 + 1167 WP_130790743 conjugal transfer protein TraB -
ELG87_RS34640 (ELG87_34645) 84890..85510 + 621 WP_130800512 TraH family protein virB1
ELG87_RS34645 (ELG87_34650) 85655..86377 - 723 Protein_85 Crp/Fnr family transcriptional regulator -
ELG87_RS34650 (ELG87_34655) 86734..87108 - 375 WP_130790741 DUF5615 family PIN-like protein -
ELG87_RS34655 (ELG87_34660) 87105..87737 - 633 WP_128408809 DUF433 domain-containing protein -
ELG87_RS34660 (ELG87_34665) 87851..88093 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG87_RS34665 (ELG87_34670) 88319..88660 + 342 WP_128408807 transcriptional repressor TraM -
ELG87_RS34670 (ELG87_34675) 88645..89349 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELG87_RS34675 (ELG87_34680) 89658..90956 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELG87_RS34680 (ELG87_34685) 90968..91408 - 441 WP_130692284 conjugal transfer protein TrbH -
ELG87_RS34685 (ELG87_34690) 91412..92224 - 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELG87_RS34690 (ELG87_34695) 92242..92904 - 663 WP_130692280 conjugal transfer protein TrbF virB8
ELG87_RS34695 (ELG87_34700) 92925..94106 - 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
ELG87_RS34700 (ELG87_34705) 94100..94300 - 201 WP_130759154 entry exclusion protein TrbK -
ELG87_RS34705 (ELG87_34710) 94297..95100 - 804 WP_130790740 P-type conjugative transfer protein TrbJ virB5
ELG87_RS34710 (ELG87_34715) 95072..97528 - 2457 WP_130790739 conjugal transfer protein TrbE virb4
ELG87_RS34715 (ELG87_34720) 97539..97838 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG87_RS34720 (ELG87_34725) 97831..98214 - 384 WP_063473648 TrbC/VirB2 family protein virB2
ELG87_RS34725 (ELG87_34730) 98204..99181 - 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
ELG87_RS34730 (ELG87_34735) 99178..99816 - 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG87_RS37715 100294..100506 + 213 WP_245458276 hypothetical protein -
ELG87_RS34745 (ELG87_34750) 101418..102632 + 1215 WP_027691186 plasmid partitioning protein RepA -
ELG87_RS34750 (ELG87_34755) 102629..103651 + 1023 WP_128408794 plasmid partitioning protein RepB -

Host bacterium

ID   3013 GenBank   NZ_SIKQ01000005
Plasmid name   pSM35_Rh07 Incompatibility group   -
Plasmid size   344412 bp Coordinate of oriT [Strand]   79714..79751 [+]
Host baterium   Rhizobium leguminosarum strain SM35

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, fixX, fixC, fixB, fixA, nifH, nifD, nifK, nifE
Anti-CRISPR   -