Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102560
Name   oriT_pSM3_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIJQ01000006 (33582..33619 [-], 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_pSM3_Rh07
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1911 GenBank   WP_130790745
Name   traA_ELG61_RS37230_pSM3_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   1530 GenBank   WP_130790739
Name   t4cp2_ELG61_RS37145_pSM3_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.



ID   1531 GenBank   WP_130790746
Name   traG_ELG61_RS37245_pSM3_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 14152..36195

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG61_RS37105 (ELG61_37105) 9682..10704 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG61_RS37110 (ELG61_37110) 10701..11915 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELG61_RS40260 12827..13039 - 213 WP_245458276 hypothetical protein -
ELG61_RS37125 (ELG61_37125) 13517..14155 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG61_RS37130 (ELG61_37130) 14152..15129 + 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
ELG61_RS37135 (ELG61_37135) 15119..15502 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELG61_RS37140 (ELG61_37140) 15495..15794 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG61_RS37145 (ELG61_37145) 15805..18261 + 2457 WP_130790739 conjugal transfer protein TrbE virb4
ELG61_RS37150 (ELG61_37150) 18233..19036 + 804 WP_130790740 P-type conjugative transfer protein TrbJ virB5
ELG61_RS37155 (ELG61_37155) 19033..19233 + 201 WP_130759154 entry exclusion protein TrbK -
ELG61_RS37160 (ELG61_37160) 19227..20408 + 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
ELG61_RS37165 (ELG61_37165) 20429..21091 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELG61_RS37170 (ELG61_37170) 21109..21921 + 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELG61_RS37175 (ELG61_37175) 21925..22365 + 441 WP_130692284 conjugal transfer protein TrbH -
ELG61_RS37180 (ELG61_37180) 22377..23675 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELG61_RS37185 (ELG61_37185) 23984..24688 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG61_RS37190 (ELG61_37190) 24673..25014 - 342 WP_128408807 transcriptional repressor TraM -
ELG61_RS37195 (ELG61_37195) 25240..25482 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG61_RS37200 (ELG61_37200) 25596..26228 + 633 WP_128408809 DUF433 domain-containing protein -
ELG61_RS37205 (ELG61_37205) 26225..26599 + 375 WP_130790741 DUF5615 family PIN-like protein -
ELG61_RS37210 (ELG61_37210) 26956..27678 + 723 Protein_27 Crp/Fnr family transcriptional regulator -
ELG61_RS37215 (ELG61_37215) 27823..28443 - 621 WP_130790742 TraH family protein virB1
ELG61_RS37220 (ELG61_37220) 28461..29627 - 1167 WP_130817194 conjugal transfer protein TraB -
ELG61_RS37225 (ELG61_37225) 29617..30180 - 564 WP_130790744 conjugative transfer signal peptidase TraF -
ELG61_RS37230 (ELG61_37230) 30177..33503 - 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
ELG61_RS37235 (ELG61_37235) 33758..34054 + 297 WP_063473650 conjugal transfer protein TraC -
ELG61_RS37240 (ELG61_37240) 34059..34274 + 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
ELG61_RS37245 (ELG61_37245) 34261..36195 + 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
ELG61_RS37250 (ELG61_37250) 36633..37081 + 449 Protein_35 thermonuclease family protein -
ELG61_RS37255 (ELG61_37255) 37324..37638 - 315 WP_064251367 hypothetical protein -
ELG61_RS40595 (ELG61_37260) 38082..38390 + 309 WP_130790747 WGR domain-containing protein -
ELG61_RS40270 38559..38702 + 144 WP_245488070 hypothetical protein -
ELG61_RS39665 38923..39084 - 162 WP_018516739 hypothetical protein -
ELG61_RS37270 (ELG61_37270) 39385..39696 - 312 WP_127431460 DUF736 domain-containing protein -
ELG61_RS39670 40147..40323 + 177 WP_018482051 hypothetical protein -

Host bacterium

ID   3004 GenBank   NZ_SIJQ01000006
Plasmid name   pSM3_Rh07 Incompatibility group   -
Plasmid size   321694 bp Coordinate of oriT [Strand]   33582..33619 [-]
Host baterium   Rhizobium leguminosarum strain SM3

Cargo genes

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