Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102539
Name   oriT_pSM37_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM37
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKS01000005 (33073..33110 [-], 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_pSM37_Rh07
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1890 GenBank   WP_130790745
Name   traA_ELG89_RS31750_pSM37_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   1493 GenBank   WP_130790739
Name   t4cp2_ELG89_RS31665_pSM37_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   1494 GenBank   WP_130790746
Name   traG_ELG89_RS31765_pSM37_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: 13643..35686

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG89_RS31630 (ELG89_31630) 9353..9814 + 462 WP_024323550 helix-turn-helix domain-containing protein -
ELG89_RS31635 (ELG89_31635) 10107..12218 + 2112 WP_130790737 recombinase family protein -
ELG89_RS37325 12318..12530 - 213 WP_245458276 hypothetical protein -
ELG89_RS31645 (ELG89_31645) 13008..13646 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG89_RS31650 (ELG89_31650) 13643..14620 + 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
ELG89_RS31655 (ELG89_31655) 14610..14993 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELG89_RS31660 (ELG89_31660) 14986..15285 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG89_RS31665 (ELG89_31665) 15296..17752 + 2457 WP_130790739 conjugal transfer protein TrbE virb4
ELG89_RS31670 (ELG89_31670) 17724..18527 + 804 WP_130790740 P-type conjugative transfer protein TrbJ virB5
ELG89_RS31675 (ELG89_31675) 18524..18724 + 201 WP_130759154 entry exclusion protein TrbK -
ELG89_RS31680 (ELG89_31680) 18718..19899 + 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
ELG89_RS31685 (ELG89_31685) 19920..20582 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELG89_RS31690 (ELG89_31690) 20600..21412 + 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELG89_RS31695 (ELG89_31695) 21416..21856 + 441 WP_130692284 conjugal transfer protein TrbH -
ELG89_RS31700 (ELG89_31700) 21868..23166 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELG89_RS31705 (ELG89_31705) 23475..24179 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG89_RS31710 (ELG89_31710) 24164..24505 - 342 WP_128408807 transcriptional repressor TraM -
ELG89_RS31715 (ELG89_31715) 24731..24973 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG89_RS31720 (ELG89_31720) 25087..25719 + 633 WP_128408809 DUF433 domain-containing protein -
ELG89_RS31725 (ELG89_31725) 25716..26090 + 375 WP_130790741 DUF5615 family PIN-like protein -
ELG89_RS31730 (ELG89_31730) 26447..27169 + 723 Protein_27 Crp/Fnr family transcriptional regulator -
ELG89_RS31735 (ELG89_31735) 27314..27934 - 621 WP_130790742 TraH family protein virB1
ELG89_RS31740 (ELG89_31740) 27952..29118 - 1167 WP_130790743 conjugal transfer protein TraB -
ELG89_RS31745 (ELG89_31745) 29108..29671 - 564 WP_130790744 conjugative transfer signal peptidase TraF -
ELG89_RS31750 (ELG89_31750) 29668..32994 - 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
ELG89_RS31755 (ELG89_31755) 33249..33545 + 297 WP_063473650 conjugal transfer protein TraC -
ELG89_RS31760 (ELG89_31760) 33550..33765 + 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
ELG89_RS31765 (ELG89_31765) 33752..35686 + 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
ELG89_RS31770 (ELG89_31770) 36124..36572 + 449 Protein_35 thermonuclease family protein -
ELG89_RS31775 (ELG89_31775) 36815..37129 - 315 WP_064251367 hypothetical protein -
ELG89_RS37655 (ELG89_31780) 37573..37881 + 309 WP_130790747 WGR domain-containing protein -
ELG89_RS37335 38050..38193 + 144 WP_245488070 hypothetical protein -
ELG89_RS36725 38414..38575 - 162 WP_018516739 hypothetical protein -
ELG89_RS31790 (ELG89_31790) 38876..39187 - 312 WP_127431460 DUF736 domain-containing protein -
ELG89_RS36730 39638..39814 + 177 WP_018482051 hypothetical protein -

Host bacterium

ID   2983 GenBank   NZ_SIKS01000005
Plasmid name   pSM37_Rh07 Incompatibility group   -
Plasmid size   101260 bp Coordinate of oriT [Strand]   33073..33110 [-]
Host baterium   Rhizobium leguminosarum strain SM37

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodD
Anti-CRISPR   -