Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102537
Name   oriT_pSM9_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIJV01000006 (45886..45923 [+], 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_pSM9_Rh07
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1888 GenBank   WP_130790745
Name   traA_ELG66_RS31135_pSM9_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   1491 GenBank   WP_130790746
Name   traG_ELG66_RS31120_pSM9_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   1492 GenBank   WP_130790739
Name   t4cp2_ELG66_RS31220_pSM9_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: 43310..65353

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG66_RS39850 39182..39358 - 177 WP_018482051 hypothetical protein -
ELG66_RS31095 (ELG66_31090) 39809..40120 + 312 WP_127431460 DUF736 domain-containing protein -
ELG66_RS39855 40421..40582 + 162 WP_018516739 hypothetical protein -
ELG66_RS40455 40803..40946 - 144 WP_245488070 hypothetical protein -
ELG66_RS40830 (ELG66_31100) 41115..41423 - 309 WP_130790747 WGR domain-containing protein -
ELG66_RS31110 (ELG66_31105) 41867..42181 + 315 WP_064251367 hypothetical protein -
ELG66_RS31115 (ELG66_31110) 42424..42872 - 449 Protein_55 thermonuclease family protein -
ELG66_RS31120 (ELG66_31115) 43310..45244 - 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
ELG66_RS31125 (ELG66_31120) 45231..45446 - 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
ELG66_RS31130 (ELG66_31125) 45451..45747 - 297 WP_063473650 conjugal transfer protein TraC -
ELG66_RS31135 (ELG66_31130) 46002..49328 + 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
ELG66_RS31140 (ELG66_31135) 49325..49888 + 564 WP_130790744 conjugative transfer signal peptidase TraF -
ELG66_RS31145 (ELG66_31140) 49878..51044 + 1167 WP_130817194 conjugal transfer protein TraB -
ELG66_RS31150 (ELG66_31145) 51062..51682 + 621 WP_130790742 TraH family protein virB1
ELG66_RS31155 (ELG66_31150) 51827..52549 - 723 Protein_63 Crp/Fnr family transcriptional regulator -
ELG66_RS31160 (ELG66_31155) 52906..53280 - 375 WP_130790741 DUF5615 family PIN-like protein -
ELG66_RS31165 (ELG66_31160) 53277..53909 - 633 WP_128408809 DUF433 domain-containing protein -
ELG66_RS31170 (ELG66_31165) 54023..54265 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG66_RS31175 (ELG66_31170) 54491..54832 + 342 WP_128408807 transcriptional repressor TraM -
ELG66_RS31180 (ELG66_31175) 54817..55521 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELG66_RS31185 (ELG66_31180) 55830..57128 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELG66_RS31190 (ELG66_31185) 57140..57580 - 441 WP_130692284 conjugal transfer protein TrbH -
ELG66_RS31195 (ELG66_31190) 57584..58396 - 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELG66_RS31200 (ELG66_31195) 58414..59076 - 663 WP_130692280 conjugal transfer protein TrbF virB8
ELG66_RS31205 (ELG66_31200) 59097..60278 - 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
ELG66_RS31210 (ELG66_31205) 60272..60472 - 201 WP_130759154 entry exclusion protein TrbK -
ELG66_RS31215 (ELG66_31210) 60469..61272 - 804 WP_130790740 P-type conjugative transfer protein TrbJ virB5
ELG66_RS31220 (ELG66_31215) 61244..63700 - 2457 WP_130790739 conjugal transfer protein TrbE virb4
ELG66_RS31225 (ELG66_31220) 63711..64010 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG66_RS31230 (ELG66_31225) 64003..64386 - 384 WP_063473648 TrbC/VirB2 family protein virB2
ELG66_RS31235 (ELG66_31230) 64376..65353 - 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
ELG66_RS31240 (ELG66_31235) 65350..65988 - 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG66_RS40465 66466..66678 + 213 WP_245458276 hypothetical protein -
ELG66_RS31255 (ELG66_31250) 67590..68804 + 1215 WP_027691186 plasmid partitioning protein RepA -
ELG66_RS31260 (ELG66_31255) 68801..69823 + 1023 WP_128408794 plasmid partitioning protein RepB -

Host bacterium

ID   2981 GenBank   NZ_SIJV01000006
Plasmid name   pSM9_Rh07 Incompatibility group   -
Plasmid size   81626 bp Coordinate of oriT [Strand]   45886..45923 [+]
Host baterium   Rhizobium leguminosarum strain SM9

Cargo genes

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