Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102559
Name   oriT_pSM11_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM11
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIJX01000006 (65924..65961 [+], 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_pSM11_Rh07
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1910 GenBank   WP_130790745
Name   traA_ELG68_RS29220_pSM11_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   1528 GenBank   WP_130790746
Name   traG_ELG68_RS29205_pSM11_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   1529 GenBank   WP_130790739
Name   t4cp2_ELG68_RS29305_pSM11_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: 63348..85391

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG68_RS38910 59220..59396 - 177 WP_018482051 hypothetical protein -
ELG68_RS29180 (ELG68_29170) 59847..60158 + 312 WP_127431460 DUF736 domain-containing protein -
ELG68_RS38915 60459..60620 + 162 WP_018516739 hypothetical protein -
ELG68_RS39480 60841..60984 - 144 WP_245510058 hypothetical protein -
ELG68_RS39870 (ELG68_29180) 61153..61461 - 309 WP_130790747 WGR domain-containing protein -
ELG68_RS29195 (ELG68_29185) 61905..62219 + 315 WP_064251367 hypothetical protein -
ELG68_RS29200 (ELG68_29190) 62462..62910 - 449 Protein_64 thermonuclease family protein -
ELG68_RS29205 (ELG68_29195) 63348..65282 - 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
ELG68_RS29210 (ELG68_29200) 65269..65484 - 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
ELG68_RS29215 (ELG68_29205) 65489..65785 - 297 WP_063473650 conjugal transfer protein TraC -
ELG68_RS29220 (ELG68_29210) 66040..69366 + 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
ELG68_RS29225 (ELG68_29215) 69414..69926 + 513 WP_245505007 conjugative transfer signal peptidase TraF -
ELG68_RS29230 (ELG68_29220) 69916..71082 + 1167 WP_130790743 conjugal transfer protein TraB -
ELG68_RS29235 (ELG68_29225) 71100..71720 + 621 WP_130790742 TraH family protein virB1
ELG68_RS29240 (ELG68_29230) 71865..72587 - 723 Protein_72 Crp/Fnr family transcriptional regulator -
ELG68_RS29245 (ELG68_29235) 72944..73318 - 375 WP_130790741 DUF5615 family PIN-like protein -
ELG68_RS29250 (ELG68_29240) 73315..73947 - 633 WP_128408809 DUF433 domain-containing protein -
ELG68_RS29255 (ELG68_29245) 74061..74303 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG68_RS29260 (ELG68_29250) 74529..74870 + 342 WP_128408807 transcriptional repressor TraM -
ELG68_RS29265 (ELG68_29255) 74855..75559 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELG68_RS29270 (ELG68_29260) 75868..77166 - 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELG68_RS29275 (ELG68_29265) 77178..77618 - 441 WP_130692284 conjugal transfer protein TrbH -
ELG68_RS29280 (ELG68_29270) 77622..78434 - 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELG68_RS29285 (ELG68_29275) 78452..79114 - 663 WP_130692280 conjugal transfer protein TrbF virB8
ELG68_RS29290 (ELG68_29280) 79135..80316 - 1182 WP_130794128 P-type conjugative transfer protein TrbL virB6
ELG68_RS29295 (ELG68_29285) 80310..80510 - 201 WP_130759154 entry exclusion protein TrbK -
ELG68_RS29300 (ELG68_29290) 80507..81310 - 804 WP_130790740 P-type conjugative transfer protein TrbJ virB5
ELG68_RS29305 (ELG68_29295) 81282..83738 - 2457 WP_130790739 conjugal transfer protein TrbE virb4
ELG68_RS29310 (ELG68_29300) 83749..84048 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG68_RS29315 (ELG68_29305) 84041..84424 - 384 WP_063473648 TrbC/VirB2 family protein virB2
ELG68_RS29320 (ELG68_29310) 84414..85391 - 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
ELG68_RS29325 (ELG68_29315) 85388..86026 - 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG68_RS39490 86504..86716 + 213 WP_245458276 hypothetical protein -
ELG68_RS29340 (ELG68_29330) 87628..88842 + 1215 WP_027691186 plasmid partitioning protein RepA -
ELG68_RS29345 (ELG68_29335) 88839..89861 + 1023 WP_128408794 plasmid partitioning protein RepB -

Host bacterium

ID   3003 GenBank   NZ_SIJX01000006
Plasmid name   pSM11_Rh07 Incompatibility group   -
Plasmid size   383510 bp Coordinate of oriT [Strand]   65924..65961 [+]
Host baterium   Rhizobium leguminosarum strain SM11

Cargo genes

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