Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102555
Name   oriT_pSM14_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM14
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKA01000006 (156988..157025 [-], 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_pSM14_Rh07
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1906 GenBank   WP_130790745
Name   traA_ELG71_RS34685_pSM14_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   1520 GenBank   WP_130790739
Name   t4cp2_ELG71_RS34600_pSM14_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   1521 GenBank   WP_130790746
Name   traG_ELG71_RS34700_pSM14_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: 137558..159601

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG71_RS34565 (ELG71_34560) 133268..133729 + 462 WP_024323550 helix-turn-helix domain-containing protein -
ELG71_RS34570 (ELG71_34565) 134022..136133 + 2112 WP_130790737 recombinase family protein -
ELG71_RS37560 136233..136445 - 213 WP_245458276 hypothetical protein -
ELG71_RS34580 (ELG71_34575) 136923..137561 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG71_RS34585 (ELG71_34580) 137558..138535 + 978 WP_130790738 P-type conjugative transfer ATPase TrbB virB11
ELG71_RS34590 (ELG71_34585) 138525..138908 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELG71_RS34595 (ELG71_34590) 138901..139200 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG71_RS34600 (ELG71_34595) 139211..141667 + 2457 WP_130790739 conjugal transfer protein TrbE virb4
ELG71_RS34605 (ELG71_34600) 141639..142442 + 804 WP_130790740 P-type conjugative transfer protein TrbJ virB5
ELG71_RS34610 (ELG71_34605) 142439..142639 + 201 WP_130759154 entry exclusion protein TrbK -
ELG71_RS34615 (ELG71_34610) 142633..143814 + 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
ELG71_RS34620 (ELG71_34615) 143835..144497 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELG71_RS34625 (ELG71_34620) 144515..145327 + 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELG71_RS34630 (ELG71_34625) 145331..145771 + 441 WP_130692284 conjugal transfer protein TrbH -
ELG71_RS34635 (ELG71_34630) 145783..147081 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELG71_RS34640 (ELG71_34635) 147390..148094 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG71_RS34645 (ELG71_34640) 148079..148420 - 342 WP_128408807 transcriptional repressor TraM -
ELG71_RS34650 (ELG71_34645) 148646..148888 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG71_RS34655 (ELG71_34650) 149002..149634 + 633 WP_128408809 DUF433 domain-containing protein -
ELG71_RS34660 (ELG71_34655) 149631..150005 + 375 WP_130790741 DUF5615 family PIN-like protein -
ELG71_RS34665 (ELG71_34660) 150362..151084 + 723 Protein_152 Crp/Fnr family transcriptional regulator -
ELG71_RS34670 (ELG71_34665) 151229..151849 - 621 WP_130790742 TraH family protein virB1
ELG71_RS34675 (ELG71_34670) 151867..153033 - 1167 WP_130790743 conjugal transfer protein TraB -
ELG71_RS34680 (ELG71_34675) 153023..153535 - 513 WP_245505007 conjugative transfer signal peptidase TraF -
ELG71_RS34685 (ELG71_34680) 153583..156909 - 3327 WP_130790745 Ti-type conjugative transfer relaxase TraA -
ELG71_RS34690 (ELG71_34685) 157164..157460 + 297 WP_063473650 conjugal transfer protein TraC -
ELG71_RS34695 (ELG71_34690) 157465..157680 + 216 WP_063473651 type IV conjugative transfer system coupling protein TraD -
ELG71_RS34700 (ELG71_34695) 157667..159601 + 1935 WP_130790746 Ti-type conjugative transfer system protein TraG virb4
ELG71_RS34705 (ELG71_34700) 160039..160487 + 449 Protein_160 thermonuclease family protein -
ELG71_RS34710 (ELG71_34705) 160730..161044 - 315 WP_064251367 hypothetical protein -
ELG71_RS37815 (ELG71_34710) 161488..161796 + 309 WP_130790747 WGR domain-containing protein -
ELG71_RS37570 161965..162108 + 144 WP_245488070 hypothetical protein -
ELG71_RS36965 162329..162490 - 162 WP_018516739 hypothetical protein -
ELG71_RS34725 (ELG71_34720) 162791..163102 - 312 WP_127431460 DUF736 domain-containing protein -
ELG71_RS36970 163553..163729 + 177 WP_018482051 hypothetical protein -

Host bacterium

ID   2999 GenBank   NZ_SIKA01000006
Plasmid name   pSM14_Rh07 Incompatibility group   -
Plasmid size   225402 bp Coordinate of oriT [Strand]   156988..157025 [-]
Host baterium   Rhizobium leguminosarum strain SM14

Cargo genes

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