Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107641
Name   oriT_pRL23b2 in_silico
Organism   Rhizobium leguminosarum bv. trifolii strain 23B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050089 (311690..311730 [+], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pRL23b2
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5135 GenBank   WP_130784879
Name   traA_HA463_RS37350_pRL23b2 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: 122892.96 Da        Isoelectric Point: 9.7033

>WP_130784879.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVCSMIADR
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKIALLGPDGKPVRNDAGKLVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKTQASAPKLERIELQGERRSENARRIERRPE
IVLDLITREKSVFDERDVAKVLYRYIDDAALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTRDM
VRLEAEMANRAIWLSGRASHGVREEVLQTTFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLAKVLESAPGRIVAEVGDGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIAHDRIHWAVRQKQNLADLGARLAAISTALGLARGSNKHSIPNTI
KGAKPMVSGITTFPKSLDHAVEDKLAADPGLKKQWEDVSTRFQLVYAQPEAVFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGVLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTADQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   5368 GenBank   WP_128409206
Name   traG_HA463_RS37335_pRL23b2 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: 69653.97 Da        Isoelectric Point: 9.3813

>WP_128409206.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSSFMKTVPADKTVLAFLDPATSIGASAALLCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDVGGIVIGERYRVDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSGHRGRAGRDVFLLD
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   5369 GenBank   WP_164015671
Name   t4cp2_HA463_RS37435_pRL23b2 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: 91687.44 Da        Isoelectric Point: 5.7027

>WP_164015671.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTLAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMSMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPISPCPFYPPNAPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATSEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLETRGVHDAASLLKYV

  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: 309113..331146

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HA463_RS37300 (HA463_37295) 304475..304786 + 312 WP_128408833 DUF736 domain-containing protein -
HA463_RS37305 (HA463_37300) 305086..305247 + 162 WP_018516739 hypothetical protein -
HA463_RS39685 (HA463_37305) 305780..306088 - 309 WP_128408835 WGR domain-containing protein -
HA463_RS37315 (HA463_37310) 306532..306846 + 315 WP_128408836 hypothetical protein -
HA463_RS37320 (HA463_37315) 307078..307227 - 150 Protein_294 thermonuclease family protein -
HA463_RS37325 (HA463_37320) 307224..308301 - 1078 Protein_295 IS630 family transposase -
HA463_RS37330 (HA463_37325) 308371..308673 - 303 Protein_296 thermonuclease family protein -
HA463_RS37335 (HA463_37330) 309113..311047 - 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
HA463_RS37340 (HA463_37335) 311034..311249 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
HA463_RS37345 (HA463_37340) 311254..311547 - 294 WP_128409207 conjugal transfer protein TraC -
HA463_RS37350 (HA463_37345) 311802..315128 + 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
HA463_RS37355 (HA463_37350) 315176..315688 + 513 WP_245458277 conjugative transfer signal peptidase TraF -
HA463_RS37360 (HA463_37355) 315678..316844 + 1167 WP_128408812 conjugal transfer protein TraB -
HA463_RS37365 (HA463_37360) 316862..317482 + 621 WP_128408811 TraH family protein virB1
HA463_RS37370 (HA463_37365) 317627..318342 - 716 Protein_304 Crp/Fnr family transcriptional regulator -
HA463_RS37375 (HA463_37370) 318699..319073 - 375 WP_128408810 DUF5615 family PIN-like protein -
HA463_RS37380 (HA463_37375) 319070..319702 - 633 WP_128408809 DUF433 domain-containing protein -
HA463_RS37385 (HA463_37380) 319816..320058 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
HA463_RS37390 (HA463_37385) 320284..320625 + 342 WP_128408807 transcriptional repressor TraM -
HA463_RS37395 (HA463_37390) 320610..321314 - 705 WP_128408806 autoinducer binding domain-containing protein -
HA463_RS37400 (HA463_37395) 321623..322921 - 1299 WP_128408805 IncP-type conjugal transfer protein TrbI virB10
HA463_RS37405 (HA463_37400) 322933..323373 - 441 WP_128408804 conjugal transfer protein TrbH -
HA463_RS37410 (HA463_37405) 323377..324189 - 813 WP_128408803 P-type conjugative transfer protein TrbG virB9
HA463_RS37415 (HA463_37410) 324207..324869 - 663 WP_128408802 conjugal transfer protein TrbF virB8
HA463_RS37420 (HA463_37415) 324890..326071 - 1182 WP_128408801 P-type conjugative transfer protein TrbL virB6
HA463_RS37425 (HA463_37420) 326065..326265 - 201 WP_128408800 entry exclusion protein TrbK -
HA463_RS37430 (HA463_37425) 326262..327065 - 804 WP_166481262 P-type conjugative transfer protein TrbJ virB5
HA463_RS37435 (HA463_37430) 327037..329493 - 2457 WP_164015671 conjugal transfer protein TrbE virb4
HA463_RS37440 (HA463_37435) 329504..329803 - 300 WP_027681723 conjugal transfer protein TrbD virB3
HA463_RS37445 (HA463_37440) 329796..330179 - 384 WP_128408797 TrbC/VirB2 family protein virB2
HA463_RS37450 (HA463_37445) 330169..331146 - 978 WP_128408796 P-type conjugative transfer ATPase TrbB virB11
HA463_RS37455 (HA463_37450) 331143..331781 - 639 WP_063473646 acyl-homoserine-lactone synthase -
HA463_RS39330 332259..332471 + 213 WP_245458276 hypothetical protein -

Host bacterium

ID   8076 GenBank   NZ_CP050089
Plasmid name   pRL23b2 Incompatibility group   -
Plasmid size   333383 bp Coordinate of oriT [Strand]   311690..311730 [+]
Host baterium   Rhizobium leguminosarum bv. trifolii strain 23B

Cargo genes

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