Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107575
Name   oriT_pRlvC in_silico
Organism   Rhizobium leguminosarum bv. viciae strain UPM791
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP025505 (384849..384889 [+], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pRlvC
TCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5089 GenBank   WP_018516732
Name   traA_RLV_RS01765_pRlvC 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: 123258.54 Da        Isoelectric Point: 9.9722

>WP_018516732.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTTALPLELTAEQNIALMRDFVVRHITAKGMVADWVYHDANGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDAKPIRNDAGKIVYELWAGSTEDFNAFRDGWFDCQNKHLALAG
LDIRIDGRSFEKQGIPLEPTIHLGVGTKAIARKAEQSDRKSETSTPKLERIELQEELRSENARRIQRRPE
IVLDLITKEKSVFDERDVAKVLYRYIDDVALFQSLMVRILRSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLQATFARHSRLSDEQRTAIEHVAGASRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRAGAKFVLVGDPEQLQPIEAGAAFRTIADRIGYAELETIYRQRDQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVENLIAAWDRDYDPSKTSLILSHLRRDVRKLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEIGEGEHRRLVMIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYFGSRSFAKSGGLIPILSRRNAKETSLDYE
KASFYGQALRFAEARGLHLMNVARTIARDRLEWTVRQKQKLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDFSTRFQLVYAKPEAAFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGLRASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPSAKRTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAGKDTDG
KTFETITSGMTAGQKAEVQSAWNSMRTVQQLSSHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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)

(697-741)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5302 GenBank   WP_018516735
Name   traG_RLV_RS01750_pRlvC insolico UniProt ID   _
Length   643 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 643 a.a.        Molecular weight: 69508.71 Da        Isoelectric Point: 9.2299

>WP_018516735.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVTGSSGTILIAAIRETMRLSAFMTVPADKTVWAFLDPATSIGASAALLCACFALRVALIGN
AAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGGK
SPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLDP
RKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDGGGVRGVRDDFFRASALQLLTALIADVCLSGRTDEH
DQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAA
LVSGKKFATNEIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGYM
RIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTV
EIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGT
NRFHMVGDTPKPA

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(162-633)

  Protein structure



No available structure.



ID   5303 GenBank   WP_018516716
Name   t4cp2_RLV_RS01855_pRlvC insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91624.26 Da        Isoelectric Point: 5.8767

>WP_018516716.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGTDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYADEESRKKSYADTVLFVFRNAVRELEQYFANTLSIRRMETRETLERGGERIARYDELLQFARFCTTG
ESHPIRLPDIPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYAANSPPLMQVASGSTSFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSSLQPLTLAAGGDHYEIGGDNVEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQFLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRTLKSEHGHDWPIHWLETRGVHDAASLLK

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 390021..404198

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RLV_RS01770 (RLV_2002) 388285..388848 + 564 WP_018516731 conjugative transfer signal peptidase TraF -
RLV_RS01775 (RLV_2003) 388838..390004 + 1167 WP_018516730 conjugal transfer protein TraB -
RLV_RS01780 (RLV_2004) 390021..390638 + 618 WP_018516729 TraH family protein virB1
RLV_RS01785 (RLV_2005) 390873..391742 - 870 WP_018516728 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
RLV_RS01790 (RLV_2006) 391735..392352 - 618 WP_026242323 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
RLV_RS01800 (RLV_2007) 392611..392883 - 273 Protein_353 DUF433 domain-containing protein -
RLV_RS01805 (RLV_2008) 392935..393147 - 213 WP_018482035 helix-turn-helix transcriptional regulator -
RLV_RS01810 (RLV_2009) 393353..393676 + 324 WP_018482034 transcriptional repressor TraM -
RLV_RS01815 (RLV_2010) 393680..394382 - 703 Protein_356 autoinducer binding domain-containing protein -
RLV_RS01820 (RLV_2011) 394694..395992 - 1299 WP_018516723 IncP-type conjugal transfer protein TrbI virB10
RLV_RS01825 (RLV_2012) 396004..396444 - 441 WP_018516722 conjugal transfer protein TrbH -
RLV_RS01830 (RLV_2013) 396448..397257 - 810 WP_026242322 P-type conjugative transfer protein TrbG virB9
RLV_RS01835 (RLV_2014) 397275..397937 - 663 WP_018516720 conjugal transfer protein TrbF virB8
RLV_RS01840 (RLV_2015) 397958..399136 - 1179 WP_018516719 P-type conjugative transfer protein TrbL virB6
RLV_RS01845 399150..399326 - 177 WP_018516718 entry exclusion protein TrbK -
RLV_RS01850 (RLV_2016) 399320..400117 - 798 WP_026242321 P-type conjugative transfer protein TrbJ virB5
RLV_RS01855 (RLV_2017) 400095..402545 - 2451 WP_018516716 conjugal transfer protein TrbE virb4
RLV_RS01860 (RLV_2018) 402556..402855 - 300 WP_018516715 conjugal transfer protein TrbD virB3
RLV_RS01865 (RLV_2019) 402848..403231 - 384 WP_018516714 TrbC/VirB2 family protein virB2
RLV_RS01870 (RLV_2020) 403221..404198 - 978 WP_018516713 P-type conjugative transfer ATPase TrbB virB11
RLV_RS01875 (RLV_2021) 404195..404833 - 639 WP_018516712 acyl-homoserine-lactone synthase -

Host bacterium

ID   8010 GenBank   NZ_CP025505
Plasmid name   pRlvC Incompatibility group   -
Plasmid size   405209 bp Coordinate of oriT [Strand]   384849..384889 [+]
Host baterium   Rhizobium leguminosarum bv. viciae strain UPM791

Cargo genes

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