Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107603
Name   oriT_pRLN3 in_silico
Organism   Rhizobium leguminosarum strain Norway
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP025015 (537136..537169 [+], 34 nt)
oriT length   34 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: 34 nt

>oriT_pRLN3
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5112 GenBank   WP_105009996
Name   traA_CUJ84_RS34840_pRLN3 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: 122765.90 Da        Isoelectric Point: 9.7558

>WP_105009996.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCTKMEFEREARTIDYTRKQGLLHEEFIIPADAPAWLRAMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYELWAGSTEDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVPEAVLQATFARHSRLSDEQRTAIEHIAGTTRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDRCVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMLGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLAYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYE
KSALYRQALRFAEARGLHLMNVARTIAHDRLQWAVRQSSRLADLGARLAAIGKALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDAMLKDQSVAQS
TLARIAGEPESFGALKGNTGLLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPSAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDAGG
KTFETVTTGMTPGQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

AAA domain (AAA_30)

(387-569)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-740)


  Protein structure



No available structure.




T4CP

ID   5335 GenBank   WP_105009699
Name   t4cp2_CUJ84_RS32525_pRLN3 insolico UniProt ID   _
Length   577 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 577 a.a.        Molecular weight: 64544.32 Da        Isoelectric Point: 9.3996

>WP_105009699.1 type IV secretory system conjugative DNA transfer family protein [Rhizobium leguminosarum]
MSNKFDLFGDLERHLSLALRWGKWGAKTGRNLKARSARQHVEELYGPEVADAVDAAVRSGRDPGPIIERA
KRDLAARQERERQIADPPPLYGSARWPTSQDLRPYLRDRKAFDDPRSIQLGTFSDEGQATPAGFAHWDGD
GHLLTIAPTRSGKGKTTIIPNLLRYQGSCVVLDPKGELFEATSQWRSTLGPVYRIAPLDGGSGKPVHRFD
PVSRVRRESDARAIAMQMFPRDPKSPAFFADDAVGFMTAIVMFVRYKAPPHRRTLATVCQMASLKGASLL
KVAKEMEAFPPSADGARASLEKDPLRGLKVLQETLTSKLYKWKDADIQRSVSGNDVSFESLKDRPATVYI
EIPFDMMKTFSGWLRVVLKTALDAMLTNPRVPDIPVLFVLDEFLNIGAFPEYRDAIRTHAGAGIRLWFFL
QDIYSIEEHYPGNSWRPFLNCAVKQFFGINDDDTAKMIGGYLGHKTHAIRTTRASASISSHLGEWYGDAS
TNTSFSMTESVQFLGRPLLTSDEVRELLGGWQGDGWRYGITDIAGTRPFKTQLVVHEKSETCRQRIGLMT
RGESDDRNDHQLSAPQK

  Protein domains


Predicted by InterproScan.

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

(136-517)

  Protein structure



No available structure.



ID   5336 GenBank   WP_105009994
Name   traG_CUJ84_RS34825_pRLN3 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: 69482.93 Da        Isoelectric Point: 9.6636

>WP_105009994.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTINRIALAVMPAALMILVVIGMTGIEQWLSGFGKTEAARLAWGRARIALPYAASAAIGVLFLFACAGSI
NIKRAGWGVLAGCIGTMLIAAVRETLRLSALMKTLPAGKTVLAYLDPATSIGASAALLCAGFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDIVGSQAFRADSAENWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
KDQTLRRVRMNLSEPEPTLRKRLQDVYDNSGSDFVKENVAAFVNLTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQLNGRALFLLDEVARLGY
MRILETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETAEYISKRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIIFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPKPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   5337 GenBank   WP_018482025
Name   t4cp2_CUJ84_RS34925_pRLN3 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: 91596.40 Da        Isoelectric Point: 5.9999

>WP_018482025.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVESRFLGVVAIDGLPVESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARRKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIARASSQLVAYGYYTPVVVL
FGSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDSVEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDSLHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRTLKSEHGHDWPIHWLETRGVQDAESLLK

  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: 546875..556375

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CUJ84_RS34855 (CUJ84_pRLN3000586) 542306..542923 + 618 WP_105009999 TraH family protein -
CUJ84_RS34860 (CUJ84_pRLN3000588) 543054..543920 - 867 WP_105010000 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
CUJ84_RS34865 (CUJ84_pRLN3000589) 543913..544530 - 618 WP_105010001 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
CUJ84_RS34870 (CUJ84_pRLN3000590) 544790..545062 - 273 Protein_488 DUF433 domain-containing protein -
CUJ84_RS34875 (CUJ84_pRLN3000591) 545114..545326 - 213 WP_018482035 helix-turn-helix transcriptional regulator -
CUJ84_RS34880 (CUJ84_pRLN3000592) 545532..545855 + 324 WP_018482034 transcriptional repressor TraM -
CUJ84_RS34885 (CUJ84_pRLN3000593) 545859..546563 - 705 WP_105010002 autoinducer binding domain-containing protein -
CUJ84_RS34890 (CUJ84_pRLN3000594) 546875..548173 - 1299 WP_018482032 IncP-type conjugal transfer protein TrbI virB10
CUJ84_RS34895 (CUJ84_pRLN3000595) 548175..548618 - 444 WP_018482031 conjugal transfer protein TrbH -
CUJ84_RS34900 (CUJ84_pRLN3000596) 548622..549434 - 813 WP_020572024 P-type conjugative transfer protein TrbG virB9
CUJ84_RS34905 (CUJ84_pRLN3000597) 549452..550114 - 663 WP_018482029 conjugal transfer protein TrbF virB8
CUJ84_RS34910 (CUJ84_pRLN3000598) 550135..551313 - 1179 WP_105010003 P-type conjugative transfer protein TrbL virB6
CUJ84_RS34915 (CUJ84_pRLN3000599) 551327..551503 - 177 WP_018482027 entry exclusion protein TrbK -
CUJ84_RS34920 (CUJ84_pRLN3000600) 551497..552294 - 798 WP_018482026 P-type conjugative transfer protein TrbJ virB5
CUJ84_RS34925 (CUJ84_pRLN3000601) 552272..554722 - 2451 WP_018482025 conjugal transfer protein TrbE virb4
CUJ84_RS34930 (CUJ84_pRLN3000602) 554733..555032 - 300 WP_018482024 conjugal transfer protein TrbD virB3
CUJ84_RS34935 (CUJ84_pRLN3000603) 555025..555408 - 384 WP_018482023 TrbC/VirB2 family protein virB2
CUJ84_RS34940 (CUJ84_pRLN3000604) 555398..556375 - 978 WP_018482022 P-type conjugative transfer ATPase TrbB virB11
CUJ84_RS34945 (CUJ84_pRLN3000605) 556372..557010 - 639 WP_018482021 acyl-homoserine-lactone synthase -

Host bacterium

ID   8038 GenBank   NZ_CP025015
Plasmid name   pRLN3 Incompatibility group   -
Plasmid size   557386 bp Coordinate of oriT [Strand]   537136..537169 [+]
Host baterium   Rhizobium leguminosarum strain Norway

Cargo genes

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