Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107658
Name   oriT_PLR8-1a|p3 in_silico
Organism   Rhizobium bangladeshense strain PLR8-1a
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP071621 (181771..181804 [+], 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_PLR8-1a|p3
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5147 GenBank   WP_207603830
Name   traA_J2J97_RS26560_PLR8-1a|p3 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: 123147.73 Da        Isoelectric Point: 9.9555

>WP_207603830.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPTDAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIGLPLELTAEQNIALVRDFVACHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLAPDGKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERVELQEERRRENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREVVLQATFTRHSRLSDEQRTAIEHVAGTTRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALLVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDARMLNDIARAKLVERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVVEAAPGRIVAEIGEREHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAIYYGSRSFAKSGGLIPILSRRNAKETSLDYE
KSALYRQALRFAEARGLHLMNVARTIAHDRLQWAVRQKKKLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRLQLIYAKPEAAFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVREAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTVVQKAEVQSAWKSMRTVQQLGAHERTTEALKQAETLRQTKSQGLSLK

  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)

(387-570)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-741)


  Protein structure



No available structure.




T4CP

ID   5382 GenBank   WP_207603827
Name   traG_J2J97_RS26545_PLR8-1a|p3 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: 69478.82 Da        Isoelectric Point: 9.1308

>WP_207603827.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVIVPAALMIPVVIGMTGIEQWLSGFGKTETARLAWGRAGIALPYLASAAVGILFLFATAGAI
NIKQAGWGVVAGCSGMILIAALRETIRLSAFMKTVPADKTVLAFLDPATSIGASAALLCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDTGGIVIGERYRVDRDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKPDIGFNVLDWVGCFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
KEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSQIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
ANRFHMIGDAPRPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   5383 GenBank   WP_207603842
Name   t4cp2_J2J97_RS26640_PLR8-1a|p3 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: 91699.43 Da        Isoelectric Point: 5.5845

>WP_207603842.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESAIDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTHRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYLANTLSIRRMETRETVERGGERIARYDELLQFARYCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENLFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWVEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERSLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARETGTREFYERIGFNERQLEIVATAIPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGHEWPIHWLETRGVHDAASLLRFE

  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: 186939..200929

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J2J97_RS26565 (J2J97_26565) 185234..185770 + 537 WP_246569464 conjugative transfer signal peptidase TraF -
J2J97_RS26570 (J2J97_26570) 185760..186922 + 1163 Protein_166 conjugal transfer protein TraB -
J2J97_RS26575 (J2J97_26575) 186939..187547 + 609 WP_207603833 TraH family protein virB1
J2J97_RS26580 (J2J97_26580) 187773..188641 - 869 Protein_168 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
J2J97_RS26585 (J2J97_26585) 188634..189251 - 618 WP_127431473 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
J2J97_RS32960 189298..189515 - 218 Protein_170 hypothetical protein -
J2J97_RS26590 (J2J97_26590) 189597..189839 - 243 WP_087002841 helix-turn-helix transcriptional regulator -
J2J97_RS26595 (J2J97_26595) 190064..190387 + 324 WP_207603834 transcriptional repressor TraM -
J2J97_RS26600 (J2J97_26600) 190391..191095 - 705 WP_207603835 autoinducer binding domain-containing protein -
J2J97_RS26605 (J2J97_26605) 191406..192704 - 1299 WP_207603836 IncP-type conjugal transfer protein TrbI virB10
J2J97_RS26610 (J2J97_26610) 192716..193156 - 441 WP_207609319 conjugal transfer protein TrbH -
J2J97_RS26615 (J2J97_26615) 193160..193972 - 813 WP_207603838 P-type conjugative transfer protein TrbG virB9
J2J97_RS26620 (J2J97_26620) 193990..194652 - 663 WP_207603839 conjugal transfer protein TrbF virB8
J2J97_RS26625 (J2J97_26625) 194673..195854 - 1182 WP_207603840 P-type conjugative transfer protein TrbL virB6
J2J97_RS26630 (J2J97_26630) 195848..196048 - 201 WP_207603981 entry exclusion protein TrbK -
J2J97_RS26635 (J2J97_26635) 196045..196848 - 804 WP_207603841 P-type conjugative transfer protein TrbJ virB5
J2J97_RS26640 (J2J97_26640) 196820..199276 - 2457 WP_207603842 conjugal transfer protein TrbE virb4
J2J97_RS26645 (J2J97_26645) 199287..199586 - 300 WP_207603843 conjugal transfer protein TrbD virB3
J2J97_RS26650 (J2J97_26650) 199579..199962 - 384 WP_207603844 TrbC/VirB2 family protein virB2
J2J97_RS26655 (J2J97_26655) 199952..200929 - 978 WP_207609320 P-type conjugative transfer ATPase TrbB virB11
J2J97_RS26660 (J2J97_26660) 200926..201564 - 639 WP_207603846 acyl-homoserine-lactone synthase -
J2J97_RS26665 (J2J97_26665) 201901..203163 + 1263 WP_207603982 plasmid partitioning protein RepA -
J2J97_RS26670 (J2J97_26670) 203160..204197 + 1038 WP_207603847 plasmid partitioning protein RepB -
J2J97_RS26675 (J2J97_26675) 204389..205602 + 1214 Protein_188 plasmid replication protein RepC -

Host bacterium

ID   8093 GenBank   NZ_CP071621
Plasmid name   PLR8-1a|p3 Incompatibility group   -
Plasmid size   382349 bp Coordinate of oriT [Strand]   181771..181804 [+]
Host baterium   Rhizobium bangladeshense strain PLR8-1a

Cargo genes

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