Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107442
Name   oriT_ATCC 14479|unnamed3 in_silico
Organism   Rhizobium leguminosarum strain ATCC 14479
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP030763 (244018..244053 [+], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      15..21, 26..32  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_ATCC 14479|unnamed3
AAGGGCGCAATTATACGTCGCTGACGCGACGTCTTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4978 GenBank   WP_112908016
Name   traA_DLJ82_RS33460_ATCC 14479|unnamed3 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: 122960.89 Da        Isoelectric Point: 9.8781

>WP_112908016.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARKIDYTRKRGLLHEEFVIPVNAPQWLRTMIADR
SVSGASEAFWNRVEAFEKRSDAQLAKDVTIALPIELSAGQNIALVRDFVGRHITANGMVADWVYHDAAGN
PHVHLMTTLRPLTEDGFGAKKVAVLGPDGNLLRNDSGKILYEAWAGSVDDFHVFRDGWFACQNEHLALAG
LDIRIDGRSFEAQGVELTPTIHLGVGTKAIERKAEQAKAKVSVWALKLERIELQEDRRVENARRIQRRPE
IVLDLITREKSVFDERDVAKILHRYIDDTGLFQSLMVRILQSPETLPLERERIEFGTGIRAPAKYTTREL
IRLEADMTNRAIWLAARNSHGVKKSVLEATFAHHSRLSQEQRSAIAHVAAAKQVAAVVGRAGAGKTTMMT
AAREAWESSGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELDWNEGRNQLDGRTVFVLDEAGMVSSRQM
AVFVEAASRAGAKLVLIGDPEQLQPIEAGAAFRAITDRIGYAELETIYRQRERWMRDASLDLARGNVATA
VDAYRANDRLLGSELKAHAVENLIADWNRDYDPTKTTLILAHLRRDVRMLNELARENLVERGIVATGFAF
RTEEGNRNFAAGDQIVFLRNEGSLGVKNGMIGKVVEAAPCRILVEVGQDEHRRQVTVDQRFYNNVDHGYA
ITIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHRDDLAVYYGSRSFAKAGGLIPILSRKNAKETTLDYE
KNSLYRQALRFSEARGLHLMNVARTIARDRLDWTVRQKQKLADLGARLLAIGSMLGVADRIAKSSLPNAI
KESKPMVSGISTFPKSIEQVVEDKLAADAGLRTQWEDVSTRFHLVYAQPEAAFSAVDVDAMLKDQSTAKA
TLAKIAAEPASFGALRGKTGIFANRSDKHDRDRAIANGPALARNLERYLRQRTEAERKYDAEERGVRLKI
SIDIPALSPAARQTLERVRDAIDRNDLAAGLEYALADKLVNAELEGLAKAVSERFGERTFLGVASKDASG
GTYKSITSGMNPTQKAEMRIAWDWIRTIQQLSAHRNTTEALKQAQTVRQTKSPGLSLK

  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)


  Protein structure



No available structure.




T4CP

ID   5181 GenBank   WP_112908014
Name   traG_DLJ82_RS33445_ATCC 14479|unnamed3 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: 70054.35 Da        Isoelectric Point: 9.9361

>WP_112908014.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTANKIALVGLPITLMILVTIGMTGSEQWLSAFGKTEAGRRMLGRAGIALPYIASATIGMIVLFASAGST
NIKLAGWSVVGGGSVTILIAALRETVRLVALLDQLPTARSALFYADPATMIGAAAALISAAFALRISLVG
NAAFATAEPKRILGRRALHGEADWMKMTQAGKLFPDAGGIVIGERYRVDKDSTAAQAFRTDSPETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVVLDPSKEVAPMIIKHRSQAGRDVHILD
PRNRDTGFNALDWIGRHGGTKEEDIAAVASWIMSDNGGARGVRDDFFRASALQLLTALIADVCLSGHTLK
EHQTLRQVRKNLAEPEPKLRERLQRIHGNSKSEFVKENVASFVNMTPETFSGVYANAVKETHWLSYLNYA
ALVSGSSFSTDELARGDLDVFINIDLKTLEAHSGLARVIIGSFLNAIYNHDGDLKERALFLLDEVARLGY
MRILETARDAGRKYGISLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQVSRSFQSKGTSRTRSKQLAARPLIQPHEVLRMRPDEQIVFTAGNPPLRCGRAIWFRRDDMRMRVV
ENRFHALAGGARER

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   5182 GenBank   WP_112908041
Name   t4cp2_DLJ82_RS33590_ATCC 14479|unnamed3 insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 91682.41 Da        Isoelectric Point: 6.2214

>WP_112908041.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVSLRVFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDLERNEVSRQINAILSRLG
SGWMIQVEAVRLATVEYASAGKSYFPDRVTRAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSTLSK
YIYADEGSRKQSYADTVLFIFRNVVREVEQYLANIISIRRMMTRETTERGGARVARYDELLQFIRFCVTG
ENHPVRLPDIPMYLDWIATAELQHGLSPKVENRFLGVVAIDGLPSESWPGILNSLDLMPLSYRWSSRFIF
LDAEEAKVHLERTRKKWQQKVRPFFDQLFQTQSRSVDHDAMSMVAETEDAIAEASSQLVAYGYYTPVVVL
FENDAERLKEQTEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWFCNIREPLINTRNLSDLIPLNSVWS
GNPQAPCPFYPSDSPPLMHVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYKDAQIFA
FDKGGSMLPLTLAAGGDHYDVGGDEGTRLSFCPLSELSSDRDRAWACEWIESLVAMQGITITPDHRNAIS
RQIGLMAAAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAETDGLALGLFQTFEIEQLMNMGERN
LVPVLTYLFRRIEKRLTGAPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGM
IDVLKESCPTKICLPNGAAREPGTREFYERIGFNQRQIQIVASAIPKREYYVASPEGRRLFDMALGPLTL
SFAGASSKDDLKRIRALHEEHGPEWPLHWLQQRGIKDAASLLDDT

  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: 264621..274093

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DLJ82_RS33530 (DLJ82_6139) 259630..261024 - 1395 WP_112908029 amidohydrolase family protein -
DLJ82_RS40745 261014..261565 - 552 WP_342637407 response regulator transcription factor -
DLJ82_RS33545 262339..263076 + 738 WP_112908032 response regulator transcription factor -
DLJ82_RS33550 (DLJ82_6142) 263463..264146 + 684 WP_245472958 autoinducer binding domain-containing protein -
DLJ82_RS33555 (DLJ82_6143) 264621..265907 - 1287 WP_112908034 IncP-type conjugal transfer protein TrbI virB10
DLJ82_RS33560 (DLJ82_6144) 265920..266354 - 435 WP_112908035 conjugal transfer protein TrbH -
DLJ82_RS33565 (DLJ82_6145) 266351..267172 - 822 WP_112908036 P-type conjugative transfer protein TrbG virB9
DLJ82_RS33570 (DLJ82_6146) 267187..267849 - 663 WP_112908037 conjugal transfer protein TrbF virB8
DLJ82_RS33575 (DLJ82_6147) 267869..269050 - 1182 WP_112908038 P-type conjugative transfer protein TrbL virB6
DLJ82_RS33585 (DLJ82_6149) 269238..270038 - 801 WP_112908040 P-type conjugative transfer protein TrbJ virB5
DLJ82_RS33590 (DLJ82_6150) 270010..272457 - 2448 WP_112908041 conjugal transfer protein TrbE virb4
DLJ82_RS33595 (DLJ82_6151) 272469..272765 - 297 WP_112908042 conjugal transfer protein TrbD virB3
DLJ82_RS33600 (DLJ82_6152) 272758..273138 - 381 WP_204361411 TrbC/VirB2 family protein virB2
DLJ82_RS33605 (DLJ82_6153) 273128..274093 - 966 WP_112908043 P-type conjugative transfer ATPase TrbB virB11
DLJ82_RS33610 (DLJ82_6154) 274107..274736 - 630 WP_112908044 acyl-homoserine-lactone synthase TraI -
DLJ82_RS33615 (DLJ82_6155) 275100..276317 + 1218 WP_018247073 plasmid partitioning protein RepA -
DLJ82_RS33620 (DLJ82_6156) 276302..277342 + 1041 WP_112908045 plasmid partitioning protein RepB -
DLJ82_RS33625 (DLJ82_6157) 277582..278847 + 1266 WP_112908046 plasmid replication protein RepC -

Host bacterium

ID   7877 GenBank   NZ_CP030763
Plasmid name   ATCC 14479|unnamed3 Incompatibility group   -
Plasmid size   771583 bp Coordinate of oriT [Strand]   244018..244053 [+]
Host baterium   Rhizobium leguminosarum strain ATCC 14479

Cargo genes

Drug resistance gene   -
Virulence gene   gmd
Metal resistance gene   hupE2
Degradation gene   bphC
Symbiosis gene   noeL
Anti-CRISPR   AcrIIA7, AcrIIA9