Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115784
Name   oriT_pCB3060_2 in_silico
Organism   Rhizobium sp. CB3060
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP104160 (519995..520030 [+], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      21..26, 31..36  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_pCB3060_2
ATCCGAAGGGCGCAATTATACGTCGCTGACGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10108 GenBank   WP_260305520
Name   traA_N2601_RS32060_pCB3060_2 insolico UniProt ID   _
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122591.56 Da        Isoelectric Point: 9.9807

>WP_260305520.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. CB3060]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADAPNWLRAMIADR
SVSGASEAFWNSVETFEKRVDAQLAKDVTIALPVELSTAQNIELVRDFVERHITSNGMVADWVYHDAPGN
PHVHLMTTLRPLAEDGFGAKKIAVTGPDGKPVRNDASKIVYQLWAGSLDDFNAFRDGWFACQNRHLARAG
LDLRVDGRSFEKQGIDLTPTIHLGVGAKAIERKSAEAERLPSLERLELQEERRAENARRIRRRPELVLDL
ITREKSVFDERDVAKILHRYIDDAGLFQSLMARILQSSDTLRLERERIEFSSGQRVPARYTTRELIRLEA
ELANRAIWLSQRSSHGVADAVREATFAHHLRLSDEQRTAIAHVIGGERIGAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLVKEAGIVSRTLSSWELRWNQGRNQLDDRTVFVLDEAGMVSSRQMALFVE
AATKSGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMREASLDLARGNIGKAVEAYR
AQGRISEADLKADAVQALIADWNRDYDPQTSSLILAHLRRDVRMLNDMTRAKLIERGLVAEGFAFRTEDG
HRKFAAGDQIVFLKNEGSLGVKNGMLAKVVEAAPGRIVAEVGEGEHRRQVTVEQRFYANLDHGYAITIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLSFYYGRRSFAKAGGLISILSRGQAKETTLDYASGRFY
AQALRFADARGLHLVNVARTVVRDRLEWTVRQKSKLAELGARLATIAGRLGLFAGAAKTTQSHRIKEAKP
MVSGITTFPKSLEQAVEDRLAADPGLKKQWEEVSTRFHLVYAQPESGFKAVNVDAMLKDESIAKSTLARI
GSEPERFGALKGKTGILASHADRQEREKAQTNAPALARNLERYLRQRAEAERKFEVEERALRLKVSIDIP
ALSQGAKQILERVRDAIDRNDLPAGLEYALADKMMKAELEGFAKAVSERFGERIFLSLAAKDPIGQTFNA
VTSGMTAGQKAEVQAAWSLMRTVQQLAAHERTTEALKHAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

AAA domain (AAA_30)

(382-569)

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

(859-955)


  Protein structure



No available structure.




T4CP

ID   11809 GenBank   WP_260305517
Name   traG_N2601_RS32045_pCB3060_2 insolico UniProt ID   _
Length   640 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 640 a.a.        Molecular weight: 69321.12 Da        Isoelectric Point: 8.5372

>WP_260305517.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. CB3060]
MTRMLLFVAPCTLMMLTAIGMTGIEDWLAQFGKSDAARQMLGRAGIALPYVAASVVGIVFLFASAGSVRI
RTAGWGVVTGSIATLVIAALREASRLSAFLGQVPTGKSIFNYLDPATAIGAAAVLMSALFGTRVAIAGNA
AFARAEPKRIVGKRALHGEADWMKLAHAEKLFAESGGIVIGERYRVDRDSCAAQSVRADSPETWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVSKHRGDANRDVFVLDPK
YSEIGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRTSALQLLTALIADVCLSGHTAESD
QTLRQVRKNLSEPEPQLRQRLQEIYDDSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGKTFTTGDLADGKTDVFINVDLKTLETHAGLARVIIGSFLNAIYNRNGEMPGRALFLLDEVARLGYMR
ILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKACVKPN
AFFRDSADNP

  Protein domains


Predicted by InterproScan.

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

(161-632)

  Protein structure



No available structure.



ID   11810 GenBank   WP_260305541
Name   t4cp2_N2601_RS32130_pCB3060_2 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: 91828.75 Da        Isoelectric Point: 6.3410

>WP_260305541.1 conjugal transfer protein TrbE [Rhizobium sp. CB3060]
MVALKRFRATDSSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATALERNELSRHINKILSRLG
SGWMIQVEAVRIPTFDYPSDDRCHFPDAVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKTYADTVLFFFKNTVREIEQYFANTLSIRRMETREAVERGGVRVARYDELLQFVRFCITG
DNHPIRLPDAPMYLDWIATAELEHGLTPKIESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDFDREALQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNVREPLINTSNLADLIPLNSVWS
GHPVAPCPFYPPSSPPLMQAASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLAAGGDHYEIGGDTQKAEKALAFCPLSDLSSDVDRAWAAEWIEMLIALQGVTITPDHRN
AISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLSLGAFQTFEIEQLMNMG
ERNLMPVLTYLFRRIEKRLDGSPSLIILDEGWVPLGHPKFRDKIREWLKVLRRLNCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAGEPGTREFYERIGFSETQIEIVSNAIPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRTLSSKHGRDWPIHWLRTRGVHDAAALLNLE

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 526265..538130

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N2601_RS32065 (N2601_32065) 523417..523983 + 567 WP_260305521 conjugative transfer signal peptidase TraF -
N2601_RS32070 (N2601_32070) 523973..525136 + 1164 WP_260305522 conjugal transfer protein TraB -
N2601_RS32075 (N2601_32075) 525224..525996 + 773 Protein_490 IS110 family transposase -
N2601_RS32080 (N2601_32080) 526265..526873 + 609 WP_260305523 TraH family protein virB1
N2601_RS32085 (N2601_32085) 527132..527368 - 237 WP_260305524 helix-turn-helix domain-containing protein -
N2601_RS32090 (N2601_32090) 527617..527931 + 315 WP_260305525 transcriptional repressor TraM -
N2601_RS32095 (N2601_32095) 527935..528639 - 705 WP_260305526 autoinducer binding domain-containing protein -
N2601_RS32100 (N2601_32100) 528798..530099 - 1302 WP_260305527 IncP-type conjugal transfer protein TrbI virB10
N2601_RS32105 (N2601_32105) 530110..530544 - 435 WP_260305528 conjugal transfer protein TrbH -
N2601_RS32110 (N2601_32110) 530548..531360 - 813 WP_260305532 P-type conjugative transfer protein TrbG virB9
N2601_RS32115 (N2601_32115) 531377..532039 - 663 WP_104825910 conjugal transfer protein TrbF virB8
N2601_RS32120 (N2601_32120) 532064..533242 - 1179 WP_260305537 P-type conjugative transfer protein TrbL virB6
N2601_RS32125 (N2601_32125) 533247..534050 - 804 WP_104825912 P-type conjugative transfer protein TrbJ virB5
N2601_RS32130 (N2601_32130) 534022..536478 - 2457 WP_260305541 conjugal transfer protein TrbE virb4
N2601_RS32135 (N2601_32135) 536488..536787 - 300 WP_260305542 conjugal transfer protein TrbD virB3
N2601_RS32140 (N2601_32140) 536780..537163 - 384 WP_260305543 TrbC/VirB2 family protein virB2
N2601_RS32145 (N2601_32145) 537153..538130 - 978 WP_260305547 P-type conjugative transfer ATPase TrbB virB11
N2601_RS32150 (N2601_32150) 538127..538765 - 639 WP_260305554 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   16217 GenBank   NZ_CP104160
Plasmid name   pCB3060_2 Incompatibility group   -
Plasmid size   539141 bp Coordinate of oriT [Strand]   519995..520030 [+]
Host baterium   Rhizobium sp. CB3060

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   LinG, dxnH, linJ
Symbiosis gene   nodD, nodA, nodE, fixN, fixO, fixQ, fixG, nodB, nodC, nodS, nodU, nodI, nodJ, nodH, nifT, nifZ, nifB, nifA, fixX, fixC, fixB, fixA, nifW, nifS, nifH, nifD, nifK, nifE, nifN, nifX, mLTONO_5203, nodM
Anti-CRISPR   -