Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108330
Name   oriT_pCB3090_2 in_silico
Organism   Rhizobium sp. CB3090
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP121664 (543065..543100 [+], 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_pCB3090_2
ATCCGAAGGGCGCAATTATACGTCGCTATCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5571 GenBank   WP_283060803
Name   traA_QA646_RS29310_pCB3090_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: 122223.93 Da        Isoelectric Point: 9.7678

>WP_283060803.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. CB3090]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYRAKQGLLHEEFVVPVDAPQWLRAMIADR
SVSGASEAFWNSVETFEKRSDAQLAKDVTIALPIELSTEQNIALMRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLAEEGFGAKKVAVKGPDGKPMRNDAGKIVYQLWAGNLDNFNAFRDGWFACENRHLALAG
LDMRVDGRSFEKQGIELTPTIHLGVGAKAIERKSAVAAGDVSLERLELHEERRAENARRIQRRPELVLDL
ITREKSVFDERDVAKILHRYVDDAGLFQSLMARIVQSPETLRLERERIEFSSGVRLPAKYTTRDLIRLEA
EMANRAIWLSQRSSHGLADAVREATFARYLRLSDEQKTAIAHVTGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVIGGALAGKAAEGLEKEAGILSRTLSSWELRWNEGHNLLDDKTVFVLDEAGMVSSRQMAVFVE
AATKAGAKLALVGDPEQLQPIEAGAAFRSIADRIGYVELETIHRQREQWMRDASLDLARGNIGKAIDAYR
AQGRINGSELKAQAVENLIADWDREYDPQTSSLILAHLRRDVRMLNDMARAKLVERGLVAEGFVFQTEDG
HRKFAAGDQVVFLKNEGSLGVKNGMLARLTDAAPGRIVAEVGEGEHCRQITVEQRFYANVDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHRQDLGFYYGRRSFAKAGGLIPILSRRQGKETTLDYANGRFY
GQALRFAEARGLHLVSVARTVLRDRLEWTFRQKSKLAELGARLAALAGKLSLATAAARTSQSHTIKEPKP
MVSGITTFSRSLEQAVEDRLAADPGLKKQWAEVSGRFHMVYAQPEAAFKAVNVDAMLGDETTAKSTIARI
GSEPQSFGALKGNIGFLASRADEQNRERAVTNAPALARNLERYLRQQTEAERKYEAEERALRLKVSLDIP
ALSPAAKQTLERVRDAIDRNDLPAALEYALSDKMVKAELEGFARAVSERFGERIFPSLTAKAPNGQTFNA
VTTGMTAGQKAQVEAAWDSIRTVQQLSAHERTSESLKQIETLRQSKSKGFSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

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

(859-955)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-567)


  Protein structure



No available structure.




T4CP

ID   5943 GenBank   WP_283060799
Name   traG_QA646_RS29295_pCB3090_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: 69474.63 Da        Isoelectric Point: 8.9613

>WP_283060799.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. CB3090]
MTRILLLVVPCALMILAAMGMTGIEHWLSAFGKTDAARQMLGRAGIALPYVVASLVGIVFLFASAGSVRV
RTAGSGVVAGAMATLFIAAIREAMRLSVFREQVPAGKSIFNYLDPATGIGAAAVLISALFGLRVAIAGNA
AFAKAEPKRIYGKRALHGEADWMKMSQAEQLFAGSGGIVIGERYRVDRDSVAAQSFRADCGETWGAGGMS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVSKHRGDADRDVFVLDPK
HSEIGFNALDWIGRFGGTKEEDIASVASWVVSDSGGRGLRDDFFRASALQLLTALIADVCLSGHTTQSDQ
TLRQVRKNLSEPEPKLRERLQSIFDHSESDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPNYAALV
SGTTFTTSDLAAGKTDVFINVDLKTLEMHSGLARVIIGSFLNAICNRNGEMHGRTLFLLDEVARLGYMRI
LETARDAGRKYGITLTMIYQSIGQMRETYGGRDATSKWFESASWISFAAINDPETAEYVSRRCGMTTVEI
DQVSRSFQSRGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNPALRCGRAIWFRRRDMEVCINGQS
FQLGRKSMSL

  Protein domains


Predicted by InterproScan.

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

(161-630)

  Protein structure



No available structure.



ID   5944 GenBank   WP_283060820
Name   t4cp2_QA646_RS29375_pCB3090_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: 92029.77 Da        Isoelectric Point: 5.8777

>WP_283060820.1 conjugal transfer protein TrbE [Rhizobium sp. CB3090]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINTILSRLG
SGWMIQVEAIRIPTFDYPSDDRCHFPDAVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKTYADTVLFIFKNAIREIEQYFANSLSIRRMETRETVERGGARVARYDELLQFVRFCITG
ENHPIRLPAAPMYLDWIATAEIEHGLTPKAENRFLAVVAIDGLPAESWPGILNSLDLMPLAYRWSSRFIF
LDAEEARRKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAITMVAETEDAIAQASSQLVAYGYYTPVIIL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSAIAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDRGNSLLPLTLAAGGDHYEIGGDAQEEGSALAFCPLSDLSEESDRAWATEWIEMLVALQGVTITPDHRN
AISRQIRLMIGAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLSLGAFQTFEIEQLMNMG
ERNLIPVLTYLFRRIEKRLDGSPSLIVLDEGWVPLGHPKFRDKIREWLKVLRKLNCAVVLATHSISDAER
SGIIDVLKESCPTKICLANGAAREPGTREFYERIGFNERQIEIVSNAIPKREYYAVTPEGRRLFDMALGP
VALSFVGASGKEDLKRIRALHSEHGRDWPIHWLQTRGVYDAESQLTIE

  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: 548225..560099

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QA646_RS29315 (QA646_29315) 546552..547055 + 504 WP_283060804 conjugative transfer signal peptidase TraF -
QA646_RS29320 (QA646_29320) 547045..548208 + 1164 WP_283060806 conjugal transfer protein TraB -
QA646_RS29325 (QA646_29325) 548225..548833 + 609 WP_283060807 TraH family protein virB1
QA646_RS29330 (QA646_29330) 549100..549336 - 237 WP_104825904 helix-turn-helix transcriptional regulator -
QA646_RS29335 (QA646_29335) 549586..549900 + 315 WP_283060809 transcriptional repressor TraM -
QA646_RS29340 (QA646_29340) 549904..550608 - 705 WP_283060811 autoinducer binding domain-containing protein -
QA646_RS29345 (QA646_29345) 550768..552066 - 1299 WP_283060813 IncP-type conjugal transfer protein TrbI virB10
QA646_RS29350 (QA646_29350) 552077..552514 - 438 WP_283060815 conjugal transfer protein TrbH -
QA646_RS29355 (QA646_29355) 552518..553330 - 813 WP_283060816 P-type conjugative transfer protein TrbG virB9
QA646_RS29360 (QA646_29360) 553346..554008 - 663 WP_283060817 conjugal transfer protein TrbF virB8
QA646_RS29365 (QA646_29365) 554033..555211 - 1179 WP_283060818 P-type conjugative transfer protein TrbL virB6
QA646_RS29370 (QA646_29370) 555216..556019 - 804 WP_283060819 P-type conjugative transfer protein TrbJ virB5
QA646_RS29375 (QA646_29375) 555991..558447 - 2457 WP_283060820 conjugal transfer protein TrbE virb4
QA646_RS29380 (QA646_29380) 558457..558756 - 300 WP_283060821 conjugal transfer protein TrbD virB3
QA646_RS29385 (QA646_29385) 558749..559132 - 384 WP_283054526 TrbC/VirB2 family protein virB2
QA646_RS29390 (QA646_29390) 559122..560099 - 978 WP_283060822 P-type conjugative transfer ATPase TrbB virB11
QA646_RS29395 (QA646_29395) 560096..560734 - 639 WP_283060823 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   8765 GenBank   NZ_CP121664
Plasmid name   pCB3090_2 Incompatibility group   -
Plasmid size   561108 bp Coordinate of oriT [Strand]   543065..543100 [+]
Host baterium   Rhizobium sp. CB3090

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsC
Degradation gene   dxnH
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, nifE, nifN, nifX, mLTONO_5203, nodM
Anti-CRISPR   -