Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108329
Name   oriT_pCB3171_2 in_silico
Organism   Rhizobium sp. CB3171
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP121654 (522310..522345 [+], 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_pCB3171_2
ATCCGAAGGGCGCAATTATACGTCGCTATCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5570 GenBank   WP_283054512
Name   traA_QA648_RS34330_pCB3171_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: 122288.11 Da        Isoelectric Point: 9.7678

>WP_283054512.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. CB3171]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYRAKQGLLHEEFVVPVDAPQWLRAMIADH
SVSGASEAFWNSVETFEKRSDAQLAKDVTIALPIELSTEQNIALMRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLAEDGFGAKKVAVKGPDGKPMRNDAGKIVYELWAGNLDNFNAFRDGWFACENRHLALAG
LDMRIDGRSFEKQGIELRPTIHLGVGAKAIERKSAVAAGDVSLERLELHEERRAENARRIQRRPELVLDL
ITREKSVFDERDVAKILHRYVDDAGLFQSLMARIVQSPETLRLERERIEFSSGVRLPAKYTTRDLIRLEA
EMANRAIWLSQRSSHGLADAVREATFARYLRLSDEQKTAIAHVTGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVIGGALAGKAAEGLEKEAGILSRTLSSWELRWNEGHNLLDDKTVFVLDEAGMVSSRQMAVFVE
AATKAGAKLALVGDPEQLQPIEAGAAFRSIADRIGYVELETIHRQREQWMRDASLDLARGNIGKAIDAYR
AQARINGSELKAQAVENLIADWDREYDLQTSSLILAHLRRDVRMLNDMARAKLVERGLVAEGFVFQTEDG
HRKFAAGDQVVFLKNEGSLGVKNGMLARLTDAAPGRIVAEVGEGEHCRQITVEQRFYANVDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHRQDLGFYYGRRSFAKAGGLIPILSRRQGKETTLDYANGRFY
GQALRFAEARGLHLVSVARTVLRDRLEWTFRQKSKLAELGARLAALAGKLSLATAAARTSQSHTIKEPKP
MVSGITTFSRSLEQAVEDRLAADPGLKKQWAEVSGRFHMVYAQPEAAFKAVNVDAMLGDETTAKSTIARI
GSEPQSFGALKGNIGFLASRADEQNRERAVTNAPALARNLERYLRQRTEAVRKYEAEERALRLKVSLDIP
ALSPAAKQTLERVRDAIDRNDLPAALEYALSDKMVKAELEGFARAVSERFGERIFPSLTAKAPNGQTFNA
ITTGMTAGQKAEVEAAWDSIRTVQQLSAHERTAESLKQIETLRQSKSKGFSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

MobA/MobL family (MobA_MobL)

(17-243)

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

(859-955)


  Protein structure



No available structure.




T4CP

ID   5941 GenBank   WP_283054511
Name   traG_QA648_RS34325_pCB3171_2 insolico UniProt ID   _
Length   731 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 731 a.a.        Molecular weight: 79566.10 Da        Isoelectric Point: 9.4241

>WP_283054511.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. CB3171]
MKKPSSKIRDEIAKLQEQLKLAETREAERIGRIALKAGLGVIEIDEGELQAAFEYLAKRFRYGEARSTGD
RKAGGARESSSPPAQNSSPQLALRRLEKPMTRILLLVVPCALMILAAMGMTGIEQWLSAFGKTDAARQML
GRAGIALPYVVASLVGIVFLFASAGSVRVRTAGSGVVAGAMATLFIAAIREAMRLSVFREQVPAGKSIFN
YLDPATGIGAAAVLISALFGLRVAIAGNAAFAKAEPKRIYGKRALHGEADWMKMSQAEQLFAGSGGIVIG
ERYRVDRDSVAAQSFRADCGETWGAGGMSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALV
VLDPSNEVAPMVSKHRGDADRDVFVLDPKHSEIGFNALDWIGRFGGTKEEDIASVASWVVSDSGGRGLRD
DFFRASALQLLTALIADVCLSGHTTQSDQTLRQVRKNLSEPEPKLRERLQSIFDHSESDFVKENVAVFVN
MTPETFSGVYANAVKETHWLSYPNYAALVSGTTFTTSDLAAGKTDVFINIDLKTLEMHSGLARVIIGSFL
NAICNRNGEMYGRTLFLLDEVARLGYMRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDATSKWFES
ASWISFAAINDPETADYISRRCGMTTVEIDQVSRSFQSRGSSRTRSKQLAARPLIQPHEVLRMRADEQIV
FTAGNPALRCGRAIWFRRRDMEACIKGQSFQ

  Protein domains


Predicted by InterproScan.

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

(260-728)

TraC-like protein (TraC)

(2-80)

  Protein structure



No available structure.



ID   5942 GenBank   WP_283054524
Name   t4cp2_QA648_RS34395_pCB3171_2 insolico UniProt ID   _
Length   822 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 822 a.a.        Molecular weight: 92383.33 Da        Isoelectric Point: 6.2243

>WP_283054524.1 conjugal transfer protein TrbE [Rhizobium sp. CB3171]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINTILSRLG
SGWMIQVEAIRIPTFDYPSDDRCHFPDAVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKTYADTVLFIFKNAIREIEQYFANSLSIRRMETRETVERGGARVARYDELLQFVRFCITG
ENHPIRLPAAPMYLDWIATAEIEHGLTPKAENRFLAVVAIDGLPAESWPGILNSLDLMPLAYRWSSRFIF
LDAEEARRKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAITMVAETEDAIAQASSQLVAYGYYTPVIIL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSAIAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDRGNSLLPLTLAAGGDHYEIGGDAQEEGSALAFCPLSDLSEESDRAWATEWIEMLVALQGVTITPDHRN
AISRQIRLMIGAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLSLGAFQTFEIEQLMNMG
ERNLIPVLTYLFRRIEKRLDGSPSLIVLDEGWVPLGHPKFRDKIREWLKVLRKLNCAVVLATHSISDAER
SGIIDVLKESCPTKICLANGAAREPGTREFYERIGFNERQIEIVSNAIPKREYYVVTPEGRRLFDMALGP
VALSFVGASGKEDLKRIRALHSEHGRDWPIHWLQTRGVHDAAVLLTVEKAAR

  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: 527470..539337

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QA648_RS34335 (QA648_34335) 525797..526300 + 504 WP_283054513 conjugative transfer signal peptidase TraF -
QA648_RS34340 (QA648_34340) 526290..527453 + 1164 WP_283054514 conjugal transfer protein TraB -
QA648_RS34345 (QA648_34345) 527470..528078 + 609 WP_283054515 TraH family protein virB1
QA648_RS34350 (QA648_34350) 528344..528580 - 237 WP_283054516 helix-turn-helix transcriptional regulator -
QA648_RS34355 (QA648_34355) 528830..529144 + 315 WP_283054517 transcriptional repressor TraM -
QA648_RS34360 (QA648_34360) 529148..529852 - 705 WP_283054518 autoinducer binding domain-containing protein -
QA648_RS34365 (QA648_34365) 530006..531304 - 1299 WP_283054519 IncP-type conjugal transfer protein TrbI virB10
QA648_RS34370 (QA648_34370) 531315..531752 - 438 WP_283054520 conjugal transfer protein TrbH -
QA648_RS34375 (QA648_34375) 531756..532568 - 813 WP_283054521 P-type conjugative transfer protein TrbG virB9
QA648_RS34380 (QA648_34380) 532584..533246 - 663 WP_283054522 conjugal transfer protein TrbF virB8
QA648_RS34385 (QA648_34385) 533271..534449 - 1179 WP_283054523 P-type conjugative transfer protein TrbL virB6
QA648_RS34390 (QA648_34390) 534454..535257 - 804 WP_283054765 P-type conjugative transfer protein TrbJ virB5
QA648_RS34395 (QA648_34395) 535217..537685 - 2469 WP_283054524 conjugal transfer protein TrbE virb4
QA648_RS34400 (QA648_34400) 537695..537994 - 300 WP_283054525 conjugal transfer protein TrbD virB3
QA648_RS34405 (QA648_34405) 537987..538370 - 384 WP_283054526 TrbC/VirB2 family protein virB2
QA648_RS34410 (QA648_34410) 538360..539337 - 978 WP_283054527 P-type conjugative transfer ATPase TrbB virB11
QA648_RS34415 (QA648_34415) 539334..539972 - 639 WP_283054528 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   8764 GenBank   NZ_CP121654
Plasmid name   pCB3171_2 Incompatibility group   -
Plasmid size   540349 bp Coordinate of oriT [Strand]   522310..522345 [+]
Host baterium   Rhizobium sp. CB3171

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
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, nifK, nifE, nifN, nifX, mLTONO_5203, nodM
Anti-CRISPR   -