Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114419
Name   oriT_pN03G-1 in_silico
Organism   Bradyrhizobium japonicum strain N03G-Bj
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP126011 (146975..147016 [+], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      9..15, 20..26  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pN03G-1
AAAGCAGGACGTCGCGGATGCGACGTATTACTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9239 GenBank   WP_212479306
Name   traA_QIH85_RS47710_pN03G-1 insolico UniProt ID   _
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 121918.26 Da        Isoelectric Point: 9.9984

>WP_212479306.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Bradyrhizobium]
MAITHFTPQLISRGSGRSAVLSAAYRHCARMEHQAEGRTVDYSAKRGLRYEEFLLPPDAPQWARELIADR
SVAGAAEAFWNAIEAFEKRSDAQLAKEFIIALPVELTIDQNVALVREFVATQVLARGQVADWVFHDEPGN
PHIHLMTTLRPLGEDGFGPKKVPVIGHDGAPLRNAAGKIVYRLWSGEKAEFLAQREGWLDLQNRHLALAG
LDIRVDGRSYAERGVDLAPTTHIGVATKAIDRKGKKAGWSPKLERVALHEERKTDNRQRILRRPEIVLDL
VSREMSVFTERDIARVLHRYVDDAGTFQHLMARILQNPEALRLEGECIALATGIREPAKYTTRELIRLEA
EMAHRAVWLAGRSSHGVREKVLAAAFERHARLSEEQRVAIAHVASVGRIAAVVGRAGAGKTTMMKAAREV
WEAAGYRVVGAALAGKAAEGLEKEAGIASRTLASWELAWSNGREQLDDKTIFVLDEAGMVSSRQMALFVE
AVVKTGAKLALVGDPDQLQPIEAGAAFRAIAERTGYAELETIYRQREQWMRDASLDLARGRVAEALQAYG
ANGKLEARKYKAQAVEALIEDWNWDYDPAKSTLILAHLRRDVRVLNEMARAKLIERGIVEDGHAFRTEDG
PRSFATGDQIVFLKNEGSLGVKNGMIARVIEARPGWFAAMIGEGEARRRVEVDQRFYANVDHGYATTIHK
SQGATVDRVKVLATLSLDRHLAYVALTRHREDVALYYGAISFGKAGGLTKILSQSRAKETTLDYERGPSY
RAALRFAEARGLHLMRVARTLVADKVRWTVRQKQKLADLGARLLALGARLGLGAARKQTIPNGAKEAKPM
VAGITTFAKSIDQVVEDKLAADPGLKKQWEEVSTRFRFVFAEPESAFRKVDVDSMLKDKATAQSTLSKLA
EKPESFGALKGKTGLLASRADKQDRQRADLNVPALARDLERFLRLRSEAEHRYEAEERAARLKVAVDIPA
LSPSAKQTLERIRDAIDRNDLPAALEFALEDKMIEAELEGFARAVSERFGERSFVGLAAKDTDGKTFETL
SGGMNAAQKEGLKAAWPDLRTAQQLAAQQRTAVALKEAKTLRQTQSKGLSLQ

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

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

(858-954)

AAA domain (AAA_30)

(382-566)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   10700 GenBank   WP_028152596
Name   t4cp2_QIH85_RS47635_pN03G-1 insolico UniProt ID   _
Length   817 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 817 a.a.        Molecular weight: 91386.01 Da        Isoelectric Point: 6.3078

>WP_028152596.1 MULTISPECIES: conjugal transfer protein TrbE [Bradyrhizobium]
MVALRSFRHSGPSFADLVPYAGLVDDGIVLLKDGSLMAGWYFAGPDSESSTDAERNDVSRQINAILARLG
SGWMIQVEALRIPTTDYPARKDGHFPDAVTRAIDEERRGHFERERGHYESRHALILTWRPPERRKSGLAK
YVYSDKDSRSASFADTALGNFRTSIREIEQYLSNLLSIQRMRTRETAERGDARIARYDELFQFVRFCITG
ENHPVRLPEVPMYLDWLVTAEYQHGLTPTVDGRYVGVVAIDGLPAESWPGILNILDLMPLTYRWSSRFMF
LDEIEARERLERTRKKWQQKVRPFFDQLFQTQSRSIDQDAMAMVAETQDAIAEAASQLVAYGYYTPVIVL
QDHDAERLREKCEGIRRVVQAEGFGARIETLNATEAFLGSLPGNWYANIREPLIHTRNLADLLPLNSVWS
GSPVAPCPFYPEGSPPLMQVASGSTPFRLNLHTDDVGHSLIFGPTGSGKSTLLALIAAQFRRYRDAQIFA
FDKGRSLMPLTLAAGGDHYEIGGGAGEGPQLAFCPLAELATDADRAWASEWIETLVVLQGVSVTPDHRNA
ISRQVALMAAAPGRSLADFVSGVQMREIKDALHHYTVDGPMGHLLDAERDGLVLGGFQTFEIEELMNMGE
RSLVPVLTYLFRRIEKRLTGAPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAERS
GIIDVLKESCPTKICLPNGAAREPGTREFYERLGFNERQIEIVSNAIPKREYYVTSPAGRRLFDMALGPV
ALAFVGASGRDDLKRITELKAVHGRTWPANWLQTRGIAHAETLLADD

  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.



ID   10701 GenBank   WP_028152606
Name   traG_QIH85_RS47725_pN03G-1 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: 68584.77 Da        Isoelectric Point: 9.2825

>WP_028152606.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Bradyrhizobium]
MTASRLLLLIVPVALMLGTVIGLTGIEHSLAGLGKTEAQRLLVARAGIAMPYIVAAAIGVVFLFAAAGSA
NIRTAAWSVVAGCAAAISMAAAREAIRLSAILANAVHGRSPPVQIDPAIMVGAGIALMAGIFALRVAVKG
NAAFAAPMPKRVRGRRALHGDADWMLVPEAAGLFSDAGGIVVGERYRVDKDSAAAEPFRAMDRQSWGIGG
RAPLLCFDATFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVIEHRRAAGRTVHVLD
PREPGTGFNALDWIGRFGGTKEEDIAAVASWIMSDSGGVRGVRDDFFRASALQLVTALIADVCLSGHTED
KNQTLRQVRANLSEPEPKLRARLQAIYDNSESQFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGSTFVSDDLAGGATDVFINLDLKTLETHAGLARVIIGAFMNAIYNRNGEVTGRALFLLDEVARLGF
MRILETARDAGRKYGITLLLLFQSIGQMRETYGGRDAASKWFESASWISFAAVNDPETAEYISKRCGMTT
VEIDQVSRSSQASGSSRTRSKQLASRPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVG
KNRFQPEEKT

  Protein domains


Predicted by InterproScan.

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

(169-635)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 129196..138772

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QIH85_RS47600 (QIH85_47600) 124423..125647 - 1225 Protein_124 plasmid replication protein RepC -
QIH85_RS47605 (QIH85_47605) 125874..126887 - 1014 WP_049808001 plasmid partitioning protein RepB -
QIH85_RS47610 (QIH85_47610) 126884..128077 - 1194 WP_028152592 plasmid partitioning protein RepA -
QIH85_RS47615 (QIH85_47615) 128570..129199 + 630 WP_063629878 acyl-homoserine-lactone synthase -
QIH85_RS47620 (QIH85_47620) 129196..130164 + 969 WP_060913174 P-type conjugative transfer ATPase TrbB virB11
QIH85_RS47625 (QIH85_47625) 130154..130543 + 390 WP_028152594 TrbC/VirB2 family protein virB2
QIH85_RS47630 (QIH85_47630) 130536..130835 + 300 WP_028152595 conjugal transfer protein TrbD virB3
QIH85_RS47635 (QIH85_47635) 130845..133298 + 2454 WP_028152596 conjugal transfer protein TrbE virb4
QIH85_RS47640 (QIH85_47640) 133270..134088 + 819 WP_038953896 P-type conjugative transfer protein TrbJ virB5
QIH85_RS47645 (QIH85_47645) 134082..134294 + 213 WP_028152598 entry exclusion protein TrbK -
QIH85_RS47650 (QIH85_47650) 134288..135475 + 1188 WP_038945592 P-type conjugative transfer protein TrbL virB6
QIH85_RS47655 (QIH85_47655) 135490..136152 + 663 WP_028152600 conjugal transfer protein TrbF virB8
QIH85_RS47660 (QIH85_47660) 136170..136994 + 825 WP_028152601 P-type conjugative transfer protein TrbG virB9
QIH85_RS47665 (QIH85_47665) 136999..137463 + 465 WP_028152602 conjugal transfer protein TrbH -
QIH85_RS47670 (QIH85_47670) 137474..138772 + 1299 WP_028152603 IncP-type conjugal transfer protein TrbI virB10
QIH85_RS47675 (QIH85_47675) 139047..139958 + 912 WP_232674644 autoinducer binding domain-containing protein -
QIH85_RS47680 (QIH85_47680) 139967..140836 - 870 WP_232674645 transcriptional repressor TraM -
QIH85_RS49635 140841..141089 - 249 WP_080586789 DUF2167 domain-containing protein -
QIH85_RS47685 (QIH85_47685) 141098..141688 - 591 WP_049807966 DUF2167 domain-containing protein -
QIH85_RS47690 (QIH85_47690) 141827..141946 + 120 Protein_143 type II toxin-antitoxin system VapC family toxin -
QIH85_RS47695 (QIH85_47695) 141977..142582 - 606 WP_035680223 TraH family protein -
QIH85_RS47700 (QIH85_47700) 142597..142919 - 323 Protein_145 nitrilase-related carbon-nitrogen hydrolase -
QIH85_RS47705 (QIH85_47705) 142977..143480 - 504 WP_038953892 conjugative transfer signal peptidase TraF -

Host bacterium

ID   14854 GenBank   NZ_CP126011
Plasmid name   pN03G-1 Incompatibility group   -
Plasmid size   165114 bp Coordinate of oriT [Strand]   146975..147016 [+]
Host baterium   Bradyrhizobium japonicum strain N03G-Bj

Cargo genes

Drug resistance gene   -
Virulence gene   bscN
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -