Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111746
Name   oriT_pBjCNPSo29a in_silico
Organism   Bradyrhizobium japonicum strain CNPSo 29
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP138300 (18100..18141 [-], 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_pBjCNPSo29a
AAAGCAGGACGTCGCGGATGCGACGTATTACTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7620 GenBank   WP_212479306
Name   traA_R3F78_RS01520_pBjCNPSo29a 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   8692 GenBank   WP_028152606
Name   traG_R3F78_RS01505_pBjCNPSo29a 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.



ID   8693 GenBank   WP_028152596
Name   t4cp2_R3F78_RS01595_pBjCNPSo29a 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 26344..35920

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R3F78_RS01525 (R3F78_01525) 21567..22139 + 573 WP_259266211 conjugative transfer signal peptidase TraF -
R3F78_RS01530 (R3F78_01530) 22197..22519 + 323 Protein_26 nitrilase-related carbon-nitrogen hydrolase -
R3F78_RS01535 (R3F78_01535) 22534..23139 + 606 WP_035680223 TraH family protein -
R3F78_RS01540 (R3F78_01540) 23170..23289 - 120 Protein_28 type II toxin-antitoxin system VapC family toxin -
R3F78_RS01545 (R3F78_01545) 23428..24018 + 591 WP_049807966 DUF2167 domain-containing protein -
R3F78_RS01550 (R3F78_01550) 24280..25149 + 870 WP_232674645 transcriptional repressor TraM -
R3F78_RS01555 (R3F78_01555) 25158..26069 - 912 WP_232674644 autoinducer binding domain-containing protein -
R3F78_RS01560 (R3F78_01560) 26344..27642 - 1299 WP_028152603 IncP-type conjugal transfer protein TrbI virB10
R3F78_RS01565 (R3F78_01565) 27653..28117 - 465 WP_028152602 conjugal transfer protein TrbH -
R3F78_RS01570 (R3F78_01570) 28122..28946 - 825 WP_028152601 P-type conjugative transfer protein TrbG virB9
R3F78_RS01575 (R3F78_01575) 28964..29626 - 663 WP_028152600 conjugal transfer protein TrbF virB8
R3F78_RS01580 (R3F78_01580) 29641..30828 - 1188 WP_038945592 P-type conjugative transfer protein TrbL virB6
R3F78_RS01585 (R3F78_01585) 30822..31034 - 213 WP_028152598 entry exclusion protein TrbK -
R3F78_RS01590 (R3F78_01590) 31028..31846 - 819 WP_038953896 P-type conjugative transfer protein TrbJ virB5
R3F78_RS01595 (R3F78_01595) 31818..34271 - 2454 WP_028152596 conjugal transfer protein TrbE virb4
R3F78_RS01600 (R3F78_01600) 34281..34580 - 300 WP_028152595 conjugal transfer protein TrbD virB3
R3F78_RS01605 (R3F78_01605) 34573..34962 - 390 WP_028152594 TrbC/VirB2 family protein virB2
R3F78_RS01610 (R3F78_01610) 34952..35920 - 969 WP_060913174 P-type conjugative transfer ATPase TrbB virB11
R3F78_RS01615 (R3F78_01615) 35917..36546 - 630 WP_063629878 acyl-homoserine-lactone synthase -
R3F78_RS01620 (R3F78_01620) 37039..38232 + 1194 WP_028152592 plasmid partitioning protein RepA -
R3F78_RS01625 (R3F78_01625) 38229..39242 + 1014 WP_049808001 plasmid partitioning protein RepB -
R3F78_RS01630 (R3F78_01630) 39469..40693 + 1225 Protein_46 plasmid replication protein RepC -

Host bacterium

ID   12181 GenBank   NZ_CP138300
Plasmid name   pBjCNPSo29a Incompatibility group   -
Plasmid size   160017 bp Coordinate of oriT [Strand]   18100..18141 [-]
Host baterium   Bradyrhizobium japonicum strain CNPSo 29

Cargo genes

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