Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101390
Name   oriT_pBjCNPSo38b in_silico
Organism   Bradyrhizobium japonicum strain CNPSo 38
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAXIOH010000002 (107348..107385 [+], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 38 nt

>oriT_pBjCNPSo38b
TCCAAGGGCGCAGTAATACGTCGCTGACGCGACGTCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1273 GenBank   WP_232674620
Name   traA_R3F79_RS48225_pBjCNPSo38b 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: 122893.31 Da        Isoelectric Point: 10.2929

>WP_232674620.1 Ti-type conjugative transfer relaxase TraA [Bradyrhizobium japonicum]
MAITHFTPQLIGRGDGRSAVLAAAYRHCAKMEFEAEGRTVDYSNKRGMIHEEFLVPADAPAWLRTMIADR
SVAGASEAFWNKVEAFEKRADAQFAKEFIIALPVELTSEQNIALMRQFVVEQVLSRGQVADWVYHDEPGN
PHVHMMTTLRPLTEDGFGPKRVAVIGEDGQPLRMKSGKIAYRLWAGDKQEFLEQRNGWLDLQNQHLALNG
HEIRVDGRSYAERGIDVVPTTHIGVAAKAIQRRAEREGRDPNLERLRVFNENRAETLRRIQRRPEIVLDM
ISREKSVFDERDVGKLLHRYVDDAATFQHLMARVLQSPDVLQLEGEQVDFATGARAPAKYTTRELIRLEA
EMVRRAVHLSGSGAFPVKPSVLAAMSARHANLSAEQRAAIAHLASGIRIAAVVGRAGAGKTTMMRAAREV
WEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWKSGRDGLDDRTVFVLDEAGMVASRQMALFVE
TASKAGAKLVLVGDPEQLQPIEAGAAFRAIVERIGYAELETIYRQRQQWMRDASLDLARGRTAQALSAYR
QQGRVFGSELKAQAIDNLIADWNRDYDPSKSTLILAHLRRDIRALNEMARAKLVEGGLLEQGHAFRTEDG
ERRFAPGDQIVFLKNEGSLGVKNGMIGKVVEAGTARLVAEIGEGECRCRVEVDQRFYRNIDHGYATTVHK
AQGATVDRVKVLATLSLDKHLAYVALTRHREDVALYYGRRSFQKAGGLIPILSQRRAKETTLDYERGALY
RAALRFAANRGLHVVRVARTLVNDRLRWTVRQKQRLAEVARRLRALAEKLGLVDGRKPIISTAHKEAKPM
IAGVTTFPKSLIDTVEDRILADPAIKKQWEDVSIRFRLVFADPERAFRATNFDAMLKDPAAASSTMARLA
SSPESFGALRGKVGMLAGKSDKQVRQRAEANAPALKRDIERYLRLRAEAEHKHEAEERAIRHRVAIDIPA
LSREARRVLERVRDAIDRNDLPSALEFALADRMVKAEIDGFNKAVAERFGDRTFLSNAAREPNGQPFEKA
AAGMDPARREQLKEAWPAMRAAQQLAAGERTAQALKQAEGQRLTQSQGQTLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)

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

(858-954)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-735)


  Protein structure



No available structure.




T4CP

ID   884 GenBank   WP_232674619
Name   traG_R3F79_RS48210_pBjCNPSo38b insolico UniProt ID   _
Length   643 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 643 a.a.        Molecular weight: 69692.74 Da        Isoelectric Point: 9.6771

>WP_232674619.1 Ti-type conjugative transfer system protein TraG [Bradyrhizobium japonicum]
MRANKIALAIVPAVLMASLCLVLTGIEAWLSKFGTTPNARLVLGRVGIALPYVVAAAIGVVFLLAAAGAT
AIRSAGWSVVFGGLLVVAIAVSREIARPHSFANALLAGDRLLAYADPSTIIGATIAALVAVFGLRVAIKG
NAAFAAAAPRRIRGRRAIHGESDWMVMTEAARLFPETGGIVVGERYRVDRDAVTDRSFRADDAETWGAGG
KSPLLCFDASFGSSHGIVFAGSGGFKTTSVTVPTALKWGGGLVVLDPSYEVAPMVTGHRHGAGRQVFVLD
PRSSGVGFNVLDWIGQHGATKEEDIAAVASWIMTDNPRQGSARDDFFRASALQLLTALIGDVCLSGHTEK
KDQHLRQVRANLSEPEPKLRQRLQTIYDNSESGFVKENVAPFIAMTPETFSGVYANAVKETHWLSYANYA
VLVSGSSFTTAELAEGRTDVFINLDLKTLENHAGLARVVIGSLLNAIYNRNGEVTGRTLFLLDEVARLGY
LRILETARDAGRKYGITLLMLYQSIGQMREAYGGRDATSKWFESASWISFSAINDPETADYISKRCGDTT
VEVDQLSRSSQMSGSSRTRSKQLARRPLMLPHEVLRMRTDEQIIFTAGNPPLRCGRAIWFRRTDMRACVG
ENRFYRREAGQRS

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   885 GenBank   WP_232674731
Name   t4cp2_R3F79_RS49085_pBjCNPSo38b insolico UniProt ID   _
Length   791 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 791 a.a.        Molecular weight: 88425.42 Da        Isoelectric Point: 5.4966

>WP_232674731.1 conjugal transfer protein TrbE [Bradyrhizobium japonicum]
MVALRTFRHSGPSFADLVPYAGLVANGIVLLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINTILARLG
SGWMIQVEAVRVPTTDYPAQQDCHFPDPVTRAIDDERRGRFEQERGHFESRHAIILSWRPPERRRAGLAR
YIYSDAESRSASYADTAIESFRTSIREVEQYLASVLSIRRMETREVEERDGTRIARYDELFQFIRFCITG
ENHPIRLPDIPMYLDWLATAELQHGLSPMVENRFLGVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFMF
LDDQDARQKLERTRKKWQQKVRPFIDRLFQTQSRSIDQDAAAMVAETEDAIAQASSQLVAYGYYTPVIVL
FDESSARLQEKAEAVRRLIQAEGFGARIETLNATEAFLGSLPGNWYANIREPLINTRNLADLIPLNSVWS
GNPTAPCPFYPPSSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLPLTLAAGGDHYEIGGDDA
DGAAALAFCPLSDLSTDNDRAWAAEWVETLVAVQGVLITPDHRNAISRQIGLMAEARGRSLSDFVSGVQM
REIKDALHHYTVDGPMGQLLDAERDGLQLGSFQTFEIEQLMNMGERNLVPVLTYLFRRIEKRLTGSPSLI
ILDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGIIDVLKESCPTKICLPNGAAREPG
TREFYERIGFNERQIEIVAAASPKREYYVASPEGRRLFNMALGPVALSFVGASGKEDLKRILALKAAEAN
WPVHWLKERGIGHAETLLADL

  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: 281087..290565

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R3F79_RS49035 (R3F79_49035) 276217..277560 + 1344 WP_253575149 IS1380-like element ISBdi2 family transposase -
R3F79_RS49040 (R3F79_49040) 277818..278420 + 603 WP_028152988 hypothetical protein -
R3F79_RS49045 (R3F79_49045) 278546..278830 + 285 WP_155258061 hypothetical protein -
R3F79_RS49050 (R3F79_49050) 279637..281085 + 1449 WP_232674895 IS4 family transposase -
R3F79_RS49055 (R3F79_49055) 281087..282394 - 1308 WP_232674733 IncP-type conjugal transfer protein TrbI virB10
R3F79_RS49060 (R3F79_49060) 282406..282858 - 453 WP_028152991 conjugal transfer protein TrbH -
R3F79_RS49065 (R3F79_49065) 282861..283700 - 840 WP_038944961 P-type conjugative transfer protein TrbG virB9
R3F79_RS49070 (R3F79_49070) 283718..284380 - 663 WP_028152993 conjugal transfer protein TrbF virB8
R3F79_RS49075 (R3F79_49075) 284424..285581 - 1158 WP_028152994 P-type conjugative transfer protein TrbL virB6
R3F79_RS49080 (R3F79_49080) 285781..286578 - 798 WP_232674732 P-type conjugative transfer protein TrbJ virB5
R3F79_RS49085 (R3F79_49085) 286550..288925 - 2376 WP_232674731 conjugal transfer protein TrbE virb4
R3F79_RS49090 (R3F79_49090) 288935..289234 - 300 WP_232674730 conjugal transfer protein TrbD virB3
R3F79_RS49095 (R3F79_49095) 289227..289607 - 381 WP_028152998 TrbC/VirB2 family protein virB2
R3F79_RS49100 (R3F79_49100) 289597..290565 - 969 WP_232674729 P-type conjugative transfer ATPase TrbB virB11
R3F79_RS49105 (R3F79_49105) 290571..291197 - 627 WP_232674728 acyl-homoserine-lactone synthase -

Host bacterium

ID   1834 GenBank   NZ_JAXIOH010000002
Plasmid name   pBjCNPSo38b Incompatibility group   -
Plasmid size   291609 bp Coordinate of oriT [Strand]   107348..107385 [+]
Host baterium   Bradyrhizobium japonicum strain CNPSo 38

Cargo genes

Drug resistance gene   -
Virulence gene   wzt
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrID1