Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101391
Name   oriT_pBjCNPSo38a in_silico
Organism   Bradyrhizobium japonicum strain CNPSo 38
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAXIOH010000004 (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_pBjCNPSo38a
AAAGCAGGACGTCGCGGATGCGACGTATTACTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1274 GenBank   WP_212479306
Name   traA_R3F79_RS49275_pBjCNPSo38a 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   886 GenBank   WP_028152606
Name   traG_R3F79_RS49260_pBjCNPSo38a 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   887 GenBank   WP_028152596
Name   t4cp2_R3F79_RS49350_pBjCNPSo38a 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
R3F79_RS49280 (R3F79_49280) 21540..22139 + 600 WP_080587024 conjugative transfer signal peptidase TraF -
R3F79_RS49285 (R3F79_49285) 22197..22519 + 323 Protein_26 nitrilase-related carbon-nitrogen hydrolase -
R3F79_RS49290 (R3F79_49290) 22534..23139 + 606 WP_035680223 TraH family protein -
R3F79_RS49295 (R3F79_49295) 23170..23289 - 120 Protein_28 type II toxin-antitoxin system VapC family toxin -
R3F79_RS49300 (R3F79_49300) 23428..24018 + 591 WP_049807966 DUF2167 domain-containing protein -
R3F79_RS49305 (R3F79_49305) 24280..25149 + 870 WP_232674645 transcriptional repressor TraM -
R3F79_RS49310 (R3F79_49310) 25158..26069 - 912 WP_232674644 autoinducer binding domain-containing protein -
R3F79_RS49315 (R3F79_49315) 26344..27642 - 1299 WP_028152603 IncP-type conjugal transfer protein TrbI virB10
R3F79_RS49320 (R3F79_49320) 27653..28117 - 465 WP_028152602 conjugal transfer protein TrbH -
R3F79_RS49325 (R3F79_49325) 28122..28946 - 825 WP_028152601 P-type conjugative transfer protein TrbG virB9
R3F79_RS49330 (R3F79_49330) 28964..29626 - 663 WP_028152600 conjugal transfer protein TrbF virB8
R3F79_RS49335 (R3F79_49335) 29641..30828 - 1188 WP_038945592 P-type conjugative transfer protein TrbL virB6
R3F79_RS49340 (R3F79_49340) 30822..31034 - 213 WP_028152598 entry exclusion protein TrbK -
R3F79_RS49345 (R3F79_49345) 31028..31846 - 819 WP_038953896 P-type conjugative transfer protein TrbJ virB5
R3F79_RS49350 (R3F79_49350) 31818..34271 - 2454 WP_028152596 conjugal transfer protein TrbE virb4
R3F79_RS49355 (R3F79_49355) 34281..34580 - 300 WP_028152595 conjugal transfer protein TrbD virB3
R3F79_RS49360 (R3F79_49360) 34573..34962 - 390 WP_028152594 TrbC/VirB2 family protein virB2
R3F79_RS49365 (R3F79_49365) 34952..35920 - 969 WP_060913174 P-type conjugative transfer ATPase TrbB virB11
R3F79_RS49370 (R3F79_49370) 35917..36486 - 570 WP_232707732 acyl-homoserine-lactone synthase -
R3F79_RS49375 (R3F79_49375) 37039..38232 + 1194 WP_028152592 plasmid partitioning protein RepA -
R3F79_RS49380 (R3F79_49380) 38229..39242 + 1014 WP_232707731 plasmid partitioning protein RepB -
R3F79_RS49385 (R3F79_49385) 39469..40693 + 1225 Protein_46 plasmid replication protein RepC -

Host bacterium

ID   1835 GenBank   NZ_JAXIOH010000004
Plasmid name   pBjCNPSo38a Incompatibility group   -
Plasmid size   167649 bp Coordinate of oriT [Strand]   18100..18141 [-]
Host baterium   Bradyrhizobium japonicum strain CNPSo 38

Cargo genes

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