Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118246
Name   oriT_pBb323S2b in_silico
Organism   Bradyrhizobium barranii subsp. barranii strain 323S2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088281 (234394..234431 [+], 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_pBb323S2b
TCCAAGGGCGCAGTAATACGTCGCTGACGCGACGTCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11597 GenBank   WP_166354441
Name   traA_G6321_RS54810_pBb323S2b 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: 123111.13 Da        Isoelectric Point: 10.2256

>WP_166354441.1 Ti-type conjugative transfer relaxase TraA [Bradyrhizobium barranii]
MAITHFTPQLIGRGDGRSAVLAAAYRHCAKMEFEAEGRTVDYSNKRGMAHEEFLVPADAPAWLRTIIADR
SVAGASEAFWNKVEAFEKRADAQFAKEFIIALPVELTTEQNIALMRQFVVEQVLSRRQVADWVYHDEPGN
PHVHLMTTLRPLTEDGFGPKRVAVIGEDGQPLRMQSGKIAYRLWAGDKQEFLEQRNGWLDLQNQHLALNG
HEIRVDGRSYAERGIDVVPTTHIGVAAKAIQRRAEREGRDPNLERLRVFDENRAETLRRIQRRPEIVLDM
ISREKSVFDQRDVGKLLHRYVDDVGTFQDLMARVLQSPDALRLEGESVDFATGARAPAKYTTRELIRLEA
EMARRADHLSGSAAFTVKAQVIAAVSARHANLSVEQRAAIAHVVSGERIAAVVGRAGAGKTTMMRAAREV
WEAAGYRVVVGALAGKAAEGLEKEAAIQSRTLASWELRWKSGRDGLDDRTVFVLDEAGMVASRQMALFVE
TASKAGSKLVLVGDPEQLQPIEAGAAFRAIVERIGYAELETIYRQRQQWMRDASLDLARGRTGEALSAYR
HHGRLFGSELKAQAIDNLIADWNRDYDPSKSTLILAHLRRDVRALNDMARAKLVERGLIEEGHAFRTEDG
ERRFAAGDQIVFLKNEGSLGVKNGMIGKVVAAEPKRLVAEIGDGEGRRHVEVDQRFYRNIDHGYATTVHK
AQGATVDRVKVLATLSLDKHLTYVALTRHREDVALYYGRRSFQKAGGLIPILSQRRAKESTLDYECGALY
RDALRFAANRGLNIFKVARTLANDRLRWTVRQKQRLADVARRLRALGEKLGLLDSRKPIIRTAHKEAKPM
VAGVTTFTKSLTDTVEDRILADPAIKKQWEDVSTRFRLVFADPERAFRATNFDAMLKDPAAASSTMARLA
ASPESFGALRGKVGLLAGKSDKQVRQRAEANAPALKRDIERYLRLRAEAEHKHEAEERAIRHRVAIDIPA
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   13575 GenBank   WP_166354443
Name   traG_G6321_RS54795_pBb323S2b 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: 69419.19 Da        Isoelectric Point: 9.1739

>WP_166354443.1 Ti-type conjugative transfer system protein TraG [Bradyrhizobium barranii]
MRANKIALAIVPAVLMASLCLVLTGIEAWLSEFGTTPNARLVLGRVGIALPYVVAAAIGVVFLLAAAGAT
AIRSAGWSVVFGGLLVVAIAASREIARPHSFANALLAGDRLLAYADPSTIIGATIAALVAVFGLRVAIKG
NAAFAAAAPRRIRGRRAIHGESDWMVMTEAARLFPETGGIVVGERYRVDRDAVTDRSFRADDAETWGAGG
KSPLLCFDASFGSSHGIVFAGSGGFKTTSVTVPTALKWGGGLVVLDPSYEVAPMVTGHRHGAGRQVFVLD
PRSSGVGFNVLDWIGQHGATKEEDIAAVASWIMTDNPRQGSARDDFFRASALQLLTALTADVCLSGHTEK
KDQHLRQVRANLSEPEPKLRQRLQTIYDNSESGFVKENVAPFIAMTPETFSGVYANAVKETHWLSYANYA
ALVSGASFTTAELAEGRTDVFINLDLKTLENYAGLARVVIGSLLNAIYNRNGEVTGRTLFLLDEVARLGY
LRILETARDAGRKYGITLLMLYQSIGQMREAYGGRDATSKWFESASWISFSAINDPETADYISKRCGDTT
VEVDQLSQSSQTSSSSRTRSKQLARRPLVLPHEVLRMRTDEQIIFTAGNPPLRCGRAIWFRRTDMRACVG
ENRFYRGEAGGRS

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 184589..190795

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G6321_RS54540 (G6321_00054540) 180558..180761 - 204 WP_011084467 hypothetical protein -
G6321_RS54545 (G6321_00054545) 181400..181621 - 222 Protein_173 hypothetical protein -
G6321_RS54550 (G6321_00054550) 182043..182441 + 399 WP_026193420 transposase -
G6321_RS54555 (G6321_00054555) 182438..182794 + 357 WP_011090953 IS66 family insertion sequence element accessory protein TnpB -
G6321_RS54560 (G6321_00054560) 182929..184473 + 1545 WP_224517700 IS66 family transposase -
G6321_RS54565 (G6321_00054565) 184589..185749 - 1161 WP_166354331 P-type conjugative transfer protein TrbL virB6
G6321_RS54570 (G6321_00054570) 185767..185949 - 183 WP_060907883 entry exclusion protein TrbK -
G6321_RS54575 (G6321_00054575) 185946..186743 - 798 WP_060907882 P-type conjugative transfer protein TrbJ virB5
G6321_RS54580 (G6321_00054580) 186816..187139 - 324 WP_224518048 hypothetical protein virb4
G6321_RS54585 (G6321_00054585) 187191..189167 - 1977 WP_224518050 conjugal transfer protein TrbE virb4
G6321_RS54590 (G6321_00054590) 189177..189476 - 300 WP_166354329 conjugal transfer protein TrbD virB3
G6321_RS54595 (G6321_00054595) 189469..189837 - 369 WP_166354327 TrbC/VirB2 family protein virB2
G6321_RS54600 (G6321_00054600) 189827..190795 - 969 WP_166354325 P-type conjugative transfer ATPase TrbB virB11
G6321_RS54605 (G6321_00054605) 190801..191427 - 627 WP_166354323 acyl-homoserine-lactone synthase -
G6321_RS54610 (G6321_00054610) 191825..193048 + 1224 WP_035696734 plasmid partitioning protein RepA -
G6321_RS54615 (G6321_00054615) 193033..194094 + 1062 WP_028180948 plasmid partitioning protein RepB -
G6321_RS54620 (G6321_00054620) 194332..195609 + 1278 WP_050995298 plasmid replication protein RepC -

Host bacterium

ID   18679 GenBank   NZ_CP088281
Plasmid name   pBb323S2b Incompatibility group   -
Plasmid size   294915 bp Coordinate of oriT [Strand]   234394..234431 [+]
Host baterium   Bradyrhizobium barranii subsp. barranii strain 323S2

Cargo genes

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