Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118245
Name   oriT_pBb323S2c in_silico
Organism   Bradyrhizobium barranii subsp. barranii strain 323S2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088279 (17957..17993 [-], 37 nt)
oriT length   37 nt
IRs (inverted repeats)      17..23, 28..34  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 37 nt

>oriT_pBb323S2c
CCAAGGGCGCAGTAATACGTCGCTGACGCGACGTCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11596 GenBank   WP_166354441
Name   traA_G6321_RS02715_pBb323S2c 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   13573 GenBank   WP_234678485
Name   traG_G6321_RS02730_pBb323S2c insolico UniProt ID   _
Length   597 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 597 a.a.        Molecular weight: 64024.21 Da        Isoelectric Point: 9.1616

>WP_234678485.1 Ti-type conjugative transfer system protein TraG [Bradyrhizobium barranii]
MKANKIALAIVPAVLMTGLCLALTGIEAWLSKFGTTPKAHLVLGRIGIALPYVIAAAIGVVFLFAAAGAT
AIRSAGWSVVFGGLLVVAIAAAREIARLHSFANALPAGDRLLAYADPSTVIGATITALVAVFGLRVAMRG
NAAFAAAAPRRIHGRRAIHGESDWMTMSEAARLFPEAGGIVVGERYRVDRDAVAGQPFRADDAETWGAAG
KSPLLCFDASFGSSHGIAFAGSGGFKTTSVTVPTALKWGGGLVVLDPSNEVAPMVRGHRHGAGRQVFVLD
PRSSGVGFNVLDWIGQHGATKEEDIAAVASWIMTDNPRQGSARDDFFRASALQLLTALIADVCLSGHTEK
KDQHLRQVRANLSEPEPKLRQRLQAIYDNSESGFVKENVAPFIAMTPETFSGVYANAVKETHWLSYANYA
ALVSGSSFTTAELAEGRTDVFINLDLKTLENHAGLARVIIGSLLNAIYNRNGEVTSRTLFLLDEVARLGY
LRILETARDAGRKYGITLLMLYQSIGQMREAYGGRDATSKWFESASWISFSAINDPETADYISKRCGDTT
VEVDQLSRSSQMSGSSRTRSKQLARRPLILPHEVLHP

  Protein domains


Predicted by InterproScan.

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

(163-596)

  Protein structure



No available structure.



ID   13574 GenBank   WP_166354547
Name   t4cp2_G6321_RS03040_pBb323S2c 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: 91446.12 Da        Isoelectric Point: 6.0776

>WP_166354547.1 conjugal transfer protein TrbE [Bradyrhizobium barranii]
MVALRSFRHSGPSFADLVPYAGLVANGVVLLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINTILARLG
SGWMIQVEAVRVPTTDYPARQDCYFPDPVTRAIDDERRSRFEQERGHFESRHAIILSWRPPERRRAGLAR
YIYSDAESRSASYADTAIESFRTSVREVEQYLASVLSIRRMETREVEERDGTRMARYDELFQFIRFCITG
ENHPIRLPDIPMYLDWLATAELQHGLSPMVENRFLGVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFMF
LDDQDARQKLERTRKKWQQKVRPFIDQLFQTQSRSIDQDAAAMVAEAEDAIAEASSQLVAYGYYTPVIVL
FDESSARLQEKAEAVRRLIQAEGFGARIETLNATEAFLGSLPGNWYANIREPLINTRNLADLIPLNSVWS
GNPTAPCPFFPPASPPLMQVASGSSPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYAGAQIFA
FDKGRSMMPLTLAAGGDHYEIGGDEVDSAAALAFCPLSDLSTDTDRAWAAEWVETLVAVQGVLITPDHRN
AISRQIGLMVKARGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAERDGLQLGSFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLTGNPSLIILDEAWLMLGHSVFRDKIREWLKVLRKANCAVLLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAVPKREYYVASPEGRRLFNMALGP
VALSFVGASGKDDLKRILALKKAEANWPVHWLKERGIGHAETLLATS

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(189-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 76350..85898

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G6321_RS03005 (G6321_00003005) 71533..72849 - 1317 WP_166354555 plasmid replication protein RepC -
G6321_RS03010 (G6321_00003010) 73129..74157 - 1029 WP_166354553 plasmid partitioning protein RepB -
G6321_RS03015 (G6321_00003015) 74154..75368 - 1215 WP_080660038 plasmid partitioning protein RepA -
G6321_RS03020 (G6321_00003020) 75781..76334 + 554 Protein_78 acyl-homoserine-lactone synthase -
G6321_RS03025 (G6321_00003025) 76350..77318 + 969 WP_166354551 P-type conjugative transfer ATPase TrbB virB11
G6321_RS03030 (G6321_00003030) 77308..77688 + 381 WP_166354549 TrbC/VirB2 family protein virB2
G6321_RS03035 (G6321_00003035) 77681..77980 + 300 WP_166354329 conjugal transfer protein TrbD virB3
G6321_RS03040 (G6321_00003040) 77990..80443 + 2454 WP_166354547 conjugal transfer protein TrbE virb4
G6321_RS03045 (G6321_00003045) 80415..81212 + 798 WP_166354545 P-type conjugative transfer protein TrbJ virB5
G6321_RS03050 (G6321_00003050) 81209..81394 + 186 WP_166354543 entry exclusion protein TrbK -
G6321_RS03055 (G6321_00003055) 81411..82571 + 1161 WP_166354541 P-type conjugative transfer protein TrbL virB6
G6321_RS03060 (G6321_00003060) 82608..83270 + 663 WP_166354539 conjugal transfer protein TrbF virB8
G6321_RS03065 (G6321_00003065) 83288..84127 + 840 WP_166354537 P-type conjugative transfer protein TrbG virB9
G6321_RS03070 (G6321_00003070) 84130..84582 + 453 WP_166354535 conjugal transfer protein TrbH -
G6321_RS03075 (G6321_00003075) 84594..85898 + 1305 WP_166354533 IncP-type conjugal transfer protein TrbI virB10
G6321_RS03080 (G6321_00003080) 86255..86974 + 720 WP_166354531 alpha/beta fold hydrolase -
G6321_RS03085 (G6321_00003085) 87037..88683 + 1647 WP_166354529 hypothetical protein -
G6321_RS03090 (G6321_00003090) 89111..89725 + 615 WP_207795166 DUF1353 domain-containing protein -

Host bacterium

ID   18678 GenBank   NZ_CP088279
Plasmid name   pBb323S2c Incompatibility group   -
Plasmid size   182079 bp Coordinate of oriT [Strand]   17957..17993 [-]
Host baterium   Bradyrhizobium barranii subsp. barranii strain 323S2

Cargo genes

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