Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118243
Name   oriT_pBb38S5b in_silico
Organism   Bradyrhizobium barranii subsp. apii strain 38S5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP096253 (39498..39553 [-], 56 nt)
oriT length   56 nt
IRs (inverted repeats)      23..29, 34..40  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 56 nt

>oriT_pBb38S5b
CCCCGGCAGGCGGGAAAACAGGACGTCGCGGATGCGACGTATTACTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11594 GenBank   WP_248594487
Name   traA_J4G48_RS49710_pBb38S5b insolico UniProt ID   _
Length   1101 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1101 a.a.        Molecular weight: 122017.19 Da        Isoelectric Point: 9.9987

>WP_248594487.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Bradyrhizobium]
MAITHFTPQLISRGSGRSAVLSAAYRHCARMEHQAEGRTVDYSTKRGLRHEEFLLPPDGPQWARELIADR
SVAGAAEAFWNAIEAFEKRSDAQLAKEFIIALPVELTVDQNIALVREFVATQVLARGQVADWVFHDEPGN
PHIHLMTTLRPLGDNGFGPKKVPVIGDDGAPLRNDFGKIVYRLWSGEKAEFLEQREGWLDLQNKHLALAG
LEIRVDGRSYAERGIDLAPTTHIGVSTKAIDRKGKKAGWSPKLERIALHEERKADNRERMLRRPEIVLDL
VTRELSVFTERDIARVVHRYVDDAGTFQHLMARILQNPDVLRLEGERIALETGIREPAKYTTRELIRLEA
EMAHRAVWLAGRSSHGVREKVLAAAFERHDRLSEEQRVAIAHVAGEGRIAAVVGRAGAGKTTMMKAAREV
WEAAGYRVVGGALAGKASEGLEKEAGIASRTLASWELAWSNGREQLDDKTIFVLDEAGMVSSRQMALFVE
AVVKTGAKLVLVGDPDQLQPIEAGAAFRAIVARTGYAELKTIYRQRAQWMRDASLDLARGRVAEALQAYG
ANGKLEARKFKAQAVTALIEDWNRDYDPAKSILILAHLRRDVRALNNMARAKLIERGLVEDGQAFCTEDG
QRKFSAGDQIVFLKNEGSLGVKNGMIARVIEARSGWFAAIIGEGERQRRVEVDQRFYANVDHGYATTIHK
SQGATVDRVKVLATLSLDRHLAYVALTRHRENVALYYGAISFGKAGGLTKILSQSRAKETTLDYERGPSY
RAALRFAEARGLHLMRVARTLVADKVRWTVRQSSRLADLGARLLALGARLGLGAARKQTIPNGTKEAKPM
VAGITTFAKSIDQVVEDKLAADPALKKQWEEISTRFRFVFADPEASFRKVDIDSMLKDKATAQSTLSKLA
EKPDSFGALKGKTGLLASRADKQDRQRADLNVPALARDLERFLRLRSEAEHRYEAEERAARLKVAVDIPA
LSPSAKQTLERIRDAIDRNDLPSALEFALEDKMIEAELEGFARAVSERFGERAFVGLSAKDADGKVFEAI
SGGTNAAQKEELKAAWPDLRTAQQLAAQQRTAEAQKEADILRQARRPGLSL

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-566)

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

(858-954)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   13570 GenBank   WP_225049235
Name   t4cp2_J4G48_RS49510_pBb38S5b 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: 91439.88 Da        Isoelectric Point: 6.3245

>WP_225049235.1 conjugal transfer protein TrbE [Bradyrhizobium barranii]
MVALHSFRHSGPSFADLVPYAGLVDDGIVLLKDGSLMAGWYFAGPDSESSTDAERNDVSRQINAILARLG
SGWMIQVEALRIPTTDYPARKDGHFPDAVTREIDEERRAHFERESGHYESRHALILSWRPPERRKSGLAK
YVYSDKDSRSASFADTALGNFRASVREIEQYLSNLLSIQRMRTRTVEERGGSRSARYDELFQFVRFCITG
ENHPVRLPEVPMYLDWLVTAEYQHGLTPTVDGRYVGVVAIDGLPAESWPGILNVLDQMPLTYRWSSRFMF
LDEIEARERLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETQDAIAEAASQLVAYGYYTPVIVL
QDHDAERLREKCEGIRRVVQAEGFGARIETLNATEAFLSSLPGNWYANVREPLIHTRNLADLLPLNSVWS
GSPIAPCPFYPESSPPLMQVASGSTPFRLNLHTDDVGHSLIFGPTGSGKSTLLALIAAQFRRYRDAQIFA
FDKGRSLMPLTLAAGGDHYEIGGGAGEGLQLAFCPLAELATDADRAWASEWIETLVVLQGVSVTPDHRNA
ISRQVTLMAAAPGRSLADFVSGVQMREIKDALHHYTVDGPMGHLLDAERDGLTLGGFQTFEIEELMNMGE
RSLVPVLTYLFRRIEKRLTGAPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAERS
GIIDVLKESCPTKICLPNGAAREPGTREFYERLGFNERQVEIVSNAIPKREYYVTSPAGRRLFEMALGPV
ALAFVGASGRDDLKRITELKTAHGRTWPAYWLQTRGIAHAETLLAHD

  Protein domains


Predicted by InterproScan.

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

(188-400)

  Protein structure



No available structure.



ID   13571 GenBank   WP_248594486
Name   traG_J4G48_RS49695_pBb38S5b insolico UniProt ID   _
Length   659 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 659 a.a.        Molecular weight: 70483.62 Da        Isoelectric Point: 9.7222

>WP_248594486.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Bradyrhizobium]
MTANRLLLLIVPMALMLGAIFGLTGIGHGLAGLGKTEAQRLLFARAGLAMPYIAAAGIGVIFLFATAGSA
SIRAAAWSVVAGCVSAISIALAREAMRLSGAPETIVPGRSAVAQIDPATMVAASVVLMGGIFALRVAVKG
NAAFAAPDPKRVRGRRALHGDADWMSMPEAARLFGNAGGIVVGERYRVDRDSAAAQPFRTTDRQSWGFGG
RPPLLCFDASFGSSHGIVFAGSGGFKTTSVTVPTALKWGGALVVLDPSNEVAPMVIAHRRAAGRTVHVLD
PHAGQRTAQGRPPEAAQEATNLPRTGFNALDWIGRFGGTKEEDIAAVASWIMSDSGGARGVRDDFFRASA
LQLLTALIADVCLSGHTEDKNQTLRQVRANLSEPEPKLRARLQAIYDNSESGFVKENVAVFVNMTPETFS
GVYANAVKETHWLSYPNYAALVSGSTFVSDDLAGGQTDVFINLDLKTLETHAGLARVIIGSFMNAIYNHN
GAVTGRALFLLDEVARLGFMRILETARDAGRKYGITLLLLFQSIGQMRETYGGRDAASKWFESASWIAFA
AVNDPETADYISKRCGMTTVEIDQVSRSSQASGSSRTRSKQLASRPLIQPHEVLRMRADEQIVFTAGNAP
LRCGRAIWFRRDDMKACVGHNRFQPEEKA

  Protein domains


Predicted by InterproScan.

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

(163-654)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1830..11192

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J4G48_RS49490 (J4G48_0049490) 1198..1833 + 636 WP_166107254 acyl-homoserine-lactone synthase -
J4G48_RS49495 (J4G48_0049495) 1830..2798 + 969 WP_225049237 P-type conjugative transfer ATPase TrbB virB11
J4G48_RS49500 (J4G48_0049500) 2788..3168 + 381 WP_224581100 TrbC/VirB2 family protein virB2
J4G48_RS49505 (J4G48_0049505) 3161..3460 + 300 WP_166107251 conjugal transfer protein TrbD virB3
J4G48_RS49510 (J4G48_0049510) 3470..5923 + 2454 WP_225049235 conjugal transfer protein TrbE virb4
J4G48_RS49515 (J4G48_0049515) 5895..6713 + 819 WP_166107246 P-type conjugative transfer protein TrbJ virB5
J4G48_RS49520 (J4G48_0049520) 6707..7894 + 1188 WP_166107244 P-type conjugative transfer protein TrbL virB6
J4G48_RS49525 (J4G48_0049525) 7910..8572 + 663 WP_208067382 conjugal transfer protein TrbF virB8
J4G48_RS49530 (J4G48_0049530) 8590..9414 + 825 WP_166107238 P-type conjugative transfer protein TrbG virB9
J4G48_RS49535 (J4G48_0049535) 9419..9883 + 465 WP_166107236 conjugal transfer protein TrbH -
J4G48_RS49540 (J4G48_0049540) 9897..11192 + 1296 WP_166107234 IncP-type conjugal transfer protein TrbI virB10
J4G48_RS49550 (J4G48_0049550) 12808..13428 + 621 WP_248594484 autoinducer binding domain-containing protein -
J4G48_RS49555 (J4G48_0049555) 13553..13759 - 207 WP_166218049 cold-shock protein -
J4G48_RS49560 (J4G48_0049560) 14188..14670 + 483 WP_225049233 Spy/CpxP family protein refolding chaperone -
J4G48_RS49565 (J4G48_0049565) 14985..15722 - 738 WP_225049231 outer membrane protein -

Host bacterium

ID   18676 GenBank   NZ_CP096253
Plasmid name   pBb38S5b Incompatibility group   -
Plasmid size   177824 bp Coordinate of oriT [Strand]   39498..39553 [-]
Host baterium   Bradyrhizobium barranii subsp. apii strain 38S5

Cargo genes

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