Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118247
Name   oriT_pBb1S5b in_silico
Organism   Bradyrhizobium barranii subsp. apii strain 1S5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP096257 (21175..21230 [-], 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_pBb1S5b
CCCCGGCAGGCGGGAAAACAGGACGTCGCGGATGCGACGTATTACTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   13576 GenBank   WP_166107292
Name   traG_HAP41_RS49135_pBb1S5b 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: 70496.67 Da        Isoelectric Point: 9.8327

>WP_166107292.1 Ti-type conjugative transfer system protein TraG [Bradyrhizobium barranii]
MTANRLLLLIVPMALMLGAIFGLTGIGHGLAGLGKTEAQRLLFARAGLAMPYIAAAGIGVIFLFATAGSA
SIRAAAWSVVAGCVSAISIALAREAMRLSGAPETIVPGRSAVAQIDPATMVAASVVLMGGIFALRVAVKG
NAAFAAPDPKRVRGRRALHGDADWMSMPEAARLFGNAGGIVVGERYRVDRDSAAAQPFRTTNRQSWGFGG
RPPLLCFDASFGSSHGIVFAGSGGFKTTSVTVPTALKWGGALVVLDPSNEVAPMVIAHRRAAGRTVHVLD
PHAGQRTAQGRPPEAAQEATNLPRTGFNALDWIGRFGGTKEEDIAAVASWIMSDSGGARGVRDDFFRASA
LQLLTALIADVCLSGHTEDKNQTLRQVRANLSEPEPKLRARLQAIYDNSESAFVKENVAVFVNMTPETFS
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.



ID   13577 GenBank   WP_166107248
Name   t4cp2_HAP41_RS49775_pBb1S5b 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: 91409.86 Da        Isoelectric Point: 6.3245

>WP_166107248.1 conjugal transfer protein TrbE [Bradyrhizobium barranii]
MVALHSFRHSGPSFADLVPYAGLVDDGIVLLKDGSLMAGWYFAGPDSESSTDAERNDVSRQINAILARLG
SGWMIQVEALRIPTTDYPARKDGHFPDAVTREIDEERRAHFERESGHYESRHALILSWRPPERRKSGLAK
YVYSDKDSRSASFADTALGNFRASVREIEQYLSNLLSIQRMRTRTVEERGGSRSARYDELFQFVRFCITG
ENHPVRLPEVPMYLDWLVTAEYQHGLTPTVDGRYVGVVAIDGLPAESWPGILNVLDQMPLTYRWSSRFMF
LDEIEARERLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETQDAIAEAASQLVAYGYYTPVIVL
QDHDAERLREKCEGIRRVVQAEGFGARIETLNATEAFLGSLPGNWYANVREPLIHTRNLADLLPLNSVWS
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 150137..159499

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HAP41_RS49725 (HAP41_0000049725) 146651..147403 + 753 WP_166107230 outer membrane protein -
HAP41_RS49730 (HAP41_0000049730) 147685..148194 - 510 WP_224581098 Spy/CpxP family protein refolding chaperone -
HAP41_RS49735 (HAP41_0000049735) 148624..148830 + 207 WP_166107232 cold-shock protein -
HAP41_RS49740 (HAP41_0000049740) 148955..149806 - 852 WP_224581099 autoinducer binding domain-containing protein -
HAP41_RS49745 (HAP41_0000049745) 150137..151432 - 1296 WP_166107234 IncP-type conjugal transfer protein TrbI virB10
HAP41_RS49750 (HAP41_0000049750) 151446..151910 - 465 WP_166107236 conjugal transfer protein TrbH -
HAP41_RS49755 (HAP41_0000049755) 151915..152739 - 825 WP_166107238 P-type conjugative transfer protein TrbG virB9
HAP41_RS49760 (HAP41_0000049760) 152757..153419 - 663 WP_166107241 conjugal transfer protein TrbF virB8
HAP41_RS49765 (HAP41_0000049765) 153435..154622 - 1188 WP_166107244 P-type conjugative transfer protein TrbL virB6
HAP41_RS49770 (HAP41_0000049770) 154616..155434 - 819 WP_166107246 P-type conjugative transfer protein TrbJ virB5
HAP41_RS49775 (HAP41_0000049775) 155406..157859 - 2454 WP_166107248 conjugal transfer protein TrbE virb4
HAP41_RS49780 (HAP41_0000049780) 157869..158168 - 300 WP_166107251 conjugal transfer protein TrbD virB3
HAP41_RS49785 (HAP41_0000049785) 158161..158541 - 381 WP_224581100 TrbC/VirB2 family protein virB2
HAP41_RS49790 (HAP41_0000049790) 158531..159499 - 969 WP_166107253 P-type conjugative transfer ATPase TrbB virB11
HAP41_RS49795 (HAP41_0000049795) 159496..160131 - 636 WP_166107254 acyl-homoserine-lactone synthase -
HAP41_RS49800 (HAP41_0000049800) 160493..161728 + 1236 WP_175618600 plasmid partitioning protein RepA -
HAP41_RS49805 (HAP41_0000049805) 161904..162917 + 1014 WP_166107255 plasmid partitioning protein RepB -
HAP41_RS49810 (HAP41_0000049810) 163133..164452 + 1320 WP_166107256 plasmid replication protein RepC -

Host bacterium

ID   18680 GenBank   NZ_CP096257
Plasmid name   pBb1S5b Incompatibility group   -
Plasmid size   184131 bp Coordinate of oriT [Strand]   21175..21230 [-]
Host baterium   Bradyrhizobium barranii subsp. apii strain 1S5

Cargo genes

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