Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105342
Name   oriT_pBq66S1MBa in_silico
Organism   Bradyrhizobium quebecense strain 66S1MB
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088023 (57817..57872 [+], 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_pBq66S1MBa
CCCCGGCAGGCGGGAAAACAGGACGTCGCGGATGCGACGTATTACTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3645 GenBank   WP_176535431
Name   traA_HU230_RS41650_pBq66S1MBa 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: 122011.19 Da        Isoelectric Point: 10.0035

>WP_176535431.1 Ti-type conjugative transfer relaxase TraA [Bradyrhizobium quebecense]
MAITHFTPQLISRGSGRSAVLSAAYRHCARMEHQAEGRTVDYSTKRGLRHEEFLLPPDGPQWARELIADR
SVAGAAEAFWNAIEAFEKRSDAQLAKEFIIALPVELTVDQNIALVREFVATQVLARGQVADWVFHDEPGN
PHIHLMTTLRPLGDNGFGPKKVPVIGDDGAPLRNDFGKIVYRLWSGEKAEFLEQREGWLDLQNKHLALAG
LEIRVDGRSYAERGIDLAPTTHIGVSTKAIDRKGKKAGWSPKLERIALHEERKADNRERMLRRPEIVLDL
VTRELSVFTERDIARVVHRYVDDAGTFQHLMARILQNPDVLRLEGERIALETGIREPAKYTTRELIRLEA
EMAHRAVWLAGRSSHGVREKVLAAAFERHDRLSEEQRVAIAHVAGEGRIAAVVGRAGAGKTTMMKAAREV
WEAAGYRVVGGALAGKASEGLEKEAGIASRTLASWELAWSNGREQLDDKTIFVLDEAGMVSSRQMALFVE
AVVKTGAKLVLVGDPDQLQPIEAGAAFRAIVARTGYAELKTIYRQRAQWMRDASLDLARGRVAEALQAYG
ANGKLEARKFKAQAVTALIEDWNRDYDPAKSILILAHLRRDVRALNNMARAKLIERGLVEDGQAFCTEDG
QRKFSAGDQIVFLKNEGSLGVKNGMIARVIEARSGWFAAIIGEGERQRRVEVDQRFYANVDHGYATTIHK
SQGATVDRVKVLATLSLDRHLAYVALTRHRENVALYYGAISFGKAGGLTKILSQSRAKETTLDYERGPSY
RAALRFAEARGLHLMRVARTLVADKVRWTVRQSSRLADLGARLLALGARLGLGAARKQTIPNGTKEARPM
VAGITTFAKSIDQVVEDKLAADPALKKQWEEISTRFRFVFADPEASFRKVDIDSMLKDKATAQSTLSKLA
EKPDSFGALKGKTGLLASRADKQDRQRADLNVPALARDLERFLRLRSEAEHRYEAEERAARLKVAVDIPA
LSPSAKQTLERIRDAIDRNDLPSALEFALEDKMIEAELEGFARAVSERFGERALVGLSAKDADGKVFEAI
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   3616 GenBank   WP_176535491
Name   t4cp2_HU230_RS42125_pBq66S1MBa 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: 91363.83 Da        Isoelectric Point: 6.3244

>WP_176535491.1 conjugal transfer protein TrbE [Bradyrhizobium quebecense]
MVALHSFRHSGPSFADLVPYAGLVDDGIVLLKDGSLMAGWYFAGPDSESSTDAERNDVSRQINAILARLG
SGWMIQVEALRIPTTDYPARKDGHFPDAVTREIDEERRAHFERESGHYESRHALILSWRPPERRKSGLAK
YVYSDKDSRSASFADTALGNFRASVREIEQYLSNLLSIQRMRTRTVEERGGSRSARYDELFQFVRFCITG
ENHPVRLPEVPMYLDWLVTAEYQHGLTPTVDGRYVGVVAIDGLPAESWPGILNILDLMPLTYRWSSRFMF
LDEIEARERLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETQDAIAEAASQLVSYGYYTPVIVL
QDHDAERLREKCEGIRRVVQAEGFGARIETLNATEAFLGSLPGNWYANVREPLIHTRNLADLLPLNSVWS
GSPVAPCPFYPESSPPLMQVASGSTPFRLNLHTDDVGHSLIFGPTGSGKSTLLALIAAQFRRYRDAQIFA
FDKGRSLMPLTLAAGGDHYEIGGGAGEGIQFAFCPLAELATDADRAWASEWIETLVVLQGVSVTPDHRNA
ISRQVALMAAAPGRSLADFVSGVQMREIKDALHHYTVDGPMGHLLDAERDGLTLGGFQTFEIEELMNMGE
RSLVPVLTYLFRRIEKRLIGAPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAERS
GIIDVLKESCPTKICLPNGAAREPGTREFYERLGFNERQVEIVSNAIPKREYYVTSPAGRRLFEMALGPV
ALAFVGASGRDDLKRITELKTAHGRTWPANWLQTRGIAHADTLLAHD

  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: 151664..161035

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HU230_RS42090 (HU230_0042090) 146800..148119 - 1320 WP_176535490 plasmid replication protein RepC -
HU230_RS42095 (HU230_0042095) 148382..149401 - 1020 WP_166218025 plasmid partitioning protein RepB -
HU230_RS42100 (HU230_0042100) 149398..150624 - 1227 WP_166218028 plasmid partitioning protein RepA -
HU230_RS42105 (HU230_0042105) 151020..151667 + 648 WP_312022737 acyl-homoserine-lactone synthase -
HU230_RS42110 (HU230_0042110) 151664..152632 + 969 WP_166218031 P-type conjugative transfer ATPase TrbB virB11
HU230_RS42115 (HU230_0042115) 152622..153011 + 390 WP_166218034 TrbC/VirB2 family protein virB2
HU230_RS42120 (HU230_0042120) 153004..153303 + 300 Protein_137 conjugal transfer protein TrbD -
HU230_RS42125 (HU230_0042125) 153313..155766 + 2454 WP_176535491 conjugal transfer protein TrbE virb4
HU230_RS42130 (HU230_0042130) 155738..156556 + 819 WP_166218040 P-type conjugative transfer protein TrbJ virB5
HU230_RS42135 (HU230_0042135) 156550..157737 + 1188 WP_166218043 P-type conjugative transfer protein TrbL virB6
HU230_RS42140 (HU230_0042140) 157753..158415 + 663 WP_166107241 conjugal transfer protein TrbF virB8
HU230_RS42145 (HU230_0042145) 158433..159257 + 825 WP_166107238 P-type conjugative transfer protein TrbG virB9
HU230_RS42150 (HU230_0042150) 159262..159726 + 465 WP_166107236 conjugal transfer protein TrbH -
HU230_RS42155 (HU230_0042155) 159740..161035 + 1296 WP_166107234 IncP-type conjugal transfer protein TrbI virB10
HU230_RS42160 (HU230_0042160) 161507..162217 + 711 WP_166107311 autoinducer binding domain-containing protein -
HU230_RS42165 (HU230_0042165) 162342..162548 - 207 WP_166218049 cold-shock protein -
HU230_RS42170 (HU230_0042170) 162978..163490 + 513 WP_224944386 Spy/CpxP family protein refolding chaperone -
HU230_RS42175 (HU230_0042175) 163771..164523 - 753 WP_166218055 outer membrane beta-barrel protein -
HU230_RS43565 164682..164859 + 178 Protein_149 SulP family inorganic anion transporter -
HU230_RS42180 (HU230_0042180) 164953..165618 + 666 WP_176535494 helix-turn-helix domain-containing protein -

Host bacterium

ID   5780 GenBank   NZ_CP088023
Plasmid name   pBq66S1MBa Incompatibility group   -
Plasmid size   187265 bp Coordinate of oriT [Strand]   57817..57872 [+]
Host baterium   Bradyrhizobium quebecense strain 66S1MB

Cargo genes

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