Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100021
Name   oriT_pDN1 in_silico
Organism   Dichelobacter nodosus
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_002636 (804..892 [-], 89 nt)
oriT length   89 nt
IRs (inverted repeats)      5..10, 16..21  (GTTTCT..AGAAAC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TAAGTGCG|CCCT
Note   _

  oriT sequence  


Download         Length: 89 nt

>oriT_pDN1
GGCAGTTTCTTGAAGAGAAACCGGTAAGTGCGCCCTCCCGCAAAATGACGGTCGGGGTTTGCGGTGTCTGTGCTCCGATGATAGCATAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Francia MV et al. (2004) A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev. 28(1):79-100. [PMID:14975531]
[2] Whittle G et al. (2000) Identification and characterization of a native Dichelobacter nodosus plasmid, pDN1. Plasmid. 43(3):230-4. [PMID:10783302]


Relaxase

ID   20 GenBank   NP_073212
Name   MobA_pDN1 insolico UniProt ID   Q9EXP9
Length   703 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 703 a.a.        Molecular weight: 78872.79 Da        Isoelectric Point: 7.6998

>NP_073212.1 mobilisation protein A (plasmid) [Dichelobacter nodosus]
MAIYHLTAKTGSRNGGQSAKAKADYIQREGRYSRDREEVLHTQSGHLPEWAERPADYWDGADLYERANGR
LFKEIEFALPVELTLDQQRELVDEFARHLTEGERLPYTLAIHAGNGENPHCHLMISERKNDGIERPADQW
FKRYNGKQPERGGAQKSESLKPKAWLEQTREAWSHYANRALEQAGHEARIDHRTLEAQGIERLPGIHLGP
NVVEMESRGIRTERADIALAIDTANGQIIDLQEYREVIEHERDRQSEEIQRDQRVSGRDRAAGPEHGDTG
GRSPAADRRGTAGQRGAGRELDEPATASHERMAAGSKGHEGSRRGTRQGRPDGPERRPWLDMEVVGRGLD
RFRDAYSGAADRIMALAGAANHRATGEHMADFQAQVKGDRTAQAIARQLKAMGCDRYDIGIRDAASGKMM
NREWTPQEVQQNAAWLKRMNAQGNDIYIRPAEQARHGLVLVDDLSSDDLDAMKQEGREPAAIIETSPKNY
QAWVKVAQDAPADHRGVIARKLAREYDADPASADSRHYGRLAGFTNRKDKYTSRTGYQPWVLCRESSGKS
ATAGPELMQQAGQVLDSIERRQERTARLAEITAPQSVRRYRRSVVDDYRSEMAGLVKRYGDDLSKCDFIA
AMKLASKGREADEIGKAMAEASPAIMERKAGHEADYIKRTVQKVMELPQVQEARAELAKQTQKQRSKGPD
LSM

  Protein domains


Predicted by InterproScan.

RepB DNA-primase from phage plasmid (RepB_primase)

(415-640)

MobA/MobL family (MobA_MobL)

(22-218)


  Protein structure


Source ID Structure
AlphaFold DB Q9EXP9

  Reference


[1] Francia MV et al. (2004) A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev. 28(1):79-100. [PMID:14975531]
[2] Whittle G et al. (2000) Identification and characterization of a native Dichelobacter nodosus plasmid, pDN1. Plasmid. 43(3):230-4. [PMID:10783302]


Auxiliary protein

ID   31 GenBank   NP_073213
Name   MobB_pDN1 insolico UniProt ID   Q9EU19
Length   136 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 136 a.a.        Molecular weight: 15085.39 Da        Isoelectric Point: 10.1732

>NP_073213.1 mobilisation protein B (plasmid) [Dichelobacter nodosus]
MSAIDRVRKSRGINELAAEIEPLAQSMATLADEARQRIAEVQQASEEQAASWTSQQQQAMSAWRQAAKDM
RAAAGELAKAGQTARSAARGWTWRLWAGVLIASVMPILALLIASWLWLEPQIIEQQGSIWLIFKLK

  Protein domains


Predicted by InterproScan.

Mobilization protein B (Mobilization_B)

(1-136)


  Protein structure


Source ID Structure
AlphaFold DB Q9EU19

  Reference


[1] Francia MV et al. (2004) A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev. 28(1):79-100. [PMID:14975531]

ID   32 GenBank   NP_073211
Name   MobC_pDN1 insolico UniProt ID   Q9EXQ0
Length   99 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 99 a.a.        Molecular weight: 11617.14 Da        Isoelectric Point: 10.3917

>NP_073211.1 mobilisation protein C (plasmid) [Dichelobacter nodosus]
MAKTAERLAKLEEQRARINAEIQRIRAREQQQKRKENTRRKVLVGAWILGKVENGEWPEQRLLDGLDSYL
ERDHDRALFGLPPKQKQQPQEHGQPEPQG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q9EXQ0

  Reference


[1] Francia MV et al. (2004) A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev. 28(1):79-100. [PMID:14975531]


Host bacterium

ID   20 GenBank   NC_002636
Plasmid name   pDN1 Incompatibility group   IncQ1
Plasmid size   5112 bp Coordinate of oriT [Strand]   804..892 [-]
Host baterium   Dichelobacter nodosus

Cargo genes

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