Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200014
Name   oriT_intD in_silico
Organism   Dichelobacter nodosus strain C305-1 intD element and flanking
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AY847513 (30074..30197 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      23..31, 39..47  (GTCTGACAA..TTTTCAGAC)
  57..64, 68..75  (CAAAGGGG..CCCCTTTG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   _

  oriT sequence  


Download         Length: 124 nt

>oriT_intD
GCATTGAGGCACGTTGCCGACTGTCTGACAAACTGACGTTTTCAGACGTCGCGTGCCAAAGGGGATCCCCCTTTGAAACCCTATTGCGGAAAAATCAATGTGGAGACTTACTGACGTAAGGAAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Tanjung LR et al. (2009) The intD mobile genetic element from Dichelobacter nodosus, the causative agent of ovine footrot, is associated with the benign phenotype. Anaerobe. 15(5):219-24. [PMID:19327404]


Relaxase

ID   228 GenBank   AAW31842
Name   DapA_intD insolico UniProt ID   Q5I738
Length   520 a.a. PDB ID   
Note   relaxase; similar to H. influenzae relaxase

  Relaxase protein sequence


Download         Length: 520 a.a.        Molecular weight: 61641.48 Da        Isoelectric Point: 8.5740

>AAW31842.1 DapA [Dichelobacter nodosus]
MTINICLMNGMNTLPAKRDLSKKQQNMNADAYVAMNLPEKKSWLAAQWHHHLKHIGYEDSPQSTHNFNYE
TITVTYVDIDHIPHIDDVPYIGDCRHLDEIPNLDEAPHINEIYGDLNDTTQIEQRNSRFSMHELRTRRGN
GNRGQRKPLSMPNLLQNDQCLDMVRNEKITFEELYTSSHERNVAAKRFIDQQNQQREVLKHHWSELINSI
DSRNFLNYISYHYGLEVDNYRIEKNKSGNERIIADDRKYSVSDFLTKKMHMTWTEAQSILRTVAAQQQIG
EQRKAAVTSRLMWQRFMRYEANKKNFSTVKSEYFTQRRMIKARYQYVHNDEISRGENAAKYRLIKMQKAA
ELAKLEQEYEEQARYYRQKMHDRYMEYLYEEAEQGNSAALGELNRIYPIRDYAQRDVFEICIKEQKHHKQ
QFSLIDLDYKVKIKRNGTIEYQDEREKTVIIDSYNSIKVTDRSVDIIVKALELAKLRYGRDGFEIRNATE
QDLVAIQAAVNKTGVEVRIMNKEKNQDRGR

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q5I738

  Reference


[1] Tanjung LR et al. (2009) The intD mobile genetic element from Dichelobacter nodosus, the causative agent of ovine footrot, is associated with the benign phenotype. Anaerobe. 15(5):219-24. [PMID:19327404]


Auxiliary protein

ID   316 GenBank   AAW31843
Name   DapB_intD insolico UniProt ID   Q5I737
Length   271 a.a. PDB ID   _
Note   mobilisation protein

  Auxiliary protein sequence


Download         Length: 271 a.a.        Molecular weight: 31834.32 Da        Isoelectric Point: 9.6303

>AAW31843.1 DapB [Dichelobacter nodosus]
MIIRFRGASHGVVTYLRDGKKSGRYYSRDELDQRVQLCGNLTELDTVLNSFDRECKTQKYFHISLSFKEK
NISEEVLKNIDVEFRKFIFSSCVEGEFYYFSEIHFPKIQSLIDMQGKNFKRYPHIHVVIPEYNLYTGKRD
NPLGLVDKRERYINAFQEYINEKYELESPKDNQRTIKTGREEVIARYEIKPDMTNKEIKQTIFSIIQNNP
QISSVTELAQVIKGFGTVTVRDSKSFGQPYINLKIVGKDKGINLKDPGFSQSLFRKPHRER

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(46-225)


  Protein structure


Source ID Structure
AlphaFold DB Q5I737

  Reference


[1] Tanjung LR et al. (2009) The intD mobile genetic element from Dichelobacter nodosus, the causative agent of ovine footrot, is associated with the benign phenotype. Anaerobe. 15(5):219-24. [PMID:19327404]

ID   317 GenBank   AAW31844
Name   DapC_intD insolico UniProt ID   Q5I742
Length   113 a.a. PDB ID   _
Note   mobilisation protein

  Auxiliary protein sequence


Download         Length: 113 a.a.        Molecular weight: 13234.20 Da        Isoelectric Point: 6.2200

>AAW31844.1 DapC [Dichelobacter nodosus]
MALETRITLRLSDELQEKYAAIADQTGNTLSEVIRQVLLESNPQFIDKLAIEDRLKIIRLISKSSNNLNQ
IARQLNSLALYNQLHYDQCIHYLRILDTIEAQQHIFLKMFNDY

  Protein domains


Predicted by InterproScan.

Bacterial mobilisation protein (MobC) (MobC)

(58-94)


  Protein structure


Source ID Structure
AlphaFold DB Q5I742

  Reference


[1] Tanjung LR et al. (2009) The intD mobile genetic element from Dichelobacter nodosus, the causative agent of ovine footrot, is associated with the benign phenotype. Anaerobe. 15(5):219-24. [PMID:19327404]


Host bacterium

ID   19 Element type   
Element name   intD element and flanking genomic sequence GenBank   AY847513
Element size   35198 bp Coordinate of oriT [Strand]   30074..30197 [-]
Host bacterium   Dichelobacter nodosus strain C305-1 intD element and flanking

Cargo genes

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