Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100079
Name   oriT_pRA2 in_silico
Organism   Pseudomonas alcaligenes
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_005909 (27593..27986 [+], 394 nt)
oriT length   394 nt
IRs (inverted repeats)      132..146, 149..163  (TGGCACACTGCCGCT..AGCGGCGGTGGGACA)
Location of nic site      175..176
Conserved sequence flanking the
  nic site    		  TACCCTG|T
Note   

  oriT sequence  


Download         Length: 394 nt

>oriT_pRA2
GCAAACCCCTAATGATGGCGGTGGGACACGCCGCAATGTTGGCCGCTGGCACGGCGCGGGGTCTCGGGGCGAAGCCCTGAGCAGGGGAGGAAAGGCCCAGCAGAACGAGTGCAACGAGTGACGCGGGCCGGTGGCACACTGCCGCTTTAGCGGCGGTGGGACATTCCCTACCCTGTCCCCTAATATGAAACCGCGTCCCGTTCAAACTTGTCTGCATCACTCACGCCCATTGAAAACCCACAAAAACCGGCACAGCACGATAAACCCGTGTATATCACAAACGCAGGTACTTGACCACATCCGCATAATGCACGATGATTGCAAGGCCAATGATTGCGCCAGCTTCAAAGGCAAACATCACCACACTGTTACCACAATCTAGCGAGGGCCAAAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Dam B et al. (2009) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Appl Environ Microbiol. 75(13):4362-73. [PMID:19411426]
[2] van Zyl LJ et al. (2003) Analysis of the mobilization region of the broad-host-range IncQ-like plasmid pTC-F14 and its ability to interact with a related plasmid, pTF-FC2. J Bacteriol. 185(20):6104-11. [PMID:14526022]


Relaxase

ID   74 GenBank   YP_025347
Name   MobA_pRA2 insolico UniProt ID   Q9XAW2
Length   854 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 854 a.a.        Molecular weight: 98487.27 Da        Isoelectric Point: 9.7752

>YP_025347.1 MobA (plasmid) [Pseudomonas alcaligenes]
MLAKVPPKRADGKTSFKSLAKYACERDHIDPETGAVERRECSTETNCLDKDTAWREMKAVSDMNGRVKDP
VYHFTVSWPAHEKPTDAQVFEAGREGMKSLGMEGHQYLAAVHRDTDNVHGHFMVNRVNPETYKAVYPDRD
YFKLDKTMREMELRQGWSHDKGPYAVHERNGQKVVDWAKDEPSHRQPDREKLPGKARQMEVMTGNESLTT
YAQGQPKKDALEALNKGGGWHELHEALGRHGLEIRQKGQGFAIHSKTDPEQTPIKASTMAQELGGGKLTK
RIGPYQEPRPEIQQEKAKREYSDQRPKADPKRDPNAREEKRDERAAERRELRDRYTAFTEEWKTAKAPAR
AAMYEDQKQRRQALTEKHKSQRETIRTSGLSTEQKKALYSVAAFDTAAKRAELNETIKGEREAFRQERPQ
SFREWTADRAQEGDRAAMRQVRGWAYQDKRTAKDMQQADAKAERGPHLGTTDTEQHDPAKPRRVTDRVSW
AVDRKTGAVDYKVDDRDAFRDSGRRLDYTEQGRKDKDSIEAGLLLAREKFAGKALKVTGPDDFRERVLQT
AIERKLDVRFSDKELEQRREAGLRQQAERERPDWSKMRGVASTGQQAEQRPQQPTQAQQPERRPTAPEQA
KEAAQAQPAQQAAPRMTDDEARAVLNRKPPAEPNQELVEINAINAHADGYRQQLDKQFREKHGERPDPER
AGGWIARFAAKSKAEAWDKEHAQIDRQVEQRKEHLRSDAPEARQFRAQAWAQAQQQYGAQHTAWEQARKQ
ATAHFEPNREGEPNMANNEQERKQQQQTQQQAQQKQAQEKQMAERAAREAQARQLAEKQKQQKEKQEKEK
EQARMMNQQMDIDR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-285)

Large polyvalent protein-associated domain 7 (LPD7)

(486-581)


  Protein structure


Source ID Structure
AlphaFold DB Q9XAW2

  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]


Auxiliary protein

ID   107 GenBank   YP_025348
Name   MobB_pRA2 insolico UniProt ID   Q9XAW1
Length   104 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 104 a.a.        Molecular weight: 11479.14 Da        Isoelectric Point: 8.5393

>YP_025348.1 MobB (plasmid) [Pseudomonas alcaligenes]
MSSSENRKRVVNLKVRCLPEEADTIRDKALDSGVSVSEFLRCAALGRKTRSTIDSQIINELRRLGGLQKH
LFTEAGGHEGGGHLSKEYADILVAIKEAIMRIES

  Protein domains


Predicted by InterproScan.

Ribbon-helix-helix protein, copG family (RHH_1)

(13-45)


  Protein structure


Source ID Structure
AlphaFold DB Q9XAW1

  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   108 GenBank   YP_025349
Name   MobC_pRA2 insolico UniProt ID   Q9XAW0
Length   116 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 116 a.a.        Molecular weight: 12565.07 Da        Isoelectric Point: 10.3779

>YP_025349.1 MobC (plasmid) [Pseudomonas alcaligenes]
MAGKQKTFDQETRQKIEATLDNLPEKPKSERPLTTKELVTELRTKIRAAQAKGYTLEEIVELFKREGAQI
SLSSVKSALKGSSPRSSRTTKPTQAGEQTAPQAASNAQPDGSHNGG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q9XAW0

  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   74 GenBank   NC_005909
Plasmid name   pRA2 Incompatibility group   IncQ2
Plasmid size   32743 bp Coordinate of oriT [Strand]   27593..27986 [+]
Host baterium   Pseudomonas alcaligenes

Cargo genes

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