Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100165
Name   oriT_pMD136 in_silico
Organism   Pediococcus pentosaceus
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_001277 (3761..3823 [+], 63 nt)
oriT length   63 nt
IRs (inverted repeats)      1..31, 33..63  (GTAAATTGATTGATTAAGCTCGTGAAACCCT..AGGGTTTCACGAGCTTAATCAATCAATTTAC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   ColE1 superfamily

  oriT sequence  


Download         Length: 63 nt

>oriT_pMD136
GTAAATTGATTGATTAAGCTCGTGAAACCCTTAGGGTTTCACGAGCTTAATCAATCAATTTAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Giacomini A et al. (2000) Nucleotide sequence and analysis of plasmid pMD136 from Pediococcus pentosaceus FBB61 (ATCC43200) involved in pediocin A production. Plasmid. 43(2):111-22. [PMID:10686129]


Relaxase

ID   159 GenBank   NP_037562
Name   MobA_pMD136 insolico UniProt ID   Q9WW30
Length   386 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 386 a.a.        Molecular weight: 44687.23 Da        Isoelectric Point: 10.0930

>NP_037562.1 mobilization protein (plasmid) [Pediococcus pentosaceus]
MATTHIKRSDSASRLVNYAEKRAVLKDGLNLDVDYAKSQLKQVREVYGNQGKTQAYASRISFSPKELDPT
NENDQQKALEIAKEVYQKTYPNQQVALYEHADTNALHVHAVIGAIDLETGRKMHGNWQEYREKLVHNTDE
ISQEHGLEVTQVDPNRYEKRTMAEIKMQAKGQPTWKDQIRQAVDKTMANRLVTDFQTFRDDLKQKTVDVW
ERGKDLTYQLTGTNYKARGNKLGTAYEKGEIYHELERRTRNHTKTRNPDTAKPDRTQPNLERNQELSGHA
NSITEQTTDRIDRTAPTDRASQSTGQSGFSNDLEQFRKQQRDQQTTINRDAQRRARTVQRANTQDKSKDN
RSLKTDKQRPKEQQRDVEKSQQQSKSNRSRNDGPSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(9-248)


  Protein structure


Source ID Structure
AlphaFold DB Q9WW30

  Reference


[1] Giacomini A et al. (2000) Nucleotide sequence and analysis of plasmid pMD136 from Pediococcus pentosaceus FBB61 (ATCC43200) involved in pediocin A production. Plasmid. 43(2):111-22. [PMID:10686129]


Auxiliary protein

ID   229 GenBank   NP_037563
Name   MobB_pMD136 insolico UniProt ID   Q9XDL9
Length   196 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 196 a.a.        Molecular weight: 23013.87 Da        Isoelectric Point: 9.3555

>NP_037563.1 mobilization protein (plasmid) [Pediococcus pentosaceus]
MKRGKFTMSWKDEPETTQRPETQIQPNLTELNQTLKEIRNYQGTQIQLQSKQQIELTEQLQQIEQASQRV
NQAFQTTLNNLENSRETNKQQSIETLKGAHEQFKEQTRKINQKTIEVLKQINNDQKSNNETLKNLSNNLN
QTVQETMDQVANRLAGEINQTHKKMSWFEIKNYLYAVIPTGLLSGLIFWFLTHFFA

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q9XDL9

  Reference


[1] Giacomini A et al. (2000) Nucleotide sequence and analysis of plasmid pMD136 from Pediococcus pentosaceus FBB61 (ATCC43200) involved in pediocin A production. Plasmid. 43(2):111-22. [PMID:10686129]

ID   230 GenBank   NP_037561
Name   MobC_pMD136 insolico UniProt ID   Q9RHE2
Length   73 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 73 a.a.        Molecular weight: 7839.15 Da        Isoelectric Point: 11.0075

>NP_037561.1 MobC-like protein (plasmid) [Pediococcus pentosaceus]
MSVPAFVKKKAQGARIIVPKIGAKDAQEITRQLAKIGSNLNQLAKHANQGGAVHAPALQELQSEVAKIWQ
QLT

  Protein domains


Predicted by InterproScan.

Bacterial mobilisation protein (MobC) (MobC)

(31-72)


  Protein structure


Source ID Structure
AlphaFold DB Q9RHE2

  Reference


[1] Giacomini A et al. (2000) Nucleotide sequence and analysis of plasmid pMD136 from Pediococcus pentosaceus FBB61 (ATCC43200) involved in pediocin A production. Plasmid. 43(2):111-22. [PMID:10686129]


T4CP

ID   159 GenBank   NP_037556
Name   ORF1_pMD136 insolico UniProt ID   Q9XDL7
Length   607 a.a. PDB ID   _
Note   shows homology to conjugative coupling proteins

  T4CP protein sequence


Download         Length: 607 a.a.        Molecular weight: 68354.13 Da        Isoelectric Point: 5.6242

>NP_037556.1 hypothetical protein pMD136_p01 (plasmid) [Pediococcus pentosaceus]
MHLVSVTIHNFRGYKNTKINIDDQLTTLIGKNDVGKSTIVDALEIFFNNTVVKLDTNDLNIYATDSKLVS
ISCEFSDIPESIIIDSNQQTNLKDEYLVNANGNLEIKKVYDCSKKTPKPQIFAVVHYPDNPEIADLLYLT
HSKLLTALKKLPPAIQETVTSRVANAPIRQAIRSAYNITNFLTKDIDLQKVDGKTLWDKIETCLPIYALF
QSDRPSNDSDAEVQDPMNTAIQESLSNAAQQLQVIQQQVIQEVTAVAEMTISKLKEMDPEIAKGLEPQYQ
ESPKWNKLFKFVIADEKGIPLNKRGSGVRRLVLLNFFRAKVSMTSDKLKTNGLIYAVEEPETAQHPDNQR
KIMQALLELGQRGNCQIIITTHLAETAKMAPKSGVRLITRQDNVTKVSDNDTALKIAAKEVGLIANITDT
NIVLYVEGPSDVLFFNSVSKILNQFDSTKYSDFTKSKNLLIVPMGGGTMKQWVNYKYLETLQLPSFYLFD
KDLDAQHQREVDELKTDPQCLYAFLTDKREIENYIAPAAIERYFSKLLKSEFSMPELNSESDVTNLLKKA
GVNQRQSYLKETLNSKVAAQMTADEFLSNDTTGFMAEFIAKITKEIS

  Protein domains


Predicted by InterproScan.

AAA ATPase domain (AAA_15)

(1-372)

  Protein structure


Source ID Structure
AlphaFold DB Q9XDL7

  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   159 GenBank   NC_001277
Plasmid name   pMD136 Incompatibility group   _
Plasmid size   19515 bp Coordinate of oriT [Strand]   3761..3823 [+]
Host baterium   Pediococcus pentosaceus

Cargo genes

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