Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100016
Name   oriT_pB10 in_silico
Organism   Uncultured bacterium IncP-1beta multiresistance
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AJ564903 (31293..31595 [+], 303 nt)
oriT length   303 nt
IRs (inverted repeats)      55..72, 75..92  (TGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCA)
Location of nic site      101..102
Conserved sequence flanking the
  nic site    		  CATCCTG|C
Note   _

  oriT sequence  


Download         Length: 303 nt

>oriT_pB10
TGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Schlüter A et al. (2003) The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group. Microbiology. 149(Pt 11):3139-53. [PMID:14600226]


Relaxase

ID   15 GenBank   CAD97516
Name   TraI_pB10 insolico UniProt ID   Q7X3D1
Length   746 a.a. PDB ID   
Note   DNA relaxase

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82038.71 Da        Isoelectric Point: 10.7900

>CAD97516.1 DNA relaxase (plasmid) [uncultured bacterium]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
LQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)


  Protein structure


Source ID Structure
AlphaFold DB Q7X3D1

  Reference


[1] Schlüter A et al. (2003) The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group. Microbiology. 149(Pt 11):3139-53. [PMID:14600226]


Auxiliary protein

ID   23 GenBank   CAD97515
Name   TraH_pB10 insolico UniProt ID   Q7AS80
Length   130 a.a. PDB ID   _
Note   relaxosome stabilisation protein

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 13936.41 Da        Isoelectric Point: 3.9776

>CAD97515.1 relaxosome stabilisation protein (plasmid) [uncultured bacterium]
MSEPKDQSIEDELDAALAALDSGPLPTSTLPEPQPSPEQATAGQPPAEATAPTPAFTPPPSTGSPTLDAL
EENRRPKASTVCEHCPNSVWFASPAEVKCYCRVMFLVTWSSKEPNQITHCDGEFLGQEQE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q7AS80

  Reference


[1] Schlüter A et al. (2003) The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group. Microbiology. 149(Pt 11):3139-53. [PMID:14600226]

ID   24 GenBank   CAD97517
Name   TraJ_pB10 insolico UniProt ID   Q7X3D0
Length   124 a.a. PDB ID   _
Note   involved in conjugative DNA transfer

  Auxiliary protein sequence


Download         Length: 124 a.a.        Molecular weight: 14206.27 Da        Isoelectric Point: 8.5329

>CAD97517.1 oriT binding protein (plasmid) [uncultured bacterium]
MENDEKEHGRRRRQHLRVPVFPEEKDEIEANAKRAGVSVARYLRDVGQGYQIKGVMDYQHVRELVRVNGD
LGRLGGLLKLWLTDDVRTLQFGEATILALLGRIEATQDEMSRIMKAVVQPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q7X3D0

  Reference


[1] Schlüter A et al. (2003) The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group. Microbiology. 149(Pt 11):3139-53. [PMID:14600226]

ID   25 GenBank   CAD97518
Name   TraK_pB10 insolico UniProt ID   Q7AS79
Length   132 a.a. PDB ID   _
Note   involved in conjugative DNA transfer

  Auxiliary protein sequence


Download         Length: 132 a.a.        Molecular weight: 14621.83 Da        Isoelectric Point: 9.9884

>CAD97518.1 oriT binding protein (plasmid) [uncultured bacterium]
MPKTYPEELAEWVKGREAKKPRQDKHVVAFLAVKSDVQAALDAGYAMKTIWEHMKETGRLRCRYETFTQH
VKRYIKAAPVASPPPPATPPDSQPKGAKPEPKAAPPASESKSEPPKIGGFTFDATPKKEDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB Q7AS79

  Reference


[1] Schlüter A et al. (2003) The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group. Microbiology. 149(Pt 11):3139-53. [PMID:14600226]


T4CP

ID   15 GenBank   CAD97514
Name   TraG_pB10 insolico UniProt ID   Q7X3D2
Length   637 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 69897.09 Da        Isoelectric Point: 8.2993

>CAD97514.1 DNA transport protein (plasmid) [uncultured bacterium]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDDGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQAET
EGEGITI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(121-620)

  Protein structure


Source ID Structure
AlphaFold DB Q7X3D2

  Reference


[1] Schlüter A et al. (2003) The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group. Microbiology. 149(Pt 11):3139-53. [PMID:14600226]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 769..11446

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_0 97..459 + 363 CAD97487 TrbA protein -
Locus_1 769..1731 + 963 CAD97488 putative ATPase, autophosphorylase virB11
Locus_2 1748..2212 + 465 CAD97489 putative prepilin virB2
Locus_3 2216..2527 + 312 CAD97490 TrbD protein virB3
Locus_4 2524..5082 + 2559 CAD97491 TrbE protein virb4
Locus_5 5079..5861 + 783 CAD97492 TrbF protein virB8
Locus_6 5858..6778 + 921 CAD97493 TrbG protein virB9
Locus_7 6781..7269 + 489 CAD97494 TrbH protein -
Locus_8 7274..8695 + 1422 CAD97495 TrbI protein virB10
Locus_9 8716..9480 + 765 CAD97496 TrbJ protein virB5
Locus_10 9490..9717 + 228 CAD97497 TrbK protein -
Locus_11 9728..11446 + 1719 CAD97498 putative DNA topoisomerase virB6
Locus_12 11464..12051 + 588 CAD97499 TrbM protein -
Locus_13 12065..12700 + 636 CAD97500 putative muramidase -
Locus_14 12729..12995 + 267 CAD97501 TrbO protein -
Locus_15 12995..13693 + 699 CAD97502 TrbP protein -
Locus_16 13709..14140 + 432 CAD97503 putative outer membrane protein -
Locus_17 14404..14904 - 501 CAD97504 putative acetyltransferase -
Locus_18 15032..15871 - 840 CAD97505 dihydropteroate synthetase -
Locus_19 15865..16212 - 348 CAD97506 small exporter protein -

Host bacterium

ID   15 GenBank   AJ564903
Plasmid name   pB10 Incompatibility group   IncP1
Plasmid size   64508 bp Coordinate of oriT [Strand]   31293..31595 [+]
Host baterium   Uncultured bacterium IncP-1beta multiresistance

Cargo genes

Drug resistance gene   resistance to amoxicillin, streptomycin, sulfonamides and tetracycline
Virulence gene   -
Metal resistance gene   mercury resistance
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -