Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100042
Name   oriT_pTP6 in_silico
Organism   Uncultured bacterium mercury resistance
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AM048832 (52447..52545 [+], 99 nt)
oriT length   99 nt
IRs (inverted repeats)      13..31, 34..52  (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site      60..61
Conserved sequence flanking the
  nic site    		  CATCCTG|C
Note   identical to the oriT of plasmid R751

  oriT sequence  


Download         Length: 99 nt

>oriT_pTP6
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Smalla K et al. (2006) Increased abundance of IncP-1beta plasmids and mercury resistance genes in mercury-polluted river sediments: first discovery of IncP-1beta plasmids with a complex mer transposon as the sole accessory element. Appl Environ Microbiol. 72(11):7253-9. [PMID:16980416]


Relaxase

ID   40 GenBank   CAJ15629
Name   TraI_pTP6 insolico UniProt ID   Q3BL02
Length   746 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82134.85 Da        Isoelectric Point: 10.8213

>CAJ15629.1 TraI DNA relaxase (plasmid) [uncultured bacterium]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQNLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHRRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
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 Q3BL02

  Reference


[1] Smalla K et al. (2006) Increased abundance of IncP-1beta plasmids and mercury resistance genes in mercury-polluted river sediments: first discovery of IncP-1beta plasmids with a complex mer transposon as the sole accessory element. Appl Environ Microbiol. 72(11):7253-9. [PMID:16980416]


Auxiliary protein

ID   66 GenBank   CAJ15630
Name   TraH_pTP6 insolico UniProt ID   Q7AS80
Length   130 a.a. PDB ID   _
Note   relaxosome stabilisation

  Auxiliary protein sequence


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

>CAJ15630.1 TraH protein (plasmid) [uncultured bacterium]
MSEPKDQSIEDELDAALAALDSGPLPTSTLPEPQPSPEQATAGQPPAEATAPTPAFTPPPSTGSPTLDAL
EENRRPKASTVCEHCPNSVWFASPAEVKCYCRVMFLVTWSSKEPNQITHCDGEFLGQEQE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q7AS80

ID   67 GenBank   CAJ15632
Name   TraJ_pTP6 insolico UniProt ID   Q7X3D0
Length   124 a.a. PDB ID   _
Note   conjugal transfer relaxosome component TraJ

  Auxiliary protein sequence


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

>CAJ15632.1 TraJ protein (plasmid) [uncultured bacterium]
MENDEKEHGRRRRQHLRVPVFPEEKDEIEANAKRAGVSVARYLRDVGQGYQIKGVMDYQHVRELVRVNGD
LGRLGGLLKLWLTDDVRTLQFGEATILALLGRIEATQDEMSRIMKAVVQPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q7X3D0

ID   68 GenBank   CAJ15633
Name   TraK_pTP6 insolico UniProt ID   Q7AS79
Length   132 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


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

>CAJ15633.1 TraK 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


T4CP

ID   40 GenBank   CAJ15628
Name   TraG_pTP6 insolico UniProt ID   Q7X3D2
Length   637 a.a. PDB ID   _
Note   conjugal transfer coupling protein TraG

  T4CP protein sequence


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

>CAJ15628.1 TraG 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


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12930..23607

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_13 8007..8435 - 429 CAJ15571 KlcA protein -
Locus_14 8604..8873 + 270 CAJ15572 hypothetical protein -
Locus_15 8870..9184 + 315 CAJ15573 hypothetical protein -
Locus_16 10536..11756 - 1221 CAJ15574 long form TrfA replication protein -
Locus_17 10536..11390 - 855 CAJ15575 short form TrfA replication protein -
Locus_18 11803..12144 - 342 CAJ15576 SSB single stranded DNA binding protein -
Locus_19 12258..12620 + 363 CAJ15577 TrbA repressor protein -
Locus_20 12930..13892 + 963 CAJ15589 TrbB protein virB11
Locus_21 13909..14373 + 465 CAJ15590 TrbC protein virB2
Locus_22 14377..14688 + 312 CAJ15591 TrbD protein virB3
Locus_23 14685..17243 + 2559 CAJ15592 TrbE protein virb4
Locus_24 17240..18022 + 783 CAJ15593 TrbF protein virB8
Locus_25 18019..18939 + 921 CAJ15594 TrbG protein virB9
Locus_26 18942..19430 + 489 CAJ15595 TrbH protein -
Locus_27 19435..20856 + 1422 CAJ15596 TrbI protein virB10
Locus_28 20877..21641 + 765 CAJ15597 TrbJ protein virB5
Locus_29 21651..21878 + 228 CAJ15598 TrbK entry exclusion protein -
Locus_30 21889..23607 + 1719 CAJ15599 TrbL protein virB6
Locus_31 23625..24212 + 588 CAJ15600 TrbM protein -
Locus_32 24226..24861 + 636 CAJ15601 TrbN protein -
Locus_33 24890..25156 + 267 CAJ15602 TrbO protein -
Locus_34 25156..25854 + 699 CAJ15603 TrbP protein -
Locus_35 25870..26301 + 432 CAJ15604 Upf30.5 protein -
Locus_36 26410..27084 + 675 CAJ15605 Upf31.0 putative adenine methylase -
Locus_37 27086..27745 - 660 CAJ15606 ParA resolvase -
Locus_38 28071..28505 - 435 CAJ15607 MerR-1 protein -

Host bacterium

ID   40 GenBank   AM048832
Plasmid name   pTP6 Incompatibility group   IncP1
Plasmid size   54344 bp Coordinate of oriT [Strand]   52447..52545 [+]
Host baterium   Uncultured bacterium mercury resistance

Cargo genes

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