Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100213
Name   oriT_pAKD33 in_silico
Organism   Uncultured bacterium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   JN106174 (29904..30207 [+], 304 nt)
oriT length   304 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   similar to oriT of the IncP-1beta multiresistance plasmid pB10

  oriT sequence  


Download         Length: 304 nt

>oriT_pAKD33
TGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Sen D et al. (2011) Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl Environ Microbiol. 77(22):7975-83. [PMID:21948829]


Relaxase

ID   206 GenBank   AEV57343
Name   TraI_pAKD33 insolico UniProt ID   Q7X3D1
Length   746 a.a. PDB ID   
Note   conjugal transfer relaxase TraI; Provisional

  Relaxase protein sequence


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

>AEV57343.1 TraI (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


Auxiliary protein

ID   288 GenBank   AEV57344
Name   TraH_pAKD33 insolico UniProt ID   Q7AS80
Length   130 a.a. PDB ID   _
Note   DNA-processing protein; relaxosome stabilisation

  Auxiliary protein sequence


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

>AEV57344.1 TraH (plasmid) [uncultured bacterium]
MSEPKDQSIEDELDAALAALDSGPLPTSTLPEPQPSPEQATAGQPPAEATAPTPAFTPPPSTGSPTLDAL
EENRRPKASTVCEHCPNSVWFASPAEVKCYCRVMFLVTWSSKEPNQITHCDGEFLGQEQE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q7AS80

ID   289 GenBank   AEV57345
Name   TraJ_pAKD33 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

>AEV57345.1 TraJ (plasmid) [uncultured bacterium]
MENDEKEHGRRRRQHLRVPVFPEEKDEIEANAKRAGVSVARYLRDVGQGYQIKGVMDYQHVRELVRVNGD
LGRLGGLLKLWLTDDVRTLQFGEATILALLGRIEATQDEMSRIMKAVVQPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q7X3D0

ID   290 GenBank   AEV57346
Name   TraK_pAKD33 insolico UniProt ID   Q7AS79
Length   132 a.a. PDB ID   _
Note   DNA-processing protein; oriT-binding protein

  Auxiliary protein sequence


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

>AEV57346.1 TraK (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   206 GenBank   AEV57342
Name   TraG_pAKD33 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

>AEV57342.1 TraG (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: 2398..13075

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_0 1..1221 - 1221 AEV57317 TrfA1 -
Locus_1 1268..1612 - 345 AEV57318 ssb protein -
Locus_2 1726..2088 + 363 AEV57319 TrbA -
Locus_3 2398..3360 + 963 AEV57320 TrbB virB11
Locus_4 3377..3841 + 465 AEV57321 TrbC virB2
Locus_5 3845..4156 + 312 AEV57322 TrbD virB3
Locus_6 4153..6711 + 2559 AEV57323 TrbE virb4
Locus_7 6708..7490 + 783 AEV57324 TrbF virB8
Locus_8 7508..8407 + 900 AEV57325 TrbG virB9
Locus_9 8410..8898 + 489 AEV57326 TrbH -
Locus_10 8903..10324 + 1422 AEV57327 TrbI virB10
Locus_11 10345..11109 + 765 AEV57328 TrbJ virB5
Locus_12 11119..11346 + 228 AEV57329 TrbK -
Locus_13 11363..13075 + 1713 AEV57330 TrbL virB6
Locus_14 13093..13680 + 588 AEV57331 TrbM -
Locus_15 13694..14329 + 636 AEV57332 TrbN -
Locus_16 14358..14624 + 267 AEV57333 TrbO -
Locus_17 14624..15322 + 699 AEV57334 TrbP -
Locus_18 15338..15769 + 432 AEV57335 Upf30.5 -
Locus_19 15840..16598 + 759 AEV57336 Upf31.0 -
Locus_20 16600..17451 - 852 AEV57337 ParA -

Host bacterium

ID   206 GenBank   JN106174
Plasmid name   pAKD33 Incompatibility group   IncP1
Plasmid size   57974 bp Coordinate of oriT [Strand]   29904..30207 [+]
Host baterium   Uncultured bacterium

Cargo genes

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