Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100220
Name   oriT_pADP-1 in_silico
Organism   Pseudomonas sp. ADP
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_004956 (11993..12052 [-], 60 nt)
oriT length   60 nt
IRs (inverted repeats)      8..26, 29..47  (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site      55..56
Conserved sequence flanking the
  nic site    		  CATCCTG|C
Note   _

  oriT sequence  


Download         Length: 60 nt

>oriT_pADP-1
AGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]


Relaxase

ID   213 GenBank   NP_862458
Name   TraI_pADP-1 insolico UniProt ID   Q937B9
Length   746 a.a. PDB ID   
Note   DNA relaxase

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82120.82 Da        Isoelectric Point: 10.8213

>NP_862458.1 TraI protein (plasmid) [Pseudomonas sp. ADP]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWVKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQNLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHRRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)


  Protein structure


Source ID Structure
AlphaFold DB Q937B9

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]


Auxiliary protein

ID   299 GenBank   NP_862459
Name   TraH_pADP-1 insolico UniProt ID   Q79BS3
Length   130 a.a. PDB ID   _
Note   relaxosome stabilization protein

  Auxiliary protein sequence


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

>NP_862459.1 TraH protein (plasmid) [Pseudomonas sp. ADP]
MSEPKDQSIEDELDAALAALDSGPLPTSTLPEPQPSPEQATAGQPPAEATAPTPAFTPPPSTGSPTLDAL
EENRRPKASTVCEHCPNSVWFASPAEVKCYCRVMFLVTWSSKEPNQITHCDGEFLGQEQE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q79BS3

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]

ID   300 GenBank   NP_862457
Name   TraJ_pADP-1 insolico UniProt ID   Q937C0
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

>NP_862457.1 TraJ protein (plasmid) [Pseudomonas sp. ADP]
MENDEKEHGRRRRQHLRVPVFPEEKDEIEANAKRAGVSVARYLRDVGQGYQIKGVMDYQHVRELVRVNGD
LGRLGGLLKLWLTDDVRTLQFGEATILALLGRIEATQDEMSRIMKAVVQPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q937C0

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]

ID   301 GenBank   NP_862456
Name   TraK_pADP-1 insolico UniProt ID   Q79BS4
Length   132 a.a. PDB ID   _
Note   TraK protein; oriT binding protein

  Auxiliary protein sequence


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

>NP_862456.1 TraK protein (plasmid) [Pseudomonas sp. ADP]
MPKTYPEELAEWVKGREAKKPRQDKHVVAFLAVKSDVQAALDAGYAMKTIWEHMKETGRLRCRYETFTQH
VKRYIKAAPVASPPPPATPPDSQPKGAKPEPKAAPPASESKSEPPKIGGFTFDATPKKEDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB Q79BS4

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]


T4CP

ID   213 GenBank   NP_862460
Name   TraG_pADP-1 insolico UniProt ID   Q937B8
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

>NP_862460.1 TraG protein (plasmid) [Pseudomonas sp. ADP]
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 Q937B8

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 77534..88211

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTY49_RS00370 (pADP-1_p073) 72897..74444 - 1548 WP_008328818 IS91-like element ISPps1 family transposase -
HTY49_RS00375 (pADP-1_p074) 74553..75762 - 1210 Protein_74 NAD(P)/FAD-dependent oxidoreductase -
HTY49_RS00380 (pADP-1_p075) 75908..76237 + 330 Protein_75 DUF4158 domain-containing protein -
HTY49_RS00385 (pADP-1_p076) 76280..76915 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
HTY49_RS00390 (pADP-1_p077) 76929..77516 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
HTY49_RS00395 (pADP-1_p078) 77534..79252 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
HTY49_RS00400 (pADP-1_p079) 79263..79490 - 228 WP_011117181 entry exclusion lipoprotein TrbK -
HTY49_RS00405 (pADP-1_p080) 79500..80264 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
HTY49_RS00410 (pADP-1_p081) 80285..81706 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
HTY49_RS00415 (pADP-1_p082) 81711..82199 - 489 WP_006122479 conjugal transfer protein TrbH -
HTY49_RS00420 (pADP-1_p083) 82202..83101 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
HTY49_RS00425 (pADP-1_p084) 83119..83901 - 783 WP_011114048 conjugal transfer protein TrbF virB8
HTY49_RS00430 (pADP-1_p085) 83898..86456 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTY49_RS00435 (pADP-1_p086) 86453..86764 - 312 WP_001207961 conjugal transfer protein TrbD virB3
HTY49_RS00440 (pADP-1_p087) 86768..87232 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
HTY49_RS00445 (pADP-1_p088) 87249..88211 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
HTY49_RS00450 (pADP-1_p089) 88521..88883 - 363 WP_011114045 transcriptional regulator -
HTY49_RS00455 (pADP-1_p090) 88997..89338 + 342 WP_000019167 single-stranded DNA-binding protein -
HTY49_RS00460 (pADP-1_p091) 89385..90399 + 1015 Protein_91 plasmid replication initiator TrfA -
HTY49_RS00465 (pADP-1_p092) 90795..92165 - 1371 WP_011117183 IS1182-like element ISPsp5 family transposase -

Host bacterium

ID   213 GenBank   NC_004956
Plasmid name   pADP-1 Incompatibility group   IncP1
Plasmid size   108845 bp Coordinate of oriT [Strand]   11993..12052 [-]
Host baterium   Pseudomonas sp. ADP

Cargo genes

Drug resistance gene   _
Virulence gene   _
Metal resistance gene   merE, merD, merA, merF, merP, merT, merR2
Degradation gene   degradation of herbicide atrazine
Symbiosis gene   -
Anti-CRISPR   -