Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100045
Name   oriT_pJP4 in_silico
Organism   Ralstonia eutropha JMP134
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AY365053 (85790..85881 [+], 92 nt)
oriT length   92 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   _

  oriT sequence  


Download         Length: 92 nt

>oriT_pJP4
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   43 GenBank   AAR31100
Name   TraI_pJP4 insolico UniProt ID   Q6UP38
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

>AAR31100.1 relaxosome stabilization protein (plasmid) [Cupriavidus pinatubonensis JMP134]
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 Q6UP38

  Reference


[1] Shintani M et al. (2010) The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms. Microbes Environ. 25(4):253-65. [PMID:21576880]
[2] Trefault N et al. (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol. 6(7):655-68. [PMID:15186344]


Auxiliary protein

ID   71 GenBank   AAR31099
Name   TraH_pJP4 insolico UniProt ID   Q6UP37
Length   130 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


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

>AAR31099.1 DNA relaxase (plasmid) [Cupriavidus pinatubonensis JMP134]
MSEPKDQSIEDELDAALAALDSGPLPTSTLPEPQPSPEQATAGQPPAEATAPTPAFTPPPSTGSPTLDAL
EENRRPKASTVCEHCPNSVWFASPAEVKCYCRVMFLVTWSSKEPNQITHCDGEFLGQEQE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q6UP37

  Reference


[1] Trefault N et al. (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol. 6(7):655-68. [PMID:15186344]

ID   72 GenBank   AAR31101
Name   TraJ_pJP4 insolico UniProt ID   Q6UP36
Length   105 a.a. PDB ID   _
Note   conjugal transfer relaxosome component TraJ

  Auxiliary protein sequence


Download         Length: 105 a.a.        Molecular weight: 11812.61 Da        Isoelectric Point: 5.8882

>AAR31101.1 oriT binding protein (plasmid) [Cupriavidus pinatubonensis JMP134]
MFPEEKDEIEANAKRAGVSVARYLRDVGQGYQIKGVMDYQHVRELVRVNGDLGRLGGLLKLWLTDDVRTL
QFGEATILALLGRIEATQDEMSRIMKAVVQPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q6UP36

  Reference


[1] Trefault N et al. (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol. 6(7):655-68. [PMID:15186344]

ID   73 GenBank   AAR31102
Name   TraK_pJP4 insolico UniProt ID   Q6UP35
Length   132 a.a. PDB ID   _
Note   oriT binding protein

  Auxiliary protein sequence


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

>AAR31102.1 oriT binding protein (plasmid) [Cupriavidus pinatubonensis JMP134]
MPKTYPEELAEWVKGREAKKPRQDKHVVAFLAVKSDVQAALDAGYAMKTIWEHMKETGRLRCRYETFTQH
VKRYIKAAPVASPPPPATPPDSQPKGAKPEPKAAPPASESKSEPPKIGGFTFDATPKKEDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB Q6UP35

  Reference


[1] Trefault N et al. (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol. 6(7):655-68. [PMID:15186344]


T4CP

ID   43 GenBank   AAR31098
Name   TraG_pJP4 insolico UniProt ID   Q6UP39
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

>AAR31098.1 DNA transport protein (plasmid) [Cupriavidus pinatubonensis JMP134]
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 Q6UP39

  Reference


[1] Trefault N et al. (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol. 6(7):655-68. [PMID:15186344]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 58243..68920

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_49 54470..54745 - 276 AAR31067 periplasmic mercury ion binding protein -
Locus_50 54758..55108 - 351 AAR31068 mercury ion transport protein -
Locus_51 55180..55614 + 435 AAR31069 mercury regulatory protein -
Locus_52 55727..56947 - 1221 AAR31070 transreplication factor -
Locus_53 55727..56581 - 855 AAR31071 transreplication factor -
Locus_54 56994..57335 - 342 AAR31072 single-strand DNA binding protein -
Locus_55 57571..57933 + 363 AAR31073 regulatory protein for mating pair formation -
Locus_56 58243..59205 + 963 AAR31074 ATPase autophosphorylase virB11
Locus_57 59222..59686 + 465 AAR31075 mating pair formation virB2
Locus_58 59690..60001 + 312 AAR31076 mating pair formation virB3
Locus_59 59998..62556 + 2559 AAR31077 mating pair formation virb4
Locus_60 62553..63335 + 783 AAR31078 mating pair formation virB8
Locus_61 63332..64252 + 921 AAR31079 mating pair formation virB9
Locus_62 64255..64743 + 489 AAR31080 mating pair formation -
Locus_63 64748..66169 + 1422 AAR31081 mating pair formation virB10
Locus_64 66190..66954 + 765 AAR31082 mating pair formation virB5
Locus_65 66964..67191 + 228 AAR31083 plasmid entry / exclusion -
Locus_66 67202..68920 + 1719 AAR31084 DNA topoisomerase virB6
Locus_67 68938..69525 + 588 AAR31085 mating pair formation -
Locus_68 69539..70174 + 636 AAR31086 mating pair formation -
Locus_69 70203..70469 + 267 AAR31087 TrbO -
Locus_70 70469..71167 + 699 AAR31088 Trbp -
Locus_71 71183..71614 + 432 AAR31089 Upf30.5 -
Locus_72 71769..72443 + 675 AAR31090 Upf31.0 -
Locus_73 72445..73104 - 660 AAR31091 resolvase -

Host bacterium

ID   43 GenBank   AY365053
Plasmid name   pJP4 Incompatibility group   IncP1
Plasmid size   87688 bp Coordinate of oriT [Strand]   85790..85881 [+]
Host baterium   Ralstonia eutropha JMP134

Cargo genes

Drug resistance gene   _
Virulence gene   _
Metal resistance gene   mercury resistance
Degradation gene   degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) and 3-chlorobenzoic acid (3-CB)
Symbiosis gene   -
Anti-CRISPR   -