Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100176
Name   oriT_R751 experimental
Organism   Klebsiella aerogenes
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_001735 (51526..51624 [+], 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   _

  oriT sequence  


Download         Length: 99 nt

>oriT_R751
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Waters VL et al. (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]
[2] Furuya N et al. (1991) Determination of the nick site at oriT of IncI1 plasmid R64: global similarity of oriT structures of IncI1 and IncP plasmids. J Bacteriol. 173(20):6612-7. [PMID:1917882]
[3] Fürste JP et al. (1989) Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin. Proc Natl Acad Sci U S A. 86(6):1771-5. [PMID:2538813]
[4] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]


Relaxase

ID   169 GenBank   NP_044272
Name   TraI_R751 insolico UniProt ID   _
Length   747 a.a. PDB ID   
Note   to recognize the conserved nick region sequence

  Relaxase protein sequence


Download         Length: 747 a.a.        Molecular weight: 82194.90 Da        Isoelectric Point: 10.8213

>NP_044272.1 hypothetical protein R751p63 [[Enterobacter] aerogenes]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGRDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)


  Protein structure



No available structure.



  Reference


[1] Waters VL et al. (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]
[2] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]


Auxiliary protein

ID   242 GenBank   NP_044273
Name   TraH_R751 insolico UniProt ID   _
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

>NP_044273.1 hypothetical protein R751p64 [[Enterobacter] aerogenes]
MSEPKDQSIEDELDAALAALDSGPLPTSTLPEPQPSPEQATAGQPPAEATAPTPAFTPPPSTGSPTLDAL
EENRRPKASTVCEHCPNSVWFASPAEVKCYCRVMFLVTWSSKEPNQITHCDGEFLGQEQE

  Protein domains



No domain identified.



  Protein structure



No available structure.



  Reference


[1] Waters VL et al. (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]
[2] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]

ID   243 GenBank   NP_044275
Name   TraJ_R751 insolico UniProt ID   _
Length   124 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


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

>NP_044275.2 hypothetical protein R751p66 [[Enterobacter] aerogenes]
MENDEKEHGRRRRQHLRVPVFPEEKDEIEANAKRAGVSVARYLRDVGQGYQIKGVMDYQHVRELVRVNGD
LGRLGGLLKLWLTDDVRTLQFGEATILALLGRIEATQDEMSRIMKAVVQPRAEP

  Protein domains



No domain identified.



  Protein structure



No available structure.



  Reference


[1] Waters VL et al. (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]
[2] Fürste JP et al. (1989) Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin. Proc Natl Acad Sci U S A. 86(6):1771-5. [PMID:2538813]
[3] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]

ID   244 GenBank   NP_044276
Name   TraK_R751 insolico UniProt ID   _
Length   132 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


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

>NP_044276.1 hypothetical protein R751p67 [[Enterobacter] aerogenes]
MPKTYPEELAEWVKGREAKKPRQDKHVVAFLAVKSDVQAALDAGYAMKTIWEHMKETGRLRCRYETFTQH
VKRYIKAAPVASPPPPATPPDSQPKGAKPEPKAAPPASESKSEPPKIGGFTFDATPKKEDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure



No available structure.



  Reference


[1] Waters VL et al. (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]
[2] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]


T4CP

ID   169 GenBank   CAA38327
Name   TraG_R751 insolico UniProt ID   Q00184
Length   637 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 69883.06 Da        Isoelectric Point: 8.2993

>CAA38327.1 traG (plasmid) [Escherichia coli]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDDGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQADT
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 Q00184

  Reference


[1] Waters VL et al. (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids. Proc Natl Acad Sci U S A. 88(4):1456-60. [PMID:1996345]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17618..28296

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTY34_RS00100 (R751p24) 13470..14474 + 1005 WP_010890123 IS110-like element IS4321 family transposase -
HTY34_RS00105 (R751p25) 15226..16449 - 1224 WP_010890124 plasmid replication initiator TrfA -
HTY34_RS00110 (R751p27) 16496..16837 - 342 WP_000019167 single-stranded DNA-binding protein -
HTY34_RS00115 (R751p28) 16951..17313 + 363 WP_010890126 transcriptional regulator -
HTY34_RS00120 (R751p30) 17618..18580 + 963 WP_010890127 P-type conjugative transfer ATPase TrbB virB11
HTY34_RS00125 (R751p31) 18597..19061 + 465 WP_010890128 conjugal transfer system pilin TrbC virB2
HTY34_RS00130 (R751p32) 19065..19376 + 312 WP_010890129 conjugal transfer protein TrbD virB3
HTY34_RS00135 (R751p33) 19373..21931 + 2559 WP_010890130 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTY34_RS00140 (R751p34) 21928..22710 + 783 WP_010890131 conjugal transfer protein TrbF virB8
HTY34_RS00145 (R751p35) 22728..23627 + 900 WP_181411753 P-type conjugative transfer protein TrbG virB9
HTY34_RS00150 (R751p36) 23630..24118 + 489 WP_010890133 conjugal transfer protein TrbH -
HTY34_RS00155 (R751p37) 24123..25544 + 1422 WP_010890134 TrbI/VirB10 family protein virB10
HTY34_RS00160 25565..26329 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
HTY34_RS00165 (R751p39) 26340..26567 + 228 WP_010890136 entry exclusion lipoprotein TrbK -
HTY34_RS00170 (R751p40) 26578..28296 + 1719 WP_010890137 P-type conjugative transfer protein TrbL virB6
HTY34_RS00175 (R751p41) 28314..28901 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
HTY34_RS00180 (R751p42) 28915..29550 + 636 WP_010890139 transglycosylase SLT domain-containing protein -
HTY34_RS00185 (R751p43) 29577..29843 + 267 WP_010890140 hypothetical protein -
HTY34_RS00190 (R751p44) 29843..30541 + 699 WP_010890141 TraX family protein -
HTY34_RS00195 (R751p46) 30557..30985 + 429 WP_010890142 OmpA family protein -
HTY34_RS00200 (R751p47) 31056..31664 + 609 WP_228275496 DNA adenine methylase -
HTY34_RS00205 (R751p48) 31911..32924 - 1014 WP_000845054 class 1 integron integrase IntI1 -

Host bacterium

ID   169 GenBank   NC_001735
Plasmid name   R751 Incompatibility group   IncP1
Plasmid size   53423 bp Coordinate of oriT [Strand]   51526..51624 [+]
Host baterium   Klebsiella aerogenes

Cargo genes

Drug resistance gene   resistance to trimethoprim, quaternary ammonium compounds (qacE)
Virulence gene   _
Metal resistance gene   _
Degradation gene   _
Symbiosis gene   -
Anti-CRISPR   -