Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100132
Name   oriT_pE001 in_silico
Organism   Escherichia coli
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_019067 (7136..7161 [-], 26 nt)
oriT length   26 nt
IRs (inverted repeats)     _
Location of nic site      18..19
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   putative oriT of IncX1 plasmids

  oriT sequence  


Download         Length: 26 nt

>oriT_pE001
GGCGTTTGCCCTATCCTGCATCACAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   127 GenBank   YP_006953019
Name   TaxC_pE001 insolico UniProt ID   G1CCM2
Length   388 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 388 a.a.        Molecular weight: 44446.83 Da        Isoelectric Point: 10.5067

>YP_006953019.1 TaxC (plasmid) [Escherichia coli]
MGVYVDKEYRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKEHMIDRANDPQHVMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDIGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFLGL

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(70-228)


  Protein structure


Source ID Structure
AlphaFold DB G1CCM2

  Reference


[1] Bielak E et al. (2011) Investigation of diversity of plasmids carrying the blaTEM-52 gene. J Antimicrob Chemother. 66(11):2465-74. [PMID:21831988]


Auxiliary protein

ID   190 GenBank   YP_006953020
Name   TaxA_pE001 insolico UniProt ID   G1CCM3
Length   204 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 204 a.a.        Molecular weight: 24095.65 Da        Isoelectric Point: 8.0185

>YP_006953020.1 TaxA (plasmid) [Escherichia coli]
MTSLTPFRNICPVTYSRFLLENFMKKVQFRIDENQHDDLLDCLKTLYPDEPALTVAKGMKLLANALLKSK
AVSKDINTFFDNNDFIKTTMYLTGKQRADIERAANRHGWTLSRECRYRIQTTLENELDFFDQELLMMNRC
RNSIDKIGRNFHYIIVNDQTRVLDKDGFYQDAERLTTEIFNLKNQFENYIMLCKGRTVSNKVEM

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB G1CCM3


T4CP

ID   127 GenBank   YP_006953056
Name   TaxB_pE001 insolico UniProt ID   G1CCQ9
Length   611 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 611 a.a.        Molecular weight: 69306.20 Da        Isoelectric Point: 6.9121

>YP_006953056.1 TaxB (plasmid) [Escherichia coli]
MSLKLPDKGQWVFIGLVMCLVTYYAGSVSVYFLNGKTPLYIWKNFDSMLLWKIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFVIWQLNKMDVALYGDAKFASDNDLKKSKLLKWETENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVFSI
GSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAKIS
EKLGYITTTSKSTSKSRGRSASQGESESEARRALVLPQELGTLDFKEEFIILKGENPVKAEKALYYLDPY
FMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(102-571)

  Protein structure


Source ID Structure
AlphaFold DB G1CCQ9


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 27642..37601

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS777_RS00170 (E001_24) 22985..23305 - 321 WP_001020837 hypothetical protein -
HS777_RS00175 (E001_25) 23365..23769 - 405 WP_001576899 hypothetical protein -
HS777_RS00180 (E001_26) 23785..24222 - 438 WP_250696074 thermonuclease family protein -
HS777_RS00185 (E001_27) 24317..24751 - 435 WP_001579348 hypothetical protein -
HS777_RS00190 24833..24991 - 159 WP_250133465 hypothetical protein -
HS777_RS00195 (E001_28) 25095..25397 - 303 WP_001576896 TrbM/KikA/MpfK family conjugal transfer protein -
HS777_RS00200 (E001_29) 25394..25807 - 414 WP_001579347 cag pathogenicity island Cag12 family protein -
HS777_RS00205 (E001_30) 25804..27639 - 1836 WP_001579346 type IV secretory system conjugative DNA transfer family protein -
HS777_RS00210 (E001_31) 27642..28673 - 1032 WP_001058476 P-type DNA transfer ATPase VirB11 virB11
HS777_RS00215 (E001_32) 28675..29880 - 1206 WP_001579345 VirB10/TraB/TrbI family type IV secretion system protein virB10
HS777_RS00220 (E001_33) 29877..30806 - 930 WP_000783381 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS777_RS00225 (E001_34) 30811..31524 - 714 WP_001579343 type IV secretion system protein virB8
HS777_RS00270 (E001_50) 31514..31642 - 129 WP_001328099 hypothetical protein -
HS777_RS00230 (E001_35) 31769..32902 - 1134 WP_001576910 type IV secretion system protein virB6
HS777_RS00235 (E001_36) 32912..33139 - 228 WP_000835348 EexN family lipoprotein -
HS777_RS00240 (E001_37) 33140..33898 - 759 WP_000744201 type IV secretion system protein -
HS777_RS00245 (E001_38) 33909..36662 - 2754 WP_001363160 VirB3 family type IV secretion system protein virb4
HS777_RS00250 (E001_39) 36681..36977 - 297 WP_000040716 TrbC/VirB2 family protein virB2
HS777_RS00255 (E001_40) 37086..37601 - 516 WP_250696073 lytic transglycosylase domain-containing protein virB1
HS777_RS00260 37634..37846 - 213 WP_000125172 hypothetical protein -
HS777_RS00265 (E001_41) 37776..38294 - 519 WP_001446885 transcription termination/antitermination NusG family protein -

Host bacterium

ID   127 GenBank   NC_019067
Plasmid name   pE001 Incompatibility group   IncX3
Plasmid size   38611 bp Coordinate of oriT [Strand]   7136..7161 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   carrying the blaTEM-52 gene
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -