Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102617
Name   oriT_pTR3 in_silico
Organism   Escherichia coli JT5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQA01000167 (29669..29751 [+], 83 nt)
oriT length   83 nt
IRs (inverted repeats)      27..34, 37..44  (AGTGCGAT..ATCGCACT)
 13..18, 32..37  (TAAATC..GATTTA)
Location of nic site      55..56
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 83 nt

>oriT_pTR3
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1950 GenBank   WP_014014966
Name   mobF_AH62_RS25045_pTR3 insolico UniProt ID   I7CZU5
Length   1068 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1068 a.a.        Molecular weight: 118452.14 Da        Isoelectric Point: 6.4309

>WP_014014966.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPDTSGT
ENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARDVELP
QHEHENHQHDHDKEGYGL

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-288)

AAA domain (AAA_30)

(480-656)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(855-899)


  Protein structure


Source ID Structure
AlphaFold DB I7CZU5


T4CP

ID   1578 GenBank   WP_014014965
Name   t4cp2_AH62_RS25050_pTR3 insolico UniProt ID   _
Length   510 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 510 a.a.        Molecular weight: 58174.11 Da        Isoelectric Point: 9.7081

>WP_014014965.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAERTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGGILQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(113-492)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3172..13454

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AH62_RS24885 181..513 + 333 WP_015060077 hypothetical protein -
AH62_RS24890 679..1287 + 609 WP_000275218 recombinase family protein -
AH62_RS24895 1284..1469 - 186 WP_014014955 ribbon-helix-helix domain-containing protein -
AH62_RS24900 1754..2062 - 309 WP_000733764 hypothetical protein -
AH62_RS24905 2066..2404 - 339 WP_000040982 hypothetical protein -
AH62_RS24910 2401..2751 - 351 WP_014014953 hypothetical protein -
AH62_RS24915 2755..3072 - 318 WP_000960955 H-NS family nucleoid-associated regulatory protein -
AH62_RS24920 3172..3954 + 783 WP_014014952 lytic transglycosylase domain-containing protein virB1
AH62_RS24930 4201..4497 + 297 WP_015060075 TrbC/VirB2 family protein virB2
AH62_RS24935 4537..4854 + 318 WP_000462629 VirB3 family type IV secretion system protein virB3
AH62_RS24940 4855..7428 + 2574 WP_014014950 VirB4 family type IV secretion/conjugal transfer ATPase virb4
AH62_RS24945 7444..8145 + 702 WP_014014949 type IV secretion system protein virB5
AH62_RS24950 8155..8397 + 243 WP_000858958 EexN family lipoprotein -
AH62_RS24955 8414..9451 + 1038 WP_014014948 type IV secretion system protein virB6
AH62_RS28930 9528..9659 + 132 WP_072000589 conjugal transfer protein TraN -
AH62_RS24960 9670..10365 + 696 WP_014014947 type IV secretion system protein virB8
AH62_RS24965 10376..11263 + 888 WP_014014946 TrbG/VirB9 family P-type conjugative transfer protein virB9
AH62_RS24970 11263..12402 + 1140 WP_014014945 type IV secretion system protein VirB10 virB10
AH62_RS24975 12453..13454 + 1002 WP_001076634 ATPase, T2SS/T4P/T4SS family virB11
AH62_RS24980 13466..13978 + 513 WP_029697418 phospholipase D family protein -
AH62_RS24985 13975..14286 + 312 WP_000570332 hypothetical protein -
AH62_RS24990 15197..15943 + 747 Protein_21 IS30-like element ISAba125 family transposase -
AH62_RS24995 15962..16993 - 1032 WP_001395480 IS630-like element ISEc33 family transposase -
AH62_RS25000 17289..18101 + 813 WP_004201164 subclass B1 metallo-beta-lactamase NDM-1 -

Host bacterium

ID   3061 GenBank   NZ_JAQA01000167
Plasmid name   pTR3 Incompatibility group   -
Plasmid size   40090 bp Coordinate of oriT [Strand]   29669..29751 [+]
Host baterium   Escherichia coli JT5

Cargo genes

Drug resistance gene   blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -