Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100436
Name   oriT_pQNR2078 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019033 (28456..29104 [+], 649 nt)
oriT length   649 nt
IRs (inverted repeats)      IR1: 198..207, 211..220  (ATTGGGTGTT..AATACCTAAT)
 IR2:319..324, 330..335  (AAAAAA..TTTTTT)
  IR3: 393..402, 405..414  (GTATTCATGC..GCATGAATAC)
Location of nic site      301..302
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 649 nt

>oriT_pQNR2078
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAACAAAAAATTGGGATCTAACCAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGGATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGAACTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACACTATTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAGAATTACATCATTATCTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   507 GenBank   YP_006903022
Name   TraI_pQNR2078 insolico UniProt ID   D7RVP6
Length   1076 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1076 a.a.        Molecular weight: 119897.16 Da        Isoelectric Point: 6.6071

>YP_006903022.1 trai protein (plasmid) [Escherichia coli]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB D7RVP6


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 6296..28128

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXG36_RS00015 (D616_p02) 2148..3581 - 1434 WP_001288433 DNA cytosine methyltransferase -
HXG36_RS00020 3675..3946 + 272 Protein_3 IS1 family transposase -
HXG36_RS00025 (D616_p04) 3966..4163 - 198 WP_013188474 hypothetical protein -
HXG36_RS00030 (D616_p25) 4168..4815 - 648 WP_001532074 restriction endonuclease -
HXG36_RS00035 (D616_p27) 4865..5098 - 234 WP_001191790 hypothetical protein -
HXG36_RS00040 (D616_p28) 5212..5526 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HXG36_RS00045 (D616_p37) 5489..5866 - 378 WP_000504250 hypothetical protein -
HXG36_RS00050 (D616_p32) 5882..6253 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HXG36_RS00055 (D616_p08) 6296..7030 + 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
HXG36_RS00060 (D616_p33) 7039..7320 + 282 WP_000440698 transcriptional repressor KorA -
HXG36_RS00065 (D616_p07) 7330..7623 + 294 WP_000209137 TrbC/VirB2 family protein virB2
HXG36_RS00070 (D616_p18) 7673..7990 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HXG36_RS00075 (D616_p17) 7990..10590 + 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXG36_RS00080 (D616_p16) 10608..11321 + 714 WP_000749362 type IV secretion system protein virB5
HXG36_RS00085 (D616_p39) 11329..11556 + 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
HXG36_RS00090 (D616_p15) 11572..12612 + 1041 WP_000886022 type IV secretion system protein virB6
HXG36_RS00095 (D616_p06) 12683..12841 + 159 WP_012561180 hypothetical protein -
HXG36_RS00100 (D616_p14) 12831..13529 + 699 WP_000646594 type IV secretion system protein virB8
HXG36_RS00105 (D616_p05) 13540..14424 + 885 WP_000735067 TrbG/VirB9 family P-type conjugative transfer protein virB9
HXG36_RS00110 (D616_p13) 14424..15584 + 1161 WP_000101712 type IV secretion system protein VirB10 virB10
HXG36_RS00115 (D616_p12) 15626..16621 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HXG36_RS00120 (D616_p31) 16621..17154 + 534 WP_000731968 phospholipase D family protein -
HXG36_RS00125 (D616_p19) 17323..18837 - 1515 Protein_24 Tn3-like element TnAs1 family transposase -
HXG36_RS00130 (D616_p21) 18903..19607 + 705 WP_001067855 IS6-like element IS26 family transposase -
HXG36_RS00135 (D616_p26) 19800..20444 - 645 WP_012954666 quinolone resistance pentapeptide repeat protein QnrB19 -
HXG36_RS00140 20538..20687 - 150 Protein_27 helix-turn-helix domain-containing protein -
HXG36_RS00145 (D616_p20) 20782..21486 + 705 WP_001067855 IS6-like element IS26 family transposase -
HXG36_RS00150 (D616_p30) 21635..22510 + 876 WP_000983082 methyl-accepting chemotaxis protein -
HXG36_RS00155 (D616_p38) 22743..23369 - 627 WP_000434930 DUF6710 family protein -
HXG36_RS00160 (D616_p11) 23369..26599 - 3231 WP_000884351 MobF family relaxase -
HXG36_RS00165 (D616_p10) 26599..28128 - 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
HXG36_RS00170 (D616_p09) 28130..28546 - 417 WP_001532083 hypothetical protein -
HXG36_RS00260 29059..29478 + 420 WP_000802909 plasmid stabilization protein StbA -
HXG36_RS00180 (D616_p23) 29487..30203 + 717 WP_000861577 StbB family protein -
HXG36_RS00185 (D616_p22) 30205..30573 + 369 WP_000414913 plasmid stabilization protein StbC -
HXG36_RS00190 (D616_p29) 30755..31099 + 345 WP_000999874 hypothetical protein -
HXG36_RS00195 (D616_p40) 31210..31530 - 321 WP_000211832 protein CcgAII -
HXG36_RS00200 (D616_p44) 31585..31764 - 180 WP_000214483 protein CcgAI -
HXG36_RS00205 (D616_p45) 32596..33105 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   897 GenBank   NC_019033
Plasmid name   pQNR2078 Incompatibility group   IncN
Plasmid size   42379 bp Coordinate of oriT [Strand]   28456..29104 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   qnrB19
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -