Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100545
Name   oriT_pNDM-BTR in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_022375 (13873..14499 [-], 627 nt)
oriT length   627 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: 627 nt

>oriT_pNDM-BTR
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   616 GenBank   YP_008574914
Name   TraI_pNDM-BTR insolico UniProt ID   _
Length   1078 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120141.30 Da        Isoelectric Point: 6.5229

>YP_008574914.1 TraI (plasmid) [Escherichia coli]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  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



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 10964..21290

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTB89_RS00045 6809..8242 - 1434 WP_001288432 DNA cytosine methyltransferase -
HTB89_RS00050 8341..8613 + 273 Protein_10 IS1 family transposase -
HTB89_RS00055 8624..8830 - 207 WP_001749967 hypothetical protein -
HTB89_RS00060 8835..9482 - 648 WP_015344958 restriction endonuclease -
HTB89_RS00065 9532..9765 - 234 WP_001191790 hypothetical protein -
HTB89_RS00070 9879..10193 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTB89_RS00075 10190..10534 - 345 WP_001749964 hypothetical protein -
HTB89_RS00080 10550..10921 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTB89_RS00085 10964..11698 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTB89_RS00090 11707..11988 + 282 WP_000440698 transcriptional repressor KorA -
HTB89_RS00095 11998..12291 + 294 WP_001749962 hypothetical protein virB2
HTB89_RS00100 12341..12658 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTB89_RS00105 12658..15258 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTB89_RS00110 15276..15989 + 714 WP_001749960 type IV secretion system protein virB5
HTB89_RS00115 15997..16224 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTB89_RS00120 16240..17280 + 1041 WP_001749958 type IV secretion system protein virB6
HTB89_RS00125 17351..17509 + 159 WP_012561180 hypothetical protein -
HTB89_RS00130 17499..18197 + 699 WP_000646594 type IV secretion system protein virB8
HTB89_RS00135 18208..19092 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTB89_RS00140 19092..20252 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTB89_RS00145 20295..21290 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTB89_RS00150 21290..21823 + 534 WP_000792636 phospholipase D family protein -
HTB89_RS00155 21904..22608 - 705 WP_001067855 IS6-like element IS26 family transposase -
HTB89_RS00160 22599..22835 + 237 WP_021740577 hypothetical protein -
HTB89_RS00165 22825..22953 - 129 WP_002210551 DUF6710 family protein -
HTB89_RS00170 23379..23558 + 180 Protein_34 helix-turn-helix domain-containing protein -
HTB89_RS00175 23623..24327 + 705 WP_001067855 IS6-like element IS26 family transposase -
HTB89_RS00180 24381..25012 - 632 Protein_36 transposase -
HTB89_RS00185 25407..26063 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -

Host bacterium

ID   1005 GenBank   NC_022375
Plasmid name   pNDM-BTR Incompatibility group   IncN
Plasmid size   59400 bp Coordinate of oriT [Strand]   13873..14499 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   dfrA14, qnrS1, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -