Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100568
Name   oriT_pEcNDM0 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_023910 (40008..40634 [+], 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_pEcNDM0
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   640 GenBank   YP_009023229
Name   PutativerelaxaseofpEcNDM0 insolico UniProt ID   F6IB82
Length   1080 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1080 a.a.        Molecular weight: 120419.59 Da        Isoelectric Point: 6.5483

>YP_009023229.1 conjugal transfer protein (plasmid) [Escherichia coli]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLSQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEHEEGGHEI

  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 F6IB82


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 19832..39680

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTA45_RS00090 (pEcNDM0_00031) 15677..17110 - 1434 WP_001288432 DNA cytosine methyltransferase -
HTA45_RS00095 (pEcNDM0_00032) 17209..17481 + 273 Protein_18 IS1 family transposase -
HTA45_RS00100 (pEcNDM0_00033) 17492..17698 - 207 WP_001749967 hypothetical protein -
HTA45_RS00105 (pEcNDM0_00034) 17703..18350 - 648 WP_015344958 restriction endonuclease -
HTA45_RS00110 (pEcNDM0_00035) 18400..18633 - 234 WP_001191790 hypothetical protein -
HTA45_RS00115 (pEcNDM0_00036) 18747..19061 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTA45_RS00120 (pEcNDM0_00037) 19058..19402 - 345 WP_001749964 hypothetical protein -
HTA45_RS00125 19418..19789 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTA45_RS00130 (pEcNDM0_00040) 19832..20566 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTA45_RS00135 (pEcNDM0_00041) 20575..20856 + 282 WP_000440698 transcriptional repressor KorA -
HTA45_RS00140 (pEcNDM0_00042) 20866..21159 + 294 WP_001749962 hypothetical protein virB2
HTA45_RS00145 (pEcNDM0_00043) 21209..21526 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTA45_RS00150 (pEcNDM0_00044) 21526..24126 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTA45_RS00155 (pEcNDM0_00045) 24144..24857 + 714 WP_001749960 type IV secretion system protein virB5
HTA45_RS00160 (pEcNDM0_00046) 24865..25092 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTA45_RS00165 (pEcNDM0_00047) 25108..26148 + 1041 WP_001749958 type IV secretion system protein virB6
HTA45_RS00170 (pEcNDM0_00048) 26219..26377 + 159 WP_012561180 hypothetical protein -
HTA45_RS00175 (pEcNDM0_00049) 26367..27065 + 699 WP_000646594 type IV secretion system protein virB8
HTA45_RS00180 (pEcNDM0_00050) 27076..27960 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTA45_RS00185 (pEcNDM0_00051) 27960..29120 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTA45_RS00190 (pEcNDM0_00052) 29162..30157 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTA45_RS00195 (pEcNDM0_00053) 30157..30690 + 534 WP_000792636 phospholipase D family protein -
HTA45_RS00335 (pEcNDM0_00054) 30864..31316 - 453 WP_001749956 DUF6710 family protein -
HTA45_RS00205 (pEcNDM0_00055) 31627..31869 + 243 WP_000844627 transposase -
HTA45_RS00210 (pEcNDM0_00056) 31901..32551 - 651 WP_000164043 tetracycline resistance transcriptional repressor TetR(A) -
HTA45_RS00215 (pEcNDM0_00057) 32657..33856 + 1200 WP_012579085 tetracycline efflux MFS transporter Tet(A) -
HTA45_RS00220 (pEcNDM0_00058) 33888..34541 - 654 Protein_43 EamA family transporter -
HTA45_RS00225 (pEcNDM0_00059) 34736..34909 - 174 WP_001749978 hypothetical protein -
HTA45_RS00230 (pEcNDM0_00060) 34909..38151 - 3243 WP_001749977 MobF family relaxase -
HTA45_RS00235 (pEcNDM0_00061) 38151..39680 - 1530 WP_001749976 type IV secretion system DNA-binding domain-containing protein virb4
HTA45_RS00240 (pEcNDM0_00062) 39682..40098 - 417 WP_001749975 hypothetical protein -
HTA45_RS00340 (pEcNDM0_00063) 40589..41008 + 420 WP_001749974 plasmid stabilization protein StbA -
HTA45_RS00250 (pEcNDM0_00064) 41017..41733 + 717 WP_001749973 StbB family protein -
HTA45_RS00255 (pEcNDM0_00065) 41735..42103 + 369 WP_001749972 plasmid stabilization protein StbC -
HTA45_RS00260 (pEcNDM0_00066) 42285..42629 + 345 WP_000999874 hypothetical protein -
HTA45_RS00265 (pEcNDM0_00068) 42740..43060 - 321 WP_001749971 protein CcgAII -
HTA45_RS00270 (pEcNDM0_00069) 43115..43294 - 180 WP_000214483 protein CcgAI -
HTA45_RS00275 (pEcNDM0_00072) 44021..44530 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   1028 GenBank   NC_023910
Plasmid name   pEcNDM0 Incompatibility group   IncN
Plasmid size   53416 bp Coordinate of oriT [Strand]   40008..40634 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, blaOXA-1, catB3, ARR-3, qacE, sul1, qnrA7, tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -