Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100567
Name   oriT_pEcNDM1 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_023909 (44820..45446 [+], 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_pEcNDM1
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   639 GenBank   YP_009023148
Name   PutativerelaxaseofpEcNDM1 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_009023148.1 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: 24644..44492

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTA19_RS00120 (B634_00031) 20489..21922 - 1434 WP_001288432 DNA cytosine methyltransferase -
HTA19_RS00125 (B634_00032) 22021..22293 + 273 Protein_24 IS1 family transposase -
HTA19_RS00130 (B634_00033) 22304..22510 - 207 WP_001749967 hypothetical protein -
HTA19_RS00135 (B634_00034) 22515..23162 - 648 WP_015344958 restriction endonuclease -
HTA19_RS00140 (B634_00035) 23212..23445 - 234 WP_001191790 hypothetical protein -
HTA19_RS00145 (B634_00036) 23559..23873 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTA19_RS00150 (B634_00037) 23870..24214 - 345 WP_001749964 hypothetical protein -
HTA19_RS00155 24230..24601 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTA19_RS00160 (B634_00040) 24644..25378 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTA19_RS00165 (B634_00041) 25387..25668 + 282 WP_000440698 transcriptional repressor KorA -
HTA19_RS00170 (B634_00042) 25678..25971 + 294 WP_001749962 hypothetical protein virB2
HTA19_RS00175 (B634_00043) 26021..26338 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTA19_RS00180 (B634_00044) 26338..28938 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTA19_RS00185 (B634_00045) 28956..29669 + 714 WP_001749960 type IV secretion system protein virB5
HTA19_RS00190 (B634_00046) 29677..29904 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTA19_RS00195 (B634_00047) 29920..30960 + 1041 WP_001749958 type IV secretion system protein virB6
HTA19_RS00200 (B634_00048) 31031..31189 + 159 WP_012561180 hypothetical protein -
HTA19_RS00205 (B634_00049) 31179..31877 + 699 WP_000646594 type IV secretion system protein virB8
HTA19_RS00210 (B634_00050) 31888..32772 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTA19_RS00215 (B634_00051) 32772..33932 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTA19_RS00220 (B634_00052) 33974..34969 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTA19_RS00225 (B634_00053) 34969..35502 + 534 WP_000792636 phospholipase D family protein -
HTA19_RS00365 (B634_00054) 35676..36128 - 453 WP_001749956 DUF6710 family protein -
HTA19_RS00235 (B634_00055) 36439..36681 + 243 WP_000844627 transposase -
HTA19_RS00240 (B634_00056) 36713..37363 - 651 WP_000164043 tetracycline resistance transcriptional repressor TetR(A) -
HTA19_RS00245 (B634_00057) 37469..38668 + 1200 WP_012579085 tetracycline efflux MFS transporter Tet(A) -
HTA19_RS00250 (B634_00058) 38700..39353 - 654 Protein_49 EamA family transporter -
HTA19_RS00255 (B634_00059) 39548..39721 - 174 WP_001749978 hypothetical protein -
HTA19_RS00260 (B634_00060) 39721..42963 - 3243 WP_001749977 MobF family relaxase -
HTA19_RS00265 (B634_00061) 42963..44492 - 1530 WP_001749976 type IV secretion system DNA-binding domain-containing protein virb4
HTA19_RS00270 (B634_00062) 44494..44910 - 417 WP_001749975 hypothetical protein -
HTA19_RS00370 (B634_00063) 45401..45820 + 420 WP_001749974 plasmid stabilization protein StbA -
HTA19_RS00280 (B634_00064) 45829..46545 + 717 WP_001749973 StbB family protein -
HTA19_RS00285 (B634_00065) 46547..46915 + 369 WP_001749972 plasmid stabilization protein StbC -
HTA19_RS00290 (B634_00066) 47097..47441 + 345 WP_000999874 hypothetical protein -
HTA19_RS00295 (B634_00068) 47552..47872 - 321 WP_001749971 protein CcgAII -
HTA19_RS00300 (B634_00069) 47927..48106 - 180 WP_000214483 protein CcgAI -
HTA19_RS00305 (B634_00072) 48833..49342 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   1027 GenBank   NC_023909
Plasmid name   pEcNDM1 Incompatibility group   IncN
Plasmid size   58228 bp Coordinate of oriT [Strand]   44820..45446 [+]
Host baterium   Escherichia coli

Cargo genes

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