Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100544
Name   oriT_pHKU1 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_022374 (40965..41591 [+], 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_pHKU1
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTTGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   615 GenBank   YP_008574857
Name   TraI_pHKU1 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_008574857.1 TraI, conjugal nickase and helicase (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: 20528..40637

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTB37_RS00105 (pHKU1_18) 16054..16203 + 150 Protein_20 LysR family transcriptional regulator -
HTB37_RS00110 (pHKU1_19) 16197..16616 + 420 WP_012579083 fosfomycin resistance glutathione transferase FosA5 -
HTB37_RS00115 (pHKU1_20) 17478..18686 + 1209 WP_001339197 IS4-like element ISVsa5 family transposase -
HTB37_RS00355 18699..19040 - 342 Protein_23 restriction endonuclease -
HTB37_RS00125 (pHKU1_21) 19096..19329 - 234 WP_001191790 hypothetical protein -
HTB37_RS00130 (pHKU1_22) 19443..19757 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTB37_RS00135 19754..20098 - 345 WP_001749964 hypothetical protein -
HTB37_RS00140 (pHKU1_23) 20114..20485 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTB37_RS00145 (pHKU1_24) 20528..21262 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTB37_RS00150 (pHKU1_25) 21271..21552 + 282 WP_000440698 transcriptional repressor KorA -
HTB37_RS00155 (pHKU1_26) 21562..21855 + 294 WP_001749962 hypothetical protein virB2
HTB37_RS00160 (pHKU1_27) 21905..22222 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTB37_RS00165 (pHKU1_28) 22222..24822 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTB37_RS00170 (pHKU1_29) 24840..25553 + 714 WP_001749960 type IV secretion system protein virB5
HTB37_RS00175 (pHKU1_30) 25561..25788 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTB37_RS00180 (pHKU1_31) 25804..26844 + 1041 WP_001749958 type IV secretion system protein virB6
HTB37_RS00185 (pHKU1_32) 26915..27073 + 159 WP_012561180 hypothetical protein -
HTB37_RS00190 (pHKU1_33) 27063..27761 + 699 WP_000646594 type IV secretion system protein virB8
HTB37_RS00195 (pHKU1_34) 27772..28656 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTB37_RS00200 (pHKU1_35) 28656..29816 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTB37_RS00205 (pHKU1_36) 29858..30853 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTB37_RS00210 (pHKU1_37) 30853..31386 + 534 WP_000792636 phospholipase D family protein -
HTB37_RS00215 31560..31688 - 129 WP_002210551 DUF6710 family protein -
HTB37_RS00360 31950..32273 - 324 WP_226331933 DUF6710 family protein -
HTB37_RS00225 (pHKU1_40) 32547..33200 + 654 Protein_44 EamA family transporter -
HTB37_RS00230 (pHKU1_41) 33232..34431 - 1200 WP_012579085 tetracycline efflux MFS transporter Tet(A) -
HTB37_RS00235 (pHKU1_42) 34537..35187 + 651 WP_000164043 tetracycline resistance transcriptional repressor TetR(A) -
HTB37_RS00240 (pHKU1_43) 35219..35461 - 243 WP_000844627 transposase -
HTB37_RS00245 35693..35866 - 174 WP_001749978 hypothetical protein -
HTB37_RS00250 (pHKU1_45) 35866..39108 - 3243 WP_001749977 MobF family relaxase -
HTB37_RS00255 (pHKU1_46) 39108..40637 - 1530 WP_001749976 type IV secretion system DNA-binding domain-containing protein virb4
HTB37_RS00260 (pHKU1_47) 40639..41055 - 417 WP_001749975 hypothetical protein -
HTB37_RS00365 (pHKU1_48) 41546..41965 + 420 WP_001749974 plasmid stabilization protein StbA -
HTB37_RS00270 (pHKU1_49) 41974..42690 + 717 WP_001749973 StbB family protein -
HTB37_RS00275 (pHKU1_50) 42692..43060 + 369 WP_000414913 plasmid stabilization protein StbC -
HTB37_RS00280 (pHKU1_51) 43242..43586 + 345 WP_000999874 hypothetical protein -
HTB37_RS00285 (pHKU1_53) 43697..44017 - 321 WP_001749971 protein CcgAII -
HTB37_RS00290 (pHKU1_54) 44072..44251 - 180 WP_000214483 protein CcgAI -
HTB37_RS00295 (pHKU1_58) 44978..45487 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   1004 GenBank   NC_022374
Plasmid name   pHKU1 Incompatibility group   IncN
Plasmid size   54373 bp Coordinate of oriT [Strand]   40965..41591 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, blaOXA-1, catB3, ARR-3, qacE, sul1, fosA5, tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -