Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100645
Name   oriT_pKPC-47e in_silico
Organism   Enterobacter hormaechei subsp. hoffmannii ECNIH3
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP008901 (36381..37007 [+], 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_pKPC-47e
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   717 GenBank   WP_012561166
Name   Relaxase_pKPC-47e insolico UniProt ID   A0A1B0VMV6
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

>WP_012561166.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
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


Source ID Structure
AlphaFold DB A0A1B0VMV6


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11795..22120

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ECNIH3_RS23990 (ECNIH3_24090) 7640..9073 - 1434 WP_001288432 DNA cytosine methyltransferase -
ECNIH3_RS23995 (ECNIH3_24095) 9172..9444 + 273 Protein_10 IS1 family transposase -
ECNIH3_RS24000 9455..9661 - 207 WP_001749967 hypothetical protein -
ECNIH3_RS24005 (ECNIH3_24100) 9666..10313 - 648 WP_012561184 restriction endonuclease -
ECNIH3_RS24010 (ECNIH3_24105) 10363..10674 - 312 WP_001452736 hypothetical protein -
ECNIH3_RS24015 (ECNIH3_24110) 10710..11024 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
ECNIH3_RS24020 (ECNIH3_24115) 11021..11365 - 345 WP_001749964 hypothetical protein -
ECNIH3_RS24025 (ECNIH3_24120) 11381..11686 - 306 WP_000960954 H-NS family nucleoid-associated regulatory protein -
ECNIH3_RS24030 (ECNIH3_24125) 11795..12529 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
ECNIH3_RS24035 (ECNIH3_24130) 12538..12819 + 282 WP_000440698 transcriptional repressor KorA -
ECNIH3_RS24040 (ECNIH3_24135) 12829..13122 + 294 WP_001749962 hypothetical protein virB2
ECNIH3_RS24045 (ECNIH3_24140) 13172..13489 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
ECNIH3_RS24050 (ECNIH3_24145) 13621..16089 + 2469 WP_224743086 VirB4 family type IV secretion/conjugal transfer ATPase virb4
ECNIH3_RS24055 (ECNIH3_24150) 16107..16820 + 714 WP_001749960 type IV secretion system protein virB5
ECNIH3_RS24060 (ECNIH3_24155) 16828..17055 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
ECNIH3_RS24065 (ECNIH3_24160) 17071..18111 + 1041 WP_001749958 type IV secretion system protein virB6
ECNIH3_RS26575 18212..18340 + 129 WP_071882546 conjugal transfer protein TraN -
ECNIH3_RS24070 (ECNIH3_24165) 18330..19028 + 699 WP_000646594 type IV secretion system protein virB8
ECNIH3_RS24075 (ECNIH3_24170) 19039..19923 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
ECNIH3_RS24080 (ECNIH3_24175) 19923..21083 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
ECNIH3_RS24085 (ECNIH3_24180) 21125..22120 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
ECNIH3_RS24090 (ECNIH3_24185) 22120..22653 + 534 WP_000792636 phospholipase D family protein -
ECNIH3_RS26580 22827..23114 - 288 Protein_31 DUF6710 family protein -
ECNIH3_RS25445 23381..23560 + 180 Protein_32 helix-turn-helix domain-containing protein -
ECNIH3_RS25450 23625..24185 + 561 Protein_33 IS6-like element IS26 family transposase -
ECNIH3_RS24110 (ECNIH3_24205) 24205..26316 - 2112 Protein_34 Tn3-like element Tn3 family transposase -

Host bacterium

ID   1105 GenBank   NZ_CP008901
Plasmid name   pKPC-47e Incompatibility group   IncN
Plasmid size   50333 bp Coordinate of oriT [Strand]   36381..37007 [+]
Host baterium   Enterobacter hormaechei subsp. hoffmannii ECNIH3

Cargo genes

Drug resistance gene   dfrA14, blaKPC-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -