Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100359
Name   oriT_pKOX105 in_silico
Organism   Klebsiella oxytoca KOX105
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_014208 (33559..34185 [-], 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_pKOX105
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   430 GenBank   YP_003675776
Name   TraI_pKOX105 insolico UniProt ID   D7RU03
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_003675776.1 TraI (plasmid) [Klebsiella oxytoca KOX105]
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 D7RU03


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 5428..15753

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS712_RS00010 (pKOX105p02) 1273..2706 - 1434 WP_001288432 DNA cytosine methyltransferase -
HS712_RS00015 2805..3077 + 273 Protein_2 IS1 family transposase -
HS712_RS00020 3088..3294 - 207 WP_001749967 hypothetical protein -
HS712_RS00025 (pKOX105p03) 3299..3946 - 648 WP_015344958 restriction endonuclease -
HS712_RS00030 3996..4229 - 234 WP_001191790 hypothetical protein -
HS712_RS00035 (pKOX105p04) 4343..4657 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HS712_RS00040 (pKOX105p05) 4654..4998 - 345 WP_001749964 hypothetical protein -
HS712_RS00045 (pKOX105p06) 5014..5385 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HS712_RS00050 (pKOX105p07) 5428..6162 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HS712_RS00055 (pKOX105p08) 6171..6452 + 282 WP_000440698 transcriptional repressor KorA -
HS712_RS00060 (pKOX105p09) 6462..6755 + 294 WP_001749962 hypothetical protein virB2
HS712_RS00065 (pKOX105p10) 6805..7122 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HS712_RS00070 (pKOX105p11) 7122..9722 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS712_RS00075 (pKOX105p12) 9740..10453 + 714 WP_001749960 type IV secretion system protein virB5
HS712_RS00080 (pKOX105p13) 10461..10688 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HS712_RS00085 (pKOX105p14) 10704..11744 + 1041 WP_001749958 type IV secretion system protein virB6
HS712_RS00090 11815..11973 + 159 WP_012561180 hypothetical protein -
HS712_RS00095 (pKOX105p15) 11963..12661 + 699 WP_000646594 type IV secretion system protein virB8
HS712_RS00100 (pKOX105p16) 12672..13556 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS712_RS00105 (pKOX105p17) 13556..14716 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HS712_RS00110 (pKOX105p18) 14758..15753 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HS712_RS00115 (pKOX105p19) 15753..16286 + 534 WP_000792636 phospholipase D family protein -
HS712_RS00380 16459..16746 - 288 Protein_23 DUF6710 family protein -
HS712_RS00130 17013..17192 + 180 Protein_24 helix-turn-helix domain-containing protein -
HS712_RS00135 (pKOX105p21) 17257..17961 + 705 WP_001067855 IS6-like element IS26 family transposase -
HS712_RS00140 18013..18138 - 126 Protein_26 APH(3') family aminoglycoside O-phosphotransferase -
HS712_RS00145 (pKOX105p22) 18209..18763 - 555 WP_003159191 aminoglycoside N-acetyltransferase AAC(6')-Ib4 -
HS712_RS00150 (pKOX105p23) 18871..19671 - 801 WP_013263789 subclass B1 metallo-beta-lactamase VIM-1 -

Host bacterium

ID   820 GenBank   NC_014208
Plasmid name   pKOX105 Incompatibility group   IncN
Plasmid size   54641 bp Coordinate of oriT [Strand]   33559..34185 [-]
Host baterium   Klebsiella oxytoca KOX105

Cargo genes

Drug resistance gene   blaVIM-1, qnrS1, blaSHV-12, dfrA14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -