Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100585
Name   oriT_pKo6 in_silico
Organism   Klebsiella pneumoniae subsp. ozaenae
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_025019 (52141..52767 [+], 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_pKo6
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   657 GenBank   YP_009062936
Name   TraI_pKo6 insolico UniProt ID   U3RB47
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_009062936.1 TraI,conjugal nickase and helicase (plasmid) [Klebsiella pneumoniae subsp. ozaenae]
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 U3RB47


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 16002..26327

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTB36_RS00075 (pKo6_0016) 11847..13280 - 1434 WP_001288432 DNA cytosine methyltransferase -
HTB36_RS00080 (pKo6_0017) 13379..13651 + 273 Protein_16 IS1 family transposase -
HTB36_RS00085 (pKo6_0018) 13662..13868 - 207 WP_001749967 hypothetical protein -
HTB36_RS00090 (pKo6_0019) 13873..14520 - 648 WP_015344958 restriction endonuclease -
HTB36_RS00095 (pKo6_0020) 14570..14803 - 234 WP_001191790 hypothetical protein -
HTB36_RS00100 (pKo6_0021) 14917..15231 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTB36_RS00105 (pKo6_0022) 15228..15572 - 345 WP_001749964 hypothetical protein -
HTB36_RS00110 15588..15959 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTB36_RS00115 (pKo6_0023) 16002..16736 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTB36_RS00120 (pKo6_0024) 16745..17026 + 282 WP_000440698 transcriptional repressor KorA -
HTB36_RS00125 (pKo6_0025) 17036..17329 + 294 WP_001749962 hypothetical protein virB2
HTB36_RS00130 (pKo6_0026) 17379..17696 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTB36_RS00135 (pKo6_0027) 17696..20296 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTB36_RS00140 (pKo6_0028) 20314..21027 + 714 WP_001749960 type IV secretion system protein virB5
HTB36_RS00145 (pKo6_0029) 21035..21262 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTB36_RS00150 (pKo6_0030) 21278..22318 + 1041 WP_001749958 type IV secretion system protein virB6
HTB36_RS00155 (pKo6_0031) 22389..22547 + 159 WP_012561180 hypothetical protein -
HTB36_RS00160 (pKo6_0032) 22537..23235 + 699 WP_000646594 type IV secretion system protein virB8
HTB36_RS00165 (pKo6_0033) 23246..24130 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTB36_RS00170 (pKo6_0034) 24130..25290 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTB36_RS00175 (pKo6_0035) 25332..26327 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTB36_RS00180 (pKo6_0036) 26327..26860 + 534 WP_000792636 phospholipase D family protein -
HTB36_RS00415 27034..27321 - 288 Protein_37 DUF6710 family protein -
HTB36_RS00200 (pKo6_0040) 28418..29809 - 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
HTB36_RS00205 (pKo6_0041) 29846..30418 - 573 WP_001493762 recombinase family protein -
HTB36_RS00210 (pKo6_0042) 30555..31100 - 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -

Host bacterium

ID   1045 GenBank   NC_025019
Plasmid name   pKo6 Incompatibility group   IncN
Plasmid size   65549 bp Coordinate of oriT [Strand]   52141..52767 [+]
Host baterium   Klebsiella pneumoniae subsp. ozaenae

Cargo genes

Drug resistance gene   blaKPC-2, dfrA14, qnrS1, aac(6')-Ib-cr, ARR-3, blaTEM-1B, blaCTX-M-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -