Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100043
Name   oriT_pKP96 in_silico
Organism   Klebsiella pneumoniae
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_011617 (54738..54747 [+], 10 nt)
oriT length   10 nt
IRs (inverted repeats)     _
Location of nic site      5..6
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   _

  oriT sequence  


Download         Length: 10 nt

>oriT_pKP96
GGTGTATAGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Shen P et al. (2008) Complete nucleotide sequence of pKP96, a 67 850 bp multiresistance plasmid encoding qnrA1, aac(6')-Ib-cr and blaCTX-M-24 from Klebsiella pneumoniae. J Antimicrob Chemother. 62(6):1252-6. [PMID:18812424]


Relaxase

ID   41 GenBank   YP_002332893
Name   TraI_pKP96 insolico UniProt ID   B6RFQ5
Length   1080 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 1080 a.a.        Molecular weight: 120419.59 Da        Isoelectric Point: 6.5483

>YP_002332893.1 conjugal transfer protein (plasmid) [Klebsiella pneumoniae]
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 B6RFQ5

  Reference


[1] Shen P et al. (2008) Complete nucleotide sequence of pKP96, a 67 850 bp multiresistance plasmid encoding qnrA1, aac(6')-Ib-cr and blaCTX-M-24 from Klebsiella pneumoniae. J Antimicrob Chemother. 62(6):1252-6. [PMID:18812424]


Auxiliary protein

ID   69 GenBank   YP_002332895
Name   TraK_pKP96 insolico UniProt ID   B6RFQ7
Length   138 a.a. PDB ID   _
Note   conjugal transfer protein

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15332.60 Da        Isoelectric Point: 5.9670

>YP_002332895.1 conjugal transfer protein (plasmid) [Klebsiella pneumoniae]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB B6RFQ7


T4CP

ID   41 GenBank   YP_002332894
Name   TraJ_pKP96 insolico UniProt ID   B6RFQ6
Length   509 a.a. PDB ID   _
Note   conjugal transfer protein; Type IV secretion-system coupling protein DNA-binding domain

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57679.73 Da        Isoelectric Point: 9.5788

>YP_002332894.1 conjugal transfer protein (plasmid) [Klebsiella pneumoniae]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVSARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELRDI

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(113-489)

  Protein structure


Source ID Structure
AlphaFold DB B6RFQ6


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 34005..54114

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS484_RS00165 (pKP96_028) 30955..32163 + 1209 WP_001339197 IS4-like element ISVsa5 family transposase -
HS484_RS00405 32176..32517 - 342 Protein_33 restriction endonuclease -
HS484_RS00175 (pKP96_029) 32573..32806 - 234 WP_001191790 hypothetical protein -
HS484_RS00180 (pKP96_030) 32920..33234 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HS484_RS00185 (pKP96_031) 33231..33575 - 345 WP_001749964 hypothetical protein -
HS484_RS00190 (pKP96_032) 33591..33962 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HS484_RS00195 (pKP96_033) 34005..34739 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HS484_RS00200 (pKP96_034) 34748..35029 + 282 WP_000440698 transcriptional repressor KorA -
HS484_RS00205 (pKP96_035) 35039..35332 + 294 WP_001749962 hypothetical protein virB2
HS484_RS00210 (pKP96_036) 35382..35699 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HS484_RS00215 (pKP96_037) 35699..38299 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS484_RS00220 (pKP96_038) 38317..39030 + 714 WP_001749960 type IV secretion system protein virB5
HS484_RS00225 (pKP96_039) 39038..39265 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HS484_RS00230 (pKP96_040) 39281..40321 + 1041 WP_001749958 type IV secretion system protein virB6
HS484_RS00235 (pKP96_041) 40392..40550 + 159 WP_012561180 hypothetical protein -
HS484_RS00240 (pKP96_042) 40540..41238 + 699 WP_000646594 type IV secretion system protein virB8
HS484_RS00245 (pKP96_043) 41249..42133 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS484_RS00250 (pKP96_044) 42133..43293 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HS484_RS00255 (pKP96_045) 43335..44330 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HS484_RS00260 (pKP96_046) 44330..44863 + 534 WP_000792636 phospholipase D family protein -
HS484_RS00265 45037..45222 - 186 WP_315970982 DUF6710 family protein -
HS484_RS00410 45427..45750 - 324 WP_226331933 DUF6710 family protein -
HS484_RS00275 (pKP96_049) 46024..46677 + 654 Protein_54 EamA family transporter -
HS484_RS00280 (pKP96_050) 46709..47908 - 1200 WP_012579085 tetracycline efflux MFS transporter Tet(A) -
HS484_RS00285 (pKP96_051) 48014..48664 + 651 WP_000164043 tetracycline resistance transcriptional repressor TetR(A) -
HS484_RS00290 (pKP96_051a) 48696..48938 - 243 WP_000844627 transposase -
HS484_RS00295 (pKP96_052) 49170..49343 - 174 WP_001749978 hypothetical protein -
HS484_RS00300 (pKP96_053) 49343..52585 - 3243 WP_001749977 MobF family relaxase -
HS484_RS00305 (pKP96_054) 52585..54114 - 1530 WP_001749976 type IV secretion system DNA-binding domain-containing protein virb4
HS484_RS00310 (pKP96_055) 54116..54532 - 417 WP_001749975 hypothetical protein -
HS484_RS00415 55023..55442 + 420 WP_001749974 plasmid stabilization protein StbA -
HS484_RS00320 (pKP96_057) 55451..56167 + 717 WP_001749973 StbB family protein -
HS484_RS00325 (pKP96_058) 56169..56537 + 369 WP_000414913 plasmid stabilization protein StbC -
HS484_RS00330 (pKP96_059) 56719..57063 + 345 WP_000999874 hypothetical protein -
HS484_RS00335 (pKP96_060) 57174..57494 - 321 WP_001749971 protein CcgAII -
HS484_RS00340 (pKP96_061) 57549..57728 - 180 WP_000214483 protein CcgAI -
HS484_RS00345 (pKP96_062) 58455..58964 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   41 GenBank   NC_011617
Plasmid name   pKP96 Incompatibility group   IncN
Plasmid size   67850 bp Coordinate of oriT [Strand]   54738..54747 [+]
Host baterium   Klebsiella pneumoniae

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, qacE, sul1, qnrA1, fosA5, blaCTX-M-14, tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -