Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105975
Name   oriT_pRHB16-C24_3 in_silico
Organism   Klebsiella pneumoniae strain RHB16-C24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP057724 (35306..35406 [+], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      80..85, 91..96  (AAAAAA..TTTTTT)
 20..26, 38..44  (TAAATCA..TGATTTA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 101 nt

>oriT_pRHB16-C24_3
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTATATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4022 GenBank   WP_001749977
Name   mobF_HVX23_RS25845_pRHB16-C24_3 insolico UniProt ID   A0A5C2CVP7
Length   1080 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


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

>WP_001749977.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
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 A0A5C2CVP7


Auxiliary protein

ID   1779 GenBank   WP_001749975
Name   WP_001749975_pRHB16-C24_3 insolico UniProt ID   A0A5C2CVS6
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


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

>WP_001749975.1 MULTISPECIES: hypothetical protein [Gammaproteobacteria]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A5C2CVS6


T4CP

ID   4033 GenBank   WP_001749976
Name   t4cp2_HVX23_RS25850_pRHB16-C24_3 insolico UniProt ID   _
Length   509 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


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

>WP_001749976.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Gammaproteobacteria]
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



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 14891..34739

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVX23_RS25705 (HVX23_25705) 10736..12169 - 1434 WP_001288432 DNA cytosine methyltransferase -
HVX23_RS25710 (HVX23_25710) 12268..12540 + 273 Protein_14 IS1 family transposase -
HVX23_RS25715 (HVX23_25715) 12551..12757 - 207 WP_001749967 hypothetical protein -
HVX23_RS25720 (HVX23_25720) 12762..13409 - 648 WP_015344958 restriction endonuclease -
HVX23_RS25725 (HVX23_25725) 13459..13692 - 234 WP_001191790 hypothetical protein -
HVX23_RS25730 (HVX23_25730) 13806..14120 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HVX23_RS25735 (HVX23_25735) 14117..14461 - 345 WP_001749964 hypothetical protein -
HVX23_RS25740 (HVX23_25740) 14477..14848 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HVX23_RS25745 (HVX23_25745) 14891..15625 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HVX23_RS25750 (HVX23_25750) 15634..15915 + 282 WP_000440698 transcriptional repressor KorA -
HVX23_RS25755 (HVX23_25755) 15925..16218 + 294 WP_001749962 hypothetical protein virB2
HVX23_RS25760 (HVX23_25760) 16268..16585 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HVX23_RS25765 (HVX23_25765) 16585..19185 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HVX23_RS25770 (HVX23_25770) 19203..19916 + 714 WP_001749960 type IV secretion system protein virB5
HVX23_RS25775 (HVX23_25775) 19924..20151 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HVX23_RS25780 (HVX23_25780) 20167..21207 + 1041 WP_001749958 type IV secretion system protein virB6
HVX23_RS26320 21308..21436 + 129 WP_071882546 conjugal transfer protein TraN -
HVX23_RS25785 (HVX23_25785) 21426..22124 + 699 WP_000646594 type IV secretion system protein virB8
HVX23_RS25790 (HVX23_25790) 22135..23019 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HVX23_RS25795 (HVX23_25795) 23019..24179 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HVX23_RS25800 (HVX23_25800) 24221..25216 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HVX23_RS25805 (HVX23_25805) 25216..25749 + 534 WP_000792636 phospholipase D family protein -
HVX23_RS26325 25923..26375 - 453 WP_001749956 DUF6710 family protein -
HVX23_RS25820 (HVX23_25820) 26649..27302 + 654 Protein_36 EamA family transporter -
HVX23_RS25825 (HVX23_25825) 27334..28533 - 1200 WP_050918514 tetracycline efflux MFS transporter Tet(A) -
HVX23_RS25830 (HVX23_25830) 28639..29289 + 651 WP_000164043 tetracycline resistance transcriptional repressor TetR(A) -
HVX23_RS25835 (HVX23_25835) 29321..29563 - 243 WP_000844627 transposase -
HVX23_RS25840 (HVX23_25840) 29795..29968 - 174 WP_001749978 hypothetical protein -
HVX23_RS25845 (HVX23_25845) 29968..33210 - 3243 WP_001749977 MobF family relaxase -
HVX23_RS25850 (HVX23_25850) 33210..34739 - 1530 WP_001749976 type IV secretion system DNA-binding domain-containing protein virb4
HVX23_RS25855 (HVX23_25855) 34741..35157 - 417 WP_001749975 hypothetical protein -
HVX23_RS26195 35637..36056 + 420 WP_001749974 plasmid stabilization protein StbA -
HVX23_RS25865 (HVX23_25865) 36065..36781 + 717 WP_001749973 StbB family protein -
HVX23_RS25870 (HVX23_25870) 36783..37151 + 369 WP_000414913 plasmid stabilization protein StbC -
HVX23_RS25875 (HVX23_25875) 37333..37677 + 345 WP_000999874 hypothetical protein -
HVX23_RS25880 (HVX23_25880) 37788..38108 - 321 WP_001749971 protein CcgAII -
HVX23_RS25885 (HVX23_25885) 38163..38342 - 180 WP_000214483 protein CcgAI -
HVX23_RS25890 (HVX23_25890) 39069..39578 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   6412 GenBank   NZ_CP057724
Plasmid name   pRHB16-C24_3 Incompatibility group   IncN
Plasmid size   48464 bp Coordinate of oriT [Strand]   35306..35406 [+]
Host baterium   Klebsiella pneumoniae strain RHB16-C24

Cargo genes

Drug resistance gene   dfrA1, aadA24, qacE, sul1, tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -