Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101458
Name   oriT_pCRE6_3 in_silico
Organism   Klebsiella pneumoniae strain S6_CRE6
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAHBNK010000004 (31669..31768 [-], 100 nt)
oriT length   100 nt
IRs (inverted repeats)      34..41, 44..51  (AGTGCGAT..ATCGCACT)
 20..25, 39..44  (TAAATC..GATTTA)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 100 nt

>oriT_pCRE6_3
TATTGAATGTTTTATTCTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATCAGTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1312 GenBank   WP_020323154
Name   mobF_KIN48_RS28755_pCRE6_3 insolico UniProt ID   A0A0R8CGS3
Length   1072 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1072 a.a.        Molecular weight: 118689.40 Da        Isoelectric Point: 6.4933

>WP_020323154.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNGQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFHVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGATEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKGRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHDDGQQAKSYGHEAGQQTGEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDYDKEGYGL

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-288)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(855-899)

AAA domain (AAA_30)

(480-656)


  Protein structure


Source ID Structure
AlphaFold DB A0A0R8CGS3


T4CP

ID   931 GenBank   WP_020323171
Name   t4cp2_KIN48_RS28750_pCRE6_3 insolico UniProt ID   _
Length   510 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 510 a.a.        Molecular weight: 58208.12 Da        Isoelectric Point: 9.7037

>WP_020323171.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVSIIAGSVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGSLLQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR

  Protein domains


Predicted by InterproScan.

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

(113-492)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 32339..55813

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KIN48_RS28710 (KIN48_28595) 28126..28803 + 678 WP_020323167 DUF5417 domain-containing protein -
KIN48_RS28715 (KIN48_28600) 28985..29191 + 207 WP_020323152 DUF905 family protein -
KIN48_RS28720 (KIN48_28605) 29265..29447 + 183 WP_000170167 hypothetical protein -
KIN48_RS28725 29506..29856 - 351 WP_223226687 hypothetical protein -
KIN48_RS28730 (KIN48_28615) 29920..30288 - 369 WP_032416596 plasmid stabilization protein StbC -
KIN48_RS28735 (KIN48_28620) 30291..31007 - 717 WP_020323147 StbB family protein -
KIN48_RS28740 31016..31447 - 432 WP_020323173 plasmid stabilization protein StbA -
KIN48_RS28745 31914..32339 + 426 WP_223831802 traK protein -
KIN48_RS28750 (KIN48_28635) 32339..33871 + 1533 WP_020323171 type IV secretion system DNA-binding domain-containing protein virb4
KIN48_RS28755 (KIN48_28640) 33876..37094 + 3219 WP_020323154 MobF family relaxase -
KIN48_RS28760 (KIN48_28645) 37091..37756 + 666 WP_020323157 DUF6710 family protein -
KIN48_RS28765 (KIN48_28650) 37749..38111 + 363 WP_020323170 hypothetical protein -
KIN48_RS28770 (KIN48_28655) 38727..39038 - 312 WP_032416518 hypothetical protein -
KIN48_RS28775 (KIN48_28660) 39035..39502 - 468 WP_046092601 phospholipase D family protein -
KIN48_RS28780 (KIN48_28665) 39559..40560 - 1002 WP_020323165 ATPase, T2SS/T4P/T4SS family virB11
KIN48_RS28785 (KIN48_28670) 40611..41744 - 1134 WP_020323153 type IV secretion system protein VirB10 virB10
KIN48_RS28790 (KIN48_28675) 41744..42631 - 888 WP_020323166 TrbG/VirB9 family P-type conjugative transfer protein virB9
KIN48_RS28795 (KIN48_28680) 42642..43337 - 696 WP_001208352 type IV secretion system protein virB8
KIN48_RS28800 (KIN48_28685) 43512..43682 - 171 Protein_50 serine hydrolase -
KIN48_RS28805 (KIN48_28690) 43737..44441 - 705 WP_001067855 IS6-like element IS26 family transposase -
KIN48_RS28810 (KIN48_28695) 44507..44722 - 216 Protein_52 nucleotidyltransferase domain-containing protein -
KIN48_RS28815 (KIN48_28700) 44792..45346 - 555 WP_063840280 AAC(6')-Ib family aminoglycoside 6'-N-acetyltransferase -
KIN48_RS28820 (KIN48_28705) 45580..46137 - 558 WP_001217881 recombinase family protein -
KIN48_RS28825 (KIN48_28710) 46299..49304 + 3006 WP_001143775 Tn3-like element Tn3 family transposase -
KIN48_RS29345 49329..49457 - 129 WP_326494730 conjugal transfer protein TraN -
KIN48_RS28830 (KIN48_28715) 49534..50571 - 1038 WP_020323169 type IV secretion system protein virB6
KIN48_RS28835 (KIN48_28720) 50588..50830 - 243 WP_000858958 EexN family lipoprotein -
KIN48_RS28840 (KIN48_28725) 50840..51541 - 702 WP_020323143 type IV secretion system protein virB5
KIN48_RS28845 (KIN48_28730) 51557..54130 - 2574 WP_020323176 VirB4 family type IV secretion/conjugal transfer ATPase virb4
KIN48_RS28850 (KIN48_28735) 54131..54448 - 318 WP_000462629 VirB3 family type IV secretion system protein virB3
KIN48_RS28855 (KIN48_28740) 54488..54829 - 342 WP_001121032 TrbC/VirB2 family protein virB2
KIN48_RS28865 (KIN48_28745) 55031..55813 - 783 WP_032416587 lytic transglycosylase domain-containing protein virB1
KIN48_RS28870 (KIN48_28750) 55913..56230 + 318 WP_032449361 H-NS histone family protein -
KIN48_RS28875 (KIN48_28755) 56234..56584 + 351 WP_032416642 hypothetical protein -
KIN48_RS28880 (KIN48_28760) 56581..56919 + 339 WP_223226685 hypothetical protein -
KIN48_RS28885 (KIN48_28765) 56923..57231 + 309 WP_032416643 hypothetical protein -
KIN48_RS28890 (KIN48_28770) 57516..57701 + 186 WP_006118530 ribbon-helix-helix domain-containing protein -
KIN48_RS28895 (KIN48_28775) 57698..58306 - 609 WP_032449362 recombinase family protein -
KIN48_RS28900 (KIN48_28780) 58472..58804 - 333 WP_020323168 hypothetical protein -

Host bacterium

ID   1902 GenBank   NZ_JAHBNK010000004
Plasmid name   pCRE6_3 Incompatibility group   IncN3
Plasmid size   58943 bp Coordinate of oriT [Strand]   31669..31768 [-]
Host baterium   Klebsiella pneumoniae strain S6_CRE6

Cargo genes

Drug resistance gene   aac(6')-Ib
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -