Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116222
Name   oriT_pKPC-349c in_silico
Organism   Citrobacter freundii complex sp. CFNIH2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP025758 (48944..49044 [+], 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      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 101 nt

>oriT_pKPC-349c
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10378 GenBank   WP_012561166
Name   mobF_WM46_RS26150_pKPC-349c insolico UniProt ID   D7RU03
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120141.30 Da        Isoelectric Point: 6.5229

>WP_012561166.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
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


Auxiliary protein

ID   6108 GenBank   WP_001749975
Name   WP_001749975_pKPC-349c 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   12115 GenBank   WP_000342688
Name   t4cp2_WM46_RS26155_pKPC-349c 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: 57762.87 Da        Isoelectric Point: 9.6551

>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI

  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: 11795..22119

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
WM46_RS25930 (WM46_25810) 7640..9073 - 1434 WP_001288432 DNA cytosine methyltransferase -
WM46_RS25935 (WM46_25815) 9172..9444 + 273 Protein_10 IS1 family transposase -
WM46_RS25940 (WM46_25820) 9455..9661 - 207 WP_001749967 hypothetical protein -
WM46_RS25945 (WM46_25825) 9666..10313 - 648 WP_012561184 restriction endonuclease -
WM46_RS25950 (WM46_25830) 10363..10674 - 312 WP_001452736 hypothetical protein -
WM46_RS25955 (WM46_25835) 10710..11024 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
WM46_RS25960 (WM46_25840) 11021..11365 - 345 WP_001749964 hypothetical protein -
WM46_RS25965 (WM46_25845) 11381..11686 - 306 WP_000960954 H-NS family nucleoid-associated regulatory protein -
WM46_RS25970 (WM46_25850) 11795..12529 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
WM46_RS25975 (WM46_25855) 12538..12819 + 282 WP_000440698 transcriptional repressor KorA -
WM46_RS25980 (WM46_25860) 12829..13122 + 294 WP_001749962 hypothetical protein virB2
WM46_RS25985 (WM46_25865) 13172..13489 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
WM46_RS25990 (WM46_25870) 13621..16089 + 2469 WP_224743086 VirB4 family type IV secretion/conjugal transfer ATPase virb4
WM46_RS25995 (WM46_25875) 16107..16820 + 714 WP_001749960 type IV secretion system protein virB5
WM46_RS26000 (WM46_25880) 16828..17055 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
WM46_RS26005 (WM46_25885) 17071..18111 + 1041 WP_001749958 type IV secretion system protein virB6
WM46_RS26015 (WM46_25895) 18330..19028 + 699 WP_000646594 virB8 family protein virB8
WM46_RS26020 (WM46_25900) 19039..19923 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
WM46_RS26025 (WM46_25905) 19923..21082 + 1160 Protein_27 type IV secretion system protein VirB10 -
WM46_RS26030 (WM46_25910) 21124..22119 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
WM46_RS26035 (WM46_25915) 22119..22652 + 534 WP_000792636 phospholipase D family protein -
WM46_RS26785 (WM46_25920) 22826..23113 - 288 Protein_30 DUF6710 family protein -
WM46_RS26045 (WM46_25925) 23380..23559 + 180 Protein_31 helix-turn-helix domain-containing protein -
WM46_RS26050 (WM46_25930) 23624..24184 + 561 Protein_32 IS6-like element IS26 family transposase -
WM46_RS26055 (WM46_25935) 24204..26315 - 2112 Protein_33 Tn3-like element Tn3 family transposase -

Host bacterium

ID   16655 GenBank   NZ_CP025758
Plasmid name   pKPC-349c Incompatibility group   IncN
Plasmid size   62588 bp Coordinate of oriT [Strand]   48944..49044 [+]
Host baterium   Citrobacter freundii complex sp. CFNIH2

Cargo genes

Drug resistance gene   dfrA14, blaKPC-3, aac(6')-Ib, ant(3'')-Ia, blaOXA-9
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -