Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103198
Name   oriT_pCRKP-1-KPC in_silico
Organism   Klebsiella pneumoniae strain CRKP-1-KPC
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX928750 (52989..53089 [+], 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_pCRKP-1-KPC
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2394 GenBank   WP_012561166
Name   TrwC_HTJ85_RS00290_pCRKP-1-KPC 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   1010 GenBank   WP_001749975
Name   WP_001749975_pCRKP-1-KPC 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   2149 GenBank   WP_000342688
Name   t4cp2_HTJ85_RS00295_pCRKP-1-KPC 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: 13196..23520

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTJ85_RS00050 8423..8968 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -
HTJ85_RS00055 9105..9677 + 573 WP_001493762 recombinase family protein -
HTJ85_RS00060 9714..11105 + 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
HTJ85_RS00065 11264..11961 + 698 WP_095033700 IS1-like element IS1B family transposase -
HTJ85_RS00415 12202..12489 + 288 Protein_13 DUF6710 family protein -
HTJ85_RS00075 12663..13196 - 534 WP_000792636 phospholipase D family protein -
HTJ85_RS00080 13196..14191 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTJ85_RS00085 14233..15393 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTJ85_RS00090 15393..16277 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTJ85_RS00095 16288..16986 - 699 WP_000646594 type IV secretion system protein virB8
HTJ85_RS00100 16976..17134 - 159 WP_012561180 hypothetical protein -
HTJ85_RS00105 17205..18245 - 1041 WP_001749958 type IV secretion system protein virB6
HTJ85_RS00110 18261..18488 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTJ85_RS00115 18496..19260 - 765 WP_013149461 type IV secretion system protein virB5
HTJ85_RS00395 19227..19775 - 549 WP_227543278 hypothetical protein virb4
HTJ85_RS00120 19772..21826 - 2055 WP_228719428 conjugal transfer protein TraB virb4
HTJ85_RS00125 21826..22143 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTJ85_RS00130 22193..22486 - 294 WP_001749962 hypothetical protein virB2
HTJ85_RS00135 22496..22777 - 282 WP_000440698 transcriptional repressor KorA -
HTJ85_RS00140 22786..23520 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTJ85_RS00145 23563..23934 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTJ85_RS00150 23950..24294 + 345 WP_001749964 hypothetical protein -
HTJ85_RS00155 24291..24605 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTJ85_RS00160 24719..24952 + 234 WP_001191790 hypothetical protein -
HTJ85_RS00165 25002..25649 + 648 WP_015344958 restriction endonuclease -
HTJ85_RS00170 25654..25860 + 207 WP_001749967 hypothetical protein -
HTJ85_RS00175 25871..26143 - 273 Protein_35 IS1 family transposase -
HTJ85_RS00180 26242..27675 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   3641 GenBank   NZ_KX928750
Plasmid name   pCRKP-1-KPC Incompatibility group   IncN
Plasmid size   65595 bp Coordinate of oriT [Strand]   52989..53089 [+]
Host baterium   Klebsiella pneumoniae strain CRKP-1-KPC

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   -