Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103510
Name   oriT_pCRKP-33_KPC in_silico
Organism   Klebsiella pneumoniae strain CRKP-33
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP102637 (47398..47498 [+], 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-33_KPC
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2630 GenBank   WP_012561166
Name   TrwC_NVS91_RS01210_pCRKP-33_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   1112 GenBank   WP_001749975
Name   WP_001749975_pCRKP-33_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   2438 GenBank   WP_258170743
Name   t4cp2_NVS91_RS01300_pCRKP-33_KPC insolico UniProt ID   _
Length   377 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 377 a.a.        Molecular weight: 43026.85 Da        Isoelectric Point: 9.0477

>WP_258170743.1 type IV secretion system DNA-binding domain-containing protein [Klebsiella pneumoniae]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
IGNDSNLLIVFYVQIMPDDLVMQLHRF

  Protein domains


Predicted by InterproScan.

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

(113-349)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9247..19572

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NVS91_RS01060 (NVS91_01060) 4474..5019 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -
NVS91_RS01065 (NVS91_01065) 5156..5728 + 573 WP_001493762 recombinase family protein -
NVS91_RS01070 (NVS91_01070) 5765..7156 + 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
NVS91_RS01075 (NVS91_01075) 7315..8012 + 698 WP_095033700 IS1-like element IS1B family transposase -
NVS91_RS01415 8253..8540 + 288 Protein_11 DUF6710 family protein -
NVS91_RS01085 (NVS91_01085) 8714..9247 - 534 WP_000792636 phospholipase D family protein -
NVS91_RS01090 (NVS91_01090) 9247..10242 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
NVS91_RS01095 (NVS91_01095) 10284..11444 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
NVS91_RS01100 (NVS91_01100) 11444..12328 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
NVS91_RS01105 (NVS91_01105) 12339..13037 - 699 WP_000646594 type IV secretion system protein virB8
NVS91_RS01420 13027..13185 - 159 WP_012561180 hypothetical protein -
NVS91_RS01110 (NVS91_01110) 13256..14296 - 1041 WP_001749958 type IV secretion system protein virB6
NVS91_RS01115 (NVS91_01115) 14312..14539 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
NVS91_RS01120 (NVS91_01120) 14547..15260 - 714 WP_001749960 type IV secretion system protein virB5
NVS91_RS01125 (NVS91_01125) 15278..17878 - 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
NVS91_RS01130 (NVS91_01130) 17878..18195 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
NVS91_RS01135 (NVS91_01135) 18245..18538 - 294 WP_001749962 hypothetical protein virB2
NVS91_RS01140 (NVS91_01140) 18548..18829 - 282 WP_000440698 transcriptional repressor KorA -
NVS91_RS01145 (NVS91_01145) 18838..19572 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
NVS91_RS01150 (NVS91_01150) 19636..19986 + 351 WP_024129965 H-NS family nucleoid-associated regulatory protein -
NVS91_RS01155 (NVS91_01155) 20002..20346 + 345 WP_001749964 hypothetical protein -
NVS91_RS01160 (NVS91_01160) 20343..20657 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
NVS91_RS01165 (NVS91_01165) 20771..21004 + 234 WP_001191790 hypothetical protein -
NVS91_RS01170 (NVS91_01170) 21054..21701 + 648 WP_015344958 restriction endonuclease -
NVS91_RS01175 (NVS91_01175) 21706..21912 + 207 WP_001749967 hypothetical protein -
NVS91_RS01180 (NVS91_01180) 21923..22195 - 273 Protein_32 IS1 family transposase -
NVS91_RS01185 (NVS91_01185) 22294..23727 + 1434 WP_001288432 DNA cytosine methyltransferase -
NVS91_RS01190 (NVS91_01190) 23761..24369 - 609 Protein_34 type II site-specific deoxyribonuclease -

Host bacterium

ID   3953 GenBank   NZ_CP102637
Plasmid name   pCRKP-33_KPC Incompatibility group   IncN
Plasmid size   62699 bp Coordinate of oriT [Strand]   47398..47498 [+]
Host baterium   Klebsiella pneumoniae strain CRKP-33

Cargo genes

Drug resistance gene   blaKPC-2, qnrS1, aac(6')-Ib-cr, ARR-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -