Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104965
Name   oriT_pNB5_KPC-2 in_silico
Organism   Klebsiella pneumoniae strain NB5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP092655 (58513..58613 [+], 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_pNB5_KPC-2
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3490 GenBank   WP_012561166
Name   mobF_MJ642_RS03105_pNB5_KPC-2 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   1553 GenBank   WP_001749975
Name   WP_001749975_pNB5_KPC-2 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   3439 GenBank   WP_000342688
Name   t4cp2_MJ642_RS03110_pNB5_KPC-2 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: 15870..26196

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MJ642_RS02855 11715..13148 - 1434 WP_001288432 DNA cytosine methyltransferase -
MJ642_RS02860 13247..13519 + 273 Protein_16 IS1 family transposase -
MJ642_RS02865 13530..13736 - 207 WP_001749967 hypothetical protein -
MJ642_RS02870 13741..14388 - 648 WP_015344958 restriction endonuclease -
MJ642_RS02875 14438..14671 - 234 WP_001191790 hypothetical protein -
MJ642_RS02880 14785..15099 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
MJ642_RS02885 15096..15440 - 345 WP_001749964 hypothetical protein -
MJ642_RS02890 15456..15827 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
MJ642_RS02895 15870..16604 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
MJ642_RS02900 16613..16894 + 282 WP_000440698 transcriptional repressor KorA -
MJ642_RS02905 16904..17197 + 294 WP_001749962 hypothetical protein virB2
MJ642_RS02910 17247..17564 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
MJ642_RS02915 17564..20164 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
MJ642_RS02920 20182..20895 + 714 WP_001749960 type IV secretion system protein virB5
MJ642_RS02925 20903..21130 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
MJ642_RS02930 21146..22186 + 1041 WP_001749958 type IV secretion system protein virB6
MJ642_RS29250 22287..22415 + 129 WP_071882546 conjugal transfer protein TraN -
MJ642_RS02935 22405..23103 + 699 WP_000646594 type IV secretion system protein virB8
MJ642_RS02940 23114..23999 + 886 Protein_33 TrbG/VirB9 family P-type conjugative transfer protein -
MJ642_RS02945 23999..25159 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
MJ642_RS02950 25201..26196 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
MJ642_RS02955 26196..26729 + 534 WP_000792636 phospholipase D family protein -
MJ642_RS29255 26903..27190 - 288 Protein_37 DUF6710 family protein -
MJ642_RS02970 28287..29678 - 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
MJ642_RS02975 29715..30287 - 573 WP_001493762 recombinase family protein -
MJ642_RS02980 30424..30969 - 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -

Host bacterium

ID   5403 GenBank   NZ_CP092655
Plasmid name   pNB5_KPC-2 Incompatibility group   IncN
Plasmid size   71683 bp Coordinate of oriT [Strand]   58513..58613 [+]
Host baterium   Klebsiella pneumoniae strain NB5

Cargo genes

Drug resistance gene   blaKPC-2, dfrA14, ARR-3, aac(6')-Ib-cr, qnrS1, blaTEM-1B, blaCTX-M-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -