Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116369
Name   oriT_pK616-KPC in_silico
Organism   Citrobacter koseri strain K616
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP136820 (55030..55130 [+], 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_pK616-KPC
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10459 GenBank   WP_012561166
Name   mobF_R1018_RS22315_pK616-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   6137 GenBank   WP_001749975
Name   WP_001749975_pK616-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   12211 GenBank   WP_000342688
Name   t4cp2_R1018_RS22320_pK616-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: 18029..28354

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R1018_RS22080 (R1018_22080) 13256..13801 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -
R1018_RS22085 (R1018_22085) 13938..14510 + 573 WP_001493762 recombinase family protein -
R1018_RS22090 (R1018_22090) 14547..15938 + 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
R1018_RS22095 (R1018_22095) 16097..16794 + 698 WP_095033700 IS1-like element IS1B family transposase -
R1018_RS22100 (R1018_22100) 17035..17322 + 288 Protein_18 DUF6710 family protein -
R1018_RS22105 (R1018_22105) 17496..18029 - 534 WP_000792636 phospholipase D family protein -
R1018_RS22110 (R1018_22110) 18029..19024 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
R1018_RS22115 (R1018_22115) 19066..20226 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
R1018_RS22120 (R1018_22120) 20226..21110 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
R1018_RS22125 (R1018_22125) 21121..21819 - 699 WP_000646594 virB8 family protein virB8
R1018_RS22130 (R1018_22130) 22038..23078 - 1041 WP_001749958 type IV secretion system protein virB6
R1018_RS22135 (R1018_22135) 23094..23321 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
R1018_RS22140 (R1018_22140) 23329..24042 - 714 WP_001749960 type IV secretion system protein virB5
R1018_RS22145 (R1018_22145) 24060..26528 - 2469 WP_224743086 VirB4 family type IV secretion/conjugal transfer ATPase virb4
R1018_RS22150 (R1018_22150) 26660..26977 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
R1018_RS22155 (R1018_22155) 27027..27320 - 294 WP_001749962 hypothetical protein virB2
R1018_RS22160 (R1018_22160) 27330..27611 - 282 WP_000440698 transcriptional repressor KorA -
R1018_RS22165 (R1018_22165) 27620..28354 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
R1018_RS22170 (R1018_22170) 28397..28768 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
R1018_RS22175 (R1018_22175) 28784..29128 + 345 WP_001749964 hypothetical protein -
R1018_RS22180 (R1018_22180) 29125..29439 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
R1018_RS22185 (R1018_22185) 29475..29786 + 312 WP_001452736 hypothetical protein -
R1018_RS22190 (R1018_22190) 29836..30483 + 648 WP_015344958 restriction endonuclease -
R1018_RS22195 (R1018_22195) 30488..30694 + 207 WP_001749967 hypothetical protein -
R1018_RS22200 (R1018_22200) 30705..30977 - 273 Protein_38 IS1 family transposase -
R1018_RS22205 (R1018_22205) 31076..32509 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   16802 GenBank   NZ_CP136820
Plasmid name   pK616-KPC Incompatibility group   IncN
Plasmid size   68199 bp Coordinate of oriT [Strand]   55030..55130 [+]
Host baterium   Citrobacter koseri strain K616

Cargo genes

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