Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114365
Name   oriT_pCF8698_KPC2 in_silico
Organism   Citrobacter freundii strain CF8698
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LN610760 (18921..19020 [-], 100 nt)
oriT length   100 nt
IRs (inverted repeats)      77..82, 90..95  (AAAAAA..TTTTTT)
 78..83, 90..95  (AAAAAA..TTTTTT)
 79..84, 90..95  (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: 100 nt

>oriT_pCF8698_KPC2
TATTTATTTTTTTATCTTTTAAATCAGTACGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGAAAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9210 GenBank   WP_012561142
Name   mobF_HXH58_RS00120_pCF8698_KPC2 insolico UniProt ID   A0A1S6KKJ9
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120195.37 Da        Isoelectric Point: 6.5230

>WP_012561142.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKADMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

AAA domain (AAA_30)

(477-653)

TrwC relaxase (TrwC)

(16-287)


  Protein structure


Source ID Structure
AlphaFold DB A0A1S6KKJ9


Auxiliary protein

ID   5398 GenBank   WP_001749975
Name   WP_001749975_pCF8698_KPC2 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   10675 GenBank   WP_000342688
Name   t4cp2_HXH58_RS00115_pCF8698_KPC2 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: 37079..47408

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXH58_RS00190 33054..33914 + 861 WP_000027057 broad-spectrum class A beta-lactamase TEM-1 -
HXH58_RS00195 34173..35054 + 882 WP_004199234 carbapenem-hydrolyzing class A beta-lactamase KPC-2 -
HXH58_RS00200 35304..36623 - 1320 WP_004152397 IS1182-like element ISKpn6 family transposase -
HXH58_RS00205 36975..37079 - 105 Protein_41 phospholipase D family protein -
HXH58_RS00210 37079..38074 - 996 WP_012561144 ATPase, T2SS/T4P/T4SS family virB11
HXH58_RS00215 38116..39276 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HXH58_RS00220 39276..40160 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HXH58_RS00225 40171..40869 - 699 WP_000646594 virB8 family protein virB8
HXH58_RS00230 40859..41017 - 159 WP_012561180 hypothetical protein -
HXH58_RS00235 41088..42128 - 1041 WP_001749958 type IV secretion system protein virB6
HXH58_RS00240 42144..42371 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HXH58_RS00245 42379..43143 - 765 WP_013149461 type IV secretion system protein virB5
HXH58_RS00250 43110..45710 - 2601 WP_012561149 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXH58_RS00255 45710..46027 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HXH58_RS00260 46078..46371 - 294 WP_001749962 hypothetical protein virB2
HXH58_RS00265 46381..46662 - 282 WP_016338364 transcriptional repressor KorA -
HXH58_RS00270 46671..47408 - 738 WP_013279384 lytic transglycosylase domain-containing protein virB1
HXH58_RS00275 47445..47822 + 378 WP_193567606 H-NS family nucleoid-associated regulatory protein -
HXH58_RS00280 47838..48182 + 345 WP_012561155 hypothetical protein -
HXH58_RS00285 48179..48493 + 315 WP_016338363 TrbM/KikA/MpfK family conjugal transfer protein -
HXH58_RS00290 48529..48840 + 312 WP_013279382 hypothetical protein -
HXH58_RS00340 48896..49156 + 261 WP_016359294 hypothetical protein -
HXH58_RS00300 49198..50166 - 969 WP_016151349 IS5 family transposase -
HXH58_RS00345 50184..50315 - 132 WP_255255389 hypothetical protein -
HXH58_RS00305 50250..50603 + 354 WP_225622145 restriction endonuclease -
HXH58_RS00310 50608..50814 + 207 WP_001749967 hypothetical protein -
HXH58_RS00315 50825..51097 - 273 Protein_64 IS1 family transposase -

Host bacterium

ID   14800 GenBank   NZ_LN610760
Plasmid name   pCF8698_KPC2 Incompatibility group   IncN
Plasmid size   54036 bp Coordinate of oriT [Strand]   18921..19020 [-]
Host baterium   Citrobacter freundii strain CF8698

Cargo genes

Drug resistance gene   aac(3)-IId, blaTEM-1B, blaKPC-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -