Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116613
Name   oriT_pCF38954-KPC2 in_silico
Organism   Citrobacter freundii strain NRZ-38954
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP104959 (55444..55543 [+], 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_pCF38954-KPC2
TATTTATTTTTTTATCTTTTAAATCAGTACGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGAAAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10588 GenBank   WP_012561142
Name   mobF_KKS41_RS00325_pCF38954-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   6215 GenBank   WP_000706094
Name   WP_000706094_pCF38954-KPC2 insolico UniProt ID   B6UZ32
Length   96 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 96 a.a.        Molecular weight: 10829.54 Da        Isoelectric Point: 8.5040

>WP_000706094.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MKIVADRLSDVNRKLDYLFDRASDADFGPLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIA
EPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB B6UZ32


T4CP

ID   12372 GenBank   WP_000342688
Name   t4cp2_KKS41_RS00330_pCF38954-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: 12849..23178

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KKS41_RS00050 (KKS41_p00055) 9161..9433 + 273 Protein_9 IS1 family transposase -
KKS41_RS00055 (KKS41_p00060) 9444..9650 - 207 WP_001749967 hypothetical protein -
KKS41_RS00060 (KKS41_p00065) 9655..10008 - 354 WP_225622145 restriction endonuclease -
KKS41_RS00065 (KKS41_p00070) 9943..10074 + 132 WP_255255389 hypothetical protein -
KKS41_RS00070 (KKS41_p00075) 10092..11059 + 968 Protein_13 IS5 family transposase -
KKS41_RS00075 11101..11511 - 411 WP_225622109 hypothetical protein -
KKS41_RS00080 (KKS41_p00085) 11417..11728 - 312 WP_013279382 hypothetical protein -
KKS41_RS00085 (KKS41_p00090) 11764..12078 - 315 WP_016338363 TrbM/KikA/MpfK family conjugal transfer protein -
KKS41_RS00090 (KKS41_p00095) 12075..12419 - 345 WP_012561155 hypothetical protein -
KKS41_RS00095 (KKS41_p00100) 12435..12740 - 306 WP_012561154 H-NS family nucleoid-associated regulatory protein -
KKS41_RS00100 (KKS41_p00105) 12849..13586 + 738 WP_013279384 lytic transglycosylase domain-containing protein virB1
KKS41_RS00105 (KKS41_p00110) 13595..13876 + 282 WP_016338364 transcriptional repressor KorA -
KKS41_RS00110 (KKS41_p00115) 13886..14179 + 294 WP_001749962 hypothetical protein virB2
KKS41_RS00115 (KKS41_p00120) 14230..14547 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
KKS41_RS00120 (KKS41_p00125) 14547..17147 + 2601 WP_012561149 VirB4 family type IV secretion/conjugal transfer ATPase virb4
KKS41_RS00125 (KKS41_p00130) 17165..17878 + 714 WP_001749960 type IV secretion system protein virB5
KKS41_RS00130 (KKS41_p00135) 17886..18113 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
KKS41_RS00135 (KKS41_p00140) 18129..19169 + 1041 WP_001749958 type IV secretion system protein virB6
KKS41_RS00140 (KKS41_p00145) 19252..19398 + 147 WP_001257173 conjugal transfer protein TraN -
KKS41_RS00145 (KKS41_p00150) 19388..20086 + 699 WP_000646594 virB8 family protein virB8
KKS41_RS00150 (KKS41_p00155) 20097..20981 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
KKS41_RS00155 (KKS41_p00160) 20981..22141 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
KKS41_RS00160 (KKS41_p00165) 22183..23178 + 996 WP_012561144 ATPase, T2SS/T4P/T4SS family virB11
KKS41_RS00165 (KKS41_p00170) 23178..23282 + 105 Protein_32 phospholipase D family protein -
KKS41_RS00170 (KKS41_p00175) 23634..24953 + 1320 WP_004152397 IS1182-like element ISKpn6 family transposase -
KKS41_RS00175 (KKS41_p00180) 25203..26084 - 882 WP_004199234 carbapenem-hydrolyzing class A beta-lactamase KPC-2 -
KKS41_RS00180 (KKS41_p00185) 26343..27203 - 861 WP_000027057 broad-spectrum class A beta-lactamase TEM-1 -

Host bacterium

ID   17046 GenBank   NZ_CP104959
Plasmid name   pCF38954-KPC2 Incompatibility group   IncN
Plasmid size   79803 bp Coordinate of oriT [Strand]   55444..55543 [+]
Host baterium   Citrobacter freundii strain NRZ-38954

Cargo genes

Drug resistance gene   blaKPC-2, blaTEM-1B, aac(3)-IId, aac(6')-Ib-cr, blaOXA-1, catB3, ARR-3, qacE, sul1, dfrA19, aph(3'')-Ib, aph(6)-Id
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -