Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101226
Name   oriT_pCF12908_KPC2 in_silico
Organism   Citrobacter freundii strain CF12908
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_VKMA01000036 (19363..19462 [-], 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_pCF12908_KPC2
TATTTATTTTTTTATCTTTTAAATCAGTACGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGAAAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1206 GenBank   WP_225624063
Name   mobF_FOT53_RS24215_pCF12908_KPC2 insolico UniProt ID   _
Length   864 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 864 a.a.        Molecular weight: 96165.98 Da        Isoelectric Point: 9.7197

>WP_225624063.1 MobF family relaxase [Citrobacter freundii]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKADMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGARLS
WTKNRLLIFPMLMQPPSTNPRAYL

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure



No available structure.




Auxiliary protein

ID   422 GenBank   WP_000706094
Name   WP_000706094_pCF12908_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   815 GenBank   WP_000342688
Name   t4cp2_FOT53_RS24210_pCF12908_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: 41720..52049

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FOT53_RS24295 (FOT53_24710) 37695..38555 + 861 WP_000027057 broad-spectrum class A beta-lactamase TEM-1 -
FOT53_RS24300 (FOT53_24715) 38814..39695 + 882 WP_004199234 carbapenem-hydrolyzing class A beta-lactamase KPC-2 -
FOT53_RS24305 (FOT53_24720) 39945..41264 - 1320 WP_004152397 IS1182-like element ISKpn6 family transposase -
FOT53_RS24310 41616..41720 - 105 Protein_43 phospholipase D family protein -
FOT53_RS24315 (FOT53_24730) 41720..42715 - 996 WP_012561144 ATPase, T2SS/T4P/T4SS family virB11
FOT53_RS24320 (FOT53_24735) 42757..43917 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
FOT53_RS24325 (FOT53_24740) 43917..44801 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
FOT53_RS24330 (FOT53_24745) 44812..45510 - 699 WP_000646594 type IV secretion system protein virB8
FOT53_RS24335 (FOT53_24750) 45500..45646 - 147 WP_001257173 conjugal transfer protein TraN -
FOT53_RS24340 (FOT53_24755) 45729..46769 - 1041 WP_001749958 type IV secretion system protein virB6
FOT53_RS24345 (FOT53_24760) 46785..47012 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
FOT53_RS24350 (FOT53_24765) 47020..47733 - 714 WP_001749960 type IV secretion system protein virB5
FOT53_RS24355 (FOT53_24770) 47751..50351 - 2601 WP_012561149 VirB4 family type IV secretion/conjugal transfer ATPase virb4
FOT53_RS24360 (FOT53_24775) 50351..50668 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
FOT53_RS24365 (FOT53_24780) 50719..51012 - 294 WP_001749962 hypothetical protein virB2
FOT53_RS24370 (FOT53_24785) 51022..51303 - 282 WP_016338364 transcriptional repressor KorA -
FOT53_RS24375 (FOT53_24790) 51312..52049 - 738 WP_013279384 lytic transglycosylase domain-containing protein virB1
FOT53_RS24380 (FOT53_24795) 52158..52463 + 306 WP_012561154 H-NS family nucleoid-associated regulatory protein -
FOT53_RS24385 (FOT53_24800) 52479..52823 + 345 WP_012561155 hypothetical protein -
FOT53_RS24390 (FOT53_24805) 52820..53134 + 315 WP_016338363 TrbM/KikA/MpfK family conjugal transfer protein -
FOT53_RS24395 (FOT53_24810) 53170..53481 + 312 WP_013279382 hypothetical protein -
FOT53_RS24680 53387..53797 + 411 WP_225622109 hypothetical protein -
FOT53_RS24405 (FOT53_24820) 53839..54807 - 969 WP_016151349 IS5 family transposase -
FOT53_RS24725 54825..54956 - 132 WP_255255389 hypothetical protein -
FOT53_RS24410 (FOT53_24825) 54891..55244 + 354 WP_225622145 restriction endonuclease -
FOT53_RS24415 (FOT53_24830) 55249..55455 + 207 WP_001749967 hypothetical protein -
FOT53_RS24420 (FOT53_24835) 55466..55738 - 273 Protein_66 IS1 family transposase -

Host bacterium

ID   1670 GenBank   NZ_VKMA01000036
Plasmid name   pCF12908_KPC2 Incompatibility group   IncN
Plasmid size   58677 bp Coordinate of oriT [Strand]   19363..19462 [-]
Host baterium   Citrobacter freundii strain CF12908

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib, aac(3)-IId, blaTEM-1B, blaKPC-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -