Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116327
Name   oriT_pCFBC2 in_silico
Organism   Citrobacter freundii strain BC73
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP117477 (55257..55357 [+], 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_pCFBC2
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10432 GenBank   WP_012561166
Name   mobF_PSC61_RS26045_pCFBC2 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   6127 GenBank   WP_000706094
Name   WP_000706094_pCFBC2 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   12179 GenBank   WP_000342688
Name   t4cp2_PSC61_RS26050_pCFBC2 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: 13818..31048

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PSC61_RS25790 (PSC61_25770) 9659..11092 - 1434 WP_001288435 DNA cytosine methyltransferase -
PSC61_RS25795 (PSC61_25775) 11191..11463 + 273 Protein_11 IS1 family transposase -
PSC61_RS25800 (PSC61_25780) 11474..11680 - 207 WP_001749967 hypothetical protein -
PSC61_RS25805 (PSC61_25785) 11685..12332 - 648 WP_015344958 restriction endonuclease -
PSC61_RS25810 (PSC61_25790) 12382..12693 - 312 WP_001452736 hypothetical protein -
PSC61_RS25815 (PSC61_25795) 12729..13043 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
PSC61_RS25820 (PSC61_25800) 13040..13384 - 345 WP_001749964 hypothetical protein -
PSC61_RS25825 (PSC61_25805) 13400..13705 - 306 WP_000960954 H-NS family nucleoid-associated regulatory protein -
PSC61_RS25830 (PSC61_25810) 13818..14552 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
PSC61_RS25835 (PSC61_25815) 14561..14842 + 282 WP_000440698 transcriptional repressor KorA -
PSC61_RS25840 (PSC61_25820) 14852..15145 + 294 WP_001749962 hypothetical protein virB2
PSC61_RS25845 (PSC61_25825) 15195..15512 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
PSC61_RS25850 (PSC61_25830) 15512..18112 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
PSC61_RS25855 (PSC61_25835) 18130..18843 + 714 WP_001749960 type IV secretion system protein virB5
PSC61_RS25860 (PSC61_25840) 18851..19078 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
PSC61_RS25865 (PSC61_25845) 19094..20134 + 1041 WP_001749958 type IV secretion system protein virB6
PSC61_RS25870 (PSC61_25850) 20217..20363 + 147 WP_001257173 conjugal transfer protein TraN -
PSC61_RS25875 (PSC61_25855) 20353..20544 + 192 WP_317024825 hypothetical protein virB8
PSC61_RS25880 (PSC61_25860) 20567..23554 - 2988 WP_032723026 Tn3 family transposase -
PSC61_RS25885 (PSC61_25865) 23721..24356 + 636 WP_000470624 recombinase family protein -
PSC61_RS25890 (PSC61_25870) 24384..25220 - 837 WP_009652884 S-formylglutathione hydrolase -
PSC61_RS25895 (PSC61_25875) 25286..25684 - 399 WP_000235177 VOC family protein -
PSC61_RS25900 (PSC61_25880) 25726..26835 - 1110 WP_000842086 S-(hydroxymethyl)glutathione dehydrogenase -
PSC61_RS25905 (PSC61_25885) 26866..27141 - 276 WP_001141270 formaldehyde-responsive transcriptional repressor FrmR -
PSC61_RS25910 (PSC61_25890) 27459..27956 + 498 WP_282916264 type IV secretion system protein virB8
PSC61_RS25915 (PSC61_25895) 27967..28851 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
PSC61_RS25920 (PSC61_25900) 28851..30011 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
PSC61_RS25925 (PSC61_25905) 30053..31048 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
PSC61_RS25930 (PSC61_25910) 31048..31581 + 534 WP_000792636 phospholipase D family protein -
PSC61_RS25935 31755..32042 - 288 Protein_39 DUF6710 family protein -
PSC61_RS25940 (PSC61_25920) 32365..33069 + 705 WP_001067855 IS6-like element IS26 family transposase -
PSC61_RS25945 (PSC61_25925) 33123..33754 - 632 Protein_41 transposase -
PSC61_RS25950 (PSC61_25930) 34149..34805 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
PSC61_RS25955 (PSC61_25935) 35124..35738 - 615 WP_014839983 recombinase family protein -

Host bacterium

ID   16760 GenBank   NZ_CP117477
Plasmid name   pCFBC2 Incompatibility group   IncN
Plasmid size   68426 bp Coordinate of oriT [Strand]   55257..55357 [+]
Host baterium   Citrobacter freundii strain BC73

Cargo genes

Drug resistance gene   blaIMP-4, qnrS1, ARR-3, aac(6')-Ib-cr
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -