Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103006
Name   oriT_pIMP-FJ1503 in_silico
Organism   Citrobacter freundii strain CRE1503
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU051710 (13790..13890 [-], 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_pIMP-FJ1503
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2255 GenBank   WP_012561166
Name   TrwC_HTH03_RS00110_pIMP-FJ1503 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   918 GenBank   WP_001749975
Name   WP_001749975_pIMP-FJ1503 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   1944 GenBank   WP_000342688
Name   t4cp2_HTH03_RS00105_pIMP-FJ1503 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: 27429..37754

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH03_RS00140 22551..23165 + 615 WP_014839983 recombinase family protein -
HTH03_RS00145 23484..24140 - 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
HTH03_RS00150 24535..25166 + 632 Protein_29 transposase -
HTH03_RS00155 25220..25924 - 705 WP_001067855 IS6-like element IS26 family transposase -
HTH03_RS00160 25989..26168 - 180 Protein_31 helix-turn-helix domain-containing protein -
HTH03_RS00345 26435..26722 + 288 Protein_32 DUF6710 family protein -
HTH03_RS00170 26896..27429 - 534 WP_000792636 phospholipase D family protein -
HTH03_RS00175 27429..28424 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTH03_RS00180 28466..29626 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTH03_RS00185 29626..30510 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTH03_RS00190 30521..31219 - 699 WP_000646594 type IV secretion system protein virB8
HTH03_RS00195 31209..31367 - 159 WP_012561180 hypothetical protein -
HTH03_RS00200 31438..32478 - 1041 WP_001749958 type IV secretion system protein virB6
HTH03_RS00205 32494..32721 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTH03_RS00210 32729..33493 - 765 WP_013149461 type IV secretion system protein virB5
HTH03_RS00215 33460..36060 - 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTH03_RS00220 36060..36377 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTH03_RS00225 36427..36720 - 294 WP_001749962 hypothetical protein virB2
HTH03_RS00230 36730..37011 - 282 WP_000440698 transcriptional repressor KorA -
HTH03_RS00235 37020..37754 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTH03_RS00240 37797..38168 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTH03_RS00245 38184..38528 + 345 WP_001749964 hypothetical protein -
HTH03_RS00250 38525..38839 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTH03_RS00255 38953..39186 + 234 WP_001191790 hypothetical protein -
HTH03_RS00260 39236..39883 + 648 WP_015344958 restriction endonuclease -
HTH03_RS00265 39888..40094 + 207 WP_001749967 hypothetical protein -
HTH03_RS00270 40105..40377 - 273 Protein_53 IS1 family transposase -
HTH03_RS00275 40476..41909 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   3449 GenBank   NZ_KU051710
Plasmid name   pIMP-FJ1503 Incompatibility group   IncN
Plasmid size   50546 bp Coordinate of oriT [Strand]   13790..13890 [-]
Host baterium   Citrobacter freundii strain CRE1503

Cargo genes

Drug resistance gene   qnrS1, blaIMP-4
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -