Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103047
Name   oriT_pIMP-HK1504 in_silico
Organism   Escherichia coli strain CRE1504
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT982614 (13779..13879 [-], 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-HK1504
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2278 GenBank   WP_012561166
Name   TrwC_HTH45_RS00110_pIMP-HK1504 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   936 GenBank   WP_001749975
Name   WP_001749975_pIMP-HK1504 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   1980 GenBank   WP_000342688
Name   t4cp2_HTH45_RS00105_pIMP-HK1504 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: 30723..41048

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH45_RS00165 26423..26602 - 180 Protein_32 helix-turn-helix domain-containing protein -
HTH45_RS00170 27012..27557 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -
HTH45_RS00175 27694..28266 + 573 WP_001493762 recombinase family protein -
HTH45_RS00180 28303..29694 + 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
HTH45_RS00370 29729..30016 + 288 Protein_36 DUF6710 family protein -
HTH45_RS00190 30190..30723 - 534 WP_000792636 phospholipase D family protein -
HTH45_RS00195 30723..31718 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTH45_RS00200 31760..32920 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTH45_RS00205 32920..33804 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTH45_RS00210 33815..34513 - 699 WP_000646594 type IV secretion system protein virB8
HTH45_RS00215 34503..34661 - 159 WP_012561180 hypothetical protein -
HTH45_RS00220 34732..35772 - 1041 WP_001749958 type IV secretion system protein virB6
HTH45_RS00225 35788..36015 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTH45_RS00230 36023..36787 - 765 WP_013149461 type IV secretion system protein virB5
HTH45_RS00235 36754..39354 - 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTH45_RS00240 39354..39671 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTH45_RS00245 39721..40014 - 294 WP_001749962 hypothetical protein virB2
HTH45_RS00250 40024..40305 - 282 WP_000440698 transcriptional repressor KorA -
HTH45_RS00255 40314..41048 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTH45_RS00260 41091..41462 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTH45_RS00265 41478..41822 + 345 WP_001749964 hypothetical protein -
HTH45_RS00270 41819..42133 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTH45_RS00275 42247..42480 + 234 WP_001191790 hypothetical protein -
HTH45_RS00280 42530..43177 + 648 WP_015344958 restriction endonuclease -
HTH45_RS00285 43182..43388 + 207 WP_001749967 hypothetical protein -
HTH45_RS00290 43399..43671 - 273 Protein_57 IS1 family transposase -
HTH45_RS00295 43770..45203 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   3490 GenBank   NZ_KT982614
Plasmid name   pIMP-HK1504 Incompatibility group   IncN
Plasmid size   54449 bp Coordinate of oriT [Strand]   13779..13879 [-]
Host baterium   Escherichia coli strain CRE1504

Cargo genes

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