Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105202
Name   oriT_pRHB42-C09_2 in_silico
Organism   Escherichia marmotae strain RHB42-C09
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058208 (31312..31412 [+], 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_pRHB42-C09_2
TATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3585 GenBank   WP_112040549
Name   mobF_HV018_RS22015_pRHB42-C09_2 insolico UniProt ID   _
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120153.38 Da        Isoelectric Point: 6.5766

>WP_112040549.1 MULTISPECIES: MobF family relaxase [Escherichia]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
SQTSQAEQSHTGKEHTHEHEHEEGGHEI

  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



No available structure.




Auxiliary protein

ID   1601 GenBank   WP_000706094
Name   WP_000706094_pRHB42-C09_2 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   3546 GenBank   WP_000342688
Name   t4cp2_HV018_RS22020_pRHB42-C09_2 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: 9020..19210

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV018_RS21865 (HV018_21810) 4736..6169 - 1434 WP_001288435 DNA cytosine methyltransferase -
HV018_RS21870 (HV018_21815) 6263..6535 + 273 Protein_4 IS1 family transposase -
HV018_RS21875 (HV018_21820) 6555..6752 - 198 WP_000844102 hypothetical protein -
HV018_RS21880 (HV018_21825) 6757..7266 - 510 WP_000893479 restriction endonuclease -
HV018_RS21885 (HV018_21830) 7454..7765 - 312 WP_001452736 hypothetical protein -
HV018_RS21890 (HV018_21835) 7801..8115 - 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
HV018_RS21895 (HV018_21840) 8078..8455 - 378 WP_000504251 hypothetical protein -
HV018_RS21900 (HV018_21845) 8471..8842 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HV018_RS21905 (HV018_21850) 9020..9619 + 600 WP_233461571 lytic transglycosylase domain-containing protein virB1
HV018_RS21910 (HV018_21855) 9628..9909 + 282 WP_000440698 transcriptional repressor KorA -
HV018_RS21915 (HV018_21860) 9919..10212 + 294 WP_000209137 TrbC/VirB2 family protein virB2
HV018_RS21920 (HV018_21865) 10262..10579 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HV018_RS21925 (HV018_21870) 10579..13179 + 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HV018_RS21930 (HV018_21875) 13197..13910 + 714 WP_000749362 type IV secretion system protein virB5
HV018_RS21935 (HV018_21880) 13918..14145 + 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
HV018_RS21940 (HV018_21885) 14161..15201 + 1041 WP_000886022 type IV secretion system protein virB6
HV018_RS21945 (HV018_21890) 15284..15430 + 147 WP_001257173 conjugal transfer protein TraN -
HV018_RS21950 (HV018_21895) 15420..16118 + 699 WP_000646594 type IV secretion system protein virB8
HV018_RS21955 (HV018_21900) 16129..17013 + 885 WP_162858269 TrbG/VirB9 family P-type conjugative transfer protein virB9
HV018_RS21960 (HV018_21905) 17013..18173 + 1161 WP_000101711 type IV secretion system protein VirB10 virB10
HV018_RS21965 (HV018_21910) 18215..19210 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HV018_RS21970 (HV018_21915) 19210..19461 + 252 Protein_24 phospholipase D-like domain-containing protein -
HV018_RS21975 (HV018_21920) 19454..19666 + 213 WP_072024976 relaxase -
HV018_RS21980 (HV018_21925) 19698..20348 - 651 WP_000164043 tetracycline resistance transcriptional repressor TetR(A) -
HV018_RS21985 (HV018_21930) 20454..21653 + 1200 WP_000804064 tetracycline efflux MFS transporter Tet(A) -
HV018_RS21990 (HV018_21935) 21685..22569 - 885 WP_000058717 EamA family transporter -
HV018_RS21995 (HV018_21940) 22707..23099 - 393 WP_001351729 isochorismatase family cysteine hydrolase -

Host bacterium

ID   5640 GenBank   NZ_CP058208
Plasmid name   pRHB42-C09_2 Incompatibility group   IncN
Plasmid size   42916 bp Coordinate of oriT [Strand]   31312..31412 [+]
Host baterium   Escherichia marmotae strain RHB42-C09

Cargo genes

Drug resistance gene   tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -