Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122253
Name   oriT1_pAR-0423-1 in_silico
Organism   Shigella flexneri strain AR-0423
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP044159 (36301..36360 [+], 60 nt)
oriT length   60 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 60 nt

>oriT1_pAR-0423-1
GGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14032 GenBank   WP_001749977
Name   mobF_F4V35_RS24055_pAR-0423-1 insolico UniProt ID   A0A5C2CVP7
Length   1080 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1080 a.a.        Molecular weight: 120419.59 Da        Isoelectric Point: 6.5483

>WP_001749977.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLSQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEHEEGGHEI

  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 A0A5C2CVP7


Auxiliary protein

ID   7799 GenBank   WP_000706094
Name   WP_000706094_pAR-0423-1 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   16420 GenBank   WP_001749976
Name   t4cp2_F4V35_RS24060_pAR-0423-1 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: 57679.73 Da        Isoelectric Point: 9.5788

>WP_001749976.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Gammaproteobacteria]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVSARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELRDI

  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: 22950..33275

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
F4V35_RS23870 18795..20228 - 1434 WP_001288432 DNA cytosine methyltransferase -
F4V35_RS23875 20327..20599 + 273 Protein_23 IS1 family transposase -
F4V35_RS23880 20610..20816 - 207 WP_001749967 hypothetical protein -
F4V35_RS23885 20821..21468 - 648 WP_015344958 restriction endonuclease -
F4V35_RS23890 21518..21829 - 312 WP_001452736 hypothetical protein -
F4V35_RS23895 21865..22179 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
F4V35_RS23900 22176..22520 - 345 WP_001749964 hypothetical protein -
F4V35_RS23905 22536..22886 - 351 WP_024129965 H-NS family nucleoid-associated regulatory protein -
F4V35_RS23910 22950..23684 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
F4V35_RS23915 23693..23974 + 282 WP_000440698 transcriptional repressor KorA -
F4V35_RS23920 23984..24277 + 294 WP_001749962 hypothetical protein virB2
F4V35_RS23925 24327..24644 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
F4V35_RS23930 24776..27244 + 2469 WP_224743086 VirB4 family type IV secretion/conjugal transfer ATPase virb4
F4V35_RS23935 27262..27975 + 714 WP_001749960 type IV secretion system protein virB5
F4V35_RS23940 27983..28210 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
F4V35_RS23945 28226..29266 + 1041 WP_001749958 type IV secretion system protein virB6
F4V35_RS23950 29349..29495 + 147 WP_001257173 conjugal transfer protein TraN -
F4V35_RS23955 29485..30183 + 699 WP_000646594 virB8 family protein virB8
F4V35_RS23960 30194..31078 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
F4V35_RS23965 31078..32238 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
F4V35_RS23970 32280..33275 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
F4V35_RS23975 33275..33808 + 534 WP_000792636 phospholipase D family protein -
F4V35_RS26000 33982..34434 - 453 WP_001749956 DUF6710 family protein -
F4V35_RS26005 34733..35020 - 288 Protein_45 MbeB family mobilization protein -
F4V35_RS26285 35058..35756 - 699 Protein_46 relaxase/mobilization nuclease domain-containing protein -
F4V35_RS23990 35698..36021 - 324 WP_000956004 MobC family plasmid mobilization relaxosome protein -
F4V35_RS23995 36086..36277 + 192 WP_000165994 Rop family plasmid primer RNA-binding protein -
F4V35_RS26290 36879..37037 + 159 WP_005093880 hypothetical protein -
F4V35_RS24010 37279..37746 + 468 WP_014526575 hypothetical protein -

Host bacterium

ID   22680 GenBank   NZ_CP044159
Plasmid name   pAR-0423-1 Incompatibility group   IncN
Plasmid size   59694 bp Coordinate of oriT [Strand]   36301..36360 [+]; 47656..47756 [+]
Host baterium   Shigella flexneri strain AR-0423

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, ARR-3, dfrA27, aadA16, qacE, sul1, qnrB6, tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -