Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100061
Name   oriT_N3 in_silico
Organism   Escherichia coli
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_015599 (10313..10360 [-], 48 nt)
oriT length   48 nt
IRs (inverted repeats)      1..7, 19..25  (TAAATCA..TGATTTA)
Location of nic site      43..44
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   _

  oriT sequence  


Download         Length: 48 nt

>oriT_N3
TAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Humphrey B et al. (2012) Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids. BMC Microbiol. 0.536805556. [PMID:22475035]


Relaxase

ID   57 GenBank   YP_004558187
Name   TraI_N3 insolico UniProt ID   F6IB82
Length   1080 a.a. PDB ID   
Note   conjugal transfer nickase and helicase

  Relaxase protein sequence


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

>YP_004558187.1 conjugal transfer nickase and helicase (plasmid) [Escherichia coli]
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 F6IB82

  Reference


[1] Humphrey B et al. (2012) Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids. BMC Microbiol. 0.536805556. [PMID:22475035]


Auxiliary protein

ID   88 GenBank   YP_004558185
Name   TraK_N3 insolico UniProt ID   D9Z5Q4
Length   138 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15332.60 Da        Isoelectric Point: 5.9670

>YP_004558185.1 conjugal transfer protein (plasmid) [Escherichia coli]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB D9Z5Q4

  Reference


[1] Humphrey B et al. (2012) Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids. BMC Microbiol. 0.536805556. [PMID:22475035]


T4CP

ID   57 GenBank   YP_004558186
Name   TraJ_N3 insolico UniProt ID   F6IB81
Length   509 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57679.73 Da        Isoelectric Point: 9.5788

>YP_004558186.1 conjugal transfer protein (plasmid) [Escherichia coli]
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


Source ID Structure
AlphaFold DB F6IB81

  Reference


[1] Humphrey B et al. (2012) Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids. BMC Microbiol. 0.536805556. [PMID:22475035]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 10946..27375

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXG20_RS00045 (pN3_009) 7332..7511 + 180 WP_000214483 protein CcgAI -
HXG20_RS00050 (pN3_010) 7566..7886 + 321 WP_001749971 protein CcgAII -
HXG20_RS00055 (pN3_011) 7997..8341 - 345 WP_000999874 hypothetical protein -
HXG20_RS00060 (pN3_012) 8523..8891 - 369 WP_000414913 plasmid stabilization protein StbC -
HXG20_RS00065 (pN3_013) 8893..9609 - 717 WP_001749973 StbB family protein -
HXG20_RS00335 (pN3_014) 9618..10037 - 420 WP_001749974 plasmid stabilization protein StbA -
HXG20_RS00075 (pN3_015) 10528..10944 + 417 WP_001749975 hypothetical protein -
HXG20_RS00080 (pN3_016) 10946..12475 + 1530 WP_001749976 type IV secretion system DNA-binding domain-containing protein virb4
HXG20_RS00085 (pN3_017) 12475..15717 + 3243 WP_001749977 MobF family relaxase -
HXG20_RS00090 (pN3_018) 15717..16343 + 627 WP_013851369 DUF6710 family protein -
HXG20_RS00095 (pN3_019) 16517..17050 - 534 WP_000792636 phospholipase D family protein -
HXG20_RS00100 (pN3_020) 17050..18045 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HXG20_RS00105 (pN3_021) 18087..19247 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HXG20_RS00110 (pN3_022) 19247..20131 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HXG20_RS00115 (pN3_023) 20142..20840 - 699 WP_000646594 type IV secretion system protein virB8
HXG20_RS00120 (pN3_024) 20830..20988 - 159 WP_012561180 hypothetical protein -
HXG20_RS00125 (pN3_025) 21059..22099 - 1041 WP_001749958 type IV secretion system protein virB6
HXG20_RS00130 (pN3_026) 22115..22342 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HXG20_RS00135 (pN3_027) 22350..23114 - 765 WP_013149461 type IV secretion system protein virB5
HXG20_RS00140 (pN3_028) 23081..25681 - 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXG20_RS00145 (pN3_029) 25681..25998 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HXG20_RS00150 (pN3_030) 26048..26341 - 294 WP_001749962 hypothetical protein virB2
HXG20_RS00155 (pN3_031) 26351..26632 - 282 WP_000440698 transcriptional repressor KorA -
HXG20_RS00160 (pN3_032) 26641..27375 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HXG20_RS00165 (pN3_033) 27418..27789 + 372 WP_250696002 H-NS family nucleoid-associated regulatory protein -
HXG20_RS00170 (pN3_034) 27805..28149 + 345 WP_001749964 hypothetical protein -
HXG20_RS00175 (pN3_035) 28146..28460 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HXG20_RS00180 (pN3_036) 28574..28807 + 234 WP_001191790 hypothetical protein -
HXG20_RS00185 (pN3_037) 28857..29504 + 648 WP_015344958 restriction endonuclease -
HXG20_RS00190 (pN3_038) 29509..29715 + 207 WP_001749967 hypothetical protein -
HXG20_RS00195 29726..29998 - 273 Protein_38 IS1 family transposase -
HXG20_RS00200 (pN3_039) 30097..31530 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   57 GenBank   NC_015599
Plasmid name   N3 Incompatibility group   IncN
Plasmid size   54205 bp Coordinate of oriT [Strand]   10313..10360 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   sul1, qacE, aadA2, tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -