Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100014
Name   oriT_R46 experimental
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_003292 (_)
oriT length   650 nt
IRs (inverted repeats)      IR1: 199..208, 212..221  (ATTAGGTGTT..AATACCTAAT)
 IR2:320..325, 331..336  (AAAAAA..TTTTTT)
  IR3: 394..403, 406..415  (GTATTCATGC..GCATGAATAC)
Location of nic site      302..303
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   _

  oriT sequence  


Download         Length: 650 nt

>oriT_R46
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAACAAAAGATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTAGGTGTTTTTAATACCTAATTATTACCGAATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATGCCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGATCTACGTAGGTTAAGGACTAACTGACTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACACTATTACAACAAAAGTACATCAAAATTACATCAAAAGTACATCACTTGAAGGTTGACAGTACAACAGAATTACATCATTATCTGGTACTGAGGTAGCCAGTACAACAAAAGTACATCAAAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Llosa M et al. (1991) Structural and functional analysis of the origin of conjugal transfer of the broad-host-range IncW plasmid R388 and comparison with the related IncN plasmid R46. Mol Gen Genet. 226(3):473-83. [PMID:2038309]
[2] Coupland GM et al. (1987) The origin of transfer (oriT) of the conjugative plasmid R46: characterization by deletion analysis and DNA sequencing. Mol Gen Genet. 208(1-2):219-25. [PMID:3039307]


Relaxase

ID   13 GenBank   NP_511201
Name   TraI_R46 experimental UniProt ID   Q56053
Length   1078 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120119.36 Da        Isoelectric Point: 6.6314

>NP_511201.1 TraI (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELAKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQRSAQEYADYEHYAEASDYDFDSSIYDDYAM
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
PDB 8A1B
AlphaFold DB Q56053

  Reference


[1] Paterson ES et al. (1999) Genetic analysis of the mobilization and leading regions of the IncN plasmids pKM101 and pCU1. J Bacteriol. 181(8):2572-83. [PMID:10198024]


Auxiliary protein

ID   20 GenBank   NP_511203
Name   TraK_R46 insolico UniProt ID   Q79SD6
Length   138 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


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

>NP_511203.1 TraK (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCLEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q79SD6

  Reference


[1] Paterson ES et al. (1999) Genetic analysis of the mobilization and leading regions of the IncN plasmids pKM101 and pCU1. J Bacteriol. 181(8):2572-83. [PMID:10198024]


T4CP

ID   13 GenBank   NP_511202
Name   TraJ_R46 insolico UniProt ID   Q79SD7
Length   509 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57762.87 Da        Isoelectric Point: 9.6551

>NP_511202.1 TraJ (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
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


Source ID Structure
AlphaFold DB Q79SD7

  Reference


[1] Paterson ES et al. (1999) Genetic analysis of the mobilization and leading regions of the IncN plasmids pKM101 and pCU1. J Bacteriol. 181(8):2572-83. [PMID:10198024]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3160..19575

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS151_RS00005 (R46_001) 64..768 + 705 WP_001067855 IS6-like element IS26 family transposase -
HS151_RS00010 (R46_002) 830..1027 - 198 WP_000844102 hypothetical protein -
HS151_RS00015 (R46_003) 1032..1673 - 642 WP_001694850 restriction endonuclease -
HS151_RS00020 (R46_004) 1729..1962 - 234 WP_001191790 hypothetical protein -
HS151_RS00025 (R46_005) 2076..2390 - 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
HS151_RS00030 (R46_006) 2353..2730 - 378 WP_010999955 hypothetical protein -
HS151_RS00035 (R46_007) 2746..3117 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HS151_RS00040 (R46_008) 3160..3894 + 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
HS151_RS00045 (R46_009) 3903..4184 + 282 WP_000440698 transcriptional repressor KorA -
HS151_RS00050 (R46_010) 4194..4487 + 294 WP_000209137 TrbC/VirB2 family protein virB2
HS151_RS00055 (R46_011) 4537..4848 + 312 WP_010999956 VirB3 family type IV secretion system protein virB3
HS151_RS00060 (R46_012) 4853..7453 + 2601 WP_010999957 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS151_RS00065 (R46_013) 7471..8184 + 714 WP_010999958 type IV secretion system protein virB5
HS151_RS00070 (R46_014) 8192..8419 + 228 WP_010999959 IncN-type entry exclusion lipoprotein EexN -
HS151_RS00075 (R46_015) 8435..9475 + 1041 WP_010999960 type IV secretion system protein virB6
HS151_RS00345 9576..9704 + 129 WP_328799154 conjugal transfer protein TraN -
HS151_RS00080 (R46_017) 9694..10392 + 699 WP_010999962 type IV secretion system protein virB8
HS151_RS00085 (R46_018) 10403..11287 + 885 WP_010999963 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS151_RS00090 (R46_019) 11287..12447 + 1161 WP_010999964 type IV secretion system protein VirB10 virB10
HS151_RS00095 (R46_020) 12486..13481 + 996 WP_010999965 ATPase, T2SS/T4P/T4SS family virB11
HS151_RS00100 (R46_021) 13481..14014 + 534 WP_000731968 phospholipase D family protein -
HS151_RS00105 (R46_022) 14184..14810 - 627 WP_010999966 DUF6710 family protein -
HS151_RS00110 (R46_023) 14810..18046 - 3237 WP_010999967 MobF family relaxase -
HS151_RS00115 (R46_024) 18046..19575 - 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
HS151_RS00120 (R46_025) 19577..19993 - 417 WP_001532083 hypothetical protein -
HS151_RS00340 20506..20925 + 420 WP_000802909 plasmid stabilization protein StbA -
HS151_RS00130 (R46_028) 20934..21650 + 717 WP_000861577 StbB family protein -
HS151_RS00135 (R46_029) 21652..22020 + 369 WP_000414913 plasmid stabilization protein StbC -
HS151_RS00140 (R46_030) 22202..22546 + 345 WP_000999874 hypothetical protein -
HS151_RS00145 (R46_031) 22657..22977 - 321 WP_000211833 protein CcgAII -
HS151_RS00150 (R46_032) 23032..23211 - 180 WP_000214483 protein CcgAI -
HS151_RS00155 (R46_033) 24042..24551 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   13 GenBank   NC_003292
Plasmid name   R46 Incompatibility group   IncN
Plasmid size   50969 bp Coordinate of oriT [Strand]   19903..20551 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

Drug resistance gene   blaOXA-2, ant(3'')-Ia, qacE, sul1, tet(C)
Virulence gene   -
Metal resistance gene   arsR, arsD, arsA, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -