Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100007
Name   oriT_pED208 in_silico
Organism   Salmonella typhi
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AF411480 (1..360 [-], 360 nt)
oriT length   360 nt
IRs (inverted repeats)      280..287, 289..296  (GCAAGATT..AATCTTGC)
Location of nic site      305..306
Conserved sequence flanking the
  nic site    		  GACGGGTGT|GG
Note   _

  oriT sequence  


Download         Length: 360 nt

>oriT_pED208
GGATTATCAATAGTCACATGTGAATCGGCCATTTATTTTATTAGAGTCAGTCTGGATTCACCAACTTCATACAGGCGAATCTGTTATACCGAAATTAGGGATTCGAATCCAGATTCGAATCTTTAATTTATCTTAATTTAGTGGTCTGATTCGTAGATGAATCTGGATTCGACTCCTTTACGATTCACTAAAGATTTGCATATGAATCTAGTATCTATGTCGGACATAGAATAACAATAAAAATATTAACGTAATACACTGAAAATAAAGGATAATCATGCAAGATTAAATCTTGCGACGGGTGTGGGACTTTGATGTTAAGGAGCAGGCATACAGAAATATGTCAGCCAGGAGGAATTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Lu J et al. (2002) Analysis and characterization of the IncFV plasmid pED208 transfer region. Plasmid. 48(1):24-37. [PMID:12206753]
[2] Di Laurenzio L et al. (1991) Characterization of the oriT region of the IncFV plasmid pED208. Mol Microbiol. 5(7):1779-90. [PMID:1943709]


Relaxase

ID   6 GenBank   AAM90727
Name   TraI_pED208 experimental UniProt ID   Q8KNJ9
Length   1767 a.a. PDB ID   
Note   OriT nicking and unwinding; similar to TraI of plasmid F

  Relaxase protein sequence


Download         Length: 1767 a.a.        Molecular weight: 193052.42 Da        Isoelectric Point: 4.9480

>AAM90727.1 TraI (plasmid) [Salmonella enterica subsp. enterica serovar Typhi]
MLSISSIKGDAGYYSHEDNYYASGSLDSRWMGEGAEKLGLKGEVASADMDAVRQGRLPDGSDLSRMVDGV
NKHRSGYDLTFSAPKSVSVMALIGEDRRFIEAHNRAVAVVMQEVEQLVSARITQEGKTETVLTGSMVAAL
YNHDTSRDLDPQVHTHALVFNATFADEKWRSLASDTRMKTGFSENLYATKIALGNLYRSALREDIESMGF
ETVAAGKHGLWELKDVPVDIFSSRSQAIREAAGPDASAKSRDVAALDTRQAKAWADPDLLKAEWRRRLTD
EKFDIDNYISQAQARVEVSGPVVAGQGGISASGQPGIASSGEAADELVQKAVGDTISALSDKKVQFTWSE
MLAGTVSRLPSAPGLFEQARAGIEAAIEGQRLIPLDREKGIFTSDIHLLNELSVHQLARTAVAEQTVLVF
PERAQERNIPAGDAVSVLSQDKSPVAILSCRGGAQALRERTEDVAMMARSQGREVMVIAADGRSGQFLSE
SPQLAGQVMLRSQINADTVLPVQGTVIVDRAERLSLKETVLLQEKALSAGAQLIFMDTENRQGTGNALSV
LKEADIPQYRFYGTQLPEVRLVSEADKRSRYSQLAQDYVRLSAEGRDVVAQVTGTREQQQLTEIIRDTRR
EAGELGREQVTLRVLEPVWLDSKTRHQRDNYRPGMVMEQWDAEKKTMTRHTIDRVAEATNSLVLQGEDGT
RLTLKVTQLDGSWSLYRSRTLEVSEGDRVRALGRELKGAIKAKEQFTVAGLENGAVRLRSGDRELRLPTE
RAVKLTHDYVEGTGAGTSASRTVLAAVGPRGLNKQTLNALAQSGSDIRIYTPLTPEQAARKVESVSAVRL
ASDQVRQSTGEANLDTAIQASRERLMSDAEQAVNLAIPSAQQGQVYLSELTLLAEAVKSGQPLADVRAEI
ARQVDSGALIKLDSVAGAGNRVLVPRVAYEMEKTIIRHIAEGKEAVQPLMALTPASVLAGLTAGQREATR
TVLENTDRFMAIQGYAGVGKTTQFRAVMGALNTLSESVRPQVIGLGPTHRAVHEMREAGVDARTLASFLS
ETRLAIQAGETPDFRNVLFLTDESSMVGNRDMAELYQLVAAGGGRMVSSGDTAQLQAISTGLPFRLVQQR
SAIDTVVMQEIVRQTPALRPAIESIIAGQVEISLRQVDDVTPQQVPRQPGAWVPDNSVMEIRAPKKEQDQ
VQNIPVAGEQTLTPEQLALVRTDIIEAIRDDWMGRTPEAQQQTLVVAELNADRHAINEAIHTARHEKGDT
GAEERTFTVLEPLRVPDNALRAAETFAEYTGAVAMMNERYWTVAEVDTQDAVVTLRNADGESVLISPQQN
TAQDISLFTPRDLTISQGDRVRFTRSDTDRGYVANSLWEVAGFTDEGAIRFRQGDQEKIVDPQAMTEDRH
IDLAYALTVYGVQGASERFAIALTGTEGGRKRMASLESTYVTLSRAKEHVQVYTDDLAGWSADARHSNAG
QTAHDLLHQKSDHESDTGNRLLATASRLDKTALGRRVLAENGLEGETMARFIAAGKKYPSPYVALPAWTR
HGKAAGALLTEIRIEDDGMRVVLSDESRLRGGEDAQFAGLQASRNGQTLIADDAQTALRLAQENPESGVV
IRLHGEERLLNAARLTGGRITEPDEVERTVRSVAEAESAAKAEDPITLPPDEQQKLAEAQEKAAQELAEQ
ARQDLLPALPGTEGDKPDPLLSASDERRLRDGTERETRELDEAVREAVAEGREPRQQVRDQMQRTEREWV
VNVPEKEIELEKTLGGD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(644-723)

TrwC relaxase (TrwC)

(12-279)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(586-638)

DNA helicase TraI (TraI_C)

(1441-1558)

AAA domain (AAA_30)

(971-1155)


  Protein structure



No available structure.



  Reference


[1] Lu J et al. (2002) Analysis and characterization of the IncFV plasmid pED208 transfer region. Plasmid. 48(1):24-37. [PMID:12206753]
[2] Di Laurenzio L et al. (1991) Characterization of the oriT region of the IncFV plasmid pED208. Mol Microbiol. 5(7):1779-90. [PMID:1943709]


Auxiliary protein

ID   11 GenBank   CAA42174
Name   TraM_pED208 experimental UniProt ID   P33788
Length   127 a.a. PDB ID   3OMY, 3ON0
Note   TraM mediates signalling between transferosome and relaxosome

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14664.68 Da        Isoelectric Point: 4.2626

>CAA42174.1 traM protein (plasmid) [Escherichia coli]
MPKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQEKREGGFNQMEYNKLMLE
NVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFFPDDEDDQE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure


Source ID Structure
PDB 3OMY
PDB 3ON0
AlphaFold DB P33788

  Reference


[1] Lu J et al. (2002) Analysis and characterization of the IncFV plasmid pED208 transfer region. Plasmid. 48(1):24-37. [PMID:12206753]
[2] Di Laurenzio L et al. (1991) Characterization of the oriT region of the IncFV plasmid pED208. Mol Microbiol. 5(7):1779-90. [PMID:1943709]

ID   12 GenBank   CAA42176
Name   TraY_pED208 experimental UniProt ID   P33789
Length   20 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 20 a.a.        Molecular weight: 2351.88 Da        Isoelectric Point: 11.0566

>CAA42176.1 traY protein, partial (plasmid) [Escherichia coli]
MKEPKSNIRKLIDIGGLIGRL

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB P33789

  Reference


[1] Lu J et al. (2002) Analysis and characterization of the IncFV plasmid pED208 transfer region. Plasmid. 48(1):24-37. [PMID:12206753]
[2] Di Laurenzio L et al. (1991) Characterization of the oriT region of the IncFV plasmid pED208. Mol Microbiol. 5(7):1779-90. [PMID:1943709]


T4CP

ID   6 GenBank   YP_009077548
Name   TraD_pED208 experimental UniProt ID   _
Length   736 a.a. PDB ID   _
Note   DNA transport; similar to TraD of plasmid F

  T4CP protein sequence


Download         Length: 736 a.a.        Molecular weight: 82751.10 Da        Isoelectric Point: 5.5334

>YP_009077548.1 TraD (plasmid) [Salmonella enterica subsp. enterica serovar Typhi]
MSLNPRDLTQGGQVAFMRLKMFLQINNLISYYVIMGTVLFGIAVLLMRMSIQNLTNGIIYWFVRVMSPFT
ERMVSQPVYNIRYYEHTLQYSARQILSDNYTVYCGQLLKQELVIAGCASLLVAFVATFAVYWYLGRTGRK
QSEDEIIGGRVLSESPKDVARLLKKRGEASDIRIDDLPLKLDSEIQNFAMHGTVSTGKSTLMRKNLKQLR
DRGDLVIIYDKGCTFVEDFYDESRDEVLNALDTRCPNWDLWEECRTISELENASTTLIPASSGEDPFWQG
SARTIFAEGAERMRKDPDRSYNKFLRTLLAIQLDQLRAFLAGTPASTLVDGKIEKTAISIRSVLTNYVKA
MRYLQGIDRPGRDKFTIREWMKGQADKSKNGWLFITSDEQNHESLKPLISLWLSIAATSLLAMGPNRQRR
VWFFYDELASLHKLATLPRIISEARKFGGCFALGFQNFAQMENIYGPKGAAEIFDLLNTKFFFRSPSAQI
AKFVEEDIGETRRKKFSEQTSFGHEQVRDGISFGKEEERVSIVSYSDVQSLNDLQCFVTLPGSYPVVKLT
MKYDSMPKVADALLLRDVQTSLDKNIEDELVRRTEEERLSLDGLFNPVKPVPEKASTVVTPPLPTQTVTA
SPVPLPAAAAVNTVSTVTTAAGSTAATAVTTEGGSASTGGTERDIEQDLPQDVPPGLNSDGEVVDFAAYE
AWAQNSHQTRDMTRREEVNINHATDKTHEMDDGREY

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(174-562)

F sex factor protein N terminal (TraD_N)

(35-126)

  Protein structure



No available structure.



  Reference


[1] Lu J et al. (2002) Analysis and characterization of the IncFV plasmid pED208 transfer region. Plasmid. 48(1):24-37. [PMID:12206753]
[2] Di Laurenzio L et al. (1991) Characterization of the oriT region of the IncFV plasmid pED208. Mol Microbiol. 5(7):1779-90. [PMID:1943709]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3771..25650

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_0 393..776 + 384 AAM90702 TraM -
Locus_1 1072..1521 + 450 AAM90701 TraJ -
Locus_2 3410..3769 + 360 AAM90703 TraA -
Locus_3 3771..4076 + 306 AAM90704 TraL traL
Locus_4 4096..4659 + 564 AAM90705 TraE traE
Locus_5 4649..5389 + 741 AAM90706 TraK traK
Locus_6 5376..6737 + 1362 AAM90707 TraB traB
Locus_7 6806..7072 + 267 AAM90708 TraR -
Locus_8 7076..7261 + 186 AAM90709 orfX1 -
Locus_9 7245..7535 + 291 AAM90710 orfX2 -
Locus_10 7532..7978 + 447 AAM90711 orfX3 -
Locus_11 7997..8611 + 615 AAM90712 TraV traV
Locus_12 8622..11213 + 2592 AAM90713 TraC virb4
Locus_13 11210..11674 + 465 AAM90714 TrbI -
Locus_14 11674..12309 + 636 AAM90715 TraW traW
Locus_15 12306..13301 + 996 AAM90716 TraU traU
Locus_16 13312..13680 + 369 AAM90717 orfX4 -
Locus_17 13677..14288 + 612 AAM90718 TrbC trbC
Locus_18 14285..16138 + 1854 AAM90719 TraN traN
Locus_19 16135..16914 + 780 AAM90720 TraF traF
Locus_20 16936..17547 + 612 AAM90721 TrbB traF
Locus_21 17547..18908 + 1362 AAM90722 TraH traH
Locus_22 18910..21744 + 2835 AAM90723 TraG traG
Locus_23 21815..22375 + 561 AAM90724 TraS -
Locus_24 22552..23289 + 738 AAM90725 TraT -
Locus_25 23440..25650 + 2211 AAM90726 TraD virb4

Host bacterium

ID   6 GenBank   AF411480
Plasmid name   pED208 Incompatibility group   IncF(IncFV)
Plasmid size   32647 bp Coordinate of oriT [Strand]   1..360 [-]
Host baterium   Salmonella typhi

Cargo genes

Drug resistance gene   _
Virulence gene   _
Metal resistance gene   _
Degradation gene   _
Symbiosis gene   -
Anti-CRISPR   -