Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113289
Name   oriT_pYUGDPS1-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain GD19PS1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP098835 (54379..54632 [+], 254 nt)
oriT length   254 nt
IRs (inverted repeats)      152..157, 159..164  (AAAAGT..ACTTTT)
 121..129, 134..142  (TTAAGGCTT..AAGCCTTAA)
 50..55, 59..64  (AATTTT..AAAATT)
Location of nic site      77..78
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 254 nt

>oriT_pYUGDPS1-1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8524 GenBank   WP_000980119
Name   mobH_NFH28_RS24650_pYUGDPS1-1 insolico UniProt ID   A0A0H3VVI8
Length   1050 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1050 a.a.        Molecular weight: 118035.42 Da        Isoelectric Point: 4.6054

>WP_000980119.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDT
VETAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVG
SCATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(108-304)


  Protein structure


Source ID Structure
AlphaFold DB A0A0H3VVI8


T4CP

ID   9840 GenBank   WP_046788497
Name   traD_NFH28_RS24645_pYUGDPS1-1 insolico UniProt ID   _
Length   694 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 694 a.a.        Molecular weight: 78171.95 Da        Isoelectric Point: 8.0177

>WP_046788497.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANETLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKFH

  Protein domains


Predicted by InterproScan.

AAA-like domain (AAA_10)

(199-249)

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

(406-609)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 215320..224527

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NFH28_RS25490 (NFH28_25490) 215320..218001 - 2682 WP_000387412 TraC family protein virb4
NFH28_RS25495 (NFH28_25495) 218010..218960 - 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
NFH28_RS25500 (NFH28_25500) 218970..219722 - 753 WP_183079335 protein-disulfide isomerase HtdT -
NFH28_RS25505 (NFH28_25505) 219841..220323 - 483 WP_000377633 hypothetical protein -
NFH28_RS25510 (NFH28_25510) 220331..221686 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
NFH28_RS25515 (NFH28_25515) 221676..222137 - 462 WP_000521240 plasmid transfer protein HtdO -
NFH28_RS25520 (NFH28_25520) 222139..223410 - 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
NFH28_RS25525 (NFH28_25525) 223410..224198 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
NFH28_RS25530 (NFH28_25530) 224210..224527 - 318 WP_000043357 type IV conjugative transfer system protein TraL traL
NFH28_RS25535 (NFH28_25535) 224578..224931 - 354 WP_000423602 hypothetical protein -
NFH28_RS25540 (NFH28_25540) 226080..226955 - 876 WP_000594612 RepB family plasmid replication initiator protein -
NFH28_RS25545 (NFH28_25545) 227432..228487 + 1056 WP_001065779 hypothetical protein -
NFH28_RS25550 (NFH28_25550) 228505..228705 + 201 WP_000594931 hypothetical protein -
NFH28_RS25555 (NFH28_25555) 228702..229418 + 717 WP_046788421 zinc finger-like domain-containing protein -

Host bacterium

ID   13724 GenBank   NZ_CP098835
Plasmid name   pYUGDPS1-1 Incompatibility group   -
Plasmid size   241147 bp Coordinate of oriT [Strand]   54379..54632 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain GD19PS1

Cargo genes

Drug resistance gene   oqxB, oqxA, aadA2, cmlA1, ant(3'')-Ia, sul3, aph(3')-Ia, floR, sul2, aph(4)-Ia, aac(3)-IVa, aac(6')-Ib-cr, blaOXA-1, catB3, ARR-3, qacE, sul1
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -