Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113539
Name   oriT_1205p1 in_silico
Organism   Shigella flexneri 4c strain 1205
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP012141 (183360..183613 [-], 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_1205p1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8676 GenBank   WP_241390991
Name   mobH_AD871_RS26185_1205p1 insolico UniProt ID   _
Length   1021 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1021 a.a.        Molecular weight: 114700.45 Da        Isoelectric Point: 4.5826

>WP_241390991.1 MobH family relaxase [Shigella flexneri]
MIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPTGIQTFNEQSILSLYREKLHSISMMLAISD
SDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGGLLSHSLEVAILSLKNAHHSELRPIGYQDE
EVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWTPSSQSLLDWARENDVVEYEIHWRKRIHNQ
HNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYTDGNDFLSKCVRTADFYSTGTDLNVLRDPI
MGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGEVYLNENAFLDFVLNDFELHKYNFPQGEAG
KTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFRNGIGKLEFYNLLKLRWIGLIFDSYKIPDS
VPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDTVETAVLKVNDLGRSTASIDVDIHSKKNEG
SSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESEDESAKDTESHVLVNQLHELLLSAPLSNDY
IVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGSLDGMWIVRDIDDLRLVQLGDNCAGFQLTY
HEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLELPPPRVNAVEEHSGDVEYHGTDSASATGP
LKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVGSCATSSSVHNEKLLPEPSELPELNREQNA
DPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAAATSVMASEEPALPPVLEESNGEHAPTDAK
GHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPASPVSGHNLNSKVFATTESDQNGEFSLISEG
DVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTLYLTQSCVEKFGSQLEAQDLFNKLPQYLVN
SGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(79-275)


  Protein structure



No available structure.




T4CP

ID   10033 GenBank   WP_046788497
Name   traD_AD871_RS26190_1205p1 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: 2429..11636

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AD871_RS25135 (AD871_25305) 1..876 + 876 WP_000594612 RepB family plasmid replication initiator protein -
AD871_RS25150 (AD871_25320) 1998..2378 + 381 WP_012006610 hypothetical protein -
AD871_RS25155 (AD871_25325) 2429..2746 + 318 WP_000043357 type IV conjugative transfer system protein TraL traL
AD871_RS25160 (AD871_25330) 2758..3546 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
AD871_RS25165 (AD871_25335) 3546..4817 + 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
AD871_RS25170 (AD871_25340) 4819..5280 + 462 WP_000521240 plasmid transfer protein HtdO -
AD871_RS25175 (AD871_25345) 5270..6625 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
AD871_RS25180 (AD871_25350) 6633..7115 + 483 WP_000377633 hypothetical protein -
AD871_RS25185 (AD871_25355) 7234..7986 + 753 WP_183079335 protein-disulfide isomerase HtdT -
AD871_RS25190 (AD871_25360) 7996..8946 + 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
AD871_RS25195 (AD871_25365) 8955..11636 + 2682 WP_000387412 TraC family protein virb4

Host bacterium

ID   13974 GenBank   NZ_CP012141
Plasmid name   1205p1 Incompatibility group   IncHI2A
Plasmid size   248368 bp Coordinate of oriT [Strand]   183360..183613 [-]
Host baterium   Shigella flexneri 4c strain 1205

Cargo genes

Drug resistance gene   sul1, qacE, ARR-3, catB3, blaOXA-1, aac(6')-Ib-cr, aac(3)-IVa, aph(4)-Ia, sul2, mph(A), fosA3, blaCTX-M-123
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -