Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117855
Name   oriT_SWHE2|unnamed1 in_silico
Organism   Shigella dysenteriae strain SWHE2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055064 (232777..233030 [+], 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_SWHE2|unnamed1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11344 GenBank   WP_001011151
Name   mobH_HUZ65_RS24775_SWHE2|unnamed1 insolico UniProt ID   A0A1P8VU63
Length   1048 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1048 a.a.        Molecular weight: 117773.04 Da        Isoelectric Point: 4.6054

>WP_001011151.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPTGI
QTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGGLL
SHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWTPS
SQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYTDG
NDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGEVY
LNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFRNG
IGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDTVE
TAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESEDE
SAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGSLD
GMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLELP
PPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVGSC
ATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAAAT
SVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPASPV
SGHNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTLYL
TQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(106-302)


  Protein structure


Source ID Structure
AlphaFold DB A0A1P8VU63


T4CP

ID   13259 GenBank   WP_001284076
Name   traD_HUZ65_RS24770_SWHE2|unnamed1 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: 78137.93 Da        Isoelectric Point: 8.0177

>WP_001284076.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANETLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH

  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: 144946..154153

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ65_RS24320 (HUZ65_24150) 140083..141336 - 1254 WP_001050364 ParA family protein -
HUZ65_RS24325 (HUZ65_24155) 144946..147627 - 2682 WP_000387412 TraC family protein virb4
HUZ65_RS24330 (HUZ65_24160) 147636..148586 - 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
HUZ65_RS24335 (HUZ65_24165) 148596..149348 - 753 WP_183079335 protein-disulfide isomerase HtdT -
HUZ65_RS24340 (HUZ65_24170) 149467..149949 - 483 WP_065311104 transcriptional regulator -
HUZ65_RS24345 (HUZ65_24175) 149957..151312 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
HUZ65_RS24350 (HUZ65_24180) 151302..151763 - 462 WP_000521240 plasmid transfer protein HtdO -
HUZ65_RS24355 (HUZ65_24185) 151765..153036 - 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
HUZ65_RS24360 (HUZ65_24190) 153036..153824 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
HUZ65_RS24365 (HUZ65_24195) 153836..154153 - 318 WP_000043356 type IV conjugative transfer system protein TraL traL
HUZ65_RS24370 (HUZ65_24200) 154204..154557 - 354 WP_000423602 hypothetical protein -
HUZ65_RS24375 (HUZ65_24205) 155706..156581 - 876 WP_000594612 RepB family plasmid replication initiator protein -
HUZ65_RS24380 (HUZ65_24210) 157058..158113 + 1056 WP_065311103 hypothetical protein -
HUZ65_RS24385 (HUZ65_24215) 158131..158331 + 201 WP_000594931 hypothetical protein -
HUZ65_RS24390 (HUZ65_24220) 158328..159044 + 717 WP_000838218 zinc finger-like domain-containing protein -

Host bacterium

ID   18288 GenBank   NZ_CP055064
Plasmid name   SWHE2|unnamed1 Incompatibility group   IncHI2A
Plasmid size   315105 bp Coordinate of oriT [Strand]   232777..233030 [+]
Host baterium   Shigella dysenteriae strain SWHE2

Cargo genes

Drug resistance gene   tet(A), aph(6)-Id, floR, aac(3)-IId, blaLAP-2, blaTEM-1B, blaCTX-M-55, qnrS13, aph(3')-Ia, dfrA14, ARR-3, mph(A), sul2, ant(3'')-Ia, lnu(F), sul3
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW, merR, merT, merP, merA, merD, merE, silE, silS, silR, silC, silF, silB, silA, silP, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -