Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101543
Name   oriT_pAR-0421-2 in_silico
Organism   Shigella flexneri strain AR-0421
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_WACK01000003 (140770..140920 [+], 151 nt)
oriT length   151 nt
IRs (inverted repeats)      93..98, 106..111  (TGGCCT..AGGCCA)
 12..17, 24..29  (AACCCT..AGGGTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT_pAR-0421-2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1368 GenBank   WP_001337757
Name   mobH_F4V33_RS15830_pAR-0421-2 insolico UniProt ID   A0A709FRI2
Length   992 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 992 a.a.        Molecular weight: 109581.85 Da        Isoelectric Point: 4.8956

>WP_001337757.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREDPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A709FRI2


T4CP

ID   995 GenBank   WP_000178856
Name   traD_F4V33_RS15835_pAR-0421-2 insolico UniProt ID   _
Length   621 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 621 a.a.        Molecular weight: 69197.66 Da        Isoelectric Point: 6.9403

>WP_000178856.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKAKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(471-598)

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

(170-297)

  Protein structure



No available structure.



ID   996 GenBank   WP_000637386
Name   traC_F4V33_RS15910_pAR-0421-2 insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 92590.87 Da        Isoelectric Point: 5.9222

>WP_000637386.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTERIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRQQAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(449-809)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 138854..164043

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
F4V33_RS15820 134879..135112 - 234 WP_001191892 hypothetical protein -
F4V33_RS15825 135094..135711 - 618 WP_001249396 hypothetical protein -
F4V33_RS15830 135879..138857 + 2979 WP_001337757 MobH family relaxase -
F4V33_RS15835 138854..140719 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
F4V33_RS15840 140769..141314 + 546 WP_000228720 hypothetical protein -
F4V33_RS15845 141271..141900 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
F4V33_RS15850 141910..142356 + 447 WP_000122506 hypothetical protein -
F4V33_RS15855 142366..142743 + 378 WP_000869261 hypothetical protein -
F4V33_RS15860 142743..143405 + 663 WP_001231463 hypothetical protein -
F4V33_RS27160 143586..143729 + 144 WP_001275801 hypothetical protein -
F4V33_RS15865 143741..144106 + 366 WP_001052531 hypothetical protein -
F4V33_RS15870 144251..144531 + 281 Protein_180 type IV conjugative transfer system protein TraL -
F4V33_RS15875 144528..145154 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
F4V33_RS15880 145138..146055 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
F4V33_RS15885 146055..147367 + 1313 Protein_183 TrbI/VirB10 family protein -
F4V33_RS15890 147364..147942 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
F4V33_RS15895 147946..148338 + 393 WP_000479535 TraA family conjugative transfer protein -
F4V33_RS15900 148539..154070 + 5532 WP_000606833 Ig-like domain-containing protein -
F4V33_RS15905 154219..154926 + 708 WP_001259347 DsbC family protein -
F4V33_RS15910 154923..157370 + 2448 WP_000637386 type IV secretion system protein TraC virb4
F4V33_RS15915 157385..157702 + 318 WP_000351984 hypothetical protein -
F4V33_RS15920 157699..158229 + 531 WP_001010738 S26 family signal peptidase -
F4V33_RS15925 158192..159457 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
F4V33_RS15930 159454..160125 + 672 WP_001337754 EAL domain-containing protein -
F4V33_RS15935 160125..161129 + 1005 WP_043940352 TraU family protein traU
F4V33_RS15940 161245..164043 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
F4V33_RS15945 164082..164942 - 861 WP_000709517 hypothetical protein -
F4V33_RS15950 165065..165706 - 642 WP_000796664 hypothetical protein -
F4V33_RS15955 166000..166320 + 321 WP_000547566 hypothetical protein -
F4V33_RS15960 166624..166809 + 186 WP_001186917 hypothetical protein -
F4V33_RS15965 167029..167997 + 969 WP_000085162 AAA family ATPase -
F4V33_RS15970 168008..168916 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   1987 GenBank   NZ_WACK01000003
Plasmid name   pAR-0421-2 Incompatibility group   IncA/C2
Plasmid size   185215 bp Coordinate of oriT [Strand]   140770..140920 [+]
Host baterium   Shigella flexneri strain AR-0421

Cargo genes

Drug resistance gene   dfrA5, ere(A), qacE, sul1, blaTEM-1B, aac(3)-IIa, blaSCO-1, blaCTX-M-3
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -