Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102871
Name   oriT_pETW41 in_silico
Organism   Edwardsiella piscicida strain ETW41
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP019441 (92019..92169 [-], 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_pETW41
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGTTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2147 GenBank   WP_001337757
Name   TraI_2_BXA22_RS17935_pETW41 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   1814 GenBank   WP_000637386
Name   traC_BXA22_RS17840_pETW41 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.



ID   1815 GenBank   WP_000178856
Name   traD_BXA22_RS17930_pETW41 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 69849..94085

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BXA22_RS17785 (BXA22_17785) 65220..65438 - 219 WP_000260293 hypothetical protein -
BXA22_RS17790 (BXA22_17790) 65452..65721 - 270 WP_000184110 hypothetical protein -
BXA22_RS17795 (BXA22_17795) 65714..65950 - 237 WP_231295916 hypothetical protein -
BXA22_RS17800 (BXA22_17800) 66009..67031 + 1023 WP_012846921 IS21 family transposase -
BXA22_RS17805 (BXA22_17805) 67028..67810 + 783 WP_012846920 IS21-like element ISSen3 family helper ATPase IstB -
BXA22_RS17810 (BXA22_17810) 67877..69745 - 1869 Protein_75 conjugal transfer mating pair stabilization protein TraN -
BXA22_RS17815 (BXA22_17815) 69849..70853 - 1005 WP_043940352 TraU family protein traU
BXA22_RS17820 (BXA22_17820) 70853..71524 - 672 WP_001337754 EAL domain-containing protein -
BXA22_RS17825 (BXA22_17825) 71521..72786 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
BXA22_RS17830 (BXA22_17830) 72749..73279 - 531 WP_001010738 S26 family signal peptidase -
BXA22_RS17835 (BXA22_17835) 73276..73593 - 318 WP_000351984 hypothetical protein -
BXA22_RS17840 (BXA22_17840) 73608..76055 - 2448 WP_000637386 type IV secretion system protein TraC virb4
BXA22_RS17845 (BXA22_17845) 76052..76759 - 708 WP_001259347 DsbC family protein -
BXA22_RS17850 (BXA22_17850) 76908..80537 - 3630 Protein_83 Ig-like domain-containing protein -
BXA22_RS17855 (BXA22_17855) 80626..81648 + 1023 WP_012846921 IS21 family transposase -
BXA22_RS17860 (BXA22_17860) 81645..82427 + 783 WP_012846920 IS21-like element ISSen3 family helper ATPase IstB -
BXA22_RS17865 (BXA22_17865) 82443..84398 - 1956 WP_231295917 DUF4165 domain-containing protein -
BXA22_RS17870 (BXA22_17870) 84599..84991 - 393 WP_000479535 TraA family conjugative transfer protein -
BXA22_RS17875 (BXA22_17875) 84995..85573 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
BXA22_RS17880 (BXA22_17880) 85570..86883 - 1314 WP_024131605 TraB/VirB10 family protein traB
BXA22_RS17885 (BXA22_17885) 86883..87800 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
BXA22_RS17890 (BXA22_17890) 87784..88410 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
BXA22_RS17895 (BXA22_17895) 88407..88688 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
BXA22_RS17900 (BXA22_17900) 88833..89198 - 366 WP_001052531 hypothetical protein -
BXA22_RS18970 89210..89353 - 144 WP_001275801 hypothetical protein -
BXA22_RS17905 (BXA22_17905) 89534..90196 - 663 WP_001231463 hypothetical protein -
BXA22_RS17910 (BXA22_17910) 90196..90573 - 378 WP_000869261 hypothetical protein -
BXA22_RS17915 (BXA22_17915) 90583..91029 - 447 WP_000122506 hypothetical protein -
BXA22_RS17920 (BXA22_17920) 91039..91668 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
BXA22_RS17925 (BXA22_17925) 91625..92209 - 585 WP_000332866 hypothetical protein -
BXA22_RS17930 (BXA22_17930) 92220..94085 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
BXA22_RS17935 (BXA22_17935) 94082..97060 - 2979 WP_001337757 MobH family relaxase -
BXA22_RS17940 (BXA22_17940) 97228..97845 + 618 WP_001249395 hypothetical protein -
BXA22_RS17945 (BXA22_17945) 97827..98060 + 234 WP_080783718 hypothetical protein -

Host bacterium

ID   3314 GenBank   NZ_CP019441
Plasmid name   pETW41 Incompatibility group   IncA/C2
Plasmid size   189588 bp Coordinate of oriT [Strand]   92019..92169 [-]
Host baterium   Edwardsiella piscicida strain ETW41

Cargo genes

Drug resistance gene   dfrA12, aadA2, qacE, sul1, catA2, mph(A), sul2, floR, tet(D), aph(3')-Ia
Virulence gene   -
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -