Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103243
Name   oriT_pIP40a in_silico
Organism   Pseudomonas aeruginosa strain IP40a
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX709966 (69982..70132 [+], 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_pIP40a
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2425 GenBank   WP_172688147
Name   TraI_2_HTK50_RS00475_pIP40a insolico UniProt ID   _
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109338.87 Da        Isoelectric Point: 4.9395

>WP_172688147.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPIFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   2187 GenBank   WP_000178857
Name   traD_HTK50_RS00480_pIP40a 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: 69225.71 Da        Isoelectric Point: 6.9403

>WP_000178857.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

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

(170-299)

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

(471-598)

  Protein structure



No available structure.



ID   2188 GenBank   WP_020833628
Name   traC_HTK50_RS00560_pIP40a 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: 92590.83 Da        Isoelectric Point: 5.9216

>WP_020833628.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
GPTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(21-255)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraG P-loop domain (P-loop_TraG)

(449-809)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 68066..93212

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTK50_RS00465 64097..64330 - 234 WP_001191890 hypothetical protein -
HTK50_RS00470 64312..64929 - 618 WP_001249395 hypothetical protein -
HTK50_RS00475 65097..68069 + 2973 WP_172688147 MobH family relaxase -
HTK50_RS00480 68066..69931 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HTK50_RS00485 69942..70526 + 585 WP_000332868 hypothetical protein -
HTK50_RS00490 70483..71112 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HTK50_RS00495 71122..71568 + 447 WP_000122507 hypothetical protein -
HTK50_RS00500 71578..71955 + 378 WP_000869297 hypothetical protein -
HTK50_RS00505 71955..72617 + 663 WP_001231464 hypothetical protein -
HTK50_RS00510 72798..72941 + 144 WP_001275801 hypothetical protein -
HTK50_RS00515 72941..73318 + 378 WP_000509509 hypothetical protein -
HTK50_RS00520 73463..73744 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTK50_RS00525 73741..74367 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HTK50_RS00530 74351..75268 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTK50_RS00535 75268..76581 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTK50_RS00540 76578..77156 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTK50_RS00545 77160..77552 + 393 WP_000479535 TraA family conjugative transfer protein -
HTK50_RS00550 77753..83239 + 5487 WP_000606835 Ig-like domain-containing protein -
HTK50_RS00555 83388..84095 + 708 WP_001259346 DsbC family protein -
HTK50_RS00560 84092..86539 + 2448 WP_020833628 type IV secretion system protein TraC virb4
HTK50_RS00565 86554..86871 + 318 Protein_112 hypothetical protein -
HTK50_RS00570 86868..87398 + 531 WP_001010740 S26 family signal peptidase -
HTK50_RS00575 87361..88626 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
HTK50_RS00580 88623..89294 + 672 WP_000575345 EAL domain-containing protein -
HTK50_RS00585 89294..90298 + 1005 WP_005507569 TraU family protein traU
HTK50_RS00590 90414..93212 + 2799 WP_072503043 conjugal transfer mating pair stabilization protein TraN traN
HTK50_RS00595 93251..94111 - 861 WP_172688148 hypothetical protein -
HTK50_RS00600 94234..94875 - 642 WP_000796664 hypothetical protein -
HTK50_RS00605 95169..95489 + 321 WP_000547566 hypothetical protein -
HTK50_RS00610 95793..95978 + 186 WP_001186917 hypothetical protein -
HTK50_RS00615 96198..97166 + 969 WP_000085162 AAA family ATPase -
HTK50_RS00620 97177..98085 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   3686 GenBank   NZ_KX709966
Plasmid name   pIP40a Incompatibility group   IncA/C2
Plasmid size   167554 bp Coordinate of oriT [Strand]   69982..70132 [+]
Host baterium   Pseudomonas aeruginosa strain IP40a

Cargo genes

Drug resistance gene   sul2, blaTEM-1D, aph(3')-Ia
Virulence gene   -
Metal resistance gene   arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -