Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103037
Name   oriT1_R16a in_silico
Organism   Escherichia coli strain K-12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX156773 (34367..34432 [-], 66 nt)
oriT length   66 nt
IRs (inverted repeats)      25..32, 35..42  (TAACCGGC..GCCGGTTA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 66 nt

>oriT1_R16a
CGAATAAGGGACAGTGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCACCCATCCTGCCCGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2270 GenBank   WP_001326173
Name   TraI_2_HTI74_RS00455_R16a insolico UniProt ID   F5BPR1
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109356.90 Da        Isoelectric Point: 4.9395

>WP_001326173.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB F5BPR1


T4CP

ID   1968 GenBank   WP_000178857
Name   traD_HTI74_RS00460_R16a 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   1969 GenBank   WP_020833628
Name   traC_HTI74_RS00540_R16a 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: 62091..87237

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTI74_RS00445 58122..58355 - 234 WP_001191890 hypothetical protein -
HTI74_RS00450 58337..58954 - 618 WP_001249395 hypothetical protein -
HTI74_RS00455 59122..62094 + 2973 WP_001326173 MobH family relaxase -
HTI74_RS00460 62091..63956 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HTI74_RS00465 63967..64551 + 585 WP_000332868 hypothetical protein -
HTI74_RS00470 64508..65137 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HTI74_RS00475 65147..65593 + 447 WP_000122507 hypothetical protein -
HTI74_RS00480 65603..65980 + 378 WP_000869297 hypothetical protein -
HTI74_RS00485 65980..66642 + 663 WP_001231464 hypothetical protein -
HTI74_RS00490 66823..66966 + 144 WP_001275801 hypothetical protein -
HTI74_RS00495 66978..67343 + 366 WP_001052531 hypothetical protein -
HTI74_RS00500 67488..67769 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTI74_RS00505 67766..68392 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HTI74_RS00510 68376..69293 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTI74_RS00515 69293..70606 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTI74_RS00520 70603..71181 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTI74_RS00525 71185..71577 + 393 WP_000479535 TraA family conjugative transfer protein -
HTI74_RS00530 71778..77264 + 5487 WP_000606835 Ig-like domain-containing protein -
HTI74_RS00535 77413..78120 + 708 WP_001259346 DsbC family protein -
HTI74_RS00540 78117..80564 + 2448 WP_020833628 type IV secretion system protein TraC virb4
HTI74_RS00545 80579..80896 + 318 WP_000351984 hypothetical protein -
HTI74_RS00550 80893..81423 + 531 WP_001010740 S26 family signal peptidase -
HTI74_RS00555 81386..82651 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
HTI74_RS00560 82648..83319 + 672 WP_000575345 EAL domain-containing protein -
HTI74_RS00565 83319..84323 + 1005 WP_005507569 TraU family protein traU
HTI74_RS00570 84439..87237 + 2799 WP_072503043 conjugal transfer mating pair stabilization protein TraN traN
HTI74_RS00575 87276..88136 - 861 WP_000709517 hypothetical protein -
HTI74_RS00580 88259..88900 - 642 WP_000796664 hypothetical protein -
HTI74_RS00585 89194..89514 + 321 WP_000547566 hypothetical protein -
HTI74_RS00590 89818..90003 + 186 WP_001186917 hypothetical protein -
HTI74_RS00595 90223..91191 + 969 WP_000085162 AAA family ATPase -
HTI74_RS00600 91202..92110 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   3480 GenBank   NZ_KX156773
Plasmid name   R16a Incompatibility group   IncA/C2
Plasmid size   173094 bp Coordinate of oriT [Strand]   34367..34432 [-]; 64007..64157 [+]
Host baterium   Escherichia coli strain K-12

Cargo genes

Drug resistance gene   sul2, blaTEM-2, aph(3')-Ia
Virulence gene   -
Metal resistance gene   arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -