Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117448
Name   oriT_pNUITM-VS2_2 in_silico
Organism   Shewanella xiamenensis strain NUITM-VS2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP026734 (49212..49362 [+], 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_pNUITM-VS2_2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11112 GenBank   WP_001337757
Name   mobH_OO995_RS22310_pNUITM-VS2_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   12981 GenBank   WP_000178856
Name   traD_OO995_RS22315_pNUITM-VS2_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   12982 GenBank   WP_000637386
Name   traC_OO995_RS22395_pNUITM-VS2_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: 47296..72487

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OO995_RS22300 (NUITMVS2_43500) 43321..43554 - 234 WP_001191892 hypothetical protein -
OO995_RS22305 (NUITMVS2_43510) 43536..44153 - 618 WP_001249396 hypothetical protein -
OO995_RS22310 (NUITMVS2_43520) 44321..47299 + 2979 WP_001337757 MobH family relaxase -
OO995_RS22315 (NUITMVS2_43530) 47296..49161 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
OO995_RS22320 (NUITMVS2_43540) 49211..49756 + 546 WP_000228720 hypothetical protein -
OO995_RS22325 (NUITMVS2_43550) 49713..50342 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
OO995_RS22330 50352..50798 + 447 WP_000122506 hypothetical protein -
OO995_RS22335 (NUITMVS2_43570) 50808..51185 + 378 WP_000869261 hypothetical protein -
OO995_RS22340 (NUITMVS2_43580) 51185..51847 + 663 WP_001231463 hypothetical protein -
OO995_RS22345 52028..52171 + 144 WP_001275801 hypothetical protein -
OO995_RS22350 (NUITMVS2_43590) 52183..52548 + 366 WP_001052531 hypothetical protein -
OO995_RS22355 (NUITMVS2_43600) 52693..52974 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
OO995_RS22360 (NUITMVS2_43610) 52971..53597 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
OO995_RS22365 (NUITMVS2_43620) 53581..54498 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
OO995_RS22370 (NUITMVS2_43630) 54498..55811 + 1314 WP_024131605 TraB/VirB10 family protein traB
OO995_RS22375 (NUITMVS2_43640) 55808..56386 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
OO995_RS22380 (NUITMVS2_43650) 56390..56782 + 393 WP_000479535 TraA family conjugative transfer protein -
OO995_RS22385 (NUITMVS2_43660) 56983..62514 + 5532 WP_000606833 Ig-like domain-containing protein -
OO995_RS22390 (NUITMVS2_43670) 62663..63370 + 708 WP_001259347 DsbC family protein -
OO995_RS22395 (NUITMVS2_43680) 63367..65814 + 2448 WP_000637386 type IV secretion system protein TraC virb4
OO995_RS22400 (NUITMVS2_43690) 65829..66146 + 318 WP_000351984 hypothetical protein -
OO995_RS22405 (NUITMVS2_43700) 66143..66673 + 531 WP_001010738 S26 family signal peptidase -
OO995_RS22410 (NUITMVS2_43710) 66636..67901 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
OO995_RS22415 (NUITMVS2_43720) 67898..68569 + 672 WP_001337754 EAL domain-containing protein -
OO995_RS22420 68569..69573 + 1005 WP_043940352 TraU family protein traU
OO995_RS22425 (NUITMVS2_43740) 69689..72487 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
OO995_RS22430 (NUITMVS2_43750) 72526..73386 - 861 WP_000709517 hypothetical protein -
OO995_RS22435 (NUITMVS2_43760) 73509..74150 - 642 WP_000796664 hypothetical protein -
OO995_RS22440 (NUITMVS2_43770) 74444..74764 + 321 WP_000547566 hypothetical protein -
OO995_RS22445 (NUITMVS2_43780) 75068..75253 + 186 WP_001186917 hypothetical protein -
OO995_RS22450 (NUITMVS2_43790) 75473..76441 + 969 WP_000085162 AAA family ATPase -
OO995_RS22455 (NUITMVS2_43800) 76452..77360 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   17881 GenBank   NZ_AP026734
Plasmid name   pNUITM-VS2_2 Incompatibility group   IncA/C2
Plasmid size   152182 bp Coordinate of oriT [Strand]   49212..49362 [+]
Host baterium   Shewanella xiamenensis strain NUITM-VS2

Cargo genes

Drug resistance gene   tet(X4)
Virulence gene   -
Metal resistance gene   ncrA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -