Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116407
Name   oriT_VGH117|unnamed in_silico
Organism   Shewanella algae strain VGH117
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032414 (108038..108188 [-], 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_VGH117|unnamed
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10487 GenBank   WP_001337757
Name   mobH_D3X10_RS00650_VGH117|unnamed 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   12239 GenBank   WP_000637386
Name   traC_D3X10_RS00570_VGH117|unnamed 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   12240 GenBank   WP_000178856
Name   traD_D3X10_RS00645_VGH117|unnamed 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: 84915..110104

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
D3X10_RS00510 (D3X10_00545) 80042..80950 - 909 WP_000739139 hypothetical protein -
D3X10_RS00515 (D3X10_00550) 80961..81929 - 969 WP_000085162 AAA family ATPase -
D3X10_RS00520 (D3X10_00555) 82149..82334 - 186 WP_001186917 hypothetical protein -
D3X10_RS00525 (D3X10_00560) 82638..82958 - 321 WP_000547566 hypothetical protein -
D3X10_RS00530 (D3X10_00565) 83252..83893 + 642 WP_000796664 hypothetical protein -
D3X10_RS00535 (D3X10_00570) 84016..84876 + 861 WP_000709517 hypothetical protein -
D3X10_RS00540 (D3X10_00575) 84915..87713 - 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
D3X10_RS00545 (D3X10_00580) 87829..88833 - 1005 WP_043940352 TraU family protein traU
D3X10_RS00550 (D3X10_00585) 88833..89504 - 672 WP_001337754 EAL domain-containing protein -
D3X10_RS00555 (D3X10_00590) 89501..90766 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
D3X10_RS00560 (D3X10_00595) 90729..91259 - 531 WP_001010738 S26 family signal peptidase -
D3X10_RS00565 (D3X10_00600) 91256..91573 - 318 WP_000351984 hypothetical protein -
D3X10_RS00570 (D3X10_00605) 91588..94035 - 2448 WP_000637386 type IV secretion system protein TraC virb4
D3X10_RS00575 (D3X10_00610) 94032..94739 - 708 WP_001259347 DsbC family protein -
D3X10_RS00580 (D3X10_00615) 94888..100419 - 5532 WP_000606833 Ig-like domain-containing protein -
D3X10_RS00585 (D3X10_00620) 100620..101012 - 393 WP_000479535 TraA family conjugative transfer protein -
D3X10_RS00590 (D3X10_00625) 101016..101594 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
D3X10_RS00595 (D3X10_00630) 101591..102903 - 1313 Protein_118 TrbI/VirB10 family protein -
D3X10_RS00600 (D3X10_00635) 102903..103820 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
D3X10_RS00605 (D3X10_00640) 103804..104430 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
D3X10_RS00610 (D3X10_00645) 104427..104707 - 281 Protein_121 type IV conjugative transfer system protein TraL -
D3X10_RS00615 (D3X10_00650) 104852..105217 - 366 WP_001052531 hypothetical protein -
D3X10_RS00620 (D3X10_00655) 105553..106215 - 663 WP_001231463 hypothetical protein -
D3X10_RS00625 (D3X10_00660) 106215..106592 - 378 WP_000869261 hypothetical protein -
D3X10_RS00630 (D3X10_00665) 106602..107048 - 447 WP_000122506 hypothetical protein -
D3X10_RS00635 (D3X10_00670) 107058..107687 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
D3X10_RS00640 (D3X10_00675) 107644..108228 - 585 WP_000332866 hypothetical protein -
D3X10_RS00645 (D3X10_00680) 108239..110104 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
D3X10_RS00650 (D3X10_00685) 110101..113079 - 2979 WP_001337757 MobH family relaxase -
D3X10_RS00655 (D3X10_00690) 113246..113863 + 618 WP_001249396 hypothetical protein -

Host bacterium

ID   16840 GenBank   NZ_CP032414
Plasmid name   VGH117|unnamed Incompatibility group   IncA/C2
Plasmid size   132551 bp Coordinate of oriT [Strand]   108038..108188 [-]
Host baterium   Shewanella algae strain VGH117

Cargo genes

Drug resistance gene   tet(A), floR, sul2, aph(3'')-Ib, aph(6)-Id
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -