Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121627
Name   oriT_pVFN3-blaOXA-193K in_silico
Organism   Vibrio furnissii strain VFN3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP089604 (74090..74240 [+], 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_pVFN3-blaOXA-193K
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13642 GenBank   WP_001337757
Name   mobH_LUM42_RS16410_pVFN3-blaOXA-193K 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   15945 GenBank   WP_000178856
Name   traD_LUM42_RS16415_pVFN3-blaOXA-193K 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   15946 GenBank   WP_000637386
Name   traC_LUM42_RS16500_pVFN3-blaOXA-193K 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: 72174..98679

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LUM42_RS16400 (LUM42_16400) 68199..68432 - 234 WP_001191892 hypothetical protein -
LUM42_RS16405 (LUM42_16405) 68414..69031 - 618 WP_001249396 hypothetical protein -
LUM42_RS16410 (LUM42_16410) 69199..72177 + 2979 WP_001337757 MobH family relaxase -
LUM42_RS16415 (LUM42_16415) 72174..74039 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
LUM42_RS16420 (LUM42_16420) 74089..74634 + 546 WP_000228720 hypothetical protein -
LUM42_RS16425 (LUM42_16425) 74591..75220 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
LUM42_RS16430 (LUM42_16430) 75230..75676 + 447 WP_000122506 hypothetical protein -
LUM42_RS16435 (LUM42_16435) 75686..76063 + 378 WP_000869261 hypothetical protein -
LUM42_RS16440 (LUM42_16440) 76134..76724 + 591 WP_002210536 hypothetical protein -
LUM42_RS16445 (LUM42_16445) 76801..78012 + 1212 WP_191694817 IS256 family transposase -
LUM42_RS16450 (LUM42_16450) 78220..78363 + 144 WP_001275801 hypothetical protein -
LUM42_RS16455 (LUM42_16455) 78375..78740 + 366 WP_001052531 hypothetical protein -
LUM42_RS16460 (LUM42_16460) 78885..79166 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
LUM42_RS16465 (LUM42_16465) 79163..79789 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
LUM42_RS16470 (LUM42_16470) 79773..80690 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
LUM42_RS16475 (LUM42_16475) 80690..82003 + 1314 WP_024131605 TraB/VirB10 family protein traB
LUM42_RS16480 (LUM42_16480) 82000..82578 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
LUM42_RS16485 (LUM42_16485) 82582..82974 + 393 WP_000479535 TraA family conjugative transfer protein -
LUM42_RS16490 (LUM42_16490) 83175..88706 + 5532 WP_000606833 Ig-like domain-containing protein -
LUM42_RS16495 (LUM42_16495) 88855..89562 + 708 WP_001259347 DsbC family protein -
LUM42_RS16500 (LUM42_16500) 89559..92006 + 2448 WP_000637386 type IV secretion system protein TraC virb4
LUM42_RS16505 (LUM42_16505) 92021..92338 + 318 WP_000351984 hypothetical protein -
LUM42_RS16510 (LUM42_16510) 92335..92865 + 531 WP_001010738 S26 family signal peptidase -
LUM42_RS16515 (LUM42_16515) 92828..94093 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
LUM42_RS16520 (LUM42_16520) 94090..94761 + 672 WP_001337754 EAL domain-containing protein -
LUM42_RS16525 (LUM42_16525) 94761..95765 + 1005 WP_043940352 TraU family protein traU
LUM42_RS16530 (LUM42_16530) 95881..98679 + 2799 WP_232658890 conjugal transfer mating pair stabilization protein TraN traN
LUM42_RS16535 (LUM42_16535) 98718..99578 - 861 WP_000709517 hypothetical protein -
LUM42_RS16540 (LUM42_16540) 99701..100342 - 642 WP_000796664 hypothetical protein -
LUM42_RS16545 (LUM42_16545) 100636..100956 + 321 WP_000547566 hypothetical protein -
LUM42_RS16550 (LUM42_16550) 101260..101445 + 186 WP_001186917 hypothetical protein -
LUM42_RS16555 (LUM42_16555) 101665..102633 + 969 WP_000085162 AAA family ATPase -
LUM42_RS16560 (LUM42_16560) 102644..103552 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   22054 GenBank   NZ_CP089604
Plasmid name   pVFN3-blaOXA-193K Incompatibility group   IncA/C2
Plasmid size   193896 bp Coordinate of oriT [Strand]   74090..74240 [+]
Host baterium   Vibrio furnissii strain VFN3

Cargo genes

Drug resistance gene   aac(3)-IId, tet(D), floR, sul2, aac(6')-Ib-cr, blaOXA-1, catB3, ARR-3, qacE, sul1, mph(A)
Virulence gene   -
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -