Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107968
Name   oriT_pIncA in_silico
Organism   Shigella sp. FC130
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MECU01000088 (110577..110727 [-], 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_pIncA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5344 GenBank   WP_069369999
Name   mobH_BGK50_RS18695_pIncA insolico UniProt ID   A0A9X5ML25
Length   995 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 995 a.a.        Molecular weight: 110008.37 Da        Isoelectric Point: 4.9482

>WP_069369999.1 MobH family relaxase [Shigella sp. FC130]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKQRKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFL
PSGVTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPL
LKKRQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   5627 GenBank   WP_011872839
Name   traC_BGK50_RS18620_pIncA 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: 92576.85 Da        Isoelectric Point: 5.9216

>WP_011872839.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
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   5628 GenBank   WP_000178857
Name   traD_BGK50_RS18690_pIncA 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 87450..112643

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BGK50_RS18560 (BGK50_10560) 82581..83486 - 906 WP_021293644 hypothetical protein -
BGK50_RS18565 (BGK50_10565) 83497..84465 - 969 WP_000085162 AAA family ATPase -
BGK50_RS18570 (BGK50_10570) 84685..84870 - 186 WP_001186917 hypothetical protein -
BGK50_RS18575 (BGK50_10575) 85174..85494 - 321 WP_000547566 hypothetical protein -
BGK50_RS18580 (BGK50_10580) 85787..86428 + 642 WP_024126923 hypothetical protein -
BGK50_RS18585 (BGK50_10585) 86551..87411 + 861 WP_069369991 hypothetical protein -
BGK50_RS18590 (BGK50_10590) 87450..90248 - 2799 WP_069369992 conjugal transfer mating pair stabilization protein TraN traN
BGK50_RS18595 (BGK50_10595) 90364..91371 - 1008 WP_069369993 TraU family protein traU
BGK50_RS18600 (BGK50_10600) 91368..92039 - 672 WP_069369994 EAL domain-containing protein -
BGK50_RS18605 (BGK50_10605) 92036..93301 - 1266 WP_069369995 TrbC family F-type conjugative pilus assembly protein traW
BGK50_RS18610 (BGK50_10610) 93264..93794 - 531 WP_021293639 S26 family signal peptidase -
BGK50_RS18615 (BGK50_10615) 93791..94108 - 318 WP_011872858 hypothetical protein -
BGK50_RS18620 (BGK50_10620) 94123..96570 - 2448 WP_011872839 type IV secretion system protein TraC virb4
BGK50_RS18625 (BGK50_10625) 96567..97274 - 708 WP_001259347 DsbC family protein -
BGK50_RS18630 (BGK50_10630) 97423..102954 - 5532 WP_069369996 Ig-like domain-containing protein -
BGK50_RS18635 (BGK50_10635) 103155..103538 - 384 WP_024126917 TraA family conjugative transfer protein -
BGK50_RS18640 (BGK50_10640) 103551..104129 - 579 WP_069369998 type IV conjugative transfer system lipoprotein TraV traV
BGK50_RS18645 (BGK50_10645) 104126..105442 - 1317 WP_069370021 TrbI/VirB10 family protein traB
BGK50_RS18650 (BGK50_10650) 105442..106359 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
BGK50_RS18655 (BGK50_10655) 106343..106969 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
BGK50_RS18660 (BGK50_10660) 106966..107247 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
BGK50_RS18665 (BGK50_10665) 107391..107756 - 366 WP_001052531 hypothetical protein -
BGK50_RS20680 107768..107911 - 144 WP_001275801 hypothetical protein -
BGK50_RS18670 (BGK50_10670) 108092..108754 - 663 WP_021293632 hypothetical protein -
BGK50_RS18675 (BGK50_10675) 108754..109131 - 378 WP_000869261 hypothetical protein -
BGK50_RS20685 109373..109549 - 177 WP_169342285 hypothetical protein -
BGK50_RS18680 (BGK50_10680) 109597..110226 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
BGK50_RS18685 (BGK50_10685) 110183..110728 - 546 WP_000228720 hypothetical protein -
BGK50_RS18690 (BGK50_10690) 110778..112643 - 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
BGK50_RS18695 (BGK50_10695) 112640..115627 - 2988 WP_069369999 MobH family relaxase -
BGK50_RS18700 (BGK50_10700) 115795..116412 + 618 WP_001249396 hypothetical protein -
BGK50_RS18705 (BGK50_10705) 116394..116627 + 234 WP_001191892 hypothetical protein -

Host bacterium

ID   8403 GenBank   NZ_MECU01000088
Plasmid name   pIncA Incompatibility group   IncA/C2
Plasmid size   145472 bp Coordinate of oriT [Strand]   110577..110727 [-]
Host baterium   Shigella sp. FC130

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -