Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105528
Name   oriT_pSHE-CTX-M in_silico
Organism   Shewanella bicestrii strain JAB-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP022359 (190763..190913 [+], 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_pSHE-CTX-M
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3768 GenBank   WP_001337757
Name   mobH_CF168_RS22160_pSHE-CTX-M 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   3759 GenBank   WP_000637386
Name   traC_CF168_RS21035_pSHE-CTX-M 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   3760 GenBank   WP_000178856
Name   traD_CF168_RS22165_pSHE-CTX-M 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: 906..20700

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CF168_RS22410 241..384 + 144 WP_001275801 hypothetical protein -
CF168_RS20990 (CF168_20990) 396..761 + 366 WP_001052531 hypothetical protein -
CF168_RS20995 (CF168_20995) 906..1187 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
CF168_RS21000 (CF168_21000) 1184..1810 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
CF168_RS21005 (CF168_21005) 1794..2711 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
CF168_RS21010 (CF168_21010) 2711..4024 + 1314 WP_024131605 TraB/VirB10 family protein traB
CF168_RS21015 (CF168_21015) 4021..4599 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
CF168_RS21020 (CF168_21020) 4603..4995 + 393 WP_000479535 TraA family conjugative transfer protein -
CF168_RS21025 (CF168_21025) 5196..10727 + 5532 WP_000606833 Ig-like domain-containing protein -
CF168_RS21030 (CF168_21030) 10876..11583 + 708 WP_001259347 DsbC family protein -
CF168_RS21035 (CF168_21035) 11580..14027 + 2448 WP_000637386 type IV secretion system protein TraC virb4
CF168_RS21040 (CF168_21040) 14042..14359 + 318 WP_000351984 hypothetical protein -
CF168_RS21045 (CF168_21045) 14356..14886 + 531 WP_001010738 S26 family signal peptidase -
CF168_RS21050 (CF168_21050) 14849..16114 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
CF168_RS21055 (CF168_21055) 16111..16782 + 672 WP_001337754 EAL domain-containing protein -
CF168_RS21060 (CF168_21060) 16782..17786 + 1005 WP_043940352 TraU family protein traU
CF168_RS21065 (CF168_21065) 17902..20700 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
CF168_RS21070 (CF168_21070) 20739..21599 - 861 WP_000709517 hypothetical protein -
CF168_RS21075 (CF168_21075) 21722..22363 - 642 WP_000796664 hypothetical protein -
CF168_RS21080 (CF168_21080) 22657..22977 + 321 WP_000547566 hypothetical protein -
CF168_RS21085 (CF168_21085) 23281..23466 + 186 WP_001186917 hypothetical protein -
CF168_RS21090 (CF168_21090) 23686..24654 + 969 WP_000085162 AAA family ATPase -
CF168_RS21095 (CF168_21095) 24665..25573 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   5966 GenBank   NZ_CP022359
Plasmid name   pSHE-CTX-M Incompatibility group   IncA/C2
Plasmid size   193338 bp Coordinate of oriT [Strand]   190763..190913 [+]
Host baterium   Shewanella bicestrii strain JAB-1

Cargo genes

Drug resistance gene   blaCTX-M-15, aac(3)-IIa, blaOXA-1, aac(6')-Ib-cr, tet(A), blaSHV-12, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   merR, merT, merP, merC, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -