Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117048
Name   oriT_pJNE7-NDM in_silico
Organism   Shewanella sp. JNE7
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP096167 (19056..19206 [+], 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_pJNE7-NDM
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10873 GenBank   WP_001337757
Name   mobH_MZ097_RS20835_pJNE7-NDM 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   12692 GenBank   WP_000178856
Name   traD_MZ097_RS20840_pJNE7-NDM 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   12693 GenBank   WP_000637386
Name   traC_MZ097_RS20920_pJNE7-NDM 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: 17140..42331

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MZ097_RS20825 (MZ097_20830) 13165..13398 - 234 WP_001191892 hypothetical protein -
MZ097_RS20830 (MZ097_20835) 13380..13997 - 618 WP_001249396 hypothetical protein -
MZ097_RS20835 (MZ097_20840) 14165..17143 + 2979 WP_001337757 MobH family relaxase -
MZ097_RS20840 (MZ097_20845) 17140..19005 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
MZ097_RS20845 (MZ097_20850) 19055..19600 + 546 WP_000228720 hypothetical protein -
MZ097_RS20850 (MZ097_20855) 19557..20186 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
MZ097_RS20855 (MZ097_20860) 20196..20642 + 447 WP_000122506 hypothetical protein -
MZ097_RS20860 (MZ097_20865) 20652..21029 + 378 WP_000869261 hypothetical protein -
MZ097_RS20865 (MZ097_20870) 21029..21691 + 663 WP_001231463 hypothetical protein -
MZ097_RS20870 (MZ097_20875) 21872..22015 + 144 WP_001275801 hypothetical protein -
MZ097_RS20875 (MZ097_20880) 22027..22392 + 366 WP_001052531 hypothetical protein -
MZ097_RS20880 (MZ097_20885) 22537..22818 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
MZ097_RS20885 (MZ097_20890) 22815..23441 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
MZ097_RS20890 (MZ097_20895) 23425..24342 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
MZ097_RS20895 (MZ097_20900) 24342..25655 + 1314 WP_024131605 TraB/VirB10 family protein traB
MZ097_RS20900 (MZ097_20905) 25652..26230 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
MZ097_RS20905 (MZ097_20910) 26234..26626 + 393 WP_000479535 TraA family conjugative transfer protein -
MZ097_RS20910 (MZ097_20915) 26827..32358 + 5532 WP_000606833 Ig-like domain-containing protein -
MZ097_RS20915 (MZ097_20920) 32507..33214 + 708 WP_001259347 DsbC family protein -
MZ097_RS20920 (MZ097_20925) 33211..35658 + 2448 WP_000637386 type IV secretion system protein TraC virb4
MZ097_RS20925 (MZ097_20930) 35673..35990 + 318 WP_000351984 hypothetical protein -
MZ097_RS20930 (MZ097_20935) 35987..36517 + 531 WP_001010738 S26 family signal peptidase -
MZ097_RS20935 (MZ097_20940) 36480..37745 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
MZ097_RS20940 (MZ097_20945) 37742..38413 + 672 WP_001337754 EAL domain-containing protein -
MZ097_RS20945 (MZ097_20950) 38413..39417 + 1005 WP_043940352 TraU family protein traU
MZ097_RS20950 (MZ097_20955) 39533..42331 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
MZ097_RS20955 (MZ097_20960) 42370..43230 - 861 WP_000709517 hypothetical protein -
MZ097_RS20960 (MZ097_20965) 43353..43994 - 642 WP_000796664 hypothetical protein -
MZ097_RS20965 (MZ097_20970) 44288..44608 + 321 WP_000547566 hypothetical protein -
MZ097_RS20970 (MZ097_20975) 44912..45097 + 186 WP_001186917 hypothetical protein -
MZ097_RS20975 (MZ097_20980) 45317..46285 + 969 WP_000085162 AAA family ATPase -
MZ097_RS20980 (MZ097_20985) 46296..47204 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   17481 GenBank   NZ_CP096167
Plasmid name   pJNE7-NDM Incompatibility group   IncA/C2
Plasmid size   137224 bp Coordinate of oriT [Strand]   19056..19206 [+]
Host baterium   Shewanella sp. JNE7

Cargo genes

Drug resistance gene   aac(3)-IId, dfrA17, aadA5, qacE, sul1, blaNDM-1, ARR-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -