Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102961
Name   oriT_pNDM15-1078 in_silico
Organism   Escherichia coli strain N15-01078
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP012902 (141859..142009 [-], 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_pNDM15-1078
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2219 GenBank   WP_001326173
Name   TraI_2_AOY10_RS00825_pNDM15-1078 insolico UniProt ID   F5BPR1
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109356.90 Da        Isoelectric Point: 4.9395

>WP_001326173.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB F5BPR1


T4CP

ID   1907 GenBank   WP_000637384
Name   traC_AOY10_RS00740_pNDM15-1078 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: 92604.86 Da        Isoelectric Point: 5.9216

>WP_000637384.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

TraG P-loop domain (P-loop_TraG)

(449-809)

  Protein structure



No available structure.



ID   1908 GenBank   WP_000178857
Name   traD_AOY10_RS00820_pNDM15-1078 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: 118782..143925

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AOY10_RS00680 (AOY10_00126) 113908..114816 - 909 WP_000739139 hypothetical protein -
AOY10_RS00685 (AOY10_00127) 114827..115795 - 969 WP_000085160 AAA family ATPase -
AOY10_RS00690 (AOY10_00128) 116015..116200 - 186 WP_001186917 hypothetical protein -
AOY10_RS00695 (AOY10_00130) 116504..116824 - 321 WP_000547566 hypothetical protein -
AOY10_RS00700 (AOY10_00131) 117119..117760 + 642 WP_000796664 hypothetical protein -
AOY10_RS00705 (AOY10_00132) 117883..118743 + 861 WP_000709517 hypothetical protein -
AOY10_RS00710 (AOY10_00133) 118782..121577 - 2796 WP_001256484 conjugal transfer mating pair stabilization protein TraN traN
AOY10_RS00715 (AOY10_00134) 121693..122697 - 1005 WP_005507569 TraU family protein traU
AOY10_RS00720 (AOY10_00135) 122697..123368 - 672 WP_000575345 EAL domain-containing protein -
AOY10_RS00725 (AOY10_00136) 123365..124630 - 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
AOY10_RS00730 (AOY10_00137) 124593..125123 - 531 WP_001010740 S26 family signal peptidase -
AOY10_RS00735 (AOY10_00138) 125120..125437 - 318 WP_000351984 hypothetical protein -
AOY10_RS00740 (AOY10_00139) 125452..127899 - 2448 WP_000637384 type IV secretion system protein TraC virb4
AOY10_RS00745 (AOY10_00140) 127896..128603 - 708 WP_001259346 DsbC family protein -
AOY10_RS00750 (AOY10_00141) 128752..134238 - 5487 WP_059453255 Ig-like domain-containing protein -
AOY10_RS00755 (AOY10_00142) 134439..134831 - 393 WP_000479535 TraA family conjugative transfer protein -
AOY10_RS00760 (AOY10_00143) 134835..135413 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
AOY10_RS00765 (AOY10_00144) 135410..136723 - 1314 WP_024131605 TraB/VirB10 family protein traB
AOY10_RS00770 (AOY10_00145) 136723..137640 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
AOY10_RS00775 (AOY10_00146) 137624..138250 - 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
AOY10_RS00780 (AOY10_00147) 138247..138528 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
AOY10_RS00785 (AOY10_00148) 138673..139038 - 366 WP_001052530 hypothetical protein -
AOY10_RS00790 (AOY10_00149) 139050..139193 - 144 WP_001275801 hypothetical protein -
AOY10_RS00795 (AOY10_00150) 139374..140036 - 663 WP_001231464 hypothetical protein -
AOY10_RS00800 (AOY10_00151) 140036..140413 - 378 WP_000869297 hypothetical protein -
AOY10_RS00805 (AOY10_00152) 140423..140869 - 447 WP_000122507 hypothetical protein -
AOY10_RS00810 (AOY10_00153) 140879..141508 - 630 WP_000743449 DUF4400 domain-containing protein tfc7
AOY10_RS00815 (AOY10_00154) 141465..142049 - 585 WP_000332868 hypothetical protein -
AOY10_RS00820 (AOY10_00155) 142060..143925 - 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
AOY10_RS00825 (AOY10_00156) 143922..146894 - 2973 WP_001326173 MobH family relaxase -
AOY10_RS00830 (AOY10_00157) 147062..147679 + 618 WP_001249395 hypothetical protein -
AOY10_RS00835 (AOY10_00158) 147661..147894 + 234 WP_001191890 hypothetical protein -

Host bacterium

ID   3404 GenBank   NZ_CP012902
Plasmid name   pNDM15-1078 Incompatibility group   IncA/C2
Plasmid size   176048 bp Coordinate of oriT [Strand]   141859..142009 [-]
Host baterium   Escherichia coli strain N15-01078

Cargo genes

Drug resistance gene   mph(E), msr(E), armA, sul1, qacE, aadA2, dfrA12, blaNDM-1, qnrA1, ant(3'')-Ia, blaOXA-10, cmlA1, ARR-3
Virulence gene   -
Metal resistance gene   merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -