Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101685
Name   oriT_pEC1110_NDM-1 in_silico
Organism   Escherichia coli strain E1110
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JADWPF010000002 (40823..40973 [+], 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_pEC1110_NDM-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1454 GenBank   WP_001326173
Name   mobH_I4V29_RS23165_pEC1110_NDM-1 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   1128 GenBank   WP_000178857
Name   traD_I4V29_RS23170_pEC1110_NDM-1 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.



ID   1129 GenBank   WP_000637384
Name   traC_I4V29_RS23245_pEC1110_NDM-1 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 38907..64050

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I4V29_RS23155 (I4V29_23165) 34938..35171 - 234 WP_001191890 hypothetical protein -
I4V29_RS23160 (I4V29_23170) 35153..35770 - 618 WP_001249395 hypothetical protein -
I4V29_RS23165 (I4V29_23175) 35938..38910 + 2973 WP_001326173 MobH family relaxase -
I4V29_RS23170 (I4V29_23180) 38907..40772 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
I4V29_RS23175 (I4V29_23185) 40822..41367 + 546 WP_000228720 hypothetical protein -
I4V29_RS23180 (I4V29_23190) 41324..41953 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
I4V29_RS23185 (I4V29_23195) 41963..42409 + 447 WP_000122507 hypothetical protein -
I4V29_RS23190 (I4V29_23200) 42419..42796 + 378 WP_000869297 hypothetical protein -
I4V29_RS23195 (I4V29_23205) 42796..43458 + 663 WP_232796075 hypothetical protein -
I4V29_RS23200 (I4V29_23210) 43794..44159 + 366 WP_001052530 hypothetical protein -
I4V29_RS23205 (I4V29_23215) 44304..44585 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
I4V29_RS23210 (I4V29_23220) 44582..45208 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
I4V29_RS23215 (I4V29_23225) 45192..46109 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
I4V29_RS23220 (I4V29_23230) 46109..47422 + 1314 WP_024131605 TraB/VirB10 family protein traB
I4V29_RS23225 (I4V29_23235) 47419..47997 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
I4V29_RS23230 (I4V29_23240) 48001..48393 + 393 WP_000479535 TraA family conjugative transfer protein -
I4V29_RS23235 (I4V29_23245) 48594..54080 + 5487 WP_000606835 Ig-like domain-containing protein -
I4V29_RS23240 (I4V29_23250) 54229..54936 + 708 WP_001259346 DsbC family protein -
I4V29_RS23245 (I4V29_23255) 54933..57380 + 2448 WP_000637384 type IV secretion system protein TraC virb4
I4V29_RS23250 (I4V29_23260) 57395..57712 + 318 WP_000351984 hypothetical protein -
I4V29_RS23255 (I4V29_23265) 57709..58239 + 531 WP_001010740 S26 family signal peptidase -
I4V29_RS23260 (I4V29_23270) 58202..59467 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
I4V29_RS23265 (I4V29_23275) 59464..60135 + 672 WP_000575345 EAL domain-containing protein -
I4V29_RS23270 (I4V29_23280) 60135..61139 + 1005 WP_005507569 TraU family protein traU
I4V29_RS23275 (I4V29_23285) 61255..64050 + 2796 WP_001256484 conjugal transfer mating pair stabilization protein TraN traN
I4V29_RS23280 (I4V29_23290) 64089..64697 - 609 WP_223152579 hypothetical protein -
I4V29_RS23285 (I4V29_23295) 65053..65694 - 642 WP_000796664 hypothetical protein -
I4V29_RS23290 (I4V29_23300) 65989..66309 + 321 WP_000547566 hypothetical protein -
I4V29_RS23295 (I4V29_23305) 66613..66798 + 186 WP_001186917 hypothetical protein -
I4V29_RS23300 (I4V29_23310) 67018..67986 + 969 WP_000085160 AAA family ATPase -
I4V29_RS23305 (I4V29_23315) 67997..68905 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   2129 GenBank   NZ_JADWPF010000002
Plasmid name   pEC1110_NDM-1 Incompatibility group   IncA/C2
Plasmid size   145165 bp Coordinate of oriT [Strand]   40823..40973 [+]
Host baterium   Escherichia coli strain E1110

Cargo genes

Drug resistance gene   sul2, dfrA12, aadA2, qacE, sul1, aph(3')-VI, blaNDM-1
Virulence gene   -
Metal resistance gene   merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -