Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111054
Name   oriT_pNDM-2262 in_silico
Organism   Citrobacter freundii strain 2262
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH892479 (54583..54733 [+], 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_pNDM-2262
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7269 GenBank   WP_001337757
Name   mobH_HTU48_RS00405_pNDM-2262 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   8275 GenBank   WP_000178856
Name   traD_HTU48_RS00410_pNDM-2262 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   8276 GenBank   WP_000637386
Name   traC_HTU48_RS00490_pNDM-2262 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: 52667..77858

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTU48_RS00395 48692..48925 - 234 WP_001191892 hypothetical protein -
HTU48_RS00400 48907..49524 - 618 WP_001249396 hypothetical protein -
HTU48_RS00405 49692..52670 + 2979 WP_001337757 MobH family relaxase -
HTU48_RS00410 52667..54532 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
HTU48_RS00415 54543..55127 + 585 WP_000332866 hypothetical protein -
HTU48_RS00420 55084..55713 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
HTU48_RS00425 55723..56169 + 447 WP_000122506 hypothetical protein -
HTU48_RS00430 56179..56556 + 378 WP_000869261 hypothetical protein -
HTU48_RS00435 56556..57218 + 663 WP_001231463 hypothetical protein -
HTU48_RS00440 57399..57542 + 144 WP_001275801 hypothetical protein -
HTU48_RS00445 57554..57919 + 366 WP_001052531 hypothetical protein -
HTU48_RS00450 58064..58345 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTU48_RS00455 58342..58968 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
HTU48_RS00460 58952..59869 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTU48_RS00465 59869..61182 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTU48_RS00470 61179..61757 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTU48_RS00475 61761..62153 + 393 WP_000479535 TraA family conjugative transfer protein -
HTU48_RS00480 62354..67885 + 5532 WP_000606833 Ig-like domain-containing protein -
HTU48_RS00485 68034..68741 + 708 WP_001259347 DsbC family protein -
HTU48_RS00490 68738..71185 + 2448 WP_000637386 type IV secretion system protein TraC virb4
HTU48_RS00495 71200..71517 + 318 WP_000351984 hypothetical protein -
HTU48_RS00500 71514..72044 + 531 WP_001010738 S26 family signal peptidase -
HTU48_RS00505 72007..73272 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
HTU48_RS00510 73269..73940 + 672 WP_001337754 EAL domain-containing protein -
HTU48_RS00515 73940..74944 + 1005 WP_043940352 TraU family protein traU
HTU48_RS00520 75048..77858 + 2811 WP_001909286 conjugal transfer mating pair stabilization protein TraN traN
HTU48_RS00525 77897..78757 - 861 WP_000709517 hypothetical protein -
HTU48_RS00530 78880..79521 - 642 WP_000796664 hypothetical protein -
HTU48_RS00535 79815..80135 + 321 WP_000547566 hypothetical protein -
HTU48_RS00540 80439..80624 + 186 WP_001186917 hypothetical protein -
HTU48_RS00545 80844..81812 + 969 WP_000085162 AAA family ATPase -
HTU48_RS00550 81823..82731 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   11489 GenBank   NZ_MH892479
Plasmid name   pNDM-2262 Incompatibility group   IncA/C2
Plasmid size   175495 bp Coordinate of oriT [Strand]   54583..54733 [+]
Host baterium   Citrobacter freundii strain 2262

Cargo genes

Drug resistance gene   fosA3, blaSFO-1, dfrA12, aadA2, qacE, sul1, blaNDM-1, msr(E), mph(E)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -