Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111813
Name   oriT_pCW-NDM-1_ in_silico
Organism   Citrobacter werkmanii isolate BB1472
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LR822055 (47529..47679 [+], 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_pCW-NDM-1_
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7659 GenBank   WP_001326173
Name   mobH_L1W29_RS00350_pCW-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   8749 GenBank   WP_000178857
Name   traD_L1W29_RS00355_pCW-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   8750 GenBank   WP_000637384
Name   traC_L1W29_RS00435_pCW-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: 45613..70756

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L1W29_RS00340 (TML_179) 41644..41877 - 234 WP_001191890 hypothetical protein -
L1W29_RS00345 (TML_118) 41859..42476 - 618 WP_001249395 hypothetical protein -
L1W29_RS00350 (TML_37) 42644..45616 + 2973 WP_001326173 MobH family relaxase -
L1W29_RS00355 (TML_40) 45613..47478 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
L1W29_RS00360 (TML_56) 47528..48073 + 546 WP_000228720 hypothetical protein -
L1W29_RS00365 (TML_53) 48030..48659 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
L1W29_RS00370 (TML_141) 48669..49115 + 447 WP_000122507 hypothetical protein -
L1W29_RS00375 (TML_152) 49125..49502 + 378 WP_000869297 hypothetical protein -
L1W29_RS00380 (TML_115) 49502..50164 + 663 WP_001231464 hypothetical protein -
L1W29_RS00385 (TML_193) 50345..50488 + 144 WP_001275801 hypothetical protein -
L1W29_RS00390 (TML_151) 50500..50865 + 366 WP_001052530 hypothetical protein -
L1W29_RS00395 (TML_61) 51010..51291 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
L1W29_RS00400 (TML_54) 51288..51914 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
L1W29_RS00405 (TML_51) 51898..52815 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
L1W29_RS00410 (TML_43) 52815..54128 + 1314 WP_024131605 TraB/VirB10 family protein traB
L1W29_RS00415 (TML_55) 54125..54703 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
L1W29_RS00420 (TML_59) 54707..55099 + 393 WP_000479535 TraA family conjugative transfer protein -
L1W29_RS00425 (TML_35) 55300..60786 + 5487 WP_000606835 Ig-like domain-containing protein -
L1W29_RS00430 (TML_80) 60935..61642 + 708 WP_001259346 DsbC family protein -
L1W29_RS00435 (TML_39) 61639..64086 + 2448 WP_000637384 type IV secretion system protein TraC virb4
L1W29_RS00440 (TML_162) 64101..64418 + 318 WP_000351984 hypothetical protein -
L1W29_RS00445 (TML_57) 64415..64945 + 531 WP_001010740 S26 family signal peptidase -
L1W29_RS00450 (TML_44) 64908..66173 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
L1W29_RS00455 (TML_82) 66170..66841 + 672 WP_000575345 EAL domain-containing protein -
L1W29_RS00460 (TML_48) 66841..67845 + 1005 WP_005507569 TraU family protein traU
L1W29_RS00465 (TML_38) 67949..70756 + 2808 WP_001447718 conjugal transfer mating pair stabilization protein TraN traN
L1W29_RS00470 (TML_111) 70795..71655 - 861 WP_000709517 hypothetical protein -
L1W29_RS00475 (TML_117) 71778..72419 - 642 WP_000796664 hypothetical protein -
L1W29_RS00480 (TML_161) 72714..73034 + 321 WP_000547566 hypothetical protein -
L1W29_RS00485 (TML_191) 73338..73523 + 186 WP_001186917 hypothetical protein -
L1W29_RS00490 (TML_4) 73743..74711 + 969 WP_000085160 AAA family ATPase -
L1W29_RS00495 (TML_110) 74722..75630 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   12248 GenBank   NZ_LR822055
Plasmid name   pCW-NDM-1_ Incompatibility group   IncA/C2
Plasmid size   161908 bp Coordinate of oriT [Strand]   47529..47679 [+]
Host baterium   Citrobacter werkmanii isolate BB1472

Cargo genes

Drug resistance gene   dfrA12, aadA2, qacE, sul1, blaNDM-1, aph(3')-VI, armA, msr(E), mph(E)
Virulence gene   -
Metal resistance gene   merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -