Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120603
Name   oriT_pCF20-4P-1-2 in_silico
Organism   Citrobacter freundii strain CF20-4P-1 isolate gut contents of Mastacembelus
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP026942 (55033..55183 [+], 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_pCF20-4P-1-2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12978 GenBank   WP_211119999
Name   mobH_OPA57_RS25590_pCF20-4P-1-2 insolico UniProt ID   _
Length   992 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 992 a.a.        Molecular weight: 109568.87 Da        Isoelectric Point: 4.8714

>WP_211119999.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEMGERAFYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREDPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   15239 GenBank   WP_000178856
Name   traD_OPA57_RS25595_pCF20-4P-1-2 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   15240 GenBank   WP_000637386
Name   traC_OPA57_RS25675_pCF20-4P-1-2 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: 53117..78308

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OPA57_RS25580 (CF204P1_49770) 49142..49375 - 234 WP_001191892 hypothetical protein -
OPA57_RS25585 (CF204P1_49780) 49357..49974 - 618 WP_001249396 hypothetical protein -
OPA57_RS25590 (CF204P1_49790) 50142..53120 + 2979 WP_211119999 MobH family relaxase -
OPA57_RS25595 (CF204P1_49800) 53117..54982 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
OPA57_RS25600 (CF204P1_49810) 55032..55577 + 546 WP_000228720 hypothetical protein -
OPA57_RS25605 (CF204P1_49820) 55534..56163 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
OPA57_RS25610 56173..56619 + 447 WP_000122506 hypothetical protein -
OPA57_RS25615 (CF204P1_49840) 56629..57006 + 378 WP_000869261 hypothetical protein -
OPA57_RS25620 (CF204P1_49850) 57006..57668 + 663 WP_001231463 hypothetical protein -
OPA57_RS25625 (CF204P1_49860) 57849..57992 + 144 WP_001275801 hypothetical protein -
OPA57_RS25630 (CF204P1_49870) 58004..58369 + 366 WP_001052531 hypothetical protein -
OPA57_RS25635 (CF204P1_49880) 58514..58795 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
OPA57_RS25640 (CF204P1_49890) 58792..59418 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
OPA57_RS25645 (CF204P1_49900) 59402..60319 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
OPA57_RS25650 (CF204P1_49910) 60319..61632 + 1314 WP_024131605 TraB/VirB10 family protein traB
OPA57_RS25655 (CF204P1_49920) 61629..62207 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
OPA57_RS25660 (CF204P1_49930) 62211..62603 + 393 WP_000479535 TraA family conjugative transfer protein -
OPA57_RS25665 (CF204P1_49940) 62804..68335 + 5532 WP_000606833 Ig-like domain-containing protein -
OPA57_RS25670 (CF204P1_49950) 68484..69191 + 708 WP_001259347 DsbC family protein -
OPA57_RS25675 (CF204P1_49960) 69188..71635 + 2448 WP_000637386 type IV secretion system protein TraC virb4
OPA57_RS25680 (CF204P1_49970) 71650..71967 + 318 WP_000351984 hypothetical protein -
OPA57_RS25685 (CF204P1_49980) 71964..72494 + 531 WP_001010738 S26 family signal peptidase -
OPA57_RS25690 (CF204P1_49990) 72457..73722 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
OPA57_RS25695 (CF204P1_50000) 73719..74390 + 672 WP_001337754 EAL domain-containing protein -
OPA57_RS25700 74390..75394 + 1005 WP_043940352 TraU family protein traU
OPA57_RS25705 (CF204P1_50020) 75510..78308 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
OPA57_RS25710 (CF204P1_50030) 78347..79207 - 861 WP_000709517 hypothetical protein -
OPA57_RS25715 (CF204P1_50040) 79330..79971 - 642 WP_000796664 hypothetical protein -
OPA57_RS25720 (CF204P1_50050) 80265..80585 + 321 WP_000547566 hypothetical protein -
OPA57_RS25725 (CF204P1_50060) 80889..81074 + 186 WP_001186917 hypothetical protein -
OPA57_RS25730 (CF204P1_50070) 81294..82262 + 969 WP_000085162 AAA family ATPase -
OPA57_RS25735 (CF204P1_50080) 82273..83181 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   21032 GenBank   NZ_AP026942
Plasmid name   pCF20-4P-1-2 Incompatibility group   IncA/C2
Plasmid size   137080 bp Coordinate of oriT [Strand]   55033..55183 [+]
Host baterium   Citrobacter freundii strain CF20-4P-1 isolate gut contents of Mastacembelus

Cargo genes

Drug resistance gene   sul1, aph(3')-VI, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -