Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121011
Name   oriT_pSTW0522-26-1 in_silico
Organism   Citrobacter portucalensis strain STW0522-26
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP022390 (45493..45643 [+], 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_pSTW0522-26-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13259 GenBank   WP_001326173
Name   mobH_JLF45_RS24865_pSTW0522-26-1 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   15541 GenBank   WP_000178857
Name   traD_JLF45_RS24870_pSTW0522-26-1 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   15542 GenBank   WP_200921652
Name   traC_JLF45_RS24960_pSTW0522-26-1 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: 92634.89 Da        Isoelectric Point: 5.9216

>WP_200921652.1 type IV secretion system protein TraC [Citrobacter portucalensis]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAITENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
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: 43577..69951

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JLF45_RS24855 39608..39841 - 234 WP_001191890 hypothetical protein -
JLF45_RS24860 (STW0522CIT26_P10660) 39823..40440 - 618 WP_001249395 hypothetical protein -
JLF45_RS24865 (STW0522CIT26_P10670) 40608..43580 + 2973 WP_001326173 MobH family relaxase -
JLF45_RS24870 (STW0522CIT26_P10680) 43577..45442 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
JLF45_RS24875 (STW0522CIT26_P10690) 45492..46037 + 546 WP_000228720 hypothetical protein -
JLF45_RS24880 (STW0522CIT26_P10700) 45994..46623 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
JLF45_RS24885 (STW0522CIT26_P10710) 46633..47079 + 447 WP_000122507 hypothetical protein -
JLF45_RS24890 (STW0522CIT26_P10720) 47089..47466 + 378 WP_000869297 hypothetical protein -
JLF45_RS24895 (STW0522CIT26_P10730) 47466..48128 + 663 WP_001231464 hypothetical protein -
JLF45_RS24900 (STW0522CIT26_P10740) 48309..48452 + 144 WP_001275801 hypothetical protein -
JLF45_RS24905 (STW0522CIT26_P10750) 48464..48829 + 366 WP_001052530 hypothetical protein -
JLF45_RS24910 (STW0522CIT26_P10760) 48974..49255 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
JLF45_RS24915 (STW0522CIT26_P10770) 49252..49878 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
JLF45_RS24920 (STW0522CIT26_P10780) 49862..50779 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
JLF45_RS24925 (STW0522CIT26_P10790) 50779..52092 + 1314 WP_024131605 TraB/VirB10 family protein traB
JLF45_RS24930 (STW0522CIT26_P10800) 52089..52667 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
JLF45_RS24935 (STW0522CIT26_P10810) 52671..53063 + 393 WP_000479535 TraA family conjugative transfer protein -
JLF45_RS24940 (STW0522CIT26_P10820) 53264..54688 + 1425 Protein_81 DUF4165 domain-containing protein -
JLF45_RS24945 (STW0522CIT26_P10840) 54752..55898 + 1147 Protein_82 IS3 family transposase -
JLF45_RS24950 (STW0522CIT26_P10850) 55914..59981 + 4068 Protein_83 Ig-like domain-containing protein -
JLF45_RS24955 (STW0522CIT26_P10860) 60130..60837 + 708 WP_001259346 DsbC family protein -
JLF45_RS24960 (STW0522CIT26_P10870) 60834..63281 + 2448 WP_200921652 type IV secretion system protein TraC virb4
JLF45_RS24965 (STW0522CIT26_P10880) 63296..63613 + 318 WP_000351984 hypothetical protein -
JLF45_RS24970 (STW0522CIT26_P10890) 63610..64140 + 531 WP_001010740 S26 family signal peptidase -
JLF45_RS24975 (STW0522CIT26_P10900) 64103..65368 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
JLF45_RS24980 (STW0522CIT26_P10910) 65365..66036 + 672 WP_000575345 EAL domain-containing protein -
JLF45_RS24985 (STW0522CIT26_P10920) 66036..67040 + 1005 WP_005507569 TraU family protein traU
JLF45_RS24990 (STW0522CIT26_P10930) 67156..69951 + 2796 WP_001256484 conjugal transfer mating pair stabilization protein TraN traN
JLF45_RS24995 (STW0522CIT26_P10940) 69990..70850 - 861 WP_000709517 hypothetical protein -
JLF45_RS25000 (STW0522CIT26_P10950) 70973..71614 - 642 WP_000796664 hypothetical protein -
JLF45_RS25005 (STW0522CIT26_P10960) 71909..72229 + 321 WP_000547566 hypothetical protein -
JLF45_RS25010 (STW0522CIT26_P10970) 72533..72718 + 186 WP_001186917 hypothetical protein -
JLF45_RS25015 (STW0522CIT26_P10980) 72938..73906 + 969 WP_000085160 AAA family ATPase -
JLF45_RS25020 (STW0522CIT26_P10990) 73917..74825 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   21440 GenBank   NZ_AP022390
Plasmid name   pSTW0522-26-1 Incompatibility group   IncA/C2
Plasmid size   146977 bp Coordinate of oriT [Strand]   45493..45643 [+]
Host baterium   Citrobacter portucalensis strain STW0522-26

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib, aadA2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -