Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101483
Name   oriT_pMRVIM0912 in_silico
Organism   Citrobacter freundii strain MRSN 11938
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JYFY02000005 (66977..67127 [-], 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_pMRVIM0912
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1326 GenBank   WP_001337757
Name   mobH_TN42_RS25940_pMRVIM0912 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   944 GenBank   WP_000637386
Name   traC_TN42_RS25860_pMRVIM0912 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.



ID   945 GenBank   WP_000178856
Name   traD_TN42_RS25935_pMRVIM0912 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 43823..69043

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
TN42_RS25800 (TN42_24150) 38950..39858 - 909 WP_000739139 hypothetical protein -
TN42_RS25805 (TN42_24155) 39869..40837 - 969 WP_000085162 AAA family ATPase -
TN42_RS25810 (TN42_24160) 41057..41242 - 186 WP_001186917 hypothetical protein -
TN42_RS25815 (TN42_24165) 41546..41866 - 321 WP_000547566 hypothetical protein -
TN42_RS25820 (TN42_24170) 42160..42801 + 642 WP_000796664 hypothetical protein -
TN42_RS25825 (TN42_24175) 42924..43784 + 861 WP_000709517 hypothetical protein -
TN42_RS25830 (TN42_24180) 43823..46621 - 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
TN42_RS31720 46737..46979 - 243 WP_046155150 TraU family protein traU
TN42_RS25835 (TN42_19725) 47005..47770 - 766 WP_044702044 TraU family protein traU
TN42_RS25840 (TN42_19730) 47770..48441 - 672 WP_001337754 EAL domain-containing protein -
TN42_RS25845 (TN42_19735) 48438..49703 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
TN42_RS25850 (TN42_19740) 49666..50196 - 531 WP_001010738 S26 family signal peptidase -
TN42_RS25855 (TN42_19745) 50193..50510 - 318 WP_000351984 hypothetical protein -
TN42_RS25860 (TN42_19750) 50525..52972 - 2448 WP_000637386 type IV secretion system protein TraC virb4
TN42_RS25865 (TN42_19755) 52969..53676 - 708 WP_001259347 DsbC family protein -
TN42_RS25870 (TN42_19760) 53825..59356 - 5532 WP_000606833 Ig-like domain-containing protein -
TN42_RS25875 (TN42_19765) 59557..59949 - 393 WP_000479535 TraA family conjugative transfer protein -
TN42_RS25880 (TN42_19770) 59953..60531 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
TN42_RS25885 (TN42_19775) 60528..61841 - 1314 WP_024131605 TraB/VirB10 family protein traB
TN42_RS25890 (TN42_19780) 61841..62758 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
TN42_RS25895 (TN42_19785) 62742..63368 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
TN42_RS25900 (TN42_19790) 63365..63646 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
TN42_RS25905 (TN42_19795) 63791..64156 - 366 WP_001052531 hypothetical protein -
TN42_RS31105 64168..64311 - 144 WP_001275801 hypothetical protein -
TN42_RS25910 (TN42_19800) 64492..65154 - 663 WP_001231463 hypothetical protein -
TN42_RS25915 (TN42_19805) 65154..65531 - 378 WP_000869261 hypothetical protein -
TN42_RS25920 (TN42_19810) 65541..65987 - 447 WP_000122506 hypothetical protein -
TN42_RS25925 (TN42_19815) 65997..66626 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
TN42_RS25930 (TN42_19820) 66583..67128 - 546 WP_000228720 hypothetical protein -
TN42_RS25935 (TN42_19825) 67178..69043 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
TN42_RS25940 (TN42_19830) 69040..72018 - 2979 WP_001337757 MobH family relaxase -
TN42_RS25945 (TN42_19835) 72186..72803 + 618 WP_001249396 hypothetical protein -
TN42_RS25950 (TN42_19840) 72785..73018 + 234 WP_001191892 hypothetical protein -

Host bacterium

ID   1927 GenBank   NZ_JYFY02000005
Plasmid name   pMRVIM0912 Incompatibility group   IncA/C2
Plasmid size   151387 bp Coordinate of oriT [Strand]   66977..67127 [-]
Host baterium   Citrobacter freundii strain MRSN 11938

Cargo genes

Drug resistance gene   catA1, tet(C), blaCTX-M-39
Virulence gene   -
Metal resistance gene   merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -