Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120591
Name   oriT_p48846_1 in_silico
Organism   Citrobacter freundii strain CF48846
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP070543 (15339..15489 [+], 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_p48846_1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12969 GenBank   WP_001337757
Name   mobH_JW295_RS02955_p48846_1 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   15229 GenBank   WP_000178856
Name   traD_JW295_RS02960_p48846_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: 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   15230 GenBank   WP_000637386
Name   traC_JW295_RS03045_p48846_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: 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: 13423..40544

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JW295_RS02945 (JW295_02945) 9448..9681 - 234 WP_001191892 hypothetical protein -
JW295_RS02950 (JW295_02950) 9663..10280 - 618 WP_001249396 hypothetical protein -
JW295_RS02955 (JW295_02955) 10448..13426 + 2979 WP_001337757 MobH family relaxase -
JW295_RS02960 (JW295_02960) 13423..15288 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
JW295_RS02965 (JW295_02965) 15338..15883 + 546 WP_000228720 hypothetical protein -
JW295_RS02970 (JW295_02970) 15840..16469 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
JW295_RS02975 (JW295_02975) 16479..16925 + 447 WP_000122506 hypothetical protein -
JW295_RS02980 (JW295_02980) 16935..17312 + 378 WP_000869261 hypothetical protein -
JW295_RS02985 (JW295_02985) 17312..17974 + 663 WP_001231463 hypothetical protein -
JW295_RS02990 (JW295_02990) 18155..18298 + 144 WP_001275801 hypothetical protein -
JW295_RS02995 (JW295_02995) 18310..18675 + 366 WP_001052531 hypothetical protein -
JW295_RS03000 (JW295_03000) 18820..19101 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
JW295_RS03005 (JW295_03005) 19098..19724 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
JW295_RS03010 (JW295_03010) 19708..20625 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
JW295_RS03015 (JW295_03015) 20625..21938 + 1314 WP_024131605 TraB/VirB10 family protein traB
JW295_RS03020 (JW295_03020) 21935..22513 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
JW295_RS03025 (JW295_03025) 22517..22909 + 393 WP_000479535 TraA family conjugative transfer protein -
JW295_RS03030 (JW295_03030) 23110..28641 + 5532 WP_000606833 Ig-like domain-containing protein -
JW295_RS03035 (JW295_03035) 29140..30546 + 1407 WP_082261857 group II intron reverse transcriptase/maturase -
JW295_RS03040 (JW295_03040) 30720..31427 + 708 WP_001259347 DsbC family protein -
JW295_RS03045 (JW295_03045) 31424..33871 + 2448 WP_000637386 type IV secretion system protein TraC virb4
JW295_RS03050 (JW295_03050) 33886..34203 + 318 WP_000351984 hypothetical protein -
JW295_RS03055 (JW295_03055) 34200..34730 + 531 WP_001010738 S26 family signal peptidase -
JW295_RS03060 (JW295_03060) 34693..35958 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
JW295_RS03065 (JW295_03065) 35955..36626 + 672 WP_001337754 EAL domain-containing protein -
JW295_RS03070 (JW295_03070) 36626..37630 + 1005 WP_043940352 TraU family protein traU
JW295_RS03075 (JW295_03075) 37746..40544 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
JW295_RS03080 (JW295_03080) 40583..41443 - 861 WP_000709517 hypothetical protein -
JW295_RS03085 (JW295_03085) 41566..42207 - 642 WP_000796664 hypothetical protein -
JW295_RS03090 (JW295_03090) 42501..42821 + 321 WP_000547566 hypothetical protein -
JW295_RS03095 (JW295_03095) 43125..43310 + 186 WP_001186917 hypothetical protein -
JW295_RS03100 (JW295_03100) 43530..44498 + 969 WP_000085162 AAA family ATPase -
JW295_RS03105 (JW295_03105) 44509..45417 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   21020 GenBank   NZ_CP070543
Plasmid name   p48846_1 Incompatibility group   -
Plasmid size   64139 bp Coordinate of oriT [Strand]   15339..15489 [+]
Host baterium   Citrobacter freundii strain CF48846

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -