Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114795
Name   oriT_pCCU4054_01 in_silico
Organism   Shewanella algae strain CCU4054
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP078520 (63780..63930 [+], 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_pCCU4054_01
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9480 GenBank   WP_001337757
Name   mobH_KE624_RS22080_pCCU4054_01 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   11030 GenBank   WP_000178856
Name   traD_KE624_RS22085_pCCU4054_01 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   11031 GenBank   WP_000637386
Name   traC_KE624_RS22160_pCCU4054_01 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: 61864..87053

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KE624_RS22075 (KE624_22075) 58105..58722 - 618 WP_001249396 hypothetical protein -
KE624_RS22080 (KE624_22080) 58889..61867 + 2979 WP_001337757 MobH family relaxase -
KE624_RS22085 (KE624_22085) 61864..63729 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
KE624_RS22090 (KE624_22090) 63740..64324 + 585 WP_000332866 hypothetical protein -
KE624_RS22095 (KE624_22095) 64281..64910 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
KE624_RS22100 (KE624_22100) 64920..65366 + 447 WP_000122506 hypothetical protein -
KE624_RS22105 (KE624_22105) 65376..65753 + 378 WP_000869261 hypothetical protein -
KE624_RS22110 (KE624_22110) 65753..66415 + 663 WP_001231463 hypothetical protein -
KE624_RS22115 (KE624_22115) 66751..67215 + 465 WP_256874027 hypothetical protein -
KE624_RS22120 (KE624_22120) 67260..67540 + 281 Protein_89 type IV conjugative transfer system protein TraL -
KE624_RS22125 (KE624_22125) 67537..68163 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
KE624_RS22130 (KE624_22130) 68147..69064 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
KE624_RS22135 (KE624_22135) 69064..70377 + 1314 WP_024131605 TraB/VirB10 family protein traB
KE624_RS22140 (KE624_22140) 70374..70952 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
KE624_RS22145 (KE624_22145) 70956..71348 + 393 WP_000479535 TraA family conjugative transfer protein -
KE624_RS22150 (KE624_22150) 71549..77080 + 5532 WP_000606833 Ig-like domain-containing protein -
KE624_RS22155 (KE624_22155) 77229..77936 + 708 WP_001259347 DsbC family protein -
KE624_RS22160 (KE624_22160) 77933..80380 + 2448 WP_000637386 type IV secretion system protein TraC virb4
KE624_RS22165 (KE624_22165) 80395..80712 + 318 WP_000351984 hypothetical protein -
KE624_RS22170 (KE624_22170) 80709..81239 + 531 WP_001010738 S26 family signal peptidase -
KE624_RS22175 (KE624_22175) 81202..82467 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
KE624_RS22180 (KE624_22180) 82464..83135 + 672 WP_001337754 EAL domain-containing protein -
KE624_RS22185 (KE624_22185) 83135..84139 + 1005 WP_043940352 TraU family protein traU
KE624_RS22190 (KE624_22190) 84255..87053 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
KE624_RS22195 (KE624_22195) 87092..87952 - 861 WP_000709517 hypothetical protein -
KE624_RS22200 (KE624_22200) 88075..88716 - 642 WP_000796664 hypothetical protein -
KE624_RS22205 (KE624_22205) 89010..89330 + 321 WP_000547566 hypothetical protein -
KE624_RS22210 (KE624_22210) 89634..89819 + 186 WP_001186917 hypothetical protein -
KE624_RS22215 (KE624_22215) 90039..91007 + 969 WP_000085162 AAA family ATPase -
KE624_RS22810 91018..91449 + 432 WP_228717829 hypothetical protein -
KE624_RS22815 91392..91925 + 534 WP_227543304 hypothetical protein -

Host bacterium

ID   15230 GenBank   NZ_CP078520
Plasmid name   pCCU4054_01 Incompatibility group   IncA/C2
Plasmid size   132646 bp Coordinate of oriT [Strand]   63780..63930 [+]
Host baterium   Shewanella algae strain CCU4054

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -