Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114793
Name   oriT_pCCU4052_01 in_silico
Organism   Shewanella algae strain CCU4052
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP078516 (61562..61712 [+], 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_pCCU4052_01
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9478 GenBank   WP_001337757
Name   mobH_KE622_RS21995_pCCU4052_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   11026 GenBank   WP_000178856
Name   traD_KE622_RS22000_pCCU4052_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   11027 GenBank   WP_000637386
Name   traC_KE622_RS22075_pCCU4052_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: 59646..84837

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KE622_RS21990 (KE622_21990) 55886..56503 - 618 WP_001249396 hypothetical protein -
KE622_RS21995 (KE622_21995) 56671..59649 + 2979 WP_001337757 MobH family relaxase -
KE622_RS22000 (KE622_22000) 59646..61511 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
KE622_RS22005 (KE622_22005) 61522..62106 + 585 WP_000332866 hypothetical protein -
KE622_RS22010 (KE622_22010) 62063..62692 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
KE622_RS22015 (KE622_22015) 62702..63148 + 447 WP_000122506 hypothetical protein -
KE622_RS22020 (KE622_22020) 63158..63535 + 378 WP_000869261 hypothetical protein -
KE622_RS22025 (KE622_22025) 63535..64197 + 663 WP_001231463 hypothetical protein -
KE622_RS22030 (KE622_22030) 64533..64898 + 366 WP_001052531 hypothetical protein -
KE622_RS22035 (KE622_22035) 65043..65324 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
KE622_RS22040 (KE622_22040) 65321..65947 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
KE622_RS22045 (KE622_22045) 65931..66848 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
KE622_RS22050 (KE622_22050) 66848..68161 + 1314 WP_024131605 TraB/VirB10 family protein traB
KE622_RS22055 (KE622_22055) 68158..68736 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
KE622_RS22060 (KE622_22060) 68740..69132 + 393 WP_000479535 TraA family conjugative transfer protein -
KE622_RS22065 (KE622_22065) 69333..74864 + 5532 WP_000606833 Ig-like domain-containing protein -
KE622_RS22070 (KE622_22070) 75013..75720 + 708 WP_001259347 DsbC family protein -
KE622_RS22075 (KE622_22075) 75717..78164 + 2448 WP_000637386 type IV secretion system protein TraC virb4
KE622_RS22080 (KE622_22080) 78179..78496 + 318 WP_000351984 hypothetical protein -
KE622_RS22085 (KE622_22085) 78493..79023 + 531 WP_001010738 S26 family signal peptidase -
KE622_RS22090 (KE622_22090) 78986..80251 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
KE622_RS22095 (KE622_22095) 80248..80919 + 672 WP_001337754 EAL domain-containing protein -
KE622_RS22100 (KE622_22100) 80919..81923 + 1005 WP_043940352 TraU family protein traU
KE622_RS22105 (KE622_22105) 82039..84837 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
KE622_RS22110 (KE622_22110) 84876..85736 - 861 WP_000709517 hypothetical protein -
KE622_RS22115 (KE622_22115) 85859..86500 - 642 WP_000796664 hypothetical protein -
KE622_RS22120 (KE622_22120) 86794..87114 + 321 WP_000547566 hypothetical protein -
KE622_RS22125 (KE622_22125) 87418..87603 + 186 WP_001186917 hypothetical protein -
KE622_RS22130 (KE622_22130) 87823..88791 + 969 WP_000085162 AAA family ATPase -
KE622_RS22135 (KE622_22135) 88802..89710 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   15228 GenBank   NZ_CP078516
Plasmid name   pCCU4052_01 Incompatibility group   IncA/C2
Plasmid size   132655 bp Coordinate of oriT [Strand]   61562..61712 [+]
Host baterium   Shewanella algae strain CCU4052

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   -