Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105752
Name   oriT_pEI-MS-17-156-1 in_silico
Organism   Edwardsiella ictaluri strain MS-17-156
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP028814 (112068..112218 [-], 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_pEI-MS-17-156-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3893 GenBank   WP_001337757
Name   mobH_DBV23_RS19030_pEI-MS-17-156-1 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   3906 GenBank   WP_000637386
Name   traC_DBV23_RS18950_pEI-MS-17-156-1 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.



ID   3907 GenBank   WP_000178856
Name   traD_DBV23_RS19025_pEI-MS-17-156-1 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 88943..114134

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DBV23_RS18890 (DBV23_18890) 84070..84978 - 909 WP_000739139 hypothetical protein -
DBV23_RS18895 (DBV23_18895) 84989..85957 - 969 WP_000085162 AAA family ATPase -
DBV23_RS18900 (DBV23_18900) 86177..86362 - 186 WP_001186917 hypothetical protein -
DBV23_RS18905 (DBV23_18905) 86666..86986 - 321 WP_000547566 hypothetical protein -
DBV23_RS18910 (DBV23_18910) 87280..87921 + 642 WP_000796664 hypothetical protein -
DBV23_RS18915 (DBV23_18915) 88044..88904 + 861 WP_000709517 hypothetical protein -
DBV23_RS18920 (DBV23_18920) 88943..91753 - 2811 WP_001909286 conjugal transfer mating pair stabilization protein TraN traN
DBV23_RS18925 (DBV23_18925) 91857..92861 - 1005 WP_043940352 TraU family protein traU
DBV23_RS18930 (DBV23_18930) 92861..93532 - 672 WP_001337754 EAL domain-containing protein -
DBV23_RS18935 (DBV23_18935) 93529..94794 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
DBV23_RS18940 (DBV23_18940) 94757..95287 - 531 WP_001010738 S26 family signal peptidase -
DBV23_RS18945 (DBV23_18945) 95284..95601 - 318 WP_000351984 hypothetical protein -
DBV23_RS18950 (DBV23_18950) 95616..98063 - 2448 WP_000637386 type IV secretion system protein TraC virb4
DBV23_RS18955 (DBV23_18955) 98060..98767 - 708 WP_001259347 DsbC family protein -
DBV23_RS18960 (DBV23_18960) 98916..104447 - 5532 WP_000606833 Ig-like domain-containing protein -
DBV23_RS18965 (DBV23_18965) 104648..105040 - 393 WP_000479535 TraA family conjugative transfer protein -
DBV23_RS18970 (DBV23_18970) 105044..105622 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
DBV23_RS18975 (DBV23_18975) 105619..106932 - 1314 WP_024131605 TraB/VirB10 family protein traB
DBV23_RS18980 (DBV23_18980) 106932..107849 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
DBV23_RS18985 (DBV23_18985) 107833..108459 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
DBV23_RS18990 (DBV23_18990) 108456..108737 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
DBV23_RS18995 (DBV23_18995) 108882..109247 - 366 WP_001052531 hypothetical protein -
DBV23_RS19000 (DBV23_19000) 109583..110245 - 663 WP_001231463 hypothetical protein -
DBV23_RS19005 (DBV23_19005) 110245..110622 - 378 WP_000869261 hypothetical protein -
DBV23_RS19010 (DBV23_19010) 110632..111078 - 447 WP_000122506 hypothetical protein -
DBV23_RS19015 (DBV23_19015) 111088..111717 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
DBV23_RS19020 (DBV23_19020) 111674..112219 - 546 WP_000228720 hypothetical protein -
DBV23_RS19025 (DBV23_19025) 112269..114134 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
DBV23_RS19030 (DBV23_19030) 114131..117109 - 2979 WP_001337757 MobH family relaxase -
DBV23_RS19035 (DBV23_19035) 117277..117894 + 618 WP_001249396 hypothetical protein -
DBV23_RS19040 (DBV23_19040) 117876..118109 + 234 WP_001191892 hypothetical protein -

Host bacterium

ID   6189 GenBank   NZ_CP028814
Plasmid name   pEI-MS-17-156-1 Incompatibility group   IncA/C2
Plasmid size   135268 bp Coordinate of oriT [Strand]   112068..112218 [-]
Host baterium   Edwardsiella ictaluri strain MS-17-156

Cargo genes

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