Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107445
Name   oriT_pP0855 in_silico
Organism   Photobacterium damselae subsp. piscicida strain P08-55
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LC225353 (37749..37899 [+], 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_pP0855
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4984 GenBank   WP_001337757
Name   mobH_HXH89_RS00245_pP0855 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   5189 GenBank   WP_000178856
Name   traD_HXH89_RS00250_pP0855 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   5190 GenBank   WP_000637386
Name   traC_HXH89_RS00330_pP0855 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: 35833..61024

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXH89_RS00235 31858..32091 - 234 WP_001191892 hypothetical protein -
HXH89_RS00240 32073..32690 - 618 WP_001249396 hypothetical protein -
HXH89_RS00245 32858..35836 + 2979 WP_001337757 MobH family relaxase -
HXH89_RS00250 35833..37698 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
HXH89_RS00255 37709..38293 + 585 WP_000332866 hypothetical protein -
HXH89_RS00260 38250..38879 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
HXH89_RS00265 38889..39335 + 447 WP_000122506 hypothetical protein -
HXH89_RS00270 39345..39722 + 378 WP_000869261 hypothetical protein -
HXH89_RS00275 39722..40384 + 663 WP_001231463 hypothetical protein -
HXH89_RS00280 40565..40708 + 144 WP_001275801 hypothetical protein -
HXH89_RS00285 40708..41085 + 378 WP_000509509 hypothetical protein -
HXH89_RS00290 41230..41511 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HXH89_RS00295 41508..42134 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
HXH89_RS00300 42118..43035 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HXH89_RS00305 43035..44348 + 1314 WP_024131605 TraB/VirB10 family protein traB
HXH89_RS00310 44345..44923 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HXH89_RS00315 44927..45319 + 393 WP_000479535 TraA family conjugative transfer protein -
HXH89_RS00320 45520..51051 + 5532 WP_000606833 Ig-like domain-containing protein -
HXH89_RS00325 51200..51907 + 708 WP_001259347 DsbC family protein -
HXH89_RS00330 51904..54351 + 2448 WP_000637386 type IV secretion system protein TraC virb4
HXH89_RS00335 54366..54683 + 318 WP_000351984 hypothetical protein -
HXH89_RS00340 54680..55210 + 531 WP_001010738 S26 family signal peptidase -
HXH89_RS00345 55173..56438 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
HXH89_RS00350 56435..57106 + 672 WP_001337754 EAL domain-containing protein -
HXH89_RS00355 57106..58110 + 1005 WP_043940352 TraU family protein traU
HXH89_RS00360 58226..61024 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
HXH89_RS00365 61063..61923 - 861 WP_000709517 hypothetical protein -
HXH89_RS00370 62046..62687 - 642 WP_000796664 hypothetical protein -
HXH89_RS00375 62981..63301 + 321 WP_000547566 hypothetical protein -
HXH89_RS00380 63605..63790 + 186 WP_001186917 hypothetical protein -
HXH89_RS00385 64010..64978 + 969 WP_000085162 AAA family ATPase -
HXH89_RS00390 64989..65897 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   7880 GenBank   NZ_LC225353
Plasmid name   pP0855 Incompatibility group   IncA/C2
Plasmid size   150115 bp Coordinate of oriT [Strand]   37749..37899 [+]
Host baterium   Photobacterium damselae subsp. piscicida strain P08-55

Cargo genes

Drug resistance gene   aph(3')-Ia, tet(D), catA1, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -