Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105791
Name   oriT_p18064-65-CSB-B-B in_silico
Organism   Shewanella algae strain 18064-CSB-B-B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP047421 (4886..5036 [+], 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_p18064-65-CSB-B-B
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3914 GenBank   WP_001326173
Name   mobH_GM320_RS00005_p18064-65-CSB-B-B insolico UniProt ID   F5BPR1
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109356.90 Da        Isoelectric Point: 4.9395

>WP_001326173.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB F5BPR1


T4CP

ID   3926 GenBank   WP_000178857
Name   traD_GM320_RS00010_p18064-65-CSB-B-B 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: 69225.71 Da        Isoelectric Point: 6.9403

>WP_000178857.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(170-299)

TraM recognition site of TraD and TraG (TraG-D_C)

(471-598)

  Protein structure



No available structure.



ID   3927 GenBank   WP_000637384
Name   traC_GM320_RS00085_p18064-65-CSB-B-B 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: 92604.86 Da        Isoelectric Point: 5.9216

>WP_000637384.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

TraG P-loop domain (P-loop_TraG)

(449-809)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2970..28113

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GM320_RS00005 (GM320_00005) 1..2973 + 2973 WP_001326173 MobH family relaxase -
GM320_RS00010 (GM320_00010) 2970..4835 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
GM320_RS00015 (GM320_00015) 4885..5430 + 546 WP_000228720 hypothetical protein -
GM320_RS00020 (GM320_00020) 5387..6016 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
GM320_RS00025 (GM320_00025) 6026..6472 + 447 WP_000122507 hypothetical protein -
GM320_RS00030 (GM320_00030) 6482..6859 + 378 WP_000869297 hypothetical protein -
GM320_RS00035 (GM320_00035) 6859..7521 + 663 WP_001231464 hypothetical protein -
GM320_RS00040 (GM320_00040) 7857..8222 + 366 WP_001052530 hypothetical protein -
GM320_RS00045 (GM320_00045) 8367..8648 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
GM320_RS00050 (GM320_00050) 8645..9271 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
GM320_RS00055 (GM320_00055) 9255..10172 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
GM320_RS00060 (GM320_00060) 10172..11485 + 1314 WP_024131605 TraB/VirB10 family protein traB
GM320_RS00065 (GM320_00065) 11482..12060 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
GM320_RS00070 (GM320_00070) 12064..12456 + 393 WP_000479535 TraA family conjugative transfer protein -
GM320_RS00075 (GM320_00075) 12657..18143 + 5487 WP_000606835 Ig-like domain-containing protein -
GM320_RS00080 (GM320_00080) 18292..18999 + 708 WP_001259346 DsbC family protein -
GM320_RS00085 (GM320_00085) 18996..21443 + 2448 WP_000637384 type IV secretion system protein TraC virb4
GM320_RS00090 (GM320_00090) 21458..21775 + 318 WP_000351984 hypothetical protein -
GM320_RS00095 (GM320_00095) 21772..22302 + 531 WP_001010740 S26 family signal peptidase -
GM320_RS00100 (GM320_00100) 22265..23530 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
GM320_RS00105 (GM320_00105) 23527..24198 + 672 WP_000575345 EAL domain-containing protein -
GM320_RS00110 (GM320_00110) 24198..25202 + 1005 WP_005507569 TraU family protein traU
GM320_RS00115 (GM320_00115) 25318..28113 + 2796 WP_001256484 conjugal transfer mating pair stabilization protein TraN traN
GM320_RS00120 (GM320_00120) 28152..29012 - 861 WP_000709517 hypothetical protein -
GM320_RS00125 (GM320_00125) 29135..29776 - 642 WP_000796664 hypothetical protein -
GM320_RS00130 (GM320_00130) 30071..30391 + 321 WP_000547566 hypothetical protein -
GM320_RS00135 (GM320_00135) 30695..30880 + 186 WP_001186917 hypothetical protein -
GM320_RS00140 (GM320_00140) 31100..32068 + 969 WP_000085160 AAA family ATPase -
GM320_RS00145 (GM320_00145) 32079..32987 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   6228 GenBank   NZ_CP047421
Plasmid name   p18064-65-CSB-B-B Incompatibility group   IncA/C2
Plasmid size   149553 bp Coordinate of oriT [Strand]   4886..5036 [+]
Host baterium   Shewanella algae strain 18064-CSB-B-B

Cargo genes

Drug resistance gene   dfrA12, qacE, sul1, armA, blaCTX-M-15
Virulence gene   -
Metal resistance gene   merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -