Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108647
Name   oriT_SF1039_p1 in_silico
Organism   Shewanella baltica strain SF1039 isolate SF1039
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OX461118 (42408..42558 [+], 151 nt)
oriT length   151 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT_SF1039_p1
TGGTCGATGTGAACCCTTTTGACCGGGTTATGAATGAATTGAAAAATCGTGGACGCAAAAACGCTCATATCCTGAGCATCCTTCAATTCGATTGGCCTGCATCAGAGGTCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGTATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5769 GenBank   WP_283631287
Name   mobH_QOT06_RS21940_SF1039_p1 insolico UniProt ID   _
Length   989 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 989 a.a.        Molecular weight: 109270.52 Da        Isoelectric Point: 4.7671

>WP_283631287.1 MobH family relaxase [Shewanella baltica]
MLKALNKLFGGRSGVIEATPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHGIERYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTTVNQPVTRLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEATGSLKILMLRLESNDLVFTNEPPAAVAAEVVGDVEDAEIE
FVDPDESDDDQDEGGVSLNDDMLAAEQEAEKALAGLGFGDAMDMLKSTSTEPEDTPAQGASETKDSPKAP
SVTTPSKGKQVKAKPKKDTEEQTEKPEAKEELSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDAF
NASTDACIADEESLKNSNEAELEQPKPDFVPEEQNSLQDDDFPMFSGSDEPPSWAIEPLPMLAVESEEAS
ATTEMSQANIPNQQEKDAKTLLSEMLAGYGEASALLEQAIMPVLEGKKTLGEVLCLMKGQAVILYPEGAR
SLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAQQLSDAVVAAIKEVEASMGGYQDVFELVS
PPDADVRKSKSAPKQQSQPMQKKNQQQKSDAGSGQAAPAKDTKGKAAQKPQKEKKGDTSSVVAGHESKPI
EEKQNVARLPKREAQPEAVVVTKVEREKELGHIEVREREEQEVREFEPPKAKTNPKDIKDEDFLPPGVTP
EKAILILKNMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGIKKHILCGMLSRAQKRPLLKNRQG
KLYLEVDET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   6180 GenBank   WP_210146616
Name   traD_QOT06_RS21945_SF1039_p1 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: 69458.93 Da        Isoelectric Point: 7.1174

>WP_210146616.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLRGRDLEFISITELQKYIKDTPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGKESTVKKVVRRI
QGKRKELPIGQPWIHGVEPKEEKLMQPLKHTEGHTLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIRAVQAYSERVRPDWEAEAAPFLEKVKNGSREKIAFA
LMRFYYEIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSTDLSDERQITD
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)

(170-292)

  Protein structure



No available structure.



ID   6181 GenBank   WP_283631306
Name   traC_QOT06_RS22015_SF1039_p1 insolico UniProt ID   _
Length   814 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 814 a.a.        Molecular weight: 92319.49 Da        Isoelectric Point: 6.0244

>WP_283631306.1 type IV secretion system protein TraC [Shewanella baltica]
MIVTIKKKLQETLIPEHLRAAGIVPVLAYDEDDHVFLMDDHSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRISAKTNKGTYDNGLIQ
DLKLFVTCKVPINNNNPSESELQNLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
AVDWEMDKPICEQIFDYGTDVEVSKNGLRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWD
EKGKEMKVDDIAERCLEGEDMRLRDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHLR
QVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLYE
NAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRLI
VGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRNRKQAA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraG P-loop domain (P-loop_TraG)

(449-808)

TraC protein (TraC_F_IV)

(22-255)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40492..65242

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QOT06_RS21930 36526..36759 - 234 WP_283631284 hypothetical protein -
QOT06_RS21935 36741..37358 - 618 WP_283631286 hypothetical protein -
QOT06_RS21940 37526..40495 + 2970 WP_283631287 MobH family relaxase -
QOT06_RS21945 40492..42357 + 1866 WP_210146616 conjugative transfer system coupling protein TraD virb4
QOT06_RS21950 42407..42952 + 546 WP_023044870 hypothetical protein -
QOT06_RS21955 42909..43538 + 630 WP_283631293 DUF4400 domain-containing protein tfc7
QOT06_RS21960 43659..44036 + 378 WP_283631294 hypothetical protein -
QOT06_RS21965 44036..44698 + 663 WP_283631296 hypothetical protein -
QOT06_RS21970 45040..45405 + 366 WP_283631298 hypothetical protein -
QOT06_RS21975 45549..45830 + 282 WP_172910019 type IV conjugative transfer system protein TraL traL
QOT06_RS21980 45827..46453 + 627 WP_283631301 TraE/TraK family type IV conjugative transfer system protein traE
QOT06_RS21985 46437..47354 + 918 WP_283631302 type-F conjugative transfer system secretin TraK traK
QOT06_RS21990 47354..48667 + 1314 WP_283631432 TrbI/VirB10 family protein traB
QOT06_RS21995 48664..49242 + 579 WP_113620233 type IV conjugative transfer system lipoprotein TraV traV
QOT06_RS22000 49255..49638 + 384 WP_283631433 TraA family conjugative transfer protein -
QOT06_RS22005 49840..55326 + 5487 WP_283631304 Ig-like domain-containing protein -
QOT06_RS22010 55475..56182 + 708 WP_283631305 DsbC family protein trbB
QOT06_RS22015 56179..58623 + 2445 WP_283631306 type IV secretion system protein TraC virb4
QOT06_RS22020 58638..58955 + 318 WP_283631307 hypothetical protein -
QOT06_RS22025 58952..59482 + 531 WP_283631309 S26 family signal peptidase -
QOT06_RS22030 59445..60710 + 1266 WP_283631310 TrbC family F-type conjugative pilus assembly protein traW
QOT06_RS22035 60707..61378 + 672 WP_071681744 EAL domain-containing protein -
QOT06_RS22040 61399..62382 + 984 WP_240433690 TraU family protein traU
QOT06_RS22045 62498..65242 + 2745 WP_283631312 conjugal transfer mating pair stabilization protein TraN traN
QOT06_RS22050 65281..66144 - 864 WP_283631314 hypothetical protein -
QOT06_RS22055 66266..66907 - 642 WP_283631316 hypothetical protein -
QOT06_RS22060 67201..67521 + 321 WP_283631318 hypothetical protein -
QOT06_RS22065 67826..68011 + 186 WP_154398366 hypothetical protein -
QOT06_RS22070 68231..69199 + 969 WP_022635552 AAA family ATPase -
QOT06_RS22075 69210..70115 + 906 WP_089140447 hypothetical protein -

Host bacterium

ID   9082 GenBank   NZ_OX461118
Plasmid name   SF1039_p1 Incompatibility group   IncA/C2
Plasmid size   141179 bp Coordinate of oriT [Strand]   42408..42558 [+]
Host baterium   Shewanella baltica strain SF1039 isolate SF1039

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -