Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104962
Name   oriT_pSX2_LC6 in_silico
Organism   Shewanella sp. LC6
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP043904 (40124..40274 [+], 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_pSX2_LC6
TGGTCGATGTGAACCCTTTTGACCGGGTTATGAATGAATTGAAAAATCGTGGCCGCAAAAATGCTCATATCCTGAGTATCCTTCAATTCGATTGGCCTGCATCAGAGGTCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGTATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3487 GenBank   WP_140907204
Name   mobH_FJD32_RS24565_pSX2_LC6 insolico UniProt ID   _
Length   987 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 987 a.a.        Molecular weight: 109366.76 Da        Isoelectric Point: 4.8804

>WP_140907204.1 MULTISPECIES: MobH family relaxase [unclassified Shewanella]
MLKALNKLFGGRSGVIEATPSGRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHGIERYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEYLSKSGPSIIEAMLEAISGTTVNQPVTRLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEATGSLKILMLRLESNDLVFTNEPPSAVAAEVVGDVEDAEIE
FVDPDESDDDEGGVSLNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSTDHEDTPAQGAAETKDSPKAASA
TTPTKGKQVKGKPKKDTEEQTEKPETKEELSPQDIAKNAPPLANDNPLQALRDVGGGLGDIDFPFDAFNA
STDTCITDEESLKNSNEAKLAQPKSDFVPEEQNSLQSEYFPMFSGSDEPPSWVIEPLPMLAVEPEETSAT
TEMSQANKPNQQEKGAKTLLSEILAGYGEASALLEQAIMPVLEGKKTLGEVLCLMKGQAVILYPEGARSL
GAPSEVLSKLSHADAIVPDPIMPGRKVRDFSGVKAIVLAQQLSDAVVAAIKEVEASMGGYQDVFELVSPP
DSDVRKSKSAPKQQSQPMQKKNQQQKSDAGSGKAAPEKDTKEKADQKPKKEKKGDTASVVDGHEIKPIEE
KQNVARLPKREAQPEAVVVTKVEREKELGHIEVREREEQEVREFEPPKAKTNPKDIKDEDFLPPGVTPEK
AILILKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGIKKHILCGMLSRAQKRPLLKKREGKL
YLEVDET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   3435 GenBank   WP_140907203
Name   traD_FJD32_RS24570_pSX2_LC6 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: 69450.96 Da        Isoelectric Point: 7.1173

>WP_140907203.1 MULTISPECIES: conjugative transfer system coupling protein TraD [unclassified Shewanella]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLRGRDLEFISITELQKYIKDTPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGKESTVKKVVRKI
QGKRKELPIGQPWIHGVEPKEEKLMQPLKHTEGHTLIVGTTGSGKTRMFDILISQAIMRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLIITHDRPNLTKLRRFLEGGAAGLVIRSVQAYSERVRPDWEAEAAPFLEKVKNGSREKIAFA
LMRFYYEIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSTDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNKPVNIFVDEAAEVINDPFIQL
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)

(170-212)

  Protein structure



No available structure.



ID   3436 GenBank   WP_140907190
Name   traC_FJD32_RS24645_pSX2_LC6 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: 92275.52 Da        Isoelectric Point: 6.0248

>WP_140907190.1 MULTISPECIES: type IV secretion system protein TraC [unclassified Shewanella]
MIVTIKKKLQETLIPEHLRAAGIIPVLAYDEDEHVFLMDDHSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRISAKTNKGTYDNGLIQ
DLKLFVTCKVPINNNNPSEGELQNLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
AVDWEMDKPICEQIFDYGTDVEVSKNGLRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDREAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWD
EKGKDMKVDDIAERCLEGEDMRLRDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHLR
QVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLYE
NAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRLI
VGDFQKLLYSTDPVDVNAIDLFVKQGMSIPEAIKAVMRSRKQAA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(21-255)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraG P-loop domain (P-loop_TraG)

(449-808)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 38208..63348

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FJD32_RS24555 (FJD32_024940) 34248..34481 - 234 WP_071681758 hypothetical protein -
FJD32_RS24560 (FJD32_024945) 34463..35080 - 618 WP_140907205 hypothetical protein -
FJD32_RS24565 (FJD32_024950) 35248..38211 + 2964 WP_140907204 MobH family relaxase -
FJD32_RS24570 (FJD32_024955) 38208..40073 + 1866 WP_140907203 conjugative transfer system coupling protein TraD virb4
FJD32_RS24575 (FJD32_024960) 40123..40668 + 546 WP_023044870 hypothetical protein -
FJD32_RS24580 (FJD32_024965) 40625..41254 + 630 WP_140907202 DUF4400 domain-containing protein tfc7
FJD32_RS25335 (FJD32_024970) 41263..41709 + 447 WP_140907201 hypothetical protein -
FJD32_RS24585 (FJD32_024975) 41719..42096 + 378 WP_140907200 hypothetical protein -
FJD32_RS24590 (FJD32_024980) 42096..42758 + 663 WP_140907199 hypothetical protein -
FJD32_RS24595 42939..43082 + 144 WP_181159838 hypothetical protein -
FJD32_RS24600 (FJD32_024985) 43094..43456 + 363 WP_240200051 hypothetical protein -
FJD32_RS24605 (FJD32_024990) 43604..43885 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
FJD32_RS24610 (FJD32_024995) 43882..44508 + 627 WP_140907197 TraE/TraK family type IV conjugative transfer system protein traE
FJD32_RS24615 (FJD32_025000) 44492..45409 + 918 WP_140907196 type-F conjugative transfer system secretin TraK traK
FJD32_RS24620 (FJD32_025005) 45409..46722 + 1314 WP_205403084 TraB/VirB10 family protein traB
FJD32_RS24625 (FJD32_025010) 46719..47297 + 579 WP_140907194 type IV conjugative transfer system lipoprotein TraV traV
FJD32_RS24630 (FJD32_025015) 47310..47693 + 384 WP_140907193 TraA family conjugative transfer protein -
FJD32_RS24635 (FJD32_025020) 47886..53372 + 5487 WP_140907192 Ig-like domain-containing protein -
FJD32_RS24640 (FJD32_025025) 53521..54228 + 708 WP_140907191 DsbC family protein trbB
FJD32_RS24645 (FJD32_025030) 54225..56669 + 2445 WP_140907190 type IV secretion system protein TraC virb4
FJD32_RS24650 (FJD32_025035) 56684..57001 + 318 WP_140907189 hypothetical protein -
FJD32_RS24655 (FJD32_025040) 56998..57528 + 531 WP_140907188 S26 family signal peptidase -
FJD32_RS24660 (FJD32_025045) 57491..58756 + 1266 WP_140907187 TrbC family F-type conjugative pilus assembly protein traW
FJD32_RS24665 (FJD32_025050) 58753..59424 + 672 WP_140907186 EAL domain-containing protein -
FJD32_RS24670 (FJD32_025055) 59445..60428 + 984 WP_231398180 TraU family protein traU
FJD32_RS24675 (FJD32_025060) 60544..63348 + 2805 WP_240200052 conjugal transfer mating pair stabilization protein TraN traN
FJD32_RS24680 (FJD32_025065) 63386..64249 - 864 WP_140907184 hypothetical protein -
FJD32_RS24685 (FJD32_025070) 64372..65013 - 642 WP_140907183 hypothetical protein -
FJD32_RS24690 (FJD32_025075) 65304..65624 + 321 WP_140907182 hypothetical protein -
FJD32_RS24695 (FJD32_025080) 65929..66114 + 186 WP_240200053 hypothetical protein -
FJD32_RS24700 (FJD32_025085) 66333..67301 + 969 WP_140907180 AAA family ATPase -
FJD32_RS24705 (FJD32_025090) 67313..68218 + 906 WP_140907179 hypothetical protein -

Host bacterium

ID   5400 GenBank   NZ_CP043904
Plasmid name   pSX2_LC6 Incompatibility group   IncA/C2
Plasmid size   119324 bp Coordinate of oriT [Strand]   40124..40274 [+]
Host baterium   Shewanella sp. LC6

Cargo genes

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