Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122357
Name   oriT1_pIncA_Silv108 in_silico
Organism   Raoultella ornithinolytica strain MQB_Silv_108
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP104451 (75125..75275 [-], 151 nt)
oriT length   151 nt
IRs (inverted repeats)      12..17, 24..29  (AACCCG..CGGGTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT1_pIncA_Silv108
TGGTCGATGTGAACCCGTTTGACCGGGTTATGAATGAGTTGAAAAGTCGTGGCCGCAAGAACGCTCATATCCTGAGCATCCTTCAATTCGACTGGCCCGCATCGGAGGTCATCATCGAGAAGCTGAGCTGTTACATCACAGATGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14096 GenBank   WP_058662807
Name   mobH_N2J37_RS28320_pIncA_Silv108 insolico UniProt ID   A0A221KLA3
Length   987 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 987 a.a.        Molecular weight: 109306.91 Da        Isoelectric Point: 4.9372

>WP_058662807.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALHKLFGGRSGAIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAYRHGIDRYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVNEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGPVKILMLRLESNDLVFTTEPPAAVTGEVVGDVEDAEIE
FVDPEEADEDQAEGDAGLNNDMLAAELEAEKALAGLGFGDAMAMLKSTSDIAEEKPEQEDTESTELPKPD
ASKKGKQQSKPGKARAEKQPQKPEVKEDLSPQDIAKNAPPLANDDPLQALKDVGGGLGDIDFPFDVFNAS
AETACTDATNLAIPDITEPVKQEEQPKPDFVPQEQNSLQNGDFPIFSDSDEPPSWAIEPLPMLTDTPEQT
IPAPDMQHAGKPKELEKDAKTLLSEMLAGYGEASTLLEQAIMPVLEGKTTLGEVLCLMKGQAVILYPEGA
RSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLVDQLSDAVVAAIKDAEASMGGYQEAFELV
SPPGSGVSKNKSAPKQQSRKKTQQQKPEVDAGAGSEQKTKDKSLQQQPKEKQGNVASLVEEQKRKPVQDQ
EKQNVARLPKREAQPVASKPKVEHERELGHVEVRERDEPEVREFEPPKAKTNPKDINEEDFLPSGVTPEK
ALLMLKDMIQKRSGRWLVTPVLEEDGCLVTSVKAFDMIAGENVGISKHILYGLLSRAQRRPLLKKRQGKL
YLEVDKA

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A221KLA3


T4CP

ID   16435 GenBank   WP_051479468
Name   traC_N2J37_RS28235_pIncA_Silv108 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: 92523.78 Da        Isoelectric Point: 5.9204

>WP_051479468.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIITIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDQSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTSLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTSKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQHLAQIRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYDDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSQKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSDGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRKQAA

  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   16436 GenBank   WP_000178858
Name   traD_N2J37_RS28315_pIncA_Silv108 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: 69248.76 Da        Isoelectric Point: 7.1093

>WP_000178858.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWMAASCAALAVEQVSTMPSEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGKESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVLTHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVKPDWEAEAAAYLEKAKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNTDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  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: 52087..77191

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N2J37_RS28175 (N2J37_28175) 47212..48117 - 906 WP_058662804 hypothetical protein -
N2J37_RS28180 (N2J37_28180) 48129..49097 - 969 WP_001553257 AAA family ATPase -
N2J37_RS28185 (N2J37_28185) 49318..49503 - 186 WP_001186892 hypothetical protein -
N2J37_RS28190 (N2J37_28190) 49814..50134 - 321 WP_012766334 hypothetical protein -
N2J37_RS28195 (N2J37_28195) 50426..51076 + 651 WP_000796641 hypothetical protein -
N2J37_RS28200 (N2J37_28200) 51188..52048 + 861 WP_000679674 hypothetical protein -
N2J37_RS28205 (N2J37_28205) 52087..54825 - 2739 WP_260990876 conjugal transfer mating pair stabilization protein TraN traN
N2J37_RS28210 (N2J37_28210) 54976..55980 - 1005 WP_000911304 TraU family protein traU
N2J37_RS28215 (N2J37_28215) 55974..56651 - 678 WP_039272402 EAL domain-containing protein -
N2J37_RS28220 (N2J37_28220) 56648..57916 - 1269 WP_039272404 TrbC family F-type conjugative pilus assembly protein traW
N2J37_RS28225 (N2J37_28225) 57879..58409 - 531 WP_000672456 S26 family signal peptidase -
N2J37_RS28230 (N2J37_28230) 58406..58723 - 318 WP_000364398 hypothetical protein -
N2J37_RS28235 (N2J37_28235) 58738..61185 - 2448 WP_051479468 type IV secretion system protein TraC virb4
N2J37_RS28240 (N2J37_28240) 61182..61889 - 708 WP_001259344 DsbC family protein -
N2J37_RS28245 (N2J37_28245) 62038..67524 - 5487 WP_039272407 Ig-like domain-containing protein -
N2J37_RS28250 (N2J37_28250) 67725..68117 - 393 WP_012766327 TraA family conjugative transfer protein -
N2J37_RS28255 (N2J37_28255) 68121..68699 - 579 WP_039272410 type IV conjugative transfer system lipoprotein TraV traV
N2J37_RS28260 (N2J37_28260) 68696..70012 - 1317 WP_039272412 TraB/VirB10 family protein traB
N2J37_RS28265 (N2J37_28265) 70009..70926 - 918 WP_012766326 type-F conjugative transfer system secretin TraK traK
N2J37_RS28270 (N2J37_28270) 70910..71536 - 627 WP_039272415 TraE/TraK family type IV conjugative transfer system protein traE
N2J37_RS28275 (N2J37_28275) 71533..71814 - 282 WP_000805626 type IV conjugative transfer system protein TraL traL
N2J37_RS28280 (N2J37_28280) 71957..72304 - 348 WP_039272417 hypothetical protein -
N2J37_RS28285 (N2J37_28285) 72317..72460 - 144 WP_168199038 hypothetical protein -
N2J37_RS28290 (N2J37_28290) 72639..73301 - 663 WP_039272419 hypothetical protein -
N2J37_RS28295 (N2J37_28295) 73301..73678 - 378 WP_000869260 hypothetical protein -
N2J37_RS28300 (N2J37_28300) 73688..74134 - 447 WP_039272421 hypothetical protein -
N2J37_RS28305 (N2J37_28305) 74145..74774 - 630 WP_000743448 DUF4400 domain-containing protein tfc7
N2J37_RS28310 (N2J37_28310) 74731..75276 - 546 WP_023356350 hypothetical protein -
N2J37_RS28315 (N2J37_28315) 75326..77191 - 1866 WP_000178858 conjugative transfer system coupling protein TraD virb4
N2J37_RS28320 (N2J37_28320) 77188..80151 - 2964 WP_058662807 MobH family relaxase -
N2J37_RS28325 (N2J37_28325) 80319..80936 + 618 WP_012766323 hypothetical protein -
N2J37_RS28330 (N2J37_28330) 80918..81151 + 234 WP_039272424 hypothetical protein -

Host bacterium

ID   22783 GenBank   NZ_CP104451
Plasmid name   pIncA_Silv108 Incompatibility group   IncA/C
Plasmid size   148888 bp Coordinate of oriT [Strand]   75125..75275 [-]; 109261..109365 [-]
Host baterium   Raoultella ornithinolytica strain MQB_Silv_108

Cargo genes

Drug resistance gene   blaSHV-12, sul1, qacE, aac(3)-Ib-aac(6')-Ib
Virulence gene   -
Metal resistance gene   merR, merT, merP, merC, merA, merD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -