Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113934
Name   oriT_pRIVM0001_VIM-1_171012_B12 in_silico
Organism   Aeromonas sp. pRIVM0001_VIM-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH220284 (34300..34450 [+], 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

>oriT_pRIVM0001_VIM-1_171012_B12
TGGTCGATGTGAACCCGTTTGACCGGGTTATGAATGAGTTGAAAAGTCGTGGCCGCAAGAACGCTCATATCCTGAGCATCCTTCAATTCGACTGGCCCGCATCGGAGGTCATCATCGAGAAGCTGAGCTGTTACATCACAGATGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8948 GenBank   WP_058662807
Name   mobH_HTS92_RS00225_pRIVM0001_VIM-1_171012_B12 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   10396 GenBank   WP_000178858
Name   traD_HTS92_RS00230_pRIVM0001_VIM-1_171012_B12 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.



ID   10397 GenBank   WP_051479468
Name   traC_HTS92_RS00310_pRIVM0001_VIM-1_171012_B12 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 32384..57488

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTS92_RS00215 28424..28657 - 234 WP_039272424 hypothetical protein -
HTS92_RS00220 28639..29256 - 618 WP_012766323 hypothetical protein -
HTS92_RS00225 29424..32387 + 2964 WP_058662807 MobH family relaxase -
HTS92_RS00230 32384..34249 + 1866 WP_000178858 conjugative transfer system coupling protein TraD virb4
HTS92_RS00235 34260..34844 + 585 WP_000332867 hypothetical protein -
HTS92_RS00240 34801..35430 + 630 WP_000743448 DUF4400 domain-containing protein tfc7
HTS92_RS00245 35441..35887 + 447 WP_039272421 hypothetical protein -
HTS92_RS00250 35897..36274 + 378 WP_000869260 hypothetical protein -
HTS92_RS00255 36274..36936 + 663 WP_039272419 hypothetical protein -
HTS92_RS00260 37115..37258 + 144 WP_168199038 hypothetical protein -
HTS92_RS00265 37271..37618 + 348 WP_039272417 hypothetical protein -
HTS92_RS00270 37761..38042 + 282 WP_000805626 type IV conjugative transfer system protein TraL traL
HTS92_RS00275 38039..38665 + 627 WP_039272415 TraE/TraK family type IV conjugative transfer system protein traE
HTS92_RS00280 38649..39566 + 918 WP_012766326 type-F conjugative transfer system secretin TraK traK
HTS92_RS00285 39563..40879 + 1317 WP_039272412 TraB/VirB10 family protein traB
HTS92_RS00290 40876..41454 + 579 WP_039272410 type IV conjugative transfer system lipoprotein TraV traV
HTS92_RS00295 41458..41850 + 393 WP_012766327 TraA family conjugative transfer protein -
HTS92_RS00300 42051..47537 + 5487 WP_039272407 Ig-like domain-containing protein -
HTS92_RS00305 47686..48393 + 708 WP_001259344 DsbC family protein -
HTS92_RS00310 48390..50837 + 2448 WP_051479468 type IV secretion system protein TraC virb4
HTS92_RS00315 50852..51169 + 318 WP_000364398 hypothetical protein -
HTS92_RS00320 51166..51696 + 531 WP_000672456 S26 family signal peptidase -
HTS92_RS00325 51659..52927 + 1269 WP_039272404 TrbC family F-type conjugative pilus assembly protein traW
HTS92_RS00330 52924..53601 + 678 WP_039272402 EAL domain-containing protein -
HTS92_RS00335 53595..54599 + 1005 WP_000911304 TraU family protein traU
HTS92_RS00340 54750..57488 + 2739 WP_058662805 conjugal transfer mating pair stabilization protein TraN traN
HTS92_RS00345 57527..58387 - 861 WP_000679674 hypothetical protein -
HTS92_RS00350 58499..59149 - 651 WP_000796641 hypothetical protein -
HTS92_RS00355 59441..59761 + 321 WP_012766334 hypothetical protein -
HTS92_RS00360 60072..60257 + 186 WP_001186892 hypothetical protein -
HTS92_RS00365 60478..61446 + 969 WP_001553257 AAA family ATPase -
HTS92_RS00370 61458..62363 + 906 WP_058662804 hypothetical protein -

Host bacterium

ID   14369 GenBank   NZ_MH220284
Plasmid name   pRIVM0001_VIM-1_171012_B12 Incompatibility group   IncA/C
Plasmid size   164885 bp Coordinate of oriT [Strand]   34300..34450 [+]
Host baterium   Aeromonas sp. pRIVM0001_VIM-1

Cargo genes

Drug resistance gene   dfrA14, mph(A), blaSHV-12, blaVIM-1, aph(3')-XV, ant(3'')-Ia, catB2, qacE, sul1, qnrS1, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -