Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113217
Name   oriT_pRM089_1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Newport strain RM089
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP117366 (50157..50307 [+], 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_pRM089_1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8478 GenBank   WP_001326173
Name   mobH_PQP78_RS23950_pRM089_1 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   9781 GenBank   WP_000178857
Name   traD_PQP78_RS23955_pRM089_1 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   9782 GenBank   WP_274892030
Name   traC_PQP78_RS24050_pRM089_1 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: 92648.87 Da        Isoelectric Point: 5.8158

>WP_274892030.1 type IV secretion system protein TraC [Salmonella enterica]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIDERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraG P-loop domain (P-loop_TraG)

(449-809)

TraC protein (TraC_F_IV)

(21-255)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 48241..57331

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PQP78_RS23940 (PQP78_23940) 44272..44505 - 234 WP_001191890 hypothetical protein -
PQP78_RS23945 (PQP78_23945) 44487..45104 - 618 WP_001249395 hypothetical protein -
PQP78_RS23950 (PQP78_23950) 45272..48244 + 2973 WP_001326173 MobH family relaxase -
PQP78_RS23955 (PQP78_23955) 48241..50106 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
PQP78_RS23960 (PQP78_23960) 50156..50701 + 546 WP_000228720 hypothetical protein -
PQP78_RS23965 (PQP78_23965) 50658..51287 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
PQP78_RS23970 (PQP78_23970) 51297..51743 + 447 WP_274892029 hypothetical protein -
PQP78_RS23975 (PQP78_23975) 51753..52130 + 378 WP_000869297 hypothetical protein -
PQP78_RS23980 (PQP78_23980) 52130..52792 + 663 WP_001231464 hypothetical protein -
PQP78_RS23985 (PQP78_23985) 53128..53493 + 366 WP_001052530 hypothetical protein -
PQP78_RS23990 (PQP78_23990) 53638..53919 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
PQP78_RS23995 (PQP78_23995) 53916..54542 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
PQP78_RS24000 (PQP78_24000) 54526..55443 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
PQP78_RS24005 (PQP78_24005) 55443..56756 + 1314 WP_024131605 TraB/VirB10 family protein traB
PQP78_RS24010 (PQP78_24010) 56753..57331 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
PQP78_RS24015 (PQP78_24015) 57335..57727 + 393 WP_000479535 TraA family conjugative transfer protein -
PQP78_RS24020 (PQP78_24020) 58012..59274 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
PQP78_RS24025 (PQP78_24025) 59598..60743 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
PQP78_RS24030 (PQP78_24030) 60837..61370 + 534 WP_001221666 lipocalin family protein -
PQP78_RS24035 (PQP78_24035) 61367..61684 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
PQP78_RS24580 61941..62306 + 366 Protein_86 LuxR family transcriptional regulator -

Host bacterium

ID   13652 GenBank   NZ_CP117366
Plasmid name   pRM089_1 Incompatibility group   IncA/C2
Plasmid size   146584 bp Coordinate of oriT [Strand]   50157..50307 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Newport strain RM089

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2
Virulence gene   -
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -