Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105558
Name   oriT_pSNE3-1928 in_silico
Organism   Salmonella enterica subsp. enterica serovar Newport str. USDA-ARS-USMARC-1928
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP025240 (51294..51444 [+], 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_pSNE3-1928
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3786 GenBank   WP_001326173
Name   mobH_AW84_RS25305_pSNE3-1928 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   3780 GenBank   WP_000178857
Name   traD_AW84_RS25310_pSNE3-1928 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   3781 GenBank   WP_000637384
Name   traC_AW84_RS25410_pSNE3-1928 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: 92604.86 Da        Isoelectric Point: 5.9216

>WP_000637384.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

TraG P-loop domain (P-loop_TraG)

(449-809)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 49378..58468

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AW84_RS25295 (AW84_25840) 45409..45642 - 234 WP_001191890 hypothetical protein -
AW84_RS25300 (AW84_25845) 45624..46241 - 618 WP_001249395 hypothetical protein -
AW84_RS25305 (AW84_25850) 46409..49381 + 2973 WP_001326173 MobH family relaxase -
AW84_RS25310 (AW84_25855) 49378..51243 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
AW84_RS25315 (AW84_25860) 51293..51838 + 546 WP_000228720 hypothetical protein -
AW84_RS25320 (AW84_25865) 51795..52424 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
AW84_RS25325 (AW84_25870) 52434..52880 + 447 WP_000122507 hypothetical protein -
AW84_RS25330 (AW84_25875) 52890..53267 + 378 WP_000869297 hypothetical protein -
AW84_RS25335 (AW84_25880) 53267..53929 + 663 WP_001231464 hypothetical protein -
AW84_RS25340 (AW84_25885) 54265..54630 + 366 WP_001052530 hypothetical protein -
AW84_RS25345 (AW84_25890) 54775..55056 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
AW84_RS25350 (AW84_25895) 55053..55631 + 579 WP_076097733 TraE/TraK family type IV conjugative transfer system protein traE
AW84_RS25355 (AW84_25900) 55663..56580 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
AW84_RS25360 (AW84_25905) 56580..57893 + 1314 WP_024131605 TraB/VirB10 family protein traB
AW84_RS25365 (AW84_25910) 57890..58468 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
AW84_RS25370 (AW84_25915) 58472..58864 + 393 WP_000479535 TraA family conjugative transfer protein -
AW84_RS25375 (AW84_25920) 59149..60411 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
AW84_RS25380 (AW84_25925) 60735..61880 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
AW84_RS25385 (AW84_25930) 61974..62507 + 534 WP_001221666 lipocalin family protein -
AW84_RS25390 (AW84_25935) 62504..62821 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
AW84_RS26480 (AW84_25940) 63078..63443 + 366 Protein_87 LuxR family transcriptional regulator -

Host bacterium

ID   5996 GenBank   NZ_CP025240
Plasmid name   pSNE3-1928 Incompatibility group   IncA/C2
Plasmid size   146581 bp Coordinate of oriT [Strand]   51294..51444 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Newport str. USDA-ARS-USMARC-1928

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -