Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104003
Name   oriT_pYU07-18_IncA/C2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain YU07-18
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP035548 (50156..50306 [+], 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_pYU07-18_IncA/C2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure



Relaxase

ID   2970 GenBank   WP_001326173
Name   mobH_D6D39_RS23985_pYU07-18_IncA/C2 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   2832 GenBank   WP_000178857
Name   traD_D6D39_RS23990_pYU07-18_IncA/C2 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   2833 GenBank   WP_000637384
Name   traC_D6D39_RS24090_pYU07-18_IncA/C2 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: 48240..57330

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
D6D39_RS23975 (D6D39_24370) 44271..44504 - 234 WP_001191890 hypothetical protein -
D6D39_RS23980 (D6D39_24375) 44486..45103 - 618 WP_001249395 hypothetical protein -
D6D39_RS23985 (D6D39_24380) 45271..48243 + 2973 WP_001326173 MobH family relaxase -
D6D39_RS23990 (D6D39_24385) 48240..50105 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
D6D39_RS23995 (D6D39_24390) 50155..50700 + 546 WP_000228720 hypothetical protein -
D6D39_RS24000 (D6D39_24395) 50657..51286 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
D6D39_RS24005 (D6D39_24400) 51296..51742 + 447 WP_000122507 hypothetical protein -
D6D39_RS24010 (D6D39_24405) 51752..52129 + 378 WP_000869297 hypothetical protein -
D6D39_RS24015 (D6D39_24410) 52129..52791 + 663 WP_001231464 hypothetical protein -
D6D39_RS24020 (D6D39_24415) 53127..53492 + 366 WP_001052530 hypothetical protein -
D6D39_RS24025 (D6D39_24420) 53637..53918 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
D6D39_RS24030 (D6D39_24425) 53915..54541 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
D6D39_RS24035 (D6D39_24430) 54525..55442 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
D6D39_RS24040 (D6D39_24435) 55442..56755 + 1314 WP_024131605 TraB/VirB10 family protein traB
D6D39_RS24045 (D6D39_24440) 56752..57330 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
D6D39_RS24050 (D6D39_24445) 57334..57726 + 393 WP_000479535 TraA family conjugative transfer protein -
D6D39_RS24055 (D6D39_24450) 58011..59273 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
D6D39_RS24060 (D6D39_24455) 59597..60742 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
D6D39_RS24065 (D6D39_24460) 60836..61369 + 534 WP_001221666 lipocalin family protein -
D6D39_RS24070 (D6D39_24465) 61366..61683 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
D6D39_RS25610 (D6D39_24470) 61940..62305 + 366 Protein_86 LuxR family transcriptional regulator -

Host bacterium

ID   4443 GenBank   NZ_CP035548
Plasmid name   pYU07-18_IncA/C2 Incompatibility group   IncA/C2
Plasmid size   153015 bp Coordinate of oriT [Strand]   50156..50306 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain YU07-18

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2, oqxB, oqxA, aadA2, dfrA12
Virulence gene   -
Metal resistance gene   silP, silA, silB, silF, silC, silR, silS, silE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -