Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 103803
• Name: oriT_pYU39_IncA/C
• Organism: Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 isolate YUHS 05-78
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP011429 (49320..49470 [+], 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

• Length: 151 nt

>oriT_pYU39_IncA/C
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Relaxase

mobH_SE14_RS24125_pYU39_IncA/C

• ID: 2824
• GenBank: WP_001326173
• Name: mobH_SE14_RS24125_pYU39_IncA/C
• UniProt ID: F5BPR1
• Length: 990 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• 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

• AlphaFold DB: F5BPR1

T4CP

traD_SE14_RS24130_pYU39_IncA/C

• ID: 2647
• GenBank: WP_000178857
• Name: traD_SE14_RS24130_pYU39_IncA/C
• UniProt ID: _
• Length: 621 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• 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.

traC_SE14_RS24225_pYU39_IncA/C

• ID: 2648
• GenBank: WP_000637384
• Name: traC_SE14_RS24225_pYU39_IncA/C
• UniProt ID: _
• Length: 815 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• 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: 47404..56494

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
SE14_RS24115	43435..43668	-	234	WP_001191890	hypothetical protein	-
SE14_RS24120 (SE14_04917)	43650..44267	-	618	WP_001249395	hypothetical protein	-
SE14_RS24125 (SE14_04918)	44435..47407	+	2973	WP_001326173	MobH family relaxase	-
SE14_RS24130 (SE14_04919)	47404..49269	+	1866	WP_000178857	conjugative transfer system coupling protein TraD	virb4
SE14_RS24135 (SE14_04920)	49319..49864	+	546	WP_000228720	hypothetical protein	-
SE14_RS24140 (SE14_04921)	49821..50450	+	630	WP_000743449	DUF4400 domain-containing protein	tfc7
SE14_RS24145 (SE14_04922)	50460..50906	+	447	WP_000122507	hypothetical protein	-
SE14_RS24150 (SE14_04923)	50916..51293	+	378	WP_000869297	hypothetical protein	-
SE14_RS24155 (SE14_04924)	51293..51955	+	663	WP_001231464	hypothetical protein	-
SE14_RS24160 (SE14_04926)	52291..52656	+	366	WP_001052530	hypothetical protein	-
SE14_RS24165 (SE14_04927)	52801..53082	+	282	WP_000805625	type IV conjugative transfer system protein TraL	traL
SE14_RS24170 (SE14_04928)	53079..53705	+	627	WP_001049717	TraE/TraK family type IV conjugative transfer system protein	traE
SE14_RS24175 (SE14_04929)	53689..54606	+	918	WP_000794249	type-F conjugative transfer system secretin TraK	traK
SE14_RS24180 (SE14_04930)	54606..55919	+	1314	WP_024131605	TraB/VirB10 family protein	traB
SE14_RS24185 (SE14_04931)	55916..56494	+	579	WP_000793435	type IV conjugative transfer system lipoprotein TraV	traV
SE14_RS24190 (SE14_04932)	56498..56890	+	393	WP_000479535	TraA family conjugative transfer protein	-
SE14_RS24195 (SE14_04933)	57175..58437	+	1263	WP_000608644	IS1380-like element ISEcp1 family transposase	-
SE14_RS24200 (SE14_04935)	58761..59906	+	1146	WP_000976514	extended-spectrum class C beta-lactamase CMY-2	-
SE14_RS24205 (SE14_04936)	60000..60533	+	534	WP_001221666	lipocalin family protein	-
SE14_RS24210 (SE14_04937)	60530..60847	-	318	WP_000118520	quaternary ammonium compound efflux SMR transporter SugE	-
SE14_RS28950	61104..61469	+	366	Protein_84	LuxR family transcriptional regulator	-

Host bacterium

• ID: 4243
• GenBank: NZ_CP011429
• Plasmid name: pYU39_IncA/C
• Incompatibility group: IncA/C2
• Plasmid size: 156323 bp
• Coordinate of oriT [Strand]: 49320..49470 [+]
• Host baterium: Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 isolate YUHS 05-78

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: silP, silA, silB, silF, silC, silR, silS, silE
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -