Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 100098
• Name: oriT_pVCR94deltaX
• Organism: Vibrio cholerae strain BI144
• Sequence Completeness: intact
• NCBI accession of oriT (coordinates [strand]): KF551948 (_)
• oriT length: 398 nt
• IRs (inverted repeats): IR1: 62..70, 71..79 (AACCCTTTC..GACAGGGTT) IR2: 143..150, 154..161 (TGGCCTGC..GGAGGCCA)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: _

oriT sequence

• Length: 398 nt

>oriT_pVCR94deltaX
CCCAAAAGGGGCATATAGGTTGCTTTTCGGTGGCTTTTTGATCGTTGAGTAAGGGAACCTATGGGAACGCTGCACGGATAGGCTCAGATAAACAGACCTTACCCTCGCATCGAGAACCGCTTGCCCTCCAGCATCGAGAGACGGTGGTAAAGAGGCATTTGGAATCTTTGATGCCATATCCAATATATCTGGAATCTTTAAATATAGATTCATATGTAAAGAGGCTGTGAAAGAATAAGAGCATCAAGATTCCAGATAGATAGAGGGAAATTTGACAAATTCCAAAGATGGGTTAGCCTAGTGACAGAACTAGATTCCAGTATTGGAATAATCAGCTTTAAATTCCAGATAGATAGTTATGTGGATAGGAATTGGATAGGAATTGGGAGGGTATTGAG

oriT secondary structure

Predicted by RNAfold.

Reference

[1] Carraro N et al. (2014) Development of pVCR94螖X from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids. Front Microbiol. 0.238888889. [PMID:24567731]

Relaxase

TraI_pVCR94deltaX

• ID: 93
• GenBank: AHC56417
• Name: TraI_pVCR94deltaX
• UniProt ID: V9SHT5
• Length: 992 a.a.
• Note: conjugative element relaxase

Relaxase protein sequence

• Length: 992 a.a.
• Molecular weight: 109595.88 Da
• Isoelectric Point: 4.8967

>AHC56417.1 TraI (plasmid) [Vibrio cholerae]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

Protein domains

Predicted by InterproScan.

• Putative helicase (TraI_2) (51-357)

Protein structure

• AlphaFold DB: V9SHT5

Reference

[1] Carraro N et al. (2014) Development of pVCR94螖X from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids. Front Microbiol. 0.238888889. [PMID:24567731]

Auxiliary protein

TraJ_pVCR94deltaX

• ID: 134
• GenBank: AHC56420
• Name: TraJ_pVCR94deltaX
• UniProt ID: V9SH95
• Length: 209 a.a.
• PDB ID: _
• Note: _

Auxiliary protein sequence

• Length: 209 a.a.
• Molecular weight: 24169.77 Da
• Isoelectric Point: 9.4782

>AHC56420.1 TraJ (plasmid) [Vibrio cholerae]
MKKPWLLVAWLLVIELLAILLLIPGDWTDRAIKRESVLVEQSLGVEARDWIQNKASTWFRSSVIDSGFYE
GMYQTLIPSEEERQKSKGMQDMGKGWFVWVKGRMEAFVNVIYQFYTRLALLAAWAPYMLILFVPAVYDGM
MTWRIKRTNFDYASPVLHRYSVRGTMYLMAGLFIAFFIPIALDPVVIPMTMMTCCVLVGLTFGNLQKRV

Protein domains

Predicted by InterproScan.

• Domain of unknown function (DUF4400) (DUF4400) (44-201)

Protein structure

• AlphaFold DB: V9SH95

Reference

[1] Carraro N et al. (2014) Development of pVCR94螖X from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids. Front Microbiol. 0.238888889. [PMID:24567731]

T4CP

TraD_pVCR94deltaX

• ID: 93
• GenBank: AHC56418
• Name: TraD_pVCR94deltaX
• UniProt ID: V9SIV0
• Length: 621 a.a.
• PDB ID: _
• Note: conjugative coupling factor TraD

T4CP protein sequence

• Length: 621 a.a.
• Molecular weight: 69225.71 Da
• Isoelectric Point: 6.9403

>AHC56418.1 TraD (plasmid) [Vibrio cholerae]
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

• AlphaFold DB: V9SIV0

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 38088..63279

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
Vcrx058	34113..34346	-	234	AHC56415	hypothetical protein	-
Vcrx059	34328..34945	-	618	AHC56416	hypothetical protein	-
Vcrx060	35113..38091	+	2979	AHC56417	TraI	-
Vcrx061	38088..39953	+	1866	AHC56418	TraD	virb4
Vcrx062	39964..40548	+	585	AHC56419	hypothetical protein	-
Vcrx063	40505..41134	+	630	AHC56420	TraJ	tfc7
Vcrx064	41144..41590	+	447	AHC56421	hypothetical protein	-
Vcrx065	41600..41977	+	378	AHC56422	hypothetical protein	-
Vcrx066	41977..42639	+	663	AHC56423	hypothetical protein	-
Vcrx067	42636..42776	+	141	AHC56424	hypothetical protein	-
Vcrx068	42820..42963	+	144	AHC56425	hypothetical protein	-
Vcrx069	42975..43340	+	366	AHC56426	hypothetical protein	-
Vcrx070	43485..43766	+	282	AHC56427	TraL	traL
Vcrx071	43763..44389	+	627	AHC56428	TraE	traE
Vcrx072	44373..45290	+	918	AHC56429	TraK	traK
Vcrx073	45287..46603	+	1317	AHC56430	TraB	traB
Vcrx074	46600..47178	+	579	AHC56431	TraV	traV
Vcrx075	47191..47574	+	384	AHC56432	TraA	-
Vcrx076	47775..53306	+	5532	AHC56433	hypothetical protein	-
Vcrx077	53455..54162	+	708	AHC56434	DsbC	-
Vcrx078	54159..56606	+	2448	AHC56435	TraC	virb4
Vcrx079	56621..56938	+	318	AHC56436	hypothetical protein	-
Vcrx080	56935..57465	+	531	AHC56437	TrhF	-
Vcrx081	57476..58693	+	1218	AHC56438	TraW	traW
Vcrx082	58690..59361	+	672	AHC56439	hypothetical protein	-
Vcrx083	59358..60365	+	1008	AHC56440	TraU	traU
Vcrx084	60481..63279	+	2799	AHC56441	TraN	traN
Vcrx085	63318..64178	-	861	AHC56442	hypothetical protein	-
Vcrx086	64301..64942	-	642	AHC56443	hypothetical protein	-
Vcrx087	65235..65555	+	321	AHC56444	hypothetical protein	-
Vcrx088	65859..66044	+	186	AHC56445	hypothetical protein	-
Vcrx089	66263..67231	+	969	AHC56446	hypothetical protein	-
Vcrx090	67242..68147	+	906	AHC56447	hypothetical protein	-

Host bacterium

• ID: 93
• GenBank: KF551948
• Plasmid name: pVCR94deltaX
• Incompatibility group: IncA/C2
• Plasmid size: 120572 bp
• Coordinate of oriT [Strand]: 39954..40504 [+]
• Host baterium: Vibrio cholerae strain BI144

Cargo genes

• Drug resistance gene: resistance to sulfamethoxazole
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -