Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 113584
• Name: oriT_pRC960-2
• Organism: Shigella flexneri Y strain C960
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_KY784668 (54580..54632 [+], 53 nt)
• oriT length: 53 nt
• IRs (inverted repeats): _
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 53 nt

>oriT_pRC960-2
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_HPG08_RS00175_pRC960-2

• ID: 10069
• GenBank: WP_015059539
• Name: t4cp2_HPG08_RS00175_pRC960-2
• UniProt ID: _
• Length: 652 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 652 a.a.
• Molecular weight: 73404.02 Da
• Isoelectric Point: 9.4339

>WP_015059539.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MNAKKMGGLILFLLLLLVGVLIASNYLGGYTALRYSSVDMSLLKWDTFHSVISTFSGNPQYKKLVFMAWF
GFSVPLIFFAIFMLIVVIGIMPKKVIYGDARLATDMDLSKSGFFPDKKSPYKHPPILIGKMFKGRYKKQF
IYFAGQQFLILYAPTRSGKGVGIVIPNCVNYPGSMVILDIKLENWFLSAGFRQKELGQKCFLFAPAGYAE
TIDQAIKGQIRSHRWNPLDCVSRSDLLRETDLAKIAAILIPASDDPIWSDSARNLFVGLGLYLLDKERFH
LDQKAKGHNAPDVLVSISAILKTSIPDNGKDLAAWMGQEVENRSWISDKTKSFFFEFMSAPDRTRGSIKT
NFSSPLNIFSNPVTAEATNFSDFDIRDIRKKPMSIYLGLTPDALITHEKIVNLFFSLLVNENCRELPEHN
PDLKYQCLILLDEFTSMGKSEVIERAVGFTAGYNLRFMFILQNEGQGQKSDMYGQEGWTTFTENSAVVLY
YPPKSKNALAKKISEEIGVRDMKISKRSISSGGGKGGSSRTRNDDVIERPVLLPEEIVSLRDKKNKARNI
AIREIITSEFSRPFIANKIIWFEEPEFKRRVDIARNNHVDIPNLFTQEVMDEIAKIAEIYLPKAGGKKVM
VAGGNVITNPDLDNHDKTDVSE

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (127-591)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 8784..33577

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HPG08_RS00025	4642..5148	+	507	WP_001326595	CaiF/GrlA family transcriptional regulator	-
HPG08_RS00030	5141..5356	+	216	WP_001127357	DUF1187 family protein	-
HPG08_RS00035	5349..5525	+	177	WP_000753050	hypothetical protein	-
HPG08_RS00040	5552..6505	+	954	WP_072089442	SPFH domain-containing protein	-
HPG08_RS00045	6879..7322	+	444	WP_000964330	NfeD family protein	-
HPG08_RS00050	7326..7496	+	171	WP_000550720	hypothetical protein	-
HPG08_RS00055	7507..7953	+	447	WP_001243165	hypothetical protein	-
HPG08_RS00060	8173..8526	+	354	WP_223286767	hypothetical protein	-
HPG08_RS00065	8523..8780	+	258	WP_000739144	hypothetical protein	-
HPG08_RS00070	8784..9779	+	996	WP_001028543	type IV secretion system protein	virB6
HPG08_RS00075	9785..10426	+	642	WP_001425343	type IV secretion system protein	-
HPG08_RS00080	10428..10682	+	255	WP_001043555	EexN family lipoprotein	-
HPG08_RS00085	10695..10982	+	288	WP_171265266	EexN family lipoprotein	-
HPG08_RS00090	11055..11690	+	636	WP_015059536	hypothetical protein	-
HPG08_RS00095	11790..12041	+	252	WP_000121741	type II toxin-antitoxin system Phd/YefM family antitoxin	-
HPG08_RS00100	12031..12312	+	282	WP_000638823	type II toxin-antitoxin system RelE/ParE family toxin	-
HPG08_RS00105	12380..12679	+	300	WP_000835764	TrbM/KikA/MpfK family conjugal transfer protein	-
HPG08_RS00110	12682..13767	+	1086	WP_252992050	pilus assembly protein	-
HPG08_RS00115	13809..15037	+	1229	WP_167389526	IS3-like element IS2 family transposase	-
HPG08_RS00120	15044..15253	+	210	WP_290367929	TcpQ domain-containing protein	-
HPG08_RS00125	15259..15696	+	438	WP_000539665	type IV pilus biogenesis protein PilM	-
HPG08_RS00130	15815..16213	+	399	WP_171265267	hypothetical protein	-
HPG08_RS00135	16234..16818	+	585	WP_001177113	lytic transglycosylase domain-containing protein	virB1
HPG08_RS00415	16818..17108	+	291	WP_000865479	conjugal transfer protein	-
HPG08_RS00145	17179..17499	+	321	WP_000362080	VirB3 family type IV secretion system protein	virB3
HPG08_RS00150	17505..19862	+	2358	WP_063078682	VirB4 family type IV secretion system protein	virb4
HPG08_RS00155	20028..20762	+	735	WP_000432282	virB8 family protein	virB8
HPG08_RS00160	20828..21529	+	702	WP_000274524	TrbG/VirB9 family P-type conjugative transfer protein	-
HPG08_RS00165	21519..22658	+	1140	WP_000790640	TrbI/VirB10 family protein	virB10
HPG08_RS00170	22677..23732	+	1056	WP_001059977	P-type DNA transfer ATPase VirB11	virB11
HPG08_RS00175	23748..25706	+	1959	WP_015059539	type IV secretory system conjugative DNA transfer family protein	-
HPG08_RS00180	25753..26289	+	537	WP_001220543	sigma 54-interacting transcriptional regulator	virb4
HPG08_RS00185	26282..27925	+	1644	WP_001035592	PilN family type IVB pilus formation outer membrane protein	-
HPG08_RS00190	27964..29286	+	1323	WP_000454142	type 4b pilus protein PilO2	-
HPG08_RS00195	29270..29764	+	495	WP_000912553	type IV pilus biogenesis protein PilP	-
HPG08_RS00200	29789..31327	+	1539	WP_000466225	GspE/PulE family protein	virB11
HPG08_RS00205	31318..32427	+	1110	WP_000974903	type II secretion system F family protein	-
HPG08_RS00210	32472..33029	+	558	WP_000095048	type 4 pilus major pilin	-
HPG08_RS00215	33095..33577	+	483	WP_001258095	lytic transglycosylase domain-containing protein	virB1
HPG08_RS00220	33581..34216	+	636	WP_000934977	A24 family peptidase	-
HPG08_RS00225	34229..35605	+	1377	WP_000750519	shufflon system plasmid conjugative transfer pilus tip adhesin PilV	-
HPG08_RS00430	35602..35833	-	232	Protein_47	shufflon system plasmid conjugative transfer pilus tip adhesin PilV	-
HPG08_RS00230	35909..36064	+	156	WP_001358489	hypothetical protein	-
HPG08_RS00235	36061..36453	-	393	WP_236918886	shufflon protein C	-
HPG08_RS00240	36964..38088	+	1125	WP_000486716	site-specific integrase	-

Host bacterium

• ID: 14019
• GenBank: NZ_KY784668
• Plasmid name: pRC960-2
• Incompatibility group: IncI2
• Plasmid size: 65538 bp
• Coordinate of oriT [Strand]: 54580..54632 [+]
• Host baterium: Shigella flexneri Y strain C960

Cargo genes

• Drug resistance gene: mcr-1.1
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -