SecReT6 ID	929
Strain	Serratia marcescens Db10
Replicon	T6SS [Browse all T6SS(s) in this replicon]
Accession	HG326223
Location	2365124..2402670
Comment	Killing of E. coli, P. fluorescens, Enterobacter cloacae, another strain of S. marcescens and susceptible mutants of Db10
Function	anti-bacterial
Experimental investigation has been performed on this T6SS.

II. T6SS components

Component	TssH	TssD	TssL	TssI	TssA	TssB	TssC	TssE	TssF
Number	1	1	1	2	1	1	1	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	1

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	SMDB11_2239 (cnu)	2360950..2361165 [+], 216	560174082	OriC-binding nucleoid-associated protein
2	SMDB11_2240 (uspC)	2361363..2361782 [+], 420	560174083	universal stress protein
3	SMDB11_2241	2361868..2362899 [+], 1032	560174084	putative zinc-binding alcohol dehydrogenase
4	SMDB11_2242 (pcp)	2362934..2363581 [-], 648	560174085	pyrrolidone-carboxylate peptidase
5	SMDB11_2243	2363679..2364611 [+], 933	560174086	LysR-family transcriptional regulator
6	SMDB11_2244	2365103..2367463 [+], 2361	560174087	type VI secretion system, effector protein VgrG-like	TssI
7	SMDB11_2245	2367474..2367863 [+], 390	560174088	hypothetical protein
8	SMDB11_2246	2367965..2368465 [+], 501	560174089	hypothetical protein
9	SMDB11_2247	2368637..2371189 [+], 2553	560174090	pentapeptide repeat-containing protein
10	SMDB11_2248	2371186..2372253 [+], 1068	560174091	pentapeptide repeat-containing protein
11	SMDB11_2249	2372284..2372919 [+], 636	560174092	hypothetical protein
12	SMDB11_2250	2372936..2373328 [+], 393	560174093	hypothetical protein
13	SMDB11_2251	2373377..2373877 [+], 501	560174094	hypothetical protein
14	SMDB11_2252	2373907..2374437 [+], 531	560174095	type VI secretion system-associated protein,SciN-like	TssJ
15	SMDB11_2253	2374478..2375824 [+], 1347	560174096	type VI secretion system-associated protein	TssK
16	SMDB11_2254	2375828..2377048 [+], 1221	560174097	type VI secretion system-associated protein	TssL
17	SMDB11_2255	2377048..2380683 [+], 3636	560174098	type VI secretion system-associated protein,IcmF-like	TssM
18	SMDB11_2256	2380702..2381421 [+], 720	560174099	type VI secretion system-associated protein
19	SMDB11_2257	2381445..2382476 [+], 1032	560174100	type VI secretion system-associated protein	TssA
20	SMDB11_2258	2382597..2383133 [+], 537	560174101	type VI secretion system-associated protein	TssB
21	SMDB11_2259	2383137..2384642 [+], 1506	560174102	type VI secretion system-associated protein	TssC
22	SMDB11_2260	2384710..2385093 [+], 384	560174103	hypothetical protein
23	SMDB11_2261	2385090..2385581 [+], 492	560174104	hypothetical protein
24	SMDB11_2262	2385581..2386036 [+], 456	560174105	hypothetical protein
25	SMDB11_2263	2386232..2386714 [+], 483	560174106	type VI secretion system, effector protein Hcp-like	TssD
26	SMDB11_2264	2386769..2387245 [+], 477	560174107	hypothetical protein
27	SMDB11_2265	2387230..2387604 [+], 375	560174108	hypothetical protein
28	SMDB11_2266	2387650..2388009 [+], 360	560174109	hypothetical protein
29	SMDB11_2267	2388490..2390232 [+], 1743	560174110	type VI secretion system-associated protein,containing FHA domain
30	SMDB11_2268	2390232..2391005 [+], 774	560174111	type VI secretion system, serine/threonine protein phosphatase, PppA-like
31	SMDB11_2269	2391034..2392020 [+], 987	560174112	hypothetical protein
32	SMDB11_2270	2392036..2392857 [+], 822	560174113	type VI secretion system-associated protein,SciE-like
33	SMDB11_2271	2392860..2393435 [+], 576	560174114	type VI secretion system,lysozyme-relatedprotein	TssE
34	SMDB11_2272	2393440..2395326 [+], 1887	560174115	type VI secretion system-associated protein	TssF
35	SMDB11_2273	2395323..2396393 [+], 1071	560174116	type VI secretion system-associated protein	TssG
36	SMDB11_2274	2396450..2399104 [+], 2655	560174117	type VI secretion system ATPase, ClpV1-like	TssH
37	SMDB11_2275	2399154..2400599 [+], 1446	560174118	type VI secretion system, serine/threonine protein kinase
38	SMDB11_2276	2400742..2402670 [+], 1929	560174119	type VI secretion system, effector protein VgrG-like	TssI
39	SMDB11_2277	2402725..2403165 [+], 441	560174120	hypothetical protein
40	SMDB11_2278	2403168..2407589 [+], 4422	560174121	Rhs-family protein

 Genes in the 5-kb flanking regions if available, or non-core components encoded by the T6SS gene cluster if any. In the 'Note' column,if available, '(e)' denotes effector while '(i)' for immunity protein

Download FASTA format files

Proteins        Genes

V. Investigation of the genomic context of the T6SS gene cluster.

1. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the mobile genetic elements database, ACLAME.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

2. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the virulence factor database, VFDB.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

3. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against against the antibiotic resistance database, ARDB.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

Homology Effector list

SMDB11_0927(Slp) , SMDB11_1083 (Tfe2), SMDB11_1112 (Ssp3), SMDB11_1610(Rhs2), SMDB11_1610 (Rhs2), SMDB11_2244 (VgrG), SMDB11_2261 (ssp1), SMDB11_2261 (Ssp1), SMDB11_2263 (Hcp), SMDB11_2264 (ssp2), SMDB11_2276 (VgrG), SMDB11_2278(Rhs1), SMDB11_2278 (Rhs1), SMDB11_3455 (Hcp), SMDB11_3456 (Hcp), SMDB11_3980 (Ssp4), SMDB11_4628 (Ssp5), SMDB11_4673 (Ssp6)   SMA3456 (Hcp protein)   SMA3455 (Hcp protein)   SMA4673 (Ssp6)   SMA4628 (Ssp5)   SMA3980 (Ssp4)   SMA2276 (VgrG)   SMA1112 (Ssp3)   SMA2244 (VgrG)   SMA2261 (Ssp1)   SMA2264 (Ssp2)   SMA2263 (Hcp protein)

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SMDB11_0927	971234..972886 [+], 1653	560172775	putative phospholipase (Slp)	SMDB11_0927(Slp)
2	SMDB11_1083	1147856..1148536 [+], 681	560172929	putative chitin-binding protein (Tfe2)	SMDB11_1083 (Tfe2)
3	SMDB11_1112	1178412..1178963 [+], 552	560172958	hypothetical protein (Ssp3)	SMDB11_1112 (Ssp3)
4	SMDB11_1610	1689650..1693942 [+], 4293	560173453	Rhs-family protein (Rhs2)	SMDB11_1610(Rhs2)
5	SMDB11_1611	1693944..1694432 [+], 489	560173454	hypothetical protein (Rhs2)	SMDB11_1610 (Rhs2)
6	SMDB11_2244	2365103..2367463 [+], 2361	560174087	type VI secretion system, effector protein VgrG-like (VgrG)	SMDB11_2244 (VgrG)
7	SMDB11_2261	2385090..2385581 [+], 492	560174104	hypothetical protein (ssp1)	SMDB11_2261 (ssp1)
8	SMDB11_2261	2385090..2385581 [+], 492	560174104	hypothetical protein (Ssp1)	SMDB11_2261 (Ssp1)
9	SMDB11_2263	2386232..2386714 [+], 483	560174106	type VI secretion system, effector protein Hcp-like (Hcp)	SMDB11_2263 (Hcp)
10	SMDB11_2264	2386769..2387245 [+], 477	560174107	hypothetical protein (ssp2)	SMDB11_2264 (ssp2)
11	SMDB11_2276	2400742..2402670 [+], 1929	560174119	type VI secretion system, effector protein VgrG-like (VgrG)	SMDB11_2276 (VgrG)
12	SMDB11_2278	2403168..2407589 [+], 4422	560174121	Rhs-family protein (Rhs1)	SMDB11_2278(Rhs1)
13	SMDB11_2278A	2407591..2408079 [+], 489	560174122	hypothetical protein (Rhs1)	SMDB11_2278 (Rhs1)
14	SMDB11_3455	3668310..3668792 [+], 483	560175282	type VI secretion system, effector protein Hcp-like (Hcp)	SMDB11_3455 (Hcp)
15	SMDB11_3456	3668840..3669322 [+], 483	560175283	type VI secretion system, effector protein Hcp-like (Hcp)	SMDB11_3456 (Hcp)
16	SMDB11_3980	4242848..4243843 [-], 996	560175802	hypothetical protein (Ssp4)	SMDB11_3980 (Ssp4)
17	SMDB11_4628	4979889..4980716 [+], 828	560176449	hypothetical protein (Ssp5)	SMDB11_4628 (Ssp5)
18	SMDB11_4673	5022150..5022797 [-], 648	560176492	hypothetical protein (Ssp6)	SMDB11_4673 (Ssp6)
Data from experimental literature

Download FASTA format files

Proteins        Genes

Homology Immunity protein list

SMDB11_0927 (Slp), SMDB11_0927 (Slp), SMDB11_1610 (Rhs2), SMDB11_2278 (Rhs1)   SMA2260 (Rap1a)   SMA2266 (Rap2b)   SMA4630 (Sip5b)   SMA2262 (Rap1b)   SMA2265 (Rap2a)   SMA4629 (Sip5a)   SMA3979 (Sip4)   SMA1111 (Sip3)

Immunity protein identified
#	Locus tag(Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SMDB11_0928	972883..973656 [+], 774	560172776	ankyrin repeat-containing protein (Slp)	SMDB11_0927 (Slp)
2	SMDB11_0929	973746..974489 [+], 744	560172777	ankyrin repeat-containing protein (Slp)	SMDB11_0927 (Slp)
3	SMDB11_1611	1693944..1694432 [+], 489	560173454	hypothetical protein (Rhs2)	SMDB11_1610 (Rhs2)
4	SMDB11_2278A	2407591..2408079 [+], 489	560174122	hypothetical protein (Rhs1)	SMDB11_2278 (Rhs1)
Data from experimental literature

Download FASTA format files

Proteins        Genes

Adaptors list

SMDB11_1609 (EagR2), SMDB11_2245 (EagR1)

Adaptor identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SMDB11_1609	1689187..1689618 [+], 432	560173452	hypothetical protein (EagR2)	SMDB11_1609 (EagR2)
2	SMDB11_2245	2367474..2367863 [+], 390	560174088	hypothetical protein (EagR1)	SMDB11_2245 (EagR1)
Data from experimental literature

Download FASTA format files

Proteins        Genes

The information on regulator interaction.

#	homolog effector locus tag	Regulator way	Function	Regulate target	Description
1	SMDB11_2275 (PpKA)	TPP	+	SMDB11_2267 (FHA)	Phosphorylation of Fha by PpkA promotes formation ofFha foci and assembly ofan active T6SS in Serratiamarcescens.
2	SMDB11_2268 (PppA)	TPP	-	SMDB11_2267 (FHA)	PppA-mediated dephosphorylation of Fha is required for partial disassembly and re-assembly of the T6SS at a new location in the cell.
3	SMDB11_2269 (RtkS)	TPP	+	SMDB11_2275 (PpKA)	RtkS is an upstream activator of PpkA which stabilises the kinase through a direct interaction.
4	SMDB11_2256 (TagF)	TPP	-	unknown	TagF negatively regulates assembly ofa functional T6SS and that PpkA-mediated phosphorylation is required to overcome this repression.

(1) Srikannathasan V et al. (2013). Structural basis for type VI secreted peptidoglycan DL-endopeptidase function, specificity and neutralization in Serratia marcescens. Acta Crystallogr D Biol Crystallogr. 69(Pt 12):2468-82. [PudMed:24311588]

(2) Heymann JB et al. (2013). Three-dimensional structure of the toxin-delivery particle antifeeding prophage of Serratia entomophila. J Biol Chem. 288(35):25276-84. [PudMed:23857636]

(3) Fritsch MJ et al. (2013). Proteomic identification of novel secreted anti-bacterial toxins of the Serratia marcescens Type VI secretion system. Mol Cell Proteomics. 12(10):2735-2749. [PudMed:23842002]

(4) English G et al. (2012). New secreted toxins and immunity proteins encoded within the Type VI secretion system gene cluster of Serratia marcescens. Mol Microbiol. 86(4):921-36. [PudMed:22957938]

(5) Rao VA et al. (2011). The structure of Serratia marcescens Lip, a membrane-bound component of the type VI secretion system. Acta Crystallogr D Biol Crystallogr. 67(Pt 12):1065-72. [PudMed:22120744]

(6) Murdoch SL et al. (2011). The opportunistic pathogen Serratia marcescens utilizes type VI secretion to target bacterial competitors. J Bacteriol. 193(21):6057-69. [PudMed:21890705]

This literature contains experimental investigation

This literature contains bioinformatics investigation