I. Summary

SecReT6 ID	330
Strain	Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_012125
Location	300684..326375
Comment
Function	N/A
T6SS Type	Type i; subtype i3
Bioinformatics investigation has been performed on this T6SS.

II. T6SS components

Component	TssH	TssD	TssL	TssI	TssA	TssB	TssC	TssE	TssF
Number	1	1	1	1	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	SPC_0270 (mltD)	295946..297313 [-], 1368	224582101	membrane-bound lytic murein transglycosylase D
2	SPC_0271 (gloB)	297385..298140 [-], 756	224582102	hydroxyacylglutathione hydrolase
3	SPC_0272 (yafS)	298229..298897 [+], 669	224582103	hypothetical protein
4	SPC_0273 (rnhA)	298894..299361 [-], 468	224582104	ribonuclease H
5	SPC_0274 (dnaQ)	299416..300156 [+], 741	224582105	DNA polymerase III subunit epsilon
6	SPC_0275	300684..301742 [-], 1059	224582106	cytoplasmic protein	TssA
7	SPC_0276	301753..302748 [-], 996	224582107	hypothetical protein	TssG
8	SPC_0277	302745..304628 [-], 1884	224582108	hypothetical protein	TssF
9	SPC_0278	304644..305138 [-], 495	224582109	hypothetical protein	TssE
10	SPC_0279	305135..305959 [-], 825	224582110	hypothetical protein	TagJ
11	SPC_0280	305946..306836 [-], 891	224582111	hypothetical protein
12	SPC_0282	307216..309855 [+], 2640	224582113	ClpB-like protein	TssH
13	SPC_0283	309955..310497 [+], 543	224582114	hypothetical protein	TssB
14	SPC_0284	310521..312029 [+], 1509	224582115	cytoplasmic protein	TssC
15	SPC_0285	312303..312482 [+], 180	224582116	hypothetical protein
16	SPC_0286	312660..312941 [+], 282	224582117	cytoplasmic protein
17	SPC_0287	313193..313678 [+], 486	224582118	hypothetical protein	TssD
18	SPC_0288	313790..314281 [+], 492	224582119	lipoprotein	TssJ
19	SPC_0289	314285..315628 [+], 1344	224582120	hypothetical protein	TssK
20	SPC_0290	315625..316929 [+], 1305	224582121	hypothetical protein	TssL
21	SPC_0291	316934..317707 [+], 774	224582122	hypothetical protein
22	SPC_0292	318119..318340 [+], 222	224582123	shiga-like toxin A subunit
23	SPC_0293	318373..321999 [+], 3627	224582124	hypothetical protein	TssM
24	SPC_0294	322032..322787 [+], 756	224582125	hypothetical protein
25	SPC_0295	322784..323200 [+], 417	224582126	hypothetical protein
26	SPC_0296	323224..323745 [+], 522	224582127	cytoplasmic protein
27	SPC_0297	323886..324095 [+], 210	224582128	hypothetical protein
28	SPC_0298	324141..326375 [+], 2235	224582129	Rhs family protein	TssI
29	SPC_0299	326435..326893 [+], 459	224582130	hypothetical 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

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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

SciK , STY2606, Hcp

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SPC_0287	313193..313678 [+], 486	224582118	hypothetical protein	SciK
2	SPC_1330	1392931..1393332 [-], 402	224583136	hypothetical protein	STY2606
3	SPC_3198	3228676..3229161 [-], 486	224584925	hypothetical protein	Hcp

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Proteins        Genes

Homology Immunity protein list

STY2607

Immunity protein identified
#	Locus tag(Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SPC_1329	1392413..1392931 [-], 519	224583135	lipoprotein	STY2607

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Proteins        Genes

(1) Blondel CJ et al. (2009). Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes. BMC Genomics. 10:354. [PudMed:19653904]

This literature contains bioinformatics investigation