I. Summary

SecReT6 ID	297
Strain	Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_011147
Location	2569899..2599898
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	2	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	SSPA2307	2569899..2572145 [-], 2247	197363515	hypothetical protein	TssI
2	SSPA2308	2572177..2572638 [-], 462	197363516	hypothetical protein
3	SSPA2309	2572640..2573383 [-], 744	197363517	hypothetical protein
4	SSPA2310	2573468..2573929 [-], 462	197363518	hypothetical protein
5	SSPA2311	2573914..2574384 [-], 471	197363519	hypothetical protein
6	SSPA2312	2574488..2574961 [-], 474	197363520	hypothetical protein
7	SSPA2313	2575458..2576225 [-], 768	197363521	hypothetical protein
8	SSPA2314	2576225..2580085 [-], 3861	197363522	inner membrane protein	TssM
9	SSPA2315	2580119..2580550 [-], 432	197363523	shiga-like toxin A subunit
10	SSPA2316	2580752..2581525 [-], 774	197363524	hypothetical protein
11	SSPA2317	2581530..2582834 [-], 1305	197363525	hypothetical protein	TssL
12	SSPA2318	2582831..2584174 [-], 1344	197363526	hypothetical protein	TssK
13	SSPA2319	2584178..2584714 [-], 537	197363527	lipoprotein	TssJ
14	SSPA2320	2584782..2585267 [-], 486	197363528	hypothetical protein	TssD
15	SSPA2321	2585410..2585793 [-], 384	197363529	periplasmic protein	STM0278 (i)
16	SSPA2322	2585778..2586263 [-], 486	197363530	cytoplasmic protein	STM0277 (e)
17	SSPA2323	2586374..2586490 [-], 117	197363531	hypothetical protein
18	SSPA2324	2586557..2587042 [-], 486	197363532	hypothetical protein	TssD
19	SSPA2325	2587294..2587626 [-], 333	197363533	cytoplasmic protein
20	SSPA2326	2588206..2589714 [-], 1509	197363534	hypothetical protein	TssC
21	SSPA2327	2589738..2590280 [-], 543	197363535	hypothetical protein	TssB
22	SSPA2328	2590342..2590632 [-], 291	197363536	hypothetical protein
23	SSPA2329	2590635..2590733 [-], 99	197363537	hypothetical protein
24	SSPA2330	2590718..2593381 [-], 2664	197363538	ClpB-like protein	TssH
25	SSPA2331	2594638..2595462 [+], 825	197363539	hypothetical protein	TagJ
26	SSPA2332	2595459..2595953 [+], 495	197363540	hypothetical protein	TssE
27	SSPA2333	2595969..2597852 [+], 1884	197363541	hypothetical protein	TssF
28	SSPA2334	2597849..2598844 [+], 996	197363542	hypothetical protein	TssG
29	SSPA2335	2598855..2599898 [+], 1044	197363543	cytoplasmic protein	TssA
30	SSPA2336	2600429..2601160 [-], 732	197363544	DNA polymerase III subunit epsilon
31	SSPA2337 (rnhA)	2601224..2601691 [+], 468	197363545	ribonuclease H
32	SSPA2338	2601688..2602410 [-], 723	197363546	hypothetical protein
33	SSPA2339	2602445..2603200 [+], 756	197363547	hydroxyacylglutathione hydrolase
34	SSPA2340 (mltD)	2603272..2604639 [+], 1368	197363548	membrane-bound lytic murein transglycosylase D

 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

STY2606 , SciK, STM0277, SciK, Hcp

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SSPA0453	560660..561028 [-], 369	197361662	hypothetical protein	STY2606
2	SSPA2320	2584782..2585267 [-], 486	197363528	hypothetical protein	SciK
3	SSPA2322	2585778..2586263 [-], 486	197363530	cytoplasmic protein	STM0277
4	SSPA2324	2586557..2587042 [-], 486	197363532	hypothetical protein	SciK
5	SSPA2797	3095472..3095957 [-], 486	197364002	hypothetical protein	Hcp

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Proteins        Genes

Homology Immunity protein list

STY2607, STM0278

Immunity protein identified
#	Locus tag(Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SSPA0452	560142..560660 [-], 519	197361661	lipoprotein	STY2607
2	SSPA2321	2585410..2585793 [-], 384	197363529	periplasmic protein	STM0278

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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