I. Summary

SecReT6 ID	45
Strain	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_004631
Location	2645055..2683159
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	2	1	0	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	0

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	t2563	2640957..2641262 [+], 306	29142940	hypothetical protein
2	t2564	2641332..2641775 [-], 444	29142941	hypothetical protein
3	t2565	2641777..2642037 [-], 261	29142942	hypothetical protein
4	t2566	2642116..2644647 [-], 2532	29142943	Rhs-family protein
5	t2567	2644743..2645036 [-], 294	29142944	hypothetical protein
6	t2568	2645055..2645732 [-], 678	29142945	hypothetical protein
7	t2569	2645735..2649799 [-], 4065	29142946	Rhs-family protein	PAAR
8	t2570	2649818..2650264 [-], 447	29142947	hypothetical protein
9	t2571	2650288..2652477 [-], 2190	29142948	Rhs-family protein	TssI
10	t2572	2652840..2652947 [-], 108	29142949	hypothetical protein
11	t2573	2652955..2653392 [-], 438	29142950	hypothetical protein
12	t2574	2653419..2653835 [-], 417	29142951	hypothetical protein
13	t2575	2653963..2654424 [-], 462	29142952	hypothetical protein
14	t2576	2654409..2654879 [-], 471	29142953	hypothetical protein
15	t2577	2654922..2655689 [-], 768	29142954	hypothetical protein
16	t2579	2659787..2660281 [-], 495	29142955	hypothetical protein
17	t2580	2660313..2661062 [-], 750	29142956	hypothetical protein
18	t2581	2661067..2662368 [-], 1302	29142957	hypothetical protein	TssL
19	t2582	2662365..2663708 [-], 1344	29142958	hypothetical protein	TssK
20	t2583	2663712..2664248 [-], 537	29142959	lipoprotein	TssJ
21	t2584	2664315..2664800 [-], 486	29142960	hypothetical protein	TssD
22	t2585	2665037..2665462 [-], 426	29142961	hypothetical protein	STY0301 (i)
23	t2586	2665434..2665835 [-], 402	29142962	hypothetical protein	STY0300 (e)
24	t2588	2667420..2667962 [-], 543	29142963	hypothetical protein	TssB
25	t2589	2668026..2668316 [-], 291	29142964	hypothetical protein
26	t2590	2668319..2668417 [-], 99	29142965	hypothetical protein
27	t2591	2668402..2671065 [-], 2664	29142966	ClpB-like protein	TssH
28	t2593	2671433..2672335 [+], 903	29142968	hypothetical protein
29	t2594	2672322..2673146 [+], 825	29142969	hypothetical protein	TagJ
30	t2595	2673143..2673637 [+], 495	29142970	hypothetical protein	TssE
31	t2597	2673653..2675536 [+], 1884	29142971	hypothetical protein	TssF
32	t2596	2675533..2676528 [+], 996	29142972	hypothetical protein	TssG
33	t2598	2676539..2676961 [+], 423	29142973	hypothetical protein	TssA
34	t2599	2676961..2677593 [+], 633	29142974	hypothetical protein	TssA
35	t2601 (dnaQ)	2678123..2678854 [-], 732	29142975	DNA polymerase III subunit epsilon
36	t2602 (rnhA)	2678918..2679385 [+], 468	29142976	ribonuclease H
37	t2603	2679382..2680104 [-], 723	29142977	hypothetical protein
38	t2604 (gloB)	2680139..2680894 [+], 756	29142978	hydroxyacylglutathione hydrolase
39	t2605 (mltD)	2680966..2682333 [+], 1368	29142979	membrane-bound lytic murein transglycosylase D
40	t2606 (yafE)	2682389..2683159 [-], 771	29142980	methyltransferase
41	t2607 (yafD)	2683237..2684016 [-], 780	29142981	hypothetical protein
42	t2608	2684169..2685344 [-], 1176	29142982	drug efflux protein
43	t2609 (yafC)	2685449..2686363 [+], 915	29142983	transcriptional regulator
44	t2610 (dkgB)	2686384..2687187 [-], 804	29142984	2,5-diketo-D-gluconate reductase B

 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, STY0300, Hcp

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	t0489	562410..562778 [-], 369	29141004	hypothetical protein	STY2606
2	t2584	2664315..2664800 [-], 486	29142960	hypothetical protein	SciK
3	t2586	2665434..2665835 [-], 402	29142962	hypothetical protein	STY0300
4	t3052	3132317..3132802 [-], 486	29143396	hypothetical protein	Hcp

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Proteins        Genes

Homology Immunity protein list

STY2607, STY0301

Immunity protein identified
#	Locus tag(Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	t0488	561892..562410 [-], 519	29141003	lipoprotein	STY2607
2	t2585	2665037..2665462 [-], 426	29142961	hypothetical protein	STY0301

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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]

(2) Boyer F et al. (2009). Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources. BMC Genomics. 10:104. [PudMed:19284603]

This literature contains bioinformatics investigation