I. Summary

SecReT6 ID	763
Strain	Salmonella enterica subsp. enterica serovar Typhi str. Ty21a
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_021176
Location	2650288..2695793
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	2	1	1	1	0	1	0	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	2

13

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	TY21A_13040	2645735..2649799 [-], 4065	488655060	Rhs-family protein	PAAR
2	TY21A_13045	2649818..2650264 [-], 447	488655061	hypothetical protein
3	TY21A_13050	2650288..2652477 [-], 2190	488655062	Rhs-family protein	TssI
4	TY21A_13055	2652840..2652947 [-], 108	488655063	hypothetical protein
5	TY21A_13060	2652955..2653392 [-], 438	488655064	conserved hypothetical pathogenicity island protein
6	TY21A_13065	2653419..2653805 [-], 387	488655065	putative secreted protein
7	TY21A_13070	2653963..2654424 [-], 462	488655066	hypothetical protein
8	TY21A_13075	2654409..2654879 [-], 471	488655067	hypothetical protein
9	TY21A_13080	2654922..2655689 [-], 768	488655068	putative cytoplasmic protein
10	TY21A_13085	2655689..2657677 [-], 1989	488655069	type VI secretion protein IcmF	TssM
11	TY21A_13090	2657574..2659550 [-], 1977	488655070	putative inner membrane protein	TssM
12	TY21A_13095	2659787..2660281 [-], 495	488655071	hypothetical protein
13	TY21A_13100	2660313..2661062 [-], 750	488655072	hypothetical protein
14	TY21A_13105	2661067..2662368 [-], 1302	488655073	hypothetical protein	TssL
15	TY21A_13110	2662365..2663708 [-], 1344	488655074	type VI secretion protein	TssK
16	TY21A_13115	2663712..2664248 [-], 537	488655075	lipoprotein	TssJ
17	TY21A_13120	2664315..2664800 [-], 486	488655076	hemolysin-coregulated protein	TssD
18	TY21A_13125	2665037..2665462 [-], 426	488655077	hypothetical protein	STY0301 (i)
19	TY21A_13130	2665434..2665835 [-], 402	488655078	hypothetical protein	STY0300 (e)
20	TY21A_13145	2667420..2667962 [-], 543	488655079	type VI secretion protein, VC_A0107 family	TssB
21	TY21A_13150	2668026..2668316 [-], 291	488655080	hypothetical protein
22	TY21A_13155	2668402..2671065 [-], 2664	488655081	ClpB-like protein	TssH
23	TY21A_13160	2671433..2672335 [+], 903	488655082	hypothetical protein
24	TY21A_13165	2672322..2673146 [+], 825	488655083	hypothetical protein	TagJ
25	TY21A_13170	2673143..2673637 [+], 495	488655084	putative cytoplasmic protein	TssE
26	TY21A_13175	2673653..2675536 [+], 1884	488655085	hypothetical protein	TssF
27	TY21A_13180	2675533..2676528 [+], 996	488655086	hypothetical protein	TssG
28	TY21A_13195	2678123..2678863 [-], 741	488655087	DNA polymerase III subunit epsilon
29	TY21A_13200 (rnhA)	2678918..2679385 [+], 468	488655088	ribonuclease H
30	TY21A_13205	2679382..2680104 [-], 723	488655089	putative methyltransferase
31	TY21A_13210	2680139..2680894 [+], 756	488655090	hydroxyacylglutathione hydrolase
32	TY21A_13215 (mltD)	2681113..2682333 [+], 1221	488655091	membrane-bound lytic murein transglycosylase D
33	TY21A_13220	2682389..2683159 [-], 771	488655092	putative methyltransferase in menaquinone/biotin biosynthesis
34	TY21A_13225	2683237..2684037 [-], 801	488655093	hypothetical protein
35	TY21A_13230	2684169..2685344 [-], 1176	488655094	putative drug efflux protein
36	TY21A_13235	2685449..2686363 [+], 915	488655095	transcriptional regulator
37	TY21A_13240 (dkgB)	2686384..2687187 [-], 804	488655096	2,5-diketo-D-gluconate reductase B
38	TY21A_13245	2693220..2695793 [-], 2574	488655097	protein disaggregation chaperone	TssH
39	TY21A_13250	2695923..2696654 [-], 732	488655098	hypothetical protein
40	TY21A_13255 (rluD)	2696651..2697631 [-], 981	488655099	23S rRNA pseudouridine synthase D
41	TY21A_13260	2697763..2698500 [+], 738	488655100	outer membrane protein assembly complex subunit YfiO
42	TY21A_13265	2698772..2699110 [+], 339	488655101	translation inhibitor protein RaiA
43	TY21A_13270 (pheA)	2699361..2700521 [+], 1161	488655102	bifunctional chorismate mutase/prephenate dehydratase

 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	TY21A_02490	562410..562778 [-], 369	488653037	hypothetical protein	STY2606
2	TY21A_13120	2664315..2664800 [-], 486	488655076	hemolysin-coregulated protein	SciK
3	TY21A_13130	2665434..2665835 [-], 402	488655078	hypothetical protein	STY0300
4	TY21A_15415	3132317..3132802 [-], 486	488655514	putative cytoplasmic 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	TY21A_02485	561892..562410 [-], 519	488653036	putative lipoprotein	STY2607
2	TY21A_13125	2665037..2665462 [-], 426	488655077	hypothetical protein	STY0301

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Proteins        Genes

N/A