I. Summary

SecReT6 ID	203
Strain	Yersinia pestis Pestoides F
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_009381
Location	2286377..2327968
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	2	1	1	1	1	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	0

13

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	YPDSF_2022	2283057..2283551 [-], 495	145599300	cytochrome c-type biogenesis protein CcmE
2	YPDSF_2023	2283548..2283850 [-], 303	145599301	heme exporter protein D
3	YPDSF_2024	2283847..2284584 [-], 738	145599302	heme exporter protein C
4	YPDSF_2025	2284647..2285306 [-], 660	145599303	heme exporter protein B
5	YPDSF_2026	2285276..2285932 [-], 657	145599304	cytochrome c biogenesis protein CcmA
6	YPDSF_2027	2286377..2286844 [-], 468	145599305	hypothetical protein
7	YPDSF_2028	2287460..2288002 [+], 543	145599306	hypothetical protein
8	YPDSF_2029	2287947..2290046 [+], 2100	145599307	membrane protein
9	YPDSF_2030	2290422..2290763 [+], 342	145599308	hypothetical protein
10	YPDSF_2031	2290838..2291203 [-], 366	145599309	membrane protein
11	YPDSF_2032	2291210..2291689 [-], 480	145599310	hypothetical protein	TssE
12	YPDSF_2033	2291770..2292576 [-], 807	145599311	hypothetical protein	TagJ
13	YPDSF_2034	2292596..2293444 [-], 849	145599312	hypothetical protein
14	YPDSF_2035	2293444..2293704 [-], 261	145599313	hypothetical protein	PAAR
15	YPDSF_2036	2293803..2296082 [-], 2280	145599314	hypothetical protein	TssI
16	YPDSF_2039	2300211..2301047 [-], 837	145599315	OmpA family protein	TssL
17	YPDSF_2040	2301063..2301842 [-], 780	145599316	transposase/IS protein
18	YPDSF_2041	2301842..2302864 [-], 1023	145599317	transposase for insertion sequence IS100
19	YPDSF_2042	2302878..2303546 [-], 669	145599318	hypothetical protein	TssL
20	YPDSF_2043	2303543..2304892 [-], 1350	145599319	hypothetical protein	TssK
21	YPDSF_2044	2304896..2305456 [-], 561	145599320	hypothetical protein	TssJ
22	YPDSF_2045	2305709..2306278 [-], 570	145599321	hypothetical protein	TssD
23	YPDSF_2046	2306520..2308022 [-], 1503	145599322	hypothetical protein	TssC
24	YPDSF_2047	2308046..2308570 [-], 525	145599323	hypothetical protein	TssB
25	YPDSF_2048	2308675..2309283 [-], 609	145599324	fimbrial protein
26	YPDSF_2049	2309268..2310458 [-], 1191	145599325	outer membrane fimbrial usher porin
27	YPDSF_2050	2310483..2311691 [+], 1209	145599326	transposase for the IS285 insertion element
28	YPDSF_2051	2311713..2313263 [-], 1551	145599327	hypothetical protein
29	YPDSF_2052	2313391..2314152 [-], 762	145599328	pili chaperone protein
30	YPDSF_2053	2314309..2314854 [-], 546	145599329	frimbrial protein
31	YPDSF_2054	2315055..2317730 [-], 2676	145599330	Clp ATPase	TssH
32	YPDSF_2055	2318513..2320393 [+], 1881	145599331	hypothetical protein	TssF
33	YPDSF_2056	2320393..2321238 [+], 846	145599332	hypothetical protein	TssG
34	YPDSF_2057	2321300..2321413 [+], 114	145599333	hypothetical protein
35	YPDSF_2058	2321512..2322693 [+], 1182	145599334	hypothetical protein	TssA
36	YPDSF_2059	2322700..2323731 [+], 1032	145599335	fimbrial protein
37	YPDSF_2060	2323771..2325108 [+], 1338	145599336	hypothetical protein
38	YPDSF_2061	2325054..2325806 [+], 753	145599337	hypothetical protein
39	YPDSF_2062	2325807..2327489 [+], 1683	145599338	hypothetical protein	TagL
40	YPDSF_2063	2327486..2327968 [+], 483	145599339	hypothetical protein
41	YPDSF_2064	2328326..2328928 [-], 603	145599340	LuxR family regulatory protein
42	YPDSF_2065	2330190..2331284 [-], 1095	145599341	murein hydrolase B
43	YPDSF_2066	2331613..2332632 [+], 1020	145599342	iron(III)-binding periplasmic 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

ROD_27741

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	YPDSF_2045	2305709..2306278 [-], 570	145599321	hypothetical protein	ROD_27741

Download FASTA format files

Proteins        Genes

N/A

(1) 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