I. Summary

SecReT6 ID	534
Strain	Pseudovibrio sp. FO-BEG1
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_016642
Location	3035230..3060247
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	2	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	1

14

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	PSE_2843	3032440..3035139 [-], 2700	374331189	hypothetical protein
2	PSE_2844 (icmF)	3035230..3038859 [-], 3630	374331190	Type VI secretion protein IcmF	TssM
3	PSE_2845 (dotU)	3038856..3040196 [-], 1341	374331191	Type IV / VI secretion system, DotU/OmpA/MotB	TssL
4	PSE_2846	3040306..3041643 [-], 1338	374331192	hypothetical protein	TssK
5	PSE_2847	3041643..3042056 [-], 414	374331193	hypothetical protein	TssJ
6	PSE_2848 (fha)	3042127..3042786 [-], 660	374331194	FHA domain-containing protein	Fha
7	PSE_2849	3042947..3043063 [-], 117	374331195	hypothetical protein	PAAR
8	PSE_2850	3043234..3043800 [-], 567	374331196	hypothetical protein
9	PSE_2851	3043836..3045944 [-], 2109	374331197	Rhs element Vgr protein	TssI
10	PSE_2852	3045986..3046279 [-], 294	374331198	hypothetical protein
11	PSE_2853	3046289..3048286 [-], 1998	374331199	hypothetical protein	TssC
12	PSE_2854	3048279..3049007 [-], 729	374331200	voltage-gated sodium channel
13	PSE_2855 (clpV)	3049297..3051891 [-], 2595	374331201	type VI secretion ATPase, ClpV1 family	TssH
14	PSE_2856	3051987..3053153 [-], 1167	374331202	hypothetical protein	TssG
15	PSE_2857	3053150..3055027 [-], 1878	374331203	Type VI secretion system	TssF
16	PSE_2858	3055029..3055535 [-], 507	374331204	Type VI secretion system, lysozyme-related protein	TssE
17	PSE_2859 (sciE)	3055528..3056379 [-], 852	374331205	virulence protein, SciE type	TagJ
18	PSE_2860 (sciM)	3056463..3056993 [-], 531	374331206	SciM protein	TssD
19	PSE_2861 (sciI)	3057127..3058632 [-], 1506	374331207	Cytoplasmic protein SciI	TssC
20	PSE_2862 (sciH)	3058625..3059047 [-], 423	374331208	Cytoplasmic protein SciH	TssB
21	PSE_2863 (impA)	3059201..3060247 [-], 1047	374331209	ImpA domain-containing protein	TssA
22	PSE_2864	3061211..3062080 [-], 870	374331210	hypothetical protein
23	PSE_2865	3062300..3063475 [-], 1176	374331211	hypothetical protein
24	PSE_2866	3063505..3064890 [-], 1386	374331212	cytochrome P450 family 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

idrA

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	PSE_p0124(hcp1)	137273..137848 [-], 576	374333545	Type VI secretion system effector, Hcp1	idrA

Download FASTA format files

Proteins        Genes

N/A

(1) Bondarev V et al. (2013). The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ Microbiol. 15(7):2095-113. [PudMed:23601235]

This literature contains bioinformatics investigation