I. Summary

SecReT6 ID	14
Strain	Pseudomonas putida KT2440
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_002947
Location	3470069..3499780
Comment
Function	N/A
T6SS Type	Type i; subtype i4b
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	1	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	2

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	PP_3081	3466346..3466822 [-], 477	26989800	PEBP family protein
2	PP_3082	3467336..3468700 [-], 1365	26989801	major facilitator superfamily protein
3	PP_3083	3469061..3469936 [+], 876	26989802	auxin efflux carrier
4	PP_3084	3470069..3472528 [-], 2460	26989803	TonB-dependent siderophore receptor
5	PP_3085	3472636..3473601 [-], 966	26989804	transmembrane sensor
6	PP_3086	3473598..3474104 [-], 507	26989805	RNA polymerase sigma-70 factor
7	PP_3087	3474193..3476709 [-], 2517	26989806	excinuclease ABC subunit A
8	PP_3088	3476877..3477962 [-], 1086	26989807	hypothetical protein	TssA
9	PP_3089	3478058..3478600 [-], 543	26989808	hypothetical protein	TssD
10	PP_3090	3478720..3481215 [-], 2496	26989809	OmpA domain-containing protein	TssM
11	PP_3091	3482117..3485920 [-], 3804	26989810	hypothetical protein	TssM
12	PP_3092	3485951..3486667 [-], 717	26989811	hypothetical protein	TssL
13	PP_3093	3486664..3488007 [-], 1344	26989812	hypothetical protein	TssK
14	PP_3094	3488004..3488726 [-], 723	26989813	hypothetical protein	TssJ
15	PP_3095	3488751..3491387 [-], 2637	26989814	chaperone-associated ATPase	TssH
16	PP_3096	3491345..3492415 [-], 1071	26989815	hypothetical protein	TssG
17	PP_3097	3492379..3494199 [-], 1821	26989816	hypothetical protein	TssF
18	PP_3098	3494199..3494681 [-], 483	26989817	hypothetical protein	TssE
19	PP_3099	3494708..3496210 [-], 1503	26989818	hypothetical protein	TssC
20	PP_3100	3496225..3496800 [-], 576	26989819	hypothetical protein	TssB
21	PP_3101	3498998..3499780 [+], 783	26989820	ADP-ribosylglycohydrolase
22	PP_3102	3504272..3504568 [-], 297	26989821	hypothetical 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

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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

Psyr_4965

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	PP_3089	3478058..3478600 [-], 543	26989808	hypothetical protein	Psyr_4965

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Proteins        Genes

N/A

The information on regulator interaction.

#	homolog effector locus tag	Regulator way	Function	Regulate target	Description
1	PP_4373 (FleQ)	c-di-GMP	-	K1-T6SS (hcp1) expression	FleQ negatively regulate hcp1 expression at all the growth phases.
2	PP_0952 (RopN)	c-di-GMP	-	PP_4373 (FleQ)	RopN negatively regulates hcp1 expression at all the growth phases,and interacts a domain characteristic of FleQ.
3	PP_0914 (BifA)	c-di-GMP	+	the levels of c-di-GMP	BifA, a cyclic-Di-GMP phosphodiesterase can lower the intracellular level of c-di-GMP.

(1) Barret M et al. (2011). Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. Microbiology. 157(Pt 6):1726-39. [PudMed:21474537]

(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