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_RS15950	3466349..3466900 [-], 552	898330895	YbhB/YbcL family Raf kinase inhibitor-like protein
2	PP_RS15955	3466949..3467257 [-], 309	518268253	hypothetical protein
3	PP_RS15960	3467339..3468637 [-], 1299	519035062	MFS transporter
4	PP_RS15965	3469064..3469939 [+], 876	499256441	AEC family transporter
5	PP_RS15970	3470072..3472489 [-], 2418	898330891	TonB-dependent receptor
6	PP_RS15975	3472639..3473601 [-], 963	898330889	FecR domain-containing protein
7	PP_RS15980	3473601..3474107 [-], 507	499256444	sigma-70 family RNA polymerase sigma factor
8	PP_RS15985	3474196..3476712 [-], 2517	499256445	excinuclease ABC subunit UvrA
9	PP_RS15990 (tssA)	3476880..3477965 [-], 1086	499256446	type VI secretion system protein TssA
10	PP_RS15995	3478061..3478579 [-], 519	898330886	type VI secretion system tube protein Hcp
11	PP_RS16000 (tssM)	3478723..3481218 [-], 2496	499256448	type VI secretion system membrane subunit TssM
12	PP_RS16005 (tagF)	3481215..3482123 [-], 909	898330884	type VI secretion system-associated protein TagF
13	PP_RS16010	3482120..3485923 [-], 3804	499256449	hypothetical protein
14	PP_RS16015 (icmH)	3485954..3486670 [-], 717	499256450	type IVB secretion system protein IcmH/DotU
15	PP_RS16020 (tssK)	3486667..3488010 [-], 1344	499256451	type VI secretion system baseplate subunit TssK
16	PP_RS16025 (tssJ)	3488007..3488729 [-], 723	490713868	type VI secretion system lipoprotein TssJ
17	PP_RS16030 (tssH)	3488754..3491351 [-], 2598	898330880	type VI secretion system ATPase TssH
18	PP_RS16035 (tssG)	3491348..3492418 [-], 1071	489341176	type VI secretion system baseplate subunit TssG
19	PP_RS16040 (tssF)	3492382..3494202 [-], 1821	499256453	type VI secretion system baseplate subunit TssF
20	PP_RS16045 (tssE)	3494202..3494684 [-], 483	489341181	type VI secretion system baseplate subunit TssE
21	PP_RS16050 (tssC)	3494711..3496213 [-], 1503	489341182	type VI secretion system contractile sheath large subunit
22	PP_RS16055 (tssB)	3496228..3496767 [-], 540	898331645	type VI secretion system contractile sheath small subunit
23	PP_RS16060	3496832..3497581 [-], 750	898330878	hypothetical protein
24	PP_RS16065	3498302..3498853 [-], 552	489341191	hypothetical protein
25	PP_RS16070	3499064..3499783 [+], 720	pseudogene	ADP-ribosylglycohydrolase family protein
26	PP_RS16075	3500053..3500325 [-], 273	1002826534	hypothetical protein
27	PP_RS28435	3500335..3500803 [-], 469	pseudogene	hypothetical protein
28	PP_RS16085	3501267..3501455 [+], 189	pseudogene	type VI secretion system tip protein VgrG
29	PP_RS16090	3501614..3502312 [+], 699	489341205	hypothetical protein
30	PP_RS16095	3502346..3502605 [+], 260	pseudogene	hypothetical protein
31	PP_RS28395	3502579..3502684 [-], 106	pseudogene	hypothetical protein
32	PP_RS16105	3502704..3503015 [-], 312	898330871	hypothetical protein
33	PP_RS16110	3503425..3503814 [-], 390	1160888979	reverse transcriptase
34	PP_RS16115	3503869..3504185 [-], 317	pseudogene	hypothetical protein
35	PP_RS16120	3504275..3504571 [-], 297	499256456	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

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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