I. Summary
SecReT6 ID23 insolico
StrainSalmonella enterica subsp. enterica serovar Typhimurium str. LT2
Repliconchromosome [Browse all T6SS(s) in this replicon]
T6SS TypeType i; subtype i3
insolico Bioinformatics investigation has been performed on this T6SS.

II. T6SS components
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1STM0260 (mltD)299923..301290 [-], 136816763643membrane-bound lytic murein transglycosylase D 
2STM0261 (gloB)301362..302117 [-], 75616763644hydroxyacylglutathione hydrolase 
3STM0262 (yafS)302152..302874 [+], 72316763645SAM-dependent methyltransferase 
4STM0263 (rnhA)302871..303338 [-], 46816763646ribonuclease H 
5STM0264 (dnaQ)303402..304133 [+], 73216763647DNA polymerase III subunit epsilon 
6STM0266304665..305720 [-], 105616763648hypothetical protein  TssA
7STM0267305731..306726 [-], 99616763649hypothetical protein  TssG
8STM0268306723..308606 [-], 188416763650hypothetical protein  TssF
9STM0269308622..309116 [-], 49516763651hypothetical protein  TssE
10STM0270309113..309937 [-], 82516763652hypothetical protein  TagJ
11STM0271309924..310826 [-], 90316763653hypothetical protein 
12STM0272311194..313833 [+], 264016763654chaperone ATPase  TssH
13STM0273313933..314475 [+], 54316763655hypothetical protein  TssB
14STM0274314499..316007 [+], 150916763656hypothetical protein  TssC
15STM0274A316070..316180 [+], 11116763657invasol SirA 
16STM0275.s316193..316639 [+], 44739546290hypothetical protein 
17STM0276316893..317378 [+], 48616763659hypothetical protein  TssD
18STM0277317683..318168 [+], 48616763660hypothetical protein  STM0277 (e)
19STM0278318153..318536 [+], 38416763661hypothetical protein  STM0278 (i)
20STM0279318679..319164 [+], 48616763662hypothetical protein  TssD
21STM0280319231..319767 [+], 53716763663outer membrane lipoprotein  TssJ
22STM0281319771..321114 [+], 134416763664hypothetical protein  TssK
23STM0282321111..322415 [+], 130516763665hypothetical protein  TssL
24STM0283322420..323193 [+], 77416763666inner membrane protein 
25STM0284323396..323827 [+], 43216763667Shiga-like toxin A subunit 
26STM0285323861..327730 [+], 387016763668inner membrane protein  TssM
27STM0286327730..328518 [+], 78916763669hypothetical protein 
28STM0287328515..328931 [+], 41716763670hypothetical protein 
29STM0288328955..329476 [+], 52216763671hypothetical protein 
30STM0289329873..332062 [+], 219016763672hypothetical protein  TssI
31STM0290332086..332532 [+], 44716763673hypothetical protein 
32STM0291332551..336645 [+], 409516763674RHS-like protein  PAAR
33STM0292337095..337835 [+], 74116763675RHS-like protein 
34STM0293337829..338275 [+], 44716763676hypothetical protein 
35STM0294338838..339275 [+], 43816763677hypothetical protein 
36STM0294.1N339328..339603 [-], 27639546291hypothetical protein 
37STM0295340044..340352 [+], 30916763678hypothetical protein 
38STM0297340755..340952 [+], 19816763680transposase 
39STM0299 (safA)342209..342721 [+], 51316763682outer membrane protein 
40STM0300 (safB)342829..343542 [+], 71416763683fimbrial assembly chaperone 
flank 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.

2. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the virulence factor database, VFDB.

3. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against against the antibiotic resistance database, ARDB.

Homology Effector list
SciK , STM0277, SciK, STY2606, Hcp

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1STM0276316893..317378 [+], 48616763659hypothetical protein SciK
2STM0277317683..318168 [+], 48616763660hypothetical protein STM0277
3STM0279318679..319164 [+], 48616763662hypothetical protein SciK
4STM23752486915..2487283 [+], 36916765702hypothetical protein STY2606
5STM31313290972..3291457 [-], 48616766431hypothetical protein Hcp

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Proteins        Genes

Homology Immunity protein list
STM0278, STY2607

Immunity protein identified
#Locus tag(Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1STM0278318153..318536 [+], 38416763661hypothetical protein STM0278
2STM23762487283..2487801 [+], 51916765703hypothetical protein STY2607

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Proteins        Genes
Regulatory element identified
SsrBRepressorPMID: 15972528

(1) Benz J et al. (2013). Structural Insights into the Effector - Immunity System Tae4/Tai4 from Salmonella typhimurium. PLoS One. 8(6):e67362. [PudMed:23826277] experimental in_silico
(2) Blondel CJ et al. (2009). Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes. BMC Genomics. 10:354. [PudMed:19653904] in_silico
(3) 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] in_silico
experimental This literature contains experimental investigation
in_silico This literature contains bioinformatics investigation