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Conserved domains on  [gi|445937280|ref|WP_000015135|]
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MULTISPECIES: DUF6531 domain-containing protein, partial [Escherichia]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RHS_core super family cl49306
RHS element core protein;
1-113 9.05e-81

RHS element core protein;


The actual alignment was detected with superfamily member NF041261:

Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 256.85  E-value: 9.05e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445937280    1 MSGKPAARQGDMTQYGGSIVQGSAGVRIGAPTGVACSVCPGGVTSGHPVNPLLGAKVLPGETDIALPGPLPFILSRTYSS 80
Cdd:NF041261    1 MSGKPAARQGDMTQYGGPIVQGSAGVRIGAPTGVACSVCPGGMTSGNPVNPLLGAKVLPGETDIALPGPLPFILSRTYSS 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 445937280   81 YRTKTPAPVGSLGPGWKMPADIRLQLRDNTLIL 113
Cdd:NF041261   81 YRTRTPAPVGVFGPGWKAPSDIRLQLRDDGLIL 113
 
Name Accession Description Interval E-value
RHS_core NF041261
RHS element core protein;
1-113 9.05e-81

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 256.85  E-value: 9.05e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445937280    1 MSGKPAARQGDMTQYGGSIVQGSAGVRIGAPTGVACSVCPGGVTSGHPVNPLLGAKVLPGETDIALPGPLPFILSRTYSS 80
Cdd:NF041261    1 MSGKPAARQGDMTQYGGPIVQGSAGVRIGAPTGVACSVCPGGMTSGNPVNPLLGAKVLPGETDIALPGPLPFILSRTYSS 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 445937280   81 YRTKTPAPVGSLGPGWKMPADIRLQLRDNTLIL 113
Cdd:NF041261   81 YRTRTPAPVGVFGPGWKAPSDIRLQLRDDGLIL 113
DUF6531 pfam20148
Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.
 46-113 2.74e-20

Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.


Pssm-ID: 466309 [Multi-domain]  Cd Length: 74  Bit Score: 77.57  E-value: 2.74e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 445937280   46 GHPVNPLLGAKVLPgETDIALPGPLPFILSRTYSSYRTKTpapvGSLGPGWKMPADIRLQLRDNTLIL 113
Cdd:pfam20148   1 GDPVNVATGNKVLE-ETDFSLPGPLPLVWTRTYNSSSERD----GPLGPGWSHPYDQRLELEGDGGVV 63
PAAR_2 cd14738
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 1-29 5.34e-06

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269823  Cd Length: 94  Bit Score: 41.46  E-value: 5.34e-06
                         10        20
                 ....*....|....*....|....*....
gi 445937280   1 MSGKPAARQGDMTQYGGSIVQGSAGVRIG 29
Cdd:cd14738   66 IGGKPAARMGDSTAHGGVIVSGVPTVLIG 94
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 3-29 2.41e-04

Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 443280  Cd Length: 87  Bit Score: 37.10  E-value: 2.41e-04
                         10        20
                 ....*....|....*....|....*..
gi 445937280   3 GKPAARQGDMTQYGGSIVQGSAGVRIG 29
Cdd:COG4104   60 GKPAARVGDKTACGGTIISGSPTVLIG 86
 
Name Accession Description Interval E-value
RHS_core NF041261
RHS element core protein;
1-113 9.05e-81

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 256.85  E-value: 9.05e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445937280    1 MSGKPAARQGDMTQYGGSIVQGSAGVRIGAPTGVACSVCPGGVTSGHPVNPLLGAKVLPGETDIALPGPLPFILSRTYSS 80
Cdd:NF041261    1 MSGKPAARQGDMTQYGGPIVQGSAGVRIGAPTGVACSVCPGGMTSGNPVNPLLGAKVLPGETDIALPGPLPFILSRTYSS 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 445937280   81 YRTKTPAPVGSLGPGWKMPADIRLQLRDNTLIL 113
Cdd:NF041261   81 YRTRTPAPVGVFGPGWKAPSDIRLQLRDDGLIL 113
DUF6531 pfam20148
Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.
 46-113 2.74e-20

Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.


Pssm-ID: 466309 [Multi-domain]  Cd Length: 74  Bit Score: 77.57  E-value: 2.74e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 445937280   46 GHPVNPLLGAKVLPgETDIALPGPLPFILSRTYSSYRTKTpapvGSLGPGWKMPADIRLQLRDNTLIL 113
Cdd:pfam20148   1 GDPVNVATGNKVLE-ETDFSLPGPLPLVWTRTYNSSSERD----GPLGPGWSHPYDQRLELEGDGGVV 63
PAAR_2 cd14738
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 1-29 5.34e-06

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269823  Cd Length: 94  Bit Score: 41.46  E-value: 5.34e-06
                         10        20
                 ....*....|....*....|....*....
gi 445937280   1 MSGKPAARQGDMTQYGGSIVQGSAGVRIG 29
Cdd:cd14738   66 IGGKPAARMGDSTAHGGVIVSGVPTVLIG 94
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 3-29 2.41e-04

Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 443280  Cd Length: 87  Bit Score: 37.10  E-value: 2.41e-04
                         10        20
                 ....*....|....*....|....*..
gi 445937280   3 GKPAARQGDMTQYGGSIVQGSAGVRIG 29
Cdd:COG4104   60 GKPAARVGDKTACGGTIISGSPTVLIG 86
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 3-48 8.42e-04

Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 443280  Cd Length: 87  Bit Score: 35.56  E-value: 8.42e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 445937280   3 GKPAARQGDMTQYGGSIVQGSAGVRIG----APTG--VACSVC-PGGVTSGHP 48
Cdd:COG4104    2 PKPAARLGDKTSHGGPVISGSPTVLIGgrpaARVGdkVSCPKHgPDTIAEGSP 54
PAAR_RHS cd14742
proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement ...
 3-29 1.54e-03

proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement hotspot (Rhs) extensions; This PAAR (proline-alanine-alanine-arginine) repeat subfamily, which forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS), contains C- and N-terminal domain extensions. These include Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences at the C-terminal, and various predicted functions at N- and C-terminal extensions. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


Pssm-ID: 269827  Cd Length: 86  Bit Score: 34.87  E-value: 1.54e-03
                         10        20
                 ....*....|....*....|....*..
gi 445937280   3 GKPAARQGDMTQYGGSIVQGSAGVRIG 29
Cdd:cd14742   60 GQPAARKGDKTTCSAVISEGSPNVFIG 86
PAAR_CT_1 cd14743
proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found ...
 2-46 8.40e-03

proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Some members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as well as uncharacterized domains. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


Pssm-ID: 269828  Cd Length: 78  Bit Score: 32.66  E-value: 8.40e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 445937280   2 SGKPAARQGDMTQYGGSIVQGSAGVRI-GAPTGVACSV--CPGGVTSG 46
Cdd:cd14743   30 DGLPAARVGDKTSCGATIVSGSINVLInGKPAAVLGSTtsHGGVVIGG 77
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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