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Conserved domains on  [gi|653619326|ref|WP_027629705|]
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PAAR domain-containing protein [Ruminiclostridium cellobioparum]

Protein Classification

PAAR domain-containing protein( domain architecture ID 10200509)

PAAR (proline-alanine-alanine-arginine) domain-containing protein forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS)

CATH:  2.60.200.60
PubMed:  23925114
SCOP:  4005541

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAAR_4 cd14740
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 4-127 2.00e-34

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of bacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). A few 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 such as DUF4150. 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: 269825  Cd Length: 121  Bit Score: 115.60  E-value: 2.00e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326   4 PAAKQGDQVTATDIHIVMIPVGSgkVPVPLPHPFTGIIDGALSSNVNIMGKPAATVDSTATNTPSHVPNGDSfqRSPSNK 83
Cdd:cd14740    1 PAARLGDPVVGDDIHIVLSPPGP--VPTPLPHPGAGLIVGGLSPTVLIGGMPAATVGSTAGNTPGGVPGGPS--VPPANP 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 653619326  84 GTIKMGSATVKINGKMAARNGDTAMTCNDPSDLPVGKVIAAGTV 127
Cdd:cd14740   77 GTIVMGSSTVFINGKPAARMGDMTATCNDPAPAPVGTVVPPGAT 120
 
Name Accession Description Interval E-value
PAAR_4 cd14740
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 4-127 2.00e-34

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of bacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). A few 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 such as DUF4150. 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: 269825  Cd Length: 121  Bit Score: 115.60  E-value: 2.00e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326   4 PAAKQGDQVTATDIHIVMIPVGSgkVPVPLPHPFTGIIDGALSSNVNIMGKPAATVDSTATNTPSHVPNGDSfqRSPSNK 83
Cdd:cd14740    1 PAARLGDPVVGDDIHIVLSPPGP--VPTPLPHPGAGLIVGGLSPTVLIGGMPAATVGSTAGNTPGGVPGGPS--VPPANP 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 653619326  84 GTIKMGSATVKINGKMAARNGDTAMTCNDPSDLPVGKVIAAGTV 127
Cdd:cd14740   77 GTIVMGSSTVFINGKPAARMGDMTATCNDPAPAPVGTVVPPGAT 120
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 1-131 3.09e-07

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: 45.19  E-value: 3.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326   1 MGQPAAKQGDqvtatdihivmipvgsgkvpvpLPHPFTGIIDGalSSNVNIMGKPAATVDSTATnTPSHVPNgdsfqrsp 80
Cdd:COG4104    1 MPKPAARLGD----------------------KTSHGGPVISG--SPTVLIGGRPAARVGDKVS-CPKHGPD-------- 47

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 653619326  81 snkgTIKMGSATVKINGKMAARNGDTaMTCndpsdlpvGKVIAAG--TVLIGG 131
Cdd:COG4104   48 ----TIAEGSPTVLINGKPAARVGDK-TAC--------GGTIISGspTVLIGG 87
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 46-106 1.57e-04

PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins.


Pssm-ID: 428491  Cd Length: 71  Bit Score: 37.55  E-value: 1.57e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 653619326   46 SSNVNIMGKPAATVDSTATNTPshvpngdsfqrsPSNKGTIKMGSATVKINGKMAARNGDT 106
Cdd:pfam05488  15 SPTVLIGGKPAARVGDLVVCPP------------CGGGGPIAEGSPTVLINGKPAAREGDK 63
 
Name Accession Description Interval E-value
PAAR_4 cd14740
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 4-127 2.00e-34

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of bacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). A few 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 such as DUF4150. 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: 269825  Cd Length: 121  Bit Score: 115.60  E-value: 2.00e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326   4 PAAKQGDQVTATDIHIVMIPVGSgkVPVPLPHPFTGIIDGALSSNVNIMGKPAATVDSTATNTPSHVPNGDSfqRSPSNK 83
Cdd:cd14740    1 PAARLGDPVVGDDIHIVLSPPGP--VPTPLPHPGAGLIVGGLSPTVLIGGMPAATVGSTAGNTPGGVPGGPS--VPPANP 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 653619326  84 GTIKMGSATVKINGKMAARNGDTAMTCNDPSDLPVGKVIAAGTV 127
Cdd:cd14740   77 GTIVMGSSTVFINGKPAARMGDMTATCNDPAPAPVGTVVPPGAT 120
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 1-131 3.09e-07

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: 45.19  E-value: 3.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326   1 MGQPAAKQGDqvtatdihivmipvgsgkvpvpLPHPFTGIIDGalSSNVNIMGKPAATVDSTATnTPSHVPNgdsfqrsp 80
Cdd:COG4104    1 MPKPAARLGD----------------------KTSHGGPVISG--SPTVLIGGRPAARVGDKVS-CPKHGPD-------- 47

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 653619326  81 snkgTIKMGSATVKINGKMAARNGDTaMTCndpsdlpvGKVIAAG--TVLIGG 131
Cdd:COG4104   48 ----TIAEGSPTVLINGKPAARVGDK-TAC--------GGTIISGspTVLIGG 87
PAAR_RHS cd14742
proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement ...
 40-130 2.58e-06

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: 42.58  E-value: 2.58e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326  40 IIDGalSSNVNIMGKPAA-TVDSTATNTpshvpngdsfqRSPSNKGTIKMGSATVKINGKMAARNGDTaMTCndpsdlpv 118
Cdd:cd14742   15 ITSG--SPNVFINGKPAArAADSTVACS-----------KHPPPPQLIAEGSETVFINGQPAARKGDK-TTC-------- 72

                         90
                 ....*....|....
gi 653619326 119 GKVIAAG--TVLIG 130
Cdd:cd14742   73 SAVISEGspNVFIG 86
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 46-106 1.57e-04

PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins.


Pssm-ID: 428491  Cd Length: 71  Bit Score: 37.55  E-value: 1.57e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 653619326   46 SSNVNIMGKPAATVDSTATNTPshvpngdsfqrsPSNKGTIKMGSATVKINGKMAARNGDT 106
Cdd:pfam05488  15 SPTVLIGGKPAARVGDLVVCPP------------CGGGGPIAEGSPTVLINGKPAAREGDK 63
PAAR_5 cd14741
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 3-129 1.76e-04

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family in bacteria as well as some archaea, 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: 269826  Cd Length: 95  Bit Score: 38.14  E-value: 1.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326   3 QPAAKQGDQVTatdiHIVMIPVGSGkvpvplphpftgiidgalSSNVNIMGKPAATVDSTATNTPSHVPNgdsfqrSPSN 82
Cdd:cd14741    1 PPAARIGDSTA----HGGPLTPGPG------------------SPNVLIGGFPAWRAGGDGHVCPLVTGP------VPHV 52

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 653619326  83 KGTIKMGSATVKINGKMAARNGDTAMtCNDPSDLPvgkVIAAGTVLI 129
Cdd:cd14741   53 GGVVAAGSTTVLINGLPAARMGDMIV-EGGPPNTI---AMGAPTVLI 95
PAAR_2 cd14738
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 29-130 2.96e-04

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: 37.23  E-value: 2.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326  29 VPVPLPHpFTGIIDGALSSNVNIMGKPAATVDSTATNTPShvPNgdsfqrspsnkgTIKMGSATVKINGKMAARNGDTAM 108
Cdd:cd14738   15 VTGPVPH-VGGPIVGPGPTTVLIGGLPAARVGDMCVCVGP--PD------------TIVQGSSTVLIGGKPAARMGDSTA 79

                         90       100
                 ....*....|....*....|....
gi 653619326 109 tcndpsdlpVGKVIAAG--TVLIG 130
Cdd:cd14738   80 ---------HGGVIVSGvpTVLIG 94
Tox-PAAR-like pfam13665
Toxin PAAR-like domain; This domain is found at the N-terminal of bacterial toxin systems, ...
 23-106 4.56e-04

Toxin PAAR-like domain; This domain is found at the N-terminal of bacterial toxin systems, including Tse7 (type IV secretion exported 7) from Pseudomonas aeruginosa, a type VI secretion exported toxin with DNase activity that induces growth arrest and ultimately DNA degradation within target cell. The structure of this domain has a PAAR-like organization necessary for interaction with T6SS VgrG tip and correct toxin delivery.


Pssm-ID: 433390  Cd Length: 108  Bit Score: 37.20  E-value: 4.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326   23 PVGSGKVPVPLPHPFTGIIDGALSSNVNIMGKPAATVDSTATNTpshvpNGDSFQ-----RSPSNKGTIK--MGSATVKI 95
Cdd:pfam13665  13 PPGPPPVPIPYPNIAMSADAAPGTKNVLIDGMPAHNLGSVFPMS-----TGDEPGvaggvVSGTVMGPAEflTGSFTVKF 87

                          90
                  ....*....|.
gi 653619326   96 NGKMAARNGDT 106
Cdd:pfam13665  88 EGKPAVRLTDL 98
PAAR_like cd14671
proline-alanine-alanine-arginine (PAAR) repeat superfamily; This domain is found in the PAAR ...
 46-105 1.14e-03

proline-alanine-alanine-arginine (PAAR) repeat superfamily; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat superfamily, 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. The PAAR-repeat proteins form a diverse superfamily with several subgroups extended both N- and C-terminally by domains with various predicted functions; the termini are exposed to solution, and do not distort the VgrG binding site. 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: 269821  Cd Length: 77  Bit Score: 35.38  E-value: 1.14e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 653619326  46 SSNVNIMGKPAATVDSTATntpshvpngdsfqrSPSNKGTIKMGSATVKINGKMAARNGD 105
Cdd:cd14671   21 SPNVFINGRPAARVGDVGD--------------HPGGGNAIVSGSGTVFINGKPAARVGD 66
PAAR_RHS cd14742
proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement ...
 83-131 3.97e-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: 34.10  E-value: 3.97e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 653619326  83 KGTIKMGSATVKINGKMAARNGDTAMTCNDPSDLPvgKVIAAG--TVLIGG 131
Cdd:cd14742   12 TGTITSGSPNVFINGKPAARAADSTVACSKHPPPP--QLIAEGseTVFING 60
 
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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