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Conserved domains on  [gi|2205660756|ref|WP_240785631|]
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S-type pyocin domain-containing protein [Rahnella sp. CJA17(1/100)]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pyocin_S pfam06958
S-type Pyocin; This family represents a conserved region approximately 180 residues long ...
 282-417 1.45e-33

S-type Pyocin; This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity.


:

Pssm-ID: 399737  Cd Length: 139  Bit Score: 124.40  E-value: 1.45e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2205660756 282 ALAGKSAPTRIRFQWVKDKYGRLIPVAYHTGADSGLDQVRVRAMRRNIFTGNYEFWADGAEKPAIIWTPDELEFKAPGNT 361
Cdd:pfam06958   5 AAQMGTVDLPVRLRIIDDEDGRLKVYGVHTGGAGVPDRVPVRAATLDAETGSYEFTADGAPGPTILWTPASPPGNGPPST 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2205660756 362 GNRDEPYLPSTITVLPLPGAEemGSTSTSLPIPDEQSFDDYILVnLPH--GMPPIYIY 417
Cdd:pfam06958  85 SSPAAPPDTPVITGTPIPPVV--GEVIEPYPAPDERDFRDYILV-FPAdsGLPPLYVV 139
PAAR_CT_2 cd14744
proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This ...
 10-88 2.65e-23

proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly beta- and gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Most members contain C-terminal domain extensions corresponding to several uncharacterized domains such as S-type pyocin, DUF2235, DUF2345 and cytotoxic proteins. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. 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: 269829  Cd Length: 78  Bit Score: 93.39  E-value: 2.65e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2205660756  10 RGQALHGDKTTTGAVCLTSLPNATEHGLGVIRIGDATTdCPKCGRRGKITSGEPHSTYDGLASAVDGSDVLCGCPPGTN 88
Cdd:cd14744     1 RGIIRLGDKTTHGGVVISGSSTFTIDGRPVARVGDKVT-CPKCKGTGPIVEGGPTFTVDGRPVALDGDRVACGCPLIPS 78
DnaT super family cl46275
DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain ...
 437-522 9.89e-04

DnaT DNA-binding domain; This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain (residues 84-153) in Swiss:P0A8J2 can bind to different types of ssDNA, which is fundamental for its physiological substrate bindings. Functional analysis indicate that both N- and C- terminals are essential to having the cooperative effect in binding ssDNA. The ssDNA bound complex displays a spiral filament assembly that is adopted by many proteins that are involved in DNA replication, such as DnaA, RecA and PriB. This domain is similar to pfam08585 except that it contains an extra loop at the N-terminus (84-99). Structural analysis indicate that this extra loop might be essential for the stabilization of the three-helix bundle.


The actual alignment was detected with superfamily member COG5529:

Pssm-ID: 480615  Cd Length: 104  Bit Score: 38.71  E-value: 9.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2205660756 437 RSREGKFEADHMPSSASVIEYYARLYPDL-SPKELEDLAKDVASIIIPKElhqqvsetYGGRNTKYQIEIDAQDLRAASD 515
Cdd:COG5529     1 FSRQAALWGIALPELAAFRAHWQKHGKEFgSQQKLARYVQQARAFVNRPP--------RRDRGTLTKTRPNGDTLVYDPD 72


                  ....*..
gi 2205660756 516 KNFDSIK 522
Cdd:COG5529    73 TNEFAVK 79
 
Name Accession Description Interval E-value
Pyocin_S pfam06958
S-type Pyocin; This family represents a conserved region approximately 180 residues long ...
 282-417 1.45e-33

S-type Pyocin; This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity.


Pssm-ID: 399737  Cd Length: 139  Bit Score: 124.40  E-value: 1.45e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2205660756 282 ALAGKSAPTRIRFQWVKDKYGRLIPVAYHTGADSGLDQVRVRAMRRNIFTGNYEFWADGAEKPAIIWTPDELEFKAPGNT 361
Cdd:pfam06958   5 AAQMGTVDLPVRLRIIDDEDGRLKVYGVHTGGAGVPDRVPVRAATLDAETGSYEFTADGAPGPTILWTPASPPGNGPPST 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2205660756 362 GNRDEPYLPSTITVLPLPGAEemGSTSTSLPIPDEQSFDDYILVnLPH--GMPPIYIY 417
Cdd:pfam06958  85 SSPAAPPDTPVITGTPIPPVV--GEVIEPYPAPDERDFRDYILV-FPAdsGLPPLYVV 139
PAAR_CT_2 cd14744
proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This ...
 10-88 2.65e-23

proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly beta- and gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Most members contain C-terminal domain extensions corresponding to several uncharacterized domains such as S-type pyocin, DUF2235, DUF2345 and cytotoxic proteins. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. 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: 269829  Cd Length: 78  Bit Score: 93.39  E-value: 2.65e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2205660756  10 RGQALHGDKTTTGAVCLTSLPNATEHGLGVIRIGDATTdCPKCGRRGKITSGEPHSTYDGLASAVDGSDVLCGCPPGTN 88
Cdd:cd14744     1 RGIIRLGDKTTHGGVVISGSSTFTIDGRPVARVGDKVT-CPKCKGTGPIVEGGPTFTVDGRPVALDGDRVACGCPLIPS 78
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 16-84 3.88e-15

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: 70.29  E-value: 3.88e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2205660756  16 GDKTTTGAVCLTSLPNATEHGLGVIRIGDATTdCPKCGRRGKITSGEPHSTYDGLASAVDGSDVLCGCP 84
Cdd:pfam05488   2 GDKTSHGGVVITGSPTVLIGGKPAARVGDLVV-CPPCGGGGPIAEGSPTVLINGKPAAREGDKTACGAT 69
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 9-83 6.72e-09

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: 52.89  E-value: 6.72e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2205660756   9 GRGQALHGDKTTTGAVCLTSLPNATEHGLGVIRIGDATTdCPKCGrRGKITSGEPHSTYDGLASAVDGSDVLCGC 83
Cdd:COG4104     2 PKPAARLGDKTSHGGPVISGSPTVLIGGRPAARVGDKVS-CPKHG-PDTIAEGSPTVLINGKPAARVGDKTACGG 74
ECs1768 COG5529
Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: ...
 437-522 9.89e-04

Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: prophages, transposons];


Pssm-ID: 444280  Cd Length: 104  Bit Score: 38.71  E-value: 9.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2205660756 437 RSREGKFEADHMPSSASVIEYYARLYPDL-SPKELEDLAKDVASIIIPKElhqqvsetYGGRNTKYQIEIDAQDLRAASD 515
Cdd:COG5529     1 FSRQAALWGIALPELAAFRAHWQKHGKEFgSQQKLARYVQQARAFVNRPP--------RRDRGTLTKTRPNGDTLVYDPD 72


                  ....*..
gi 2205660756 516 KNFDSIK 522
Cdd:COG5529    73 TNEFAVK 79
 
Name Accession Description Interval E-value
Pyocin_S pfam06958
S-type Pyocin; This family represents a conserved region approximately 180 residues long ...
 282-417 1.45e-33

S-type Pyocin; This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity.


Pssm-ID: 399737  Cd Length: 139  Bit Score: 124.40  E-value: 1.45e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2205660756 282 ALAGKSAPTRIRFQWVKDKYGRLIPVAYHTGADSGLDQVRVRAMRRNIFTGNYEFWADGAEKPAIIWTPDELEFKAPGNT 361
Cdd:pfam06958   5 AAQMGTVDLPVRLRIIDDEDGRLKVYGVHTGGAGVPDRVPVRAATLDAETGSYEFTADGAPGPTILWTPASPPGNGPPST 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2205660756 362 GNRDEPYLPSTITVLPLPGAEemGSTSTSLPIPDEQSFDDYILVnLPH--GMPPIYIY 417
Cdd:pfam06958  85 SSPAAPPDTPVITGTPIPPVV--GEVIEPYPAPDERDFRDYILV-FPAdsGLPPLYVV 139
PAAR_CT_2 cd14744
proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This ...
 10-88 2.65e-23

proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly beta- and gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Most members contain C-terminal domain extensions corresponding to several uncharacterized domains such as S-type pyocin, DUF2235, DUF2345 and cytotoxic proteins. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. 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: 269829  Cd Length: 78  Bit Score: 93.39  E-value: 2.65e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2205660756  10 RGQALHGDKTTTGAVCLTSLPNATEHGLGVIRIGDATTdCPKCGRRGKITSGEPHSTYDGLASAVDGSDVLCGCPPGTN 88
Cdd:cd14744     1 RGIIRLGDKTTHGGVVISGSSTFTIDGRPVARVGDKVT-CPKCKGTGPIVEGGPTFTVDGRPVALDGDRVACGCPLIPS 78
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 16-84 3.88e-15

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: 70.29  E-value: 3.88e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2205660756  16 GDKTTTGAVCLTSLPNATEHGLGVIRIGDATTdCPKCGRRGKITSGEPHSTYDGLASAVDGSDVLCGCP 84
Cdd:pfam05488   2 GDKTSHGGVVITGSPTVLIGGKPAARVGDLVV-CPPCGGGGPIAEGSPTVLINGKPAAREGDKTACGAT 69
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 9-83 6.72e-09

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: 52.89  E-value: 6.72e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2205660756   9 GRGQALHGDKTTTGAVCLTSLPNATEHGLGVIRIGDATTdCPKCGrRGKITSGEPHSTYDGLASAVDGSDVLCGC 83
Cdd:COG4104     2 PKPAARLGDKTSHGGPVISGSPTVLIGGRPAARVGDKVS-CPKHG-PDTIAEGSPTVLINGKPAARVGDKTACGG 74
PAAR_CT_2 cd14744
proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This ...
 38-105 3.15e-08

proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly beta- and gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Most members contain C-terminal domain extensions corresponding to several uncharacterized domains such as S-type pyocin, DUF2235, DUF2345 and cytotoxic proteins. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. 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: 269829  Cd Length: 78  Bit Score: 50.63  E-value: 3.15e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2205660756  38 GVIRIGDATTdcpkCGrrGKITSGEPHSTYDGLASAVDGSDVLCGCPPGTNRVIAPAGQWMGRGKSPA 105
Cdd:cd14744     2 GIIRLGDKTT----HG--GVVISGSSTFTIDGRPVARVGDKVTCPKCKGTGPIVEGGPTFTVDGRPVA 63
ECs1768 COG5529
Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: ...
 437-522 9.89e-04

Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: prophages, transposons];


Pssm-ID: 444280  Cd Length: 104  Bit Score: 38.71  E-value: 9.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2205660756 437 RSREGKFEADHMPSSASVIEYYARLYPDL-SPKELEDLAKDVASIIIPKElhqqvsetYGGRNTKYQIEIDAQDLRAASD 515
Cdd:COG5529     1 FSRQAALWGIALPELAAFRAHWQKHGKEFgSQQKLARYVQQARAFVNRPP--------RRDRGTLTKTRPNGDTLVYDPD 72


                  ....*..
gi 2205660756 516 KNFDSIK 522
Cdd:COG5529    73 TNEFAVK 79
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 42-105 4.37e-03

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: 36.01  E-value: 4.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2205660756  42 IGDATTDCpkcgrrGKITSGEPHSTYDGLASAVDGSDVLCGCPPGTNRVIAPAGQWMGRGKSPA 105
Cdd:pfam05488   1 LGDKTSHG------GVVITGSPTVLIGGKPAARVGDLVVCPPCGGGGPIAEGSPTVLINGKPAA 58
PAAR_CT_1 cd14743
proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found ...
 35-82 6.03e-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: 35.74  E-value: 6.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2205660756  35 HGLGVIRIGDATTdcpkCGrrGKITSGEPHSTYDGLASAVDGSDVLCG 82
Cdd:cd14743    30 DGLPAARVGDKTS----CG--ATIVSGSINVLINGKPAAVLGSTTSHG 71
 
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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