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Conserved domains on  [gi|500121502|ref|WP_011797507|]
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S24 family peptidase [Paracidovorax citrulli]

Protein Classification

S24 family peptidase( domain architecture ID 10158216)

S24 family peptidase is involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 122-228 6.34e-19

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


:

Pssm-ID: 442176  Cd Length: 121  Bit Score: 79.24  E-value: 6.34e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502 122 DGGMRTIALTHEWLERRSLRARDLIAIAVGDDSMQPSLHPGDVVAVDTRDPSPADGQVFVVDYEGACLVRRVVR-DSGAW 200
Cdd:COG2932   12 GGAFNEVEEPVDKLEFPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYVVRTDGELLVKRLQRrPDGKL 91

                         90       100       110
                 ....*....|....*....|....*....|.
gi 500121502 201 WLAAENAlRFPRKQLTAPSA---RLVGRVVH 228
Cdd:COG2932   92 RLISDNP-AYPPIEIPPEDAdeiEIIGRVVW 121
Cro super family cl46781
Cro; Members of this family are involved in the repression of transcription by binding as a ...
 14-60 4.21e-03

Cro; Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands.


The actual alignment was detected with superfamily member COG4197:

Pssm-ID: 481121  Cd Length: 68  Bit Score: 34.89  E-value: 4.21e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 500121502  14 LDEAINHLtaGNVTAFGRLLGYRDGAfVRQMLSGSRAVSDKTVRAIE 60
Cdd:COG4197    1 LEKAIEAL--GSQSALARALGVSQQA-VSQWLNGKRRVPAERCLAIE 44
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 122-228 6.34e-19

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


Pssm-ID: 442176  Cd Length: 121  Bit Score: 79.24  E-value: 6.34e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502 122 DGGMRTIALTHEWLERRSLRARDLIAIAVGDDSMQPSLHPGDVVAVDTRDPSPADGQVFVVDYEGACLVRRVVR-DSGAW 200
Cdd:COG2932   12 GGAFNEVEEPVDKLEFPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYVVRTDGELLVKRLQRrPDGKL 91

                         90       100       110
                 ....*....|....*....|....*....|.
gi 500121502 201 WLAAENAlRFPRKQLTAPSA---RLVGRVVH 228
Cdd:COG2932   92 RLISDNP-AYPPIEIPPEDAdeiEIIGRVVW 121
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 146-227 5.52e-14

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.


Pssm-ID: 119397 [Multi-domain]  Cd Length: 81  Bit Score: 64.89  E-value: 5.52e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502 146 IAIAVGDDSMQPSLHPGDVVAVDTRDPsPADGQVFVVDYEGACLVRRVVRD-SGAWWLAAENAlRFPRKQLTAPSARLVG 224
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVDPSDT-PRDGDIVVARLDGELTVKRLQRRgGGRLRLISDNP-AYPPIEIDEEELEIVG 78


                 ...
gi 500121502 225 RVV 227
Cdd:cd06529   79 VVG 81
Peptidase_S24 pfam00717
Peptidase S24-like;
109-227 1.02e-11

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 59.91  E-value: 1.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502  109 LGERQGAEPACTADGGMRTIALTHEWLerrsLRARDLIAIAVGDDSMQPSLHPGDVVAVDtRDPSPADGQVFVVDYEGAC 188
Cdd:pfam00717   3 IGRVAAGAPILAEEEIEGYLPLPESLL----SPPGNLFALRVKGDSMEPGIPDGDLVLVD-PSREARNGDIVVARLDGEA 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 500121502  189 LVRRVVRDSGAWWLAAENA----LRFPRKQltapSARLVGRVV 227
Cdd:pfam00717  78 TVKRLYRDGGGIRLISLNPeyppIELPAED----DVEIIGRVV 116
sod_Ni_protease TIGR02754
nickel-type superoxide dismutase maturation protease; Members of this protein family are ...
 150-227 4.85e-04

nickel-type superoxide dismutase maturation protease; Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad. [Cellular processes, Detoxification, Protein fate, Protein modification and repair]


Pssm-ID: 274282 [Multi-domain]  Cd Length: 90  Bit Score: 38.20  E-value: 4.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502  150 VGDDSMQPSLHPGD---VVAVDTRDPSPADGQVFVVDY---EGACLVRRV--VRDSGAWWLAAENALRFPRKQLTA-PSA 220
Cdd:TIGR02754   3 VTGVSMSPTLPPGDriiVVPWLKIFRVPPIGNVVVVRHplqPYGLIIKRLaaVDDNGLFLLGDNPKASTDSRQLGPvPRS 82


                  ....*..
gi 500121502  221 RLVGRVV 227
Cdd:TIGR02754  83 LLLGKVL 89
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
14-60 4.21e-03

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 34.89  E-value: 4.21e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 500121502  14 LDEAINHLtaGNVTAFGRLLGYRDGAfVRQMLSGSRAVSDKTVRAIE 60
Cdd:COG4197    1 LEKAIEAL--GSQSALARALGVSQQA-VSQWLNGKRRVPAERCLAIE 44
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 122-228 6.34e-19

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


Pssm-ID: 442176  Cd Length: 121  Bit Score: 79.24  E-value: 6.34e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502 122 DGGMRTIALTHEWLERRSLRARDLIAIAVGDDSMQPSLHPGDVVAVDTRDPSPADGQVFVVDYEGACLVRRVVR-DSGAW 200
Cdd:COG2932   12 GGAFNEVEEPVDKLEFPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYVVRTDGELLVKRLQRrPDGKL 91

                         90       100       110
                 ....*....|....*....|....*....|.
gi 500121502 201 WLAAENAlRFPRKQLTAPSA---RLVGRVVH 228
Cdd:COG2932   92 RLISDNP-AYPPIEIPPEDAdeiEIIGRVVW 121
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 146-227 5.52e-14

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.


Pssm-ID: 119397 [Multi-domain]  Cd Length: 81  Bit Score: 64.89  E-value: 5.52e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502 146 IAIAVGDDSMQPSLHPGDVVAVDTRDPsPADGQVFVVDYEGACLVRRVVRD-SGAWWLAAENAlRFPRKQLTAPSARLVG 224
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVDPSDT-PRDGDIVVARLDGELTVKRLQRRgGGRLRLISDNP-AYPPIEIDEEELEIVG 78


                 ...
gi 500121502 225 RVV 227
Cdd:cd06529   79 VVG 81
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 147-226 2.47e-12

The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases.


Pssm-ID: 119396 [Multi-domain]  Cd Length: 84  Bit Score: 60.74  E-value: 2.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502 147 AIAVGDDSMQPSLHPGDVVAVDTRDPSPADGQVFVVDYEG-ACLVRRVVRD--SGAWWLAAENALRFPRKQLTAPSARLV 223
Cdd:cd06462    2 ALRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPGgELTVKRVIGLpgEGHYFLLGDNPNSPDSRIDGPPELDIV 81


                 ...
gi 500121502 224 GRV 226
Cdd:cd06462   82 GVV 84
Peptidase_S24 pfam00717
Peptidase S24-like;
109-227 1.02e-11

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 59.91  E-value: 1.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502  109 LGERQGAEPACTADGGMRTIALTHEWLerrsLRARDLIAIAVGDDSMQPSLHPGDVVAVDtRDPSPADGQVFVVDYEGAC 188
Cdd:pfam00717   3 IGRVAAGAPILAEEEIEGYLPLPESLL----SPPGNLFALRVKGDSMEPGIPDGDLVLVD-PSREARNGDIVVARLDGEA 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 500121502  189 LVRRVVRDSGAWWLAAENA----LRFPRKQltapSARLVGRVV 227
Cdd:pfam00717  78 TVKRLYRDGGGIRLISLNPeyppIELPAED----DVEIIGRVV 116
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 150-229 1.11e-09

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 56.08  E-value: 1.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502 150 VGDDSMQ-PSLHPGDVVAVDtRDPSPADGQVFVVDYEGACLVRRVVRDSGAWWLAAENAlRFPRKQLTAPSARLVGRVVH 228
Cdd:COG1974  117 VKGDSMIdAGILDGDLVIVD-RQLEAENGDIVVALIDGEATVKRLYKEGGRVRLQPENP-AYPPIIIEGDDVEILGVVVG 194


                 .
gi 500121502 229 V 229
Cdd:COG1974  195 V 195
sod_Ni_protease TIGR02754
nickel-type superoxide dismutase maturation protease; Members of this protein family are ...
 150-227 4.85e-04

nickel-type superoxide dismutase maturation protease; Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad. [Cellular processes, Detoxification, Protein fate, Protein modification and repair]


Pssm-ID: 274282 [Multi-domain]  Cd Length: 90  Bit Score: 38.20  E-value: 4.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500121502  150 VGDDSMQPSLHPGD---VVAVDTRDPSPADGQVFVVDY---EGACLVRRV--VRDSGAWWLAAENALRFPRKQLTA-PSA 220
Cdd:TIGR02754   3 VTGVSMSPTLPPGDriiVVPWLKIFRVPPIGNVVVVRHplqPYGLIIKRLaaVDDNGLFLLGDNPKASTDSRQLGPvPRS 82


                  ....*..
gi 500121502  221 RLVGRVV 227
Cdd:TIGR02754  83 LLLGKVL 89
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
14-60 4.21e-03

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 34.89  E-value: 4.21e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 500121502  14 LDEAINHLtaGNVTAFGRLLGYRDGAfVRQMLSGSRAVSDKTVRAIE 60
Cdd:COG4197    1 LEKAIEAL--GSQSALARALGVSQQA-VSQWLNGKRRVPAERCLAIE 44
 
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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