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Conserved domains on  [gi|763843978|gb|KJC03820|]
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protein samA' (plasmid) [Citrobacter freundii]

Protein Classification

S24/S26 family peptidase( domain architecture ID 586)

S24/S26 family peptidase similar to human signal peptidase complex catalytic subunit SEC11C, a component of the microsomal signal peptidase complex which removes signal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum

EC:  3.4.21.-
Gene Ontology:  GO:0017171

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_S24_S26 super family cl10465
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 2-137 4.24e-55

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.


The actual alignment was detected with superfamily member PRK10276:

Pssm-ID: 447902  Cd Length: 139  Bit Score: 169.21  E-value: 4.24e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   2 ILFVTPASEPALSTAPLFTERCPAGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDMGLHSGDLMVVDKAEKP 81
Cdd:PRK10276   1 MLFIKPAELREIVTFPLFSDLVQCGFPSPAADYVEQRIDLNELLIQHPSATYFVKASGDSMIDAGISDGDLLIVDSAITA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 763843978  82 MQGDIVIAETDGEFTVKRLQLKPRIALLPMNPAY-PTLYP--EELQIFGVVMAFIHKTR 137
Cdd:PRK10276  81 SHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYsPITISseDTLDVFGVVTHIVKAMR 139
 
Name Accession Description Interval E-value
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
2-137 4.24e-55

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 169.21  E-value: 4.24e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   2 ILFVTPASEPALSTAPLFTERCPAGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDMGLHSGDLMVVDKAEKP 81
Cdd:PRK10276   1 MLFIKPAELREIVTFPLFSDLVQCGFPSPAADYVEQRIDLNELLIQHPSATYFVKASGDSMIDAGISDGDLLIVDSAITA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 763843978  82 MQGDIVIAETDGEFTVKRLQLKPRIALLPMNPAY-PTLYP--EELQIFGVVMAFIHKTR 137
Cdd:PRK10276  81 SHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYsPITISseDTLDVFGVVTHIVKAMR 139
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 5-135 2.22e-47

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 151.61  E-value: 2.22e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   5 VTPASEPALStAPLFTeRCPAGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDMGLHSGDLMVVDKAEKPMQG 84
Cdd:COG1974   67 LLPASPEVVG-LPLLG-RVAAGFPIPAEENIEEYLDLPEELVKNPGATFALRVKGDSMIDAGILDGDLVIVDRQLEAENG 144

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 763843978  85 DIVIAETDGEFTVKRLQLKP-RIALLPMNPAYPTLY--PEELQIFGVVMAFIHK 135
Cdd:COG1974  145 DIVVALIDGEATVKRLYKEGgRVRLQPENPAYPPIIieGDDVEILGVVVGVIRR 198
Peptidase_S24 pfam00717
Peptidase S24-like;
25-130 3.51e-31

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 107.68  E-value: 3.51e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   25 AGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDmGLHSGDLMVVDKAEKPMQGDIVIAETDGEFTVKRLQLKP 104
Cdd:pfam00717   8 AGAPILAEEEIEGYLPLPESLLSPPGNLFALRVKGDSMEP-GIPDGDLVLVDPSREARNGDIVVARLDGEATVKRLYRDG 86

                          90       100       110
                  ....*....|....*....|....*....|
gi 763843978  105 -RIALLPMNPAYPTLY---PEELQIFGVVM 130
Cdd:pfam00717  87 gGIRLISLNPEYPPIElpaEDDVEIIGRVV 116
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 53-129 4.11e-25

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: 91.08  E-value: 4.11e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978  53 YFVRAIGDSMKDMgLHSGDLMVVDKAEKPMQGDIVIAETDGEFTVKRLQLKP--RIALLPMNPAYPTLY--PEELQIFGV 128
Cdd:cd06529    1 FALRVKGDSMEPT-IPDGDLVLVDPSDTPRDGDIVVARLDGELTVKRLQRRGggRLRLISDNPAYPPIEidEEELEIVGV 79


                 .
gi 763843978 129 V 129
Cdd:cd06529   80 V 80
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 22-135 4.00e-15

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 68.59  E-value: 4.00e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   22 RCPAGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDMGLHSGDLMVVDKAEKPMQGDIVIAETDGEFTVKRL- 100
Cdd:TIGR00498  81 RVAAGEPILAEQHIEEYFPIDFSLLKKPSAVFLLKVMGDSMVDAGICDGDLLIVRSQKDARNGEIVAAMIDGEVTVKRFy 160

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 763843978  101 QLKPRIALLPMNPAYPT--LYPEELQIFGVVMAFIHK 135
Cdd:TIGR00498 161 KDGTKVELKPENPEFDPivLNAEDVTILGKVVGVIRN 197
 
Name Accession Description Interval E-value
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
2-137 4.24e-55

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 169.21  E-value: 4.24e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   2 ILFVTPASEPALSTAPLFTERCPAGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDMGLHSGDLMVVDKAEKP 81
Cdd:PRK10276   1 MLFIKPAELREIVTFPLFSDLVQCGFPSPAADYVEQRIDLNELLIQHPSATYFVKASGDSMIDAGISDGDLLIVDSAITA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 763843978  82 MQGDIVIAETDGEFTVKRLQLKPRIALLPMNPAY-PTLYP--EELQIFGVVMAFIHKTR 137
Cdd:PRK10276  81 SHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYsPITISseDTLDVFGVVTHIVKAMR 139
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 5-135 2.22e-47

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 151.61  E-value: 2.22e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   5 VTPASEPALStAPLFTeRCPAGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDMGLHSGDLMVVDKAEKPMQG 84
Cdd:COG1974   67 LLPASPEVVG-LPLLG-RVAAGFPIPAEENIEEYLDLPEELVKNPGATFALRVKGDSMIDAGILDGDLVIVDRQLEAENG 144

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 763843978  85 DIVIAETDGEFTVKRLQLKP-RIALLPMNPAYPTLY--PEELQIFGVVMAFIHK 135
Cdd:COG1974  145 DIVVALIDGEATVKRLYKEGgRVRLQPENPAYPPIIieGDDVEILGVVVGVIRR 198
Peptidase_S24 pfam00717
Peptidase S24-like;
25-130 3.51e-31

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 107.68  E-value: 3.51e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   25 AGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDmGLHSGDLMVVDKAEKPMQGDIVIAETDGEFTVKRLQLKP 104
Cdd:pfam00717   8 AGAPILAEEEIEGYLPLPESLLSPPGNLFALRVKGDSMEP-GIPDGDLVLVDPSREARNGDIVVARLDGEATVKRLYRDG 86

                          90       100       110
                  ....*....|....*....|....*....|
gi 763843978  105 -RIALLPMNPAYPTLY---PEELQIFGVVM 130
Cdd:pfam00717  87 gGIRLISLNPEYPPIElpaEDDVEIIGRVV 116
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 53-129 4.11e-25

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: 91.08  E-value: 4.11e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978  53 YFVRAIGDSMKDMgLHSGDLMVVDKAEKPMQGDIVIAETDGEFTVKRLQLKP--RIALLPMNPAYPTLY--PEELQIFGV 128
Cdd:cd06529    1 FALRVKGDSMEPT-IPDGDLVLVDPSDTPRDGDIVVARLDGELTVKRLQRRGggRLRLISDNPAYPPIEidEEELEIVGV 79


                 .
gi 763843978 129 V 129
Cdd:cd06529   80 V 80
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 53-129 2.24e-16

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: 68.83  E-value: 2.24e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978  53 YFVRAIGDSMKDmGLHSGDLMVVDKAEK-PMQGDIVIAETDG-EFTVKRLQLKP---RIALLPMNPAYPT---LYPEELQ 124
Cdd:cd06462    1 FALRVEGDSMEP-TIPDGDLVLVDKSSYePKRGDIVVFRLPGgELTVKRVIGLPgegHYFLLGDNPNSPDsriDGPPELD 79


                 ....*
gi 763843978 125 IFGVV 129
Cdd:cd06462   80 IVGVV 84
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 17-130 1.73e-15

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 67.68  E-value: 1.73e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978  17 PLFTERCPAGFPS-PAADYTEDELdlnAYCIRRPSATYFVRAIGDSMKDMgLHSGDLMVVDKAEKPMQ-GDIVIAETDGE 94
Cdd:COG2932    2 PLYDGEASAGGGAfNEVEEPVDKL---EFPGLPPDNLFAVRVSGDSMEPT-IRDGDIVLVDPSDTEIRdGGIYVVRTDGE 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 763843978  95 FTVKRLQLKP--RIALLPMNPAYPTLY-----PEELQIFGVVM 130
Cdd:COG2932   78 LLVKRLQRRPdgKLRLISDNPAYPPIEippedADEIEIIGRVV 120
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 22-135 4.00e-15

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 68.59  E-value: 4.00e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763843978   22 RCPAGFPSPAADYTEDELDLNAYCIRRPSATYFVRAIGDSMKDMGLHSGDLMVVDKAEKPMQGDIVIAETDGEFTVKRL- 100
Cdd:TIGR00498  81 RVAAGEPILAEQHIEEYFPIDFSLLKKPSAVFLLKVMGDSMVDAGICDGDLLIVRSQKDARNGEIVAAMIDGEVTVKRFy 160

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 763843978  101 QLKPRIALLPMNPAYPT--LYPEELQIFGVVMAFIHK 135
Cdd:TIGR00498 161 KDGTKVELKPENPEFDPivLNAEDVTILGKVVGVIRN 197
 
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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