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Conserved domains on  [gi|1168688947|ref|WP_080281262|]
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SOS response-associated peptidase family protein [Oenococcus oeni]

Protein Classification

SOS response-associated peptidase family protein( domain architecture ID 4904)

SOS response-associated peptidase (SRAP) family protein may catalyze the conversion of the apurinic/apyrimidinic (AP, or abasic) sites in DNA to its reactive, ring-opened aldehyde form, and the reversal of DNA-protein cross-links

CATH:  3.90.1680.10
Gene Ontology:  GO:0009432|GO:0003697|GO:0008233
PubMed:  32663791|35934051
SCOP:  4003435

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SRAP super family cl03646
SOS response associated peptidase (SRAP); The SRAP family functions as a DNA-associated ...
 9-160 8.24e-31

SOS response associated peptidase (SRAP); The SRAP family functions as a DNA-associated autoproteolytic switch that recruits diverse repair enzymes onto DNA damage. We propose that the human protein Q96FZ2:UniProtKB, the eukaryotic member of the SRAP family, which has been recently shown to bind specifically to DNA with 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, is a sensor for these oxidized bases generated by the TET (tetrahedral aminopeptidase of the M42 family) enzymes from methylcytosine. Hence, its autoproteolytic activity might help it act as a switch that recruits DNA repair enzymes to remove these oxidized methylcytosine species as part of the DNA demethylation pathway downstream of the TET enzymes.


The actual alignment was detected with superfamily member COG2135:

Pssm-ID: 470848  Cd Length: 222  Bit Score: 111.49  E-value: 8.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947   9 EIQRIYQLALDNGYQLK-SGEIFPTdQTALIV--AGKKQVRIVQMPWGF-PGF-KEKQI---IINARAETIMNKEIFADA 80
Cdd:COG2135    13 ELAERFGAEDAPGGDLEpRYNIAPT-QPVPVVreTDDGPRELRLARWGLvPSWaKDPKKgprLINARAETVAEKPSFRAA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947  81 FIKYRCVYPTSGFFEWTKD---KQKIYFNYQEKPsALYIAGFYNFFDGQAKSIL-----ITTVPNASVAPIYNRMPLILK 152
Cdd:COG2135    92 FRRRRCLIPADGFYEWRKEggkKQPYYIHRKDGE-PFAFAGLWERWRDPDGEWLltftiLTTEANGLMAPIHDRMPVILP 170


                  ....*...
gi 1168688947 153 KEEINRWI 160
Cdd:COG2135   171 PEDWDAWL 178
 
Name Accession Description Interval E-value
SRAP COG2135
ssDNA abasic site-binding protein YedK/HMCES, SRAP family [Replication, recombination and ...
 9-160 8.24e-31

ssDNA abasic site-binding protein YedK/HMCES, SRAP family [Replication, recombination and repair];


Pssm-ID: 441738  Cd Length: 222  Bit Score: 111.49  E-value: 8.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947   9 EIQRIYQLALDNGYQLK-SGEIFPTdQTALIV--AGKKQVRIVQMPWGF-PGF-KEKQI---IINARAETIMNKEIFADA 80
Cdd:COG2135    13 ELAERFGAEDAPGGDLEpRYNIAPT-QPVPVVreTDDGPRELRLARWGLvPSWaKDPKKgprLINARAETVAEKPSFRAA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947  81 FIKYRCVYPTSGFFEWTKD---KQKIYFNYQEKPsALYIAGFYNFFDGQAKSIL-----ITTVPNASVAPIYNRMPLILK 152
Cdd:COG2135    92 FRRRRCLIPADGFYEWRKEggkKQPYYIHRKDGE-PFAFAGLWERWRDPDGEWLltftiLTTEANGLMAPIHDRMPVILP 170


                  ....*...
gi 1168688947 153 KEEINRWI 160
Cdd:COG2135   171 PEDWDAWL 178
SRAP pfam02586
SOS response associated peptidase (SRAP); The SRAP family functions as a DNA-associated ...
 29-159 6.71e-30

SOS response associated peptidase (SRAP); The SRAP family functions as a DNA-associated autoproteolytic switch that recruits diverse repair enzymes onto DNA damage. We propose that the human protein Q96FZ2:UniProtKB, the eukaryotic member of the SRAP family, which has been recently shown to bind specifically to DNA with 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, is a sensor for these oxidized bases generated by the TET (tetrahedral aminopeptidase of the M42 family) enzymes from methylcytosine. Hence, its autoproteolytic activity might help it act as a switch that recruits DNA repair enzymes to remove these oxidized methylcytosine species as part of the DNA demethylation pathway downstream of the TET enzymes.


Pssm-ID: 460605  Cd Length: 213  Bit Score: 108.77  E-value: 6.71e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947  29 IFPTDQTALIVAGK--KQVRIVQMPWGF-PGF-KEKQI---IINARAETIMNKEIFADAFIKYRCVYPTSGFFEWTKD-K 100
Cdd:pfam02586  34 VAPTQPVPVVRARDpgGDRVLRLMRWGLvPSWaKDPKIgprTINARSETLAEKPSFRSAFRRRRCLVPADGFYEWKKGgK 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1168688947 101 QKI-YFNYQEKPSALYIAGFYNFFDGQAKSIL-----ITTVPNASVAPIYNRMPLILKKEEINRW 159
Cdd:pfam02586 114 GKQpYYIHRKDGRPLAFAGLWEVWRDPDGEPLytftiITTEANGLLAPIHDRMPVILDPEDWDAW 178
PRK09951 PRK09951
hypothetical protein; Provisional
 52-160 1.33e-08

hypothetical protein; Provisional


Pssm-ID: 182162  Cd Length: 222  Bit Score: 52.55  E-value: 1.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947  52 WGF-PGFKEKQIIINARAETIMNKEIFADAFIKYRCVYPTSGFFEWTK--DKQKIYFNYQEKPSALYIA--GFYNFFDG- 125
Cdd:PRK09951   61 WGYaPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFADGWFEWKKegDKKQPYFIYRADGQPIFMAaiGSTPFERGd 140

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1168688947 126 QAKSILI-TTVPNASVAPIYNRMPLILKKEEINRWI 160
Cdd:PRK09951  141 EAEGFLIvTAAADQGLVDIHDRRPLVLSPEAAREWM 176
 
Name Accession Description Interval E-value
SRAP COG2135
ssDNA abasic site-binding protein YedK/HMCES, SRAP family [Replication, recombination and ...
 9-160 8.24e-31

ssDNA abasic site-binding protein YedK/HMCES, SRAP family [Replication, recombination and repair];


Pssm-ID: 441738  Cd Length: 222  Bit Score: 111.49  E-value: 8.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947   9 EIQRIYQLALDNGYQLK-SGEIFPTdQTALIV--AGKKQVRIVQMPWGF-PGF-KEKQI---IINARAETIMNKEIFADA 80
Cdd:COG2135    13 ELAERFGAEDAPGGDLEpRYNIAPT-QPVPVVreTDDGPRELRLARWGLvPSWaKDPKKgprLINARAETVAEKPSFRAA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947  81 FIKYRCVYPTSGFFEWTKD---KQKIYFNYQEKPsALYIAGFYNFFDGQAKSIL-----ITTVPNASVAPIYNRMPLILK 152
Cdd:COG2135    92 FRRRRCLIPADGFYEWRKEggkKQPYYIHRKDGE-PFAFAGLWERWRDPDGEWLltftiLTTEANGLMAPIHDRMPVILP 170


                  ....*...
gi 1168688947 153 KEEINRWI 160
Cdd:COG2135   171 PEDWDAWL 178
SRAP pfam02586
SOS response associated peptidase (SRAP); The SRAP family functions as a DNA-associated ...
 29-159 6.71e-30

SOS response associated peptidase (SRAP); The SRAP family functions as a DNA-associated autoproteolytic switch that recruits diverse repair enzymes onto DNA damage. We propose that the human protein Q96FZ2:UniProtKB, the eukaryotic member of the SRAP family, which has been recently shown to bind specifically to DNA with 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, is a sensor for these oxidized bases generated by the TET (tetrahedral aminopeptidase of the M42 family) enzymes from methylcytosine. Hence, its autoproteolytic activity might help it act as a switch that recruits DNA repair enzymes to remove these oxidized methylcytosine species as part of the DNA demethylation pathway downstream of the TET enzymes.


Pssm-ID: 460605  Cd Length: 213  Bit Score: 108.77  E-value: 6.71e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947  29 IFPTDQTALIVAGK--KQVRIVQMPWGF-PGF-KEKQI---IINARAETIMNKEIFADAFIKYRCVYPTSGFFEWTKD-K 100
Cdd:pfam02586  34 VAPTQPVPVVRARDpgGDRVLRLMRWGLvPSWaKDPKIgprTINARSETLAEKPSFRSAFRRRRCLVPADGFYEWKKGgK 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1168688947 101 QKI-YFNYQEKPSALYIAGFYNFFDGQAKSIL-----ITTVPNASVAPIYNRMPLILKKEEINRW 159
Cdd:pfam02586 114 GKQpYYIHRKDGRPLAFAGLWEVWRDPDGEPLytftiITTEANGLLAPIHDRMPVILDPEDWDAW 178
PRK09951 PRK09951
hypothetical protein; Provisional
 52-160 1.33e-08

hypothetical protein; Provisional


Pssm-ID: 182162  Cd Length: 222  Bit Score: 52.55  E-value: 1.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168688947  52 WGF-PGFKEKQIIINARAETIMNKEIFADAFIKYRCVYPTSGFFEWTK--DKQKIYFNYQEKPSALYIA--GFYNFFDG- 125
Cdd:PRK09951   61 WGYaPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFADGWFEWKKegDKKQPYFIYRADGQPIFMAaiGSTPFERGd 140

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1168688947 126 QAKSILI-TTVPNASVAPIYNRMPLILKKEEINRWI 160
Cdd:PRK09951  141 EAEGFLIvTAAADQGLVDIHDRRPLVLSPEAAREWM 176
 
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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