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Conserved domains on  [gi|46048169|ref|NP_840073|]
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methionine-R-sulfoxide reductase B1-A [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SelR super family cl15841
SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate ...
 6-104 5.64e-29

SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.


The actual alignment was detected with superfamily member COG0229:

Pssm-ID: 472838  Cd Length: 133  Bit Score: 101.31  E-value: 5.64e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169   6 FSGGeiYKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVSKQEER-WGAY--KVRCGKCGNGLGHEFvN 82
Cdd:COG0229  33 FSGE--YWDNKEEGIYVCAGCGAPLFSSDTKFDSGTGWPSFTKPIDPGAVEEKEDRsHGMVrtEVRCARCGAHLGHVF-D 109

                        90       100
                ....*....|....*....|...
gi 46048169  83 DGPK-HGLsRFUIFSSSLKFIPK 104
Cdd:COG0229 110 DGPPpTGL-RYCINSAALRFIPK 131
 
Name Accession Description Interval E-value
MsrB COG0229
Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, ...
 6-104 5.64e-29

Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 439999  Cd Length: 133  Bit Score: 101.31  E-value: 5.64e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169   6 FSGGeiYKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVSKQEER-WGAY--KVRCGKCGNGLGHEFvN 82
Cdd:COG0229  33 FSGE--YWDNKEEGIYVCAGCGAPLFSSDTKFDSGTGWPSFTKPIDPGAVEEKEDRsHGMVrtEVRCARCGAHLGHVF-D 109

                        90       100
                ....*....|....*....|...
gi 46048169  83 DGPK-HGLsRFUIFSSSLKFIPK 104
Cdd:COG0229 110 DGPPpTGL-RYCINSAALRFIPK 131
SelR pfam01641
SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate ...
 6-103 2.79e-28

SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.


Pssm-ID: 460278  Cd Length: 120  Bit Score: 98.97  E-value: 2.79e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169     6 FSGGeiYKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVSKQEERWGAYK---VRCGKCGNGLGHEFvN 82
Cdd:pfam01641  23 FTGE--YWDNKEPGIYVCAGCGTPLFSSDTKFDSGCGWPSFYDPIPGDAVKEKEDTSHGMVrteVRCARCGGHLGHVF-D 99

                          90       100
                  ....*....|....*....|..
gi 46048169    83 DGPK-HGLsRFUIFSSSLKFIP 103
Cdd:pfam01641 100 DGPPpTGL-RYCINSASLKFIP 120
TIGR00357 TIGR00357
methionine-R-sulfoxide reductase; This model describes a domain found in PilB, a protein ...
 12-109 6.27e-27

methionine-R-sulfoxide reductase; This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested. [Protein fate, Protein modification and repair, Cellular processes, Adaptations to atypical conditions]


Pssm-ID: 129454  Cd Length: 134  Bit Score: 96.38  E-value: 6.27e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169    12 YKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVS-KQEERWGAYK--VRCGKCGNGLGHEFvNDGPKHG 88
Cdd:TIGR00357  32 YWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAyERDESHGMIRteVRCRNCDAHLGHVF-DDGPEPT 110

                          90       100
                  ....*....|....*....|.
gi 46048169    89 LSRFUIFSSSLKFIPKVKNEQ 109
Cdd:TIGR00357 111 GLRYCINSAALKFIPLEEMEE 131
PRK05550 PRK05550
bifunctional methionine sulfoxide reductase B/A protein; Provisional
 6-103 1.65e-19

bifunctional methionine sulfoxide reductase B/A protein; Provisional


Pssm-ID: 235499 [Multi-domain]  Cd Length: 283  Bit Score: 80.33  E-value: 1.65e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169    6 FSGgeIYKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIhEDSVSKQEERWGA-YKVRCGKCGNGLGHEFVNDG 84
Cdd:PRK05550  24 FSG--EYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEI-PGAVKRLPDADGRrTEIVCANCGAHLGHVFEGEG 100

                         90
                 ....*....|....*....
gi 46048169   85 PKHGLSRFUIFSSSLKFIP 103
Cdd:PRK05550 101 LTPKNTRHCVNSASLDFVP 119
 
Name Accession Description Interval E-value
MsrB COG0229
Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, ...
 6-104 5.64e-29

Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 439999  Cd Length: 133  Bit Score: 101.31  E-value: 5.64e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169   6 FSGGeiYKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVSKQEER-WGAY--KVRCGKCGNGLGHEFvN 82
Cdd:COG0229  33 FSGE--YWDNKEEGIYVCAGCGAPLFSSDTKFDSGTGWPSFTKPIDPGAVEEKEDRsHGMVrtEVRCARCGAHLGHVF-D 109

                        90       100
                ....*....|....*....|...
gi 46048169  83 DGPK-HGLsRFUIFSSSLKFIPK 104
Cdd:COG0229 110 DGPPpTGL-RYCINSAALRFIPK 131
SelR pfam01641
SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate ...
 6-103 2.79e-28

SelR domain; Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.


Pssm-ID: 460278  Cd Length: 120  Bit Score: 98.97  E-value: 2.79e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169     6 FSGGeiYKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVSKQEERWGAYK---VRCGKCGNGLGHEFvN 82
Cdd:pfam01641  23 FTGE--YWDNKEPGIYVCAGCGTPLFSSDTKFDSGCGWPSFYDPIPGDAVKEKEDTSHGMVrteVRCARCGGHLGHVF-D 99

                          90       100
                  ....*....|....*....|..
gi 46048169    83 DGPK-HGLsRFUIFSSSLKFIP 103
Cdd:pfam01641 100 DGPPpTGL-RYCINSASLKFIP 120
TIGR00357 TIGR00357
methionine-R-sulfoxide reductase; This model describes a domain found in PilB, a protein ...
 12-109 6.27e-27

methionine-R-sulfoxide reductase; This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested. [Protein fate, Protein modification and repair, Cellular processes, Adaptations to atypical conditions]


Pssm-ID: 129454  Cd Length: 134  Bit Score: 96.38  E-value: 6.27e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169    12 YKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVS-KQEERWGAYK--VRCGKCGNGLGHEFvNDGPKHG 88
Cdd:TIGR00357  32 YWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAyERDESHGMIRteVRCRNCDAHLGHVF-DDGPEPT 110

                          90       100
                  ....*....|....*....|.
gi 46048169    89 LSRFUIFSSSLKFIPKVKNEQ 109
Cdd:TIGR00357 111 GLRYCINSAALKFIPLEEMEE 131
PRK05550 PRK05550
bifunctional methionine sulfoxide reductase B/A protein; Provisional
 6-103 1.65e-19

bifunctional methionine sulfoxide reductase B/A protein; Provisional


Pssm-ID: 235499 [Multi-domain]  Cd Length: 283  Bit Score: 80.33  E-value: 1.65e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169    6 FSGgeIYKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIhEDSVSKQEERWGA-YKVRCGKCGNGLGHEFVNDG 84
Cdd:PRK05550  24 FSG--EYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEI-PGAVKRLPDADGRrTEIVCANCGAHLGHVFEGEG 100

                         90
                 ....*....|....*....
gi 46048169   85 PKHGLSRFUIFSSSLKFIP 103
Cdd:PRK05550 101 LTPKNTRHCVNSASLDFVP 119
PRK05508 PRK05508
methionine-R-sulfoxide reductase;
6-106 7.75e-19

methionine-R-sulfoxide reductase;


Pssm-ID: 180121  Cd Length: 119  Bit Score: 75.14  E-value: 7.75e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169    6 FSGgeIYKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIhEDSVSKQEERWGA-YKVRCGKCGNGLGHEFVNDG 84
Cdd:PRK05508  21 FSG--EYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEI-KGAVKRIPDADGRrTEIVCANCGGHLGHVFEGEG 97

                         90       100
                 ....*....|....*....|..
gi 46048169   85 PKHGLSRFUIFSSSLKFIPKVK 106
Cdd:PRK05508  98 FTPKNTRHCVNSISLKFVPDKG 119
PRK14018 PRK14018
bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide ...
 12-110 4.86e-15

bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB;


Pssm-ID: 184456 [Multi-domain]  Cd Length: 521  Bit Score: 69.13  E-value: 4.86e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46048169   12 YKDHFESGMYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVSKQEERwgAY-----KVRCGKCGNGLGHEFvNDGPK 86
Cdd:PRK14018 410 YDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKVVTEHDDF--SYnmrrtEVRSRAADSHLGHVF-PDGPR 486

                         90       100
                 ....*....|....*....|....*
gi 46048169   87 -HGLSRFUIFSSSLKFIPKVKNEQQ 110
Cdd:PRK14018 487 dKGGLRYCINGASLKFIPLEQMDAA 511
accD CHL00174
acetyl-CoA carboxylase beta subunit; Reviewed
 4-40 5.36e-04

acetyl-CoA carboxylase beta subunit; Reviewed


Pssm-ID: 214384 [Multi-domain]  Cd Length: 296  Bit Score: 37.58  E-value: 5.36e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 46048169    4 CSFSGGEIYKDHFESGMYVCAQCGYEL-FSSRSKYEHS 40
Cdd:CHL00174  41 CENCYGLNYKKFLKSKMNICEQCGYHLkMSSSDRIELL 78
 
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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