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Conserved domains on  [gi|1563805980|emb|VEU76277|]
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Free methionine-R-sulfoxide reductase [Mycoplasmopsis columboralis]

Protein Classification

GAF domain-containing protein( domain architecture ID 10005003)

GAF (cyclic GMP, adenylyl cyclase, FhlA) domain-containing protein similar to Saccharomyces cerevisiae free methionine-R-sulfoxide reductase (fRMsr), which catalyzes the reversible oxidation-reduction of the R-enantiomer of free methionine sulfoxide to methionine, protecting the cell from oxidative stress

CATH:  3.30.450.40
Gene Ontology:  GO:0005515
PubMed:  9433123|12518043
SCOP:  4001852

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 7-138 3.28e-55

GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, Signal transduction mechanisms];


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 170.01  E-value: 3.28e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980   7 LIDNEKKIYTILANTSAFIWEKFDNLNWAGFY-VNEDNTLYLHAFQGKVACSVIPFNRGVCGHAATIQKTVVVDDVNTFK 85
Cdd:COG1956    19 LLAGETDLIANLANISALLFEALPDYNWVGFYlVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLVPDVHAFP 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1563805980  86 DHIVCDSNSKSEVVIPVIVKNKLFAVLDIDAPVYKRFDTQTVKSLEEIVSILE 138
Cdd:COG1956    99 GHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLA 151
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 7-138 3.28e-55

GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, Signal transduction mechanisms];


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 170.01  E-value: 3.28e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980   7 LIDNEKKIYTILANTSAFIWEKFDNLNWAGFY-VNEDNTLYLHAFQGKVACSVIPFNRGVCGHAATIQKTVVVDDVNTFK 85
Cdd:COG1956    19 LLAGETDLIANLANISALLFEALPDYNWVGFYlVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLVPDVHAFP 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1563805980  86 DHIVCDSNSKSEVVIPVIVKNKLFAVLDIDAPVYKRFDTQTVKSLEEIVSILE 138
Cdd:COG1956    99 GHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLA 151
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 38-142 2.24e-06

GAF domain; The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433019 [Multi-domain]  Cd Length: 137  Bit Score: 44.38  E-value: 2.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980  38 YVNEDNTLYLHAFQGKVACSVI--PFNRGVCGHAATIQKTVVVDDVNTFKDHI---VCDSNSKSEVVIPVIVKNKLFAVL 112
Cdd:pfam13185  28 LVDDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRVVGVL 107

                          90       100       110
                  ....*....|....*....|....*....|
gi 1563805980 113 DIDAPVYKRFDTQTVKSLEEIVSILEHELE 142
Cdd:pfam13185 108 ALGSNRPGAFDEEDLELLELLAEQAAIAIE 137
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 37-145 2.08e-03

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 36.21  E-value: 2.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980   37 FYVNEDNTLYLHAFQG-KVACSVIPF--NRGVCGHAATIQKTVVVDDVNT---FKDHIVCDSNS-KSEVVIPVIVKNKLF 109
Cdd:smart00065  27 VDENDRGELVLVAADGlTLPTLGIRFplDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQGvRSFLAVPLVADGELV 106

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1563805980  110 AVLDIDAPVYKR-FDTQTVKSLEEI-----VSILEHELEKLL 145
Cdd:smart00065 107 GVLALHNKKSPRpFTEEDEELLQALanqlaIALANAQLYEEL 148
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 7-138 3.28e-55

GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, Signal transduction mechanisms];


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 170.01  E-value: 3.28e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980   7 LIDNEKKIYTILANTSAFIWEKFDNLNWAGFY-VNEDNTLYLHAFQGKVACSVIPFNRGVCGHAATIQKTVVVDDVNTFK 85
Cdd:COG1956    19 LLAGETDLIANLANISALLFEALPDYNWVGFYlVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLVPDVHAFP 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1563805980  86 DHIVCDSNSKSEVVIPVIVKNKLFAVLDIDAPVYKRFDTQTVKSLEEIVSILE 138
Cdd:COG1956    99 GHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLA 151
GAF COG2203
GAF domain [Signal transduction mechanisms];
37-144 5.19e-08

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 50.58  E-value: 5.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980  37 FYVNED-NTLYLHAFQGKVACSV--IPFNRGVCGHAATIQKTVVVDDVNT------FKDHIVCDSNSKSEVVIPVIVKNK 107
Cdd:COG2203   231 LLVDEDgGELELVAAPGLPEEELgrLPLGEGLAGRALRTGEPVVVNDASTdprfapSLRELLLALGIRSLLCVPLLVDGR 310

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1563805980 108 LFAVLDIDAPVYKRFDTQTVKSLEEIVSILEHELEKL 144
Cdd:COG2203   311 LIGVLALYSKEPRAFTEEDLELLEALADQAAIAIERA 347
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 38-142 2.24e-06

GAF domain; The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433019 [Multi-domain]  Cd Length: 137  Bit Score: 44.38  E-value: 2.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980  38 YVNEDNTLYLHAFQGKVACSVI--PFNRGVCGHAATIQKTVVVDDVNTFKDHI---VCDSNSKSEVVIPVIVKNKLFAVL 112
Cdd:pfam13185  28 LVDDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRVVGVL 107

                          90       100       110
                  ....*....|....*....|....*....|
gi 1563805980 113 DIDAPVYKRFDTQTVKSLEEIVSILEHELE 142
Cdd:pfam13185 108 ALGSNRPGAFDEEDLELLELLAEQAAIAIE 137
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 37-141 1.27e-03

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 36.69  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980  37 FYVNEDNTLYLHAFQGKVACSVIPFNRGVCGHAATIQKTVVVDDVNT---FKD--HIVCDSNSKSEVVIPVIVKNKLFAV 111
Cdd:pfam01590  25 YLPDADGLEYLPPGARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAAGdprFLDplLLLRNFGIRSLLAVPIIDDGELLGV 104

                          90       100       110
                  ....*....|....*....|....*....|
gi 1563805980 112 LDIDAPvYKRFDTQTVKSLEEIVSILEHEL 141
Cdd:pfam01590 105 LVLHHP-RPPFTEEELELLEVLADQVAIAL 133
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 37-145 2.08e-03

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 36.21  E-value: 2.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1563805980   37 FYVNEDNTLYLHAFQG-KVACSVIPF--NRGVCGHAATIQKTVVVDDVNT---FKDHIVCDSNS-KSEVVIPVIVKNKLF 109
Cdd:smart00065  27 VDENDRGELVLVAADGlTLPTLGIRFplDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQGvRSFLAVPLVADGELV 106

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1563805980  110 AVLDIDAPVYKR-FDTQTVKSLEEI-----VSILEHELEKLL 145
Cdd:smart00065 107 GVLALHNKKSPRpFTEEDEELLQALanqlaIALANAQLYEEL 148
 
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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