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Conserved domains on  [gi|518847189|ref|WP_020003079|]
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GAF domain-containing protein [Mycoplasmopsis synoviae]

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:  12518043|11032796
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, ...
 2-144 1.51e-64

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 193.89  E-value: 1.51e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189   2 LVQQYKSLIADEVKIYSILANTSAFIYQNFKNLNWAGFYLAEG-EVLYLSSFQGKIACTQIPFSRGVCGKAAREQKTIVV 80
Cdd:COG1956   12 LLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLV 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518847189  81 DDVHEFKDHIACDSASNSEVVIPIIVNSKLYGVLDLDSPLKSNFkDKEIVLTLEKIATELANKI 144
Cdd:COG1956   92 PDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRF-DEEDQAGLEALAALLAEAL 154
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-144 1.51e-64

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 193.89  E-value: 1.51e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189   2 LVQQYKSLIADEVKIYSILANTSAFIYQNFKNLNWAGFYLAEG-EVLYLSSFQGKIACTQIPFSRGVCGKAAREQKTIVV 80
Cdd:COG1956   12 LLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLV 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518847189  81 DDVHEFKDHIACDSASNSEVVIPIIVNSKLYGVLDLDSPLKSNFkDKEIVLTLEKIATELANKI 144
Cdd:COG1956   92 PDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRF-DEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 36-141 5.69e-09

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: 51.31  E-value: 5.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189   36 WAGFYLAEGEVLYLSSFQGKI-ACTQIPFSRGVCGKAAREQKTIVVDDV---HEFKDHIACDSASNSEVVIPIIVNSKLY 111
Cdd:pfam13185  25 FILLVDDDGRLAAWGGAADELsAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGRVV 104

                          90       100       110
                  ....*....|....*....|....*....|
gi 518847189  112 GVLDLDSPLKSNFKDKEIVLtLEKIATELA 141
Cdd:pfam13185 105 GVLALGSNRPGAFDEEDLEL-LELLAEQAA 133
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 43-141 7.93e-05

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: 40.44  E-value: 7.93e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189    43 EGEVLYLSSFQGKIACTQIPF--SRGVCGKAAREQKTIVVDDVHE---FKDHIACD-SASNSEVVIPIIVNSKLYGVLDL 116
Cdd:smart00065  32 RGELVLVAADGLTLPTLGIRFplDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLAL 111

                           90       100
                   ....*....|....*....|....*..
gi 518847189   117 DSPlKSN--FKDKEIVLtLEKIATELA 141
Cdd:smart00065 112 HNK-KSPrpFTEEDEEL-LQALANQLA 136
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-144 1.51e-64

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 193.89  E-value: 1.51e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189   2 LVQQYKSLIADEVKIYSILANTSAFIYQNFKNLNWAGFYLAEG-EVLYLSSFQGKIACTQIPFSRGVCGKAAREQKTIVV 80
Cdd:COG1956   12 LLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLV 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518847189  81 DDVHEFKDHIACDSASNSEVVIPIIVNSKLYGVLDLDSPLKSNFkDKEIVLTLEKIATELANKI 144
Cdd:COG1956   92 PDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRF-DEEDQAGLEALAALLAEAL 154
GAF COG2203
GAF domain [Signal transduction mechanisms];
36-144 8.52e-12

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 61.75  E-value: 8.52e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189  36 WAGFYL--AEGEVLYLSSFQG--KIACTQIPFSRGVCGKAAREQKTIVVDDVHEFKDHIACDSAS------NSEVVIPII 105
Cdd:COG2203  227 RGAILLvdEDGGELELVAAPGlpEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLL 306

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 518847189 106 VNSKLYGVLDLDSPLKSNFKDKEIVLtLEKIATELANKI 144
Cdd:COG2203  307 VDGRLIGVLALYSKEPRAFTEEDLEL-LEALADQAAIAI 344
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 36-141 5.69e-09

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: 51.31  E-value: 5.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189   36 WAGFYLAEGEVLYLSSFQGKI-ACTQIPFSRGVCGKAAREQKTIVVDDV---HEFKDHIACDSASNSEVVIPIIVNSKLY 111
Cdd:pfam13185  25 FILLVDDDGRLAAWGGAADELsAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGRVV 104

                          90       100       110
                  ....*....|....*....|....*....|
gi 518847189  112 GVLDLDSPLKSNFKDKEIVLtLEKIATELA 141
Cdd:pfam13185 105 GVLALGSNRPGAFDEEDLEL-LELLAEQAA 133
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 19-144 1.42e-07

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: 47.47  E-value: 1.42e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189   19 ILANTSAFIYQNFkNLNWAGFYLAEGE-VLYLSSFQGKIACTQIPFSRGVCGKAAREQKTIVVDDVHE---FKD--HIAC 92
Cdd:pfam01590   5 ILQTILEELRELL-GADRCALYLPDADgLEYLPPGARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAAGdprFLDplLLLR 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 518847189   93 DSASNSEVVIPIIVNSKLYGVLDLDSPlKSNFKDKEIVLtLEKIATELANKI 144
Cdd:pfam01590  84 NFGIRSLLAVPIIDDGELLGVLVLHHP-RPPFTEEELEL-LEVLADQVAIAL 133
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
40-141 2.04e-05

Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 42.19  E-value: 2.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189  40 YLA--EGEVLYLSSFQG----KIACTQIPFSRGVCGKAAREQKTIVVDDVHEfkdHIACDSAS-------NSEVVIPIIV 106
Cdd:COG3605   42 YLLdpDGGRLELRATEGlnpeAVGKVRLPLGEGLVGLVAERGEPLNLADAAS---HPRFKYFPetgeegfRSFLGVPIIR 118

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 518847189 107 NSKLYGVLDLDSPLKSNFKDKEiVLTLEKIATELA 141
Cdd:COG3605  119 RGRVLGVLVVQSREPREFTEEE-VEFLVTLAAQLA 152
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 43-141 7.93e-05

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: 40.44  E-value: 7.93e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518847189    43 EGEVLYLSSFQGKIACTQIPF--SRGVCGKAAREQKTIVVDDVHE---FKDHIACD-SASNSEVVIPIIVNSKLYGVLDL 116
Cdd:smart00065  32 RGELVLVAADGLTLPTLGIRFplDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLAL 111

                           90       100
                   ....*....|....*....|....*..
gi 518847189   117 DSPlKSN--FKDKEIVLtLEKIATELA 141
Cdd:smart00065 112 HNK-KSPrpFTEEDEEL-LQALANQLA 136
 
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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