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Conserved domains on  [gi|126102594|gb|ABN75272|]
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GAF domain protein [Cereibacter sphaeroides ATCC 17029]

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, ...
 1-147 1.50e-74

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 219.31  E-value: 1.50e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594   1 MDYDQLDQTIEALCHGEQDTVALMATVACEIHHAHPLSDWTGFYRVTGPELLKIGPYQGAHGCLVIPFSRGVCGAAARTG 80
Cdd:COG1956    7 EDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEG 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 126102594  81 RIQLVPDVEAFPDHIACSSTTRSEIVLPVRNgEGRLLGVLDLDSNTPAAFTEEDAARLQALLDRTFR 147
Cdd:COG1956   87 ETQLVPDVHAFPGHIACDSASRSEIVVPIFK-DGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAE 152
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-147 1.50e-74

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 219.31  E-value: 1.50e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594   1 MDYDQLDQTIEALCHGEQDTVALMATVACEIHHAHPLSDWTGFYRVTGPELLKIGPYQGAHGCLVIPFSRGVCGAAARTG 80
Cdd:COG1956    7 EDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEG 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 126102594  81 RIQLVPDVEAFPDHIACSSTTRSEIVLPVRNgEGRLLGVLDLDSNTPAAFTEEDAARLQALLDRTFR 147
Cdd:COG1956   87 ETQLVPDVHAFPGHIACDSASRSEIVVPIFK-DGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAE 152
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 14-141 1.04e-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: 53.24  E-value: 1.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594   14 CHGEQDTVALMATVACEIHhAHPLSdWTGFYRVTGPELLKIGPYQGAHGCLVIPFSRGVCGAAARTGRIQLVPDVEAFPD 93
Cdd:pfam13185   1 AADLEELLDAVLEAAVELG-ASAVG-FILLVDDDGRLAAWGGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPA 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 126102594   94 HIACSSTT---RSEIVLPVRNGeGRLLGVLDLDSNTPAAFTEEDAARLQAL 141
Cdd:pfam13185  79 KKGLPAGHaglRSFLSVPLVSG-GRVVGVLALGSNRPGAFDEEDLELLELL 128
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 66-141 3.51e-07

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: 46.61  E-value: 3.51e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594    66 IPFSRGVCGAAARTGRIQLVPDVEA---FPDHIACSST-TRSEIVLPVRNGeGRLLGVLDLDSNT-PAAFTEEDAARLQA 140
Cdd:smart00065  52 FPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQgVRSFLAVPLVAD-GELVGVLALHNKKsPRPFTEEDEELLQA 130


                   .
gi 126102594   141 L 141
Cdd:smart00065 131 L 131
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-147 1.50e-74

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 219.31  E-value: 1.50e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594   1 MDYDQLDQTIEALCHGEQDTVALMATVACEIHHAHPLSDWTGFYRVTGPELLKIGPYQGAHGCLVIPFSRGVCGAAARTG 80
Cdd:COG1956    7 EDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEG 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 126102594  81 RIQLVPDVEAFPDHIACSSTTRSEIVLPVRNgEGRLLGVLDLDSNTPAAFTEEDAARLQALLDRTFR 147
Cdd:COG1956   87 ETQLVPDVHAFPGHIACDSASRSEIVVPIFK-DGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAE 152
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 14-141 1.04e-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: 53.24  E-value: 1.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594   14 CHGEQDTVALMATVACEIHhAHPLSdWTGFYRVTGPELLKIGPYQGAHGCLVIPFSRGVCGAAARTGRIQLVPDVEAFPD 93
Cdd:pfam13185   1 AADLEELLDAVLEAAVELG-ASAVG-FILLVDDDGRLAAWGGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPA 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 126102594   94 HIACSSTT---RSEIVLPVRNGeGRLLGVLDLDSNTPAAFTEEDAARLQAL 141
Cdd:pfam13185  79 KKGLPAGHaglRSFLSVPLVSG-GRVVGVLALGSNRPGAFDEEDLELLELL 128
GAF COG2203
GAF domain [Signal transduction mechanisms];
66-141 1.02e-07

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 49.81  E-value: 1.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594  66 IPFSRGVCGAAARTGRIQLVPDVEAFPDHIACSST------TRSEIVLPVRNGeGRLLGVLDLDSNTPAAFTEEDAARLQ 139
Cdd:COG2203  256 LPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRElllalgIRSLLCVPLLVD-GRLIGVLALYSKEPRAFTEEDLELLE 334


                 ..
gi 126102594 140 AL 141
Cdd:COG2203  335 AL 336
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 66-141 3.51e-07

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: 46.61  E-value: 3.51e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594    66 IPFSRGVCGAAARTGRIQLVPDVEA---FPDHIACSST-TRSEIVLPVRNGeGRLLGVLDLDSNT-PAAFTEEDAARLQA 140
Cdd:smart00065  52 FPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQgVRSFLAVPLVAD-GELVGVLALHNKKsPRPFTEEDEELLQA 130


                   .
gi 126102594   141 L 141
Cdd:smart00065 131 L 131
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 39-141 2.67e-06

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: 44.01  E-value: 2.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594   39 DWTGFYRVTGPELLKIGPYQGAHGCLVIPFSRGVCGAAARTGRIQLVPDVEAFPDHIACSST-----TRSEIVLPVRNGe 113
Cdd:pfam01590  20 DRCALYLPDADGLEYLPPGARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAAGDPRFLDPLLLlrnfgIRSLLAVPIIDD- 98

                          90       100
                  ....*....|....*....|....*...
gi 126102594  114 GRLLGVLDLDSNTPaAFTEEDAARLQAL 141
Cdd:pfam01590  99 GELLGVLVLHHPRP-PFTEEELELLEVL 125
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
66-141 1.45e-05

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 42.96  E-value: 1.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126102594  66 IPFSRGVCGAAARTGRIQLVPDVEAFPDHIACSST----TRSEIVLPVRNGeGRLLGVLDLDSNTPAAFTEEDAARLQAL 141
Cdd:COG3605   69 LPLGEGLVGLVAERGEPLNLADAASHPRFKYFPETgeegFRSFLGVPIIRR-GRVLGVLVVQSREPREFTEEEVEFLVTL 147
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 101-141 2.73e-03

FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 442823 [Multi-domain]  Cd Length: 338  Bit Score: 36.75  E-value: 2.73e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 126102594 101 TRSEIVLPVRNGeGRLLGVLDLDSNTPAAFTEEDAARLQAL 141
Cdd:COG3604   73 RQLFLGVPLRVG-GEVLGVLTLDSRRPGAFSEEDLRLLETL 112
 
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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