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Conserved domains on  [gi|404236527|emb|CBY57929|]
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GAF domain protein [Listeria monocytogenes SLCC2479]

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, ...
 8-162 7.12e-85

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 245.89  E-value: 7.12e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527   8 TGTKEENYALALKQVQAMIHGEPNLIANLSNVSSIINQALSDINWVGFYLLEKEtNQLVLGPFQGLPACIRIPLGKGVCG 87
Cdd:COG1956    2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGG-GELVLGPFQGPPACTRIPFGKGVCG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 404236527  88 SAASDQKTYIVENVHDFPGHIACDAASNSEIVLPIVKNNQLLGVLDIDSPLFNRFNEVDQLWLEKIRDAIVQEIN 162
Cdd:COG1956   81 TAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-162 7.12e-85

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 245.89  E-value: 7.12e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527   8 TGTKEENYALALKQVQAMIHGEPNLIANLSNVSSIINQALSDINWVGFYLLEKEtNQLVLGPFQGLPACIRIPLGKGVCG 87
Cdd:COG1956    2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGG-GELVLGPFQGPPACTRIPFGKGVCG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 404236527  88 SAASDQKTYIVENVHDFPGHIACDAASNSEIVLPIVKNNQLLGVLDIDSPLFNRFNEVDQLWLEKIRDAIVQEIN 162
Cdd:COG1956   81 TAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 34-151 2.30e-12

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: 60.56  E-value: 2.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527   34 ANLSNVSSIINQALSDINW--VGFYLLEKETNQLVL--GPFQGLPACIRIPLGKGVCGSAASDQKTYIVENVHDFPGHI- 108
Cdd:pfam13185   2 ADLEELLDAVLEAAVELGAsaVGFILLVDDDGRLAAwgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKg 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 404236527  109 --ACDAASNSEIVLPIVKNNQLLGVLDIDSPLFNRFNEVDQLWLE 151
Cdd:pfam13185  82 lpAGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLE 126
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 52-147 7.31e-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: 40.83  E-value: 7.31e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527    52 WVGFYLL-EKETNQLVLGPFQGL-PAC--IRIPLGKGVCGSAASDQKTYIVENVHD---FPGHIACDA-ASNSEIVLPIV 123
Cdd:smart00065  21 RVLIYLVdENDRGELVLVAADGLtLPTlgIRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYqGVRSFLAVPLV 100

                           90       100
                   ....*....|....*....|....*
gi 404236527   124 KNNQLLGVLDIDSPLFNR-FNEVDQ 147
Cdd:smart00065 101 ADGELVGVLALHNKKSPRpFTEEDE 125
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-162 7.12e-85

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 245.89  E-value: 7.12e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527   8 TGTKEENYALALKQVQAMIHGEPNLIANLSNVSSIINQALSDINWVGFYLLEKEtNQLVLGPFQGLPACIRIPLGKGVCG 87
Cdd:COG1956    2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGG-GELVLGPFQGPPACTRIPFGKGVCG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 404236527  88 SAASDQKTYIVENVHDFPGHIACDAASNSEIVLPIVKNNQLLGVLDIDSPLFNRFNEVDQLWLEKIRDAIVQEIN 162
Cdd:COG1956   81 TAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 34-151 2.30e-12

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: 60.56  E-value: 2.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527   34 ANLSNVSSIINQALSDINW--VGFYLLEKETNQLVL--GPFQGLPACIRIPLGKGVCGSAASDQKTYIVENVHDFPGHI- 108
Cdd:pfam13185   2 ADLEELLDAVLEAAVELGAsaVGFILLVDDDGRLAAwgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKg 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 404236527  109 --ACDAASNSEIVLPIVKNNQLLGVLDIDSPLFNRFNEVDQLWLE 151
Cdd:pfam13185  82 lpAGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLE 126
GAF COG2203
GAF domain [Signal transduction mechanisms];
18-161 1.30e-11

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 61.75  E-value: 1.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527  18 ALKQVQAMIHGEPNLIANLSNVSSIINQALsDINWVGFYLLEKETNQLVLGPFQGLPA--CIRIPLGKGVCGSAASDQKT 95
Cdd:COG2203  194 LLNEISQALRSALDLEELLQRILELAGELL-GADRGAILLVDEDGGELELVAAPGLPEeeLGRLPLGEGLAGRALRTGEP 272

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 404236527  96 YIVENVHDFPGHIACDAAS------NSEIVLPIVKNNQLLGVLDIDSPLFNRFNEVDQLWLEKIRDAIVQEI 161
Cdd:COG2203  273 VVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEALADQAAIAI 344
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
56-151 7.77e-08

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 49.51  E-value: 7.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527  56 YLLEKETNQLVLGPFQGLPAC----IRIPLGKGVCGSAASDQKTYIVENVHDFPGHIACDAA----SNSEIVLPIVKNNQ 127
Cdd:COG3605   42 YLLDPDGGRLELRATEGLNPEavgkVRLPLGEGLVGLVAERGEPLNLADAASHPRFKYFPETgeegFRSFLGVPIIRRGR 121

                         90       100
                 ....*....|....*....|....
gi 404236527 128 LLGVLDIDSPLFNRFNEVDQLWLE 151
Cdd:COG3605  122 VLGVLVVQSREPREFTEEEVEFLV 145
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 52-147 7.31e-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: 40.83  E-value: 7.31e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527    52 WVGFYLL-EKETNQLVLGPFQGL-PAC--IRIPLGKGVCGSAASDQKTYIVENVHD---FPGHIACDA-ASNSEIVLPIV 123
Cdd:smart00065  21 RVLIYLVdENDRGELVLVAADGLtLPTlgIRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYqGVRSFLAVPLV 100

                           90       100
                   ....*....|....*....|....*
gi 404236527   124 KNNQLLGVLDIDSPLFNR-FNEVDQ 147
Cdd:smart00065 101 ADGELVGVLALHNKKSPRpFTEEDE 125
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 118-161 1.44e-04

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: 40.99  E-value: 1.44e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 404236527 118 IVLPIVKNNQLLGVLDIDSPLFNRFNEVDQLWLEKIRDAIVQEI 161
Cdd:COG3604   77 LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLAAVAI 120
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 31-161 8.36e-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: 34.76  E-value: 8.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404236527   31 NLIANLSNVSSIINQALsDINWVGFYLLEKE-TNQLVLGPFQGLPACIRIPLGKGVcgSAASDQKTYIVENV-----HDF 104
Cdd:pfam01590   1 DLEEILQTILEELRELL-GADRCALYLPDADgLEYLPPGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAagdprFLD 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 404236527  105 PGHIACDAASNSEIVLPIVKNNQLLGVLDIDSPlFNRFNEVDQLWLEKIRDAIVQEI 161
Cdd:pfam01590  78 PLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHP-RPPFTEEELELLEVLADQVAIAL 133
 
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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