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Conserved domains on  [gi|446416485|ref|WP_000494340|]
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MULTISPECIES: GAF domain-containing protein [Bacillus]

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, ...
 8-158 1.48e-92

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 265.15  E-value: 1.48e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485   8 AGSRVQQYETVIKQLDALLTGESNVVANLSNASALLNQFLDRVNWVGFYVTEG-NQLVLGPFQGMPACVRIPFGRGVCGV 86
Cdd:COG1956    2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGT 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446416485  87 AAETKTTQLVADVHQFPGHIACDSASNSEIVVPIVKEGAVIGVLDIDSPEKNRFDEVDQRYLEKFVETLLKH 158
Cdd:COG1956   82 AAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-158 1.48e-92

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 265.15  E-value: 1.48e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485   8 AGSRVQQYETVIKQLDALLTGESNVVANLSNASALLNQFLDRVNWVGFYVTEG-NQLVLGPFQGMPACVRIPFGRGVCGV 86
Cdd:COG1956    2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGT 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446416485  87 AAETKTTQLVADVHQFPGHIACDSASNSEIVVPIVKEGAVIGVLDIDSPEKNRFDEVDQRYLEKFVETLLKH 158
Cdd:COG1956   82 AAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 48-149 1.70e-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: 60.94  E-value: 1.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485   48 DRVNWVGFYVTEGNQLVLG-PFQGMPACVRIPFGRGVCGVAAETKTTQLVADVHQFPGHI---ACDSASNSEIVVPIVKE 123
Cdd:pfam13185  21 SAVGFILLVDDDGRLAAWGgAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSG 100

                          90       100
                  ....*....|....*....|....*.
gi 446416485  124 GAVIGVLDIDSPEKNRFDEVDQRYLE 149
Cdd:pfam13185 101 GRVVGVLALGSNRPGAFDEEDLELLE 126
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 36-151 1.98e-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: 47.76  E-value: 1.98e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485    36 LSNASALLNQFL--DRVNWVGFYVTEGNQLVLGPFQG-MPAC--VRIPFGRGVCGVAAETKTTQLVADVHQ---FPGHIA 107
Cdd:smart00065   6 LQTILEELRQLLgaDRVLIYLVDENDRGELVLVAADGlTLPTlgIRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLL 85

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 446416485   108 CD-SASNSEIVVPIVKEGAVIGVLDIDSPEKNR-FDEVDQRYLEKF 151
Cdd:smart00065  86 GRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQAL 131
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-158 1.48e-92

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 265.15  E-value: 1.48e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485   8 AGSRVQQYETVIKQLDALLTGESNVVANLSNASALLNQFLDRVNWVGFYVTEG-NQLVLGPFQGMPACVRIPFGRGVCGV 86
Cdd:COG1956    2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGT 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446416485  87 AAETKTTQLVADVHQFPGHIACDSASNSEIVVPIVKEGAVIGVLDIDSPEKNRFDEVDQRYLEKFVETLLKH 158
Cdd:COG1956   82 AAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 48-149 1.70e-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: 60.94  E-value: 1.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485   48 DRVNWVGFYVTEGNQLVLG-PFQGMPACVRIPFGRGVCGVAAETKTTQLVADVHQFPGHI---ACDSASNSEIVVPIVKE 123
Cdd:pfam13185  21 SAVGFILLVDDDGRLAAWGgAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSG 100

                          90       100
                  ....*....|....*....|....*.
gi 446416485  124 GAVIGVLDIDSPEKNRFDEVDQRYLE 149
Cdd:pfam13185 101 GRVVGVLALGSNRPGAFDEEDLELLE 126
GAF COG2203
GAF domain [Signal transduction mechanisms];
11-155 3.67e-12

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 63.29  E-value: 3.67e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485  11 RVQQYETVIKQLDALLTGESNVVANLSNASALLNQFL--DRVnWVGFYVTEGNQLVL--GPFQGMPACVRIPFGRGVCGV 86
Cdd:COG2203  187 LELERLALLNEISQALRSALDLEELLQRILELAGELLgaDRG-AILLVDEDGGELELvaAPGLPEEELGRLPLGEGLAGR 265

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446416485  87 AAETKTTQLVADVHQFPGHIACDSAS------NSEIVVPIVKEGAVIGVLDIDSPEKNRFDEVDQRYLEKFVETL 155
Cdd:COG2203  266 ALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEALADQA 340
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
20-155 5.27e-12

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 60.68  E-value: 5.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485  20 KQLDALLTGeSNVVANLSNASALLNQFLDRVNW--------VGFYVTEGNQLVLGPFQGMPAC----VRIPFGRGVCGVA 87
Cdd:COG3605    1 EMLKALRRI-SEAVASALDLDEALDRIVRRIAEalgvdvcsIYLLDPDGGRLELRATEGLNPEavgkVRLPLGEGLVGLV 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446416485  88 AETKTTQLVADVHQFPGHIACDSA----SNSEIVVPIVKEGAVIGVLDIDSPEKNRFDEVDqrylEKFVETL 155
Cdd:COG3605   80 AERGEPLNLADAASHPRFKYFPETgeegFRSFLGVPIIRRGRVLGVLVVQSREPREFTEEE----VEFLVTL 147
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 36-151 1.98e-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: 47.76  E-value: 1.98e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485    36 LSNASALLNQFL--DRVNWVGFYVTEGNQLVLGPFQG-MPAC--VRIPFGRGVCGVAAETKTTQLVADVHQ---FPGHIA 107
Cdd:smart00065   6 LQTILEELRQLLgaDRVLIYLVDENDRGELVLVAADGlTLPTlgIRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLL 85

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 446416485   108 CD-SASNSEIVVPIVKEGAVIGVLDIDSPEKNR-FDEVDQRYLEKF 151
Cdd:smart00065  86 GRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQAL 131
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 116-151 2.61e-05

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: 42.91  E-value: 2.61e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446416485 116 IVVPIVKEGAVIGVLDIDSPEKNRFDEVDQRYLEKF 151
Cdd:COG3604   77 LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETL 112
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 36-155 1.60e-04

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: 39.38  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446416485   36 LSNASALLNQFLDrVNWVGFYVTEGNQLVL---GPFQGMPACVRIPFGRGVcgVAAETKTTQLVADV-----HQFPGHIA 107
Cdd:pfam01590   6 LQTILEELRELLG-ADRCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAagdprFLDPLLLL 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 446416485  108 CDSASNSEIVVPIVKEGAVIGVLDIDSPeKNRFDEVDQRYLEKFVETL 155
Cdd:pfam01590  83 RNFGIRSLLAVPIIDDGELLGVLVLHHP-RPPFTEEELELLEVLADQV 129
 
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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