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Conserved domains on  [gi|1342405021|gb|AVB21389|]
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GAF domain-containing protein [Pseudomonas avellanae]

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, ...
 14-159 4.62e-82

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 238.57  E-value: 4.62e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  14 YALLAAQLESLLADERDFIANAAQFSAFLYTQIDDLNWAGFYL-NRDEELVLGPFQGQIACVRIPFGRGVCGVAAQSRQT 92
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGET 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1342405021  93 QRVQDVHAFAGHIACDSASNSELVVPLVKDGRLVGVLDLDSPSVGRFSEVDQAGVERLAAIFLAATD 159
Cdd:COG1956    89 QLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 14-159 4.62e-82

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 238.57  E-value: 4.62e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  14 YALLAAQLESLLADERDFIANAAQFSAFLYTQIDDLNWAGFYL-NRDEELVLGPFQGQIACVRIPFGRGVCGVAAQSRQT 92
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGET 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1342405021  93 QRVQDVHAFAGHIACDSASNSELVVPLVKDGRLVGVLDLDSPSVGRFSEVDQAGVERLAAIFLAATD 159
Cdd:COG1956    89 QLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 55-152 3.52e-10

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: 54.78  E-value: 3.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  55 YLNRDEELVL--GPFQGQIACVRIPFGRGVCGVAAQSRQTQRVQDV---HAFAGHIACDSASNSELVVPLVKDGRLVGVL 129
Cdd:pfam13185  28 LVDDDGRLAAwgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGRVVGVL 107

                          90       100
                  ....*....|....*....|...
gi 1342405021 130 DLDSPSVGRFSEVDQAGVERLAA 152
Cdd:pfam13185 108 ALGSNRPGAFDEEDLELLELLAE 130
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 74-152 1.00e-06

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: 45.84  E-value: 1.00e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021   74 VRIPFGRGVCGVAAQSRQTQRVQDVHA---FAGHIACD-SASNSELVVPLVKDGRLVGVLDLDSPSVGR-FSEVDQAGVE 148
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ....
gi 1342405021  149 RLAA 152
Cdd:smart00065 130 ALAN 133
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
117-158 1.71e-04

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 40.54  E-value: 1.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1342405021 117 VPLVKDGRLVGVLDLDSPSVGRFSEVDQAGVERLAAifLAAT 158
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAA--LAAA 154
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 14-159 4.62e-82

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 238.57  E-value: 4.62e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  14 YALLAAQLESLLADERDFIANAAQFSAFLYTQIDDLNWAGFYL-NRDEELVLGPFQGQIACVRIPFGRGVCGVAAQSRQT 92
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGET 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1342405021  93 QRVQDVHAFAGHIACDSASNSELVVPLVKDGRLVGVLDLDSPSVGRFSEVDQAGVERLAAIFLAATD 159
Cdd:COG1956    89 QLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 55-152 3.52e-10

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: 54.78  E-value: 3.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  55 YLNRDEELVL--GPFQGQIACVRIPFGRGVCGVAAQSRQTQRVQDV---HAFAGHIACDSASNSELVVPLVKDGRLVGVL 129
Cdd:pfam13185  28 LVDDDGRLAAwgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGRVVGVL 107

                          90       100
                  ....*....|....*....|...
gi 1342405021 130 DLDSPSVGRFSEVDQAGVERLAA 152
Cdd:pfam13185 108 ALGSNRPGAFDEEDLELLELLAE 130
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
74-152 1.57e-07

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 48.35  E-value: 1.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  74 VRIPFGRGVCGVAAQSRQTQRVQDVHAfagHIACDSAS-------NSELVVPLVKDGRLVGVLDLDSPSVGRFSEVDQAG 146
Cdd:COG3605    67 VRLPLGEGLVGLVAERGEPLNLADAAS---HPRFKYFPetgeegfRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEF 143


                  ....*.
gi 1342405021 147 VERLAA 152
Cdd:COG3605   144 LVTLAA 149
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 74-152 1.00e-06

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: 45.84  E-value: 1.00e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021   74 VRIPFGRGVCGVAAQSRQTQRVQDVHA---FAGHIACD-SASNSELVVPLVKDGRLVGVLDLDSPSVGR-FSEVDQAGVE 148
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ....
gi 1342405021  149 RLAA 152
Cdd:smart00065 130 ALAN 133
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 32-157 4.66e-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: 42.14  E-value: 4.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  32 IANAAQFSAFLYTQIDDLNWAGFYLNRDEELVLGPFQGQIACVRIPFGRGVCGVAAQSRQTQRVQDVHAFAGHIACdsas 111
Cdd:COG3604     1 ALLALRLLGLPLLLLLALALLLLVLLLLALLLRGDLLASALVLEESLELLALALSEALLAAQARQAALAARERQLF---- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1342405021 112 nseLVVPLVKDGRLVGVLDLDSPSVGRFSEVDQAGVERLAAIFLAA 157
Cdd:COG3604    77 ---LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLAAVA 119
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 48-152 5.07e-05

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: 40.93  E-value: 5.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  48 DLNWAGFYLNRDEELVL---GPFQGQIACVRIPFGRGVcgVAAQSRQTQRVQDV-----HAFAGHIACDSASNSELVVPL 119
Cdd:pfam01590  18 GADRCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAagdprFLDPLLLLRNFGIRSLLAVPI 95

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1342405021 120 VKDGRLVGVLDLDSPSvGRFSEVDQAGVERLAA 152
Cdd:pfam01590  96 IDDGELLGVLVLHHPR-PPFTEEELELLEVLAD 127
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
117-158 1.71e-04

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 40.54  E-value: 1.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1342405021 117 VPLVKDGRLVGVLDLDSPSVGRFSEVDQAGVERLAAifLAAT 158
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAA--LAAA 154
GAF COG2203
GAF domain [Signal transduction mechanisms];
75-153 4.83e-04

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 39.41  E-value: 4.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1342405021  75 RIPFGRGVCGVAAQSRQTQRVQDVHAFAGHIACDSAS------NSELVVPLVKDGRLVGVLDLDSPSVGRFSEVDQAGVE 148
Cdd:COG2203   255 RLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLE 334


                  ....*
gi 1342405021 149 RLAAI 153
Cdd:COG2203   335 ALADQ 339
 
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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