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Conserved domains on  [gi|1132288715|ref|WP_075948167|]
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GAF domain-containing protein [Pseudomonas reinekei]

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, ...
 14-159 3.56e-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: 246.66  E-value: 3.56e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715  14 YGMLHAQLESLLADERDFIANAAQFSAFLFNQLDDLNWAGFYL-NRNEELVLGPFQGQIACVRIPFGRGVCGTAAATLQT 92
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGET 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1132288715  93 QRVEDVHAFPGHIACDSASNSELVVPLVKDGRLIGVLDLDSPKLARFTAQDQAGIEQLAAIFLHLTD 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 3.56e-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: 246.66  E-value: 3.56e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715  14 YGMLHAQLESLLADERDFIANAAQFSAFLFNQLDDLNWAGFYL-NRNEELVLGPFQGQIACVRIPFGRGVCGTAAATLQT 92
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGET 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1132288715  93 QRVEDVHAFPGHIACDSASNSELVVPLVKDGRLIGVLDLDSPKLARFTAQDQAGIEQLAAIFLHLTD 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 ...
 65-152 3.95e-11

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: 57.48  E-value: 3.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715  65 GPFQGQIACVRIPFGRGVCGTAAATLQTQRVEDVHAFPGHI---ACDSASNSELVVPLVKDGRLIGVLDLDSPKLARFTA 141
Cdd:pfam13185  40 GAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDE 119

                          90
                  ....*....|.
gi 1132288715 142 QDQAGIEQLAA 152
Cdd:pfam13185 120 EDLELLELLAE 130
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 74-152 9.77e-08

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: 48.53  E-value: 9.77e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715   74 VRIPFGRGVCGTAAATLQTQRVEDVHA---FPGHIACD-SASNSELVVPLVKDGRLIGVLDLDSPKLAR-FTAQDQAGIE 148
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ....
gi 1132288715  149 QLAA 152
Cdd:smart00065 130 ALAN 133
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
117-153 5.38e-03

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 36.30  E-value: 5.38e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1132288715 117 VPLVKDGRLIGVLDLDSPKLARFTAQDQAGIEQLAAI 153
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAAL 151
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 14-159 3.56e-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: 246.66  E-value: 3.56e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715  14 YGMLHAQLESLLADERDFIANAAQFSAFLFNQLDDLNWAGFYL-NRNEELVLGPFQGQIACVRIPFGRGVCGTAAATLQT 92
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAEGET 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1132288715  93 QRVEDVHAFPGHIACDSASNSELVVPLVKDGRLIGVLDLDSPKLARFTAQDQAGIEQLAAIFLHLTD 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 ...
 65-152 3.95e-11

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: 57.48  E-value: 3.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715  65 GPFQGQIACVRIPFGRGVCGTAAATLQTQRVEDVHAFPGHI---ACDSASNSELVVPLVKDGRLIGVLDLDSPKLARFTA 141
Cdd:pfam13185  40 GAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDE 119

                          90
                  ....*....|.
gi 1132288715 142 QDQAGIEQLAA 152
Cdd:pfam13185 120 EDLELLELLAE 130
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
74-152 6.61e-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: 6.61e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715  74 VRIPFGRGVCGTAAATLQTQRVEDVHAFPGHIACDSA----SNSELVVPLVKDGRLIGVLDLDSPKLARFTAQDQAGIEQ 149
Cdd:COG3605    67 VRLPLGEGLVGLVAERGEPLNLADAASHPRFKYFPETgeegFRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFLVT 146


                  ...
gi 1132288715 150 LAA 152
Cdd:COG3605   147 LAA 149
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 74-152 9.77e-08

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: 48.53  E-value: 9.77e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715   74 VRIPFGRGVCGTAAATLQTQRVEDVHA---FPGHIACD-SASNSELVVPLVKDGRLIGVLDLDSPKLAR-FTAQDQAGIE 148
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ....
gi 1132288715  149 QLAA 152
Cdd:smart00065 130 ALAN 133
GAF COG2203
GAF domain [Signal transduction mechanisms];
75-153 2.72e-06

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 45.95  E-value: 2.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715  75 RIPFGRGVCGTAAATLQTQRVEDVHAFPGHIACDSAS------NSELVVPLVKDGRLIGVLDLDSPKLARFTAQDQAGIE 148
Cdd:COG2203   255 RLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLE 334


                  ....*
gi 1132288715 149 QLAAI 153
Cdd:COG2203   335 ALADQ 339
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 48-152 4.03e-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: 4.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132288715  48 DLNWAGFYLNR---NEELVLGPFQGQIACVRIPFGRGVcgTAAATLQTQRVEDV-----HAFPGHIACDSASNSELVVPL 119
Cdd:pfam01590  18 GADRCALYLPDadgLEYLPPGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAagdprFLDPLLLLRNFGIRSLLAVPI 95

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1132288715 120 VKDGRLIGVLDLDSPKlARFTAQDQAGIEQLAA 152
Cdd:pfam01590  96 IDDGELLGVLVLHHPR-PPFTEEELELLEVLAD 127
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 115-154 2.61e-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: 39.83  E-value: 2.61e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1132288715 115 LVVPLVKDGRLIGVLDLDSPKLARFTAQDQAGIEQLAAIF 154
Cdd:COG3604    77 LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLA 116
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
117-153 5.38e-03

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 36.30  E-value: 5.38e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1132288715 117 VPLVKDGRLIGVLDLDSPKLARFTAQDQAGIEQLAAI 153
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAAL 151
 
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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