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Conserved domains on  [gi|565849319|ref|WP_023932077|]
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GAF domain-containing protein [Photobacterium leiognathi]

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, ...
 2-152 2.17e-86

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 249.36  E-value: 2.17e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 565849319   2 ENTRSFYDRLTRQAVALIEGETDLIANMSNISALLNMELEQINWVGFYLLK-DNELVLGPFQGKPACVRIPVGKGVCGTA 80
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 565849319  81 VKDNKVQRVDDVHAFPGHIACDAVSQSEIVIPLNVRGKCIGVLDIDSPYLSRFDQNDEQGLVSLVEALQKVL 152
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-152 2.17e-86

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 249.36  E-value: 2.17e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 565849319   2 ENTRSFYDRLTRQAVALIEGETDLIANMSNISALLNMELEQINWVGFYLLK-DNELVLGPFQGKPACVRIPVGKGVCGTA 80
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 565849319  81 VKDNKVQRVDDVHAFPGHIACDAVSQSEIVIPLNVRGKCIGVLDIDSPYLSRFDQNDEQGLVSLVEALQKVL 152
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 32-146 8.16e-08

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: 48.23  E-value: 8.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 565849319   32 ISALLNMELEQINWVGFYLLKDNELVLG-PFQGKPACVRIPVGKGVCGTAVKDNKVQRVDDVHAFPGHI---ACDAVSQS 107
Cdd:pfam13185  12 LEAAVELGASAVGFILLVDDDGRLAAWGgAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRS 91

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 565849319  108 EIVIPLNVRGKCIGVLDIDSPYLSRFDQNDEQGLVSLVE 146
Cdd:pfam13185  92 FLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAE 130
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 68-141 3.82e-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: 3.82e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 565849319    68 VRIPVGKGVCGTAVKDNKVQRVDDVHA---FPGHIACDAVS-QSEIVIPLNVRGKCIGVLDIDSPYLSR-FDQNDEQGL 141
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQGvRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELL 128
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-152 2.17e-86

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 249.36  E-value: 2.17e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 565849319   2 ENTRSFYDRLTRQAVALIEGETDLIANMSNISALLNMELEQINWVGFYLLK-DNELVLGPFQGKPACVRIPVGKGVCGTA 80
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 565849319  81 VKDNKVQRVDDVHAFPGHIACDAVSQSEIVIPLNVRGKCIGVLDIDSPYLSRFDQNDEQGLVSLVEALQKVL 152
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF COG2203
GAF domain [Signal transduction mechanisms];
10-144 4.81e-08

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 50.96  E-value: 4.81e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 565849319  10 RLTRQAVALIEGETDLIANMSNISALLnMELEQINWVGFYLLKDN----ELVLGPFQGKPACVRIPVGKGVCGTAVKDNK 85
Cdd:COG2203  193 ALLNEISQALRSALDLEELLQRILELA-GELLGADRGAILLVDEDggelELVAAPGLPEEELGRLPLGEGLAGRALRTGE 271

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 565849319  86 VQRVDDVHAFPGHIACDAVS------QSEIVIPLNVRGKCIGVLDIDSPYLSRFDQNDEQGLVSL 144
Cdd:COG2203  272 PVVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEAL 336
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 32-146 8.16e-08

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: 48.23  E-value: 8.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 565849319   32 ISALLNMELEQINWVGFYLLKDNELVLG-PFQGKPACVRIPVGKGVCGTAVKDNKVQRVDDVHAFPGHI---ACDAVSQS 107
Cdd:pfam13185  12 LEAAVELGASAVGFILLVDDDGRLAAWGgAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRS 91

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 565849319  108 EIVIPLNVRGKCIGVLDIDSPYLSRFDQNDEQGLVSLVE 146
Cdd:pfam13185  92 FLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAE 130
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 68-141 3.82e-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: 3.82e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 565849319    68 VRIPVGKGVCGTAVKDNKVQRVDDVHA---FPGHIACDAVS-QSEIVIPLNVRGKCIGVLDIDSPYLSR-FDQNDEQGL 141
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQGvRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELL 128
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
68-148 1.04e-06

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 46.04  E-value: 1.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 565849319  68 VRIPVGKGVCGTAVKDNKVQRVDDVHAFPGHIACDAVSQ----SEIVIPLNVRGKCIGVLDIDSPYLSRFDQNDEQGLVS 143
Cdd:COG3605   67 VRLPLGEGLVGLVAERGEPLNLADAASHPRFKYFPETGEegfrSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFLVT 146


                 ....*
gi 565849319 144 LVEAL 148
Cdd:COG3605  147 LAAQL 151
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 29-148 1.38e-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: 36.69  E-value: 1.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 565849319   29 MSNISALLNMEleqinWVGFYLLKDNELVL---GPFQGKPACVRIPVGKGVcgTAVKDNKVQRVDDVHAFPGHIACDAV- 104
Cdd:pfam01590  10 LEELRELLGAD-----RCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAAGDPRFLDPLLLl 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 565849319  105 ----SQSEIVIPLNVRGKCIGVLDIDSPYlSRFDQNDEQGLVSLVEAL 148
Cdd:pfam01590  83 rnfgIRSLLAVPIIDDGELLGVLVLHHPR-PPFTEEELELLEVLADQV 129
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 109-139 7.23e-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: 35.59  E-value: 7.23e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 565849319 109 IVIPLNVRGKCIGVLDIDSPYLSRFDQNDEQ 139
Cdd:COG3604   77 LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLR 107
 
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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