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Conserved domains on  [gi|1747407832|ref|WP_149981051|]
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MULTISPECIES: GAF domain-containing protein [Pseudoalteromonas]

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, ...
 1-153 2.18e-89

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 257.06  E-value: 2.18e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832   1 MQKQEFYQSLVKQTESLITGEPNIIANMANISALLFTSLDDVNWAGFYLMDSPTELVLGPFQGNPACIRIPVGKGVCGTA 80
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1747407832  81 AATAQTQLVEDVHAFAGHIACDAASNSEIVIPIHKNGEVFAVLDIDSPSIARFDADDKQGLEALIACFEATIA 153
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-153 2.18e-89

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 257.06  E-value: 2.18e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832   1 MQKQEFYQSLVKQTESLITGEPNIIANMANISALLFTSLDDVNWAGFYLMDSPTELVLGPFQGNPACIRIPVGKGVCGTA 80
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1747407832  81 AATAQTQLVEDVHAFAGHIACDAASNSEIVIPIHKNGEVFAVLDIDSPSIARFDADDKQGLEALIACFEATIA 153
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 45-144 1.36e-09

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: 53.24  E-value: 1.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832  45 AGFYLMDSPTELVL---GPFQGNPACIRIPVGKGVCGTAAATAQTQLVEDV---HAFAGHIACDAASNSEIVIPIHKNGE 118
Cdd:pfam13185  23 VGFILLVDDDGRLAawgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGR 102

                          90       100
                  ....*....|....*....|....*.
gi 1747407832 119 VFAVLDIDSPSIARFDADDKQGLEAL 144
Cdd:pfam13185 103 VVGVLALGSNRPGAFDEEDLELLELL 128
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 68-144 4.18e-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: 4.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832   68 IRIPVGKGVCGTAAATAQTQLVEDVHA---FAGHIACDA-ASNSEIVIPIHKNGEVFAVLDIDSPSIAR-FDADDKQGLE 142
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ..
gi 1747407832  143 AL 144
Cdd:smart00065 130 AL 131
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-153 2.18e-89

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 257.06  E-value: 2.18e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832   1 MQKQEFYQSLVKQTESLITGEPNIIANMANISALLFTSLDDVNWAGFYLMDSPTELVLGPFQGNPACIRIPVGKGVCGTA 80
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1747407832  81 AATAQTQLVEDVHAFAGHIACDAASNSEIVIPIHKNGEVFAVLDIDSPSIARFDADDKQGLEALIACFEATIA 153
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 45-144 1.36e-09

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: 53.24  E-value: 1.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832  45 AGFYLMDSPTELVL---GPFQGNPACIRIPVGKGVCGTAAATAQTQLVEDV---HAFAGHIACDAASNSEIVIPIHKNGE 118
Cdd:pfam13185  23 VGFILLVDDDGRLAawgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGR 102

                          90       100
                  ....*....|....*....|....*.
gi 1747407832 119 VFAVLDIDSPSIARFDADDKQGLEAL 144
Cdd:pfam13185 103 VVGVLALGSNRPGAFDEEDLELLELL 128
GAF COG2203
GAF domain [Signal transduction mechanisms];
41-144 2.98e-09

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 54.43  E-value: 2.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832  41 DVNWAGFYLMDSPT---ELVLGPFQGNPACIRIPVGKGVCGTAAATAQTQLVEDVHAFAGHIACDAAS------NSEIVI 111
Cdd:COG2203   224 GADRGAILLVDEDGgelELVAAPGLPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCV 303

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1747407832 112 PIHKNGEVFAVLDIDSPSIARFDADDKQGLEAL 144
Cdd:COG2203   304 PLLVDGRLIGVLALYSKEPRAFTEEDLELLEAL 336
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 68-144 4.18e-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: 4.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832   68 IRIPVGKGVCGTAAATAQTQLVEDVHA---FAGHIACDA-ASNSEIVIPIHKNGEVFAVLDIDSPSIAR-FDADDKQGLE 142
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ..
gi 1747407832  143 AL 144
Cdd:smart00065 130 AL 131
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
68-144 8.93e-07

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: 8.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832  68 IRIPVGKGVCGTAAATAQTQLVEDVHAfagHIACDAAS-------NSEIVIPIHKNGEVFAVLDIDSPSIARFDADDKQG 140
Cdd:COG3605    67 VRLPLGEGLVGLVAERGEPLNLADAAS---HPRFKYFPetgeegfRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEF 143


                  ....
gi 1747407832 141 LEAL 144
Cdd:COG3605   144 LVTL 147
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 41-144 1.16e-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: 42.47  E-value: 1.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747407832  41 DVNWAGFYLMDSPTELVLGPFQGNPACIRIPVGKGVCGTAAATAQTQLVEDV-----HAFAGHIACDAASNSEIVIPIHK 115
Cdd:pfam01590  18 GADRCALYLPDADGLEYLPPGARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAagdprFLDPLLLLRNFGIRSLLAVPIID 97

                          90       100
                  ....*....|....*....|....*....
gi 1747407832 116 NGEVFAVLDIDSPSiARFDADDKQGLEAL 144
Cdd:pfam01590  98 DGELLGVLVLHHPR-PPFTEEELELLEVL 125
 
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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