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Conserved domains on  [gi|1551409143|gb|AZV79837|]
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GAF domain-containing protein [Parasedimentitalea marina]

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, ...
 2-150 2.42e-68

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 203.52  E-value: 2.42e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1551409143   2 TVDYIHLAKTIAALTEGESDQVALMATVTCEVHHSDDRFDWTGFYRVTAPEVLKIGPYQGGHGCLKIPFSRGVCGAAART 81
Cdd:COG1956     6 EEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAE 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1551409143  82 GEAQLVADVDAFEGHIACASSTRSELVLPVHDGfGALIGVFDIDSNVPDAFSQQDADALTAILSEVFGR 150
Cdd:COG1956    86 GETQLVPDVHAFPGHIACDSASRSEIVVPIFKD-GEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-150 2.42e-68

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 203.52  E-value: 2.42e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1551409143   2 TVDYIHLAKTIAALTEGESDQVALMATVTCEVHHSDDRFDWTGFYRVTAPEVLKIGPYQGGHGCLKIPFSRGVCGAAART 81
Cdd:COG1956     6 EEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAE 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1551409143  82 GEAQLVADVDAFEGHIACASSTRSELVLPVHDGfGALIGVFDIDSNVPDAFSQQDADALTAILSEVFGR 150
Cdd:COG1956    86 GETQLVPDVHAFPGHIACDSASRSEIVVPIFKD-GEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 57-147 3.53e-07

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: 46.69  E-value: 3.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1551409143  57 GPYQGGHGCLKIPFSRGVCGAAARTGEAQLVADVDA---FEGHIACASSTRSELVLPVHDGfGALIGVFDIDSNVPDAFS 133
Cdd:pfam13185  40 GAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAAdpaKKGLPAGHAGLRSFLSVPLVSG-GRVVGVLALGSNRPGAFD 118

                          90
                  ....*....|....
gi 1551409143 134 QQDADALTAILSEV 147
Cdd:pfam13185 119 EEDLELLELLAEQA 132
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-150 2.42e-68

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 203.52  E-value: 2.42e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1551409143   2 TVDYIHLAKTIAALTEGESDQVALMATVTCEVHHSDDRFDWTGFYRVTAPEVLKIGPYQGGHGCLKIPFSRGVCGAAART 81
Cdd:COG1956     6 EEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGGGELVLGPFQGPPACTRIPFGKGVCGTAAAE 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1551409143  82 GEAQLVADVDAFEGHIACASSTRSELVLPVHDGfGALIGVFDIDSNVPDAFSQQDADALTAILSEVFGR 150
Cdd:COG1956    86 GETQLVPDVHAFPGHIACDSASRSEIVVPIFKD-GEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 57-147 3.53e-07

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: 46.69  E-value: 3.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1551409143  57 GPYQGGHGCLKIPFSRGVCGAAARTGEAQLVADVDA---FEGHIACASSTRSELVLPVHDGfGALIGVFDIDSNVPDAFS 133
Cdd:pfam13185  40 GAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAAdpaKKGLPAGHAGLRSFLSVPLVSG-GRVVGVLALGSNRPGAFD 118

                          90
                  ....*....|....
gi 1551409143 134 QQDADALTAILSEV 147
Cdd:pfam13185 119 EEDLELLELLAEQA 132
GAF COG2203
GAF domain [Signal transduction mechanisms];
67-143 3.86e-07

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 48.27  E-value: 3.86e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1551409143  67 KIPFSRGVCGAAARTGEAQLVADVDAFEGHIACASS------TRSELVLPVHDGfGALIGVFDIDSNVPDAFSQQDADAL 140
Cdd:COG2203   255 RLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRElllalgIRSLLCVPLLVD-GRLIGVLALYSKEPRAFTEEDLELL 333


                  ...
gi 1551409143 141 TAI 143
Cdd:COG2203   334 EAL 336
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
68-143 1.29e-03

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 37.18  E-value: 1.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1551409143  68 IPFSRGVCGAAARTGEAQLVADVDAfegHIACASS-------TRSELVLPVHDGfGALIGVFDIDSNVPDAFSQQDADAL 140
Cdd:COG3605    69 LPLGEGLVGLVAERGEPLNLADAAS---HPRFKYFpetgeegFRSFLGVPIIRR-GRVLGVLVVQSREPREFTEEEVEFL 144


                  ...
gi 1551409143 141 TAI 143
Cdd:COG3605   145 VTL 147
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 40-143 9.93e-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: 34.38  E-value: 9.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1551409143  40 FDWTGFYRVTAPEVLKIGPYQGGHGCLKIPFSRGVCGAAARTGEAQLVADVDAFEGHIACASS-----TRSELVLPVHDG 114
Cdd:pfam01590  19 ADRCALYLPDADGLEYLPPGARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAAGDPRFLDPLLLlrnfgIRSLLAVPIIDD 98

                          90       100
                  ....*....|....*....|....*....
gi 1551409143 115 fGALIGVFDIDSNVPdAFSQQDADALTAI 143
Cdd:pfam01590  99 -GELLGVLVLHHPRP-PFTEEELELLEVL 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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