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Conserved domains on  [gi|76562247|gb|ABA44831|]
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GAF domain protein [Streptococcus agalactiae A909]

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, ...
 22-156 5.03e-66

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 198.51  E-value: 5.03e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247  22 SDETNALANLSNASAMLNAMLPNSVFTGFYLFDG-EELILGPFQGGVSCVHITLGKGVCGESAQTAKTLIVDDVTKHANY 100
Cdd:COG1956  21 AGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLVPDVHAFPGH 100

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 76562247 101 ISCDSKAMSEIVVPMFKNGKLLGVLDLDSSLVADYDEIDQEYLEKFVGILVEHTIW 156
Cdd:COG1956 101 IACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 22-156 5.03e-66

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 198.51  E-value: 5.03e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247  22 SDETNALANLSNASAMLNAMLPNSVFTGFYLFDG-EELILGPFQGGVSCVHITLGKGVCGESAQTAKTLIVDDVTKHANY 100
Cdd:COG1956  21 AGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLVPDVHAFPGH 100

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 76562247 101 ISCDSKAMSEIVVPMFKNGKLLGVLDLDSSLVADYDEIDQEYLEKFVGILVEHTIW 156
Cdd:COG1956 101 IACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 50-144 6.42e-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: 54.39  E-value: 6.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247    50 FYLFDGEELIL---GPFQGGVSCVHITLGKGVCGESAQTAKTLIVDDVTKHANYIS---CDSKAMSEIVVPMFKNGKLLG 123
Cdd:pfam13185  26 ILLVDDDGRLAawgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKGlpaGHAGLRSFLSVPLVSGGRVVG 105

                          90       100
                  ....*....|....*....|.
gi 76562247   124 VLDLDSSLVADYDEIDQEYLE 144
Cdd:pfam13185 106 VLALGSNRPGAFDEEDLELLE 126
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 70-154 2.27e-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: 45.06  E-value: 2.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247     70 VHITLGKGVCGESAQTAKTLIVDDVTKHANY------ISCDSKAMseIVVPMFKNGKLLGVLDLDSSLVAD-YDEIDQEY 142
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEADPLFaedllgRYQGVRSF--LAVPLVADGELVGVLALHNKKSPRpFTEEDEEL 127

                           90
                   ....*....|....*
gi 76562247    143 LEKF---VGILVEHT 154
Cdd:smart00065 128 LQALanqLAIALANA 142
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 22-156 5.03e-66

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 198.51  E-value: 5.03e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247  22 SDETNALANLSNASAMLNAMLPNSVFTGFYLFDG-EELILGPFQGGVSCVHITLGKGVCGESAQTAKTLIVDDVTKHANY 100
Cdd:COG1956  21 AGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQLVPDVHAFPGH 100

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 76562247 101 ISCDSKAMSEIVVPMFKNGKLLGVLDLDSSLVADYDEIDQEYLEKFVGILVEHTIW 156
Cdd:COG1956 101 IACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
GAF COG2203
GAF domain [Signal transduction mechanisms];
50-153 1.42e-11

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 61.75  E-value: 1.42e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247  50 FYLFDGE----ELILGPFQGGVSCVHITLGKGVCGESAQTAKTLIVDDVTKHANYISCDSKAM------SEIVVPMFKNG 119
Cdd:COG2203 230 ILLVDEDggelELVAAPGLPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELLlalgirSLLCVPLLVDG 309

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 76562247 120 KLLGVLDLDSSLVADYDEIDQEYLEKF---VGILVEH 153
Cdd:COG2203 310 RLIGVLALYSKEPRAFTEEDLELLEALadqAAIAIER 346
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 50-144 6.42e-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: 54.39  E-value: 6.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247    50 FYLFDGEELIL---GPFQGGVSCVHITLGKGVCGESAQTAKTLIVDDVTKHANYIS---CDSKAMSEIVVPMFKNGKLLG 123
Cdd:pfam13185  26 ILLVDDDGRLAawgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKGlpaGHAGLRSFLSVPLVSGGRVVG 105

                          90       100
                  ....*....|....*....|.
gi 76562247   124 VLDLDSSLVADYDEIDQEYLE 144
Cdd:pfam13185 106 VLALGSNRPGAFDEEDLELLE 126
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
51-144 8.20e-09

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 52.21  E-value: 8.20e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247  51 YLFD--GEELIL----GPFQGGVSCVHITLGKGVCGESAQTAKTLIVDDVTKHANYiscdsKAMSE---------IVVPM 115
Cdd:COG3605  42 YLLDpdGGRLELrateGLNPEAVGKVRLPLGEGLVGLVAERGEPLNLADAASHPRF-----KYFPEtgeegfrsfLGVPI 116

                        90       100
                ....*....|....*....|....*....
gi 76562247 116 FKNGKLLGVLDLDSSLVADYDEIDQEYLE 144
Cdd:COG3605 117 IRRGRVLGVLVVQSREPREFTEEEVEFLV 145
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 70-154 2.27e-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: 45.06  E-value: 2.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76562247     70 VHITLGKGVCGESAQTAKTLIVDDVTKHANY------ISCDSKAMseIVVPMFKNGKLLGVLDLDSSLVAD-YDEIDQEY 142
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEADPLFaedllgRYQGVRSF--LAVPLVADGELVGVLALHNKKSPRpFTEEDEEL 127

                           90
                   ....*....|....*
gi 76562247    143 LEKF---VGILVEHT 154
Cdd:smart00065 128 LQALanqLAIALANA 142
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 77-146 8.44e-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: 40.15  E-value: 8.44e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 76562247    77 GVCGESAQTAKTLIVDDVTKHANYISCDSKA-----MSEIVVPMFKNGKLLGVLDLDSSlVADYDEIDQEYLEKF 146
Cdd:pfam01590  52 GTGVTVLRTGRPLVVPDAAGDPRFLDPLLLLrnfgiRSLLAVPIIDDGELLGVLVLHHP-RPPFTEEELELLEVL 125
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 111-146 2.59e-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: 37.13  E-value: 2.59e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 76562247 111 IVVPMFKNGKLLGVLDLDSSLVADYDEIDQEYLEKF 146
Cdd:COG3604  77 LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETL 112
 
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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