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Conserved domains on  [gi|489800094|ref|WP_003703982|]
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MULTISPECIES: GAF domain-containing protein [Ligilactobacillus]

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, ...
 5-149 9.83e-80

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 232.41  E-value: 9.83e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094   5 LLSQQLDALLTNETNFIANLSNASALLYQSLSDINWAGFYLYDEtNDELHLGPFQGKVACMHIKNGSGVCGTALQQQKVL 84
Cdd:COG1956   11 ELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDG-GGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQ 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489800094  85 RVDNVHEFAGHIACDSASNSEIVVPLIKDDKIIGVLDIDSPSLSRFSPEDEVELVEFSKTLLKHI 149
Cdd:COG1956   90 LVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 5-149 9.83e-80

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 232.41  E-value: 9.83e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094   5 LLSQQLDALLTNETNFIANLSNASALLYQSLSDINWAGFYLYDEtNDELHLGPFQGKVACMHIKNGSGVCGTALQQQKVL 84
Cdd:COG1956   11 ELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDG-GGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQ 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489800094  85 RVDNVHEFAGHIACDSASNSEIVVPLIKDDKIIGVLDIDSPSLSRFSPEDEVELVEFSKTLLKHI 149
Cdd:COG1956   90 LVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 37-140 1.73e-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: 57.86  E-value: 1.73e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094   37 DINWAGFYLYDETNDELHLGPFQGKVACMHI--KNGSGVCGTALQQQKVLRVDNV---HEFAGHIACDSASNSEIVVPLI 111
Cdd:pfam13185  19 GASAVGFILLVDDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLV 98

                          90       100
                  ....*....|....*....|....*....
gi 489800094  112 KDDKIIGVLDIDSPSLSRFSPEDeVELVE 140
Cdd:pfam13185  99 SGGRVVGVLALGSNRPGAFDEED-LELLE 126
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 44-140 6.93e-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: 6.93e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094    44 YLYDETN---------DELHLGPFQGkvacmHIKNGSGVCGTALQQQKVLRVDNVHE---FAGHIACD-SASNSEIVVPL 110
Cdd:smart00065  25 YLVDENDrgelvlvaaDGLTLPTLGI-----RFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPL 99

                           90       100       110
                   ....*....|....*....|....*....|
gi 489800094   111 IKDDKIIGVLDIDSPSLSRFSPEDEVELVE 140
Cdd:smart00065 100 VADGELVGVLALHNKKSPRPFTEEDEELLQ 129
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 5-149 9.83e-80

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 232.41  E-value: 9.83e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094   5 LLSQQLDALLTNETNFIANLSNASALLYQSLSDINWAGFYLYDEtNDELHLGPFQGKVACMHIKNGSGVCGTALQQQKVL 84
Cdd:COG1956   11 ELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDG-GGELVLGPFQGPPACTRIPFGKGVCGTAAAEGETQ 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489800094  85 RVDNVHEFAGHIACDSASNSEIVVPLIKDDKIIGVLDIDSPSLSRFSPEDEVELVEFSKTLLKHI 149
Cdd:COG1956   90 LVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF COG2203
GAF domain [Signal transduction mechanisms];
40-140 1.37e-11

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 60.98  E-value: 1.37e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094  40 WAGFYLYDETNDELHL--GPFQGKVACMHIKNGSGVCGTALQQQKVLRVDNVHEFAGHIACDSAS------NSEIVVPLI 111
Cdd:COG2203  227 RGAILLVDEDGGELELvaAPGLPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLL 306

                         90       100
                 ....*....|....*....|....*....
gi 489800094 112 KDDKIIGVLDIDSPSLSRFSPEDeVELVE 140
Cdd:COG2203  307 VDGRLIGVLALYSKEPRAFTEED-LELLE 334
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 37-140 1.73e-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: 57.86  E-value: 1.73e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094   37 DINWAGFYLYDETNDELHLGPFQGKVACMHI--KNGSGVCGTALQQQKVLRVDNV---HEFAGHIACDSASNSEIVVPLI 111
Cdd:pfam13185  19 GASAVGFILLVDDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLV 98

                          90       100
                  ....*....|....*....|....*....
gi 489800094  112 KDDKIIGVLDIDSPSLSRFSPEDeVELVE 140
Cdd:pfam13185  99 SGGRVVGVLALGSNRPGAFDEED-LELLE 126
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 44-140 6.93e-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: 6.93e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094    44 YLYDETN---------DELHLGPFQGkvacmHIKNGSGVCGTALQQQKVLRVDNVHE---FAGHIACD-SASNSEIVVPL 110
Cdd:smart00065  25 YLVDENDrgelvlvaaDGLTLPTLGI-----RFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPL 99

                           90       100       110
                   ....*....|....*....|....*....|
gi 489800094   111 IKDDKIIGVLDIDSPSLSRFSPEDEVELVE 140
Cdd:smart00065 100 VADGELVGVLALHNKKSPRPFTEEDEELLQ 129
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
44-140 1.51e-06

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 45.66  E-value: 1.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094  44 YLYDETNDELHL----GPFQGKVACMHIKNGSGVCGTALQQQKVLRVDNVHEfagHIACDSAS-------NSEIVVPLIK 112
Cdd:COG3605   42 YLLDPDGGRLELrateGLNPEAVGKVRLPLGEGLVGLVAERGEPLNLADAAS---HPRFKYFPetgeegfRSFLGVPIIR 118

                         90       100
                 ....*....|....*....|....*...
gi 489800094 113 DDKIIGVLDIDSPSLSRFSpEDEVELVE 140
Cdd:COG3605  119 RGRVLGVLVVQSREPREFT-EEEVEFLV 145
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 40-140 2.76e-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: 2.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094   40 WAGFYLYDET-NDELHLGPFQGKVACMHIKNGSGVcgTALQQQKVLRVDNV-----HEFAGHIACDSASNSEIVVPLIKD 113
Cdd:pfam01590  21 RCALYLPDADgLEYLPPGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAagdprFLDPLLLLRNFGIRSLLAVPIIDD 98

                          90       100
                  ....*....|....*....|....*..
gi 489800094  114 DKIIGVLDIDSPSlSRFSpEDEVELVE 140
Cdd:pfam01590  99 GELLGVLVLHHPR-PPFT-EEELELLE 123
GAF_3 pfam13492
GAF domain;
24-142 9.36e-06

GAF domain;


Pssm-ID: 433253 [Multi-domain]  Cd Length: 129  Bit Score: 42.36  E-value: 9.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094   24 LSNASALLYQSLSDINWAGFYLYDETNDELHL--GPFQGKVACMHIKNGSGVCGTALQQQKVLRVDnvhEFAGHIACDSA 101
Cdd:pfam13492   5 ILEALLKLLVRLLGAERAAVYLLDEDGNKLQVaaGYDGEPDPSESLDADSPLARRALSSGEPISGL---GSAGEDGLPDG 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 489800094  102 SNseIVVPLIKDDKIIGVLDIDSPSLSRFSPEDEVELVEFS 142
Cdd:pfam13492  82 PA--LVVPLVAGRRVIGVLALASSKPRAFDAEDLRLLESLA 120
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 40-142 2.98e-05

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: 42.53  E-value: 2.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489800094  40 WAGFYLYDETNDELHLGPFQGKVACMHIKNGSGVCGTALQQQKVLRVDNVHEFAGHIACdsasnseIVVPLIKDDKIIGV 119
Cdd:COG3604   18 LALLLLVLLLLALLLRGDLLASALVLEESLELLALALSEALLAAQARQAALAARERQLF-------LGVPLRVGGEVLGV 90

                         90       100
                 ....*....|....*....|...
gi 489800094 120 LDIDSPSLSRFSPEDEVELVEFS 142
Cdd:COG3604   91 LTLDSRRPGAFSEEDLRLLETLA 113
 
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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