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Conserved domains on  [gi|1678513889|gb|QCX52533|]
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GAF domain-containing protein [Elizabethkingia sp. JS20170427COW]

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, ...
 1-147 2.66e-74

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 218.54  E-value: 2.66e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889   1 MKELKQRLSLLIQSEEDTQAKLQKICTLLDQEIEYFNWTGFYFRDGDkEELVLGPYVGATtDHIRIPFGKGICGQVAVSG 80
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGG-GELVLGPFQGPP-ACTRIPFGKGVCGTAAAEG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1678513889  81 ETFLVPDVYAQDNYLSCSLDTQSEIVVPIFKNGKNIGQIDIDSHHKDPFSQEDQQLLEWLCEEVGKL 147
Cdd:COG1956    87 ETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-147 2.66e-74

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 218.54  E-value: 2.66e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889   1 MKELKQRLSLLIQSEEDTQAKLQKICTLLDQEIEYFNWTGFYFRDGDkEELVLGPYVGATtDHIRIPFGKGICGQVAVSG 80
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGG-GELVLGPFQGPP-ACTRIPFGKGVCGTAAAEG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1678513889  81 ETFLVPDVYAQDNYLSCSLDTQSEIVVPIFKNGKNIGQIDIDSHHKDPFSQEDQQLLEWLCEEVGKL 147
Cdd:COG1956    87 ETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 41-145 1.97e-13

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: 62.87  E-value: 1.97e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889  41 FYFRDGDKEELVLGPYVGATTDHIRIPFGKGICGQVAVSGETFLVPDV---YAQDNYLSCSLDTQSEIVVPIFKNGKNIG 117
Cdd:pfam13185  26 ILLVDDDGRLAAWGGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGRVVG 105

                          90       100
                  ....*....|....*....|....*...
gi 1678513889 118 QIDIDSHHKDPFSQEDQQLLEWLCEEVG 145
Cdd:pfam13185 106 VLALGSNRPGAFDEEDLELLELLAEQAA 133
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 17-145 7.50e-11

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: 56.62  E-value: 7.50e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889   17 DTQAKLQKICTLLDQEIEYFNWTGFYFRDGDKEELVLGPYVGATTDHIRIPF--GKGICGQVAVSGETFLVPDVYAQDNY 94
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFplDEGLAGRVAETGRPLNIPDVEADPLF 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1678513889   95 LSCSL----DTQSEIVVPIFKNGKNIGQIDIDS-HHKDPFSQEDQQLLEWLCEEVG 145
Cdd:smart00065  81 AEDLLgryqGVRSFLAVPLVADGELVGVLALHNkKSPRPFTEEDEELLQALANQLA 136
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-147 2.66e-74

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 218.54  E-value: 2.66e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889   1 MKELKQRLSLLIQSEEDTQAKLQKICTLLDQEIEYFNWTGFYFRDGDkEELVLGPYVGATtDHIRIPFGKGICGQVAVSG 80
Cdd:COG1956     9 YDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGG-GELVLGPFQGPP-ACTRIPFGKGVCGTAAAEG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1678513889  81 ETFLVPDVYAQDNYLSCSLDTQSEIVVPIFKNGKNIGQIDIDSHHKDPFSQEDQQLLEWLCEEVGKL 147
Cdd:COG1956    87 ETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEA 153
GAF COG2203
GAF domain [Signal transduction mechanisms];
6-145 1.55e-19

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 84.09  E-value: 1.55e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889   6 QRLSLLIQSEEDTQAKLQKICTLLdqeIEYFN--WTGFYFRDGDKEELVLGPYVGATTDHI-RIPFGKGICGQVAVSGET 82
Cdd:COG2203   196 NEISQALRSALDLEELLQRILELA---GELLGadRGAILLVDEDGGELELVAAPGLPEEELgRLPLGEGLAGRALRTGEP 272

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1678513889  83 FLVPDVYAQDNYLSC------SLDTQSEIVVPIFKNGKNIGQIDIDSHHKDPFSQEDQQLLEWLCEEVG 145
Cdd:COG2203   273 VVVNDASTDPRFAPSlrelllALGIRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEALADQAA 341
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
6-138 3.75e-14

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 66.07  E-value: 3.75e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889   6 QRLSLLIQSEEDTQAKLQKICTLLdqeIEYFNWTG--FYFRDGDKEELVLGPYVGATTD---HIRIPFGKGICGQVAVSG 80
Cdd:COG3605     7 RRISEAVASALDLDEALDRIVRRI---AEALGVDVcsIYLLDPDGGRLELRATEGLNPEavgKVRLPLGEGLVGLVAERG 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1678513889  81 ETFLVPDVYAQDNYLSCSL----DTQSEIVVPIFKNGKNIGQIDIDSHHKDPFSQEDQQLLE 138
Cdd:COG3605    84 EPLNLADAASHPRFKYFPEtgeeGFRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFLV 145
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 41-145 1.97e-13

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: 62.87  E-value: 1.97e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889  41 FYFRDGDKEELVLGPYVGATTDHIRIPFGKGICGQVAVSGETFLVPDV---YAQDNYLSCSLDTQSEIVVPIFKNGKNIG 117
Cdd:pfam13185  26 ILLVDDDGRLAAWGGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGRVVG 105

                          90       100
                  ....*....|....*....|....*...
gi 1678513889 118 QIDIDSHHKDPFSQEDQQLLEWLCEEVG 145
Cdd:pfam13185 106 VLALGSNRPGAFDEEDLELLELLAEQAA 133
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 17-145 7.50e-11

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: 56.62  E-value: 7.50e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889   17 DTQAKLQKICTLLDQEIEYFNWTGFYFRDGDKEELVLGPYVGATTDHIRIPF--GKGICGQVAVSGETFLVPDVYAQDNY 94
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFplDEGLAGRVAETGRPLNIPDVEADPLF 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1678513889   95 LSCSL----DTQSEIVVPIFKNGKNIGQIDIDS-HHKDPFSQEDQQLLEWLCEEVG 145
Cdd:smart00065  81 AEDLLgryqGVRSFLAVPLVADGELVGVLALHNkKSPRPFTEEDEELLQALANQLA 136
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 63-145 1.96e-07

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: 47.09  E-value: 1.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678513889  63 HIRIPFGKGIcgQVAVSGETFLVPDVYAQDNYLSC-----SLDTQSEIVVPIFKNGKNIGQIDIDsHHKDPFSQEDQQLL 137
Cdd:pfam01590  46 GLEIPPGTGV--TVLRTGRPLVVPDAAGDPRFLDPllllrNFGIRSLLAVPIIDDGELLGVLVLH-HPRPPFTEEELELL 122


                  ....*...
gi 1678513889 138 EWLCEEVG 145
Cdd:pfam01590 123 EVLADQVA 130
 
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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