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Conserved domains on  [gi|991863588|gb|AMG31879|]
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GAF domain-containing protein [Grimontia hollisae]

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, ...
 2-152 1.85e-78

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 229.33  E-value: 1.85e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588   2 ENKADFYSLFTRQAVSLIQDEPNLIANLSNISALLFQSVDDINWAGFYL-DDGSELVLGPFQGKPACVRIPYGRGVCGRA 80
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 991863588  81 FSNRRIERVEDVHLFDDHIVCDAASNSEIVLPLYQGEKCIGVLDIDSPKKARFDQEDETGLTLLVNELQKHL 152
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-152 1.85e-78

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 229.33  E-value: 1.85e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588   2 ENKADFYSLFTRQAVSLIQDEPNLIANLSNISALLFQSVDDINWAGFYL-DDGSELVLGPFQGKPACVRIPYGRGVCGRA 80
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 991863588  81 FSNRRIERVEDVHLFDDHIVCDAASNSEIVLPLYQGEKCIGVLDIDSPKKARFDQEDETGLTLLVNELQKHL 152
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 27-146 1.48e-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: 52.85  E-value: 1.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588   27 ANLSNISALLFQSVDDINWAGF----YLDDGSELVL--GPFQGKPACVRIPYGRGVCGRAFSNRRIERVEDV---HLFDD 97
Cdd:pfam13185   2 ADLEELLDAVLEAAVELGASAVgfilLVDDDGRLAAwgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKG 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 991863588   98 HIVCDAASNSEIVLPLYQGEKCIGVLDIDSPKKARFDQEDETGLTLLVN 146
Cdd:pfam13185  82 LPAGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAE 130
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 51-148 3.35e-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: 44.29  E-value: 3.35e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588    51 DDGSELVLGPFQG-KPACVRIPY--GRGVCGRAFSNRRIERVEDVH---LFDDHIVCDA-ASNSEIVLPLYQGEKCIGVL 123
Cdd:smart00065  30 NDRGELVLVAADGlTLPTLGIRFplDEGLAGRVAETGRPLNIPDVEadpLFAEDLLGRYqGVRSFLAVPLVADGELVGVL 109

                           90       100
                   ....*....|....*....|....*.
gi 991863588   124 DIDSPKKAR-FDQEDETGLTLLVNEL 148
Cdd:smart00065 110 ALHNKKSPRpFTEEDEELLQALANQL 135
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-152 1.85e-78

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 229.33  E-value: 1.85e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588   2 ENKADFYSLFTRQAVSLIQDEPNLIANLSNISALLFQSVDDINWAGFYL-DDGSELVLGPFQGKPACVRIPYGRGVCGRA 80
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLvDGGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 991863588  81 FSNRRIERVEDVHLFDDHIVCDAASNSEIVLPLYQGEKCIGVLDIDSPKKARFDQEDETGLTLLVNELQKHL 152
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 27-146 1.48e-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: 52.85  E-value: 1.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588   27 ANLSNISALLFQSVDDINWAGF----YLDDGSELVL--GPFQGKPACVRIPYGRGVCGRAFSNRRIERVEDV---HLFDD 97
Cdd:pfam13185   2 ADLEELLDAVLEAAVELGASAVgfilLVDDDGRLAAwgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLaadPAKKG 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 991863588   98 HIVCDAASNSEIVLPLYQGEKCIGVLDIDSPKKARFDQEDETGLTLLVN 146
Cdd:pfam13185  82 LPAGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAE 130
GAF COG2203
GAF domain [Signal transduction mechanisms];
45-144 5.56e-07

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 47.88  E-value: 5.56e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588  45 WAGFYLDDGSELVL--GPFQGKPACVRIPYGRGVCGRAFSNRRIERVEDVHLFDDHIVCDAAS------NSEIVLPLYQG 116
Cdd:COG2203  229 AILLVDEDGGELELvaAPGLPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVD 308

                         90       100
                 ....*....|....*....|....*...
gi 991863588 117 EKCIGVLDIDSPKKARFDQEDETGLTLL 144
Cdd:COG2203  309 GRLIGVLALYSKEPRAFTEEDLELLEAL 336
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 51-148 3.35e-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: 44.29  E-value: 3.35e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588    51 DDGSELVLGPFQG-KPACVRIPY--GRGVCGRAFSNRRIERVEDVH---LFDDHIVCDA-ASNSEIVLPLYQGEKCIGVL 123
Cdd:smart00065  30 NDRGELVLVAADGlTLPTLGIRFplDEGLAGRVAETGRPLNIPDVEadpLFAEDLLGRYqGVRSFLAVPLVADGELVGVL 109

                           90       100
                   ....*....|....*....|....*.
gi 991863588   124 DIDSPKKAR-FDQEDETGLTLLVNEL 148
Cdd:smart00065 110 ALHNKKSPRpFTEEDEELLQALANQL 135
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
68-148 8.85e-05

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 40.65  E-value: 8.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588  68 VRIPYGRGVCGRAFSNRRIERVEDVHLfDDHIVCDAA-----SNSEIVLPLYQGEKCIGVLDIDSPKKARFDQEDETGLT 142
Cdd:COG3605   67 VRLPLGEGLVGLVAERGEPLNLADAAS-HPRFKYFPEtgeegFRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFLV 145


                 ....*.
gi 991863588 143 LLVNEL 148
Cdd:COG3605  146 TLAAQL 151
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 24-148 1.54e-04

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: 39.38  E-value: 1.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991863588   24 NLIANLSNISALLFQSVDDiNWAGFYLDDGSELVL---GPFQGKPACVRIPYGRGVcgRAFSNRRIERVEDV-----HLF 95
Cdd:pfam01590   1 DLEEILQTILEELRELLGA-DRCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAagdprFLD 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 991863588   96 DDHIVCDAASNSEIVLPLYQGEKCIGVLDIDSPkKARFDQEDETGLTLLVNEL 148
Cdd:pfam01590  78 PLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHP-RPPFTEEELELLEVLADQV 129
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 109-146 1.66e-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: 37.52  E-value: 1.66e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 991863588 109 IVLPLYQGEKCIGVLDIDSPKKARFDQEDETGLTLLVN 146
Cdd:COG3604   77 LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLAS 114
 
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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