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Conserved domains on  [gi|1943293572|gb|QPT34225|]
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GAF domain-containing protein [Proteus penneri]

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, ...
 1-153 7.04e-88

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 253.60  E-value: 7.04e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572   1 MPKSLFYQELTDNLSALLSGENDLIASLANTSALLYEKLDTINWVGFYLNDG-DSLVLGPFQGKIACVRIGFGKGVCGTA 79
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1943293572  80 YSENRILRVDDVHQFSGHIACDSASQSEIVLPLKVNGQIIGVLDIDSPIFDRFDKKDEIGLKALCDVLCEHLKT 153
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-153 7.04e-88

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 253.60  E-value: 7.04e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572   1 MPKSLFYQELTDNLSALLSGENDLIASLANTSALLYEKLDTINWVGFYLNDG-DSLVLGPFQGKIACVRIGFGKGVCGTA 79
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1943293572  80 YSENRILRVDDVHQFSGHIACDSASQSEIVLPLKVNGQIIGVLDIDSPIFDRFDKKDEIGLKALCDVLCEHLKT 153
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 44-145 8.07e-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: 51.31  E-value: 8.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572  44 WVGFYlNDGDSLVLGPFQGKIACVRI--GFGKGVCGTAYSENRILRVDDV---HQFSGHIACDSASQSEIVLPLKVNGQI 118
Cdd:pfam13185  25 FILLV-DDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGRV 103

                          90       100
                  ....*....|....*....|....*..
gi 1943293572 119 IGVLDIDSPIFDRFDKKDEIGLKALCD 145
Cdd:pfam13185 104 VGVLALGSNRPGAFDEEDLELLELLAE 130
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 67-147 6.74e-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: 43.52  E-value: 6.74e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572   67 VRIGFGKGVCGTAYSENRILRVDDVHQ---FSGHIACD-SASQSEIVLPLKVNGQIIGVLDIDSPIFDR-FDKKDEIGLK 141
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ....*.
gi 1943293572  142 ALCDVL 147
Cdd:smart00065 130 ALANQL 135
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-153 7.04e-88

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 253.60  E-value: 7.04e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572   1 MPKSLFYQELTDNLSALLSGENDLIASLANTSALLYEKLDTINWVGFYLNDG-DSLVLGPFQGKIACVRIGFGKGVCGTA 79
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1943293572  80 YSENRILRVDDVHQFSGHIACDSASQSEIVLPLKVNGQIIGVLDIDSPIFDRFDKKDEIGLKALCDVLCEHLKT 153
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
GAF COG2203
GAF domain [Signal transduction mechanisms];
14-147 1.31e-10

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 58.67  E-value: 1.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572  14 LSALLSGENDLIASLANTSALLYEKLDTiNWVGFYLNDGDSLVL----GPFQGKIACVRIGFGKGVCGTAYSENRILRVD 89
Cdd:COG2203   198 ISQALRSALDLEELLQRILELAGELLGA-DRGAILLVDEDGGELelvaAPGLPEEELGRLPLGEGLAGRALRTGEPVVVN 276

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1943293572  90 DVHQFSGHIACDSAS------QSEIVLPLKVNGQIIGVLDIDSPIFDRFDKKDEIGLKALCDVL 147
Cdd:COG2203   277 DASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEALADQA 340
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 44-145 8.07e-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: 51.31  E-value: 8.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572  44 WVGFYlNDGDSLVLGPFQGKIACVRI--GFGKGVCGTAYSENRILRVDDV---HQFSGHIACDSASQSEIVLPLKVNGQI 118
Cdd:pfam13185  25 FILLV-DDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLVSGGRV 103

                          90       100
                  ....*....|....*....|....*..
gi 1943293572 119 IGVLDIDSPIFDRFDKKDEIGLKALCD 145
Cdd:pfam13185 104 VGVLALGSNRPGAFDEEDLELLELLAE 130
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 23-147 2.60e-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: 2.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572  23 DLIASLANTSALLYEKLDTiNWVGFYLNDGDSLVLGPFQGKIACVRIGFGK-GVCGTAYSENRILRVDDV-----HQFSG 96
Cdd:pfam01590   1 DLEEILQTILEELRELLGA-DRCALYLPDADGLEYLPPGARWLKAAGLEIPpGTGVTVLRTGRPLVVPDAagdprFLDPL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1943293572  97 HIACDSASQSEIVLPLKVNGQIIGVLDIDSPIfDRFDKKDEIGLKALCDVL 147
Cdd:pfam01590  80 LLLRNFGIRSLLAVPIIDDGELLGVLVLHHPR-PPFTEEELELLEVLADQV 129
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 67-147 6.74e-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: 43.52  E-value: 6.74e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572   67 VRIGFGKGVCGTAYSENRILRVDDVHQ---FSGHIACD-SASQSEIVLPLKVNGQIIGVLDIDSPIFDR-FDKKDEIGLK 141
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ....*.
gi 1943293572  142 ALCDVL 147
Cdd:smart00065 130 ALANQL 135
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
48-149 1.43e-04

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 40.26  E-value: 1.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1943293572  48 YLNDGDS--LVL----GPFQGKIACVRIGFGKGVCGTAYSENRILRVDDVHQfsgHIACDSAS-------QSEIVLPLKV 114
Cdd:COG3605    42 YLLDPDGgrLELrateGLNPEAVGKVRLPLGEGLVGLVAERGEPLNLADAAS---HPRFKYFPetgeegfRSFLGVPIIR 118

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1943293572 115 NGQIIGVLDIDSPIFDRFDKKDEIGLKALCDVLCE 149
Cdd:COG3605   119 RGRVLGVLVVQSREPREFTEEEVEFLVTLAAQLAE 153
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 101-147 3.46e-04

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: 39.83  E-value: 3.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1943293572 101 DSASQSEIVLPLKVNGQIIGVLDIDSPIFDRFDKKDEIGLKALCDVL 147
Cdd:COG3604    70 ARERQLFLGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLA 116
 
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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