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Conserved domains on  [gi|2321362383|gb|UYP77436|]
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GAF domain-containing protein [Xanthomonas campestris pv. campestris]

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, ...
 8-159 5.53e-76

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 223.17  E-value: 5.53e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383   8 TGSKPEQYAQLTAQAQALVHGEPDRIANAANLAALIFNSLPSLNWAGFYFYDG-RELVVGPFQGLPACVRIPLDKGVCGA 86
Cdd:COG1956     2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGT 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2321362383  87 AASTRQTQRIADVDAFPGHIACDSASRSELVIPLVRGDTLIGVLDLDSPELDRFDADDQRGLEAIAQVFVGAL 159
Cdd:COG1956    82 AAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-159 5.53e-76

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 223.17  E-value: 5.53e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383   8 TGSKPEQYAQLTAQAQALVHGEPDRIANAANLAALIFNSLPSLNWAGFYFYDG-RELVVGPFQGLPACVRIPLDKGVCGA 86
Cdd:COG1956     2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGT 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2321362383  87 AASTRQTQRIADVDAFPGHIACDSASRSELVIPLVRGDTLIGVLDLDSPELDRFDADDQRGLEAIAQVFVGAL 159
Cdd:COG1956    82 AAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 55-153 6.28e-12

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: 59.40  E-value: 6.28e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383  55 FYFYDGRELVV---GPFQGLPACVRIPLDKGVCGAAASTRQTQRIADVDAFPGHI---ACDSASRSELVIPLVRGDTLIG 128
Cdd:pfam13185  26 ILLVDDDGRLAawgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRVVG 105

                          90       100
                  ....*....|....*....|....*
gi 2321362383 129 VLDLDSPELDRFDADDQRGLEAIAQ 153
Cdd:pfam13185 106 VLALGSNRPGAFDEEDLELLELLAE 130
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 75-153 9.35e-10

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: 53.92  E-value: 9.35e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383   75 VRIPLDKGVCGAAASTRQTQRIADVDA---FPGHIACD-SASRSELVIPLVRGDTLIGVLDLDSPELDR-FDADDQRGLE 149
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ....
gi 2321362383  150 AIAQ 153
Cdd:smart00065 130 ALAN 133
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
118-152 4.46e-03

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 36.30  E-value: 4.46e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2321362383 118 IPLVRGDTLIGVLDLDSPELDRFDADDQRGLEAIA 152
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALA 149
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-159 5.53e-76

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 223.17  E-value: 5.53e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383   8 TGSKPEQYAQLTAQAQALVHGEPDRIANAANLAALIFNSLPSLNWAGFYFYDG-RELVVGPFQGLPACVRIPLDKGVCGA 86
Cdd:COG1956     2 ATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGT 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2321362383  87 AASTRQTQRIADVDAFPGHIACDSASRSELVIPLVRGDTLIGVLDLDSPELDRFDADDQRGLEAIAQVFVGAL 159
Cdd:COG1956    82 AAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 55-153 6.28e-12

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: 59.40  E-value: 6.28e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383  55 FYFYDGRELVV---GPFQGLPACVRIPLDKGVCGAAASTRQTQRIADVDAFPGHI---ACDSASRSELVIPLVRGDTLIG 128
Cdd:pfam13185  26 ILLVDDDGRLAawgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRVVG 105

                          90       100
                  ....*....|....*....|....*
gi 2321362383 129 VLDLDSPELDRFDADDQRGLEAIAQ 153
Cdd:pfam13185 106 VLALGSNRPGAFDEEDLELLELLAE 130
GAF COG2203
GAF domain [Signal transduction mechanisms];
62-159 3.70e-10

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 57.51  E-value: 3.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383  62 ELVVGPFQGLPACVRIPLDKGVCGAAASTRQTQRIADVDAFPGHIACDSAS------RSELVIPLVRGDTLIGVLDLDSP 135
Cdd:COG2203   241 ELVAAPGLPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSK 320

                          90       100
                  ....*....|....*....|....
gi 2321362383 136 ELDRFDADDQRGLEAIAQVFVGAL 159
Cdd:COG2203   321 EPRAFTEEDLELLEALADQAAIAI 344
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 75-153 9.35e-10

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: 53.92  E-value: 9.35e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383   75 VRIPLDKGVCGAAASTRQTQRIADVDA---FPGHIACD-SASRSELVIPLVRGDTLIGVLDLDSPELDR-FDADDQRGLE 149
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRyQGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQ 129


                   ....
gi 2321362383  150 AIAQ 153
Cdd:smart00065 130 ALAN 133
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
75-159 3.96e-09

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 52.98  E-value: 3.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383  75 VRIPLDKGVCGAAASTRQTQRIADVDAFPGHIACDSA----SRSELVIPLVRGDTLIGVLDLDSPELDRFDADDQRGLEA 150
Cdd:COG3605    67 VRLPLGEGLVGLVAERGEPLNLADAASHPRFKYFPETgeegFRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFLVT 146


                  ....*....
gi 2321362383 151 IAQVFVGAL 159
Cdd:COG3605   147 LAAQLAEAI 155
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 109-160 1.69e-06

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: 46.38  E-value: 1.69e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2321362383 109 DSASRSELVIPLVRGDTLIGVLDLDSPELDRFDADDQRGLEAIAQVFVGALT 160
Cdd:COG3604    70 ARERQLFLGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLAAVAIL 121
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 57-159 4.20e-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: 43.62  E-value: 4.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321362383  57 FYDGRELVVgPFQGLPACVRIPLDKGVCGAAASTRQTQRIADVDAFPGHIAC-----DSASRSELVIPLVRGDTLIGVLD 131
Cdd:pfam01590  28 DADGLEYLP-PGARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAAGDPRFLDPllllrNFGIRSLLAVPIIDDGELLGVLV 106

                          90       100
                  ....*....|....*....|....*...
gi 2321362383 132 LDSPElDRFDADDQRGLEAIAQVFVGAL 159
Cdd:pfam01590 107 LHHPR-PPFTEEELELLEVLADQVAIAL 133
GAF_3 pfam13492
GAF domain;
116-159 1.22e-04

GAF domain;


Pssm-ID: 433253 [Multi-domain]  Cd Length: 129  Bit Score: 39.66  E-value: 1.22e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2321362383 116 LVIPLVRGDTLIGVLDLDSPELDRFDADDQRGLEAIAQVFVGAL 159
Cdd:pfam13492  84 LVVPLVAGRRVIGVLALASSKPRAFDAEDLRLLESLAAQIATAI 127
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
118-152 4.46e-03

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 36.30  E-value: 4.46e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2321362383 118 IPLVRGDTLIGVLDLDSPELDRFDADDQRGLEAIA 152
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALA 149
 
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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