NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1232570523|gb|OYY12205.1|]
View 

diguanylate cyclase [Sphingobacteriia bacterium 35-36-14]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 10-155 7.92e-70

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 207.76  E-value: 7.92e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523  10 GSKSDQYQALIPQISGLLTGENNLIANLANTAAALKEQF-GWFWVGFYLVD-QNELVLGPFQGPVACTRIQKGRGVCGSS 87
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALpDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1232570523  88 WKEGRTLIVPDVEKFPGHIACSSLSKSEIVVPLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVALL 155
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALL 150
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 10-155 7.92e-70

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 207.76  E-value: 7.92e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523  10 GSKSDQYQALIPQISGLLTGENNLIANLANTAAALKEQF-GWFWVGFYLVD-QNELVLGPFQGPVACTRIQKGRGVCGSS 87
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALpDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1232570523  88 WKEGRTLIVPDVEKFPGHIACSSLSKSEIVVPLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVALL 155
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALL 150
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 46-158 1.22e-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: 61.33  E-value: 1.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523  46 EQFGWFWVGFYLV--DQNELVLGPFQGPVACTRIQK--GRGVCGSSWKEGRTLIVPDVEKFPGHIACSSLS---KSEIVV 118
Cdd:pfam13185  16 VELGASAVGFILLvdDDGRLAAWGGAADELSAALDDppGEGLVGEALRTGRPVIVNDLAADPAKKGLPAGHaglRSFLSV 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1232570523 119 PLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVALLKIV 158
Cdd:pfam13185  96 PLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAEQAAIA 135
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 52-155 7.64e-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: 48.92  E-value: 7.64e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523   52 WVGFYLVDQN---ELVLGPFQGPVACTRIQK---GRGVCGSSWKEGRTLIVPDVEK---FPGHIACSSLS-KSEIVVPLV 121
Cdd:smart00065  21 RVLIYLVDENdrgELVLVAADGLTLPTLGIRfplDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQGvRSFLAVPLV 100

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1232570523  122 KDGLIWGVLDVDSSDY-DQFDDIDQHYLEQIVALL 155
Cdd:smart00065 101 ADGELVGVLALHNKKSpRPFTEEDEELLQALANQL 135
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
118-154 8.74e-04

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 38.61  E-value: 8.74e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1232570523 118 VPLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVAL 154
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAAL 151
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 10-155 7.92e-70

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 207.76  E-value: 7.92e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523  10 GSKSDQYQALIPQISGLLTGENNLIANLANTAAALKEQF-GWFWVGFYLVD-QNELVLGPFQGPVACTRIQKGRGVCGSS 87
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALpDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1232570523  88 WKEGRTLIVPDVEKFPGHIACSSLSKSEIVVPLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVALL 155
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALL 150
GAF COG2203
GAF domain [Signal transduction mechanisms];
46-155 5.66e-14

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 68.30  E-value: 5.66e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523  46 EQFGWFWVGFYLVDQN----ELVLGPFQGPVACTRIQKGRGVCGSSWKEGRTLIVPDVEKFPGHIACSSLS------KSE 115
Cdd:COG2203   221 ELLGADRGAILLVDEDggelELVAAPGLPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSL 300

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1232570523 116 IVVPLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVALL 155
Cdd:COG2203   301 LCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEALADQA 340
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 46-158 1.22e-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: 61.33  E-value: 1.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523  46 EQFGWFWVGFYLV--DQNELVLGPFQGPVACTRIQK--GRGVCGSSWKEGRTLIVPDVEKFPGHIACSSLS---KSEIVV 118
Cdd:pfam13185  16 VELGASAVGFILLvdDDGRLAAWGGAADELSAALDDppGEGLVGEALRTGRPVIVNDLAADPAKKGLPAGHaglRSFLSV 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1232570523 119 PLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVALLKIV 158
Cdd:pfam13185  96 PLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAEQAAIA 135
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 52-155 6.96e-08

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: 48.63  E-value: 6.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523  52 WVGFYLVDQNELVL---GPFQGPVACTRIQKGRGVcgSSWKEGRTLIVPDVEKFPGHIACSSL-----SKSEIVVPLVKD 123
Cdd:pfam01590  21 RCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAAGDPRFLDPLLLlrnfgIRSLLAVPIIDD 98

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1232570523 124 GLIWGVLDVDSSDyDQFDDIDQHYLEQIVALL 155
Cdd:pfam01590  99 GELLGVLVLHHPR-PPFTEEELELLEVLADQV 129
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 52-155 7.64e-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: 48.92  E-value: 7.64e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523   52 WVGFYLVDQN---ELVLGPFQGPVACTRIQK---GRGVCGSSWKEGRTLIVPDVEK---FPGHIACSSLS-KSEIVVPLV 121
Cdd:smart00065  21 RVLIYLVDENdrgELVLVAADGLTLPTLGIRfplDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQGvRSFLAVPLV 100

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1232570523  122 KDGLIWGVLDVDSSDY-DQFDDIDQHYLEQIVALL 155
Cdd:smart00065 101 ADGELVGVLALHNKKSpRPFTEEDEELLQALANQL 135
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 116-155 2.35e-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: 42.91  E-value: 2.35e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1232570523 116 IVVPLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVALL 155
Cdd:COG3604    77 LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLA 116
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
56-155 2.40e-05

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 42.19  E-value: 2.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232570523  56 YLVDQ--NELVL----GPFQGPVACTRIQKGRGVCGSSWKEGRTLIVPDVEKfpgHIACSSLS-------KSEIVVPLVK 122
Cdd:COG3605    42 YLLDPdgGRLELrateGLNPEAVGKVRLPLGEGLVGLVAERGEPLNLADAAS---HPRFKYFPetgeegfRSFLGVPIIR 118

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1232570523 123 DGLIWGVLDVDSSDYDQFDDIDQHYLEQIVALL 155
Cdd:COG3605   119 RGRVLGVLVVQSREPREFTEEEVEFLVTLAAQL 151
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
118-154 8.74e-04

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 38.61  E-value: 8.74e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1232570523 118 VPLVKDGLIWGVLDVDSSDYDQFDDIDQHYLEQIVAL 154
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAAL 151
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH