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Conserved domains on  [gi|1033839865|gb|ANH80718|]
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diguanylate cyclase [Niabella ginsenosidivorans]

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, ...
 8-155 4.59e-82

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 238.96  E-value: 4.59e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865   8 NKGTREEQYQSLLPQISAIIEGEPDLIANLSNITAALKEQF-NWWWVGFYLVK-NDELVLGPFQGPVACTRIKKGRGVCG 85
Cdd:COG1956     1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALpDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865  86 TAWLKATTLIVPDVQKFPGHIACSSVSKSEIVVPVIHNNVVVAVLDADSEHPDHFDATDQKYLEQLTGTI 155
Cdd:COG1956    81 TAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALL 150
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-155 4.59e-82

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 238.96  E-value: 4.59e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865   8 NKGTREEQYQSLLPQISAIIEGEPDLIANLSNITAALKEQF-NWWWVGFYLVK-NDELVLGPFQGPVACTRIKKGRGVCG 85
Cdd:COG1956     1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALpDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865  86 TAWLKATTLIVPDVQKFPGHIACSSVSKSEIVVPVIHNNVVVAVLDADSEHPDHFDATDQKYLEQLTGTI 155
Cdd:COG1956    81 TAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALL 150
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 37-155 6.04e-11

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: 56.71  E-value: 6.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865  37 LSNITAALkEQFNWWWVGFYLVKNDELVLGPFQGPVA----CTRIKKGRGVCGTAWLKATTLIVPDVQKFPGHIACSSVS 112
Cdd:pfam13185   8 LDAVLEAA-VELGASAVGFILLVDDDGRLAAWGGAADelsaALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKGLPAGH 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1033839865 113 ---KSEIVVPVIHNNVVVAVLDADSEHPDHFDATDQKYLEQLTGTI 155
Cdd:pfam13185  87 aglRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAEQA 132
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 76-152 4.59e-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: 43.91  E-value: 4.59e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865   76 RIKKGRGVCGTAWLKATTLIVPDVQK---FPGHIACSSVS-KSEIVVPVIHNNVVVAVLDADS-EHPDHFDATDQKYLEQ 150
Cdd:smart00065  51 RFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQGvRSFLAVPLVADGELVGVLALHNkKSPRPFTEEDEELLQA 130


                   ..
gi 1033839865  151 LT 152
Cdd:smart00065 131 LA 132
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-155 4.59e-82

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 238.96  E-value: 4.59e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865   8 NKGTREEQYQSLLPQISAIIEGEPDLIANLSNITAALKEQF-NWWWVGFYLVK-NDELVLGPFQGPVACTRIKKGRGVCG 85
Cdd:COG1956     1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALpDYNWVGFYLVDgGGELVLGPFQGPPACTRIPFGKGVCG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865  86 TAWLKATTLIVPDVQKFPGHIACSSVSKSEIVVPVIHNNVVVAVLDADSEHPDHFDATDQKYLEQLTGTI 155
Cdd:COG1956    81 TAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALL 150
GAF COG2203
GAF domain [Signal transduction mechanisms];
12-155 1.86e-16

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 75.62  E-value: 1.86e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865  12 REEQYQSLLPQISAIIEGEPDLIANLSNITAALKEQFNWWWVGFYLVKND----ELVLGPFQGPVACTRIKKGRGVCGTA 87
Cdd:COG2203   187 LELERLALLNEISQALRSALDLEELLQRILELAGELLGADRGAILLVDEDggelELVAAPGLPEEELGRLPLGEGLAGRA 266

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1033839865  88 WLKATTLIVPDVQKFPGHIACSSVS------KSEIVVPVIHNNVVVAVLDADSEHPDHFDATDQKYLEQLTGTI 155
Cdd:COG2203   267 LRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEALADQA 340
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 37-155 6.04e-11

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: 56.71  E-value: 6.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865  37 LSNITAALkEQFNWWWVGFYLVKNDELVLGPFQGPVA----CTRIKKGRGVCGTAWLKATTLIVPDVQKFPGHIACSSVS 112
Cdd:pfam13185   8 LDAVLEAA-VELGASAVGFILLVDDDGRLAAWGGAADelsaALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKGLPAGH 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1033839865 113 ---KSEIVVPVIHNNVVVAVLDADSEHPDHFDATDQKYLEQLTGTI 155
Cdd:pfam13185  87 aglRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAEQA 132
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
18-156 2.08e-06

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 45.27  E-value: 2.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865  18 SLLPQISAIIEGEPDLIANLSNITAALKEQFNWWWVGFYLVKND--ELVL----GPFQGPVACTRIKKGRGVCGTAWLKA 91
Cdd:COG3605     4 KALRRISEAVASALDLDEALDRIVRRIAEALGVDVCSIYLLDPDggRLELrateGLNPEAVGKVRLPLGEGLVGLVAERG 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1033839865  92 TTLIVPDVQKfpgHIACSSVS-------KSEIVVPVIHNNVVVAVLDADSEHPDHFDATDQKYLE----QLTGTIV 156
Cdd:COG3605    84 EPLNLADAAS---HPRFKYFPetgeegfRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFLVtlaaQLAEAIA 156
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 76-152 4.59e-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: 43.91  E-value: 4.59e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865   76 RIKKGRGVCGTAWLKATTLIVPDVQK---FPGHIACSSVS-KSEIVVPVIHNNVVVAVLDADS-EHPDHFDATDQKYLEQ 150
Cdd:smart00065  51 RFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYQGvRSFLAVPLVADGELVGVLALHNkKSPRPFTEEDEELLQA 130


                   ..
gi 1033839865  151 LT 152
Cdd:smart00065 131 LA 132
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 32-151 9.79e-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: 42.85  E-value: 9.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1033839865  32 DLIANLSNITAALKEQFNWWWVGFYLVKNDELVL---GPFQGPVACTRIKKGRGVcgTAWLKATTLIVPDVQKFPGHIAC 108
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAAGDPRFLDP 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1033839865 109 SSV-----SKSEIVVPVIHNNVVVAVLDADSEHPdHFDATDQKYLEQL 151
Cdd:pfam01590  79 LLLlrnfgIRSLLAVPIIDDGELLGVLVLHHPRP-PFTEEELELLEVL 125
 
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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