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Conserved domains on  [gi|831209361|gb|AKM11197|]
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hypothetical protein AB433_16410 [Croceicoccus naphthovorans]

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, ...
 8-162 3.71e-72

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 213.92  E-value: 3.71e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361   8 DPSDKPTLYRELAEAVDAITAGEPDGVANMANCAALFGLFITDCNWAGFYRA-VGDTLVLGPFTGNPACIRIPFGTGVCG 86
Cdd:COG1956    1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVdGGGELVLGPFQGPPACTRIPFGKGVCG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 831209361  87 AAAAaaSGKTQLVRDVHAFPGHIACDAASRSELVVPIVKDGAVIAVIDLDSPSLARFDEADRAGIESVASILADRL 162
Cdd:COG1956   81 TAAA--EGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-162 3.71e-72

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 213.92  E-value: 3.71e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361   8 DPSDKPTLYRELAEAVDAITAGEPDGVANMANCAALFGLFITDCNWAGFYRA-VGDTLVLGPFTGNPACIRIPFGTGVCG 86
Cdd:COG1956    1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVdGGGELVLGPFQGPPACTRIPFGKGVCG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 831209361  87 AAAAaaSGKTQLVRDVHAFPGHIACDAASRSELVVPIVKDGAVIAVIDLDSPSLARFDEADRAGIESVASILADRL 162
Cdd:COG1956   81 TAAA--EGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 74-159 8.75e-08

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: 48.62  E-value: 8.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361   74 ACIRIPFGTGVCGAAAAaaSGKTQLVRDVHAFPGHI---ACDAASRSELVVPIVKDGAVIAVIDLDSPSLARFDEADRAG 150
Cdd:pfam13185  47 AALDDPPGEGLVGEALR--TGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLEL 124


                  ....*....
gi 831209361  151 IESVASILA 159
Cdd:pfam13185 125 LELLAEQAA 133
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 76-159 9.47e-05

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: 40.44  E-value: 9.47e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361    76 IRIPFGTGVCGAAAAaaSGKTQLVRDVHA---FPGHIACDA-ASRSELVVPIVKDGAVIAVIDLDSPSLAR-FDEADRAG 150
Cdd:smart00065  50 IRFPLDEGLAGRVAE--TGRPLNIPDVEAdplFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEEL 127


                   ....*....
gi 831209361   151 IESVASILA 159
Cdd:smart00065 128 LQALANQLA 136
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 8-162 3.71e-72

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 213.92  E-value: 3.71e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361   8 DPSDKPTLYRELAEAVDAITAGEPDGVANMANCAALFGLFITDCNWAGFYRA-VGDTLVLGPFTGNPACIRIPFGTGVCG 86
Cdd:COG1956    1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVdGGGELVLGPFQGPPACTRIPFGKGVCG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 831209361  87 AAAAaaSGKTQLVRDVHAFPGHIACDAASRSELVVPIVKDGAVIAVIDLDSPSLARFDEADRAGIESVASILADRL 162
Cdd:COG1956   81 TAAA--EGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 74-159 8.75e-08

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: 48.62  E-value: 8.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361   74 ACIRIPFGTGVCGAAAAaaSGKTQLVRDVHAFPGHI---ACDAASRSELVVPIVKDGAVIAVIDLDSPSLARFDEADRAG 150
Cdd:pfam13185  47 AALDDPPGEGLVGEALR--TGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLEL 124


                  ....*....
gi 831209361  151 IESVASILA 159
Cdd:pfam13185 125 LELLAEQAA 133
GAF COG2203
GAF domain [Signal transduction mechanisms];
48-159 1.02e-07

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 50.19  E-value: 1.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361  48 ITDCNWAGFYRAVGDTLVL----GPFTGNPACIRIPFGTGVCGAAAAaaSGKTQLVRDVHAFPGHIACDAAS------RS 117
Cdd:COG2203  222 LLGADRGAILLVDEDGGELelvaAPGLPEEELGRLPLGEGLAGRALR--TGEPVVVNDASTDPRFAPSLRELllalgiRS 299

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 831209361 118 ELVVPIVKDGAVIAVIDLDSPSLARFDEADRAGIESVASILA 159
Cdd:COG2203  300 LLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEALADQAA 341
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 48-159 1.51e-05

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: 42.47  E-value: 1.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361   48 ITDCNWAGFYRAVGDTLVL---GPFTGNPACIRIPFGTGVcgaaAAAASGKTQLVRDV-----HAFPGHIACDAASRSEL 119
Cdd:pfam01590  16 LLGADRCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV----TVLRTGRPLVVPDAagdprFLDPLLLLRNFGIRSLL 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 831209361  120 VVPIVKDGAVIAVIDLDSPSlARFDEADRAGIESVASILA 159
Cdd:pfam01590  92 AVPIIDDGELLGVLVLHHPR-PPFTEEELELLEVLADQVA 130
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
76-159 3.33e-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: 3.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361  76 IRIPFGTGVCGAAAAaaSGKTQLVRDVHAFPGHIACDAA----SRSELVVPIVKDGAVIAVIDLDSPSLARFDEADRAGI 151
Cdd:COG3605   67 VRLPLGEGLVGLVAE--RGEPLNLADAASHPRFKYFPETgeegFRSFLGVPIIRRGRVLGVLVVQSREPREFTEEEVEFL 144


                 ....*...
gi 831209361 152 ESVASILA 159
Cdd:COG3605  145 VTLAAQLA 152
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 76-159 9.47e-05

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: 40.44  E-value: 9.47e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 831209361    76 IRIPFGTGVCGAAAAaaSGKTQLVRDVHA---FPGHIACDA-ASRSELVVPIVKDGAVIAVIDLDSPSLAR-FDEADRAG 150
Cdd:smart00065  50 IRFPLDEGLAGRVAE--TGRPLNIPDVEAdplFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEEL 127


                   ....*....
gi 831209361   151 IESVASILA 159
Cdd:smart00065 128 LQALANQLA 136
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 112-159 5.67e-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: 39.06  E-value: 5.67e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 831209361 112 DAASRSELVVPIVKDGAVIAVIDLDSPSLARFDEADRAGIESVASILA 159
Cdd:COG3604   70 ARERQLFLGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLAA 117
 
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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