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Conserved domains on  [gi|2504596314|ref|WP_282188762|]
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GAF domain-containing protein [Streptococcus salivarius]

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, ...
 2-157 3.63e-71

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 211.61  E-value: 3.63e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314   2 TNEEKKLAYELMLAQAKVLFANEDNALANFSNASALLNTTLPNSVFTGFYLMDNvKNELILGPFQGNVSCVRIALGMGVC 81
Cdd:COG1956     1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDG-GGELVLGPFQGPPACTRIPFGKGVC 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2504596314  82 GQSAAENRTLIVEDVTKHANYIACDSAARSEIVVPMVKDGKLVGVLDLDSHQVGDYNQVDQDYLEAFVKILLEKTE 157
Cdd:COG1956    80 GTAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-157 3.63e-71

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 211.61  E-value: 3.63e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314   2 TNEEKKLAYELMLAQAKVLFANEDNALANFSNASALLNTTLPNSVFTGFYLMDNvKNELILGPFQGNVSCVRIALGMGVC 81
Cdd:COG1956     1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDG-GGELVLGPFQGPPACTRIPFGKGVC 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2504596314  82 GQSAAENRTLIVEDVTKHANYIACDSAARSEIVVPMVKDGKLVGVLDLDSHQVGDYNQVDQDYLEAFVKILLEKTE 157
Cdd:COG1956    80 GTAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 49-148 5.45e-13

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: 62.48  E-value: 5.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314  49 GFYLMDNVKNELIL--GPFQGNVSCVRIALGMGVCGQSAAENRTLIVEDVTKHANYI---ACDSAARSEIVVPMVKDGKL 123
Cdd:pfam13185  24 GFILLVDDDGRLAAwgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRV 103

                          90       100
                  ....*....|....*....|....*
gi 2504596314 124 VGVLDLDSHQVGDYNQVDQDYLEAF 148
Cdd:pfam13185 104 VGVLALGSNRPGAFDEEDLELLELL 128
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 72-148 2.51e-07

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: 47.38  E-value: 2.51e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314   72 VRIALGMGVCGQSAAENRTLIVEDVTKHANY---IACD-SAARSEIVVPMVKDGKLVGVLDLDS-HQVGDYNQVDQDYLE 146
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEADPLFaedLLGRyQGVRSFLAVPLVADGELVGVLALHNkKSPRPFTEEDEELLQ 129


                   ..
gi 2504596314  147 AF 148
Cdd:smart00065 130 AL 131
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 2-157 3.63e-71

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 211.61  E-value: 3.63e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314   2 TNEEKKLAYELMLAQAKVLFANEDNALANFSNASALLNTTLPNSVFTGFYLMDNvKNELILGPFQGNVSCVRIALGMGVC 81
Cdd:COG1956     1 EATSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDG-GGELVLGPFQGPPACTRIPFGKGVC 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2504596314  82 GQSAAENRTLIVEDVTKHANYIACDSAARSEIVVPMVKDGKLVGVLDLDSHQVGDYNQVDQDYLEAFVKILLEKTE 157
Cdd:COG1956    80 GTAAAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALD 155
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 49-148 5.45e-13

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: 62.48  E-value: 5.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314  49 GFYLMDNVKNELIL--GPFQGNVSCVRIALGMGVCGQSAAENRTLIVEDVTKHANYI---ACDSAARSEIVVPMVKDGKL 123
Cdd:pfam13185  24 GFILLVDDDGRLAAwgGAADELSAALDDPPGEGLVGEALRTGRPVIVNDLAADPAKKglpAGHAGLRSFLSVPLVSGGRV 103

                          90       100
                  ....*....|....*....|....*
gi 2504596314 124 VGVLDLDSHQVGDYNQVDQDYLEAF 148
Cdd:pfam13185 104 VGVLALGSNRPGAFDEEDLELLELL 128
GAF COG2203
GAF domain [Signal transduction mechanisms];
2-148 1.10e-11

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 62.13  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314   2 TNEEKKLAYELMLAQAKVLfanedNALANFSNASALLNTTL------PNSVFTGFYLMDNVKNELILGPFQGNVS--CVR 73
Cdd:COG2203   181 LTQRARLELERLALLNEIS-----QALRSALDLEELLQRILelagelLGADRGAILLVDEDGGELELVAAPGLPEeeLGR 255

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314  74 IALGMGVCGQSAAENRTLIVEDVTKHANYIACDSAA------RSEIVVPMVKDGKLVGVLDLDSHQVGDYNQVDQDYLEA 147
Cdd:COG2203   256 LPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEA 335


                  .
gi 2504596314 148 F 148
Cdd:COG2203   336 L 336
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
51-148 1.68e-10

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 56.83  E-value: 1.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314  51 YLMDNVKNELIL----GPFQGNVSCVRIALGMGVCGQSAAENRTLIVEDVTKHANYIACDSAA----RSEIVVPMVKDGK 122
Cdd:COG3605    42 YLLDPDGGRLELrateGLNPEAVGKVRLPLGEGLVGLVAERGEPLNLADAASHPRFKYFPETGeegfRSFLGVPIIRRGR 121

                          90       100
                  ....*....|....*....|....*.
gi 2504596314 123 LVGVLDLDSHQVGDYNQVDQDYLEAF 148
Cdd:COG3605   122 VLGVLVVQSREPREFTEEEVEFLVTL 147
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 72-148 2.51e-07

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: 47.38  E-value: 2.51e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2504596314   72 VRIALGMGVCGQSAAENRTLIVEDVTKHANY---IACD-SAARSEIVVPMVKDGKLVGVLDLDS-HQVGDYNQVDQDYLE 146
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEADPLFaedLLGRyQGVRSFLAVPLVADGELVGVLALHNkKSPRPFTEEDEELLQ 129


                   ..
gi 2504596314  147 AF 148
Cdd:smart00065 130 AL 131
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 79-148 2.30e-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: 41.70  E-value: 2.30e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2504596314  79 GVCGQSAAENRTLIVEDVTKHANYIACDSAA-----RSEIVVPMVKDGKLVGVLDLDsHQVGDYNQVDQDYLEAF 148
Cdd:pfam01590  52 GTGVTVLRTGRPLVVPDAAGDPRFLDPLLLLrnfgiRSLLAVPIIDDGELLGVLVLH-HPRPPFTEEELELLEVL 125
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 106-148 2.53e-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: 40.22  E-value: 2.53e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2504596314 106 DSAARSEIVVPMVKDGKLVGVLDLDSHQVGDYNQVDQDYLEAF 148
Cdd:COG3604    70 ARERQLFLGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETL 112
 
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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