NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1539516125|emb|VEB96745|]
View 

Free methionine-R-sulfoxide reductase [Cedecea lapagei]

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, ...
 1-151 2.96e-84

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


:

Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 244.35  E-value: 2.96e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539516125   1 MSKEQFYADLNRDFSALMAGETSFLATLANTSALLFERLDGVNWAGFYLLEA-QTLVLGPFQGKIACVRIPVGKGVCGTA 79
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1539516125  80 VATGTIQRVEDVHAFDGHIACDAASNSEIVLPLTVDGQTIGVLDIDSTEYGRFSEEDEIGLKTLVSGLTDVL 151
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-151 2.96e-84

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 244.35  E-value: 2.96e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539516125   1 MSKEQFYADLNRDFSALMAGETSFLATLANTSALLFERLDGVNWAGFYLLEA-QTLVLGPFQGKIACVRIPVGKGVCGTA 79
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1539516125  80 VATGTIQRVEDVHAFDGHIACDAASNSEIVLPLTVDGQTIGVLDIDSTEYGRFSEEDEIGLKTLVSGLTDVL 151
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 41-151 4.10e-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: 57.48  E-value: 4.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539516125  41 GVNWAGFYLL--EAQTLVLGPFQGKIACVRI--PVGKGVCGTAVATGTIQRVEDV---HAFDGHIACDAASNSEIVLPLT 113
Cdd:pfam13185  19 GASAVGFILLvdDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLV 98

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1539516125 114 VDGQTIGVLDIDSTEYGRFSEEDEIGLKTLVSGLTDVL 151
Cdd:pfam13185  99 SGGRVVGVLALGSNRPGAFDEEDLELLELLAEQAAIAI 136
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 67-137 1.48e-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: 50.84  E-value: 1.48e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1539516125   67 VRIPVGKGVCGTAVATGTIQRVEDVHA---FDGHIACDA-ASNSEIVLPLTVDGQTIGVLDIDSTEYGR-FSEEDE 137
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDE 125
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
110-145 9.33e-03

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 35.53  E-value: 9.33e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1539516125 110 LPLTVDGQTIGVLDIDSTEYGRFSEEDEIGLKTLVS 145
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAA 150
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 1-151 2.96e-84

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


Pssm-ID: 441559 [Multi-domain]  Cd Length: 156  Bit Score: 244.35  E-value: 2.96e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539516125   1 MSKEQFYADLNRDFSALMAGETSFLATLANTSALLFERLDGVNWAGFYLLEA-QTLVLGPFQGKIACVRIPVGKGVCGTA 79
Cdd:COG1956     3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1539516125  80 VATGTIQRVEDVHAFDGHIACDAASNSEIVLPLTVDGQTIGVLDIDSTEYGRFSEEDEIGLKTLVSGLTDVL 151
Cdd:COG1956    83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEAL 154
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 41-151 4.10e-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: 57.48  E-value: 4.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539516125  41 GVNWAGFYLL--EAQTLVLGPFQGKIACVRI--PVGKGVCGTAVATGTIQRVEDV---HAFDGHIACDAASNSEIVLPLT 113
Cdd:pfam13185  19 GASAVGFILLvdDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGLRSFLSVPLV 98

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1539516125 114 VDGQTIGVLDIDSTEYGRFSEEDEIGLKTLVSGLTDVL 151
Cdd:pfam13185  99 SGGRVVGVLALGSNRPGAFDEEDLELLELLAEQAAIAI 136
GAF COG2203
GAF domain [Signal transduction mechanisms];
12-143 5.20e-10

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 57.13  E-value: 5.20e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539516125  12 RDFSALMAGETSfLATLANTSALLFERLDGVNWAGFYLLEAQTLVL----GPFQGKIACVRIPVGKGVCGTAVATGTIQR 87
Cdd:COG2203   196 NEISQALRSALD-LEELLQRILELAGELLGADRGAILLVDEDGGELelvaAPGLPEEELGRLPLGEGLAGRALRTGEPVV 274

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1539516125  88 VEDVHAFDGHIACDAAS------NSEIVLPLTVDGQTIGVLDIDSTEYGRFSEEDEIGLKTL 143
Cdd:COG2203   275 VNDASTDPRFAPSLRELllalgiRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEAL 336
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 67-137 1.48e-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: 50.84  E-value: 1.48e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1539516125   67 VRIPVGKGVCGTAVATGTIQRVEDVHA---FDGHIACDA-ASNSEIVLPLTVDGQTIGVLDIDSTEYGR-FSEEDE 137
Cdd:smart00065  50 IRFPLDEGLAGRVAETGRPLNIPDVEAdplFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDE 125
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
48-143 5.86e-08

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 49.89  E-value: 5.86e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539516125  48 YLL--EAQTLVL----GPFQGKIACVRIPVGKGVCGTAVATGTIQRVEDVHAFDGHIACDAA----SNSEIVLPLTVDGQ 117
Cdd:COG3605    42 YLLdpDGGRLELrateGLNPEAVGKVRLPLGEGLVGLVAERGEPLNLADAASHPRFKYFPETgeegFRSFLGVPIIRRGR 121

                          90       100
                  ....*....|....*....|....*.
gi 1539516125 118 TIGVLDIDSTEYGRFSEEDEIGLKTL 143
Cdd:COG3605   122 VLGVLVVQSREPREFTEEEVEFLVTL 147
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 26-137 4.35e-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: 4.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539516125  26 ATLANTSALLFERLdGVNWAGFYLLEAQTLVL---GPFQGKIACVRIPVGKGVcgTAVATGTIQRVEDV-----HAFDGH 97
Cdd:pfam01590   4 EILQTILEELRELL-GADRCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAagdprFLDPLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1539516125  98 IACDAASNSEIVLPLTVDGQTIGVLDIDSTEyGRFSEEDE 137
Cdd:pfam01590  81 LLRNFGIRSLLAVPIIDDGELLGVLVLHHPR-PPFTEEEL 119
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 108-143 1.93e-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: 40.60  E-value: 1.93e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1539516125 108 IVLPLTVDGQTIGVLDIDSTEYGRFSEEDEIGLKTL 143
Cdd:COG3604    77 LGVPLRVGGEVLGVLTLDSRRPGAFSEEDLRLLETL 112
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
110-145 9.33e-03

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 35.53  E-value: 9.33e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1539516125 110 LPLTVDGQTIGVLDIDSTEYGRFSEEDEIGLKTLVS 145
Cdd:PRK05022  115 LPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAA 150
 
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