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Conserved domains on  [gi|238547725|dbj|BAH64076|]
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hypothetical protein KP1_3475 [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044]

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, ...
 20-172 1.10e-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: 241.27  E-value: 1.10e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725  20 MSKTEFYADLNRDFQALMAGETSFLAMIANTSALLFERLSEVNWAGFYLLEG-DTLVLGPFQGKLACVRIPVGRGVCGAA 98
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 238547725  99 VAQAQVQRVEDVHAFDGHIACDAASNSEIVFPLRVNGQIIGVLDIDSPAYGRFTAEDEQGLRTLVEHLEKLIAA 172
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 20-172 1.10e-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: 241.27  E-value: 1.10e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725  20 MSKTEFYADLNRDFQALMAGETSFLAMIANTSALLFERLSEVNWAGFYLLEG-DTLVLGPFQGKLACVRIPVGRGVCGAA 98
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 238547725  99 VAQAQVQRVEDVHAFDGHIACDAASNSEIVFPLRVNGQIIGVLDIDSPAYGRFTAEDEQGLRTLVEHLEKLIAA 172
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 53-171 2.14e-10

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: 55.94  E-value: 2.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725   53 LLFERLSEVNWA--GFYLL--EGDTLVLGPFQGKLACVRI--PVGRGVCGAAVAQAQVQRVEDV---HAFDGHIACDAAS 123
Cdd:pfam13185  10 AVLEAAVELGASavGFILLvdDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGL 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 238547725  124 NSEIVFPLRVNGQIIGVLDIDSPAYGRFTAEDEQGLRTLVEHLEKLIA 171
Cdd:pfam13185  90 RSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAEQAAIAIE 137
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 28-175 6.40e-09

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: 52.38  E-value: 6.40e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725    28 DLNRDFQALMAGETSFLAMIaNTSALLFERLSEvNWAGFYLLEGDTLVLGPfqgklacVRIPVGRGVCGAAVAQAQVQRV 107
Cdd:smart00065   1 DLEELLQTILEELRQLLGAD-RVLIYLVDENDR-GELVLVAADGLTLPTLG-------IRFPLDEGLAGRVAETGRPLNI 71

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 238547725   108 EDVHA---FDGHIACDA-ASNSEIVFPLRVNGQIIGVLDIDSPAYGR-FTAEDEQGLRTLVEHLEKLIAATDY 175
Cdd:smart00065  72 PDVEAdplFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQALANQLAIALANAQL 144
 
Name Accession Description Interval E-value
MsrC COG1956
GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, ...
 20-172 1.10e-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: 241.27  E-value: 1.10e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725  20 MSKTEFYADLNRDFQALMAGETSFLAMIANTSALLFERLSEVNWAGFYLLEG-DTLVLGPFQGKLACVRIPVGRGVCGAA 98
Cdd:COG1956    3 TSKEEDYDELLAQLSALLAGETDLIANLANISALLFEALPDYNWVGFYLVDGgGELVLGPFQGPPACTRIPFGKGVCGTA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 238547725  99 VAQAQVQRVEDVHAFDGHIACDAASNSEIVFPLRVNGQIIGVLDIDSPAYGRFTAEDEQGLRTLVEHLEKLIAA 172
Cdd:COG1956   83 AAEGETQLVPDVHAFPGHIACDSASRSEIVVPIFKDGEVIGVLDIDSPTPGRFDEEDQAGLEALAALLAEALDA 156
GAF_2 pfam13185
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 53-171 2.14e-10

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: 55.94  E-value: 2.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725   53 LLFERLSEVNWA--GFYLL--EGDTLVLGPFQGKLACVRI--PVGRGVCGAAVAQAQVQRVEDV---HAFDGHIACDAAS 123
Cdd:pfam13185  10 AVLEAAVELGASavGFILLvdDDGRLAAWGGAADELSAALddPPGEGLVGEALRTGRPVIVNDLaadPAKKGLPAGHAGL 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 238547725  124 NSEIVFPLRVNGQIIGVLDIDSPAYGRFTAEDEQGLRTLVEHLEKLIA 171
Cdd:pfam13185  90 RSFLSVPLVSGGRVVGVLALGSNRPGAFDEEDLELLELLAEQAAIAIE 137
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 28-175 6.40e-09

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: 52.38  E-value: 6.40e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725    28 DLNRDFQALMAGETSFLAMIaNTSALLFERLSEvNWAGFYLLEGDTLVLGPfqgklacVRIPVGRGVCGAAVAQAQVQRV 107
Cdd:smart00065   1 DLEELLQTILEELRQLLGAD-RVLIYLVDENDR-GELVLVAADGLTLPTLG-------IRFPLDEGLAGRVAETGRPLNI 71

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 238547725   108 EDVHA---FDGHIACDA-ASNSEIVFPLRVNGQIIGVLDIDSPAYGR-FTAEDEQGLRTLVEHLEKLIAATDY 175
Cdd:smart00065  72 PDVEAdplFAEDLLGRYqGVRSFLAVPLVADGELVGVLALHNKKSPRpFTEEDEELLQALANQLAIALANAQL 144
PtsP COG3605
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
67-171 9.25e-08

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


Pssm-ID: 442824 [Multi-domain]  Cd Length: 188  Bit Score: 49.51  E-value: 9.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725  67 YLL--EGDTLVL----GPFQGKLACVRIPVGRGVCGAAVAQAQVQRVEDVHAFDGHIACDAA----SNSEIVFPLRVNGQ 136
Cdd:COG3605   42 YLLdpDGGRLELrateGLNPEAVGKVRLPLGEGLVGLVAERGEPLNLADAASHPRFKYFPETgeegFRSFLGVPIIRRGR 121

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 238547725 137 IIGVLDIDSPAYGRFTAEDEQGLRTLVEHLEKLIA 171
Cdd:COG3605  122 VLGVLVVQSREPREFTEEEVEFLVTLAAQLAEAIA 156
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 44-170 9.12e-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: 43.24  E-value: 9.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725   44 LAMIANTSALLFERLSEVNWAGFYLLEGDTLVL---GPFQGKLACVRIPVGRGVcgAAVAQAQVQRVEDV-----HAFDG 115
Cdd:pfam01590   2 LEEILQTILEELRELLGADRCALYLPDADGLEYlppGARWLKAAGLEIPPGTGV--TVLRTGRPLVVPDAagdprFLDPL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 238547725  116 HIACDAASNSEIVFPLRVNGQIIGVLDIDSPAyGRFTAEDEQGLRTLVEHLEKLI 170
Cdd:pfam01590  80 LLLRNFGIRSLLAVPIIDDGELLGVLVLHHPR-PPFTEEELELLEVLADQVAIAL 133
GAF COG2203
GAF domain [Signal transduction mechanisms];
57-166 1.27e-05

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 44.80  E-value: 1.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725  57 RLSEVNWAGFYLLEGDTLVL----GPFQGKLACVRIPVGRGVCGAAVAQAQVQRVEDVHAFDGHIACDAAS------NSE 126
Cdd:COG2203  221 ELLGADRGAILLVDEDGGELelvaAPGLPEEELGRLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELllalgiRSL 300

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 238547725 127 IVFPLRVNGQIIGVLDIDSPAYGRFTAEDEQGLRTLVEHL 166
Cdd:COG2203  301 LCVPLLVDGRLIGVLALYSKEPRAFTEEDLELLEALADQA 340
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 52-170 1.78e-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: 44.07  E-value: 1.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238547725  52 ALLFERLSEVNWAGFYLLEGDTLVLGPFQGKLACVRIPVGRGVCGAAVAQAQVQRVEDVHAFDGHIACdaasnseIVFPL 131
Cdd:COG3604    9 GLPLLLLLALALLLLVLLLLALLLRGDLLASALVLEESLELLALALSEALLAAQARQAALAARERQLF-------LGVPL 81

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 238547725 132 RVNGQIIGVLDIDSPAYGRFTAEDEQGLRTLVEHLEKLI 170
Cdd:COG3604   82 RVGGEVLGVLTLDSRRPGAFSEEDLRLLETLASLAAVAI 120
 
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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