NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|349602217|gb|AEP96392|]
View 

phytochrome b, partial [Urelytrum digitatum]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 208-362 1.18e-57

Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilize the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue.


:

Pssm-ID: 425635  Cd Length: 178  Bit Score: 185.16  E-value: 1.18e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217  208 ILRTQTLLCDMLLR--DSPTGIVTQSPSIMDLV*CDGAALY*HGKYYPLGVTPTESZIKDIIEWLT*CHgDSTGLSTDSL 285
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217  286 ADAgYLGAAALGDAVCGMAVAYI--TPSDYLFWFRSHTAKEIKWGGAKHHPEDKDD-GQRMHPRSSFKAFLEVVKSRSLP 362
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPIsrKPGNYLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 15-207 9.15e-24

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: 95.53  E-value: 9.15e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217    15 D*KLLCDTVVEHVRELTGYDRVMV*RFHEDEHGEVVAESRRDNLEPYLGLHYPATDipQASRFLFRQNRVRMIADCHATP 94
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEADP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217    95 VRviqDPGL*QPLCLVGSTLRAPhgchaqymanmgsiaslvmavIISGGgddeqtgrggissamKLWGLVVCHHtspRCI 174
Cdd:smart00065  79 LF---AEDLLGRYQGVRSFLAVP---------------------LVADG---------------ELVGVLALHN---KKS 116

                          170       180       190
                   ....*....|....*....|....*....|...
gi 349602217   175 P*PLRYACEFLMQAFGLQLNMELQLAHQLSEKH 207
Cdd:smart00065 117 PRPFTEEDEELLQALANQLAIALANAQLYEELR 149
 
Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 208-362 1.18e-57

Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilize the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue.


Pssm-ID: 425635  Cd Length: 178  Bit Score: 185.16  E-value: 1.18e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217  208 ILRTQTLLCDMLLR--DSPTGIVTQSPSIMDLV*CDGAALY*HGKYYPLGVTPTESZIKDIIEWLT*CHgDSTGLSTDSL 285
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217  286 ADAgYLGAAALGDAVCGMAVAYI--TPSDYLFWFRSHTAKEIKWGGAKHHPEDKDD-GQRMHPRSSFKAFLEVVKSRSLP 362
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPIsrKPGNYLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 15-207 9.15e-24

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: 95.53  E-value: 9.15e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217    15 D*KLLCDTVVEHVRELTGYDRVMV*RFHEDEHGEVVAESRRDNLEPYLGLHYPATDipQASRFLFRQNRVRMIADCHATP 94
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEADP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217    95 VRviqDPGL*QPLCLVGSTLRAPhgchaqymanmgsiaslvmavIISGGgddeqtgrggissamKLWGLVVCHHtspRCI 174
Cdd:smart00065  79 LF---AEDLLGRYQGVRSFLAVP---------------------LVADG---------------ELVGVLALHN---KKS 116

                          170       180       190
                   ....*....|....*....|....*....|...
gi 349602217   175 P*PLRYACEFLMQAFGLQLNMELQLAHQLSEKH 207
Cdd:smart00065 117 PRPFTEEDEELLQALANQLAIALANAQLYEELR 149
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 15-197 4.14e-11

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: 60.19  E-value: 4.14e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217   15 D*KLLCDTVVEHVRELTGYDRVMV*RFhedehgevvaesrrdnlePYLGLHYpatdIPQASRFLFRQNRVRMIadchATP 94
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLP------------------DADGLEY----LPPGARWLKAAGLEIPP----GTG 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217   95 VRVIQDPgl*QPLCLVGStlrAPHGCHAQ---YMANMGSIASLVMAVIISGggddeqtgrggissamKLWGLVVCHHTSP 171
Cdd:pfam01590  55 VTVLRTG---RPLVVPDA---AGDPRFLDpllLLRNFGIRSLLAVPIIDDG----------------ELLGVLVLHHPRP 112

                         170       180
                  ....*....|....*....|....*.
gi 349602217  172 Rcip*PLRYACEFLmQAFGLQLNMEL 197
Cdd:pfam01590 113 P----FTEEELELL-EVLADQVAIAL 133
GAF COG2203
GAF domain [Signal transduction mechanisms];
19-172 3.73e-03

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 39.41  E-value: 3.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217  19 LCDTVVEHVRELTGYDRVMV*RFHEDEHGEVVAESRRDNLEPYLGLHYPATDIPQAsrflFRQNRVRMIADCHatpvrvi 98
Cdd:COG2203  211 LLQRILELAGELLGADRGAILLVDEDGGELELVAAPGLPEEELGRLPLGEGLAGRA----LRTGEPVVVNDAS------- 279

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 349602217  99 QDPGL*qplclvgstlrapHGCHAQYMANMGSIASLVMAVIISGggddeqtgrggissamKLWGLVVCHHTSPR 172
Cdd:COG2203  280 TDPRF--------------APSLRELLLALGIRSLLCVPLLVDG----------------RLIGVLALYSKEPR 323
 
Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 208-362 1.18e-57

Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilize the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue.


Pssm-ID: 425635  Cd Length: 178  Bit Score: 185.16  E-value: 1.18e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217  208 ILRTQTLLCDMLLR--DSPTGIVTQSPSIMDLV*CDGAALY*HGKYYPLGVTPTESZIKDIIEWLT*CHgDSTGLSTDSL 285
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217  286 ADAgYLGAAALGDAVCGMAVAYI--TPSDYLFWFRSHTAKEIKWGGAKHHPEDKDD-GQRMHPRSSFKAFLEVVKSRSLP 362
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPIsrKPGNYLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 15-207 9.15e-24

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: 95.53  E-value: 9.15e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217    15 D*KLLCDTVVEHVRELTGYDRVMV*RFHEDEHGEVVAESRRDNLEPYLGLHYPATDipQASRFLFRQNRVRMIADCHATP 94
Cdd:smart00065   1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEADP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217    95 VRviqDPGL*QPLCLVGSTLRAPhgchaqymanmgsiaslvmavIISGGgddeqtgrggissamKLWGLVVCHHtspRCI 174
Cdd:smart00065  79 LF---AEDLLGRYQGVRSFLAVP---------------------LVADG---------------ELVGVLALHN---KKS 116

                          170       180       190
                   ....*....|....*....|....*....|...
gi 349602217   175 P*PLRYACEFLMQAFGLQLNMELQLAHQLSEKH 207
Cdd:smart00065 117 PRPFTEEDEELLQALANQLAIALANAQLYEELR 149
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 15-197 4.14e-11

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: 60.19  E-value: 4.14e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217   15 D*KLLCDTVVEHVRELTGYDRVMV*RFhedehgevvaesrrdnlePYLGLHYpatdIPQASRFLFRQNRVRMIadchATP 94
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLP------------------DADGLEY----LPPGARWLKAAGLEIPP----GTG 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217   95 VRVIQDPgl*QPLCLVGStlrAPHGCHAQ---YMANMGSIASLVMAVIISGggddeqtgrggissamKLWGLVVCHHTSP 171
Cdd:pfam01590  55 VTVLRTG---RPLVVPDA---AGDPRFLDpllLLRNFGIRSLLAVPIIDDG----------------ELLGVLVLHHPRP 112

                         170       180
                  ....*....|....*....|....*.
gi 349602217  172 Rcip*PLRYACEFLmQAFGLQLNMEL 197
Cdd:pfam01590 113 P----FTEEELELL-EVLADQVAIAL 133
GAF COG2203
GAF domain [Signal transduction mechanisms];
19-172 3.73e-03

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 39.41  E-value: 3.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349602217  19 LCDTVVEHVRELTGYDRVMV*RFHEDEHGEVVAESRRDNLEPYLGLHYPATDIPQAsrflFRQNRVRMIADCHatpvrvi 98
Cdd:COG2203  211 LLQRILELAGELLGADRGAILLVDEDGGELELVAAPGLPEEELGRLPLGEGLAGRA----LRTGEPVVVNDAS------- 279

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 349602217  99 QDPGL*qplclvgstlrapHGCHAQYMANMGSIASLVMAVIISGggddeqtgrggissamKLWGLVVCHHTSPR 172
Cdd:COG2203  280 TDPRF--------------APSLRELLLALGIRSLLCVPLLVDG----------------RLIGVLALYSKEPR 323
 
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