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Conserved domains on  [gi|526480703|gb|AGR87986|]
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phytochrome A, partial [Diospyros wallichii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 228-390 1.03e-65

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: 206.74  E-value: 1.03e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703  228 ILRTQTLLCDMLMR--DAPLGIVSQSPNVMDLVKCDGAALLYKNKIYKLGATPTDLQLRDIVSWLSEYHmDSTGLSTDSL 305
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703  306 YDAgFPGALALGDVVCGMAAVRITSNDM--LFWFRSHTAAEIRWGGAKHEPGEKDD-GRKMHPRASFKAFLQVVKSRSLP 382
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158


                  ....*...
gi 526480703  383 WKDYEMDA 390
Cdd:pfam00360 159 WSEVEIEA 166
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 35-219 1.03e-13

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: 68.18  E-value: 1.03e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703    35 IERLCDTMVQEVFELTGYDRVMAYKFHDDDHGEVVAELTKPDLEPYLGLHYPATDipQAARFLFMKNKVRMICDCrakhv 114
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDV----- 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703   115 kvlqdeklpfdltlcgstLRAPHSCHLQYMENMNSIASLVMAVVVNEgdeegensdtarpqkrkRLWGLVVCHNTTprfV 194
Cdd:smart00065  75 ------------------EADPLFAEDLLGRYQGVRSFLAVPLVADG-----------------ELVGVLALHNKK---S 116

                          170       180
                   ....*....|....*....|....*
gi 526480703   195 PFPLRYACEFLAQVFAIHINKELEL 219
Cdd:smart00065 117 PRPFTEEDEELLQALANQLAIALAN 141
 
Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 228-390 1.03e-65

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: 206.74  E-value: 1.03e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703  228 ILRTQTLLCDMLMR--DAPLGIVSQSPNVMDLVKCDGAALLYKNKIYKLGATPTDLQLRDIVSWLSEYHmDSTGLSTDSL 305
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703  306 YDAgFPGALALGDVVCGMAAVRITSNDM--LFWFRSHTAAEIRWGGAKHEPGEKDD-GRKMHPRASFKAFLQVVKSRSLP 382
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158


                  ....*...
gi 526480703  383 WKDYEMDA 390
Cdd:pfam00360 159 WSEVEIEA 166
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 35-219 1.03e-13

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: 68.18  E-value: 1.03e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703    35 IERLCDTMVQEVFELTGYDRVMAYKFHDDDHGEVVAELTKPDLEPYLGLHYPATDipQAARFLFMKNKVRMICDCrakhv 114
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDV----- 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703   115 kvlqdeklpfdltlcgstLRAPHSCHLQYMENMNSIASLVMAVVVNEgdeegensdtarpqkrkRLWGLVVCHNTTprfV 194
Cdd:smart00065  75 ------------------EADPLFAEDLLGRYQGVRSFLAVPLVADG-----------------ELVGVLALHNKK---S 116

                          170       180
                   ....*....|....*....|....*
gi 526480703   195 PFPLRYACEFLAQVFAIHINKELEL 219
Cdd:smart00065 117 PRPFTEEDEELLQALANQLAIALAN 141
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 34-217 2.96e-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: 60.57  E-value: 2.96e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703   34 SIERLCDTMVQEVFELTGYDRVMAYkfhdddhgevvaeltkpdLEPYLGLHYpatdIPQAARFLfmknKVRMICDCRAKH 113
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALY------------------LPDADGLEY----LPPGARWL----KAAGLEIPPGTG 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703  114 VKVLQDEKlpfDLTLCGStlrAPHSCHLQ---YMENMNSIASLVMAVVVNEgdeegensdtarpqkrkRLWGLVVCHNTT 190
Cdd:pfam01590  55 VTVLRTGR---PLVVPDA---AGDPRFLDpllLLRNFGIRSLLAVPIIDDG-----------------ELLGVLVLHHPR 111

                         170       180
                  ....*....|....*....|....*..
gi 526480703  191 PRFvpfpLRYACEFLaQVFAIHINKEL 217
Cdd:pfam01590 112 PPF----TEEELELL-EVLADQVAIAL 133
 
Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 228-390 1.03e-65

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: 206.74  E-value: 1.03e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703  228 ILRTQTLLCDMLMR--DAPLGIVSQSPNVMDLVKCDGAALLYKNKIYKLGATPTDLQLRDIVSWLSEYHmDSTGLSTDSL 305
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703  306 YDAgFPGALALGDVVCGMAAVRITSNDM--LFWFRSHTAAEIRWGGAKHEPGEKDD-GRKMHPRASFKAFLQVVKSRSLP 382
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158


                  ....*...
gi 526480703  383 WKDYEMDA 390
Cdd:pfam00360 159 WSEVEIEA 166
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 35-219 1.03e-13

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: 68.18  E-value: 1.03e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703    35 IERLCDTMVQEVFELTGYDRVMAYKFHDDDHGEVVAELTKPDLEPYLGLHYPATDipQAARFLFMKNKVRMICDCrakhv 114
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDV----- 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703   115 kvlqdeklpfdltlcgstLRAPHSCHLQYMENMNSIASLVMAVVVNEgdeegensdtarpqkrkRLWGLVVCHNTTprfV 194
Cdd:smart00065  75 ------------------EADPLFAEDLLGRYQGVRSFLAVPLVADG-----------------ELVGVLALHNKK---S 116

                          170       180
                   ....*....|....*....|....*
gi 526480703   195 PFPLRYACEFLAQVFAIHINKELEL 219
Cdd:smart00065 117 PRPFTEEDEELLQALANQLAIALAN 141
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 34-217 2.96e-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: 60.57  E-value: 2.96e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703   34 SIERLCDTMVQEVFELTGYDRVMAYkfhdddhgevvaeltkpdLEPYLGLHYpatdIPQAARFLfmknKVRMICDCRAKH 113
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALY------------------LPDADGLEY----LPPGARWL----KAAGLEIPPGTG 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526480703  114 VKVLQDEKlpfDLTLCGStlrAPHSCHLQ---YMENMNSIASLVMAVVVNEgdeegensdtarpqkrkRLWGLVVCHNTT 190
Cdd:pfam01590  55 VTVLRTGR---PLVVPDA---AGDPRFLDpllLLRNFGIRSLLAVPIIDDG-----------------ELLGVLVLHHPR 111

                         170       180
                  ....*....|....*....|....*..
gi 526480703  191 PRFvpfpLRYACEFLaQVFAIHINKEL 217
Cdd:pfam01590 112 PPF----TEEELELL-EVLADQVAIAL 133
 
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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