phyA, partial [Quercus phillyraeoides]
Protein Classification
GAF domain-containing protein( domain architecture ID 10637617)
GAF domain-containing protein
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| GAF_2 super family | cl21515 | GAF domain; The GAF domain is named after some of the proteins it is found in, including ... |
206-291 | 1.25e-24 | ||||
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). The actual alignment was detected with superfamily member pfam00360: Pssm-ID: 473894 Cd Length: 178 Bit Score: 97.34 E-value: 1.25e-24
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| GAF | smart00065 | Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ... |
13-197 | 8.54e-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: 64.71 E-value: 8.54e-13
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| Name | Accession | Description | Interval | E-value | ||||
| PHY | pfam00360 | Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ... |
206-291 | 1.25e-24 | ||||
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: 97.34 E-value: 1.25e-24
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| GAF | smart00065 | Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ... |
13-197 | 8.54e-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: 64.71 E-value: 8.54e-13
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| GAF | pfam01590 | GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ... |
12-195 | 6.66e-12 | ||||
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: 61.73 E-value: 6.66e-12
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| Name | Accession | Description | Interval | E-value | ||||
| PHY | pfam00360 | Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ... |
206-291 | 1.25e-24 | ||||
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: 97.34 E-value: 1.25e-24
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| GAF | smart00065 | Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ... |
13-197 | 8.54e-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: 64.71 E-value: 8.54e-13
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| GAF | pfam01590 | GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ... |
12-195 | 6.66e-12 | ||||
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: 61.73 E-value: 6.66e-12
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