helix turn helix transcriptional regulator similar to SrmR transcriptional regulatory gene governing the expression of a polyketide synthase gene in Streptomyces ambofaciens
PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the ...
566-621
1.22e-13
PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the C-terminus of PucR-like transcriptional regulators such as Swiss:O32138 and is likely to be DNA-binding.
Pssm-ID: 433305 [Multi-domain] Cd Length: 56 Bit Score: 65.55 E-value: 1.22e-13
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
76-203
1.92e-11
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: 62.40 E-value: 1.92e-11
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
75-203
2.02e-09
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: 56.32 E-value: 2.02e-09
PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the ...
566-621
1.22e-13
PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the C-terminus of PucR-like transcriptional regulators such as Swiss:O32138 and is likely to be DNA-binding.
Pssm-ID: 433305 [Multi-domain] Cd Length: 56 Bit Score: 65.55 E-value: 1.22e-13
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
76-203
1.92e-11
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: 62.40 E-value: 1.92e-11
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
75-203
2.02e-09
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: 56.32 E-value: 2.02e-09
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
76-203
5.05e-09
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: 54.79 E-value: 5.05e-09
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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