effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
882-998
8.96e-15
effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels
:
Pssm-ID: 237999 [Multi-domain] Cd Length: 115 Bit Score: 71.59 E-value: 8.96e-15
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
613-726
1.30e-09
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.
:
Pssm-ID: 459842 [Multi-domain] Cd Length: 238 Bit Score: 59.97 E-value: 1.30e-09
Sodium/hydrogen exchanger family; Na/H antiporters are key transporters in maintaining the pH ...
19-367
1.83e-23
Sodium/hydrogen exchanger family; Na/H antiporters are key transporters in maintaining the pH of actively metabolising cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminus and a large cytoplasmic region at the carboxyl terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family.
Pssm-ID: 425982 [Multi-domain] Cd Length: 377 Bit Score: 103.87 E-value: 1.83e-23
Na+/H+ antiporter, bacterial form; The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC ...
18-423
2.32e-16
Na+/H+ antiporter, bacterial form; The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals. Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in (1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles. This model is specific for the bacterial members of this family. [Transport and binding proteins, Cations and iron carrying compounds]
Pssm-ID: 129911 [Multi-domain] Cd Length: 525 Bit Score: 83.78 E-value: 2.32e-16
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
882-998
8.96e-15
effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels
Pssm-ID: 237999 [Multi-domain] Cd Length: 115 Bit Score: 71.59 E-value: 8.96e-15
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
613-726
1.30e-09
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.
Pssm-ID: 459842 [Multi-domain] Cd Length: 238 Bit Score: 59.97 E-value: 1.30e-09
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
884-1001
1.05e-07
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
Pssm-ID: 197516 [Multi-domain] Cd Length: 120 Bit Score: 51.63 E-value: 1.05e-07
Sodium/hydrogen exchanger family; Na/H antiporters are key transporters in maintaining the pH ...
19-367
1.83e-23
Sodium/hydrogen exchanger family; Na/H antiporters are key transporters in maintaining the pH of actively metabolising cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminus and a large cytoplasmic region at the carboxyl terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family.
Pssm-ID: 425982 [Multi-domain] Cd Length: 377 Bit Score: 103.87 E-value: 1.83e-23
Na+/H+ antiporter, bacterial form; The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC ...
18-423
2.32e-16
Na+/H+ antiporter, bacterial form; The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals. Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in (1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles. This model is specific for the bacterial members of this family. [Transport and binding proteins, Cations and iron carrying compounds]
Pssm-ID: 129911 [Multi-domain] Cd Length: 525 Bit Score: 83.78 E-value: 2.32e-16
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
882-998
8.96e-15
effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels
Pssm-ID: 237999 [Multi-domain] Cd Length: 115 Bit Score: 71.59 E-value: 8.96e-15
sodium/hydrogen exchanger 3; The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A. ...
74-384
1.17e-09
sodium/hydrogen exchanger 3; The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36)The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals.Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in(1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles.This model is specific for the eukaryotic members members of this family. [Transport and binding proteins, Cations and iron carrying compounds]
Pssm-ID: 273294 [Multi-domain] Cd Length: 559 Bit Score: 62.49 E-value: 1.17e-09
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
613-726
1.30e-09
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.
Pssm-ID: 459842 [Multi-domain] Cd Length: 238 Bit Score: 59.97 E-value: 1.30e-09
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
884-1001
1.05e-07
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
Pssm-ID: 197516 [Multi-domain] Cd Length: 120 Bit Score: 51.63 E-value: 1.05e-07
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.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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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.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
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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.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
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specific hits meet or exceed a domain-specific e-value threshold
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and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
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the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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