glutamate receptor 1.1 [Arabidopsis thaliana]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| PBP1_GABAb_receptor_plant | cd19990 | periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close ... |
31-397 | 1.06e-144 | ||||||
periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close homologs in other plants; This group includes the ligand-binding domain of Arabidopsis thaliana glutamate receptors, which have sequence similarity with animal ionotropic glutamate receptor and its close homologs in other plants. The ligand-binding domain of GABAb receptors are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb receptor or GABAbR). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha-i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example. : Pssm-ID: 380645 [Multi-domain] Cd Length: 373 Bit Score: 430.50 E-value: 1.06e-144
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| Periplasmic_Binding_Protein_Type_2 super family | cl21456 | Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ... |
421-737 | 4.92e-69 | ||||||
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences. The actual alignment was detected with superfamily member cd13686: Pssm-ID: 473866 [Multi-domain] Cd Length: 232 Bit Score: 227.40 E-value: 4.92e-69
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| Name | Accession | Description | Interval | E-value | ||||||
| PBP1_GABAb_receptor_plant | cd19990 | periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close ... |
31-397 | 1.06e-144 | ||||||
periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close homologs in other plants; This group includes the ligand-binding domain of Arabidopsis thaliana glutamate receptors, which have sequence similarity with animal ionotropic glutamate receptor and its close homologs in other plants. The ligand-binding domain of GABAb receptors are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb receptor or GABAbR). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha-i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example. Pssm-ID: 380645 [Multi-domain] Cd Length: 373 Bit Score: 430.50 E-value: 1.06e-144
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| ANF_receptor | pfam01094 | Receptor family ligand binding region; This family includes extracellular ligand binding ... |
45-377 | 2.09e-71 | ||||||
Receptor family ligand binding region; This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure. Pssm-ID: 460062 [Multi-domain] Cd Length: 347 Bit Score: 238.05 E-value: 2.09e-71
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| GluR_Plant | cd13686 | Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily ... |
421-737 | 4.92e-69 | ||||||
Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily contains the glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270404 [Multi-domain] Cd Length: 232 Bit Score: 227.40 E-value: 4.92e-69
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| Lig_chan | pfam00060 | Ligand-gated ion channel; This family includes the four transmembrane regions of the ... |
540-780 | 1.59e-51 | ||||||
Ligand-gated ion channel; This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors. Pssm-ID: 459656 [Multi-domain] Cd Length: 267 Bit Score: 180.97 E-value: 1.59e-51
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| LivK | COG0683 | ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid ... |
28-385 | 1.13e-23 | ||||||
ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid transport and metabolism]; Pssm-ID: 440447 [Multi-domain] Cd Length: 314 Bit Score: 102.70 E-value: 1.13e-23
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| PBPe | smart00079 | Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ... |
655-739 | 5.31e-08 | ||||||
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb Pssm-ID: 197504 [Multi-domain] Cd Length: 133 Bit Score: 52.29 E-value: 5.31e-08
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
448-529 | 2.12e-05 | ||||||
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms]; Pssm-ID: 440596 [Multi-domain] Cd Length: 223 Bit Score: 46.51 E-value: 2.12e-05
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| glnH | PRK09495 | glutamine ABC transporter periplasmic protein; Reviewed |
702-737 | 4.08e-04 | ||||||
glutamine ABC transporter periplasmic protein; Reviewed Pssm-ID: 236540 [Multi-domain] Cd Length: 247 Bit Score: 42.81 E-value: 4.08e-04
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| Name | Accession | Description | Interval | E-value | ||||||
| PBP1_GABAb_receptor_plant | cd19990 | periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close ... |
31-397 | 1.06e-144 | ||||||
periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close homologs in other plants; This group includes the ligand-binding domain of Arabidopsis thaliana glutamate receptors, which have sequence similarity with animal ionotropic glutamate receptor and its close homologs in other plants. The ligand-binding domain of GABAb receptors are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb receptor or GABAbR). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha-i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example. Pssm-ID: 380645 [Multi-domain] Cd Length: 373 Bit Score: 430.50 E-value: 1.06e-144
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| ANF_receptor | pfam01094 | Receptor family ligand binding region; This family includes extracellular ligand binding ... |
45-377 | 2.09e-71 | ||||||
Receptor family ligand binding region; This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure. Pssm-ID: 460062 [Multi-domain] Cd Length: 347 Bit Score: 238.05 E-value: 2.09e-71
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| GluR_Plant | cd13686 | Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily ... |
421-737 | 4.92e-69 | ||||||
Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily contains the glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270404 [Multi-domain] Cd Length: 232 Bit Score: 227.40 E-value: 4.92e-69
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| Lig_chan | pfam00060 | Ligand-gated ion channel; This family includes the four transmembrane regions of the ... |
540-780 | 1.59e-51 | ||||||
Ligand-gated ion channel; This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors. Pssm-ID: 459656 [Multi-domain] Cd Length: 267 Bit Score: 180.97 E-value: 1.59e-51
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| LivK | COG0683 | ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid ... |
28-385 | 1.13e-23 | ||||||
ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid transport and metabolism]; Pssm-ID: 440447 [Multi-domain] Cd Length: 314 Bit Score: 102.70 E-value: 1.13e-23
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| Peripla_BP_6 | pfam13458 | Periplasmic binding protein; This family includes a diverse range of periplasmic binding ... |
29-365 | 2.96e-20 | ||||||
Periplasmic binding protein; This family includes a diverse range of periplasmic binding proteins. Pssm-ID: 433225 [Multi-domain] Cd Length: 342 Bit Score: 93.11 E-value: 2.96e-20
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| PBP1_glutamate_receptors-like | cd06269 | ligand-binding domain of family C G-protein couples receptors (GPCRs), membrane bound guanylyl ... |
50-294 | 5.30e-20 | ||||||
ligand-binding domain of family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as natriuretic peptide receptors (NPRs), and N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of ionotropic glutamate rece; This CD represents the ligand-binding domain of the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the ionotropic glutamate receptors, all of which are structurally similar and related to the periplasmic-binding fold type 1 family. The family C GPCRs consists of metabotropic glutamate receptor (mGluR), a calcium-sensing receptor (CaSR), gamma-aminobutyric acid receptor (GABAbR), the promiscuous L-alpha-amino acid receptor GPR6A, families of taste and pheromone receptors, and orphan receptors. Truncated splicing variants of the orphan receptors are not included in this CD. The family C GPCRs are activated by endogenous agonists such as amino acids, ions, and sugar based molecules. Their amino terminal ligand-binding region is homologous to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). The ionotropic glutamate receptors (iGluRs) have an integral ion channel and are subdivided into three major groups based on their pharmacology and structural similarities: NMDA receptors, AMPA receptors, and kainate receptors. The family of membrane bound guanylyl cyclases is further divided into three subfamilies: the ANP receptor (GC-A)/C-type natriuretic peptide receptor (GC-B), the heat-stable enterotoxin receptor (GC-C)/sensory organ specific membrane GCs such as retinal receptors (GC-E, GC-F), and olfactory receptors (GC-D and GC-G). Pssm-ID: 380493 [Multi-domain] Cd Length: 332 Bit Score: 92.10 E-value: 5.30e-20
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| PBP2_iGluR_ligand_binding | cd00998 | The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ... |
445-737 | 1.32e-19 | ||||||
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic binding protein type II superfamily; This subfamily represents the ligand binding of ionotropic glutamate receptors. iGluRs are heterotetrameric ion channels that comprises of three functionally distinct subtypes based on their pharmacology and structural similarities: AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid), NMDA (N-methyl-D-aspartate), and kainate receptors. All three types of channels are also activated by the physiological neurotransmitter, glutamate. iGluRs are concentrated at postsynaptic sites, where they exert a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I. Pssm-ID: 270219 [Multi-domain] Cd Length: 243 Bit Score: 88.97 E-value: 1.32e-19
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| PBP1_ABC_transporter_LIVBP-like | cd06268 | periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the ... |
31-225 | 2.08e-14 | ||||||
periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type 1 periplasmic binding fold protein superfamily; Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type 1 periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC-type Leucine-Isoleucine-Valine-Binding Proteins (LIVBP), which are homologous to the aliphatic amidase transcriptional repressor, AmiC, of Pseudomonas aeruginosa. The uncharacterized periplasmic components of various ABC-type transport systems are included in this group. Pssm-ID: 380492 [Multi-domain] Cd Length: 298 Bit Score: 74.67 E-value: 2.08e-14
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| PBP2_iGluR_Kainate_GluR7 | cd13723 | GluR7 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ... |
446-633 | 2.09e-12 | ||||||
GluR7 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270441 [Multi-domain] Cd Length: 369 Bit Score: 69.72 E-value: 2.09e-12
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| PBP1_ABC_ligand_binding-like | cd19984 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
37-225 | 5.13e-12 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380639 [Multi-domain] Cd Length: 296 Bit Score: 67.63 E-value: 5.13e-12
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| PBP2_iGluR_putative | cd13717 | The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ... |
444-633 | 2.25e-10 | ||||||
The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270435 [Multi-domain] Cd Length: 360 Bit Score: 63.09 E-value: 2.25e-10
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| PBP1_ABC_HAAT-like | cd06348 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
31-365 | 2.75e-10 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380571 [Multi-domain] Cd Length: 342 Bit Score: 62.64 E-value: 2.75e-10
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| PBP1_iGluR_Kainate | cd06382 | N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate ... |
45-389 | 6.25e-10 | ||||||
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1 and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. Pssm-ID: 380605 Cd Length: 335 Bit Score: 61.47 E-value: 6.25e-10
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| PBP1_SBP-like | cd06328 | periplasmic substrate-binding domain of active transport proteins (substrate binding proteins ... |
31-170 | 1.19e-09 | ||||||
periplasmic substrate-binding domain of active transport proteins (substrate binding proteins or SBPs); Periplasmic substrate-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. Pssm-ID: 380551 [Multi-domain] Cd Length: 336 Bit Score: 60.78 E-value: 1.19e-09
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| PBP1_ABC_ligand_binding-like | cd06346 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
31-303 | 2.10e-09 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380569 [Multi-domain] Cd Length: 314 Bit Score: 59.88 E-value: 2.10e-09
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| PBP1_ABC_LivK_ligand_binding-like | cd06347 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
59-365 | 4.23e-09 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380570 [Multi-domain] Cd Length: 334 Bit Score: 59.09 E-value: 4.23e-09
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| PBP1_ABC_ligand_binding-like | cd06341 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type ... |
59-217 | 1.86e-08 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters such as leucine-isoleucine-valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally. Pssm-ID: 380564 [Multi-domain] Cd Length: 340 Bit Score: 56.93 E-value: 1.86e-08
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| PBP2_iGluR_non_NMDA_like | cd13685 | The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ... |
420-529 | 2.03e-08 | ||||||
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors including AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) receptors (GluR1-4), kainate receptors (GluR5-7 and KA1/2), and orphan receptors delta 1/2. iGluRs form tetrameric ligand-gated ion channels, which are concentrated at postsynaptic sites in excitatory synapses where they fulfill a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine#binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I. Pssm-ID: 270403 [Multi-domain] Cd Length: 252 Bit Score: 56.04 E-value: 2.03e-08
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| PBP1_ABC_ligand_binding-like | cd19982 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type ... |
43-190 | 4.25e-08 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, their ligand specificity has not been determined experimentally. Pssm-ID: 380637 [Multi-domain] Cd Length: 302 Bit Score: 55.75 E-value: 4.25e-08
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| PBPe | smart00079 | Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ... |
655-739 | 5.31e-08 | ||||||
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb Pssm-ID: 197504 [Multi-domain] Cd Length: 133 Bit Score: 52.29 E-value: 5.31e-08
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| Lig_chan-Glu_bd | pfam10613 | Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ... |
445-523 | 9.56e-08 | ||||||
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060. Pssm-ID: 463166 [Multi-domain] Cd Length: 111 Bit Score: 50.98 E-value: 9.56e-08
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| PBP2_ArtJ_like | cd13697 | Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding ... |
437-534 | 9.60e-08 | ||||||
Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding protein fold; The ArtJ domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270415 [Multi-domain] Cd Length: 228 Bit Score: 53.69 E-value: 9.60e-08
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| PBP2_iGluR_Kainate | cd13714 | Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains ... |
437-529 | 1.58e-07 | ||||||
Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270432 [Multi-domain] Cd Length: 251 Bit Score: 53.31 E-value: 1.58e-07
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| PBP1_ABC_HAAT-like | cd19986 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
31-244 | 2.37e-07 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380641 [Multi-domain] Cd Length: 297 Bit Score: 53.40 E-value: 2.37e-07
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| PBP1_ABC_ligand_binding-like | cd06335 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type ... |
59-225 | 2.64e-07 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally. Pssm-ID: 380558 [Multi-domain] Cd Length: 348 Bit Score: 53.38 E-value: 2.64e-07
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| SBP_bac_3 | pfam00497 | Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ... |
448-737 | 3.23e-07 | ||||||
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 425719 [Multi-domain] Cd Length: 221 Bit Score: 51.91 E-value: 3.23e-07
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| PBP2_peptides_like | cd13530 | Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ... |
448-529 | 3.95e-07 | ||||||
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1, but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. Pssm-ID: 270248 [Multi-domain] Cd Length: 217 Bit Score: 51.48 E-value: 3.95e-07
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| PBP1_NPR_GC-like | cd06352 | ligand-binding domain of membrane guanylyl-cyclase receptors; Ligand-binding domain of ... |
60-365 | 4.83e-07 | ||||||
ligand-binding domain of membrane guanylyl-cyclase receptors; Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The ligand binding domain of the NPRs exhibits strong structural similarity to the type 1 periplasmic binding fold protein family. Pssm-ID: 380575 [Multi-domain] Cd Length: 391 Bit Score: 52.74 E-value: 4.83e-07
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| PBP1_RPA0668_benzoate-like | cd20014 | type 1 periplasmic binding-protein component of an ABC system (RPA0668), involved in in the ... |
31-134 | 7.43e-07 | ||||||
type 1 periplasmic binding-protein component of an ABC system (RPA0668), involved in in the active transport of lignin-derived benzoate derivative compounds, and its close homologs; This group includes RPA0668 from Rhodopseudomonas palustris and its close homologs in other bacteria. Rpa0668 is the periplasmic binding-protein component of an ABC system that is involved in the active transport of lignin-derived benzoate derivative compounds. Members of this group has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP). Pssm-ID: 380667 [Multi-domain] Cd Length: 346 Bit Score: 52.24 E-value: 7.43e-07
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| PBP1_GABAb_receptor | cd06366 | ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for ... |
152-403 | 8.07e-07 | ||||||
ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA); Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb receptor or GABAbR). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha-i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example. Pssm-ID: 380589 [Multi-domain] Cd Length: 404 Bit Score: 52.25 E-value: 8.07e-07
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| PBP1_ABC_ligand_binding-like | cd06345 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
31-190 | 2.55e-06 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380568 [Multi-domain] Cd Length: 356 Bit Score: 50.34 E-value: 2.55e-06
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| PBP1_ABC_RPA1789-like | cd06333 | type 1 periplasmic binding-protein component (CouP) of an ABC system (CouPSTU; RPA1789, ... |
67-226 | 2.87e-06 | ||||||
type 1 periplasmic binding-protein component (CouP) of an ABC system (CouPSTU; RPA1789, RPA1791-1793), involved in active transport of lignin-derived aromatic substrates, and its close homologs; This group includes RPA1789 (CouP) from Rhodopseudomonas palustris and its close homologs in other bacteria. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791-1793) that is involved in the active transport of lignin-derived aromatic substrates. Members of this group has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP). Pssm-ID: 380556 [Multi-domain] Cd Length: 342 Bit Score: 50.24 E-value: 2.87e-06
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| PBP2_iGluR_kainate_KA1 | cd13724 | The ligand-binding domain of the kainate subtype KA1 of ionotropic glutamate receptors, a ... |
446-563 | 3.99e-06 | ||||||
The ligand-binding domain of the kainate subtype KA1 of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the KA1 subunit of kainate receptor. While this ligand-binding domain is structurally homologous to the periplasmic binding fold type II superfamily, the N_terminal domain of kainate receptors belongs to the periplasmic-binding fold type I. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. Pssm-ID: 270442 [Multi-domain] Cd Length: 333 Bit Score: 49.63 E-value: 3.99e-06
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| PBP1_ABC_HAAT-like | cd19983 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
67-225 | 4.86e-06 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of hydrophobic amino acids or peptides; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of hydrophobic amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380638 [Multi-domain] Cd Length: 303 Bit Score: 49.12 E-value: 4.86e-06
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| PBP2_GluR0 | cd00997 | Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ... |
437-524 | 4.96e-06 | ||||||
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate receptor domain GluR0. These domains are found in the GluR0 proteins that have been shown to function as prokaryotic L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. The GluR0 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270218 [Multi-domain] Cd Length: 218 Bit Score: 48.49 E-value: 4.96e-06
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| PBPb | smart00062 | Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ... |
422-529 | 5.04e-06 | ||||||
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe Pssm-ID: 214497 [Multi-domain] Cd Length: 219 Bit Score: 48.48 E-value: 5.04e-06
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
448-529 | 2.12e-05 | ||||||
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms]; Pssm-ID: 440596 [Multi-domain] Cd Length: 223 Bit Score: 46.51 E-value: 2.12e-05
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| PBP1_SAP_GC-like | cd06370 | Ligand-binding domain of membrane bound guanylyl cyclases; Ligand-binding domain of membrane ... |
50-297 | 2.25e-05 | ||||||
Ligand-binding domain of membrane bound guanylyl cyclases; Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model. Pssm-ID: 380593 [Multi-domain] Cd Length: 400 Bit Score: 47.63 E-value: 2.25e-05
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| PBP1_ABC_ligand_binding-like | cd06340 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type ... |
67-190 | 3.39e-05 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, their ligand specificity has not been determined experimentally. Pssm-ID: 380563 [Multi-domain] Cd Length: 352 Bit Score: 46.78 E-value: 3.39e-05
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| PBP2_iGluR_AMPA | cd13715 | The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ... |
425-737 | 3.43e-05 | ||||||
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtypes of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This family represents the ligand-binding domain of the AMPA receptor subunits, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Pssm-ID: 270433 [Multi-domain] Cd Length: 261 Bit Score: 46.20 E-value: 3.43e-05
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| PBP1_ABC_ligand_binding-like | cd19980 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
59-360 | 3.82e-05 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380635 [Multi-domain] Cd Length: 334 Bit Score: 46.45 E-value: 3.82e-05
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| PBP2_GlnH | cd00994 | Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ... |
655-737 | 6.18e-05 | ||||||
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; This periplasmic substrate-binding component serves as an initial receptor in the ABC transport of glutamine in bacteria and eukaryota. GlnH belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270216 [Multi-domain] Cd Length: 218 Bit Score: 44.96 E-value: 6.18e-05
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| PBP1_ABC_LIVBP-like | cd06342 | type 1 periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active ... |
31-365 | 6.56e-05 | ||||||
type 1 periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); This subgroup includes the type 1 periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few. Pssm-ID: 380565 [Multi-domain] Cd Length: 334 Bit Score: 45.98 E-value: 6.56e-05
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| PBP1_GPCR_family_C-like | cd06350 | ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory ... |
73-296 | 7.25e-05 | ||||||
ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate; categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (m; Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The metabotropic glutamate receptors (mGluR) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. The mGluRs are coupled to G proteins and are thus distinct from the iGluRs which internally contain ligand-gated ion channels. The mGluR structure is divided into three regions: the extracellular region, the seven-spanning transmembrane region and the cytoplasmic region. The extracellular region is further divided into the ligand-binding domain (LBD) and the cysteine-rich domain. The LBD has sequence similarity to the LIVBP, which is a bacterial periplasmic protein (PBP), as well as to the extracellular region of both iGluR and the gamma-aminobutyric acid (GABA)b receptor. iGluRs are divided into three main subtypes based on pharmacological profile: NMDA, AMPA, and kainate receptors. All family C GPCRs have a large extracellular N terminus that contain a domain with homology to bacterial periplasmic amino acid-binding proteins. Pssm-ID: 380573 Cd Length: 350 Bit Score: 45.75 E-value: 7.25e-05
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| PBP1_ABC_HAAT-like | cd06349 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ... |
43-198 | 8.04e-05 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. Pssm-ID: 380572 [Multi-domain] Cd Length: 338 Bit Score: 45.64 E-value: 8.04e-05
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| PBP1_ABC_ligand_binding-like | cd06337 | type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type ... |
61-127 | 8.11e-05 | ||||||
type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally. Pssm-ID: 380560 [Multi-domain] Cd Length: 354 Bit Score: 45.75 E-value: 8.11e-05
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| PBP1_SBP-like | cd06327 | periplasmic substrate-binding domain of active transport proteins (substrate binding proteins ... |
31-154 | 8.94e-05 | ||||||
periplasmic substrate-binding domain of active transport proteins (substrate binding proteins or SBPs); Periplasmic substrate-binding domain of active transport proteins found in gram-negative, gram-positive bacteria, and archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. Pssm-ID: 380550 [Multi-domain] Cd Length: 336 Bit Score: 45.64 E-value: 8.94e-05
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| PBP1_SBP-like | cd19989 | periplasmic substrate-binding domain of active transport proteins; Periplasmic ... |
68-170 | 1.40e-04 | ||||||
periplasmic substrate-binding domain of active transport proteins; Periplasmic substrate-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. Pssm-ID: 380644 [Multi-domain] Cd Length: 299 Bit Score: 44.57 E-value: 1.40e-04
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| PBP2_iGluR_NMDA_Nr2 | cd13718 | The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) ... |
451-530 | 1.43e-04 | ||||||
The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. Pssm-ID: 270436 [Multi-domain] Cd Length: 283 Bit Score: 44.64 E-value: 1.43e-04
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| PBP1_AmiC-like | cd06331 | type 1 periplasmic components of amide-binding protein (AmiC) and the active transport system ... |
31-122 | 1.80e-04 | ||||||
type 1 periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF); This group includes the type 1 periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems. Pssm-ID: 380554 [Multi-domain] Cd Length: 333 Bit Score: 44.52 E-value: 1.80e-04
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| PBP2_iGluR_NMDA | cd13687 | The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ... |
447-530 | 2.33e-04 | ||||||
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; The ligand-binding domain of the ionotropic NMDA subtype is structurally homologous to the periplasmic-binding fold type II superfamily, while the N-terminal domain belongs to the periplasmic-binding fold type I. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. Pssm-ID: 270405 [Multi-domain] Cd Length: 239 Bit Score: 43.39 E-value: 2.33e-04
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| glnH | PRK09495 | glutamine ABC transporter periplasmic protein; Reviewed |
702-737 | 4.08e-04 | ||||||
glutamine ABC transporter periplasmic protein; Reviewed Pssm-ID: 236540 [Multi-domain] Cd Length: 247 Bit Score: 42.81 E-value: 4.08e-04
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| PBP2_Dsm1740 | cd13629 | Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ... |
450-537 | 7.17e-04 | ||||||
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily includes the periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBPII proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. Pssm-ID: 270347 [Multi-domain] Cd Length: 221 Bit Score: 41.79 E-value: 7.17e-04
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| PBP1_Nba-like | cd06359 | type 1 periplasmic binding component of active transport systems predicted to be involved in ... |
31-151 | 8.79e-04 | ||||||
type 1 periplasmic binding component of active transport systems predicted to be involved in 2-nitrobenzoic acid degradation pathway; This group includes the type 1 periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; their substrate specificities are not well characterized. Pssm-ID: 380582 [Multi-domain] Cd Length: 333 Bit Score: 42.24 E-value: 8.79e-04
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| PBP2_Arg_Lys_His | cd13624 | Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ... |
488-537 | 1.12e-03 | ||||||
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 periplasmic binding protein fold; This group includes the periplasmic substrate-binding protein ArtJ of the ATP-binding cassette (ABC) transport system from the thermophilic bacterium Geobacillus stearothermophilus, which is specific for arginine, lysine, and histidine. ArtJ belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270342 [Multi-domain] Cd Length: 219 Bit Score: 41.33 E-value: 1.12e-03
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| PBP2_FliY | cd13712 | Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ... |
452-529 | 1.83e-03 | ||||||
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic binding protein fold; This group contains cystine binding domain FliY and its related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270430 [Multi-domain] Cd Length: 219 Bit Score: 40.45 E-value: 1.83e-03
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| PBP2_Cystine_like | cd13626 | Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ... |
450-529 | 3.41e-03 | ||||||
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein fold; Cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Also, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270344 [Multi-domain] Cd Length: 219 Bit Score: 39.61 E-value: 3.41e-03
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| PBP1_As_SBP-like | cd06330 | periplasmic substrate-binding domain of active transport proteins; Periplasmic ... |
67-170 | 3.72e-03 | ||||||
periplasmic substrate-binding domain of active transport proteins; Periplasmic substrate-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic (As) and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Pssm-ID: 380553 [Multi-domain] Cd Length: 342 Bit Score: 40.24 E-value: 3.72e-03
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| PBP2_AA_binding_like_1 | cd13625 | Substrate-binding domain of putative amino acid-binding protein; the type 2 ... |
658-736 | 4.86e-03 | ||||||
Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold; This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270343 [Multi-domain] Cd Length: 230 Bit Score: 39.28 E-value: 4.86e-03
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| PBP2_Cystine_like | cd13626 | Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ... |
657-737 | 5.42e-03 | ||||||
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein fold; Cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Also, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270344 [Multi-domain] Cd Length: 219 Bit Score: 39.22 E-value: 5.42e-03
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| PBP2_iGluR_Kainate_GluR5 | cd13722 | GluR5 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ... |
425-526 | 5.63e-03 | ||||||
GluR5 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270440 [Multi-domain] Cd Length: 250 Bit Score: 39.26 E-value: 5.63e-03
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| PBP2_YfhD_N | cd01009 | The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ... |
466-518 | 6.01e-03 | ||||||
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes the solute binding domain YfhD_N. These domains are found in the YfhD proteins that are predicted to function as lytic transglycosylases that cleave the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamin in peptidoglycan, while the YfhD_N domain might act as an auxiliary or regulatory subunit. In addition to periplasmic solute binding domain, they have an SLT domain, typically found in soluble lytic transglycosylases, and a C-terminal low complexity domain. The YfhD proteins might have been recruited to create localized cell wall openings required for transport of large substrates such as DNA. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270230 [Multi-domain] Cd Length: 223 Bit Score: 39.12 E-value: 6.01e-03
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| PBP2_Arg_3 | cd13622 | Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ... |
448-516 | 6.08e-03 | ||||||
Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding fold; This subgroup is similar to the HisJ-like family that comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270340 [Multi-domain] Cd Length: 222 Bit Score: 39.21 E-value: 6.08e-03
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| PBP1_aromatic_compounds-like | cd06332 | type 1 periplasmic binding proteins of active transport systems predicted to be involved in ... |
31-189 | 6.87e-03 | ||||||
type 1 periplasmic binding proteins of active transport systems predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; This group includes the type 1 periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea. Pssm-ID: 380555 [Multi-domain] Cd Length: 336 Bit Score: 39.50 E-value: 6.87e-03
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