glutamate receptor ionotropic, NMDA 1 isoform X7 [Heterocephalus glaber]
Protein Classification
glutamate receptor ionotropic, NMDA 1; glutamate receptor( domain architecture ID 10294632)
glutamate receptor ionotropic, NMDA 1 is a component of NMDA (N-methyl-D-aspartate) receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium| glutamate receptor is a glutamate-gated receptor that probably acts as a non-selective cation channel and may be involved in light-signal transduction and calcium homeostasis via the regulation of calcium influx into cells
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| PBP2_iGluR_NMDA_Nr1 | cd13719 | The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) ... |
263-667 | 0e+00 | |||||||
The ligand-binding domain of the NR1 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 NR1, an essential channel-forming subunit of the NMDA receptor. 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 ccomposed 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. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site. : Pssm-ID: 270437 [Multi-domain] Cd Length: 277 Bit Score: 524.23 E-value: 0e+00
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| Periplasmic_Binding_Protein_type1 super family | cl10011 | Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ... |
1-251 | 2.26e-113 | |||||||
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold. The actual alignment was detected with superfamily member cd06379: Pssm-ID: 471960 Cd Length: 364 Bit Score: 352.41 E-value: 2.26e-113
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| CaM_bdg_C0 | pfam10562 | Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; This is a very short highly ... |
703-731 | 1.03e-09 | |||||||
Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue. : Pssm-ID: 402271 Cd Length: 29 Bit Score: 54.44 E-value: 1.03e-09
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| PHA03378 super family | cl33729 | EBNA-3B; Provisional |
748-903 | 3.54e-08 | |||||||
EBNA-3B; Provisional The actual alignment was detected with superfamily member PHA03378: Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 57.38 E-value: 3.54e-08
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| Name | Accession | Description | Interval | E-value | |||||||
| PBP2_iGluR_NMDA_Nr1 | cd13719 | The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) ... |
263-667 | 0e+00 | |||||||
The ligand-binding domain of the NR1 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 NR1, an essential channel-forming subunit of the NMDA receptor. 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 ccomposed 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. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site. Pssm-ID: 270437 [Multi-domain] Cd Length: 277 Bit Score: 524.23 E-value: 0e+00
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| PBP1_iGluR_NMDA_NR1 | cd06379 | N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR1, an ... |
1-251 | 2.26e-113 | |||||||
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed 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. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site Pssm-ID: 380602 Cd Length: 364 Bit Score: 352.41 E-value: 2.26e-113
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| Lig_chan | pfam00060 | Ligand-gated ion channel; This family includes the four transmembrane regions of the ... |
428-691 | 1.51e-81 | |||||||
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: 264.56 E-value: 1.51e-81
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| PBPe | smart00079 | Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ... |
531-663 | 9.58e-45 | |||||||
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: 157.45 E-value: 9.58e-45
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| ANF_receptor | pfam01094 | Receptor family ligand binding region; This family includes extracellular ligand binding ... |
1-225 | 1.52e-23 | |||||||
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: 103.23 E-value: 1.52e-23
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
325-660 | 1.42e-11 | |||||||
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: 65.00 E-value: 1.42e-11
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| CaM_bdg_C0 | pfam10562 | Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; This is a very short highly ... |
703-731 | 1.03e-09 | |||||||
Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue. Pssm-ID: 402271 Cd Length: 29 Bit Score: 54.44 E-value: 1.03e-09
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
748-903 | 3.54e-08 | |||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 57.38 E-value: 3.54e-08
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| PRK11260 | PRK11260 | cystine ABC transporter substrate-binding protein; |
366-413 | 3.11e-05 | |||||||
cystine ABC transporter substrate-binding protein; Pssm-ID: 183061 [Multi-domain] Cd Length: 266 Bit Score: 46.64 E-value: 3.11e-05
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| KLF9_13_N-like | cd21975 | Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like ... |
756-899 | 9.01e-05 | |||||||
Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF9, KLF13, KLF14, KLF16, and similar proteins. Pssm-ID: 409240 [Multi-domain] Cd Length: 163 Bit Score: 43.91 E-value: 9.01e-05
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| DUF3729 | pfam12526 | Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins ... |
825-903 | 4.87e-03 | |||||||
Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with pfam01443, pfam01661, pfam05417, pfam01660, pfam00978. There is a single completely conserved residue L that may be functionally important. Pssm-ID: 372164 [Multi-domain] Cd Length: 115 Bit Score: 37.75 E-value: 4.87e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| PBP2_iGluR_NMDA_Nr1 | cd13719 | The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) ... |
263-667 | 0e+00 | |||||||
The ligand-binding domain of the NR1 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 NR1, an essential channel-forming subunit of the NMDA receptor. 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 ccomposed 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. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site. Pssm-ID: 270437 [Multi-domain] Cd Length: 277 Bit Score: 524.23 E-value: 0e+00
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| PBP2_iGluR_NMDA | cd13687 | The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ... |
263-661 | 5.00e-118 | |||||||
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: 359.64 E-value: 5.00e-118
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| PBP1_iGluR_NMDA_NR1 | cd06379 | N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR1, an ... |
1-251 | 2.26e-113 | |||||||
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed 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. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site Pssm-ID: 380602 Cd Length: 364 Bit Score: 352.41 E-value: 2.26e-113
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| PBP1_iGluR_NMDA | cd06367 | N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the ionotropic ... |
1-244 | 1.44e-83 | |||||||
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptors; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptors. 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. 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: 380590 [Multi-domain] Cd Length: 357 Bit Score: 273.35 E-value: 1.44e-83
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| Lig_chan | pfam00060 | Ligand-gated ion channel; This family includes the four transmembrane regions of the ... |
428-691 | 1.51e-81 | |||||||
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: 264.56 E-value: 1.51e-81
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| PBP2_iGluR_Kainate_GluR7 | cd13723 | GluR7 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ... |
325-662 | 9.80e-59 | |||||||
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: 205.69 E-value: 9.80e-59
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| PBP2_iGluR_putative | cd13717 | The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ... |
264-660 | 4.22e-54 | |||||||
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: 192.51 E-value: 4.22e-54
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| PBP2_iGluR_NMDA_Nr2 | cd13718 | The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) ... |
266-660 | 4.63e-51 | |||||||
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: 181.00 E-value: 4.63e-51
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| PBP2_iGluR_non_NMDA_like | cd13685 | The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ... |
264-660 | 1.01e-49 | |||||||
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: 176.22 E-value: 1.01e-49
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| PBP2_iGluR_NMDA_Nr3 | cd13720 | The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ... |
264-660 | 1.42e-48 | |||||||
The ligand-binding domain of the NR3 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 NR3 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: 270438 [Multi-domain] Cd Length: 283 Bit Score: 174.27 E-value: 1.42e-48
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| PBPe | smart00079 | Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ... |
531-663 | 9.58e-45 | |||||||
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: 157.45 E-value: 9.58e-45
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| PBP2_iGluR_ligand_binding | cd00998 | The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ... |
265-660 | 2.58e-40 | |||||||
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: 149.06 E-value: 2.58e-40
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| Lig_chan-Glu_bd | pfam10613 | Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ... |
264-412 | 9.60e-39 | |||||||
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: 139.58 E-value: 9.60e-39
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| PBP2_iGluR_Kainate | cd13714 | Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains ... |
325-660 | 5.29e-38 | |||||||
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: 142.68 E-value: 5.29e-38
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| PBP1_glutamate_receptors-like | cd06269 | ligand-binding domain of family C G-protein couples receptors (GPCRs), membrane bound guanylyl ... |
1-241 | 2.41e-31 | |||||||
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: 125.61 E-value: 2.41e-31
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| PBP2_iGluR_kainate_KA1 | cd13724 | The ligand-binding domain of the kainate subtype KA1 of ionotropic glutamate receptors, a ... |
325-660 | 2.03e-30 | |||||||
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: 123.20 E-value: 2.03e-30
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| PBP2_iGluR_AMPA | cd13715 | The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ... |
325-666 | 2.68e-27 | |||||||
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: 112.06 E-value: 2.68e-27
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| PBP2_iGluR_Kainate_GluR6 | cd13721 | GluR6 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ... |
325-662 | 1.60e-24 | |||||||
GluR6 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: 270439 [Multi-domain] Cd Length: 251 Bit Score: 103.56 E-value: 1.60e-24
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| ANF_receptor | pfam01094 | Receptor family ligand binding region; This family includes extracellular ligand binding ... |
1-225 | 1.52e-23 | |||||||
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: 103.23 E-value: 1.52e-23
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| PBP2_iGluR_AMPA_GluR1 | cd13729 | The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ... |
325-666 | 4.44e-23 | |||||||
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR1 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the AMPA receptor subunit GluR1, 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. The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. 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: 270447 [Multi-domain] Cd Length: 260 Bit Score: 99.71 E-value: 4.44e-23
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| PBP2_iGluR_Kainate_GluR5 | cd13722 | GluR5 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ... |
325-424 | 3.26e-21 | |||||||
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: 93.96 E-value: 3.26e-21
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| PBP2_iGluR_AMPA_GluR2 | cd13726 | The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ... |
325-666 | 3.43e-21 | |||||||
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR2 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the AMPA receptor subunit GluR2, 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. The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. 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: 270444 [Multi-domain] Cd Length: 259 Bit Score: 94.32 E-value: 3.43e-21
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| PBP2_iGluR_delta_like | cd13716 | The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of ... |
266-660 | 3.81e-21 | |||||||
The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of iGluRs belongs to the periplasmic-binding fold type I. Although the delta receptors are members of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. Pssm-ID: 270434 [Multi-domain] Cd Length: 257 Bit Score: 94.14 E-value: 3.81e-21
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| PBP2_iGluR_AMPA_GluR4 | cd13727 | The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ... |
325-415 | 6.88e-21 | |||||||
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR4 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the AMPA receptor subunit GluR4, 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.The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. 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: 270445 [Multi-domain] Cd Length: 259 Bit Score: 93.17 E-value: 6.88e-21
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| PBP2_iGluR_delta_1 | cd13730 | The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the ... |
266-660 | 1.33e-20 | |||||||
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the delta1 receptor of an orphan glutamate receptor family. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of delta receptors belongs to the periplasmic-binding fold type I. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRdelta2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. Pssm-ID: 270448 [Multi-domain] Cd Length: 257 Bit Score: 92.33 E-value: 1.33e-20
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| PBP2_iGluR_kainate_KA2 | cd13725 | The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a ... |
325-660 | 1.21e-19 | |||||||
The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the KA2 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: 270443 [Multi-domain] Cd Length: 250 Bit Score: 89.38 E-value: 1.21e-19
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| PBP2_iGluR_AMPA_GluR3 | cd13728 | The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ... |
325-415 | 6.90e-19 | |||||||
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR3 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the AMPA receptor subunit GluR3, 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. The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. 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: 270446 [Multi-domain] Cd Length: 259 Bit Score: 87.44 E-value: 6.90e-19
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| PBP1_GABAb_receptor | cd06366 | ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for ... |
1-251 | 4.04e-18 | |||||||
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: 87.69 E-value: 4.04e-18
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| PBP1_iGluR_NMDA_NR2 | cd06378 | N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of ... |
62-235 | 1.24e-17 | |||||||
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor 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: 380601 Cd Length: 356 Bit Score: 85.42 E-value: 1.24e-17
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| PBP2_iGluR_delta_2 | cd13731 | The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the ... |
266-660 | 1.89e-17 | |||||||
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the delta-2 receptor of an orphan glutamate receptor family. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of delta receptors belongs to the periplasmic-binding fold type I. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. Pssm-ID: 270449 [Multi-domain] Cd Length: 257 Bit Score: 83.16 E-value: 1.89e-17
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| Lig_chan-Glu_bd | smart00918 | Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ... |
318-374 | 4.95e-17 | |||||||
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. Pssm-ID: 214911 [Multi-domain] Cd Length: 62 Bit Score: 75.75 E-value: 4.95e-17
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| SBP_bac_3 | pfam00497 | Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ... |
325-422 | 2.33e-12 | |||||||
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: 67.32 E-value: 2.33e-12
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
325-660 | 1.42e-11 | |||||||
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: 65.00 E-value: 1.42e-11
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| PBP2_peptides_like | cd13530 | Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ... |
325-421 | 3.15e-10 | |||||||
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: 61.11 E-value: 3.15e-10
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| PBP2_Cystine_like | cd13626 | Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ... |
325-413 | 6.57e-10 | |||||||
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: 60.02 E-value: 6.57e-10
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| PBP2_Arg_Lys_His | cd13624 | Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ... |
325-413 | 9.42e-10 | |||||||
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: 59.43 E-value: 9.42e-10
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| CaM_bdg_C0 | pfam10562 | Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; This is a very short highly ... |
703-731 | 1.03e-09 | |||||||
Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue. Pssm-ID: 402271 Cd Length: 29 Bit Score: 54.44 E-value: 1.03e-09
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| PBP1_iGluR_Kainate_KA1_2 | cd06394 | N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the KA1 and KA2 ... |
69-225 | 3.78e-09 | |||||||
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. 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. 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 AMPA 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: 380616 Cd Length: 379 Bit Score: 59.54 E-value: 3.78e-09
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
748-903 | 3.54e-08 | |||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 57.38 E-value: 3.54e-08
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| PBPb | smart00062 | Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ... |
325-420 | 4.82e-08 | |||||||
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe Pssm-ID: 214497 [Multi-domain] Cd Length: 219 Bit Score: 54.64 E-value: 4.82e-08
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| PBP2_GlnH | cd00994 | Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ... |
325-412 | 9.75e-08 | |||||||
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: 53.82 E-value: 9.75e-08
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| PBP1_GABAb_receptor_plant | cd19990 | periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close ... |
72-233 | 1.46e-07 | |||||||
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: 54.54 E-value: 1.46e-07
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| PBP2_Dsm1740 | cd13629 | Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ... |
325-425 | 4.23e-07 | |||||||
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: 51.80 E-value: 4.23e-07
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| PBP2_AA_binding_like_2 | cd13627 | Substrate-binding domain of putative amino acid-binding protein; the type 2 ... |
363-412 | 8.25e-07 | |||||||
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: 270345 [Multi-domain] Cd Length: 243 Bit Score: 51.25 E-value: 8.25e-07
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| PBP2_FliY | cd13712 | Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ... |
365-417 | 1.14e-06 | |||||||
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: 50.46 E-value: 1.14e-06
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| PBP2_BsGlnH | cd13689 | Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ... |
325-422 | 1.21e-06 | |||||||
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 periplasmic-bindig protein fold; This group includes periplasmic glutamine-binding domain GlnP from Bacillus subtilis and its related proteins. The GlnP 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: 270407 [Multi-domain] Cd Length: 229 Bit Score: 50.69 E-value: 1.21e-06
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| PBP2_Ala | cd13628 | Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ... |
310-440 | 1.39e-06 | |||||||
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 periplasmic binding protein; This periplasmic substrate component serves as an initial receptor in the ABC transport of glutamine in eubacteria and archaea. After binding the alanine with high affinity, this domain Interacts 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. This alanine specific domain 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: 270346 [Multi-domain] Cd Length: 219 Bit Score: 50.16 E-value: 1.39e-06
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
750-891 | 1.44e-06 | |||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 52.38 E-value: 1.44e-06
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
758-927 | 1.62e-06 | |||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 52.25 E-value: 1.62e-06
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| PBP2_mlr5654_like | cd13702 | Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ... |
365-413 | 2.15e-06 | |||||||
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold; This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which serve as initial receptors in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group 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: 270420 [Multi-domain] Cd Length: 223 Bit Score: 49.63 E-value: 2.15e-06
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| PBP1_NPR_GC-like | cd06352 | ligand-binding domain of membrane guanylyl-cyclase receptors; Ligand-binding domain of ... |
1-238 | 2.25e-06 | |||||||
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: 50.82 E-value: 2.25e-06
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
753-895 | 3.98e-06 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 50.94 E-value: 3.98e-06
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| PBP2_HisK | cd13704 | The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ... |
324-464 | 5.24e-06 | |||||||
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding fold protein; This subfamily includes the periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain 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 through their function as an initial high-affinity binding component. 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. Pssm-ID: 270422 [Multi-domain] Cd Length: 220 Bit Score: 48.35 E-value: 5.24e-06
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| PBP1_mGluR | cd06362 | ligand binding domain of metabotropic glutamate receptors (mGluR); Ligand binding domain of ... |
151-235 | 6.84e-06 | |||||||
ligand binding domain of metabotropic glutamate receptors (mGluR); Ligand binding domain of the metabotropic glutamate receptors (mGluR), which are members of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. mGluRs bind to glutamate and function as an excitatory neurotransmitter; they are involved in learning, memory, anxiety, and the perception of pain. Eight subtypes of mGluRs have been cloned so far, and are classified into three groups according to their sequence similarities, transduction mechanisms, and pharmacological profiles. Group I is composed of mGlu1R and mGlu5R that both stimulate PLC hydrolysis. Group II includes mGlu2R and mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R, mGlu6R, mGlu7R, and mGlu8R, which form group III. Pssm-ID: 380585 [Multi-domain] Cd Length: 460 Bit Score: 49.60 E-value: 6.84e-06
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| PBP2_YxeM | cd13709 | Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ... |
365-422 | 7.28e-06 | |||||||
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein fold; This group contains cystine-binding domain (YxeM) of a periplasmic receptor-dependent ATP-binding cassette transporter and its closely 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: 270427 [Multi-domain] Cd Length: 227 Bit Score: 48.11 E-value: 7.28e-06
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| PBP2_Cys_DEBP_like | cd01000 | Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ... |
373-420 | 1.07e-05 | |||||||
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 periplasmic-binding protein fold; This family comprises of the periplasmic-binding protein component of ABC transporters specific for cysteine and carboxylic amino acids, as well as their closely related proteins. The cysteine and aspartate-glutamate binding domains belong 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: 270221 [Multi-domain] Cd Length: 228 Bit Score: 47.69 E-value: 1.07e-05
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| PBP2_GluR0 | cd00997 | Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ... |
524-660 | 1.18e-05 | |||||||
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: 47.33 E-value: 1.18e-05
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| PBP1_iGluR_Kainate | cd06382 | N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate ... |
61-236 | 1.36e-05 | |||||||
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: 48.37 E-value: 1.36e-05
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| PBP1_pheromone_receptor | cd06365 | Ligand-binding domain of the V2R pheromone receptor, a member of the family C receptors within ... |
145-249 | 2.20e-05 | |||||||
Ligand-binding domain of the V2R pheromone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily; Ligand-binding domain of the V2R pheromone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptor, the GABAb receptor, the calcium-sensing receptor (CaSR), the T1R taste receptor, and a small group of uncharacterized orphan receptors. Pssm-ID: 380588 [Multi-domain] Cd Length: 464 Bit Score: 48.02 E-value: 2.20e-05
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| PBP2_Cystine_like_1 | cd13713 | Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ... |
365-420 | 2.36e-05 | |||||||
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold; This group contains uncharacterized periplasmic cystine-binding domain of 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. 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: 270431 [Multi-domain] Cd Length: 218 Bit Score: 46.51 E-value: 2.36e-05
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| PBP2_GlnP | cd13619 | Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ... |
325-412 | 2.83e-05 | |||||||
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily; Periplasmic glutamine binding domain GlnP serves as an initial receptor in the ABC transport of glutamine in eubacteria. GlnP 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: 270337 [Multi-domain] Cd Length: 220 Bit Score: 46.15 E-value: 2.83e-05
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| PRK11260 | PRK11260 | cystine ABC transporter substrate-binding protein; |
366-413 | 3.11e-05 | |||||||
cystine ABC transporter substrate-binding protein; Pssm-ID: 183061 [Multi-domain] Cd Length: 266 Bit Score: 46.64 E-value: 3.11e-05
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| PBP2_Arg_3 | cd13622 | Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ... |
324-402 | 5.60e-05 | |||||||
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: 45.37 E-value: 5.60e-05
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| PBP2_GluR0 | cd00997 | Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ... |
325-410 | 6.32e-05 | |||||||
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: 45.41 E-value: 6.32e-05
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| PBP1_iGluR_AMPA_GluR1 | cd06390 | N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit ... |
5-236 | 8.52e-05 | |||||||
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed 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. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs). Pssm-ID: 380613 [Multi-domain] Cd Length: 367 Bit Score: 46.09 E-value: 8.52e-05
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| KLF9_13_N-like | cd21975 | Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like ... |
756-899 | 9.01e-05 | |||||||
Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF9, KLF13, KLF14, KLF16, and similar proteins. Pssm-ID: 409240 [Multi-domain] Cd Length: 163 Bit Score: 43.91 E-value: 9.01e-05
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
772-903 | 1.14e-04 | |||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 46.47 E-value: 1.14e-04
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| PBP2_Peb1a_like | cd13691 | Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 ... |
324-413 | 1.16e-04 | |||||||
Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 periplasmic-binding protein fold; This group includes periplasmic aspartate/glutamate binding domain Peb1a and its closely related protein. The Peb1a is an important virulence factor in the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonization. The Peb1a 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: 270409 [Multi-domain] Cd Length: 228 Bit Score: 44.75 E-value: 1.16e-04
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| PBP2_Dsm1740 | cd13629 | Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ... |
579-660 | 1.21e-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: 44.48 E-value: 1.21e-04
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
761-933 | 1.64e-04 | |||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 45.70 E-value: 1.64e-04
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
745-902 | 1.86e-04 | |||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 45.25 E-value: 1.86e-04
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
772-903 | 2.20e-04 | |||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 45.25 E-value: 2.20e-04
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| PBP2_ml15202_like | cd13701 | Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ... |
325-410 | 2.58e-04 | |||||||
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold; This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which are involved in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group 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: 270419 [Multi-domain] Cd Length: 227 Bit Score: 43.60 E-value: 2.58e-04
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| PBP2_AatB_like | cd00996 | Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong ... |
365-421 | 3.31e-04 | |||||||
Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong to the type 2 periplasmic binding fold protein superfamily; This subfamily includes periplasmic binding domain of ATP-binding cassette transporter-like systems that serve as initial receptors in the ABC transport of amino acids and their derivatives in eubacteria. After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The Abp proteins belong to the PBPI 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: 270217 [Multi-domain] Cd Length: 227 Bit Score: 43.34 E-value: 3.31e-04
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
768-903 | 3.49e-04 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 44.78 E-value: 3.49e-04
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
753-903 | 3.55e-04 | |||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 44.59 E-value: 3.55e-04
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| PRK14951 | PRK14951 | DNA polymerase III subunits gamma and tau; Provisional |
829-903 | 3.71e-04 | |||||||
DNA polymerase III subunits gamma and tau; Provisional Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 44.32 E-value: 3.71e-04
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| PBP1_CaSR | cd06364 | ligand-binding domain of the CaSR calcium-sensing receptor, a member of the family C receptors ... |
152-249 | 4.56e-04 | |||||||
ligand-binding domain of the CaSR calcium-sensing receptor, a member of the family C receptors within the G-protein coupled receptor superfamily; Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. CaSR provides feedback control of extracellular calcium homeostasis by responding sensitively to acute fluctuations in extracellular ionized Ca2+ concentration. This ligand-binding domain has homology to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). CaSR is widely expressed in mammalian tissues and is active in tissues that are not directly involved in extracellular calcium homeostasis. Moreover, CaSR responds to aromatic, aliphatic, and polar amino acids, but not to positively charged or branched chain amino acids, which suggests that changes in plasma amino acid levels are likely to modulate whole body calcium metabolism. Additionally, the family C GPCRs includes at least two receptors with broad-spectrum amino acid-sensing properties: GPRC6A which recognizes basic and various aliphatic amino acids, its gold-fish homolog the 5.24 chemoreceptor, and a specific taste receptor (T1R) which responds to aliphatic, polar, charged, and branched amino acids, but not to aromatic amino acids. Pssm-ID: 380587 [Multi-domain] Cd Length: 473 Bit Score: 43.78 E-value: 4.56e-04
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
761-894 | 4.70e-04 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 44.01 E-value: 4.70e-04
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| PBP2_HisJ_LAO_like | cd01001 | Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ... |
325-401 | 5.28e-04 | |||||||
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and related proteins; the type 2 periplasmic-binding protein fold; This family 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: 270222 [Multi-domain] Cd Length: 228 Bit Score: 42.67 E-value: 5.28e-04
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| PBP1_iGluR_AMPA | cd06380 | N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA receptor; ... |
1-236 | 5.72e-04 | |||||||
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system. 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. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current. Pssm-ID: 380603 [Multi-domain] Cd Length: 390 Bit Score: 43.42 E-value: 5.72e-04
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| PBP2_Mlr3796_like | cd13695 | The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic ... |
346-420 | 5.99e-04 | |||||||
The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Mesorhizobium loti and its related proteins. The putative Mlr3796-like 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: 270413 [Multi-domain] Cd Length: 232 Bit Score: 42.55 E-value: 5.99e-04
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| KLF16_N | cd21573 | N-terminal domain of Kruppel-like factor 16; Kruppel-like factor 16 (KLF16; also known as ... |
852-910 | 6.49e-04 | |||||||
N-terminal domain of Kruppel-like factor 16; Kruppel-like factor 16 (KLF16; also known as Krueppel-like factor 16, Basic transcription element binding protein 4/BTEB4, or Novel Sp1-like zinc finger transcription factor/2NSLP2) is a protein that in humans is encoded by the KLF16 gene. KLF16 functions as a transcription activator. It is thought to modulate dopaminergic transmission in the brain and also regulates the expression of several genes essential for metabolic and endocrine processes in sex steroid-sensitive uterine cells. KLF16 selectively binds three distinct KLF-binding sites (GC, CA, and BTE boxes). KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF16 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF16. Pssm-ID: 409237 [Multi-domain] Cd Length: 125 Bit Score: 40.74 E-value: 6.49e-04
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| PBP2_SMa0082_like | cd01072 | The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic ... |
373-441 | 6.90e-04 | |||||||
The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Sinorhizobium meliloti and its related proteins. The putative SMa0082-like 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: 270233 [Multi-domain] Cd Length: 238 Bit Score: 42.25 E-value: 6.90e-04
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| PBP2_Ngo0372_TcyA | cd13711 | Substrate binding domain of ABC transporters involved in cystine import; the type 2 ... |
365-422 | 8.05e-04 | |||||||
Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold; This subgroup includes cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette transporters from Neisseria gonorrhoeae and Bacillus subtilis and their 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: 270429 [Multi-domain] Cd Length: 222 Bit Score: 41.90 E-value: 8.05e-04
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| PBP2_GltS | cd13620 | Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ... |
364-413 | 8.06e-04 | |||||||
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily; This family comprises of the periplasmic-binding protein component (GltS) of an ABC transporter specific for glutamate or arginine from Lactococcus lactis, as well as its closely related proteins. The GltS 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: 270338 [Multi-domain] Cd Length: 227 Bit Score: 41.94 E-value: 8.06e-04
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
736-903 | 8.21e-04 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 43.24 E-value: 8.21e-04
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| PBP2_GluB | cd13690 | Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ... |
373-413 | 8.35e-04 | |||||||
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein fold; This group includes periplasmic glutamate-binding domain GluB from Corynebacterium efficiens and its related proteins. The GluB 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: 270408 [Multi-domain] Cd Length: 231 Bit Score: 41.87 E-value: 8.35e-04
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| PRK07003 | PRK07003 | DNA polymerase III subunit gamma/tau; |
774-887 | 1.12e-03 | |||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 42.91 E-value: 1.12e-03
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| PBP2_MidA_like | cd01004 | Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ... |
325-412 | 1.30e-03 | |||||||
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 periplasmic binding protein fold; This subgroup includes the periplasmic binding component of ABC transporter involved in uptake of mimosine MidA and its similar proteins. This periplasmic binding domain 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: 270225 [Multi-domain] Cd Length: 230 Bit Score: 41.46 E-value: 1.30e-03
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| PBP2_Ehub_like | cd01002 | Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 ... |
365-422 | 1.46e-03 | |||||||
Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 periplasmic binding protein fold; This family represents the periplasmic substrate-binding component of ABC transport systems that involved in uptake of osmoprotectants (also termed compatible solutes) such as ectoine and hydroxyectoine. To counteract the efflux of water, bacteria and archaea accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain 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. Pssm-ID: 270223 [Multi-domain] Cd Length: 242 Bit Score: 41.50 E-value: 1.46e-03
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
753-928 | 1.47e-03 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 42.47 E-value: 1.47e-03
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| PBP2_GltI_DEBP | cd13688 | Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ... |
373-423 | 1.76e-03 | |||||||
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic binding protein fold; This subfamily represents the periplasmic-binding protein component of ABC transporter specific for carboxylic amino acids, including GtlI from Escherichia coli. The aspartate-glutamate binding 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: 270406 [Multi-domain] Cd Length: 238 Bit Score: 41.08 E-value: 1.76e-03
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| PRK14951 | PRK14951 | DNA polymerase III subunits gamma and tau; Provisional |
828-895 | 2.05e-03 | |||||||
DNA polymerase III subunits gamma and tau; Provisional Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 42.01 E-value: 2.05e-03
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
779-903 | 2.51e-03 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.70 E-value: 2.51e-03
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| MltF | COG4623 | Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ... |
325-442 | 2.52e-03 | |||||||
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, Signal transduction mechanisms]; Pssm-ID: 443662 [Multi-domain] Cd Length: 421 Bit Score: 41.20 E-value: 2.52e-03
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| PBP2_AA_binding_like_1 | cd13625 | Substrate-binding domain of putative amino acid-binding protein; the type 2 ... |
366-400 | 2.54e-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: 40.44 E-value: 2.54e-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 ... |
325-442 | 2.61e-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: 40.27 E-value: 2.61e-03
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
772-898 | 3.16e-03 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.31 E-value: 3.16e-03
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| PBP2_OccT_like | cd13699 | Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding ... |
325-410 | 4.32e-03 | |||||||
Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding protein fold; This group includes periplasmic octopine-binding protein and related proteins. This group 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 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: 270417 [Multi-domain] Cd Length: 211 Bit Score: 39.66 E-value: 4.32e-03
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| PBP2_Atu4678_like | cd13696 | The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ... |
373-420 | 4.77e-03 | |||||||
The substrate binding domain of putative amino acid transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Agrobacterium tumefaciens and its related proteins. The putative Atu4678-like 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: 270414 [Multi-domain] Cd Length: 227 Bit Score: 39.67 E-value: 4.77e-03
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| DUF3729 | pfam12526 | Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins ... |
825-903 | 4.87e-03 | |||||||
Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with pfam01443, pfam01661, pfam05417, pfam01660, pfam00978. There is a single completely conserved residue L that may be functionally important. Pssm-ID: 372164 [Multi-domain] Cd Length: 115 Bit Score: 37.75 E-value: 4.87e-03
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| PBP1_iGluR_AMPA_GluR2 | cd06389 | N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit ... |
143-236 | 5.17e-03 | |||||||
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed 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. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs). Pssm-ID: 380612 [Multi-domain] Cd Length: 372 Bit Score: 40.38 E-value: 5.17e-03
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| PBP2_Cysteine | cd13694 | Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ... |
373-413 | 5.44e-03 | |||||||
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein fold; This subfamily comprises of the periplasmic-binding protein component of ABC transporter specific for cysteine and its closely related proteins. The cysteine-binding domains belong 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: 270412 [Multi-domain] Cd Length: 229 Bit Score: 39.64 E-value: 5.44e-03
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
818-903 | 6.43e-03 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 40.54 E-value: 6.43e-03
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| PBP1_ABC_LIVBP-like | cd06342 | type 1 periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active ... |
65-222 | 7.22e-03 | |||||||
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: 39.82 E-value: 7.22e-03
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| GluR_Plant | cd13686 | Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily ... |
325-414 | 9.75e-03 | |||||||
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: 38.66 E-value: 9.75e-03
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