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Conserved domains on  [gi|1370486819|ref|XP_024309793|]
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glutamate receptor ionotropic, delta-2 isoform X12 [Homo sapiens]

Protein Classification

glutamate receptor( domain architecture ID 10294646)

glutamate receptor ionotropic, AMPA is a receptor for glutamate that functions as a ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP2_iGluR_delta_2 cd13731
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the ...
121-487 0e+00

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: 535.00  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 121 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADI 200
Cdd:cd13731     1 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 201 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgs 280
Cdd:cd13731    81 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAE---------------------------------------------- 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 281 mtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEIPY 360
Cdd:cd13731   115 ----------------------------------------------------------------SIQSLQDLSKQTDIPY 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 361 GTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFY 440
Cdd:cd13731   131 GTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFY 210
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 487
Cdd:cd13731   211 TVGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 257
Periplasmic_Binding_Protein_type1 super family cl10011
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
1-110 3.13e-75

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 cd06391:

Pssm-ID: 471960 [Multi-domain]  Cd Length: 402  Bit Score: 247.65  E-value: 3.13e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFE 80
Cdd:cd06391   293 MEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGLLEFGENGGNPNVHFE 372
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819  81 ILGTNYGEELGRGVRKLGCWNPVTGLNGSL 110
Cdd:cd06391   373 ILGTNYGEELGRGVRKLGCWNPVTGLNGSL 402
 
Name Accession Description Interval E-value
PBP2_iGluR_delta_2 cd13731
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the ...
121-487 0e+00

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: 535.00  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 121 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADI 200
Cdd:cd13731     1 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 201 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgs 280
Cdd:cd13731    81 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAE---------------------------------------------- 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 281 mtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEIPY 360
Cdd:cd13731   115 ----------------------------------------------------------------SIQSLQDLSKQTDIPY 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 361 GTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFY 440
Cdd:cd13731   131 GTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFY 210
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 487
Cdd:cd13731   211 TVGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 257
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
247-522 2.63e-82

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: 261.47  E-value: 2.63e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 247 DLSLWACIAGTVLLVGLLVYLLNWLNPPRLQMGSMT---STTLYNSMWFVYGSFVQQGGEVPYTTLATRMMMGAWWLFAL 323
Cdd:pfam00060   1 SLEVWLGILVAFLIVGVVLFLLERFSPYEWRGPLETeenRFTLSNSLWFSFGALVQQGHRENPRSLSGRIVVGVWWFFAL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 324 IVISSYTANLAAFLTITRIESSIQSLQDLSKQTEIPYGTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSEnnv 403
Cdd:pfam00060  81 ILLSSYTANLAAFLTVERMQSPIQSLEDLAKQTKIEYGTVRGSSTYLFFRNSKIPSYKRMWEYMESAKPSVKDALNE--- 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 404 lesqAGIQKVKYGNYAFVWDAavLEYVAINDPDCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKH 483
Cdd:pfam00060 158 ----EGVALVRNGIYAYALLS--ENYYLFQRECCDTMIVGETFATGGYGIATPKGSPLTDLLSLAILELEESGELDKLEK 231
                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1370486819 484 KWWPKNGQCDLYSSVDTKQKggaLDIKSFAGVFCILAAG 522
Cdd:pfam00060 232 KWWPKSGECDSKSSASSSSQ---LGLKSFAGLFLILGIG 267
PBP1_iGluR_delta_2 cd06391
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 ...
1-110 3.13e-75

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. 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. 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. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related 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 tumor necrosis factor family that is secreted from cerebellar granule cells.


Pssm-ID: 380614 [Multi-domain]  Cd Length: 402  Bit Score: 247.65  E-value: 3.13e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFE 80
Cdd:cd06391   293 MEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGLLEFGENGGNPNVHFE 372
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819  81 ILGTNYGEELGRGVRKLGCWNPVTGLNGSL 110
Cdd:cd06391   373 ILGTNYGEELGRGVRKLGCWNPVTGLNGSL 402
PBPe smart00079
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ...
345-488 1.18e-46

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: 161.30  E-value: 1.18e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819  345 SIQSLQDLSKQTEIPYGTVLDSAVYEHVRMKGLNPferdsmYSQMWRMINRSngsENNVLESQAGIQKVKYGNYAFVWDA 424
Cdd:smart00079   1 PITSVEDLAKQTKIEYGTQDGSSTLAFFKRSGNPE------YSRMWPYMKSP---EVFVKSYAEGVQRVRVSNYAFIMES 71
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370486819  425 AVLEYVAINDpdCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWPK 488
Cdd:smart00079  72 PYLDYELSRN--CDLMTVGEEFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELEKLRNKWWKD 133
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
124-237 5.69e-16

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: 77.33  E-value: 5.69e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLE-EPFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGI 202
Cdd:COG0834     1 LRVGVDPDyPPFSFRDED-----GKLVGFDVDLARAIAKRLGLKVEFVPVP------------WDRLIPALQSGKVDLII 63
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1370486819 203 SALTITPDRENVVDFTTRYMDYSVGVLLRRAEKTV 237
Cdd:COG0834    64 AGMTITPEREKQVDFSDPYYTSGQVLLVRKDNSGI 98
ANF_receptor pfam01094
Receptor family ligand binding region; This family includes extracellular ligand binding ...
1-85 1.23e-12

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: 69.72  E-value: 1.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKKLEDRKWHSmaslSCIRknSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFE 80
Cdd:pfam01094 267 PVSYGALAYDAVYLLAHALHNLLRDDKPGR----ACGA--LGPWNGGQKLLRYLKNVNFTGLTGNVQFDENGDRINPDYD 340

                  ....*
gi 1370486819  81 ILGTN 85
Cdd:pfam01094 341 ILNLN 345
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
133-234 6.83e-06

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 48.18  E-value: 6.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:PRK11260   53 PFSFQGED-----GKLTGFEVEFAEALAKHLGVKASLKPTK------------WDGMLASLDSKRIDVVINQVTISDERK 115
                          90       100
                  ....*....|....*....|..
gi 1370486819 213 NVVDFTTRYMDYSVGVLLRRAE 234
Cdd:PRK11260  116 KKYDFSTPYTVSGIQALVKKGN 137
 
Name Accession Description Interval E-value
PBP2_iGluR_delta_2 cd13731
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the ...
121-487 0e+00

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: 535.00  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 121 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADI 200
Cdd:cd13731     1 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 201 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgs 280
Cdd:cd13731    81 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAE---------------------------------------------- 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 281 mtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEIPY 360
Cdd:cd13731   115 ----------------------------------------------------------------SIQSLQDLSKQTDIPY 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 361 GTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFY 440
Cdd:cd13731   131 GTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFY 210
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 487
Cdd:cd13731   211 TVGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 257
PBP2_iGluR_delta_like cd13716
The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of ...
121-487 2.33e-174

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: 497.44  E-value: 2.33e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 121 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADI 200
Cdd:cd13716     1 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALANYLGFKYEIYVAPDHKYGSQQEDGTWNGLIGELVFKRADI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 201 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgs 280
Cdd:cd13716    81 GISALTITPERENVVDFTTRYMDYSVGVLLRKAE---------------------------------------------- 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 281 mtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEIPY 360
Cdd:cd13716   115 ----------------------------------------------------------------SIQSLQDLSKQTDIPY 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 361 GTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFY 440
Cdd:cd13716   131 GTVLDSAVYEYVRSKGTNPFERDSMYSQMWRMINRSNGSENNVSESSEGIRKVKYGNYAFVWDAAVLEYVAINDDDCSFY 210
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 487
Cdd:cd13716   211 TVGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 257
PBP2_iGluR_delta_1 cd13730
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the ...
121-487 3.23e-128

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: 379.69  E-value: 3.23e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 121 GVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADI 200
Cdd:cd13730     1 GLTLKVVTVLEEPFVMVAENILGQPKRYKGFSIDVLDALAKALGFKYEIYQAPDGKYGHQLHNTSWNGMIGELISKRADL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 201 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgs 280
Cdd:cd13730    81 AISAITITPERESVVDFSKRYMDYSVGILIKKPE---------------------------------------------- 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 281 mtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEIPY 360
Cdd:cd13730   115 ----------------------------------------------------------------PIRTFQDLSKQVEMSY 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 361 GTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFY 440
Cdd:cd13730   131 GTVRDSAVYEYFRAKGTNPLEQDSTFAELWRTISKNGGADNCVSSPSEGIRKAKKGNYAFLWDVAVVEYAALTDDDCSVT 210
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 487
Cdd:cd13730   211 VIGNSISSKGYGIALQHGSPYRDLFSQRILELQDTGDLDVLKQKWWP 257
PBP2_iGluR_non_NMDA_like cd13685
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ...
122-487 3.54e-95

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: 294.48  E-value: 3.54e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 122 VVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIG 201
Cdd:cd13685     2 KTLRVTTILEPPFVMKKRDSLSGNPRFEGYCIDLLEELAKILGFDYEIYLVPDGKYGSRDENGNWNGMIGELVRGEADIA 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRRaektvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgsm 281
Cdd:cd13685    82 VAPLTITAEREEVVDFTKPFMDTGISILMRK------------------------------------------------- 112
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 282 tsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriESSIQSLQDLSKQTEIPYG 361
Cdd:cd13685   113 -------------------------------------------------------------PTPIESLEDLAKQSKIEYG 131
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 362 TVLDSAVYEHVRMKGLNPFERDSmYSQMWRMINRSngseNNVLESQAGIQKVKYGN--YAFVWDAAVLEYVAINdpDCSF 439
Cdd:cd13685   132 TLKGSSTFTFFKNSKNPEYRRYE-YTKIMSAMSPS----VLVASAAEGVQRVRESNggYAFIGEATSIDYEVLR--NCDL 204
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 1370486819 440 YTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWP 487
Cdd:cd13685   205 TKVGEVFSEKGYGIAVQQGSPLRDELSLAILELQESGELEKLKEKWWN 252
PBP2_iGluR_putative cd13717
The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ...
123-486 1.79e-85

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: 273.02  E-value: 1.79e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRVVTVLEEPFVMVSENvlgKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGI 202
Cdd:cd13717     3 VYRIGTVESPPFVYRDRD---GSPIWEGYCIDLIEEISEILNFDYEIVEPEDGKFGTMDENGEWNGLIGDLVRKEADIAL 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 203 SALTITPDRENVVDFTTRYMDYsVG--VLLRRAEKTVDMFACLAPFDLSLWaciagtvllvgllvyllnwlnpprlqmgs 280
Cdd:cd13717    80 AALSVMAEREEVVDFTVPYYDL-VGitILMKKPERPTSLFKFLTVLELEVW----------------------------- 129
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 281 mTSTTLYNSMWFVYGSFVQQGG-EVPyTTLATRMMMGAWWLFALIVISSYTANLAAFLTITRIESSIQSLQDLSKQTEIP 359
Cdd:cd13717   130 -REFTLKESLWFCLTSLTPQGGgEAP-KNLSGRLLVATWWLFVFIIIASYTANLAAFLTVSRLQTPVESLDDLARQYKIQ 207
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 360 YGTVLDSAVYEH-VRMKG-----------------LNPFERDSM----------YSQMWRMINRSNGSENnvleSQAGIQ 411
Cdd:cd13717   208 YTVVKNSSTHTYfERMKNaedtlyemwkdmslndsLSPVERAKLavwdypvsekYTKIYQAMQEAGLVAN----AEEGVK 283
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370486819 412 KVKYGN---YAFVWDAAVLEYVAINDpdCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 486
Cdd:cd13717   284 RVRESTsagFAFIGDATDIKYEILTN--CDLQEVGEEFSRKPYAIAVQQGSPLKDELNYAILELQNDRFLEKLKAKWW 359
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
247-522 2.63e-82

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: 261.47  E-value: 2.63e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 247 DLSLWACIAGTVLLVGLLVYLLNWLNPPRLQMGSMT---STTLYNSMWFVYGSFVQQGGEVPYTTLATRMMMGAWWLFAL 323
Cdd:pfam00060   1 SLEVWLGILVAFLIVGVVLFLLERFSPYEWRGPLETeenRFTLSNSLWFSFGALVQQGHRENPRSLSGRIVVGVWWFFAL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 324 IVISSYTANLAAFLTITRIESSIQSLQDLSKQTEIPYGTVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSNGSEnnv 403
Cdd:pfam00060  81 ILLSSYTANLAAFLTVERMQSPIQSLEDLAKQTKIEYGTVRGSSTYLFFRNSKIPSYKRMWEYMESAKPSVKDALNE--- 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 404 lesqAGIQKVKYGNYAFVWDAavLEYVAINDPDCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKH 483
Cdd:pfam00060 158 ----EGVALVRNGIYAYALLS--ENYYLFQRECCDTMIVGETFATGGYGIATPKGSPLTDLLSLAILELEESGELDKLEK 231
                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1370486819 484 KWWPKNGQCDLYSSVDTKQKggaLDIKSFAGVFCILAAG 522
Cdd:pfam00060 232 KWWPKSGECDSKSSASSSSQ---LGLKSFAGLFLILGIG 267
PBP2_iGluR_Kainate_GluR7 cd13723
GluR7 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
124-486 2.29e-76

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: 249.61  E-value: 2.29e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMV--SENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIG 201
Cdd:cd13723     4 LIVTTVLEEPFVMFrkSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLA 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRRAEKT-VDMFACLAPFDLSLWACI------AGTVLLVGLLVYLLNWLNPP 274
Cdd:cd13723    84 VAPLTITHVREKAIDFSKPFMTLGVSILYRKPNGTnPSVFSFLNPLSPDIWMYVllaylgVSCVLFVIARFSPYEWYDAH 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 275 RLQMGSMT---STTLYNSMWFVYGSFVQQGGEVPYTTLATRMMMGAWWLFALIVISSYTANLAAFLTITRIESSIQSLQD 351
Cdd:cd13723   164 PCNPGSEVvenNFTLLNSFWFGMGSLMQQGSELMPKALSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADD 243
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 352 LSKQTEIPYGTVLDSAVYEHVRMKGLNPFERdsmysqMWRMInrSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYva 431
Cdd:cd13723   244 LAKQTKIEYGAVKDGATMTFFKKSKISTFEK------MWAFM--SSKPSALVKNNEEGIQRALTADYALLMESTTIEY-- 313
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1370486819 432 INDPDCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 486
Cdd:cd13723   314 VTQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWW 368
PBP1_iGluR_delta_2 cd06391
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 ...
1-110 3.13e-75

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. 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. 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. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related 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 tumor necrosis factor family that is secreted from cerebellar granule cells.


Pssm-ID: 380614 [Multi-domain]  Cd Length: 402  Bit Score: 247.65  E-value: 3.13e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFE 80
Cdd:cd06391   293 MEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGLLEFGENGGNPNVHFE 372
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819  81 ILGTNYGEELGRGVRKLGCWNPVTGLNGSL 110
Cdd:cd06391   373 ILGTNYGEELGRGVRKLGCWNPVTGLNGSL 402
PBP1_iGluR_delta-like cd06381
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of an orphan family ...
1-110 3.32e-75

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2; This CD represents the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. 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. 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. Phylogenetic 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: 380604 [Multi-domain]  Cd Length: 401  Bit Score: 247.60  E-value: 3.32e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFE 80
Cdd:cd06381   292 LQISNLYLYDSVLMLANAFHRKLEDRKWHSMASLNCIRKSTKPWNGGRSMLDTIKKGHITGLTGVMEFREDSSNPYVQFE 371
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819  81 ILGTNYGEELGRGVRKLGCWNPVTGLNGSL 110
Cdd:cd06381   372 ILGTTYSETFGKDMRKLATWDSEKGLNGSL 401
PBP2_iGluR_Kainate cd13714
Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains ...
122-486 3.81e-59

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: 199.69  E-value: 3.81e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 122 VVLRVVTVLEEPFVMV--SENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQED-GTWNGLVGELVFKRA 198
Cdd:cd13714     2 KTLIVTTILEEPYVMLkeSAKPLTGNDRFEGFCIDLLKELAKILGFNYTIRLVPDGKYGSYDPEtGEWNGMVRELIDGRA 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 199 DIGISALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqm 278
Cdd:cd13714    82 DLAVADLTITYERESVVDFTKPFMNLGISILYRKPT-------------------------------------------- 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 279 gsmtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEI 358
Cdd:cd13714   118 ------------------------------------------------------------------PIESADDLAKQTKI 131
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 359 PYGTVLDSAVYEhvrmkglnpFERDSMYSQMWRMINRSNGSENNVLES--QAGIQKVKYGNYAFVWDAAVLEYVAINdpD 436
Cdd:cd13714   132 KYGTLRGGSTMT---------FFRDSNISTYQKMWNFMMSAKPSVFVKsnEEGVARVLKGKYAFLMESTSIEYVTQR--N 200
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 1370486819 437 CSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 486
Cdd:cd13714   201 CNLTQIGGLLDSKGYGIATPKGSPYRDKLSLAILKLQEKGKLEMLKNKWW 250
PBP1_iGluR_delta_1 cd06392
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta1 ...
1-110 4.15e-55

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. 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. 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. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdelta1 is expressed in many areas in the developing CNS, including the hippocampus and the caudate putamen. 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: 380615  Cd Length: 402  Bit Score: 193.69  E-value: 4.15e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFE 80
Cdd:cd06392   293 LQVSNLYLYDSVLMLANAFHRKLEDRKWHSMASLNCIRKSTKPWNGGRSMLDTIKKGHITGLTGVMEFREDGANPYVQFE 372
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819  81 ILGTNYGEELGRGVRKLGCWNPVTGLNGSL 110
Cdd:cd06392   373 ILGTSYSETFGKDVRRLATWDSEKGLNGSL 402
PBP2_iGluR_ligand_binding cd00998
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ...
124-486 7.42e-54

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: 185.27  E-value: 7.42e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMVSENVLGKP--KKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPqEDGTWNGLVGELVFKRADIG 201
Cdd:cd00998     3 LKVVVPLEPPFVMFVTGSNAVTgnGRFEGYCIDLLKELSQSLGFTYEYYLVPDGKFGAP-VNGSWNGMVGEVVRGEADLA 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRraektvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgsm 281
Cdd:cd00998    82 VGPITITSERSVVIDFTQPFMTSGIGIMIP-------------------------------------------------- 111
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 282 tsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriessIQSLQDLSKQTEIPYG 361
Cdd:cd00998   112 ----------------------------------------------------------------IRSIDDLKRQTDIEFG 127
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 362 TVLDSAVYEHVRMKGLNPFERDSMYSQMWRMINRSngsennvleSQAGIQKVKYGN-YAFVWDAAVLEYVAINDPdCSFY 440
Cdd:cd00998   128 TVENSFTETFLRSSGIYPFYKTWMYSEARVVFVNN---------IAEGIERVRKGKvYAFIWDRPYLEYYARQDP-CKLI 197
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*.
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 486
Cdd:cd00998   198 KTGGGFGSIGYGFALPKNSPLTNDLSTAILKLVESGVLQKLKNKWL 243
PBP2_iGluR_NMDA cd13687
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ...
124-485 3.73e-49

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: 172.05  E-value: 3.73e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMVsenvlgkpKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGS--PQEDGTWNGLVGELVFKRADIG 201
Cdd:cd13687     4 LKVVTLEEAPFVYV--------KCCYGFCIDLLKKLAEDVNFTYDLYLVTDGKFGTvnKSINGEWNGMIGELVSGRADMA 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRRAEKtvdmfaclapfdlslwacIAGtvllvgllvyllnwLNPPRLQMGSm 281
Cdd:cd13687    76 VASLTINPERSEVIDFSKPFKYTGITILVKKRNE------------------LSG--------------INDPRLRNPS- 122
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 282 tsttlynsmwfvygsfvqqggeVPYTtlatrmmmgawwlfalivissytanlaafltitriessiqslqdlskqteipYG 361
Cdd:cd13687   123 ----------------------PPFR----------------------------------------------------FG 128
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 362 TVLDSAVYEHVRmkglnpferdSMYSQMWRMINRsngseNNVLESQAGIQKVKYGNY-AFVWDAAVLEYVAINDPDCSFY 440
Cdd:cd13687   129 TVPNSSTERYFR----------RQVELMHRYMEK-----YNYETVEEAIQALKNGKLdAFIWDSAVLEYEASQDEGCKLV 193
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKW 485
Cdd:cd13687   194 TVGSLFARSGYGIGLQKNSPWKRNVSLAILQFHESGFMEELDKKW 238
PBP2_iGluR_AMPA cd13715
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
126-492 2.87e-47

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: 167.92  E-value: 2.87e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 126 VVTVLEEPFVMVSENVLGKP----KKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSP-QEDGTWNGLVGELVFKRADI 200
Cdd:cd13715     6 VTTILEEPYVMMKKNHEGEPlegnERYEGYCVDLADEIAKHLGIKYELRIVKDGKYGARdADTGIWNGMVGELVRGEADI 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 201 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAektvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgs 280
Cdd:cd13715    86 AIAPLTITLVRERVIDFSKPFMSLGISIMIKKP----------------------------------------------- 118
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 281 mtsttlynsmwfvygsfvqqggeVPyttlatrmmmgawwlfalivissytanlaafltitriessIQSLQDLSKQTEIPY 360
Cdd:cd13715   119 -----------------------VP----------------------------------------IESAEDLAKQTEIAY 135
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 361 GTVLDSAVYEhvrmkglnpFERDS---MYSQMWRMINrSNGSENNVLESQAGIQKVK--YGNYAFVWDAAVLEYVAINDP 435
Cdd:cd13715   136 GTLDSGSTKE---------FFRRSkiaVYDKMWEYMN-SAEPSVFVRTTDEGIARVRksKGKYAYLLESTMNEYINQRKP 205
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1370486819 436 dCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWPKNGQC 492
Cdd:cd13715   206 -CDTMKVGGNLDSKGYGIATPKGSPLRNPLNLAVLKLKENGELDKLKNKWWYDKGEC 261
PBPe smart00079
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ...
345-488 1.18e-46

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: 161.30  E-value: 1.18e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819  345 SIQSLQDLSKQTEIPYGTVLDSAVYEHVRMKGLNPferdsmYSQMWRMINRSngsENNVLESQAGIQKVKYGNYAFVWDA 424
Cdd:smart00079   1 PITSVEDLAKQTKIEYGTQDGSSTLAFFKRSGNPE------YSRMWPYMKSP---EVFVKSYAEGVQRVRVSNYAFIMES 71
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370486819  425 AVLEYVAINDpdCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWPK 488
Cdd:smart00079  72 PYLDYELSRN--CDLMTVGEEFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELEKLRNKWWKD 133
PBP2_iGluR_kainate_KA1 cd13724
The ligand-binding domain of the kainate subtype KA1 of ionotropic glutamate receptors, a ...
124-486 1.61e-46

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: 168.27  E-value: 1.61e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMVSEN--VLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIG 201
Cdd:cd13724     4 LVVTTILENPYLMLKGNhqEMEGNDRYEGFCVDMLKELAEILRFNYKIRLVGDGVYGVPEANGTWTGMVGELIARKADLA 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLR-RAEKTVDMFACLAPFDLSLWACI------AGTVLLVGLLVYLLNWLNPP 274
Cdd:cd13724    84 VAGLTITAEREKVIDFSKPFMTLGISILYRvHMGRKPGYFSFLDPFSPGVWLFMllaylaVSCVLFLVARLTPYEWYSPH 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 275 RLQMGS----MTSTTLYNSMWFVYGSFVQQGgevpyttlatrmmmgawwlfalivissytanlaafltiTRIESSIQSLQ 350
Cdd:cd13724   164 PCAQGRcnllVNQYSLGNSLWFPVGGFMQQG--------------------------------------STIAPPIESVD 205
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 351 DLSKQTEIPYGTVLDSAVYEhvrmkglnpFERDSMYSQMWRMINRSNGSENNVL--ESQAGIQKVKYGNYAFVWDAAVLE 428
Cdd:cd13724   206 DLADQTAIEYGTIHGGSSMT---------FFQNSRYQTYQRMWNYMYSKQPSVFvkSTEEGIARVLNSNYAFLLESTMNE 276
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1370486819 429 YVaiNDPDCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 486
Cdd:cd13724   277 YY--RQRNCNLTQIGGLLDTKGYGIGMPVGSVFRDEFDLAILQLQENNRLEILKRKWW 332
Lig_chan-Glu_bd pfam10613
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
122-232 3.72e-46

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: 159.22  E-value: 3.72e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 122 VVLRVVTVLEEPFVMVSENVLGkPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDG-TWNGLVGELVFKRADI 200
Cdd:pfam10613   1 KTLIVTTILEPPFVMLKENLEG-NDRYEGFCIDLLKELAEILGFKYEIRLVPDGKYGSLDPTTgEWNGMIGELIDGKADL 79
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1370486819 201 GISALTITPDRENVVDFTTRYMDYSVGVLLRR 232
Cdd:pfam10613  80 AVAPLTITSEREKVVDFTKPFMTLGISILMKK 111
PBP2_iGluR_Kainate_GluR6 cd13721
GluR6 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
124-486 1.56e-38

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: 143.24  E-value: 1.56e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMV--SENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQE-DGTWNGLVGELVFKRADI 200
Cdd:cd13721     4 LIVTTILEEPYVLFkkSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDvNGQWNGMVRELIDHKADL 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 201 GISALTITPDRENVVDFTTRYMDYSVGVLLRRAektvdmfaclapfdlslwaciagtvllvgllvyllnwlNPprlqmgs 280
Cdd:cd13721    84 AVAPLAITYVREKVIDFSKPFMTLGISILYRKG--------------------------------------TP------- 118
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 281 mtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriessIQSLQDLSKQTEIPY 360
Cdd:cd13721   119 -----------------------------------------------------------------IDSADDLAKQTKIEY 133
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 361 GTVLDSAVYEHVRMkglnpfERDSMYSQMWRMINrSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVaiNDPDCSFY 440
Cdd:cd13721   134 GAVEDGATMTFFKK------SKISTYDKMWAFMS-SRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFV--TQRNCNLT 204
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*.
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 486
Cdd:cd13721   205 QIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWW 250
PBP2_iGluR_AMPA_GluR1 cd13729
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
126-492 7.66e-37

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: 138.62  E-value: 7.66e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 126 VVTVLEEPFVMVSENV--LGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDG-TWNGLVGELVFKRADIGI 202
Cdd:cd13729     6 VTTILESPYVMLKKNHeqFEGNDRYEGYCVELAAEIAKHVGYSYKLEIVSDGKYGARDPETkMWNGMVGELVYGKADVAV 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 203 SALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgsmt 282
Cdd:cd13729    86 APLTITLVREEVIDFSKPFMSLGISIMIKKPT------------------------------------------------ 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 283 sttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitrieSSIQSLQDLSKQTEIPYGT 362
Cdd:cd13729   118 -------------------------------------------------------------SPIESAEDLAKQTEIAYGT 136
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 363 VLDSAVYEHVRMKGLNPFERdsMYSQMwrminRSNGSENNVLESQAGIQKVKY--GNYAFVWDAAVLEYVAINDPdCSFY 440
Cdd:cd13729   137 LDAGSTKEFFRRSKIAVFEK--MWSYM-----KSADPSVFVKTTDEGVMRVRKskGKYAYLLESTMNEYIEQRKP-CDTM 208
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWPKNGQC 492
Cdd:cd13729   209 KVGGNLDSKGYGIATPKGSALRNPVNLAVLKLNEQGLLDKLKNKWWYDKGEC 260
PBP2_iGluR_Kainate_GluR5 cd13722
GluR5 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
124-486 7.81e-36

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: 135.56  E-value: 7.81e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMV--SENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIG 201
Cdd:cd13722     4 LIVTTILEEPYVMYrkSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLA 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRRAektvdmfaclapfdlslwaciagtvllvgllvyllnwlNPprlqmgsm 281
Cdd:cd13722    84 VAPLTITYVREKVIDFSKPFMTLGISILYRKG--------------------------------------TP-------- 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 282 tsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriessIQSLQDLSKQTEIPYG 361
Cdd:cd13722   118 ----------------------------------------------------------------IDSADDLAKQTKIEYG 133
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 362 TVLDSAVYEHVRMKGLnpferdSMYSQMWR-MINRSNGSEnnVLESQAGIQKVKYGNYAFVWDAAVLEYVAinDPDCSFY 440
Cdd:cd13722   134 AVRDGSTMTFFKKSKI------STYEKMWAfMSSRQQTAL--VKNSDEGIQRVLTTDYALLMESTSIEYVT--QRNCNLT 203
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*.
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 486
Cdd:cd13722   204 QIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWW 249
PBP2_iGluR_AMPA_GluR4 cd13727
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
126-492 5.56e-35

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: 133.62  E-value: 5.56e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 126 VVTVLEEPFVMVSEN--VLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDG-TWNGLVGELVFKRADIGI 202
Cdd:cd13727     6 VTTIMESPYVMYKKNheMFEGNDKFEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDPETkIWNGMVGELVYGKAEIAV 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 203 SALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgsmt 282
Cdd:cd13727    86 APLTITLVREEVIDFSKPFMSLGISIMIKKPQ------------------------------------------------ 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 283 sttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEIPYGT 362
Cdd:cd13727   118 --------------------------------------------------------------PIESAEDLAKQTEIAYGT 135
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 363 VLDSAVYEHVRMKGLnpferdSMYSQMWRMINRSNGS--ENNVLESQAGIQKVKyGNYAFVWDAAVLEYVAINDPdCSFY 440
Cdd:cd13727   136 LDSGSTKEFFRRSKI------AVYEKMWTYMKSAEPSvfTRTTAEGVARVRKSK-GKFAFLLESTMNEYIEQRKP-CDTM 207
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWPKNGQC 492
Cdd:cd13727   208 KVGGNLDSKGYGVATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 259
PBP2_iGluR_AMPA_GluR2 cd13726
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
126-492 8.86e-35

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: 132.84  E-value: 8.86e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 126 VVTVLEEPFVMVSEN--VLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGS-PQEDGTWNGLVGELVFKRADIGI 202
Cdd:cd13726     6 VTTILESPYVMMKKNheMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGArDADTKIWNGMVGELVYGKADIAI 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 203 SALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgsmt 282
Cdd:cd13726    86 APLTITLVREEVIDFSKPFMSLGISIMIKKGT------------------------------------------------ 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 283 sttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEIPYGT 362
Cdd:cd13726   118 --------------------------------------------------------------PIESAEDLSKQTEIAYGT 135
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 363 VLDSAVYEHVRMKGLnpferdSMYSQMWRMInRSNGSENNVLESQAGIQKVK--YGNYAFVWDAAVLEYVAINDPdCSFY 440
Cdd:cd13726   136 LDSGSTKEFFRRSKI------AVFDKMWTYM-RSAEPSVFVRTTAEGVARVRksKGKYAYLLESTMNEYIEQRKP-CDTM 207
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWPKNGQC 492
Cdd:cd13726   208 KVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 259
PBP2_iGluR_NMDA_Nr2 cd13718
The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
124-485 1.84e-32

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: 127.07  E-value: 1.84e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMVS--ENVLGKPKK-----------------------YQ---GFSIDVLDALSNYLGFNYEIYVAPDH 175
Cdd:cd13718     4 LKIVTLEEAPFVIVEpvDPLTGTCMRntvpcrkqlnhenstdadenryvKKcckGFCIDILKKLAKDVGFTYDLYLVTNG 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 176 KYGSpQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRAEKtvdmfaclapfdlslwacIA 255
Cdd:cd13718    84 KHGK-KINGVWNGMIGEVVYKRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNQ------------------VS 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 256 GtvllvgllvyllnwLNPPRLQMgsmtsttlynsmwfvygsfvqqggevPYttlatrmmmgawwlfalivissytanlaa 335
Cdd:cd13718   145 G--------------LSDKKFQR--------------------------PH----------------------------- 155
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 336 fltitriessiqslqdlSKQTEIPYGTVLDSAVYEHVRmkglnpferdSMYSQMWRMINRSNgsENNVlesQAGIQKVKY 415
Cdd:cd13718   156 -----------------DQSPPFRFGTVPNGSTERNIR----------NNYPEMHQYMRKYN--QKGV---EDALVSLKT 203
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370486819 416 GNY-AFVWDAAVLEYVAINDPDCSFYTIGNTV--ADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKW 485
Cdd:cd13718   204 GKLdAFIYDAAVLNYMAGQDEGCKLVTIGSGKwfAMTGYGIALQKNSKWKRPFDLALLQFRGDGELERLERLW 276
PBP2_iGluR_kainate_KA2 cd13725
The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a ...
124-486 2.34e-32

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: 125.59  E-value: 2.34e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMVSENV--LGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIG 201
Cdd:cd13725     4 LVVTTILENPYVMRRPNFqaLSGNERFEGFCVDMLRELAELLRFRYRLRLVEDGLYGAPEPNGSWTGMVGELINRKADLA 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLrraektvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgsm 281
Cdd:cd13725    84 VAAFTITAEREKVIDFSKPFMTLGISILY--------------------------------------------------- 112
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 282 tsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitRIESSIQSLQDLSKQTEIPYG 361
Cdd:cd13725   113 -----------------------------------------------------------RVHMPVESADDLADQTNIEYG 133
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 362 TVLDSAVYEhvrmkglnpFERDSMYSQMWRMINRSNGSENNVL--ESQAGIQKVKYGNYAFVWDAAVLEYVaiNDPDCSF 439
Cdd:cd13725   134 TIHAGSTMT---------FFQNSRYQTYQRMWNYMQSKQPSVFvkSTEEGIARVLNSRYAFLLESTMNEYH--RRLNCNL 202
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1370486819 440 YTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 486
Cdd:cd13725   203 TQIGGLLDTKGYGIGMPLGSPFRDEITLAILQLQENNRLEILKRKWW 249
PBP2_iGluR_NMDA_Nr1 cd13719
The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
124-485 5.62e-32

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: 125.55  E-value: 5.62e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMVS------------------ENVLGKPKKYQ---GFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQE 182
Cdd:cd13719     4 LKIVTIHEEPFVYVRptpsdgtcreeftvncpnFNISGRPTVPFccyGYCIDLLIKLARKMNFTYELHLVADGQFGTQER 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 183 DG-----TWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRAEKtvdmfaclapfdlslwacIAGt 257
Cdd:cd13719    84 VNnsnkkEWNGMMGELVSGRADMIVAPLTINPERAQYIEFSKPFKYQGLTILVKKEIR------------------LTG- 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 258 vllvgllvyllnwLNPPRLQmgsmtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytaNLAAFL 337
Cdd:cd13719   145 -------------INDPRLR------------------------------------------------------NPSEKF 157
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 338 TitriessiqslqdlskqteipYGTVLDSAVYEHVRMKglnpFERDSMYSQMwrminrsngSENNVLESQAGIQKVKYGN 417
Cdd:cd13719   158 I---------------------YATVKGSSVDMYFRRQ----VELSTMYRHM---------EKHNYETAEEAIQAVRDGK 203
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370486819 418 -YAFVWDAAVLEYVAINdpDCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKW 485
Cdd:cd13719   204 lHAFIWDSSRLEFEASQ--DCDLVTAGELFGRSGYGIGLQKNSPWTDNVSLAILKMHESGFMEDLDKTW 270
PBP2_iGluR_AMPA_GluR3 cd13728
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
126-492 6.45e-30

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: 119.03  E-value: 6.45e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 126 VVTVLEEPFVMVSEN--VLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQ-EDGTWNGLVGELVFKRADIGI 202
Cdd:cd13728     6 VTTILESPYVMYKKNheQLEGNERYEGYCVDLAYEIAKHVRIKYKLSIVGDGKYGARDpETKIWNGMVGELVYGRADIAV 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 203 SALTITPDRENVVDFTTRYMDYSVGVLLRRAEktvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgsmt 282
Cdd:cd13728    86 APLTITLVREEVIDFSKPFMSLGISIMIKKPQ------------------------------------------------ 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 283 sttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfalivissytanlaafltitriesSIQSLQDLSKQTEIPYGT 362
Cdd:cd13728   118 --------------------------------------------------------------PIESAEDLAKQTEIAYGT 135
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 363 VLDSAVYEHVRMKGLnpferdSMYSQMWRMINRSNGS--ENNVLESQAGIQKVKyGNYAFVWDAAVLEYVAINDPdCSFY 440
Cdd:cd13728   136 LDSGSTKEFFRRSKI------AVYEKMWSYMKSAEPSvfTKTTADGVARVRKSK-GKFAFLLESTMNEYIEQRKP-CDTM 207
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1370486819 441 TIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWWPKNGQC 492
Cdd:cd13728   208 KVGGNLDSKGYGVATPKGSALGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 259
PBP2_iGluR_NMDA_Nr3 cd13720
The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
123-486 8.39e-29

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: 116.49  E-value: 8.39e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRVVTVLEEPFVMVSE----------------------------NVLG-----KPKKYQ----GFSIDVLDALSNYLGF 165
Cdd:cd13720     3 HLRVVTLLEHPFVFTREvdeeglcpagqlcldpmtndsstldalfSSLHssndtVPIKFRkccyGYCIDLLEKLAEDLGF 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 166 NYEIYVAPDHKYGsPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRraektvdmfaclap 245
Cdd:cd13720    83 DFDLYIVGDGKYG-AWRNGRWTGLVGDLLSGRAHMAVTSFSINSARSQVIDFTSPFFSTSLGILVR-------------- 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 246 fdlslwaciagtvllvgllvyllnwlnpPRLQmgsmtsttlynsmwfvygsfvqqggevpyttlatrmmmgawwlfaliv 325
Cdd:cd13720   148 ----------------------------TRDE------------------------------------------------ 151
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 326 issytanlaafltITRIESSIQSLQDLSKQteipYGTVLDSAVYEHVRMKglNPferdsmysQMWRMINRSNGSenNVLE 405
Cdd:cd13720   152 -------------LSGIHDPKLHHPSQGFR----FGTVRESSAEYYVKKS--FP--------EMHEHMRRYSLP--NTPE 202
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 406 sqaGIQKVKYGNY---AFVWDAAVLEYVAINDPDCSFYTIGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILK 482
Cdd:cd13720   203 ---GVEYLKNDPEkldAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQNSPLTSNISELISQYKSNGFMDLLH 279

                  ....
gi 1370486819 483 HKWW 486
Cdd:cd13720   280 DKWY 283
Lig_chan-Glu_bd smart00918
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
133-194 7.61e-24

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: 95.01  E-value: 7.61e-24
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370486819  133 PFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELV 194
Cdd:smart00918   1 PYVMLKESPDGGNDRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGARLPNGSWNGMVGELV 62
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
123-244 5.11e-18

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: 83.45  E-value: 5.11e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRVVTVLE-EPFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIG 201
Cdd:cd13530     1 TLRVGTDADyPPFEYIDKN-----GKLVGFDVDLANAIAKRLGVKVEF------------VDTDFDGLIPALQSGKIDVA 63
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRRAEKTVDMFACLA 244
Cdd:cd13530    64 ISGMTITPERAKVVDFSDPYYYTGQVLVVKKDSKITKTVADLK 106
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
124-237 5.69e-16

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: 77.33  E-value: 5.69e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLE-EPFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGI 202
Cdd:COG0834     1 LRVGVDPDyPPFSFRDED-----GKLVGFDVDLARAIAKRLGLKVEFVPVP------------WDRLIPALQSGKVDLII 63
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1370486819 203 SALTITPDRENVVDFTTRYMDYSVGVLLRRAEKTV 237
Cdd:COG0834    64 AGMTITPEREKQVDFSDPYYTSGQVLLVRKDNSGI 98
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
133-239 1.81e-15

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: 76.18  E-value: 1.81e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:pfam00497  11 PFEYVDEN-----GKLVGFDVDLAKAIAKRLGVKVEF------------VPVSWDGLIPALQSGKVDLIIAGMTITPERA 73
                          90       100
                  ....*....|....*....|....*..
gi 1370486819 213 NVVDFTTRYMDYSVGVLLRRAEKTVDM 239
Cdd:pfam00497  74 KQVDFSDPYYYSGQVILVRKKDSSKSI 100
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
123-237 7.45e-13

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: 68.29  E-value: 7.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRVVTVLE-EPFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIG 201
Cdd:cd13624     1 TLVVGTDATfPPFEFVDEN-----GKIVGFDIDLIKAIAKEAGFEVEF------------KNMAFDGLIPALQSGKIDII 63
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRRAEKTV 237
Cdd:cd13624    64 ISGMTITEERKKSVDFSDPYYEAGQAIVVRKDSTII 99
ANF_receptor pfam01094
Receptor family ligand binding region; This family includes extracellular ligand binding ...
1-85 1.23e-12

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: 69.72  E-value: 1.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKKLEDRKWHSmaslSCIRknSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFE 80
Cdd:pfam01094 267 PVSYGALAYDAVYLLAHALHNLLRDDKPGR----ACGA--LGPWNGGQKLLRYLKNVNFTGLTGNVQFDENGDRINPDYD 340

                  ....*
gi 1370486819  81 ILGTN 85
Cdd:pfam01094 341 ILNLN 345
PBP2_GlnH cd00994
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ...
147-237 1.56e-12

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: 67.30  E-value: 1.56e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 147 KYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSV 226
Cdd:cd00994    20 KYVGFDIDLWEAIAKEAGFKYEL------------QPMDFKGIIPALQTGRIDIAIAGITITEERKKVVDFSDPYYDSGL 87
                          90
                  ....*....|.
gi 1370486819 227 GVLLRRAEKTV 237
Cdd:cd00994    88 AVMVKADNNSI 98
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
124-485 3.80e-11

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: 63.12  E-value: 3.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPFVMVSENVLgkpkkyQGFSIDVLDALSNYLGFNYEiYVAPDhkygspqedgTWNGLVGELVFKRADIGIS 203
Cdd:cd00997     5 LTVATVPRPPFVFYNDGEL------TGFSIDLWRAIAERLGWETE-YVRVD----------SVSALLAAVAEGEADIAIA 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 204 ALTITPDRENVVDFTTRYMDYSVGVLLRraektvdmfaclapfdlslwaciagtvllvgllvyllnwlnpprlqmgsmtS 283
Cdd:cd00997    68 AISITAEREAEFDFSQPIFESGLQILVP---------------------------------------------------N 96
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 284 TTLYNSMWFVYGSFVqqgGEVPYTTLATrmmmgawWLfalivissyTANLAAFLTITRIESSIQSLQDlsKQTEipygtv 363
Cdd:cd00997    97 TPLINSVNDLYGKRV---ATVAGSTAAD-------YL---------RRHDIDVVEVPNLEAAYTALQD--KDAD------ 149
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 364 ldsavyehvrmkglnpferdsmysqmwrminrsngsennvlesqagiqkvkygnyAFVWDAAVLEYVAINDPDCSFYTIG 443
Cdd:cd00997   150 -------------------------------------------------------AVVFDAPVLRYYAAHDGNGKAEVTG 174
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1370486819 444 NTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKW 485
Cdd:cd00997   175 SVFLEENYGIVFPTGSPLRKPINQALLNLREDGTYDELYEKW 216
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
133-237 9.69e-11

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: 62.22  E-value: 9.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlGKPkkyQGFSIDVLDALSNYLGFNYEIYVapdhkygspqedGTWNGLVGELVFKRADIgISALTITPDRE 212
Cdd:cd13704    14 PYEFLDEN--GNP---TGFNVDLLRAIAEEMGLKVEIRL------------GPWSEVLQALENGEIDV-LIGMAYSEERA 75
                          90       100
                  ....*....|....*....|....*
gi 1370486819 213 NVVDFTTRYMDYSVGVLLRRAEKTV 237
Cdd:cd13704    76 KLFDFSDPYLEVSVSIFVRKGSSII 100
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
143-221 7.26e-10

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: 59.40  E-value: 7.26e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370486819 143 GKPKKYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRY 221
Cdd:cd13628    18 GDRGKIVGFDIELAKTIAKKLGLKLQI------------QEYDFNGLIPALASGQADLALAGITPTPERKKVVDFSEPY 84
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
133-232 7.57e-10

Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 59.26  E-value: 7.57e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819  133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIYVApdhkygspqedgTWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:smart00062  12 PFSFADED-----GELTGFDVDLAKAIAKELGLKVEFVEV------------SFDSLLTALKSGKIDVVAAGMTITPERA 74
                           90       100
                   ....*....|....*....|
gi 1370486819  213 NVVDFTTRYMDYSVGVLLRR 232
Cdd:smart00062  75 KQVDFSDPYYRSGQVILVRK 94
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
146-229 3.89e-09

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: 57.64  E-value: 3.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 146 KKYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTrYMDYS 225
Cdd:cd01004    22 GKLIGFDVDLAKAIAKRLGLKVEI------------VNVSFDGLIPALQSGRYDIIMSGITDTPERAKQVDFVD-YMKDG 88

                  ....
gi 1370486819 226 VGVL 229
Cdd:cd01004    89 LGVL 92
PBP2_HisJ_LAO_like cd01001
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ...
133-239 3.67e-08

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: 54.61  E-value: 3.67e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFvmvseNVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:cd01001    14 PF-----NFLDADGKLVGFDIDLANALCKRMKVKCEIVTQP------------WDGLIPALKAGKYDAIIASMSITDKRR 76
                          90       100
                  ....*....|....*....|....*..
gi 1370486819 213 NVVDFTTRYMDYSVGVLLRRAEKTVDM 239
Cdd:cd01001    77 QQIDFTDPYYRTPSRFVARKDSPITDT 103
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
123-232 3.92e-08

The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine kinase receptors, and related proteins; This family comprises the periplasmic sensor domain of the two-component sensor-kinase systems, such as the sensor protein BvgS of Bordetella pertussis and histidine kinase receptors (HisK), and uncharacterized related proteins. Typically, the two-component system consists of a membrane spanning sensor-kinase and a cytoplasmic response regulator. It serves as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. The N-terminal sensing domain of the sensor kinase detects extracellular signals, such as small molecule ligands and ions, which then modulate the catalytic activity of the cytoplasmic kinase domain through a phosphorylation cascade. The periplasmic 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 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: 270228 [Multi-domain]  Cd Length: 220  Bit Score: 54.46  E-value: 3.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRVVTVLE-EPFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIYVAPDhkygspqedgtWNGLVGELVFKRADIg 201
Cdd:cd01007     3 VIRVGVDPDwPPFEFIDEG-----GEPQGIAADYLKLIAKKLGLKFEYVPGDS-----------WSELLEALKAGEIDL- 65
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRR 232
Cdd:cd01007    66 LSSVSKTPEREKYLLFTKPYLSSPLVIVTRK 96
PBP2_GltS cd13620
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ...
143-235 6.82e-07

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: 50.80  E-value: 6.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 143 GKpKKYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYM 222
Cdd:cd13620    25 GK-NQVVGADIDIAKAIAKELGVKLEI------------KSMDFDNLLASLQSGKVDMAISGMTPTPERKKSVDFSDVYY 91
                          90
                  ....*....|...
gi 1370486819 223 DYSVGVLLRRAEK 235
Cdd:cd13620    92 EAKQSLLVKKADL 104
PBP1_GABAb_receptor_plant cd19990
periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close ...
3-106 7.13e-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: 51.85  E-value: 7.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   3 ISNLYIYDTVLLLANAFHKKLEDRKwhsmaslscirkNSKPWQGGRSMLETIKKGGVSGLTGELEFgENGGNPNVH-FEI 81
Cdd:cd19990   283 IYALRAYDAIWALAHAVEKLNSSGG------------NISVSDSGKKLLEEILSTKFKGLSGEVQF-VDGQLAPPPaFEI 349
                          90       100
                  ....*....|....*....|....*
gi 1370486819  82 LGTNygeelGRGVRKLGCWNPVTGL 106
Cdd:cd19990   350 VNVI-----GKGYRELGFWSPGSGF 369
PBP2_YxeM cd13709
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ...
123-238 1.35e-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: 50.04  E-value: 1.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRV-VTVLEEPFVMVSENVLgkpkkyQGFSIDVLDALSNYLGFNYEIYVApdhkygspqedgTWNGLVGELVFKRADIG 201
Cdd:cd13709     2 VIKVgSSGSSYPFTFKENGKL------KGFEVDVWNAIGKRTGYKVEFVTA------------DFSGLFGMLDSGKVDTI 63
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1370486819 202 ISALTITPDRENVVDFTTRYMDYSVGVLLRRAEKTVD 238
Cdd:cd13709    64 ANQITITPERQEKYDFSEPYVYDGAQIVVKKDNNSIK 100
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
150-222 2.12e-06

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: 49.20  E-value: 2.12e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370486819 150 GFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYM 222
Cdd:cd13713    24 GFDVDVAKAIAKRLGVKVEPVTTA------------WDGIIAGLWAGRYDIIIGSMTITEERLKVVDFSNPYY 84
PBP2_GlnP cd13619
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ...
146-237 2.95e-06

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: 48.85  E-value: 2.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 146 KKYQGFSIDVLDALSNYLGFNYEIyvapdhkygSPQEdgtWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYS 225
Cdd:cd13619    20 GKYVGIDVDLLNAIAKDQGFKVEL---------KPMG---FDAAIQAVQSGQADGVIAGMSITDERKKTFDFSDPYYDSG 87
                          90
                  ....*....|..
gi 1370486819 226 VGVLLRRAEKTV 237
Cdd:cd13619    88 LVIAVKKDNTSI 99
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
123-221 3.62e-06

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: 48.34  E-value: 3.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRVVTVLE-EPFVMVSENvlGKPkkyQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIG 201
Cdd:cd13629     1 VLRVGMEAGyPPFEMTDKK--GEL---IGFDVDLAKALAKDLGVKVEF------------VNTAWDGLIPALQTGKFDLI 63
                          90       100
                  ....*....|....*....|
gi 1370486819 202 ISALTITPDRENVVDFTTRY 221
Cdd:cd13629    64 ISGMTITPERNLKVNFSNPY 83
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
133-234 6.83e-06

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 48.18  E-value: 6.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:PRK11260   53 PFSFQGED-----GKLTGFEVEFAEALAKHLGVKASLKPTK------------WDGMLASLDSKRIDVVINQVTISDERK 115
                          90       100
                  ....*....|....*....|..
gi 1370486819 213 NVVDFTTRYMDYSVGVLLRRAE 234
Cdd:PRK11260  116 KKYDFSTPYTVSGIQALVKKGN 137
PBP1_iGluR_AMPA cd06380
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA receptor; ...
8-106 7.62e-06

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: 48.81  E-value: 7.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   8 IYDTVLLLANAFHKKLEDR------KWHSMASLS------CIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNP 75
Cdd:cd06380   280 AVDAVLVIAEAFQSLLRQNddifrfTFHGELYNNgskgidCDPNPPLPWEHGKAIMKALKKVRFEGLTGNVQFDDFGQRK 359
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1370486819  76 NVHFEILgtnygeELG--RGVRKLGCWNPVTGL 106
Cdd:cd06380   360 NYTLDVI------ELTsnRGLRKIGTWSEGDGF 386
PBP2_mlr5654_like cd13702
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
147-221 7.65e-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: 47.70  E-value: 7.65e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370486819 147 KYQGFSIDVLDALSNYLGFNYEIyVAPDhkygspqedgtWNGLVGELVFKRADIGISALTITPDRENVVDFTTRY 221
Cdd:cd13702    23 KLGGFDVDIANALCAEMKAKCEI-VAQD-----------WDGIIPALQAKKFDAIIASMSITPERKKQVDFTDPY 85
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
133-221 8.68e-06

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: 47.31  E-value: 8.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:cd13626    12 PFTFKDED-----GKLTGFDVEVGREIAKRLGLKVEF------------KATEWDGLLPGLNSGKFDVIANQVTITPERE 74

                  ....*....
gi 1370486819 213 NVVDFTTRY 221
Cdd:cd13626    75 EKYLFSDPY 83
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
147-234 1.04e-05

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: 47.21  E-value: 1.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 147 KYQGFSIDVLDALSNYLGFNYEIYVAPDhkygspqedgtWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMdYSV 226
Cdd:cd01009    20 GPRGFEYELAKAFADYLGVELEIVPADN-----------LEELLEALEEGKGDLAAAGLTITPERKKKVDFSFPYY-YVV 87

                  ....*...
gi 1370486819 227 GVLLRRAE 234
Cdd:cd01009    88 QVLVYRKG 95
glnH PRK09495
glutamine ABC transporter periplasmic protein; Reviewed
147-237 1.42e-05

glutamine ABC transporter periplasmic protein; Reviewed


Pssm-ID: 236540 [Multi-domain]  Cd Length: 247  Bit Score: 47.05  E-value: 1.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 147 KYQGFSIDVLDALSNYLGFNYEIyvapdhkygSPQEdgtWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSV 226
Cdd:PRK09495   45 KYVGFDIDLWAAIAKELKLDYTL---------KPMD---FSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGL 112
                          90
                  ....*....|.
gi 1370486819 227 GVLLRRAEKTV 237
Cdd:PRK09495  113 LVMVKANNNDI 123
PBP1_iGluR_N_LIVBP-like cd06351
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, ...
1-109 1.90e-05

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs); N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). 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. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors characterized by their response to glutamate agonists: N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. On the other hand, non-NMDA receptors have faster kinetics, are weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute to several forms of synaptic plasticity and are suggested to play an important role in the development of synaptic pathways.


Pssm-ID: 380574  Cd Length: 348  Bit Score: 47.34  E-value: 1.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKkledrkwhsmaslscirknskpwqggrsmletikkggvsglTGELEFGENGGNPNVHFE 80
Cdd:cd06351   285 LQLSSAFYFDLALRSALAFKE-----------------------------------------TGYGTFDLQSTQPFNGHS 323
                          90       100
                  ....*....|....*....|....*....
gi 1370486819  81 ILGTNYgeelGRGVRKLGCWNPVTGLNGS 109
Cdd:cd06351   324 FMKFEM----DINVRKIRGWSEYESVNSK 348
GluR_Plant cd13686
Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily ...
134-229 1.98e-05

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: 46.36  E-value: 1.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 134 FVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEiyvapdHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDREN 213
Cdd:cd13686    16 FVKVTRDPITNSTSVTGFCIDVFEAAVKRLPYAVP------YEFIPFNDAGSYDDLVYQVYLKKFDAAVGDITITANRSL 89
                          90
                  ....*....|....*.
gi 1370486819 214 VVDFTTRYMDYSVGVL 229
Cdd:cd13686    90 YVDFTLPYTESGLVMV 105
PBP2_Arg_STM4351 cd13700
Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding ...
133-232 1.98e-05

Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding protein fold; This group includes domains similar to Escherichia coli arginine third transport system. STM4351 is the high arginine specific periplasmic-binding protein of ABC transport system. STM4351 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: 270418 [Multi-domain]  Cd Length: 222  Bit Score: 46.28  E-value: 1.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIyvapdhkygSPQedgTWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:cd13700    14 PFESIGAK-----GEIVGFDIDLANALCKQMQAECTF---------TNQ---AFDSLIPSLKFKKFDAVISGMDITPERE 76
                          90       100
                  ....*....|....*....|
gi 1370486819 213 NVVDFTTRYMDYSVGVLLRR 232
Cdd:cd13700    77 KQVSFSTPYYENSAVVIAKK 96
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
147-244 2.09e-05

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: 46.21  E-value: 2.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 147 KYQGFSIDVLDALSNYLGFNYEiyvapdhkygspQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSV 226
Cdd:cd13625    25 KIVGFDRDLLDEMAKKLGVKVE------------QQDLPWSGILPGLLAGKFDMVATSVTITKERAKRFAFTLPIAEATA 92
                          90
                  ....*....|....*...
gi 1370486819 227 GVLLRRAEKTVDMFACLA 244
Cdd:cd13625    93 ALLKRAGDDSIKTIEDLA 110
PBP2_HisJ_LAO cd13703
Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; ...
132-221 2.18e-05

Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; the type 2 periplasmic-binding protein fold; This subgroup includes the periplasmic-binding proteins, HisJ and LAO, that serve as initial receptors in the ABC transport of histidine and lysine-arginine-ornithine amino acids. They are 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: 270421 [Multi-domain]  Cd Length: 229  Bit Score: 46.47  E-value: 2.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 132 EPFVMVSENvlGKPkkyQGFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGISALTITPDR 211
Cdd:cd13703    13 PPFESKDAD--GEL---TGFDIDLGNALCAEMKVKCTWVEQD------------FDGLIPGLLARKFDAIISSMSITEER 75
                          90
                  ....*....|
gi 1370486819 212 ENVVDFTTRY 221
Cdd:cd13703    76 KKVVDFTDKY 85
PBP2_OccT_like cd13699
Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding ...
150-221 2.35e-05

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: 45.83  E-value: 2.35e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370486819 150 GFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGISALTITPDRENVVDFTTRY 221
Cdd:cd13699    26 GFEIDLANVLCERMKVKCTFVVQD------------WDGMIPALNAGKFDVIMDAMSITAERKKVIDFSTPY 85
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
133-236 2.55e-05

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: 45.84  E-value: 2.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFvmvseNVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:cd13712    12 PF-----NFKDETGQLTGFEVDVAKALAAKLGVKPEFVTTE------------WSGILAGLQAGKYDVIINQVGITPERQ 74
                          90       100
                  ....*....|....*....|....
gi 1370486819 213 NVVDFTTRYMdYSVGVLLRRAEKT 236
Cdd:cd13712    75 KKFDFSQPYT-YSGIQLIVRKNDT 97
PBP2_Cysteine cd13694
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ...
133-239 4.92e-05

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: 45.04  E-value: 4.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYL-GFNYEI-YVAPDHKYGSPQedgtwnglvgeLVFKRADIGISALTITPD 210
Cdd:cd13694    20 PFGYVDEN-----GKFQGFDIDLAKQIAKDLfGSGVKVeFVLVEAANRVPY-----------LTSGKVDLILANFTVTPE 83
                          90       100
                  ....*....|....*....|....*....
gi 1370486819 211 RENVVDFTTRYMDYSVGVLLRRAEKTVDM 239
Cdd:cd13694    84 RAEVVDFANPYMKVALGVVSPKDSNITSV 112
PBP2_ml15202_like cd13701
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
133-221 6.35e-05

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: 44.76  E-value: 6.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIGISALTITPDRE 212
Cdd:cd13701    15 PFTSKDAS-----GKWSGWEIDLIDALCARLDARCEI------------TPVAWDGIIPALQSGKIDMIWNSMSITDERK 77

                  ....*....
gi 1370486819 213 NVVDFTTRY 221
Cdd:cd13701    78 KVIDFSDPY 86
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
123-232 8.71e-05

Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, Signal transduction mechanisms];


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 45.44  E-value: 8.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRVVTVLEEPFVMVSENvlgkpkKYQGFSIDVLDALSNYLGFNYEIYVAPDHkygspqedgtwNGLVGELVFKRADIGI 202
Cdd:COG4623    23 VLRVLTRNSPTTYFIYRG------GPMGFEYELAKAFADYLGVKLEIIVPDNL-----------DELLPALNAGEGDIAA 85
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819 203 SALTITPDRENVVDFTTRYMDYSVGVLLRR 232
Cdd:COG4623    86 AGLTITPERKKQVRFSPPYYSVSQVLVYRK 115
PBP2_SMa0082_like cd01072
The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic ...
120-228 8.81e-05

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: 44.56  E-value: 8.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 120 RGVVLRVVTVLEEPFVMVSENvlGKPkkyQGFSIDVLDALSNYLGFNYEIY-VAPDHKYGSPQEDgtwnglvgelvfkRA 198
Cdd:cd01072    12 RGKLKVGVLVDAPPFGFVDAS--MQP---QGYDVDVAKLLAKDLGVKLELVpVTGANRIPYLQTG-------------KV 73
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819 199 DIGISALTITPDRENVVDFTTRYMDYSVGV 228
Cdd:cd01072    74 DMLIASLGITPERAKVVDFSQPYAAFYLGV 103
PBP2_PheC cd01069
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ...
147-236 1.47e-04

Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes cyclohexadienyl dehydratase PheC. These proteins catalyze the decarboxylation of prephenate to phenylpyruvate in the alternative phenylalanine biosynthesis pathway in some proteobacteria and archaea. The PheC 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. Since they the PheC proteins are so similar to periplasmic binding proteins, (PBP), it is evolutionarily plausible that several pre-existing PBP proteins might have been recruited to perform the enzymatic function.


Pssm-ID: 270231 [Multi-domain]  Cd Length: 232  Bit Score: 43.87  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 147 KYQGFSIDVLDALSNYLGFnyEIYVAPDhkygspqedgTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSV 226
Cdd:cd01069    31 QYEGYDIDMAEALAKSLGV--KVEFVPT----------SWPTLMDDLAADKFDIAMGGISITLERQRQAFFSAPYLRFGK 98
                          90
                  ....*....|
gi 1370486819 227 GVLLRRAEKT 236
Cdd:cd01069    99 TPLVRCADVD 108
PBP1_iGluR_non_NMDA-like cd06368
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA ...
1-110 1.59e-04

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-D-aspartate) subtypes of ionotropic glutamate receptors; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-D-asparate) subtypes of ionotropic 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. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-D-aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. Non-NMDA receptors have faster kinetics, are most often only weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute several forms of synaptic plasticity and are thought to play an important role in the development of synaptic pathways. Non-NMDA receptors include alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate (AMPA) and kainate receptors.


Pssm-ID: 380591 [Multi-domain]  Cd Length: 339  Bit Score: 44.28  E-value: 1.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   1 MEISNLYIYDTVLLLANAFHKkledrkwhsmaslscirknskpwqggrsmletikkggvsglTGELEFGENGGNPNVHFE 80
Cdd:cd06368   276 PPYEAALMFDAVLLLADAFRR-----------------------------------------TGDLRFNGTGLRSNFTLR 314
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819  81 ILGTNYGeelgrGVRKLGCWNPVTGLNGSL 110
Cdd:cd06368   315 ILELGYG-----GLRKIGFWDSNTRLAMNL 339
PBP1_iGluR_AMPA_GluR4 cd06388
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit ...
9-106 2.12e-04

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 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: 380611 [Multi-domain]  Cd Length: 373  Bit Score: 44.24  E-value: 2.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   9 YDTVLLLANAFH----KKLEDRKWHSMASlsCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFEILgt 84
Cdd:cd06388   275 YDGVLVMAETFRnlrrQKIDISRRGNAGD--CLANPAAPWGQGIDMERTLKQVRIQGLTGNVQFDHYGRRVNYTMDVF-- 350
                          90       100
                  ....*....|....*....|..
gi 1370486819  85 nygEELGRGVRKLGCWNPVTGL 106
Cdd:cd06388   351 ---ELKSTGPRKVGYWNDMDKL 369
PBP2_Arg_3 cd13622
Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ...
133-222 3.34e-04

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: 42.67  E-value: 3.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 133 PFVMVSENvlgkpKKYQGFSIDVLDALSNYL--GFNYEIYvapdhkygspqedgTWNGLVGELVFKRADIGISALTITPD 210
Cdd:cd13622    14 PFEMQGTN-----NELFGFDIDLMNEICKRIqrTCQYKPM--------------RFDDLLAALNNGKVDVAISSISITPE 74
                          90
                  ....*....|..
gi 1370486819 211 RENVVDFTTRYM 222
Cdd:cd13622    75 RSKNFIFSLPYL 86
PRK11917 PRK11917
bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
144-241 3.85e-04

bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed


Pssm-ID: 183381 [Multi-domain]  Cd Length: 259  Bit Score: 42.60  E-value: 3.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 144 KPKKYQGFSIDVLDALSNY-LGFNYEI-YVAPDHKYGSPQEDgtwNGLVgelvfkraDIGISALTITPDRENVVDFTTRY 221
Cdd:PRK11917   57 ATGEIKGFEIDVAKLLAKSiLGDDKKIkLVAVNAKTRGPLLD---NGSV--------DAVIATFTITPERKRIYNFSEPY 125
                          90       100
                  ....*....|....*....|
gi 1370486819 222 MDYSVGVLLRRaEKTVDMFA 241
Cdd:PRK11917  126 YQDAIGLLVLK-EKNYKSLA 144
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
123-235 4.28e-04

The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein; This group contains the second domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS 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: 270425 [Multi-domain]  Cd Length: 221  Bit Score: 42.21  E-value: 4.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 123 VLRVVtVLEE--PFVMVSENvlgkpKKYQGFSIDVLDALSNYLGFNYEIYVAPdhkygSPQEdgtwngLVGELVFKRADI 200
Cdd:cd13707     3 VVRVV-VNPDlaPLSFFDSN-----GQFRGISADLLELISLRTGLRFEVVRAS-----SPAE------MIEALRSGEADM 65
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1370486819 201 gISALTITPDRENVVDFTTRYMDYSVGVLLRRAEK 235
Cdd:cd13707    66 -IAALTPSPEREDFLLFTRPYLTSPFVLVTRKDAA 99
PBP1_iGluR_AMPA_GluR2 cd06389
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit ...
9-103 4.35e-04

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: 43.08  E-value: 4.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   9 YDTVLLLANAF---HKKLEDRKWHSMASlSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFGENGGNPNVHFEILgtn 85
Cdd:cd06389   274 YDAVQVMTEAFrnlRKQRIEISRRGNAG-DCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIM--- 349
                          90
                  ....*....|....*...
gi 1370486819  86 ygEELGRGVRKLGCWNPV 103
Cdd:cd06389   350 --ELKTNGPRKIGYWSEV 365
PBP2_ArtJ cd00999
The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold ...
147-223 8.02e-04

The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold protein superfamily; An arginine-binding protein found in Chlamydiae trachomatis (CT-ArtJ) and pneumoniae (CPn-ArtJ) and its closely related proteins. CT- and CPn-ArtJ are shown to have different immunogenic properties despite a high sequence similarity. The ArtJ proteins display the type 2 periplasmic binding fold organized in two alpha-beta domains with arginine-binding region at their interface.


Pssm-ID: 270220 [Multi-domain]  Cd Length: 223  Bit Score: 41.54  E-value: 8.02e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1370486819 147 KYQGFSIDVLDALSNYLGFNYEIyvapdhkygspqEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMD 223
Cdd:cd00999    25 ELVGFDIDLAEAISEKLGKKLEW------------RDMAFDALIPNLLTGKIDAIAAGMSATPERAKRVAFSPPYGE 89
PBP2_BsGlnH cd13689
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ...
145-221 1.51e-03

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: 40.68  E-value: 1.51e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370486819 145 PKKYQ--GFSIDVLDALSNYLGfnyeiyVAPDHKYGSPQedgtwnGLVGELVFKRADIGISALTITPDRENVVDFTTRY 221
Cdd:cd13689    26 PKTREivGFDVDLCKAIAKKLG------VKLELKPVNPA------ARIPELQNGRVDLVAANLTYTPERAEQIDFSDPY 92
PBP2_Atu4678_like cd13696
The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ...
124-233 1.76e-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: 40.44  E-value: 1.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 124 LRVVTVLEEPfVMVSENVLGKPkkyQGFSIDVLDALSNYLGFNYEIYVAPdhkygSPQEdgtwnglVGELVFKRADIGIS 203
Cdd:cd13696    10 LRCGVCLDFP-PFGFRDAAGNP---VGYDVDYAKDLAKALGVKPEIVETP-----SPNR-------IPALVSGRVDVVVA 73
                          90       100       110
                  ....*....|....*....|....*....|
gi 1370486819 204 ALTITPDRENVVDFTTRYMDYSVGVLLRRA 233
Cdd:cd13696    74 NTTRTLERAKTVAFSIPYVVAGMVVLTRKD 103
PBP2_Ngo0372_TcyA cd13711
Substrate binding domain of ABC transporters involved in cystine import; the type 2 ...
150-236 3.21e-03

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: 39.59  E-value: 3.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819 150 GFSIDVLDALSNYLGFNYEIYVAPdhkygspqedgtWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMdYSVGVL 229
Cdd:cd13711    25 GFDVEVARAVAKKLGVKVEFVETQ------------WDSMIAGLDAGRFDVVANQVGITDERKKKYDFSTPYI-YSRAVL 91

                  ....*..
gi 1370486819 230 LRRAEKT 236
Cdd:cd13711    92 IVRKDNS 98
PBP1_iGluR_NMDA_NR1 cd06379
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR1, an ...
8-82 4.45e-03

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: 40.01  E-value: 4.45e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1370486819   8 IYDTVLLLANAFHKKLEDRKWHSMASLSCiRKNSKPWQGGRSMLETIKKGGVS-GLTGELEFGENGGNPNVHFEIL 82
Cdd:cd06379   254 IRDSVSVVAQAIRELFRSSENITDPPVDC-RDDTNIWKSGQKFFRVLKSVKLSdGRTGRVEFNDKGDRIGAEYDII 328
PBP1_iGluR_Kainate cd06382
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate ...
8-107 5.13e-03

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: 39.51  E-value: 5.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370486819   8 IYDTVLLLANAFHKkledrkwhsmaslscirknskpwqggrsmletikkggvsGLTGELEFGENGGNPNVHFEILgtnyg 87
Cdd:cd06382   277 MYDAVNLFANALKE---------------------------------------GLTGPIKFDEEGQRTDFKLDIL----- 312
                          90       100
                  ....*....|....*....|.
gi 1370486819  88 eELGR-GVRKLGCWNPVTGLN 107
Cdd:cd06382   313 -ELTEgGLVKVGTWNPTDGLN 332
PBP2_AA_binding_like_2 cd13627
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
186-231 8.14e-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: 270345 [Multi-domain]  Cd Length: 243  Bit Score: 38.54  E-value: 8.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370486819 186 WNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLR 231
Cdd:cd13627    61 WNGLIPALNSGDIDLIIAGMSKTPEREKTIDFSDPYYISNIVMVVK 106
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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