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Conserved domains on  [gi|310703673|ref|NP_612555|]
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glutamate receptor ionotropic, NMDA 3A isoform 1 precursor [Rattus norvegicus]

Protein Classification

glutamate receptor( domain architecture ID 11570956)

glutamate receptor is a glutamate-gated receptor that probably acts as a non-selective cation channel and may be involved in light-signal transduction and calcium homeostasis via the regulation of calcium influx into cells

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP1_iGluR_NMDA_NR3 cd06377
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of ...
40-496 0e+00

N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.


:

Pssm-ID: 380600 [Multi-domain]  Cd Length: 373  Bit Score: 535.09  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   40 ILKRIGHAVRVGAVHLQPWTTAPRAASRAQeggragaqrddpesgtwrPPAPSqgarwlgsalhgrgppgsrklgegaga 119
Cdd:cd06377     1 VLKRIGHTVRLGALLPHPWFTRGRAGAALA------------------VDLPT--------------------------- 35
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  120 etlwprdallfavenlnrveGLLPYNLSLEVVMAIEAglgdlplmpfsspsspwSSDPFSFLQSVCHTVVVQGVSALLAF 199
Cdd:cd06377    36 --------------------GLLPYNLSLEVVVAAPW-----------------ARDPASLTRSLCHSVVVQGVAALLAF 78
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  200 PQSQGEMMELDLVSSVLHIPVLSIVRHEFPR--ESQNPLHLQLSLENSLSSDADVTVSILTMNNWYNFSLLLCQEdWNIT 277
Cdd:cd06377    79 PQSRGELLQLDFLSAALEIPVVSILRREFPRplRSQNPFHLQLDLQSSLESLEDVLVSLLQANSWEDVSLLLCQP-WDPT 157
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  278 DFLLLTENNSKFHLESVINITANLSStkDLLSFLQVQMDNIRNSTPTMVMFGCDMDSIRQIFEMSTQFGLspPELHWVLG 357
Cdd:cd06377   158 SFLLLWQNNSQFHLGTVLNLSVLDES--DLQRSLQQHLESLKDPSPAIVMFGCDAARARRVFEAAPPGGL--PEFHWLLG 233
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  358 DSQNVEELRTEGLPLGLIAHGKTTQSVFEYYVQDAMELVARAVATATMIQPELALLPSTMNCMDVKTT-NLTSGQYLSRF 436
Cdd:cd06377   234 TPLPVEELPTEGLPPGLLALGETSRPSLEAYVQDAVELVARALSSAALVHPELALLPATVNCNDLKTGgSESSGQYLSRF 313
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  437 LANTTFRGLSGSIKVKGSTIISSENNFFIWNLQHDPMGKPMWTRLGSWQGGRIVMDSGIW 496
Cdd:cd06377   314 LANTSFQGRTGTVWVTGSSQVHSERHFKVWSLRRDPLGAPTWATVGSWQDGKLDMEPGAW 373
PBP2_iGluR_NMDA_Nr3 cd13720
The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
512-908 4.43e-177

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: 520.18  E-value: 4.43e-177
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  512 KLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDM 591
Cdd:cd13720     1 RPHLRVVTLLEHPFVFTREVDEEGLCPAGQLCLDPMTNDSSTLDALFSSLHSSNDTVPIKFRKCCYGYCIDLLEKLAEDL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  592 NFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDtaapigafmw 671
Cdd:cd13720    81 GFDFDLYIVGDGKYGAWRNGRWTGLVGDLLSGRAHMAVTSFSINSARSQVIDFTSPFFSTSLGILVRTRD---------- 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  672 plhwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtgrflmnlwai 751
Cdd:cd13720       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  752 fcmfclstytanlaavmvgekiyeELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQY 831
Cdd:cd13720   151 ------------------------ELSGIHDPKLHHPSQGFRFGTVRESSAEYYVKKSFPEMHEHMRRYSLPNTPEGVEY 206
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 310703673  832 LKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 908
Cdd:cd13720   207 LKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQNSPLTSNISELISQYKSNGFMDLLHDKWY 283
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
674-941 7.83e-75

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: 248.38  E-value: 7.83e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   674 HWTMWLGIFVALHITAIFLTLYEWKSPFGMTPKGRNRNKVFSFSSALNVCYALLFGRTAaIKPPKCWTGRFLMNLWAIFC 753
Cdd:pfam00060    1 SLEVWLGILVAFLIVGVVLFLLERFSPYEWRGPLETEENRFTLSNSLWFSFGALVQQGH-RENPRSLSGRIVVGVWWFFA 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   754 MFCLSTYTANLAAVMVGEKIYEELSGIHDpkLhHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLK 833
Cdd:pfam00060   80 LILLSSYTANLAAFLTVERMQSPIQSLED--L-AKQTKIEYGTVRGSSTYLFFRNSKIPSYKRMWEYMESAKPSVKDALN 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   834 NDPEKLDAFIMDKALLD---YEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYKV 910
Cdd:pfam00060  157 EEGVALVRNGIYAYALLsenYYLFQRECCDTMIVGETFATGGYGIATPKGSPLTDLLSLAILELEESGELDKLEKKWWPK 236
                          250       260       270
                   ....*....|....*....|....*....|..
gi 310703673   911 VP-CGKRSFAVTETlQMGIKHFSGLFVLLCIG 941
Cdd:pfam00060  237 SGeCDSKSSASSSS-QLGLKSFAGLFLILGIG 267
 
Name Accession Description Interval E-value
PBP1_iGluR_NMDA_NR3 cd06377
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of ...
40-496 0e+00

N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.


Pssm-ID: 380600 [Multi-domain]  Cd Length: 373  Bit Score: 535.09  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   40 ILKRIGHAVRVGAVHLQPWTTAPRAASRAQeggragaqrddpesgtwrPPAPSqgarwlgsalhgrgppgsrklgegaga 119
Cdd:cd06377     1 VLKRIGHTVRLGALLPHPWFTRGRAGAALA------------------VDLPT--------------------------- 35
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  120 etlwprdallfavenlnrveGLLPYNLSLEVVMAIEAglgdlplmpfsspsspwSSDPFSFLQSVCHTVVVQGVSALLAF 199
Cdd:cd06377    36 --------------------GLLPYNLSLEVVVAAPW-----------------ARDPASLTRSLCHSVVVQGVAALLAF 78
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  200 PQSQGEMMELDLVSSVLHIPVLSIVRHEFPR--ESQNPLHLQLSLENSLSSDADVTVSILTMNNWYNFSLLLCQEdWNIT 277
Cdd:cd06377    79 PQSRGELLQLDFLSAALEIPVVSILRREFPRplRSQNPFHLQLDLQSSLESLEDVLVSLLQANSWEDVSLLLCQP-WDPT 157
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  278 DFLLLTENNSKFHLESVINITANLSStkDLLSFLQVQMDNIRNSTPTMVMFGCDMDSIRQIFEMSTQFGLspPELHWVLG 357
Cdd:cd06377   158 SFLLLWQNNSQFHLGTVLNLSVLDES--DLQRSLQQHLESLKDPSPAIVMFGCDAARARRVFEAAPPGGL--PEFHWLLG 233
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  358 DSQNVEELRTEGLPLGLIAHGKTTQSVFEYYVQDAMELVARAVATATMIQPELALLPSTMNCMDVKTT-NLTSGQYLSRF 436
Cdd:cd06377   234 TPLPVEELPTEGLPPGLLALGETSRPSLEAYVQDAVELVARALSSAALVHPELALLPATVNCNDLKTGgSESSGQYLSRF 313
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  437 LANTTFRGLSGSIKVKGSTIISSENNFFIWNLQHDPMGKPMWTRLGSWQGGRIVMDSGIW 496
Cdd:cd06377   314 LANTSFQGRTGTVWVTGSSQVHSERHFKVWSLRRDPLGAPTWATVGSWQDGKLDMEPGAW 373
PBP2_iGluR_NMDA_Nr3 cd13720
The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
512-908 4.43e-177

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: 520.18  E-value: 4.43e-177
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  512 KLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDM 591
Cdd:cd13720     1 RPHLRVVTLLEHPFVFTREVDEEGLCPAGQLCLDPMTNDSSTLDALFSSLHSSNDTVPIKFRKCCYGYCIDLLEKLAEDL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  592 NFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDtaapigafmw 671
Cdd:cd13720    81 GFDFDLYIVGDGKYGAWRNGRWTGLVGDLLSGRAHMAVTSFSINSARSQVIDFTSPFFSTSLGILVRTRD---------- 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  672 plhwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtgrflmnlwai 751
Cdd:cd13720       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  752 fcmfclstytanlaavmvgekiyeELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQY 831
Cdd:cd13720   151 ------------------------ELSGIHDPKLHHPSQGFRFGTVRESSAEYYVKKSFPEMHEHMRRYSLPNTPEGVEY 206
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 310703673  832 LKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 908
Cdd:cd13720   207 LKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQNSPLTSNISELISQYKSNGFMDLLHDKWY 283
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
674-941 7.83e-75

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: 248.38  E-value: 7.83e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   674 HWTMWLGIFVALHITAIFLTLYEWKSPFGMTPKGRNRNKVFSFSSALNVCYALLFGRTAaIKPPKCWTGRFLMNLWAIFC 753
Cdd:pfam00060    1 SLEVWLGILVAFLIVGVVLFLLERFSPYEWRGPLETEENRFTLSNSLWFSFGALVQQGH-RENPRSLSGRIVVGVWWFFA 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   754 MFCLSTYTANLAAVMVGEKIYEELSGIHDpkLhHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLK 833
Cdd:pfam00060   80 LILLSSYTANLAAFLTVERMQSPIQSLED--L-AKQTKIEYGTVRGSSTYLFFRNSKIPSYKRMWEYMESAKPSVKDALN 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   834 NDPEKLDAFIMDKALLD---YEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYKV 910
Cdd:pfam00060  157 EEGVALVRNGIYAYALLsenYYLFQRECCDTMIVGETFATGGYGIATPKGSPLTDLLSLAILELEESGELDKLEKKWWPK 236
                          250       260       270
                   ....*....|....*....|....*....|..
gi 310703673   911 VP-CGKRSFAVTETlQMGIKHFSGLFVLLCIG 941
Cdd:pfam00060  237 SGeCDSKSSASSSS-QLGLKSFAGLFLILGIG 267
PBPe smart00079
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ...
776-909 2.88e-36

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: 133.57  E-value: 2.88e-36
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673    776 ELSGIHDPKLHhpsQGFRFGTVRESSAEDYVRQSFP----EMHEYM--RRYNVPATPDGVQYLKNDPeklDAFIMDKALL 849
Cdd:smart00079    1 PITSVEDLAKQ---TKIEYGTQDGSSTLAFFKRSGNpeysRMWPYMksPEVFVKSYAEGVQRVRVSN---YAFIMESPYL 74
                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673    850 DYEVSIDadCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYK 909
Cdd:smart00079   75 DYELSRN--CDLMTVGEEFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELEKLRNKWWK 132
Lig_chan-Glu_bd pfam10613
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
514-658 9.28e-31

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: 116.85  E-value: 9.28e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   514 HLRVVTLIEHPFVftrevddeglcpagqlcldpmtndssMLDRLFSSlhssNDTvpikfkkcCYGYCIDLLEQLAEDMNF 593
Cdd:pfam10613    2 TLIVTTILEPPFV--------------------------MLKENLEG----NDR--------YEGFCIDLLKELAEILGF 43
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 310703673   594 DFDLYIVGDGKYGA--WKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVR 658
Cdd:pfam10613   44 KYEIRLVPDGKYGSldPTTGEWNGMIGELIDGKADLAVAPLTITSEREKVVDFTKPFMTLGISILMK 110
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
578-909 9.75e-14

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: 71.55  E-value: 9.75e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGdgkygawknghWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:COG0834    23 GFDVDLARAIAKRLGLKVEFVPVP-----------WDRLIPALQSGKVDLIIAGMTITPEREKQVDFSDPYYTSGQVLLV 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  658 RTRDTaapigafmwplhwtmwlgifvalhitaifltlyEWKSPfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikpp 737
Cdd:COG0834    92 RKDNS---------------------------------GIKSL------------------------------------- 101
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  738 kcwtgrflmnlwaifcmfclstytanlaavmvgekiyEELSgihdpklhhpsqGFRFGTVRESSAEDYVRQSFPEMHeyM 817
Cdd:COG0834   102 -------------------------------------ADLK------------GKTVGVQAGTTYEEYLKKLGPNAE--I 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  818 RRYnvPATPDGVQYLKNDpeKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSP-LTSNISELISQYKS 896
Cdd:COG0834   131 VEF--DSYAEALQALASG--RVDAVVTDEPVAAYLLAKNPGDDLKIVGEPLSGEPYGIAVRKGDPeLLEAVNKALAALKA 206
                         330
                  ....*....|...
gi 310703673  897 HGFMDVLHDKWYK 909
Cdd:COG0834   207 DGTLDKILEKWFG 219
 
Name Accession Description Interval E-value
PBP1_iGluR_NMDA_NR3 cd06377
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of ...
40-496 0e+00

N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.


Pssm-ID: 380600 [Multi-domain]  Cd Length: 373  Bit Score: 535.09  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   40 ILKRIGHAVRVGAVHLQPWTTAPRAASRAQeggragaqrddpesgtwrPPAPSqgarwlgsalhgrgppgsrklgegaga 119
Cdd:cd06377     1 VLKRIGHTVRLGALLPHPWFTRGRAGAALA------------------VDLPT--------------------------- 35
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  120 etlwprdallfavenlnrveGLLPYNLSLEVVMAIEAglgdlplmpfsspsspwSSDPFSFLQSVCHTVVVQGVSALLAF 199
Cdd:cd06377    36 --------------------GLLPYNLSLEVVVAAPW-----------------ARDPASLTRSLCHSVVVQGVAALLAF 78
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  200 PQSQGEMMELDLVSSVLHIPVLSIVRHEFPR--ESQNPLHLQLSLENSLSSDADVTVSILTMNNWYNFSLLLCQEdWNIT 277
Cdd:cd06377    79 PQSRGELLQLDFLSAALEIPVVSILRREFPRplRSQNPFHLQLDLQSSLESLEDVLVSLLQANSWEDVSLLLCQP-WDPT 157
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  278 DFLLLTENNSKFHLESVINITANLSStkDLLSFLQVQMDNIRNSTPTMVMFGCDMDSIRQIFEMSTQFGLspPELHWVLG 357
Cdd:cd06377   158 SFLLLWQNNSQFHLGTVLNLSVLDES--DLQRSLQQHLESLKDPSPAIVMFGCDAARARRVFEAAPPGGL--PEFHWLLG 233
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  358 DSQNVEELRTEGLPLGLIAHGKTTQSVFEYYVQDAMELVARAVATATMIQPELALLPSTMNCMDVKTT-NLTSGQYLSRF 436
Cdd:cd06377   234 TPLPVEELPTEGLPPGLLALGETSRPSLEAYVQDAVELVARALSSAALVHPELALLPATVNCNDLKTGgSESSGQYLSRF 313
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  437 LANTTFRGLSGSIKVKGSTIISSENNFFIWNLQHDPMGKPMWTRLGSWQGGRIVMDSGIW 496
Cdd:cd06377   314 LANTSFQGRTGTVWVTGSSQVHSERHFKVWSLRRDPLGAPTWATVGSWQDGKLDMEPGAW 373
PBP2_iGluR_NMDA_Nr3 cd13720
The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
512-908 4.43e-177

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: 520.18  E-value: 4.43e-177
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  512 KLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDM 591
Cdd:cd13720     1 RPHLRVVTLLEHPFVFTREVDEEGLCPAGQLCLDPMTNDSSTLDALFSSLHSSNDTVPIKFRKCCYGYCIDLLEKLAEDL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  592 NFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDtaapigafmw 671
Cdd:cd13720    81 GFDFDLYIVGDGKYGAWRNGRWTGLVGDLLSGRAHMAVTSFSINSARSQVIDFTSPFFSTSLGILVRTRD---------- 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  672 plhwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtgrflmnlwai 751
Cdd:cd13720       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  752 fcmfclstytanlaavmvgekiyeELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQY 831
Cdd:cd13720   151 ------------------------ELSGIHDPKLHHPSQGFRFGTVRESSAEYYVKKSFPEMHEHMRRYSLPNTPEGVEY 206
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 310703673  832 LKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 908
Cdd:cd13720   207 LKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQNSPLTSNISELISQYKSNGFMDLLHDKWY 283
PBP2_iGluR_NMDA cd13687
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ...
512-908 1.87e-113

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: 351.94  E-value: 1.87e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  512 KLHLRVVTLIEHPFVFTrevddeglcpagqlcldpmtndssmldrlfsslhssndtvpikfkKCCYGYCIDLLEQLAEDM 591
Cdd:cd13687     1 STHLKVVTLEEAPFVYV---------------------------------------------KCCYGFCIDLLKKLAEDV 35
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  592 NFDFDLYIVGDGKYG---AWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDTaapiga 668
Cdd:cd13687    36 NFTYDLYLVTDGKFGtvnKSINGEWNGMIGELVSGRADMAVASLTINPERSEVIDFSKPFKYTGITILVKKRNE------ 109
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  669 fmwplhwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtgrflmnl 748
Cdd:cd13687       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  749 waifcmfclstytanlaavmvgekiyeeLSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDG 828
Cdd:cd13687   110 ----------------------------LSGINDPRLRNPSPPFRFGTVPNSSTERYFRRQVELMHRYMEKYNYETVEEA 161
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  829 VQYLKNDpeKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 908
Cdd:cd13687   162 IQALKNG--KLDAFIWDSAVLEYEASQDEGCKLVTVGSLFARSGYGIGLQKNSPWKRNVSLAILQFHESGFMEELDKKWL 239
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
674-941 7.83e-75

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: 248.38  E-value: 7.83e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   674 HWTMWLGIFVALHITAIFLTLYEWKSPFGMTPKGRNRNKVFSFSSALNVCYALLFGRTAaIKPPKCWTGRFLMNLWAIFC 753
Cdd:pfam00060    1 SLEVWLGILVAFLIVGVVLFLLERFSPYEWRGPLETEENRFTLSNSLWFSFGALVQQGH-RENPRSLSGRIVVGVWWFFA 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   754 MFCLSTYTANLAAVMVGEKIYEELSGIHDpkLhHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLK 833
Cdd:pfam00060   80 LILLSSYTANLAAFLTVERMQSPIQSLED--L-AKQTKIEYGTVRGSSTYLFFRNSKIPSYKRMWEYMESAKPSVKDALN 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   834 NDPEKLDAFIMDKALLD---YEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYKV 910
Cdd:pfam00060  157 EEGVALVRNGIYAYALLsenYYLFQRECCDTMIVGETFATGGYGIATPKGSPLTDLLSLAILELEESGELDKLEKKWWPK 236
                          250       260       270
                   ....*....|....*....|....*....|..
gi 310703673   911 VP-CGKRSFAVTETlQMGIKHFSGLFVLLCIG 941
Cdd:pfam00060  237 SGeCDSKSSASSSS-QLGLKSFAGLFLILGIG 267
PBP2_iGluR_NMDA_Nr2 cd13718
The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
512-907 2.30e-66

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: 225.29  E-value: 2.30e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  512 KLHLRVVTLIEHPFVFTREVDdeglcPAGQLCLDpmtnDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDM 591
Cdd:cd13718     1 KFHLKIVTLEEAPFVIVEPVD-----PLTGTCMR----NTVPCRKQLNHENSTDADENRYVKKCCKGFCIDILKKLAKDV 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  592 NFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDTaapigafmw 671
Cdd:cd13718    72 GFTYDLYLVTNGKHGKKINGVWNGMIGEVVYKRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNQ--------- 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  672 plhwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtgrflmnlwai 751
Cdd:cd13718       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  752 fcmfclstytanlaavmvgekiyeeLSGIHDPKLHHPSQ---GFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDG 828
Cdd:cd13718   143 -------------------------VSGLSDKKFQRPHDqspPFRFGTVPNGSTERNIRNNYPEMHQYMRKYNQKGVEDA 197
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  829 VQYLKNdpEKLDAFIMDKALLDYEVSIDADCKLLTVGKP--FAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDK 906
Cdd:cd13718   198 LVSLKT--GKLDAFIYDAAVLNYMAGQDEGCKLVTIGSGkwFAMTGYGIALQKNSKWKRPFDLALLQFRGDGELERLERL 275

                  .
gi 310703673  907 W 907
Cdd:cd13718   276 W 276
PBP2_iGluR_NMDA_Nr1 cd13719
The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
514-913 5.52e-56

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: 195.66  E-value: 5.52e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  514 HLRVVTLIEHPFVFTREVDDEGLCpagqLCLDPMTNDSSMLdrlfsslhSSNDTVPikfkKCCYGYCIDLLEQLAEDMNF 593
Cdd:cd13719     3 HLKIVTIHEEPFVYVRPTPSDGTC----REEFTVNCPNFNI--------SGRPTVP----FCCYGYCIDLLIKLARKMNF 66
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  594 DFDLYIVGDGKYGAW--KNG----HWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRtrdtaapig 667
Cdd:cd13719    67 TYELHLVADGQFGTQerVNNsnkkEWNGMMGELVSGRADMIVAPLTINPERAQYIEFSKPFKYQGLTILVK--------- 137
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  668 afmwplhwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaiKPPKcwtgrflmn 747
Cdd:cd13719   138 -------------------------------------------------------------------KEIR--------- 141
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  748 lwaifcmfclstytanlaavmvgekiyeeLSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQ--SFPEMHEYMRRYNVPAT 825
Cdd:cd13719   142 -----------------------------LTGINDPRLRNPSEKFIYATVKGSSVDMYFRRqvELSTMYRHMEKHNYETA 192
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  826 PDGVQYLKNDpeKLDAFIMDKALLDYEVSidADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHD 905
Cdd:cd13719   193 EEAIQAVRDG--KLHAFIWDSSRLEFEAS--QDCDLVTAGELFGRSGYGIGLQKNSPWTDNVSLAILKMHESGFMEDLDK 268

                  ....*...
gi 310703673  906 KWYKVVPC 913
Cdd:cd13719   269 TWIRYQEC 276
PBP2_iGluR_non_NMDA_like cd13685
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ...
515-907 6.81e-43

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: 156.96  E-value: 6.81e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  515 LRVVTLIEHPFVFTREVDDEGlcpagqlcldpmtndssmldrlfsslhssNDTVpikfkkccYGYCIDLLEQLAEDMNFD 594
Cdd:cd13685     4 LRVTTILEPPFVMKKRDSLSG-----------------------------NPRF--------EGYCIDLLEELAKILGFD 46
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  595 FDLYIVGDGKYGAWK-NGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDtaaPIGAFmwpl 673
Cdd:cd13685    47 YEIYLVPDGKYGSRDeNGNWNGMIGELVRGEADIAVAPLTITAEREEVVDFTKPFMDTGISILMRKPT---PIESL---- 119
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  674 hwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtgrflmnlwaifc 753
Cdd:cd13685       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  754 mfclstytanlaavmvgekiyEELSgihdpklhhPSQGFRFGTVRESSAEDY---------VRQSFPEMHEYMRRYN-VP 823
Cdd:cd13685   120 ---------------------EDLA---------KQSKIEYGTLKGSSTFTFfknsknpeyRRYEYTKIMSAMSPSVlVA 169
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  824 ATPDGVQYLKNDPEKLdAFIMDKALLDYEVSIdaDCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVL 903
Cdd:cd13685   170 SAAEGVQRVRESNGGY-AFIGEATSIDYEVLR--NCDLTKVGEVFSEKGYGIAVQQGSPLRDELSLAILELQESGELEKL 246

                  ....
gi 310703673  904 HDKW 907
Cdd:cd13685   247 KEKW 250
PBP2_iGluR_putative cd13717
The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ...
577-909 1.68e-42

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: 159.39  E-value: 1.68e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  577 YGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAW-KNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFF-STSLG 654
Cdd:cd13717    26 EGYCIDLIEEISEILNFDYEIVEPEDGKFGTMdENGEWNGLIGDLVRKEADIALAALSVMAEREEVVDFTVPYYdLVGIT 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  655 ILVRTRDTAAPIGAFMWPLHWTMWlgifvalhitAIFlTLYE--WkspFGMTpkgrnrnkvfSFSSAlnvcyallfGRTA 732
Cdd:cd13717   106 ILMKKPERPTSLFKFLTVLELEVW----------REF-TLKEslW---FCLT----------SLTPQ---------GGGE 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  733 AikpPKCWTGRFLMNLWAIFCMFCLSTYTANLAAVMVGEKIYEELSGIHDpkLHHPSQgFRFGTVRESSAEDY------- 805
Cdd:cd13717   153 A---PKNLSGRLLVATWWLFVFIIIASYTANLAAFLTVSRLQTPVESLDD--LARQYK-IQYTVVKNSSTHTYfermkna 226
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  806 -------------------------------VRQSFPEMHEYMRRYNVPAT-PDGVQYLKNDPEKLDAFIMDKALLDYEV 853
Cdd:cd13717   227 edtlyemwkdmslndslspveraklavwdypVSEKYTKIYQAMQEAGLVANaEEGVKRVRESTSAGFAFIGDATDIKYEI 306
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 310703673  854 SIdaDCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYK 909
Cdd:cd13717   307 LT--NCDLQEVGEEFSRKPYAIAVQQGSPLKDELNYAILELQNDRFLEKLKAKWWN 360
PBP2_iGluR_ligand_binding cd00998
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ...
514-907 1.42e-41

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: 152.91  E-value: 1.42e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  514 HLRVVTLIEHPFVFtrevddeglcpagqlcldPMTNDSSMLDrlfsslhssndtvpikfKKCCYGYCIDLLEQLAEDMNF 593
Cdd:cd00998     2 TLKVVVPLEPPFVM------------------FVTGSNAVTG-----------------NGRFEGYCIDLLKELSQSLGF 46
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  594 DFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRdtaapigafmwpl 673
Cdd:cd00998    47 TYEYYLVPDGKFGAPVNGSWNGMVGEVVRGEADLAVGPITITSERSVVIDFTQPFMTSGIGIMIPIR------------- 113
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  674 hwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtgrflmnlwaifc 753
Cdd:cd00998       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  754 mfclstytanlaavmvgekiyeelsGIHDPKLHHPsqgFRFGTVRESSAEDYVRQSFP------EMHEYMRRYNVPATPD 827
Cdd:cd00998   114 -------------------------SIDDLKRQTD---IEFGTVENSFTETFLRSSGIypfyktWMYSEARVVFVNNIAE 165
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  828 GVQYLKNdpEKLDAFIMDKALLDYEVSIDaDCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKW 907
Cdd:cd00998   166 GIERVRK--GKVYAFIWDRPYLEYYARQD-PCKLIKTGGGFGSIGYGFALPKNSPLTNDLSTAILKLVESGVLQKLKNKW 242
PBPe smart00079
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ...
776-909 2.88e-36

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: 133.57  E-value: 2.88e-36
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673    776 ELSGIHDPKLHhpsQGFRFGTVRESSAEDYVRQSFP----EMHEYM--RRYNVPATPDGVQYLKNDPeklDAFIMDKALL 849
Cdd:smart00079    1 PITSVEDLAKQ---TKIEYGTQDGSSTLAFFKRSGNpeysRMWPYMksPEVFVKSYAEGVQRVRVSN---YAFIMESPYL 74
                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673    850 DYEVSIDadCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYK 909
Cdd:smart00079   75 DYELSRN--CDLMTVGEEFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELEKLRNKWWK 132
PBP2_iGluR_Kainate_GluR7 cd13723
GluR7 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
578-909 1.66e-35

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: 139.44  E-value: 1.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKN-GHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGIL 656
Cdd:cd13723    32 GYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDkGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSIL 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  657 VRTRDTAAP-IGAFMWPLHWTMWLGIFVA-LHITAIFLTL-----YEWKSPFGMTPKGRNRNKVFSFSSALNVCYALLFG 729
Cdd:cd13723   112 YRKPNGTNPsVFSFLNPLSPDIWMYVLLAyLGVSCVLFVIarfspYEWYDAHPCNPGSEVVENNFTLLNSFWFGMGSLMQ 191
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  730 RTAAIKpPKCWTGRFLMNLWAIFCMFCLSTYTANLAAVMVGEKIYEELSGIHDPKlhhPSQGFRFGTVRESSAEDYVRQS 809
Cdd:cd13723   192 QGSELM-PKALSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLA---KQTKIEYGAVKDGATMTFFKKS 267
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  810 FPEMHEYMRRYnVPATPDGVqyLKNDPEKLD-AFIMDKALLDYEVSID----ADCKLLTVGKPFAIEGYGIGLPPNSPLT 884
Cdd:cd13723   268 KISTFEKMWAF-MSSKPSAL--VKNNEEGIQrALTADYALLMESTTIEyvtqRNCNLTQIGGLIDSKGYGIGTPMGSPYR 344
                         330       340
                  ....*....|....*....|....*
gi 310703673  885 SNISELISQYKSHGFMDVLHDKWYK 909
Cdd:cd13723   345 DKITIAILQLQEEDKLHIMKEKWWR 369
PBP1_iGluR_NMDA cd06367
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the ionotropic ...
142-491 1.07e-31

N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptors; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.


Pssm-ID: 380590 [Multi-domain]  Cd Length: 357  Bit Score: 127.74  E-value: 1.07e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  142 LPYNLSLEVVMAIEAGLGDLPLmpfsspsspwssdpfsflqSVCHtVVVQGVSALLAFPQSQGE---MMELDLVSSVLHI 218
Cdd:cd06367    32 LPVQLRVELVTMPEPDPKSIIT-------------------RICD-LLSDSKVQGVVFSDDTDQeaiAQILDFIAAQTLT 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  219 PVLSIVRhefpRES-----QNPLHLQLSLENSLSSDADVTVSILTMNNWYNFSLLLC--QEDWNITDFLLLTENNSKFHL 291
Cdd:cd06367    92 PVLGLHG----RSSmimadKSEHSMFLQFGPPIEQQASVMLNIMEEYDWYIVSLVTTyfPGYQDFVNKLRSTIENSGWEL 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  292 ESVINITAnlsSTKDLLSFLQVQMDNIRNSTPTMVMFGCDMDSIRQIFEMSTQFGLSPPELHWVLGDSQNVEELRTEGLP 371
Cdd:cd06367   168 EEVLQLDM---SLDDGDSKLQAQLKKLQSPEARVILLYCTKEEATYVFEVAASVGLTGYGYTWLVGSLVAGTDTVPAEFP 244
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  372 LGLIAHGKTTQSVFEYYVQDAMELVARAVatATMIQPELALLPSTMNCMDVKTTNLTSGQYLSRFLANTTFRGLSGSIKV 451
Cdd:cd06367   245 TGLISLSYDEWYNLPARIRDGVAIVATAA--SEMLSEHEQIPDPPSSCVNNQEIRKYTGPMLKRYLINVTFEGRDLSFSE 322
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 310703673  452 KGstiISSENNFFIWNLQHDpmgkPMWTRLGSWQGGRIVM 491
Cdd:cd06367   323 DG---YQMHPKLVIILLNNE----RKWERVGKWKDSSLIM 355
Lig_chan-Glu_bd pfam10613
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
514-658 9.28e-31

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: 116.85  E-value: 9.28e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   514 HLRVVTLIEHPFVftrevddeglcpagqlcldpmtndssMLDRLFSSlhssNDTvpikfkkcCYGYCIDLLEQLAEDMNF 593
Cdd:pfam10613    2 TLIVTTILEPPFV--------------------------MLKENLEG----NDR--------YEGFCIDLLKELAEILGF 43
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 310703673   594 DFDLYIVGDGKYGA--WKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVR 658
Cdd:pfam10613   44 KYEIRLVPDGKYGSldPTTGEWNGMIGELIDGKADLAVAPLTITSEREKVVDFTKPFMTLGISILMK 110
PBP2_iGluR_Kainate cd13714
Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains ...
511-909 7.62e-30

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: 119.18  E-value: 7.62e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  511 NKlHLRVVTLIEHPFVFTREvDDEGLcpagqlcldpmtndssmldrlfsslhSSNDtvpiKFKkccyGYCIDLLEQLAED 590
Cdd:cd13714     1 NK-TLIVTTILEEPYVMLKE-SAKPL--------------------------TGND----RFE----GFCIDLLKELAKI 44
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  591 MNFDFDLYIVGDGKYGAW--KNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFfstslgilvrtrdtaapiga 668
Cdd:cd13714    45 LGFNYTIRLVPDGKYGSYdpETGEWNGMVRELIDGRADLAVADLTITYERESVVDFTKPF-------------------- 104
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  669 fmwplhwtMWLGIfvalhitAIfltLYewKSPfgmTPkgrnrnkvfsFSSAlnvcyallfgrtaaikppkcwtgrflmnl 748
Cdd:cd13714   105 --------MNLGI-------SI---LY--RKP---TP----------IESA----------------------------- 122
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  749 waifcmfclstytanlaavmvgekiyEELSgihdpklhhPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDG 828
Cdd:cd13714   123 --------------------------DDLA---------KQTKIKYGTLRGGSTMTFFRDSNISTYQKMWNFMMSAKPSV 167
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  829 vqYLKNDPEKLD-------AFIMDKALLDYEVsiDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMD 901
Cdd:cd13714   168 --FVKSNEEGVArvlkgkyAFLMESTSIEYVT--QRNCNLTQIGGLLDSKGYGIATPKGSPYRDKLSLAILKLQEKGKLE 243

                  ....*...
gi 310703673  902 VLHDKWYK 909
Cdd:cd13714   244 MLKNKWWK 251
PBP2_iGluR_kainate_KA1 cd13724
The ligand-binding domain of the kainate subtype KA1 of ionotropic glutamate receptors, a ...
578-909 3.78e-22

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: 98.93  E-value: 3.78e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGA-WKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGIL 656
Cdd:cd13724    32 GFCVDMLKELAEILRFNYKIRLVGDGVYGVpEANGTWTGMVGELIARKADLAVAGLTITAEREKVIDFSKPFMTLGISIL 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  657 VRTRDTAAP-IGAFMWPLHWTMWLGIFVA-LHITAIF-----LTLYEWKSPFGMTpKGRNRNKV--FSFSSALNVCYALL 727
Cdd:cd13724   112 YRVHMGRKPgYFSFLDPFSPGVWLFMLLAyLAVSCVLflvarLTPYEWYSPHPCA-QGRCNLLVnqYSLGNSLWFPVGGF 190
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  728 FGRTAAIKPPkcwtgrflmnlwaifcmfclstytanlaavmvgekiYEELSGIHDpklhhpSQGFRFGTVRESSAEDYVR 807
Cdd:cd13724   191 MQQGSTIAPP------------------------------------IESVDDLAD------QTAIEYGTIHGGSSMTFFQ 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  808 QSfpEMHEYMRRYNVPATPDGVQYLKNDPEKLD-------AFIMDKALLDYEVSidADCKLLTVGKPFAIEGYGIGLPPN 880
Cdd:cd13724   229 NS--RYQTYQRMWNYMYSKQPSVFVKSTEEGIArvlnsnyAFLLESTMNEYYRQ--RNCNLTQIGGLLDTKGYGIGMPVG 304
                         330       340
                  ....*....|....*....|....*....
gi 310703673  881 SPLTSNISELISQYKSHGFMDVLHDKWYK 909
Cdd:cd13724   305 SVFRDEFDLAILQLQENNRLEILKRKWWE 333
PBP2_iGluR_delta_like cd13716
The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of ...
515-908 1.45e-21

The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of iGluRs belongs to the periplasmic-binding fold type I. Although the delta receptors are members of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans.


Pssm-ID: 270434 [Multi-domain]  Cd Length: 257  Bit Score: 95.68  E-value: 1.45e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  515 LRVVTLIEHPFVFTREvddeglcpagqlcldpmtndsSMLDRlfsslhssndtvPIKFKkccyGYCIDLLEQLAEDMNFD 594
Cdd:cd13716     4 LRVVTVLEEPFVMVSE---------------------NVLGK------------PKKYQ----GFSIDVLDALANYLGFK 46
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  595 FDLYIVGDGKYGA-WKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRtrdTAAPIGAFmwpl 673
Cdd:cd13716    47 YEIYVAPDHKYGSqQEDGTWNGLIGELVFKRADIGISALTITPERENVVDFTTRYMDYSVGVLLR---KAESIQSL---- 119
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  674 hwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtgrflmnlwaifc 753
Cdd:cd13716       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  754 mfclstytanlaavmvgekiyEELSGIHDpklhhpsqgFRFGTVRESSAEDYVR----------QSFPEMHEYMRR---- 819
Cdd:cd13716   120 ---------------------QDLSKQTD---------IPYGTVLDSAVYEYVRskgtnpferdSMYSQMWRMINRsngs 169
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  820 -YNVPATPDGVQYLKNDPEkldAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHG 898
Cdd:cd13716   170 eNNVSESSEGIRKVKYGNY---AFVWDAAVLEYVAINDDDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQNG 246
                         410
                  ....*....|
gi 310703673  899 FMDVLHDKWY 908
Cdd:cd13716   247 DMDILKHKWW 256
PBP2_iGluR_AMPA cd13715
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
578-655 2.76e-21

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: 94.73  E-value: 2.76e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWK--NGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFstSLGI 655
Cdd:cd13715    34 GYCVDLADEIAKHLGIKYELRIVKDGKYGARDadTGIWNGMVGELVRGEADIAIAPLTITLVRERVIDFSKPFM--SLGI 111
PBP2_iGluR_delta_1 cd13730
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the ...
513-908 1.05e-20

The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the delta1 receptor of an orphan glutamate receptor family. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of delta receptors belongs to the periplasmic-binding fold type I. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRdelta2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans.


Pssm-ID: 270448 [Multi-domain]  Cd Length: 257  Bit Score: 93.10  E-value: 1.05e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  513 LHLRVVTLIEHPFVFTREvddeglcpagqlcldpmtndsSMLDRlfsslhssndtvPIKFKkccyGYCIDLLEQLAEDMN 592
Cdd:cd13730     2 LTLKVVTVLEEPFVMVAE---------------------NILGQ------------PKRYK----GFSIDVLDALAKALG 44
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  593 FDFDLYIVGDGKYGA-WKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDtaaPIGAFMw 671
Cdd:cd13730    45 FKYEIYQAPDGKYGHqLHNTSWNGMIGELISKRADLAISAITITPERESVVDFSKRYMDYSVGILIKKPE---PIRTFQ- 120
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  672 plhwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfSFSSALNVCYallfgrtaaikppkcwtgrflmnlwai 751
Cdd:cd13730   121 -------------------------------------------DLSKQVEMSY--------------------------- 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  752 fcmfclstytanlaavmvgekiyeelsgihdpklhhpsqgfrfGTVRESSAEDYVR----------QSFPEMHEYMRRYN 821
Cdd:cd13730   131 -------------------------------------------GTVRDSAVYEYFRakgtnpleqdSTFAELWRTISKNG 167
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  822 -----VPATPDGVQYLKNDPEkldAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKS 896
Cdd:cd13730   168 gadncVSSPSEGIRKAKKGNY---AFLWDVAVVEYAALTDDDCSVTVIGNSISSKGYGIALQHGSPYRDLFSQRILELQD 244
                         410
                  ....*....|..
gi 310703673  897 HGFMDVLHDKWY 908
Cdd:cd13730   245 TGDLDVLKQKWW 256
Lig_chan-Glu_bd smart00918
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
558-621 1.45e-20

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: 86.15  E-value: 1.45e-20
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 310703673    558 FSSLHSSNDTVPikfkKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAW-KNGHWTGLVGDLL 621
Cdd:smart00918    2 YVMLKESPDGGN----DRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGARlPNGSWNGMVGELV 62
PBP2_iGluR_delta_2 cd13731
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the ...
515-908 6.57e-20

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: 90.86  E-value: 6.57e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  515 LRVVTLIEHPFVFTREvddeglcpagqlcldpmtndsSMLDRlfsslhssndtvPIKFKkccyGYCIDLLEQLAEDMNFD 594
Cdd:cd13731     4 LRVVTVLEEPFVMVSE---------------------NVLGK------------PKKYQ----GFSIDVLDALSNYLGFN 46
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  595 FDLYIVGDGKYGAWK-NGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVR-----------TRDT 662
Cdd:cd13731    47 YEIYVAPDHKYGSPQeDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRraesiqslqdlSKQT 126
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  663 AAPIGafmwplhwtmwlgifvalhiTAIFLTLYEWKSPFGMTPKGRNrnkvfsfssalnvcyallfgrtaaikppkcwtg 742
Cdd:cd13731   127 DIPYG--------------------TVLDSAVYEHVRMKGLNPFERD--------------------------------- 153
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  743 rflmnlwaifcmfclSTYtanlaavmvgekiyeelsgihdpklhhpSQGFRFGTvRESSAEDyvrqsfpemheymrryNV 822
Cdd:cd13731   154 ---------------SMY----------------------------SQMWRMIN-RSNGSEN----------------NV 173
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  823 PATPDGVQYLKNDPEkldAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDV 902
Cdd:cd13731   174 LESQAGIQKVKYGNY---AFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDI 250

                  ....*.
gi 310703673  903 LHDKWY 908
Cdd:cd13731   251 LKHKWW 256
PBP2_iGluR_kainate_KA2 cd13725
The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a ...
578-909 1.64e-19

The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the KA2 subunit of kainate receptor. While this ligand-binding domain is structurally homologous to the periplasmic binding fold type II superfamily, the N_terminal domain of kainate receptors belongs to the periplasmic-binding fold type I. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined.


Pssm-ID: 270443 [Multi-domain]  Cd Length: 250  Bit Score: 89.38  E-value: 1.64e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWK-NGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGIL 656
Cdd:cd13725    32 GFCVDMLRELAELLRFRYRLRLVEDGLYGAPEpNGSWTGMVGELINRKADLAVAAFTITAEREKVIDFSKPFMTLGISIL 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  657 VRTRdtaAPIgafmwplhwtmwlgifvalhitaifltlyewKSPFGMtpkgrnrnkvfsfSSALNVCYALLFGRTaaikp 736
Cdd:cd13725   112 YRVH---MPV-------------------------------ESADDL-------------ADQTNIEYGTIHAGS----- 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  737 pkcwTGRFLMNlwaifcmfclSTYtanlaavmvgekiyeelsgihdpklhhpsqgfrfgtvressaedyvrQSFPEMHEY 816
Cdd:cd13725   140 ----TMTFFQN----------SRY-----------------------------------------------QTYQRMWNY 158
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  817 MRRYN----VPATPDGVQYLKNDPEkldAFIMDKALLDYEVSIdaDCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELIS 892
Cdd:cd13725   159 MQSKQpsvfVKSTEEGIARVLNSRY---AFLLESTMNEYHRRL--NCNLTQIGGLLDTKGYGIGMPLGSPFRDEITLAIL 233
                         330
                  ....*....|....*..
gi 310703673  893 QYKSHGFMDVLHDKWYK 909
Cdd:cd13725   234 QLQENNRLEILKRKWWE 250
PBP2_iGluR_AMPA_GluR1 cd13729
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
578-666 5.06e-18

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: 85.08  E-value: 5.06e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGAW--KNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFstSLGI 655
Cdd:cd13729    32 GYCVELAAEIAKHVGYSYKLEIVSDGKYGARdpETKMWNGMVGELVYGKADVAVAPLTITLVREEVIDFSKPFM--SLGI 109
                          90
                  ....*....|.
gi 310703673  656 LVRTRDTAAPI 666
Cdd:cd13729   110 SIMIKKPTSPI 120
PBP2_iGluR_Kainate_GluR6 cd13721
GluR6 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
578-658 1.09e-17

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: 83.92  E-value: 1.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWK--NGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGI 655
Cdd:cd13721    32 GYCIDLLRELSTILGFTYEIRLVEDGKYGAQDdvNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISI 111

                  ...
gi 310703673  656 LVR 658
Cdd:cd13721   112 LYR 114
PBP2_iGluR_AMPA_GluR2 cd13726
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
578-658 7.36e-17

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: 81.61  E-value: 7.36e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGA--WKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGI 655
Cdd:cd13726    32 GYCVDLAAEIAKHCGFKYKLTIVGDGKYGArdADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISI 111

                  ...
gi 310703673  656 LVR 658
Cdd:cd13726   112 MIK 114
PBP2_iGluR_AMPA_GluR3 cd13728
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
578-658 9.08e-16

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: 78.58  E-value: 9.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGAW--KNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGI 655
Cdd:cd13728    32 GYCVDLAYEIAKHVRIKYKLSIVGDGKYGARdpETKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISI 111

                  ...
gi 310703673  656 LVR 658
Cdd:cd13728   112 MIK 114
PBP2_iGluR_AMPA_GluR4 cd13727
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
578-658 1.01e-15

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: 78.54  E-value: 1.01e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKNGH--WTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGI 655
Cdd:cd13727    32 GYCVDLASEIAKHIGIKYKIAIVPDGKYGARDPETkiWNGMVGELVYGKAEIAVAPLTITLVREEVIDFSKPFMSLGISI 111

                  ...
gi 310703673  656 LVR 658
Cdd:cd13727   112 MIK 114
PBP2_iGluR_Kainate_GluR5 cd13722
GluR5 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
578-658 1.88e-15

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: 77.40  E-value: 1.88e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKN-GHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGIL 656
Cdd:cd13722    32 GYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDkGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISIL 111

                  ..
gi 310703673  657 VR 658
Cdd:cd13722   112 YR 113
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
578-909 9.75e-14

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: 71.55  E-value: 9.75e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGdgkygawknghWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:COG0834    23 GFDVDLARAIAKRLGLKVEFVPVP-----------WDRLIPALQSGKVDLIIAGMTITPEREKQVDFSDPYYTSGQVLLV 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  658 RTRDTaapigafmwplhwtmwlgifvalhitaifltlyEWKSPfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikpp 737
Cdd:COG0834    92 RKDNS---------------------------------GIKSL------------------------------------- 101
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  738 kcwtgrflmnlwaifcmfclstytanlaavmvgekiyEELSgihdpklhhpsqGFRFGTVRESSAEDYVRQSFPEMHeyM 817
Cdd:COG0834   102 -------------------------------------ADLK------------GKTVGVQAGTTYEEYLKKLGPNAE--I 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  818 RRYnvPATPDGVQYLKNDpeKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSP-LTSNISELISQYKS 896
Cdd:COG0834   131 VEF--DSYAEALQALASG--RVDAVVTDEPVAAYLLAKNPGDDLKIVGEPLSGEPYGIAVRKGDPeLLEAVNKALAALKA 206
                         330
                  ....*....|...
gi 310703673  897 HGFMDVLHDKWYK 909
Cdd:COG0834   207 DGTLDKILEKWFG 219
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
578-907 6.02e-12

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: 66.50  E-value: 6.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDlyivgdgkygaWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13530    24 GFDVDLANAIAKRLGVKVE-----------FVDTDFDGLIPALQSGKIDVAISGMTITPERAKVVDFSDPYYYTGQVLVV 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  658 RtrdtaapigafmwplhwtmwlgifvalhitaifltlyewkspfgmtpKGRNRNKVFsfssalnvcyallfgrtaaikpp 737
Cdd:cd13530    93 K-----------------------------------------------KDSKITKTV----------------------- 102
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  738 kcwtgrflmnlwaifcmfclstytANLAavmvGEKIyeelsgihdpklhhpsqgfrfGTVRESSAEDYVRQSFP--EMHE 815
Cdd:cd13530   103 ------------------------ADLK----GKKV---------------------GVQAGTTGEDYAKKNLPnaEVVT 133
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  816 YmrrynvPATPDGVQYLKNDpeKLDAFIMDKALLDYEVSiDADCKLLTVGKPFAIEGYGIGLPP-NSPLTSNISELISQY 894
Cdd:cd13530   134 Y------DNYPEALQALKAG--RIDAVITDAPVAKYYVK-KNGPDLKVVGEPLTPEPYGIAVRKgNPELLDAINKALAEL 204
                         330
                  ....*....|...
gi 310703673  895 KSHGFMDVLHDKW 907
Cdd:cd13530   205 KADGTLDKLLEKW 217
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
578-669 2.00e-11

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: 65.01  E-value: 2.00e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673   578 GYCIDLLEQLAEDMNFDFDLYIVGdgkygawknghWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:pfam00497   23 GFDVDLAKAIAKRLGVKVEFVPVS-----------WDGLIPALQSGKVDLIIAGMTITPERAKQVDFSDPYYYSGQVILV 91
                           90
                   ....*....|..
gi 310703673   658 RTRDTAAPIGAF 669
Cdd:pfam00497   92 RKKDSSKSIKSL 103
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
578-662 7.82e-10

Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 periplasmic binding protein fold; This group includes the periplasmic substrate-binding protein ArtJ of the ATP-binding cassette (ABC) transport system from the thermophilic bacterium Geobacillus stearothermophilus, which is specific for arginine, lysine, and histidine. ArtJ belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270342 [Multi-domain]  Cd Length: 219  Bit Score: 60.20  E-value: 7.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDlyivgdgkygaWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13624    24 GFDIDLIKAIAKEAGFEVE-----------FKNMAFDGLIPALQSGKIDIIISGMTITEERKKSVDFSDPYYEAGQAIVV 92

                  ....*
gi 310703673  658 RTRDT 662
Cdd:cd13624    93 RKDST 97
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
578-658 1.87e-09

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 58.88  E-value: 1.87e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673    578 GYCIDLLEQLAEDMNFDFDlyivgdgkygaWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:smart00062   24 GFDVDLAKAIAKELGLKVE-----------FVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYRSGQVILV 92

                    .
gi 310703673    658 R 658
Cdd:smart00062   93 R 93
PBP2_GlnH cd00994
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ...
565-663 4.85e-08

Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; This periplasmic substrate-binding component serves as an initial receptor in the ABC transport of glutamine in bacteria and eukaryota. GlnH belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270216 [Multi-domain]  Cd Length: 218  Bit Score: 54.97  E-value: 4.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  565 NDTVPIKFKKC--CYGYCIDLLEQLAEDMNFDFDlyivgdgkygaWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVI 642
Cdd:cd00994     8 TTFVPFEFKQDgkYVGFDIDLWEAIAKEAGFKYE-----------LQPMDFKGIIPALQTGRIDIAIAGITITEERKKVV 76
                          90       100
                  ....*....|....*....|.
gi 310703673  643 DFTSPFFSTSLGILVRTRDTA 663
Cdd:cd00994    77 DFSDPYYDSGLAVMVKADNNS 97
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
791-908 2.61e-07

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: 52.72  E-value: 2.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  791 GFRFGTVRESSAEDYVRQSFPEMHEymrrynVPATPDGVQYLKNDpeKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAI 870
Cdd:cd00997   108 GKRVATVAGSTAADYLRRHDIDVVE------VPNLEAAYTALQDK--DADAVVFDAPVLRYYAAHDGNGKAEVTGSVFLE 179
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 310703673  871 EGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 908
Cdd:cd00997   180 ENYGIVFPTGSPLRKPINQALLNLREDGTYDELYEKWF 217
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
577-659 5.90e-07

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: 51.82  E-value: 5.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  577 YGYCIDLLEQLAEDMNFDFDLYIvgdgkygawknGHWTGLVGDLLSGTANMaVTSFSINTARSQVIDFTSPFFSTSLGIL 656
Cdd:cd13704    25 TGFNVDLLRAIAEEMGLKVEIRL-----------GPWSEVLQALENGEIDV-LIGMAYSEERAKLFDFSDPYLEVSVSIF 92

                  ...
gi 310703673  657 VRT 659
Cdd:cd13704    93 VRK 95
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
578-658 6.36e-07

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: 51.57  E-value: 6.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYivgdgkygawknghWTGLVGDLLS----GTANMAVTSFSINTARSQVIDFTSPFFSTSL 653
Cdd:cd00997    25 GFSIDLWRAIAERLGWETEYV--------------RVDSVSALLAavaeGEADIAIAAISITAEREAEFDFSQPIFESGL 90

                  ....*
gi 310703673  654 GILVR 658
Cdd:cd00997    91 QILVP 95
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
578-668 6.37e-07

Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily includes the periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBPII proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 270347 [Multi-domain]  Cd Length: 221  Bit Score: 51.42  E-value: 6.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLyivgdgkygawKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13629    24 GFDVDLAKALAKDLGVKVEF-----------VNTAWDGLIPALQTGKFDLIISGMTITPERNLKVNFSNPYLVSGQTLLV 92
                          90
                  ....*....|.
gi 310703673  658 RTRDTAAPIGA 668
Cdd:cd13629    93 NKKSAAGIKSL 103
PBP2_GlnP cd13619
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ...
581-662 4.06e-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: 49.24  E-value: 4.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  581 IDLLEQLAEDMNFDFDlyivgdgkygaWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTR 660
Cdd:cd13619    27 VDLLNAIAKDQGFKVE-----------LKPMGFDAAIQAVQSGQADGVIAGMSITDERKKTFDFSDPYYDSGLVIAVKKD 95

                  ..
gi 310703673  661 DT 662
Cdd:cd13619    96 NT 97
PBP2_GltI_DEBP cd13688
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ...
790-907 4.64e-06

Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic binding protein fold; This subfamily represents the periplasmic-binding protein component of ABC transporter specific for carboxylic amino acids, including GtlI from Escherichia coli. The aspartate-glutamate binding domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270406 [Multi-domain]  Cd Length: 238  Bit Score: 49.17  E-value: 4.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  790 QGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLKNDpeKLDAFIMDKALLDYEVSI-DADCKLLTVGKPF 868
Cdd:cd13688   120 AGKTVGVTAGTTTEDALRTVNPLAGLQASVVPVKDHAEGFAALETG--KADAFAGDDILLAGLAARsKNPDDLALIPRPL 197
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 310703673  869 AIEGYGIGLPPNSP---LTSNISelISQYKSHGFMDVLHDKW 907
Cdd:cd13688   198 SYEPYGLMLRKDDPdfrLLVDRA--LAQLYQSGEIEKLYDKW 237
PBP2_HisJ_LAO_like cd01001
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ...
578-663 5.36e-06

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: 48.83  E-value: 5.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDlyivgdgkygaWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd01001    26 GFDIDLANALCKRMKVKCE-----------IVTQPWDGLIPALKAGKYDAIIASMSITDKRRQQIDFTDPYYRTPSRFVA 94

                  ....*.
gi 310703673  658 RtRDTA 663
Cdd:cd01001    95 R-KDSP 99
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
791-907 7.82e-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: 7.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  791 GFRFGTVRESSAEDYVRQSFPEMHeyMRRYNVPAtpDGVQYLKNDpeKLDAFIMDkALLDYEVSIDADCKLLTVGKPFAI 870
Cdd:cd13629   110 GVTIAVKLGTTGDQAARKLFPKAT--ILVFDDEA--AAVLEVVNG--KADAFIYD-QPTPARFAKKNDPTLVALLEPFTY 182
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 310703673  871 EGYGIGLPPNSPLTSN-ISELISQYKSHGFMDVLHDKW 907
Cdd:cd13629   183 EPLGFAIRKGDPDLLNwLNNFLKQIKGDGTLDELYDKW 220
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
578-662 1.96e-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: 47.37  E-value: 1.96e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVgdgkygawkngHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13625    28 GFDRDLLDEMAKKLGVKVEQQDL-----------PWSGILPGLLAGKFDMVATSVTITKERAKRFAFTLPIAEATAALLK 96

                  ....*
gi 310703673  658 RTRDT 662
Cdd:cd13625    97 RAGDD 101
PBP1_iGluR_NMDA_NR2 cd06378
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of ...
209-491 3.21e-05

N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.


Pssm-ID: 380601  Cd Length: 356  Bit Score: 47.67  E-value: 3.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  209 LDLVSSVLHIPVLSI------VRHEfpresQNPLHLQLSLENSLSSDADVTVSILTMNNWYNFSLLLCQ----EDWniTD 278
Cdd:cd06378    80 LDFISLQTYLPILGIsggsanVLLD-----KEEGSTFLQLGPSIEQQATVMLNILEEYDWHQFSVVTSLfpgyRDF--VD 152
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  279 FLLLTENNSKFHLESVINITANLSSTKDLLSfLQVQMDNIrnSTPTMVMFgCDMDSIRQIFEMSTQFGLSPPELHW---- 354
Cdd:cd06378   153 AIRSTIDNSFVGWELQDVLTLDMSNDGSDAK-TLRQLKKI--EAQVILLY-CTKEEAQYIFEAAEEAGLTGYGYVWivps 228
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  355 -VLGDSqnveELRTEGLPLGLIA-HGKTTQSVFEYYVQDAMELVARAVatATMIQPELALLPSTMNCMDVKTTNLTSGQY 432
Cdd:cd06378   229 lVLGNT----DPPPAEFPVGLISvHFDTWDYSLRARVRDGVAIIATGA--EAMLSEHGFLPEPKSDCYAPNETREPANET 302
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 310703673  433 LSRFLANTTFRGLSGSIKVKGsTIISSEnnFFIWNLQHDpmgkPMWTRLGSWQGGRIVM 491
Cdd:cd06378   303 LHRYLINVTWEGRDLSFNEDG-YLVNPE--LVIINLNRE----RLWEKVGKWESGSLQM 354
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
790-907 8.62e-05

Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 periplasmic-binding protein fold; This family comprises of the periplasmic-binding protein component of ABC transporters specific for cysteine and carboxylic amino acids, as well as their closely related proteins. The cysteine and aspartate-glutamate binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270221 [Multi-domain]  Cd Length: 228  Bit Score: 45.38  E-value: 8.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  790 QGFRFGTVRESSAEDYVRQSFPEMheymRRYNVPATPDGVQYLKNDpeKLDAFIMDKALLDYEVSIDADcKLLTVGKPFA 869
Cdd:cd01000   116 KGKTILVLQGSTAEAALRKAAPEA----QLLEFDDYAEAFQALESG--RVDAMATDNSLLAGWAAENPD-DYVILPKPFS 188
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 310703673  870 IEGYGIGLPPNSP-LTSNISELISQYKSHGFMDVLHDKW 907
Cdd:cd01000   189 QEPYGIAVRKGDTeLLKAVNATIAKLKADGELAEIYKKW 227
PBP2_GluB cd13690
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ...
620-663 1.20e-04

Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein fold; This group includes periplasmic glutamate-binding domain GluB from Corynebacterium efficiens and its related proteins. The GluB domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270408 [Multi-domain]  Cd Length: 231  Bit Score: 44.95  E-value: 1.20e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 310703673  620 LLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDTA 663
Cdd:cd13690    67 LQNGTVDLVVATYSITPERRKQVDFAGPYYTAGQRLLVRAGSKI 110
PBP2_ml15202_like cd13701
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
578-658 2.78e-04

Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold; This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which are involved in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270419 [Multi-domain]  Cd Length: 227  Bit Score: 43.60  E-value: 2.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGdgkygawknghWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13701    27 GWEIDLIDALCARLDARCEITPVA-----------WDGIIPALQSGKIDMIWNSMSITDERKKVIDFSDPYYETPTAIVG 95

                  .
gi 310703673  658 R 658
Cdd:cd13701    96 A 96
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
578-662 3.00e-04

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: 43.46  E-value: 3.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDlyivgdgkygaWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13626    24 GFDVEVGREIAKRLGLKVE-----------FKATEWDGLLPGLNSGKFDVIANQVTITPEREEKYLFSDPYLVSGAQIIV 92

                  ....*
gi 310703673  658 RTRDT 662
Cdd:cd13626    93 KKDNT 97
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
578-658 1.51e-03

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: 41.36  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGDgkygawknghWTGLVGDLLSGTANMaVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd01007    26 GIAADYLKLIAKKLGLKFEYVPGDS----------WSELLEALKAGEIDL-LSSVSKTPEREKYLLFTKPYLSSPLVIVT 94

                  .
gi 310703673  658 R 658
Cdd:cd01007    95 R 95
PBP2_mlr5654_like cd13702
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
613-657 1.67e-03

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: 41.15  E-value: 1.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 310703673  613 WTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13702    50 WDGIIPALQAKKFDAIIASMSITPERKKQVDFTDPYYTNPLVFVA 94
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
578-668 1.79e-03

Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic binding protein fold; This group contains cystine binding domain FliY and its related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270430 [Multi-domain]  Cd Length: 219  Bit Score: 41.22  E-value: 1.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMnfdfdlyivgdGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13712    24 GFEVDVAKALAAKL-----------GVKPEFVTTEWSGILAGLQAGKYDVIINQVGITPERQKKFDFSQPYTYSGIQLIV 92
                          90
                  ....*....|.
gi 310703673  658 RTRDTAAPIGA 668
Cdd:cd13712    93 RKNDTRTFKSL 103
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
563-652 2.26e-03

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: 40.92  E-value: 2.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  563 SSNDTVPIKFKKC----CYGYCIDLLEQLAEDMNFDFDLyivgdgkygawKNGHWTGLVGDLLSGTANMAVTSFSINTAR 638
Cdd:cd13628     6 TSPDYPPFEFKIGdrgkIVGFDIELAKTIAKKLGLKLQI-----------QEYDFNGLIPALASGQADLALAGITPTPER 74
                          90
                  ....*....|....
gi 310703673  639 SQVIDFTSPFFSTS 652
Cdd:cd13628    75 KKVVDFSEPYYEAS 88
PBP2_YxeM cd13709
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ...
563-658 2.89e-03

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: 40.41  E-value: 2.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  563 SSNDTVPIKFKKC--CYGYCIDLLEQLAEDMNFDFDlyivgdgkygaWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQ 640
Cdd:cd13709     7 SSGSSYPFTFKENgkLKGFEVDVWNAIGKRTGYKVE-----------FVTADFSGLFGMLDSGKVDTIANQITITPERQE 75
                          90
                  ....*....|....*...
gi 310703673  641 VIDFTSPFFSTSLGILVR 658
Cdd:cd13709    76 KYDFSEPYVYDGAQIVVK 93
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
613-666 2.90e-03

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: 40.35  E-value: 2.90e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 310703673  613 WTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDTAAPI 666
Cdd:cd13713    48 WDGIIAGLWAGRYDIIIGSMTITEERLKVVDFSNPYYYSGAQIFVRKDSTITSL 101
PBP2_BsGlnH cd13689
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ...
791-909 3.09e-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: 3.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  791 GFRFGTVRESSAEDYVRQSFPEMheymrryNVPA---TPDGVQYLKNDpeKLDAFIMDKALL--DYEVSIDADcKLLTVG 865
Cdd:cd13689   115 GKRVGAVKGSTSEAAIREKLPKA-------SVVTfddTAQAFLALQQG--KVDAITTDETILagLLAKAPDPG-NYEILG 184
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 310703673  866 KPFAIEGYGIGLPPNSP-LTSNISELISQYKSHGFMDVLHDKWYK 909
Cdd:cd13689   185 EALSYEPYGIGVPKGESaLRDFVNETLADLEKDGEADKIYDKWFG 229
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
620-658 3.40e-03

Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 periplasmic-binding protein fold; This family comprises of the periplasmic-binding protein component of ABC transporters specific for cysteine and carboxylic amino acids, as well as their closely related proteins. The cysteine and aspartate-glutamate binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270221 [Multi-domain]  Cd Length: 228  Bit Score: 40.37  E-value: 3.40e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 310703673  620 LLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVR 658
Cdd:cd01000    66 LQSGKVDLIIATMTITPERAKEVDFSVPYYADGQGLLVR 104
PBP2_PheC cd01069
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ...
578-661 4.40e-03

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: 40.02  E-value: 4.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVgdgkygAWKNghwtgLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd01069    34 GYDIDMAEALAKSLGVKVEFVPT------SWPT-----LMDDLAADKFDIAMGGISITLERQRQAFFSAPYLRFGKTPLV 102

                  ....
gi 310703673  658 RTRD 661
Cdd:cd01069   103 RCAD 106
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
578-663 6.30e-03

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: 39.51  E-value: 6.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703673  578 GYCIDLLEQLAEDMNFDFDLYIVGdgkygawkngHWTGLVGDLLSGTANMAVTSFSiNTARSQVIDFTSPFFSTSLGILV 657
Cdd:cd13707    26 GISADLLELISLRTGLRFEVVRAS----------SPAEMIEALRSGEADMIAALTP-SPEREDFLLFTRPYLTSPFVLVT 94

                  ....*.
gi 310703673  658 RTRDTA 663
Cdd:cd13707    95 RKDAAA 100
 
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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