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Conserved domains on  [gi|568966813|ref|XP_006513352|]
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glutamate receptor ionotropic, NMDA 3B isoform X3 [Mus musculus]

Protein Classification

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 ...
141-481 2.95e-172

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: 499.65  E-value: 2.95e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 141 TPSPRLPHNLSLELVAVASPTRDPASLARGLCQVLAPPGVVASITFPEARPELRLLQFLAAATETPVLSVLRREVRAPLG 220
Cdd:cd06377   33 LPTGLLPYNLSLEVVVAAPWARDPASLTRSLCHSVVVQGVAALLAFPQSRGELLQLDFLSAALEIPVVSILRREFPRPLR 112
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 221 APTPFHLQLDWASPLETILDVLVSLVRAHAWEDIALVLCRVRDPSGLVTLWTSRASQAPKFVLDLSQLDS--GNDSLRAT 298
Cdd:cd06377  113 SQNPFHLQLDLQSSLESLEDVLVSLLQANSWEDVSLLLCQPWDPTSFLLLWQNNSQFHLGTVLNLSVLDEsdLQRSLQQH 192
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 299 LALLGTlegggtPVSAAVLLGCSTAHAHEVLEAAPPG----PQWLLGTPLPAEALPKTGLPPGVLVLGETGQPSLEAAVH 374
Cdd:cd06377  193 LESLKD------PSPAIVMFGCDAARARRVFEAAPPGglpeFHWLLGTPLPVEELPTEGLPPGLLALGETSRPSLEAYVQ 266
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 375 DMVELVARALSSMALMHPERALLPAAVNCEDLKTGGSESTARTLARFLSNTSFQGRTGAVWVAGSSQVHVSRHFKVWSLR 454
Cdd:cd06377  267 DAVELVARALSSAALVHPELALLPATVNCNDLKTGGSESSGQYLSRFLANTSFQGRTGTVWVTGSSQVHSERHFKVWSLR 346
                        330       340
                 ....*....|....*....|....*..
gi 568966813 455 RDPLGAPAWATVGSWQDGQLDFQPGAA 481
Cdd:cd06377  347 RDPLGAPTWATVGSWQDGKLDMEPGAW 373
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
494-646 4.75e-95

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd13720:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 283  Bit Score: 297.15  E-value: 4.75e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 494 RPKLRVVTLVEHPFVFTRESDEDGQCPAGQLCLDPGTNDSARLDALFTALE--NGSVPRTLRRCCYGYCIDLLERLAEDL 571
Cdd:cd13720    1 RPHLRVVTLLEHPFVFTREVDEEGLCPAGQLCLDPMTNDSSTLDALFSSLHssNDTVPIKFRKCCYGYCIDLLEKLAEDL 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568966813 572 AFDFELYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTASPI 646
Cdd:cd13720   81 GFDFDLYIVGDGKYGAWRNGRWTGLVGDLLSGRAHMAVTSFSINSARSQVIDFTSPFFSTSLGILVRTRDELSGI 155
Lig_chan super family cl27683
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
654-762 3.57e-33

Ligand-gated ion channel; This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.


The actual alignment was detected with superfamily member pfam00060:

Pssm-ID: 459656 [Multi-domain]  Cd Length: 267  Bit Score: 128.97  E-value: 3.57e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813  654 HWSMWVGVFAALHLTALFLTLYEWRSPYGLTPRGRNRGTVFSYSSALNLCYAILFGRTvSSKTPKCPTGRFLMNLWAIFC 733
Cdd:pfam00060   1 SLEVWLGILVAFLIVGVVLFLLERFSPYEWRGPLETEENRFTLSNSLWFSFGALVQQG-HRENPRSLSGRIVVGVWWFFA 79
                          90       100
                  ....*....|....*....|....*....
gi 568966813  734 LLVLSSYTANLAAVMVGDKTFEELSGIHD 762
Cdd:pfam00060  80 LILLSSYTANLAAFLTVERMQSPIQSLED 108
 
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 ...
141-481 2.95e-172

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: 499.65  E-value: 2.95e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 141 TPSPRLPHNLSLELVAVASPTRDPASLARGLCQVLAPPGVVASITFPEARPELRLLQFLAAATETPVLSVLRREVRAPLG 220
Cdd:cd06377   33 LPTGLLPYNLSLEVVVAAPWARDPASLTRSLCHSVVVQGVAALLAFPQSRGELLQLDFLSAALEIPVVSILRREFPRPLR 112
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 221 APTPFHLQLDWASPLETILDVLVSLVRAHAWEDIALVLCRVRDPSGLVTLWTSRASQAPKFVLDLSQLDS--GNDSLRAT 298
Cdd:cd06377  113 SQNPFHLQLDLQSSLESLEDVLVSLLQANSWEDVSLLLCQPWDPTSFLLLWQNNSQFHLGTVLNLSVLDEsdLQRSLQQH 192
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 299 LALLGTlegggtPVSAAVLLGCSTAHAHEVLEAAPPG----PQWLLGTPLPAEALPKTGLPPGVLVLGETGQPSLEAAVH 374
Cdd:cd06377  193 LESLKD------PSPAIVMFGCDAARARRVFEAAPPGglpeFHWLLGTPLPVEELPTEGLPPGLLALGETSRPSLEAYVQ 266
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 375 DMVELVARALSSMALMHPERALLPAAVNCEDLKTGGSESTARTLARFLSNTSFQGRTGAVWVAGSSQVHVSRHFKVWSLR 454
Cdd:cd06377  267 DAVELVARALSSAALVHPELALLPATVNCNDLKTGGSESSGQYLSRFLANTSFQGRTGTVWVTGSSQVHSERHFKVWSLR 346
                        330       340
                 ....*....|....*....|....*..
gi 568966813 455 RDPLGAPAWATVGSWQDGQLDFQPGAA 481
Cdd:cd06377  347 RDPLGAPTWATVGSWQDGKLDMEPGAW 373
PBP2_iGluR_NMDA_Nr3 cd13720
The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
494-646 4.75e-95

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: 297.15  E-value: 4.75e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 494 RPKLRVVTLVEHPFVFTRESDEDGQCPAGQLCLDPGTNDSARLDALFTALE--NGSVPRTLRRCCYGYCIDLLERLAEDL 571
Cdd:cd13720    1 RPHLRVVTLLEHPFVFTREVDEEGLCPAGQLCLDPMTNDSSTLDALFSSLHssNDTVPIKFRKCCYGYCIDLLEKLAEDL 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568966813 572 AFDFELYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTASPI 646
Cdd:cd13720   81 GFDFDLYIVGDGKYGAWRNGRWTGLVGDLLSGRAHMAVTSFSINSARSQVIDFTSPFFSTSLGILVRTRDELSGI 155
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
654-762 3.57e-33

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: 128.97  E-value: 3.57e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813  654 HWSMWVGVFAALHLTALFLTLYEWRSPYGLTPRGRNRGTVFSYSSALNLCYAILFGRTvSSKTPKCPTGRFLMNLWAIFC 733
Cdd:pfam00060   1 SLEVWLGILVAFLIVGVVLFLLERFSPYEWRGPLETEENRFTLSNSLWFSFGALVQQG-HRENPRSLSGRIVVGVWWFFA 79
                          90       100
                  ....*....|....*....|....*....
gi 568966813  734 LLVLSSYTANLAAVMVGDKTFEELSGIHD 762
Cdd:pfam00060  80 LILLSSYTANLAAFLTVERMQSPIQSLED 108
Lig_chan-Glu_bd pfam10613
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
497-638 3.76e-32

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: 120.32  E-value: 3.76e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813  497 LRVVTLVEHPFVFTRESDEDgqcpagqlcldpgtNDSarldalftalengsvprtlrrcCYGYCIDLLERLAEDLAFDFE 576
Cdd:pfam10613   3 LIVTTILEPPFVMLKENLEG--------------NDR----------------------YEGFCIDLLKELAEILGFKYE 46
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568966813  577 LYIVGDGKYGALRD--GRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVR 638
Cdd:pfam10613  47 IRLVPDGKYGSLDPttGEWNGMIGELIDGKADLAVAPLTITSEREKVVDFTKPFMTLGISILMK 110
Lig_chan-Glu_bd smart00918
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
551-601 6.91e-19

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: 81.14  E-value: 6.91e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568966813   551 TLRRCCYGYCIDLLERLAEDLAFDFELYIVGDGKYGA-LRDGRWTGLVGDLL 601
Cdd:smart00918  11 GGNDRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGArLPNGSWNGMVGELV 62
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
558-638 1.42e-11

ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms];


Pssm-ID: 440596 [Multi-domain]  Cd Length: 223  Bit Score: 64.62  E-value: 1.42e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVgdgkygalrdgRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:COG0834   23 GFDVDLARAIAKRLGLKVEFVPV-----------PWDRLIPALQSGKVDLIIAGMTITPEREKQVDFSDPYYTSGQVLLV 91

                 .
gi 568966813 638 R 638
Cdd:COG0834   92 R 92
 
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 ...
141-481 2.95e-172

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: 499.65  E-value: 2.95e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 141 TPSPRLPHNLSLELVAVASPTRDPASLARGLCQVLAPPGVVASITFPEARPELRLLQFLAAATETPVLSVLRREVRAPLG 220
Cdd:cd06377   33 LPTGLLPYNLSLEVVVAAPWARDPASLTRSLCHSVVVQGVAALLAFPQSRGELLQLDFLSAALEIPVVSILRREFPRPLR 112
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 221 APTPFHLQLDWASPLETILDVLVSLVRAHAWEDIALVLCRVRDPSGLVTLWTSRASQAPKFVLDLSQLDS--GNDSLRAT 298
Cdd:cd06377  113 SQNPFHLQLDLQSSLESLEDVLVSLLQANSWEDVSLLLCQPWDPTSFLLLWQNNSQFHLGTVLNLSVLDEsdLQRSLQQH 192
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 299 LALLGTlegggtPVSAAVLLGCSTAHAHEVLEAAPPG----PQWLLGTPLPAEALPKTGLPPGVLVLGETGQPSLEAAVH 374
Cdd:cd06377  193 LESLKD------PSPAIVMFGCDAARARRVFEAAPPGglpeFHWLLGTPLPVEELPTEGLPPGLLALGETSRPSLEAYVQ 266
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 375 DMVELVARALSSMALMHPERALLPAAVNCEDLKTGGSESTARTLARFLSNTSFQGRTGAVWVAGSSQVHVSRHFKVWSLR 454
Cdd:cd06377  267 DAVELVARALSSAALVHPELALLPATVNCNDLKTGGSESSGQYLSRFLANTSFQGRTGTVWVTGSSQVHSERHFKVWSLR 346
                        330       340
                 ....*....|....*....|....*..
gi 568966813 455 RDPLGAPAWATVGSWQDGQLDFQPGAA 481
Cdd:cd06377  347 RDPLGAPTWATVGSWQDGKLDMEPGAW 373
PBP2_iGluR_NMDA_Nr3 cd13720
The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
494-646 4.75e-95

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: 297.15  E-value: 4.75e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 494 RPKLRVVTLVEHPFVFTRESDEDGQCPAGQLCLDPGTNDSARLDALFTALE--NGSVPRTLRRCCYGYCIDLLERLAEDL 571
Cdd:cd13720    1 RPHLRVVTLLEHPFVFTREVDEEGLCPAGQLCLDPMTNDSSTLDALFSSLHssNDTVPIKFRKCCYGYCIDLLEKLAEDL 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568966813 572 AFDFELYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTASPI 646
Cdd:cd13720   81 GFDFDLYIVGDGKYGAWRNGRWTGLVGDLLSGRAHMAVTSFSINSARSQVIDFTSPFFSTSLGILVRTRDELSGI 155
PBP1_iGluR_NMDA cd06367
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the ionotropic ...
144-471 2.08e-93

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: 295.69  E-value: 2.08e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 144 PRLPHNLSLELVAvaSPTRDPASLARGLCQVLAPPgVVASITFPEARPE---LRLLQFLAAATETPVLSVLRREVRAPlG 220
Cdd:cd06367   30 FTLPVQLRVELVT--MPEPDPKSIITRICDLLSDS-KVQGVVFSDDTDQeaiAQILDFIAAQTLTPVLGLHGRSSMIM-A 105
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 221 APTPFHLQLDWASPLETILDVLVSLVRAHAWEDIALVLCRVRDPSGLVTLWTSRASQA-----PKFVLDLSqLDSGNDSL 295
Cdd:cd06367  106 DKSEHSMFLQFGPPIEQQASVMLNIMEEYDWYIVSLVTTYFPGYQDFVNKLRSTIENSgweleEVLQLDMS-LDDGDSKL 184
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 296 RATLALLgtleggGTPVSAAVLLGCSTAHAHEVLEAAPP------GPQWLLGTPLPAEALPKTGLPPGVLVLGETGQPSL 369
Cdd:cd06367  185 QAQLKKL------QSPEARVILLYCTKEEATYVFEVAASvgltgyGYTWLVGSLVAGTDTVPAEFPTGLISLSYDEWYNL 258
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 370 EAAVHDMVELVARALSSMALMHpeRALLPAAVNCEDLKTGGsESTARTLARFLSNTSFQGRTGAVWVagsSQVHVSRHFK 449
Cdd:cd06367  259 PARIRDGVAIVATAASEMLSEH--EQIPDPPSSCVNNQEIR-KYTGPMLKRYLINVTFEGRDLSFSE---DGYQMHPKLV 332
                        330       340
                 ....*....|....*....|..
gi 568966813 450 VWSLRRDplgaPAWATVGSWQD 471
Cdd:cd06367  333 IILLNNE----RKWERVGKWKD 350
PBP2_iGluR_NMDA cd13687
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ...
494-646 1.82e-50

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: 176.67  E-value: 1.82e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 494 RPKLRVVTLVEHPFVFTResdedgqcpagqlcldpgtndsarldalftalengsvprtlrrCCYGYCIDLLERLAEDLAF 573
Cdd:cd13687    1 STHLKVVTLEEAPFVYVK-------------------------------------------CCYGFCIDLLKKLAEDVNF 37
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568966813 574 DFELYIVGDGKYG---ALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTASPI 646
Cdd:cd13687   38 TYDLYLVTDGKFGtvnKSINGEWNGMIGELVSGRADMAVASLTINPERSEVIDFSKPFKYTGITILVKKRNELSGI 113
PBP2_iGluR_NMDA_Nr2 cd13718
The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
497-644 1.72e-37

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: 141.71  E-value: 1.72e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 497 LRVVTLVEHPFVFTRESDedgqcPAGQLCLDPGTNDSARLDALFTALENGsvPRTLRRCCYGYCIDLLERLAEDLAFDFE 576
Cdd:cd13718    4 LKIVTLEEAPFVIVEPVD-----PLTGTCMRNTVPCRKQLNHENSTDADE--NRYVKKCCKGFCIDILKKLAKDVGFTYD 76
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568966813 577 LYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTAS 644
Cdd:cd13718   77 LYLVTNGKHGKKINGVWNGMIGEVVYKRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNQVS 144
PBP2_iGluR_non_NMDA_like cd13685
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ...
494-642 3.09e-33

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: 128.46  E-value: 3.09e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 494 RPKLRVVTLVEHPFVFTRESDEDGqcpagqlcldpgtndSARLdalftalengsvprtlrrccYGYCIDLLERLAEDLAF 573
Cdd:cd13685    1 NKTLRVTTILEPPFVMKKRDSLSG---------------NPRF--------------------EGYCIDLLEELAKILGF 45
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 574 DFELYIVGDGKYGA-LRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDT 642
Cdd:cd13685   46 DYEIYLVPDGKYGSrDENGNWNGMIGELVRGEADIAVAPLTITAEREEVVDFTKPFMDTGISILMRKPTP 115
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
654-762 3.57e-33

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: 128.97  E-value: 3.57e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813  654 HWSMWVGVFAALHLTALFLTLYEWRSPYGLTPRGRNRGTVFSYSSALNLCYAILFGRTvSSKTPKCPTGRFLMNLWAIFC 733
Cdd:pfam00060   1 SLEVWLGILVAFLIVGVVLFLLERFSPYEWRGPLETEENRFTLSNSLWFSFGALVQQG-HRENPRSLSGRIVVGVWWFFA 79
                          90       100
                  ....*....|....*....|....*....
gi 568966813  734 LLVLSSYTANLAAVMVGDKTFEELSGIHD 762
Cdd:pfam00060  80 LILLSSYTANLAAFLTVERMQSPIQSLED 108
PBP2_iGluR_NMDA_Nr1 cd13719
The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
496-638 5.97e-33

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: 128.63  E-value: 5.97e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 496 KLRVVTLVEHPFVFTRESDEDGQCpagqLCLDPGTNDsarldaLFTALENGSVPRtlrrCCYGYCIDLLERLAEDLAFDF 575
Cdd:cd13719    3 HLKIVTIHEEPFVYVRPTPSDGTC----REEFTVNCP------NFNISGRPTVPF----CCYGYCIDLLIKLARKMNFTY 68
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568966813 576 ELYIVGDGKYGALR------DGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVR 638
Cdd:cd13719   69 ELHLVADGQFGTQErvnnsnKKEWNGMMGELVSGRADMIVAPLTINPERAQYIEFSKPFKYQGLTILVK 137
PBP2_iGluR_putative cd13717
The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ...
494-758 1.24e-32

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: 129.73  E-value: 1.24e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 494 RPKLRVVTLVEHPFVFTRESDEDGQcpagqlcldpgtndsarldalftalengsvprtlrrccYGYCIDLLERLAEDLAF 573
Cdd:cd13717    1 RRVYRIGTVESPPFVYRDRDGSPIW--------------------------------------EGYCIDLIEEISEILNF 42
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 574 DFELYIVGDGKYGALRD-GRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFF-STSLGIMVRTRDTASPIGAFMW 651
Cdd:cd13717   43 DYEIVEPEDGKFGTMDEnGEWNGLIGDLVRKEADIALAALSVMAEREEVVDFTVPYYdLVGITILMKKPERPTSLFKFLT 122
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 652 PLHWSMWvgvfaalhltaLFLTLYE--WRSPYGLTPRGrnrgtvfsyssalnlcyailfgrtvSSKTPKCPTGRFLMNLW 729
Cdd:cd13717  123 VLELEVW-----------REFTLKEslWFCLTSLTPQG-------------------------GGEAPKNLSGRLLVATW 166
                        250       260       270
                 ....*....|....*....|....*....|....*
gi 568966813 730 AIFCLLVLSSYTANLAAVMVGDK------TFEELS 758
Cdd:cd13717  167 WLFVFIIIASYTANLAAFLTVSRlqtpveSLDDLA 201
Lig_chan-Glu_bd pfam10613
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
497-638 3.76e-32

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: 120.32  E-value: 3.76e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813  497 LRVVTLVEHPFVFTRESDEDgqcpagqlcldpgtNDSarldalftalengsvprtlrrcCYGYCIDLLERLAEDLAFDFE 576
Cdd:pfam10613   3 LIVTTILEPPFVMLKENLEG--------------NDR----------------------YEGFCIDLLKELAEILGFKYE 46
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568966813  577 LYIVGDGKYGALRD--GRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVR 638
Cdd:pfam10613  47 IRLVPDGKYGSLDPttGEWNGMIGELIDGKADLAVAPLTITSEREKVVDFTKPFMTLGISILMK 110
PBP2_iGluR_ligand_binding cd00998
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ...
497-640 1.31e-27

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: 112.08  E-value: 1.31e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 497 LRVVTLVEHPFVFTRESDEDGqcpagqlcldpgtndsarldalftalengsvprTLRRCCYGYCIDLLERLAEDLAFDFE 576
Cdd:cd00998    3 LKVVVPLEPPFVMFVTGSNAV---------------------------------TGNGRFEGYCIDLLKELSQSLGFTYE 49
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568966813 577 LYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTR 640
Cdd:cd00998   50 YYLVPDGKFGAPVNGSWNGMVGEVVRGEADLAVGPITITSERSVVIDFTQPFMTSGIGIMIPIR 113
PBP2_iGluR_Kainate_GluR7 cd13723
GluR7 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
497-752 1.60e-27

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: 115.17  E-value: 1.60e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 497 LRVVTLVEHPFVFTRESDEdgqcpagqlcldpgtndsarldalfTALENGSVPrtlrrccyGYCIDLLERLAEDLAFDFE 576
Cdd:cd13723    4 LIVTTVLEEPFVMFRKSDR-------------------------TLYGNDRFE--------GYCIDLLKELAHILGFSYE 50
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 577 LYIVGDGKYGALRD-GRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTASP-IGAFMWPLH 654
Cdd:cd13723   51 IRLVEDGKYGAQDDkGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRKPNGTNPsVFSFLNPLS 130
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 655 WSMW-------VGVFAALHLTALFlTLYEWRSPYGLTPRGRNRGTVFSYSSALNLCYAILFGRTvSSKTPKCPTGRFLMN 727
Cdd:cd13723  131 PDIWmyvllayLGVSCVLFVIARF-SPYEWYDAHPCNPGSEVVENNFTLLNSFWFGMGSLMQQG-SELMPKALSTRIIGG 208
                        250       260
                 ....*....|....*....|....*
gi 568966813 728 LWAIFCLLVLSSYTANLAAVMVGDK 752
Cdd:cd13723  209 IWWFFTLIIISSYTANLAAFLTVER 233
PBP2_iGluR_Kainate cd13714
Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains ...
497-635 2.87e-27

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: 111.09  E-value: 2.87e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 497 LRVVTLVEHPFVFTRESDE--DGqcpagqlcldpgtNDsarldaLFtalengsvprtlrrccYGYCIDLLERLAEDLAFD 574
Cdd:cd13714    4 LIVTTILEEPYVMLKESAKplTG-------------ND------RF----------------EGFCIDLLKELAKILGFN 48
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568966813 575 FELYIVGDGKYGALRD--GRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFstSLGI 635
Cdd:cd13714   49 YTIRLVPDGKYGSYDPetGEWNGMVRELIDGRADLAVADLTITYERESVVDFTKPFM--NLGI 109
PBP2_iGluR_AMPA cd13715
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
558-638 6.23e-24

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: 102.05  E-value: 6.23e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDGKYGAL--RDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGI 635
Cdd:cd13715   34 GYCVDLADEIAKHLGIKYELRIVKDGKYGARdaDTGIWNGMVGELVRGEADIAIAPLTITLVRERVIDFSKPFMSLGISI 113

                 ...
gi 568966813 636 MVR 638
Cdd:cd13715  114 MIK 116
PBP2_iGluR_AMPA_GluR1 cd13729
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
558-646 1.01e-19

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: 89.70  E-value: 1.01e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDGKYGAlRDGR---WTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFstSLG 634
Cdd:cd13729   32 GYCVELAAEIAKHVGYSYKLEIVSDGKYGA-RDPEtkmWNGMVGELVYGKADVAVAPLTITLVREEVIDFSKPFM--SLG 108
                         90
                 ....*....|..
gi 568966813 635 IMVRTRDTASPI 646
Cdd:cd13729  109 ISIMIKKPTSPI 120
PBP2_iGluR_kainate_KA1 cd13724
The ligand-binding domain of the kainate subtype KA1 of ionotropic glutamate receptors, a ...
558-681 2.72e-19

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: 89.69  E-value: 2.72e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDGKYGALR-DGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIM 636
Cdd:cd13724   32 GFCVDMLKELAEILRFNYKIRLVGDGVYGVPEaNGTWTGMVGELIARKADLAVAGLTITAEREKVIDFSKPFMTLGISIL 111
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 568966813 637 VRTRDTASP-IGAFMWPLHWSMW-------VGVFAALHLTALfLTLYEWRSPY 681
Cdd:cd13724  112 YRVHMGRKPgYFSFLDPFSPGVWlfmllayLAVSCVLFLVAR-LTPYEWYSPH 163
PBP2_iGluR_delta_like cd13716
The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of ...
497-649 5.93e-19

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: 87.20  E-value: 5.93e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 497 LRVVTLVEHPFVFTRESdedgqcPAGQlcldpgtndsarldalftalengsvPRTLRrccyGYCIDLLERLAEDLAFDFE 576
Cdd:cd13716    4 LRVVTVLEEPFVMVSEN------VLGK-------------------------PKKYQ----GFSIDVLDALANYLGFKYE 48
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568966813 577 LYIVGDGKYGA-LRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRtrdTASPIGAF 649
Cdd:cd13716   49 IYVAPDHKYGSqQEDGTWNGLIGELVFKRADIGISALTITPERENVVDFTTRYMDYSVGVLLR---KAESIQSL 119
Lig_chan-Glu_bd smart00918
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
551-601 6.91e-19

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: 81.14  E-value: 6.91e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568966813   551 TLRRCCYGYCIDLLERLAEDLAFDFELYIVGDGKYGA-LRDGRWTGLVGDLL 601
Cdd:smart00918  11 GGNDRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGArLPNGSWNGMVGELV 62
PBP2_iGluR_Kainate_GluR6 cd13721
GluR6 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
497-638 9.24e-19

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: 86.61  E-value: 9.24e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 497 LRVVTLVEHPFVFTRESDEDgqcpagqlcldpgTNDSARLDalftalengsvprtlrrccyGYCIDLLERLAEDLAFDFE 576
Cdd:cd13721    4 LIVTTILEEPYVLFKKSDKP-------------LYGNDRFE--------------------GYCIDLLRELSTILGFTYE 50
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568966813 577 LYIVGDGKYGALRD--GRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVR 638
Cdd:cd13721   51 IRLVEDGKYGAQDDvnGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYR 114
PBP2_iGluR_AMPA_GluR2 cd13726
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
558-638 2.58e-18

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: 85.46  E-value: 2.58e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDGKYGAlRDGR---WTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLG 634
Cdd:cd13726   32 GYCVDLAAEIAKHCGFKYKLTIVGDGKYGA-RDADtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGIS 110

                 ....
gi 568966813 635 IMVR 638
Cdd:cd13726  111 IMIK 114
PBP2_iGluR_delta_1 cd13730
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the ...
497-638 4.30e-18

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: 84.62  E-value: 4.30e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 497 LRVVTLVEHPFVFTRESdedgqcPAGQlcldpgtndsarldalftalengsvPRTLRrccyGYCIDLLERLAEDLAFDFE 576
Cdd:cd13730    4 LKVVTVLEEPFVMVAEN------ILGQ-------------------------PKRYK----GFSIDVLDALAKALGFKYE 48
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568966813 577 LYIVGDGKYGA-LRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVR 638
Cdd:cd13730   49 IYQAPDGKYGHqLHNTSWNGMIGELISKRADLAISAITITPERESVVDFSKRYMDYSVGILIK 111
PBP2_iGluR_kainate_KA2 cd13725
The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a ...
541-640 5.17e-18

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: 84.37  E-value: 5.17e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 541 TALENgsvPRTLRRCCY----------GYCIDLLERLAEDLAFDFELYIVGDGKYGALR-DGRWTGLVGDLLAGRAHMAV 609
Cdd:cd13725    8 TILEN---PYVMRRPNFqalsgnerfeGFCVDMLRELAELLRFRYRLRLVEDGLYGAPEpNGSWTGMVGELINRKADLAV 84
                         90       100       110
                 ....*....|....*....|....*....|.
gi 568966813 610 TSFSINSARSQVVDFTSPFFSTSLGIMVRTR 640
Cdd:cd13725   85 AAFTITAEREKVIDFSKPFMTLGISILYRVH 115
PBP2_iGluR_delta_2 cd13731
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the ...
497-638 6.25e-18

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: 84.31  E-value: 6.25e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 497 LRVVTLVEHPFVFTRESdedgqcPAGQlcldpgtndsarldalftalengsvPRTLRrccyGYCIDLLERLAEDLAFDFE 576
Cdd:cd13731    4 LRVVTVLEEPFVMVSEN------VLGK-------------------------PKKYQ----GFSIDVLDALSNYLGFNYE 48
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568966813 577 LYIVGDGKYGALR-DGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVR 638
Cdd:cd13731   49 IYVAPDHKYGSPQeDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLR 111
PBP2_iGluR_AMPA_GluR4 cd13727
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
558-638 1.82e-17

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: 82.77  E-value: 1.82e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDGKYGAlRDGR---WTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLG 634
Cdd:cd13727   32 GYCVDLASEIAKHIGIKYKIAIVPDGKYGA-RDPEtkiWNGMVGELVYGKAEIAVAPLTITLVREEVIDFSKPFMSLGIS 110

                 ....
gi 568966813 635 IMVR 638
Cdd:cd13727  111 IMIK 114
PBP2_iGluR_AMPA_GluR3 cd13728
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
558-638 5.38e-17

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: 81.66  E-value: 5.38e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDGKYGAlRDGR---WTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLG 634
Cdd:cd13728   32 GYCVDLAYEIAKHVRIKYKLSIVGDGKYGA-RDPEtkiWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGIS 110

                 ....
gi 568966813 635 IMVR 638
Cdd:cd13728  111 IMIK 114
PBP2_iGluR_Kainate_GluR5 cd13722
GluR5 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
558-638 5.64e-16

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: 78.55  E-value: 5.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDGKYGALRD-GRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIM 636
Cdd:cd13722   32 GYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDkGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISIL 111

                 ..
gi 568966813 637 VR 638
Cdd:cd13722  112 YR 113
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
558-649 4.10e-13

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: 69.24  E-value: 4.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813  558 GYCIDLLERLAEDLAFDFELyivgdgkygalRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:pfam00497  23 GFDVDLAKAIAKRLGVKVEF-----------VPVSWDGLIPALQSGKVDLIIAGMTITPERAKQVDFSDPYYYSGQVILV 91
                          90
                  ....*....|..
gi 568966813  638 RTRDTASPIGAF 649
Cdd:pfam00497  92 RKKDSSKSIKSL 103
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
558-638 5.14e-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: 66.12  E-value: 5.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELyivgdgkygalRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd13530   24 GFDVDLANAIAKRLGVKVEF-----------VDTDFDGLIPALQSGKIDVAISGMTITPERAKVVDFSDPYYYTGQVLVV 92

                 .
gi 568966813 638 R 638
Cdd:cd13530   93 K 93
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
558-638 1.42e-11

ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms];


Pssm-ID: 440596 [Multi-domain]  Cd Length: 223  Bit Score: 64.62  E-value: 1.42e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVgdgkygalrdgRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:COG0834   23 GFDVDLARAIAKRLGLKVEFVPV-----------PWDRLIPALQSGKVDLIIAGMTITPEREKQVDFSDPYYTSGQVLLV 91

                 .
gi 568966813 638 R 638
Cdd:COG0834   92 R 92
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
558-638 4.68e-09

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 57.34  E-value: 4.68e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813   558 GYCIDLLERLAEDLAFDFELYIVGdgkygalrdgrWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:smart00062  24 GFDVDLAKAIAKELGLKVEFVEVS-----------FDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYRSGQVILV 92

                   .
gi 568966813   638 R 638
Cdd:smart00062  93 R 93
PBP2_GlnH cd00994
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ...
558-643 5.40e-09

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: 56.90  E-value: 5.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELyivgdgkygalRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd00994   23 GFDIDLWEAIAKEAGFKYEL-----------QPMDFKGIIPALQTGRIDIAIAGITITEERKKVVDFSDPYYDSGLAVMV 91

                 ....*.
gi 568966813 638 RTRDTA 643
Cdd:cd00994   92 KADNNS 97
PBP1_iGluR_NMDA_NR2 cd06378
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of ...
282-478 3.21e-08

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: 56.15  E-value: 3.21e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 282 VLDLSQLDSGNDSLRA-TLALLGTLEgggTPVsaaVLLGCSTAHAHEVLEAAP------PGPQWLLgtplPAEALPKTGL 354
Cdd:cd06378  167 LQDVLTLDMSNDGSDAkTLRQLKKIE---AQV---ILLYCTKEEAQYIFEAAEeagltgYGYVWIV----PSLVLGNTDP 236
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 355 PP-----GVL-VLGETGQPSLEAAVHDMVELVARALSSmalMHPERALLP-AAVNCEDlKTGGSESTARTLARFLSNTSF 427
Cdd:cd06378  237 PPaefpvGLIsVHFDTWDYSLRARVRDGVAIIATGAEA---MLSEHGFLPePKSDCYA-PNETREPANETLHRYLINVTW 312
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568966813 428 QGRTGAvWVAGSSQVHVSrhFKVWSLRRDPLgapaWATVGSWQDGQLDFQP 478
Cdd:cd06378  313 EGRDLS-FNEDGYLVNPE--LVIINLNRERL----WEKVGKWESGSLQMKY 356
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
538-642 6.42e-08

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: 53.92  E-value: 6.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 538 ALFTALENGSVprtlrrccYGYCIDLLERLAEDLAFDFElYIvgdgkygalrDGRWTGLVGDLLAGRAHMAVTSFSINSA 617
Cdd:cd13625   16 APFEFVENGKI--------VGFDRDLLDEMAKKLGVKVE-QQ----------DLPWSGILPGLLAGKFDMVATSVTITKE 76
                         90       100
                 ....*....|....*....|....*
gi 568966813 618 RSQVVDFTSPFFSTSLGIMVRTRDT 642
Cdd:cd13625   77 RAKRFAFTLPIAEATAALLKRAGDD 101
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
558-648 8.72e-08

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: 53.34  E-value: 8.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVgdgkygalrdgRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd13629   24 GFDVDLAKALAKDLGVKVEFVNT-----------AWDGLIPALQTGKFDLIISGMTITPERNLKVNFSNPYLVSGQTLLV 92
                         90
                 ....*....|.
gi 568966813 638 RTRDTASPIGA 648
Cdd:cd13629   93 NKKSAAGIKSL 103
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
558-638 1.33e-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: 53.11  E-value: 1.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYivgdgkygalrdgrWTGLVGDLLA----GRAHMAVTSFSINSARSQVVDFTSPFFSTSL 633
Cdd:cd00997   25 GFSIDLWRAIAERLGWETEYV--------------RVDSVSALLAavaeGEADIAIAAISITAEREAEFDFSQPIFESGL 90

                 ....*
gi 568966813 634 GIMVR 638
Cdd:cd00997   91 QILVP 95
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
558-642 1.94e-07

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: 52.50  E-value: 1.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELyivgdgkygalRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd13624   24 GFDIDLIKAIAKEAGFEVEF-----------KNMAFDGLIPALQSGKIDIIISGMTITEERKKSVDFSDPYYEAGQAIVV 92

                 ....*
gi 568966813 638 RTRDT 642
Cdd:cd13624   93 RKDST 97
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
557-639 2.03e-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: 52.59  E-value: 2.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 557 YGYCIDLLERLAEDLAFDFELYIvgdgkygalrdGRWTGLVGDLLAGRAHMaVTSFSINSARSQVVDFTSPFFSTSLGIM 636
Cdd:cd13704   25 TGFNVDLLRAIAEEMGLKVEIRL-----------GPWSEVLQALENGEIDV-LIGMAYSEERAKLFDFSDPYLEVSVSIF 92

                 ...
gi 568966813 637 VRT 639
Cdd:cd13704   93 VRK 95
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
593-646 6.56e-06

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


Pssm-ID: 270431 [Multi-domain]  Cd Length: 218  Bit Score: 48.05  E-value: 6.56e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568966813 593 WTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTASPI 646
Cdd:cd13713   48 WDGIIAGLWAGRYDIIIGSMTITEERLKVVDFSNPYYYSGAQIFVRKDSTITSL 101
PBP2_mlr5654_like cd13702
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
593-637 1.39e-05

Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold; This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which 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: 46.93  E-value: 1.39e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 568966813 593 WTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd13702   50 WDGIIPALQAKKFDAIIASMSITPERKKQVDFTDPYYTNPLVFVA 94
PBP2_GlnP cd13619
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ...
561-642 1.98e-05

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


Pssm-ID: 270337 [Multi-domain]  Cd Length: 220  Bit Score: 46.54  E-value: 1.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 561 IDLLERLAEDLAFDFELYIVGdgkygalrdgrWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTR 640
Cdd:cd13619   27 VDLLNAIAKDQGFKVELKPMG-----------FDAAIQAVQSGQADGVIAGMSITDERKKTFDFSDPYYDSGLVIAVKKD 95

                 ..
gi 568966813 641 DT 642
Cdd:cd13619   96 NT 97
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
557-632 2.55e-05

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: 46.31  E-value: 2.55e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568966813 557 YGYCIDLLERLAEDLAFDFELyivgdgkygalRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTS 632
Cdd:cd13628   24 VGFDIELAKTIAKKLGLKLQI-----------QEYDFNGLIPALASGQADLALAGITPTPERKKVVDFSEPYYEAS 88
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
558-646 3.19e-05

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: 45.99  E-value: 3.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDgkygalrdgrWTGLVGDLLAGRAHMaVTSFSINSARSQVVDFTSPFFSTSLGIMv 637
Cdd:cd01007   26 GIAADYLKLIAKKLGLKFEYVPGDS----------WSELLEALKAGEIDL-LSSVSKTPEREKYLLFTKPYLSSPLVIV- 93

                 ....*....
gi 568966813 638 rTRDTASPI 646
Cdd:cd01007   94 -TRKDAPFI 101
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
558-645 8.74e-05

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 45.82  E-value: 8.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDgkygalrdgrWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLgIMV 637
Cdd:COG4623   44 GFEYELAKAFADYLGVKLEIIVPDN----------LDELLPALNAGEGDIAAAGLTITPERKKQVRFSPPYYSVSQ-VLV 112

                 ....*...
gi 568966813 638 RTRDTASP 645
Cdd:COG4623  113 YRKGSPRP 120
PBP2_HisJ_LAO_like cd01001
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ...
558-643 1.05e-04

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


Pssm-ID: 270222 [Multi-domain]  Cd Length: 228  Bit Score: 44.21  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVgdgkygalrdgRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd01001   26 GFDIDLANALCKRMKVKCEIVTQ-----------PWDGLIPALKAGKYDAIIASMSITDKRRQQIDFTDPYYRTPSRFVA 94

                 ....*.
gi 568966813 638 RtRDTA 643
Cdd:cd01001   95 R-KDSP 99
PBP2_PheC cd01069
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ...
558-630 1.68e-04

Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes cyclohexadienyl dehydratase PheC. These proteins catalyze the decarboxylation of prephenate to phenylpyruvate in the alternative phenylalanine biosynthesis pathway in some proteobacteria and archaea. The PheC proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Since they the PheC proteins are so similar to periplasmic binding proteins, (PBP), it is evolutionarily plausible that several pre-existing PBP proteins might have been recruited to perform the enzymatic function.


Pssm-ID: 270231 [Multi-domain]  Cd Length: 232  Bit Score: 43.87  E-value: 1.68e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGdgkygalrdgrWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFS 630
Cdd:cd01069   34 GYDIDMAEALAKSLGVKVEFVPTS-----------WPTLMDDLAADKFDIAMGGISITLERQRQAFFSAPYLR 95
PBP2_GltI_DEBP cd13688
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ...
558-639 2.22e-04

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: 43.40  E-value: 2.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAF-----DFELYIV---GDGKYGALRDGRWtglvgDLLAGRAhmavtsfSINSARSQVVDFTSPFF 629
Cdd:cd13688   32 GYSVDLCNAIADALKKklalpDLKVRYVpvtPQDRIPALTSGTI-----DLECGAT-------TNTLERRKLVDFSIPIF 99
                         90
                 ....*....|
gi 568966813 630 STSLGIMVRT 639
Cdd:cd13688  100 VAGTRLLVRK 109
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
558-644 2.60e-04

The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein; This group contains the second domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270425 [Multi-domain]  Cd Length: 221  Bit Score: 42.98  E-value: 2.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGDgkygalrdgrWTGLVGDLLAGRAHMAVTSFSiNSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd13707   26 GISADLLELISLRTGLRFEVVRASS----------PAEMIEALRSGEADMIAALTP-SPEREDFLLFTRPYLTSPFVLVT 94

                 ....*..
gi 568966813 638 RTRDTAS 644
Cdd:cd13707   95 RKDAAAP 101
PBP2_GluB cd13690
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ...
558-643 4.50e-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: 42.64  E-value: 4.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLafdfelyIVGDGK---YGALRDGRwtglVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLG 634
Cdd:cd13690   33 GFDVDIARAVARAI-------GGDEPKvefREVTSAER----EALLQNGTVDLVVATYSITPERRKQVDFAGPYYTAGQR 101

                 ....*....
gi 568966813 635 IMVRTRDTA 643
Cdd:cd13690  102 LLVRAGSKI 110
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
558-638 5.41e-04

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


Pssm-ID: 270225 [Multi-domain]  Cd Length: 230  Bit Score: 42.23  E-value: 5.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGdgkygalrdgrWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFtSPFFSTSLGIMV 637
Cdd:cd01004   26 GFDVDLAKAIAKRLGLKVEIVNVS-----------FDGLIPALQSGRYDIIMSGITDTPERAKQVDF-VDYMKDGLGVLV 93

                 .
gi 568966813 638 R 638
Cdd:cd01004   94 A 94
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
558-648 5.89e-04

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: 41.99  E-value: 5.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVgdgkygalrdgRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd13712   24 GFEVDVAKALAAKLGVKPEFVTT-----------EWSGILAGLQAGKYDVIINQVGITPERQKKFDFSQPYTYSGIQLIV 92
                         90
                 ....*....|.
gi 568966813 638 RTRDTASPIGA 648
Cdd:cd13712   93 RKNDTRTFKSL 103
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
562-632 6.33e-04

The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes the solute binding domain YfhD_N. These domains are found in the YfhD proteins that are predicted to function as lytic transglycosylases that cleave the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamin in peptidoglycan, while the YfhD_N domain might act as an auxiliary or regulatory subunit. In addition to periplasmic solute binding domain, they have an SLT domain, typically found in soluble lytic transglycosylases, and a C-terminal low complexity domain. The YfhD proteins might have been recruited to create localized cell wall openings required for transport of large substrates such as DNA. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270230 [Multi-domain]  Cd Length: 223  Bit Score: 41.81  E-value: 6.33e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568966813 562 DLLERLAEDLafDFELYIVgdgKYGALRDgrwtgLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTS 632
Cdd:cd01009   27 ELAKAFADYL--GVELEIV---PADNLEE-----LLEALEEGKGDLAAAGLTITPERKKKVDFSFPYYYVV 87
GluR_Plant cd13686
Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily ...
558-641 1.29e-03

Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily contains the glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270404 [Multi-domain]  Cd Length: 232  Bit Score: 40.97  E-value: 1.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDL----LERLAEDLAFDFELYiVGDGKYGAL----RDGRWTGLVGDllagrahmavtsFSINSARSQVVDFTSPFF 629
Cdd:cd13686   32 GFCIDVfeaaVKRLPYAVPYEFIPF-NDAGSYDDLvyqvYLKKFDAAVGD------------ITITANRSLYVDFTLPYT 98
                         90
                 ....*....|..
gi 568966813 630 STSLGIMVRTRD 641
Cdd:cd13686   99 ESGLVMVVPVKD 110
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
558-642 1.88e-03

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


Pssm-ID: 270344 [Multi-domain]  Cd Length: 219  Bit Score: 40.38  E-value: 1.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELYIVGdgkygalrdgrWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd13626   24 GFDVEVGREIAKRLGLKVEFKATE-----------WDGLLPGLNSGKFDVIANQVTITPEREEKYLFSDPYLVSGAQIIV 92

                 ....*
gi 568966813 638 RTRDT 642
Cdd:cd13626   93 KKDNT 97
PBP2_GltS cd13620
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ...
558-641 2.11e-03

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


Pssm-ID: 270338 [Multi-domain]  Cd Length: 227  Bit Score: 40.40  E-value: 2.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568966813 558 GYCIDLLERLAEDLAFDFELyivgdgkygalRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMV 637
Cdd:cd13620   31 GADIDIAKAIAKELGVKLEI-----------KSMDFDNLLASLQSGKVDMAISGMTPTPERKKSVDFSDVYYEAKQSLLV 99

                 ....
gi 568966813 638 RTRD 641
Cdd:cd13620  100 KKAD 103
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
600-638 3.04e-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: 39.98  E-value: 3.04e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 568966813 600 LLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVR 638
Cdd:cd01000   66 LQSGKVDLIIATMTITPERAKEVDFSVPYYADGQGLLVR 104
 
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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