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Conserved domains on  [gi|1825730066|ref|NP_001077089|]
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glutamate receptor 2 isoform 3 [Homo sapiens]

Protein Classification

glutamate receptor( domain architecture ID 10294620)

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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Periplasmic_Binding_Protein_type1 super family cl10011
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
1-351 0e+00

Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.


The actual alignment was detected with superfamily member cd06389:

Pssm-ID: 471960 [Multi-domain]  Cd Length: 372  Bit Score: 740.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   1 MVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQ 80
Cdd:cd06389    21 MVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQ 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  81 MRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDEMYRSLFQDLELKKERRV 160
Cdd:cd06389   101 MRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLELKKERRV 180
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 161 ILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPG 240
Cdd:cd06389   181 ILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPG 260
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 241 AHTTTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGK 320
Cdd:cd06389   261 AHTTTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGK 340
                         330       340       350
                  ....*....|....*....|....*....|.
gi 1825730066 321 RINYTINIMELKTNGPRKIGYWSEVDKMVVT 351
Cdd:cd06389   341 RINYTINIMELKTNGPRKIGYWSEVDKMVVT 371
PBP2_iGluR_AMPA cd13715
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
366-747 1.75e-179

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: 516.14  E-value: 1.75e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEM--LEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVY 443
Cdd:cd13715     1 NRTYIVTTILEEPYVMMKKNHEGepLEGNERYEGYCVDLADEIAKHLGIKYELRIVKDGKYGARDADTGIWNGMVGELVR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 444 GKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspy 523
Cdd:cd13715    81 GEADIAIAPLTITLVRERVIDFSKPFMSLGISIMIKKPV----------------------------------------- 119
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 524 ewhteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltverm 603
Cdd:cd13715       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 604 vsPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMN 683
Cdd:cd13715   120 --PIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYDKMWEYMNSAEPSVFVRTTDEGIARVRKSKGKYAYLLESTMN 197
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1825730066 684 EYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYDKGEC 747
Cdd:cd13715   198 EYINQRKPCDTMKVGGNLDSKGYGIATPKGSPLRNPLNLAVLKLKENGELDKLKNKWWYDKGEC 261
 
Name Accession Description Interval E-value
PBP1_iGluR_AMPA_GluR2 cd06389
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit ...
1-351 0e+00

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380612 [Multi-domain]  Cd Length: 372  Bit Score: 740.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   1 MVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQ 80
Cdd:cd06389    21 MVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQ 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  81 MRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDEMYRSLFQDLELKKERRV 160
Cdd:cd06389   101 MRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLELKKERRV 180
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 161 ILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPG 240
Cdd:cd06389   181 ILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPG 260
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 241 AHTTTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGK 320
Cdd:cd06389   261 AHTTTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGK 340
                         330       340       350
                  ....*....|....*....|....*....|.
gi 1825730066 321 RINYTINIMELKTNGPRKIGYWSEVDKMVVT 351
Cdd:cd06389   341 RINYTINIMELKTNGPRKIGYWSEVDKMVVT 371
PBP2_iGluR_AMPA cd13715
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
366-747 1.75e-179

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: 516.14  E-value: 1.75e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEM--LEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVY 443
Cdd:cd13715     1 NRTYIVTTILEEPYVMMKKNHEGepLEGNERYEGYCVDLADEIAKHLGIKYELRIVKDGKYGARDADTGIWNGMVGELVR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 444 GKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspy 523
Cdd:cd13715    81 GEADIAIAPLTITLVRERVIDFSKPFMSLGISIMIKKPV----------------------------------------- 119
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 524 ewhteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltverm 603
Cdd:cd13715       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 604 vsPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMN 683
Cdd:cd13715   120 --PIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYDKMWEYMNSAEPSVFVRTTDEGIARVRKSKGKYAYLLESTMN 197
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1825730066 684 EYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYDKGEC 747
Cdd:cd13715   198 EYINQRKPCDTMKVGGNLDSKGYGIATPKGSPLRNPLNLAVLKLKENGELDKLKNKWWYDKGEC 261
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
498-776 2.44e-121

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: 366.63  E-value: 2.44e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 498 EIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEefedgretqSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGG 577
Cdd:pfam00060   3 EVWLGILVAFLIVGVVLFLLERFSPYEWRGP---------LETEENRFTLSNSLWFSFGALVQQGHRENPRSLSGRIVVG 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 578 VWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFV 657
Cdd:pfam00060  74 VWWFFALILLSSYTANLAAFLTVERMQSPIQSLEDLAKQTKIEYGTVRGSSTYLFFRNSKIPSYKRMWEYMESAKPSVKD 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 658 RTTAEGVARVRKSKGKYAYLLEstmNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLK 737
Cdd:pfam00060 154 ALNEEGVALVRNGIYAYALLSE---NYYLFQRECCDTMIVGETFATGGYGIATPKGSPLTDLLSLAILELEESGELDKLE 230
                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1825730066 738 NKWWYDKGECGAKDSGSKEktSALSLSNVAGVFYILVGG 776
Cdd:pfam00060 231 KKWWPKSGECDSKSSASSS--SQLGLKSFAGLFLILGIG 267
PBPe smart00079
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ...
606-743 6.34e-55

Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb


Pssm-ID: 197504 [Multi-domain]  Cd Length: 133  Bit Score: 185.57  E-value: 6.34e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSaePSVFVRTTAEGVARVRKSKgkYAYLLESTMNEY 685
Cdd:smart00079   1 PITSVEDLAKQTKIEYGTQDGSSTLAFFKRSGNPEYSRMWPYMKS--PEVFVKSYAEGVQRVRVSN--YAFIMESPYLDY 76
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1825730066  686 IEQRkPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYD 743
Cdd:smart00079  77 ELSR-NCDLMTVGEEFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELEKLRNKWWKD 133
ANF_receptor pfam01094
Receptor family ligand binding region; This family includes extracellular ligand binding ...
9-334 2.40e-49

Receptor family ligand binding region; This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.


Pssm-ID: 460062 [Multi-domain]  Cd Length: 347  Bit Score: 177.96  E-value: 2.40e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   9 FRLTPHIdnLEVANSFAVTNAFCSQFSRG-VYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT-----HPFVIQMR 82
Cdd:pfam01094  23 TKLEYII--LDTCCDPSLALAAALDLLKGeVVAIIGPSCSSVASAVASLANEWKVPLISYGSTSPALsdlnrYPTFLRTT 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  83 PD---LKGALLSLIEYYQWDKFAYLY-DSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKkDEMYRSLFQDLElKKER 158
Cdd:pfam01094 101 PSdtsQADAIVDILKHFGWKRVALIYsDDDYGESGLQALEDALRERGIRVAYKAVIPPAQDD-DEIARKLLKEVK-SRAR 178
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 159 RVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGA--NVSGFQIVDYDDSLVSKFIERWSTLEEK 236
Cdd:pfam01094 179 VIVVCCSSETARRLLKAARELGMMGEGYVWIATDGLTTSLVILNPSTLEAagGVLGFRLHPPDSPEFSEFFWEKLSDEKE 258
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 237 EYPGAHTTTIKYtSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGdclanpavPWGQGVEIERALKQVQVEGLSGNIKFD 316
Cdd:pfam01094 259 LYENLGGLPVSY-GALAYDAVYLLAHALHNLLRDDKPGRACGALG--------PWNGGQKLLRYLKNVNFTGLTGNVQFD 329
                         330
                  ....*....|....*...
gi 1825730066 317 QNGKRINYTINIMELKTN 334
Cdd:pfam01094 330 ENGDRINPDYDILNLNGS 347
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
387-480 3.54e-14

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


Pssm-ID: 440596 [Multi-domain]  Cd Length: 223  Bit Score: 72.71  E-value: 3.54e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFS 466
Cdd:COG0834    13 SFRDEDGKLVGFDVDLARAIAKRLGLKVEFVPVP-------------WDRLIPALQSGKVDLIIAGMTITPEREKQVDFS 79
                          90
                  ....*....|....
gi 1825730066 467 KPFMSLGISIMIKK 480
Cdd:COG0834    80 DPYYTSGQVLLVRK 93
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
397-501 1.51e-07

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 53.57  E-value: 1.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTivgdgkygardaDTKiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISI 476
Cdd:PRK11260   65 GFEVEFAEALAKHLGVKASLK------------PTK-WDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQA 131
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1825730066 477 MIKkpqKSKPGVFSFLDPLA-----------YEIWM 501
Cdd:PRK11260  132 LVK---KGNEGTIKTAADLKgkkvgvglgtnYEQWL 164
LivK COG0683
ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid ...
37-335 2.86e-05

ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid transport and metabolism];


Pssm-ID: 440447 [Multi-domain]  Cd Length: 314  Bit Score: 46.85  E-value: 2.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  37 GVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTD-----GTHPFVIQMRPDLKGALLSLIEY----YQWDKFAYLYDS 107
Cdd:COG0683    71 KVDAIVGPLSSGVALAVAPVAEEAGVPLISPSATAPaltgpECSPYVFRTAPSDAQQAEALADYlakkLGAKKVALLYDD 150
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 108 DR-GLSTLQAVLDSAAEKKWQVTAINVgnINNDKKDemYRSLFQDLELKKerrvildcerdkvndiVDQVITIGkhvkgy 186
Cdd:COG0683   151 YAyGQGLAAAFKAALKAAGGEVVGEEY--YPPGTTD--FSAQLTKIKAAG----------------PDAVFLAG------ 204
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 187 hyiianlgfTDGDLLKIqfgganVSGFQIVDYDDSLVSKFIERWstleEKEYpGAHTTTIkytSALTYDAVQVMTEAFRN 266
Cdd:COG0683   205 ---------YGGDAALF------IKQAREAGLKGPLNKAFVKAY----KAKY-GREPSSY---AAAGYDAALLLAEAIEK 261
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1825730066 267 lrkqrieisrrgnAGDclANPAvpwgqgvEIERALKQVQVEGLSGNIKFDQNGKRINyTINIMELKTNG 335
Cdd:COG0683   262 -------------AGS--TDRE-------AVRDALEGLKFDGVTGPITFDPDGQGVQ-PVYIVQVKADG 307
 
Name Accession Description Interval E-value
PBP1_iGluR_AMPA_GluR2 cd06389
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit ...
1-351 0e+00

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380612 [Multi-domain]  Cd Length: 372  Bit Score: 740.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   1 MVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQ 80
Cdd:cd06389    21 MVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQ 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  81 MRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDEMYRSLFQDLELKKERRV 160
Cdd:cd06389   101 MRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLELKKERRV 180
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 161 ILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPG 240
Cdd:cd06389   181 ILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPG 260
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 241 AHTTTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGK 320
Cdd:cd06389   261 AHTTTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGK 340
                         330       340       350
                  ....*....|....*....|....*....|.
gi 1825730066 321 RINYTINIMELKTNGPRKIGYWSEVDKMVVT 351
Cdd:cd06389   341 RINYTINIMELKTNGPRKIGYWSEVDKMVVT 371
PBP2_iGluR_AMPA cd13715
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
366-747 1.75e-179

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: 516.14  E-value: 1.75e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEM--LEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVY 443
Cdd:cd13715     1 NRTYIVTTILEEPYVMMKKNHEGepLEGNERYEGYCVDLADEIAKHLGIKYELRIVKDGKYGARDADTGIWNGMVGELVR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 444 GKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspy 523
Cdd:cd13715    81 GEADIAIAPLTITLVRERVIDFSKPFMSLGISIMIKKPV----------------------------------------- 119
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 524 ewhteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltverm 603
Cdd:cd13715       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 604 vsPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMN 683
Cdd:cd13715   120 --PIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYDKMWEYMNSAEPSVFVRTTDEGIARVRKSKGKYAYLLESTMN 197
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1825730066 684 EYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYDKGEC 747
Cdd:cd13715   198 EYINQRKPCDTMKVGGNLDSKGYGIATPKGSPLRNPLNLAVLKLKENGELDKLKNKWWYDKGEC 261
PBP2_iGluR_AMPA_GluR1 cd13729
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
366-747 5.94e-177

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: 509.57  E-value: 5.94e-177
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGK 445
Cdd:cd13729     1 NRTYIVTTILESPYVMLKKNHEQFEGNDRYEGYCVELAAEIAKHVGYSYKLEIVSDGKYGARDPETKMWNGMVGELVYGK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13729    81 ADVAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPT------------------------------------------- 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvS 605
Cdd:cd13729   118 -------------------------------------------------------------------------------S 118
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEY 685
Cdd:cd13729   119 PIESAEDLAKQTEIAYGTLDAGSTKEFFRRSKIAVFEKMWSYMKSADPSVFVKTTDEGVMRVRKSKGKYAYLLESTMNEY 198
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1825730066 686 IEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYDKGEC 747
Cdd:cd13729   199 IEQRKPCDTMKVGGNLDSKGYGIATPKGSALRNPVNLAVLKLNEQGLLDKLKNKWWYDKGEC 260
PBP1_iGluR_AMPA_GluR1 cd06390
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit ...
10-351 1.88e-173

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380613 [Multi-domain]  Cd Length: 367  Bit Score: 504.86  E-value: 1.88e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  10 RLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGAL 89
Cdd:cd06390    29 KLLPQIDIVNISDSFEMTYTFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRPELQDAL 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  90 LSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINndkkDEMYRSLFQDLELKKERRVILDCERDKV 169
Cdd:cd06390   109 ISVIEHYKWQKFVYIYDADRGLSVLQKVLDTAAEKNWQVTAVNILTTT----EEGYRMLFQDLDKKKERLVVVDCESERL 184
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 170 NDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTTTIKYT 249
Cdd:cd06390   185 NAILGQIVKLEKNGIGYHYILANLGFMDIDLTKFKESGANVTGFQLVNYTDTIPARIMQQWKNSDSRDLPRVDWKRPKYT 264
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 250 SALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIM 329
Cdd:cd06390   265 SALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVI 344
                         330       340
                  ....*....|....*....|..
gi 1825730066 330 ELKTNGPRKIGYWSEVDKMVVT 351
Cdd:cd06390   345 EMKHDGIRKIGYWNEDDKLVPA 366
PBP1_iGluR_AMPA_GluR3 cd06387
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit ...
9-349 1.35e-171

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380610 [Multi-domain]  Cd Length: 375  Bit Score: 500.32  E-value: 1.35e-171
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   9 FRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGA 88
Cdd:cd06387    35 FHLNYHVDHLDSSNSFSVTNAFCSQFSRGVYAIFGFYDQMSMNTLTSFCGALHTSFITPSFPTDADVQFVIQMRPALKGA 114
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  89 LLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNInndKKDEMYRSLFQDLELKKERRVILDCERDK 168
Cdd:cd06387   115 ILSLLAHYKWEKFVYLYDTERGFSILQAIMEAAVQNNWQVTARSVGNI---KDVQEFRRIIEEMDRRQEKRYLIDCEVER 191
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 169 VNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTTTIKY 248
Cdd:cd06387   192 INTILEQVVILGKHSRGYHYMLANLGFTDILLERVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKNAPLKY 271
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 249 TSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINI 328
Cdd:cd06387   272 TSALTHDAILVIAEAFRYLRRQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDV 351
                         330       340
                  ....*....|....*....|.
gi 1825730066 329 MELKTNGPRKIGYWSEVDKMV 349
Cdd:cd06387   352 YEMKPSGSRKAGYWNEYERFV 372
PBP2_iGluR_AMPA_GluR2 cd13726
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
366-747 3.07e-171

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: 494.93  E-value: 3.07e-171
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGK 445
Cdd:cd13726     1 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13726    81 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGT------------------------------------------- 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvs 605
Cdd:cd13726       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEY 685
Cdd:cd13726   118 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEY 197
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1825730066 686 IEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYDKGEC 747
Cdd:cd13726   198 IEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 259
PBP2_iGluR_AMPA_GluR4 cd13727
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
366-747 2.07e-168

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: 487.62  E-value: 2.07e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGK 445
Cdd:cd13727     1 NRTVVVTTIMESPYVMYKKNHEMFEGNDKFEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDPETKIWNGMVGELVYGK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13727    81 AEIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQ------------------------------------------- 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvs 605
Cdd:cd13727       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEY 685
Cdd:cd13727   118 PIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMKSAEPSVFTRTTAEGVARVRKSKGKFAFLLESTMNEY 197
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1825730066 686 IEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYDKGEC 747
Cdd:cd13727   198 IEQRKPCDTMKVGGNLDSKGYGVATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 259
PBP1_iGluR_AMPA_GluR4 cd06388
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit ...
5-350 7.82e-165

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380611 [Multi-domain]  Cd Length: 373  Bit Score: 482.99  E-value: 7.82e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   5 STSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPD 84
Cdd:cd06388    31 SEAPFNLVPHVDNIETANSFAVTNAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGESQFVLQLRPS 110
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  85 LKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINndkkDEMYRSLFQDLELKKERRVILDC 164
Cdd:cd06388   111 LRGALLSLLDHYEWNRFVFLYDTDRGYSILQAIMEKAGQNGWQVSAICVENFN----DASYRRLLEDLDRRQEKKFVIDC 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 165 ERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTT 244
Cdd:cd06388   187 EIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISLERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSETP 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 245 TiKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINY 324
Cdd:cd06388   267 P-KYTSALTYDGVLVMAETFRNLRRQKIDISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNVQFDHYGRRVNY 345
                         330       340
                  ....*....|....*....|....*.
gi 1825730066 325 TINIMELKTNGPRKIGYWSEVDKMVV 350
Cdd:cd06388   346 TMDVFELKSTGPRKVGYWNDMDKLVL 371
PBP1_iGluR_AMPA cd06380
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA receptor; ...
1-350 3.15e-151

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current.


Pssm-ID: 380603 [Multi-domain]  Cd Length: 390  Bit Score: 448.65  E-value: 3.15e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   1 MVQFSTSEFRLTPHIDNLEvANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT---HPF 77
Cdd:cd06380    27 NNNNRFRLFPLTERIDITN-ADSFSVSRAICSQLSRGVFAIFGSSDASSLNTIQSYSDTFHMPYITPSFPKNEPsdsNPF 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  78 VIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEK-KWQVTAINVGNINNDkkdEMYRSLFQDLELKK 156
Cdd:cd06380   106 ELSLRPSYIEAIVDLIRHYGWKKVVYLYDSDEGLLRLQQLYDYLKEKsNISVRVRRVRNVNDA---YEFLRTLRELDREK 182
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 157 E-RRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEE 235
Cdd:cd06380   183 EdKRIVLDLSSERYQKILEQIVEDGMNRRNYHYLLANLDFLDLDLERFLHGGVNITGFQLVDTNNKTVKDFLQRWKKLDP 262
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 236 KEYPGAHTTTIKYTSALTYDAVQVMTEAFRNLRKQRIEI----------SRRGNAGDCLANPAVPWGQGVEIERALKQVQ 305
Cdd:cd06380   263 REYPGAGTDTIPYEAALAVDAVLVIAEAFQSLLRQNDDIfrftfhgelyNNGSKGIDCDPNPPLPWEHGKAIMKALKKVR 342
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*.
gi 1825730066 306 VEGLSGNIKFDQNGKRINYTINIMELK-TNGPRKIGYWSEVDKMVV 350
Cdd:cd06380   343 FEGLTGNVQFDDFGQRKNYTLDVIELTsNRGLRKIGTWSEGDGFLL 388
PBP2_iGluR_AMPA_GluR3 cd13728
The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic ...
366-747 1.90e-149

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: 439.13  E-value: 1.90e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGK 445
Cdd:cd13728     1 NRTIVVTTILESPYVMYKKNHEQLEGNERYEGYCVDLAYEIAKHVRIKYKLSIVGDGKYGARDPETKIWNGMVGELVYGR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13728    81 ADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQ------------------------------------------- 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvs 605
Cdd:cd13728       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEY 685
Cdd:cd13728   118 PIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWSYMKSAEPSVFTKTTADGVARVRKSKGKFAFLLESTMNEY 197
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1825730066 686 IEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYDKGEC 747
Cdd:cd13728   198 IEQRKPCDTMKVGGNLDSKGYGVATPKGSALGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 259
PBP2_iGluR_Kainate_GluR7 cd13723
GluR7 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
366-741 4.60e-146

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: 434.89  E-value: 4.60e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDaDTKIWNGMVGELVYGK 445
Cdd:cd13723     1 NRSLIVTTVLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQD-DKGQWNGMVKELIDHK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEW 525
Cdd:cd13723    80 ADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSCVLFVIARFSPYEW 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 H-TEEFEDGRETQSsestNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMV 604
Cdd:cd13723   160 YdAHPCNPGSEVVE----NNFTLLNSFWFGMGSLMQQGSELMPKALSTRIIGGIWWFFTLIIISSYTANLAAFLTVERME 235
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 605 SPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMrSAEPSVFVRTTAEGVARVRKSkgKYAYLLESTMNE 684
Cdd:cd13723   236 SPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFM-SSKPSALVKNNEEGIQRALTA--DYALLMESTTIE 312
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1825730066 685 YIEQRKpCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13723   313 YVTQRN-CNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWW 368
PBP2_iGluR_Kainate cd13714
Kainate receptor of the type 2 periplasmic-binding fold superfamily; This group contains ...
366-741 3.97e-124

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: 373.41  E-value: 3.97e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGK 445
Cdd:cd13714     1 NKTLIVTTILEEPYVMLKESAKPLTGNDRFEGFCIDLLKELAKILGFNYTIRLVPDGKYGSYDPETGEWNGMVRELIDGR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13714    81 ADLAVADLTITYERESVVDFTKPFMNLGISILYRKPT------------------------------------------- 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvs 605
Cdd:cd13714       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRksKGKYAYLLESTMNEY 685
Cdd:cd13714   118 PIESADDLAKQTKIKYGTLRGGSTMTFFRDSNISTYQKMWNFMMSAKPSVFVKSNEEGVARVL--KGKYAFLMESTSIEY 195
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1825730066 686 IEQRkPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13714   196 VTQR-NCNLTQIGGLLDSKGYGIATPKGSPYRDKLSLAILKLQEKGKLEMLKNKWW 250
Lig_chan pfam00060
Ligand-gated ion channel; This family includes the four transmembrane regions of the ...
498-776 2.44e-121

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: 366.63  E-value: 2.44e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 498 EIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEefedgretqSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGG 577
Cdd:pfam00060   3 EVWLGILVAFLIVGVVLFLLERFSPYEWRGP---------LETEENRFTLSNSLWFSFGALVQQGHRENPRSLSGRIVVG 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 578 VWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFV 657
Cdd:pfam00060  74 VWWFFALILLSSYTANLAAFLTVERMQSPIQSLEDLAKQTKIEYGTVRGSSTYLFFRNSKIPSYKRMWEYMESAKPSVKD 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 658 RTTAEGVARVRKSKGKYAYLLEstmNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLK 737
Cdd:pfam00060 154 ALNEEGVALVRNGIYAYALLSE---NYYLFQRECCDTMIVGETFATGGYGIATPKGSPLTDLLSLAILELEESGELDKLE 230
                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1825730066 738 NKWWYDKGECGAKDSGSKEktSALSLSNVAGVFYILVGG 776
Cdd:pfam00060 231 KKWWPKSGECDSKSSASSS--SQLGLKSFAGLFLILGIG 267
PBP2_iGluR_kainate_KA1 cd13724
The ligand-binding domain of the kainate subtype KA1 of ionotropic glutamate receptors, a ...
366-741 1.27e-113

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: 349.31  E-value: 1.27e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADtKIWNGMVGELVYGK 445
Cdd:cd13724     1 NTTLVVTTILENPYLMLKGNHQEMEGNDRYEGFCVDMLKELAEILRFNYKIRLVGDGVYGVPEAN-GTWTGMVGELIARK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEW 525
Cdd:cd13724    80 ADLAVAGLTITAEREKVIDFSKPFMTLGISILYRVHMGRKPGYFSFLDPFSPGVWLFMLLAYLAVSCVLFLVARLTPYEW 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 HTEefEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPrslsgrivggvwwfftliiissytanlaafltvermvs 605
Cdd:cd13724   160 YSP--HPCAQGRCNLLVNQYSLGNSLWFPVGGFMQQGSTIAP-------------------------------------- 199
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSkgKYAYLLESTMNEY 685
Cdd:cd13724   200 PIESVDDLADQTAIEYGTIHGGSSMTFFQNSRYQTYQRMWNYMYSKQPSVFVKSTEEGIARVLNS--NYAFLLESTMNEY 277
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1825730066 686 IEQRKpCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13724   278 YRQRN-CNLTQIGGLLDTKGYGIGMPVGSVFRDEFDLAILQLQENNRLEILKRKWW 332
PBP2_iGluR_non_NMDA_like cd13685
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ...
366-742 1.31e-110

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: 338.39  E-value: 1.31e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHemLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDaDTKIWNGMVGELVYGK 445
Cdd:cd13685     1 NKTLRVTTILEPPFVMKKRDS--LSGNPRFEGYCIDLLEELAKILGFDYEIYLVPDGKYGSRD-ENGNWNGMIGELVRGE 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPqkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13685    78 ADIAVAPLTITAEREEVVDFTKPFMDTGISILMRKP-------------------------------------------- 113
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvS 605
Cdd:cd13685   114 -------------------------------------------------------------------------------T 114
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKM--WTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMN 683
Cdd:cd13685   115 PIESLEDLAKQSKIEYGTLKGSSTFTFFKNSKNPEYRRYeyTKIMSAMSPSVLVASAAEGVQRVRESNGGYAFIGEATSI 194
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1825730066 684 EYIEQRkPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWY 742
Cdd:cd13685   195 DYEVLR-NCDLTKVGEVFSEKGYGIAVQQGSPLRDELSLAILELQESGELEKLKEKWWN 252
PBP2_iGluR_putative cd13717
The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 ...
371-741 1.85e-88

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: 284.58  E-value: 1.85e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 371 VTTILESPYVMMKKNhemleGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKiWNGMVGELVYGKADIAI 450
Cdd:cd13717     6 IGTVESPPFVYRDRD-----GSPIWEGYCIDLIEEISEILNFDYEIVEPEDGKFGTMDENGE-WNGLIGDLVRKEADIAL 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 451 APLTITLVREEVIDFSKPFMSL-GISIMIKKPqKSKPGVFSFLDPLAYEIWmcivfayigvsvvlflvsrfspyewhtee 529
Cdd:cd13717    80 AALSVMAEREEVVDFTVPYYDLvGITILMKKP-ERPTSLFKFLTVLELEVW----------------------------- 129
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 530 fedgretqssestNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIES 609
Cdd:cd13717   130 -------------REFTLKESLWFCLTSLTPQGGGEAPKNLSGRLLVATWWLFVFIIIASYTANLAAFLTVSRLQTPVES 196
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 610 AEDLSKQTEIAYGTLDSGSTKEFFRR--------------------------SKIAVFD--------KMWTYMRSAepsV 655
Cdd:cd13717   197 LDDLARQYKIQYTVVKNSSTHTYFERmknaedtlyemwkdmslndslspverAKLAVWDypvsekytKIYQAMQEA---G 273
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 656 FVRTTAEGVARVRKS-KGKYAYLLESTMNEYiEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLD 734
Cdd:cd13717   274 LVANAEEGVKRVREStSAGFAFIGDATDIKY-EILTNCDLQEVGEEFSRKPYAIAVQQGSPLKDELNYAILELQNDRFLE 352

                  ....*..
gi 1825730066 735 KLKNKWW 741
Cdd:cd13717   353 KLKAKWW 359
PBP2_iGluR_ligand_binding cd00998
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ...
367-741 1.20e-85

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: 272.71  E-value: 1.20e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 367 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDadTKIWNGMVGELVYGKA 446
Cdd:cd00998     1 KTLKVVVPLEPPFVMFVTGSNAVTGNGRFEGYCIDLLKELSQSLGFTYEYYLVPDGKFGAPV--NGSWNGMVGEVVRGEA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 447 DIAIAPLTITLVREEVIDFSKPFMSLGISIMIkkpqkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyewh 526
Cdd:cd00998    79 DLAVGPITITSERSVVIDFTQPFMTSGIGIMI------------------------------------------------ 110
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 527 teefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvsP 606
Cdd:cd00998   111 -------------------------------------------------------------------------------P 111
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 607 IESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRsaEPSVFVRTTAEGVARVRKSKGkYAYLLESTMNEYI 686
Cdd:cd00998   112 IRSIDDLKRQTDIEFGTVENSFTETFLRSSGIYPFYKTWMYSE--ARVVFVNNIAEGIERVRKGKV-YAFIWDRPYLEYY 188
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1825730066 687 EQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd00998   189 ARQDPCKLIKTGGGFGSIGYGFALPKNSPLTNDLSTAILKLVESGVLQKLKNKWL 243
PBP2_iGluR_Kainate_GluR6 cd13721
GluR6 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
366-741 5.29e-79

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: 255.33  E-value: 5.29e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGK 445
Cdd:cd13721     1 NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPqkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13721    81 ADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKG-------------------------------------------- 116
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvS 605
Cdd:cd13721   117 -------------------------------------------------------------------------------T 117
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSkgKYAYLLESTMNEY 685
Cdd:cd13721   118 PIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTS--DYAFLMESTTIEF 195
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1825730066 686 IEQRKpCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13721   196 VTQRN-CNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWW 250
PBP1_iGluR_N_LIVBP-like cd06351
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, ...
9-349 1.68e-73

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs); N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors characterized by their response to glutamate agonists: N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. On the other hand, non-NMDA receptors have faster kinetics, are weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute to several forms of synaptic plasticity and are suggested to play an important role in the development of synaptic pathways.


Pssm-ID: 380574  Cd Length: 348  Bit Score: 244.18  E-value: 1.68e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   9 FRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT--------HPFVIQ 80
Cdd:cd06351    34 LSVQYDSIEANKSNAFVLLEAICNKYATGTPALILDTTKSSINSLTSALGAPHISASYGQQGDLRQwrdldeakQKYLLQ 113
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  81 MRPD--LKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINN----DKKDEMYRSLFQDLEL 154
Cdd:cd06351   114 VRPPeaLRSIVLHLNITNAWIKFVDSYDMEHYKSLLQNIQTRAVQNNVIVAIAKVGKREReeqlDINNFFILGTLQSIRM 193
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 155 KKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLE 234
Cdd:cd06351   194 VLEVRPAYFERNFAWHAITQNEVEISSQSDNAHIMFMNPMAYDILLETVYRDRLGLTRTTYNLNENPMVQQFIQRWVRLD 273
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 235 EKEYPGAHTTTIKYTSALTYDAVQVMTEAFRNlrkqrieisrrgnagdclanpavpwgqgveieralkqvqveglSGNIK 314
Cdd:cd06351   274 EREFPEAKNAELQLSSAFYFDLALRSALAFKE-------------------------------------------TGYGT 310
                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1825730066 315 FDQNGKRINYTINIMELKTN-GPRKIGYWSEVDKMV 349
Cdd:cd06351   311 FDLQSTQPFNGHSFMKFEMDiNVRKIRGWSEYESVN 346
PBP2_iGluR_Kainate_GluR5 cd13722
GluR5 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group ...
366-741 9.81e-70

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: 230.71  E-value: 9.81e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDaDTKIWNGMVGELVYGK 445
Cdd:cd13722     1 NRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQN-DKGEWNGMVKELIDHR 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPqkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13722    80 ADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKG-------------------------------------------- 115
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvS 605
Cdd:cd13722   116 -------------------------------------------------------------------------------T 116
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSkgKYAYLLESTMNEY 685
Cdd:cd13722   117 PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQTALVKNSDEGIQRVLTT--DYALLMESTSIEY 194
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1825730066 686 IEQRKpCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13722   195 VTQRN-CNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWW 249
PBP2_iGluR_kainate_KA2 cd13725
The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a ...
366-741 5.10e-69

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: 228.44  E-value: 5.10e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 366 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKiWNGMVGELVYGK 445
Cdd:cd13725     1 NKTLVVTTILENPYVMRRPNFQALSGNERFEGFCVDMLRELAELLRFRYRLRLVEDGLYGAPEPNGS-WTGMVGELINRK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 446 ADIAIAPLTITLVREEVIDFSKPFMSLGISIMIkkpqkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyew 525
Cdd:cd13725    80 ADLAVAAFTITAEREKVIDFSKPFMTLGISILY----------------------------------------------- 112
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 526 hteefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltveRMVS 605
Cdd:cd13725   113 ----------------------------------------------------------------------------RVHM 116
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSkgKYAYLLESTMNEY 685
Cdd:cd13725   117 PVESADDLADQTNIEYGTIHAGSTMTFFQNSRYQTYQRMWNYMQSKQPSVFVKSTEEGIARVLNS--RYAFLLESTMNEY 194
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1825730066 686 iEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13725   195 -HRRLNCNLTQIGGLLDTKGYGIGMPLGSPFRDEITLAILQLQENNRLEILKRKWW 249
PBP1_iGluR_non_NMDA-like cd06368
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA ...
9-344 7.14e-60

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-D-aspartate) subtypes of ionotropic glutamate receptors; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-D-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-D-aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. Non-NMDA receptors have faster kinetics, are most often only weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute several forms of synaptic plasticity and are thought to play an important role in the development of synaptic pathways. Non-NMDA receptors include alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate (AMPA) and kainate receptors.


Pssm-ID: 380591 [Multi-domain]  Cd Length: 339  Bit Score: 206.83  E-value: 7.14e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   9 FRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT-HPFVIQMRP--DL 85
Cdd:cd06368    35 FRITYSIEAIDSNSHFDATDKACDLLEKGVVAIVGPSSSDSNNALQSICDALDVPHITVHDDPRLSkSQYSLSLYPrnQL 114
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  86 KGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGninNDKKDEMYRSLFQDLELKKERRVILDCE 165
Cdd:cd06368   115 SQAVSDLLKYWRWKRFVLVYDDDDRLRRLQELLEAARFSKRFVSVRKVD---LDYKTLDETPLLKRKDCSLFSRILIDLS 191
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 166 RDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKI-QFGGANVSGFQIVDyDDSLVSKFIERWSTLEEKEYPGAHTT 244
Cdd:cd06368   192 PEKAYTFLLQALEMGMTIELYHYFLTTMDLSLLLDLELfRYNHANITGFQLVD-NNSMYKEDINRLAFNWSRFRQHIKIE 270
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 245 ----TIKYTSALTYDAVQVMTEAFRNlrkqrieisrrgnagdclanpavpwgqgveieralkqvqveglSGNIKFDQNGK 320
Cdd:cd06368   271 snlrGPPYEAALMFDAVLLLADAFRR-------------------------------------------TGDLRFNGTGL 307
                         330       340
                  ....*....|....*....|....
gi 1825730066 321 RINYTINIMELKTNGPRKIGYWSE 344
Cdd:cd06368   308 RSNFTLRILELGYGGLRKIGFWDS 331
Lig_chan-Glu_bd pfam10613
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
367-480 4.78e-58

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: 193.50  E-value: 4.78e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 367 KTVVVTTILESPYVMMKKNhemLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKA 446
Cdd:pfam10613   1 KTLIVTTILEPPFVMLKEN---LEGNDRYEGFCIDLLKELAEILGFKYEIRLVPDGKYGSLDPTTGEWNGMIGELIDGKA 77
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1825730066 447 DIAIAPLTITLVREEVIDFSKPFMSLGISIMIKK 480
Cdd:pfam10613  78 DLAVAPLTITSEREKVVDFTKPFMTLGISILMKK 111
PBP1_iGluR_Kainate cd06382
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate ...
9-351 1.09e-57

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1 and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined.


Pssm-ID: 380605  Cd Length: 335  Bit Score: 200.53  E-value: 1.09e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   9 FRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFI--TPSFPTDGTHPFVIQMRPD-- 84
Cdd:cd06382    33 TKLVPDIERVPRDDSFEASKKVCELLEEGVAAIFGPSSPSSSDIVQSICDALEIPHIetRWDPKESNRDTFTINLYPDpd 112
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  85 -LKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNdkkdemYRSLFQDLELKKERRVILD 163
Cdd:cd06382   113 aLSKAYADLVKSLNWKSFTILYEDDEGLIRLQELLKLPKPKDIPITVRQLDPGDD------YRPVLKEIKKSGETRIILD 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 164 CERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHT 243
Cdd:cd06382   187 CSPDRLVDVLKQAQQVGMLTEYYHYILTNLDLHTLDLEPFKYSGANITGFRLVDPENPEVKNVLKDWSKREKEGFNKDIG 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 244 TTIKYT-SALTYDAVQVMTEAFRNlrkqrieisrrgnagdclanpavpwgqgveieralkqvqveGLSGNIKFDQNGKRI 322
Cdd:cd06382   267 PGQITTeTALMYDAVNLFANALKE-----------------------------------------GLTGPIKFDEEGQRT 305
                         330       340
                  ....*....|....*....|....*....
gi 1825730066 323 NYTINIMELKTNGPRKIGYWSEVDKMVVT 351
Cdd:cd06382   306 DFKLDILELTEGGLVKVGTWNPTDGLNIT 334
PBPe smart00079
Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic ...
606-743 6.34e-55

Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb


Pssm-ID: 197504 [Multi-domain]  Cd Length: 133  Bit Score: 185.57  E-value: 6.34e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  606 PIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSaePSVFVRTTAEGVARVRKSKgkYAYLLESTMNEY 685
Cdd:smart00079   1 PITSVEDLAKQTKIEYGTQDGSSTLAFFKRSGNPEYSRMWPYMKS--PEVFVKSYAEGVQRVRVSN--YAFIMESPYLDY 76
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1825730066  686 IEQRkPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYD 743
Cdd:smart00079  77 ELSR-NCDLMTVGEEFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELEKLRNKWWKD 133
ANF_receptor pfam01094
Receptor family ligand binding region; This family includes extracellular ligand binding ...
9-334 2.40e-49

Receptor family ligand binding region; This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.


Pssm-ID: 460062 [Multi-domain]  Cd Length: 347  Bit Score: 177.96  E-value: 2.40e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066   9 FRLTPHIdnLEVANSFAVTNAFCSQFSRG-VYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT-----HPFVIQMR 82
Cdd:pfam01094  23 TKLEYII--LDTCCDPSLALAAALDLLKGeVVAIIGPSCSSVASAVASLANEWKVPLISYGSTSPALsdlnrYPTFLRTT 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  83 PD---LKGALLSLIEYYQWDKFAYLY-DSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKkDEMYRSLFQDLElKKER 158
Cdd:pfam01094 101 PSdtsQADAIVDILKHFGWKRVALIYsDDDYGESGLQALEDALRERGIRVAYKAVIPPAQDD-DEIARKLLKEVK-SRAR 178
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 159 RVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGA--NVSGFQIVDYDDSLVSKFIERWSTLEEK 236
Cdd:pfam01094 179 VIVVCCSSETARRLLKAARELGMMGEGYVWIATDGLTTSLVILNPSTLEAagGVLGFRLHPPDSPEFSEFFWEKLSDEKE 258
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 237 EYPGAHTTTIKYtSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGdclanpavPWGQGVEIERALKQVQVEGLSGNIKFD 316
Cdd:pfam01094 259 LYENLGGLPVSY-GALAYDAVYLLAHALHNLLRDDKPGRACGALG--------PWNGGQKLLRYLKNVNFTGLTGNVQFD 329
                         330
                  ....*....|....*...
gi 1825730066 317 QNGKRINYTINIMELKTN 334
Cdd:pfam01094 330 ENGDRINPDYDILNLNGS 347
PBP2_iGluR_NMDA cd13687
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate ...
371-740 1.10e-40

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: 149.71  E-value: 1.10e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 371 VTTILESPYVMMKKNhemlegneryEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDA-DTKIWNGMVGELVYGKADIA 449
Cdd:cd13687     6 VVTLEEAPFVYVKCC----------YGFCIDLLKKLAEDVNFTYDLYLVTDGKFGTVNKsINGEWNGMIGELVSGRADMA 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 450 IAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyewhtee 529
Cdd:cd13687    76 VASLTINPERSEVIDFSKPFKYTGITILVKKRNE---------------------------------------------- 109
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 530 fedgretqssestnefgifnslwfslgafmqqgcdisprsLSGrivggvwwfftliiissytanlaafLTVERMVSPIES 609
Cdd:cd13687   110 ----------------------------------------LSG-------------------------INDPRLRNPSPP 124
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 610 aedlskqteIAYGTLDSGSTKEFFRRSkiavFDKMWTYMRSAEpsvfVRTTAEGVARVRKSKGKyAYLLESTMNEY-IEQ 688
Cdd:cd13687   125 ---------FRFGTVPNSSTERYFRRQ----VELMHRYMEKYN----YETVEEAIQALKNGKLD-AFIWDSAVLEYeASQ 186
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1825730066 689 RKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKW 740
Cdd:cd13687   187 DEGCKLVTVGSLFARSGYGIGLQKNSPWKRNVSLAILQFHESGFMEELDKKW 238
PBP2_iGluR_delta_1 cd13730
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the ...
368-741 3.65e-39

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: 145.87  E-value: 3.65e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 368 TVVVTTILESPYVMMKKNheMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKiWNGMVGELVYGKAD 447
Cdd:cd13730     3 TLKVVTVLEEPFVMVAEN--ILGQPKRYKGFSIDVLDALAKALGFKYEIYQAPDGKYGHQLHNTS-WNGMIGELISKRAD 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 448 IAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyewht 527
Cdd:cd13730    80 LAISAITITPERESVVDFSKRYMDYSVGILIKKPE--------------------------------------------- 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 528 eefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvsPI 607
Cdd:cd13730   115 ------------------------------------------------------------------------------PI 116
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 608 ESAEDLSKQTEIAYGTLDSGSTKEFFRRS------KIAVFDKMW-TYMRSAEPSVFVRTTAEGVARVRksKGKYAYLLES 680
Cdd:cd13730   117 RTFQDLSKQVEMSYGTVRDSAVYEYFRAKgtnpleQDSTFAELWrTISKNGGADNCVSSPSEGIRKAK--KGNYAFLWDV 194
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1825730066 681 TMNEYIE-QRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13730   195 AVVEYAAlTDDDCSVTVIGNSISSKGYGIALQHGSPYRDLFSQRILELQDTGDLDVLKQKWW 256
PBP2_iGluR_delta_like cd13716
The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of ...
368-741 7.71e-39

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: 144.98  E-value: 7.71e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 368 TVVVTTILESPYVMMKKNheMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKiWNGMVGELVYGKAD 447
Cdd:cd13716     3 VLRVVTVLEEPFVMVSEN--VLGKPKKYQGFSIDVLDALANYLGFKYEIYVAPDHKYGSQQEDGT-WNGLIGELVFKRAD 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 448 IAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyewht 527
Cdd:cd13716    80 IGISALTITPERENVVDFTTRYMDYSVGVLLRKAE--------------------------------------------- 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 528 eefedgretqssestnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvsPI 607
Cdd:cd13716   115 ------------------------------------------------------------------------------SI 116
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 608 ESAEDLSKQTEIAYGTLDSGSTKEFFRRSKI------AVFDKMW-TYMRSAEPSVFVRTTAEGVARVRksKGKYAYLLES 680
Cdd:cd13716   117 QSLQDLSKQTDIPYGTVLDSAVYEYVRSKGTnpferdSMYSQMWrMINRSNGSENNVSESSEGIRKVK--YGNYAFVWDA 194
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1825730066 681 TMNEYIEQRKP-CDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13716   195 AVLEYVAINDDdCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 256
PBP2_iGluR_delta_2 cd13731
The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the ...
371-741 2.54e-34

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: 132.08  E-value: 2.54e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 371 VTTILESPYVMMKKNheMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKiWNGMVGELVYGKADIAI 450
Cdd:cd13731     6 VVTVLEEPFVMVSEN--VLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGT-WNGLVGELVFKRADIGI 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 451 APLTITLVREEVIDFSKPFMSLGISIMIKKpqkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyewhteef 530
Cdd:cd13731    83 SALTITPDRENVVDFTTRYMDYSVGVLLRR-------------------------------------------------- 112
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 531 edgretqsSEStnefgifnslwfslgafmqqgcdisprslsgrivggvwwfftliiissytanlaafltvermvspIESA 610
Cdd:cd13731   113 --------AES-----------------------------------------------------------------IQSL 119
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 611 EDLSKQTEIAYGTLDSGSTKEFFRRSKIAVF--DKMWTYM-----RSAEPSVFVRTTAEGVARVRksKGKYAYLLESTMN 683
Cdd:cd13731   120 QDLSKQTDIPYGTVLDSAVYEHVRMKGLNPFerDSMYSQMwrminRSNGSENNVLESQAGIQKVK--YGNYAFVWDAAVL 197
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1825730066 684 EYIEQRKP-CDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13731   198 EYVAINDPdCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQNGDMDILKHKWW 256
PBP2_iGluR_NMDA_Nr1 cd13719
The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
371-740 3.66e-28

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: 114.77  E-value: 3.66e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 371 VTTILESPYVMMKK---------------NHEMLEGNERY----EGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDA-- 429
Cdd:cd13719     6 IVTIHEEPFVYVRPtpsdgtcreeftvncPNFNISGRPTVpfccYGYCIDLLIKLARKMNFTYELHLVADGQFGTQERvn 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 430 --DTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKskpgvfsfldplayeiwmcivfay 507
Cdd:cd13719    86 nsNKKEWNGMMGELVSGRADMIVAPLTINPERAQYIEFSKPFKYQGLTILVKKEIR------------------------ 141
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 508 igvsvvlflvsrfspyewhteefedgretqssestnefgifnslwfslgafmqqgcdisprsLSGrivggvwwfftliii 587
Cdd:cd13719   142 --------------------------------------------------------------LTG--------------- 144
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 588 ssytanlaafLTVERMVSPIEsaedlskqtEIAYGTLDSGSTKEFFRRSkiAVFDKMWTYMrsaEPSVfVRTTAEGVARV 667
Cdd:cd13719   145 ----------INDPRLRNPSE---------KFIYATVKGSSVDMYFRRQ--VELSTMYRHM---EKHN-YETAEEAIQAV 199
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1825730066 668 RKSKGKyAYLLESTMNEYiEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKW 740
Cdd:cd13719   200 RDGKLH-AFIWDSSRLEF-EASQDCDLVTAGELFGRSGYGIGLQKNSPWTDNVSLAILKMHESGFMEDLDKTW 270
PBP2_iGluR_NMDA_Nr2 cd13718
The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
397-740 1.57e-26

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: 110.12  E-value: 1.57e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISI 476
Cdd:cd13718    58 GFCIDILKKLAKDVGFTYDLYLVTNGKHGKKINGV--WNGMIGEVVYKRADMAVGSLTINEERSEVVDFSVPFVETGISV 135
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 477 MIKKpqkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyewhteefedgRETQSSESTNEFgifnslwfslg 556
Cdd:cd13718   136 MVAR-----------------------------------------------------SNQVSGLSDKKF----------- 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 557 afmQQGCDISPrslsgrivggvwwfftliiissytanlaafltvermvsPIEsaedlskqteiaYGTLDSGSTKEFFRRS 636
Cdd:cd13718   152 ---QRPHDQSP--------------------------------------PFR------------FGTVPNGSTERNIRNN 178
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 637 kiavFDKMWTYMRsaepSVFVRTTAEGVARVRKSKGKyAYLLESTMNEYIEQR-KPCDTMKVGGN--LDSKGYGIATPKG 713
Cdd:cd13718   179 ----YPEMHQYMR----KYNQKGVEDALVSLKTGKLD-AFIYDAAVLNYMAGQdEGCKLVTIGSGkwFAMTGYGIALQKN 249
                         330       340
                  ....*....|....*....|....*..
gi 1825730066 714 SSLRTPVNLAVLKLSEQGVLDKLKNKW 740
Cdd:cd13718   250 SKWKRPFDLALLQFRGDGELERLERLW 276
Lig_chan-Glu_bd smart00918
Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the ...
378-442 9.07e-25

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: 97.70  E-value: 9.07e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1825730066  378 PYVMMKKNHEmlEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADtKIWNGMVGELV 442
Cdd:smart00918   1 PYVMLKESPD--GGNDRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGARLPN-GSWNGMVGELV 62
PBP2_iGluR_NMDA_Nr3 cd13720
The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) ...
397-741 3.49e-23

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: 100.31  E-value: 3.49e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTIVGDGKYGA-RDADtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGIS 475
Cdd:cd13720    67 GYCIDLLEKLAEDLGFDFDLYIVGDGKYGAwRNGR---WTGLVGDLLSGRAHMAVTSFSINSARSQVIDFTSPFFSTSLG 143
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 476 IMIkKPQkskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyewhteefedgretqssestnefgifnslwfsl 555
Cdd:cd13720   144 ILV-RTR------------------------------------------------------------------------- 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 556 gafmQQGCDISPRSLSGRIVGgvwwfftliiissytanlaafltvERMVSPIESAEDlskqteiaygtldsgstkEFFRR 635
Cdd:cd13720   150 ----DELSGIHDPKLHHPSQG------------------------FRFGTVRESSAE------------------YYVKK 183
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 636 SkiavFDKMWTYMRSAEpsvfVRTTAEGVARVRKSKGKYAYLLEST--MNEYIEQRKPCDTMKVGGNLDSKGYGIATPKG 713
Cdd:cd13720   184 S----FPEMHEHMRRYS----LPNTPEGVEYLKNDPEKLDAFIMDKalLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQN 255
                         330       340
                  ....*....|....*....|....*...
gi 1825730066 714 SSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:cd13720   256 SPLTSNISELISQYKSNGFMDLLHDKWY 283
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
369-480 5.24e-19

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: 86.54  E-value: 5.24e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 369 VVVTTILESPYVMMKKNhemlegnERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADI 448
Cdd:cd13530     3 RVGTDADYPPFEYIDKN-------GKLVGFDVDLANAIAKRLGVKVEFVDTD-------------FDGLIPALQSGKIDV 62
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1825730066 449 AIAPLTITLVREEVIDFSKPFMSLGISIMIKK 480
Cdd:cd13530    63 AISGMTITPERAKVVDFSDPYYYTGQVLVVKK 94
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
378-493 3.12e-14

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: 72.71  E-value: 3.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 378 PYVMMKKNHEmlegnerYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITL 457
Cdd:pfam00497  11 PFEYVDENGK-------LVGFDVDLAKAIAKRLGVKVEFVPVS-------------WDGLIPALQSGKVDLIIAGMTITP 70
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1825730066 458 VREEVIDFSKPFMSLGISIMIKKpQKSKPGVFSFLD 493
Cdd:pfam00497  71 ERAKQVDFSDPYYYSGQVILVRK-KDSSKSIKSLAD 105
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
387-480 3.54e-14

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


Pssm-ID: 440596 [Multi-domain]  Cd Length: 223  Bit Score: 72.71  E-value: 3.54e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFS 466
Cdd:COG0834    13 SFRDEDGKLVGFDVDLARAIAKRLGLKVEFVPVP-------------WDRLIPALQSGKVDLIIAGMTITPEREKQVDFS 79
                          90
                  ....*....|....
gi 1825730066 467 KPFMSLGISIMIKK 480
Cdd:COG0834    80 DPYYTSGQVLLVRK 93
PBP1_iGluR_delta-like cd06381
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of an orphan family ...
10-345 7.00e-14

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


Pssm-ID: 380604 [Multi-domain]  Cd Length: 401  Bit Score: 74.64  E-value: 7.00e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  10 RLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVS--FI---TPSFPTDGTH--------P 76
Cdd:cd06381    35 KITYSIKVIEANNPFQAVQEACDLMTQGILALVTSTGCASANALQSLTDAMHIPhlFVqrnPGGSPRTACHlnpspdgeA 114
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  77 FVIQMRPD--LKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINV-GNINndkkdEMYRSLFQDL- 152
Cdd:cd06381   115 YTLASRPPvrLNDVMLRLVTELRWQKFVMFYDSEYDIRGLQSFLDQASRLGLDVSLQKVdKNIS-----HVFTSLFTTMk 189
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 153 --ELKKE----RRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKI-------------QFGGANVSgf 213
Cdd:cd06381   190 teELNRYrdtlRRAILLLSPQGAHSFINEAVETNLASKDSHWVFVNEEISDPEILDLvhsalgrmtvvrqIFPSAKDN-- 267
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 214 QIVDYDDSLVSkfierwSTLEEKEYPGAHTTTIkyTSALTYDAVQVMTEAFRNLRKQRIEISRRgnAGDCLANPAVPWGQ 293
Cdd:cd06381   268 QKCFRNNHRIS------SLLCDPQEGYLQMLQI--SNLYLYDSVLMLANAFHRKLEDRKWHSMA--SLNCIRKSTKPWNG 337
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1825730066 294 GVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIM-----ELKTNGPRKIGYWSEV 345
Cdd:cd06381   338 GRSMLDTIKKGHITGLTGVMEFREDSSNPYVQFEILgttysETFGKDMRKLATWDSE 394
PBP1_iGluR_Kainate_KA1_2 cd06394
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the KA1 and KA2 ...
148-342 2.98e-13

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMPA receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined.


Pssm-ID: 380616  Cd Length: 379  Bit Score: 72.25  E-value: 2.98e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 148 LFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFI 227
Cdd:cd06394   180 LLKEIRDDKVSTIIIDANASISHLILKKASELGMTSAFYKYILTTMDFPLLHLDGIVDDQSNILGFSMFNTSHPFYLEFV 259
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 228 ER----W-STLEEKEYPGAhtttiKYTSALTYDAVQVMTEAFRNL-RKQRIEISRRGnagdclANPAVPWGQGVEIERAL 301
Cdd:cd06394   260 RSlnmsWrENCDASTYPGP-----ALSSALMFDAVHVVVSAVRELnRSQEIGVKPLS------CTSAQIWQHGTSLMNYL 328
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1825730066 302 KQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIGYW 342
Cdd:cd06394   329 RMVEYDGLTGRVEFNSKGQRTNYTLRILEKSRQGHREIGVW 369
PBP1_iGluR_delta_2 cd06391
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 ...
10-352 1.54e-12

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq and tumor necrosis factor family that is secreted from cerebellar granule cells.


Pssm-ID: 380614 [Multi-domain]  Cd Length: 402  Bit Score: 70.45  E-value: 1.54e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  10 RLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVS--FI------TPSF---PTDGTHP-- 76
Cdd:cd06391    35 KITFSVTFVDGNNPFQAVQEACELMNQGILALVSSIGCTSAGSLQSLADAMHIPhlFIqrstagTPRSgcgLTRSNRNdd 114
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  77 FVIQMRPD--LKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDEMYRSL-FQDLE 153
Cdd:cd06391   115 YTLSVRPPvyLNDVILRVVTEYAWQKFIIFYDSEYDIRGIQEFLDKVSQQGMDVALQKVENNINKMITTLFDTMrIEELN 194
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 154 LKKE--RRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFggANVSGFQIVDYDDSLVSKFIERW- 230
Cdd:cd06391   195 RYRDtlRRAILVMNPATAKSFITEVVETNLVAFDCHWIIINEEINDVDVQELVR--RSIGRLTIIRQTFPVPQNISQRCf 272
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 231 -------STLEEKEYPGAHTTTIkyTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAgdCLANPAVPWGQGVEIERALKQ 303
Cdd:cd06391   273 rgnhrisSSLCDPKDPFAQNMEI--SNLYIYDTVLLLANAFHKKLEDRKWHSMASLS--CIRKNSKPWQGGRSMLETIKK 348
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1825730066 304 VQVEGLSGNIKFDQNGKRINYTINIM-----ELKTNGPRKIGYWSEVDKMVVTL 352
Cdd:cd06391   349 GGVSGLTGLLEFGENGGNPNVHFEILgtnygEELGRGVRKLGCWNPVTGLNGSL 402
PBP2_GlnH cd00994
Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold; ...
387-480 2.34e-12

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


Pssm-ID: 270216 [Multi-domain]  Cd Length: 218  Bit Score: 67.30  E-value: 2.34e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNErYEGYCVDLAAEIAKHCGFKYKLTivgdgkygarDADtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFS 466
Cdd:cd00994    14 EFKQDGK-YVGFDIDLWEAIAKEAGFKYELQ----------PMD---FKGIIPALQTGRIDIAIAGITITEERKKVVDFS 79
                          90
                  ....*....|....
gi 1825730066 467 KPFMSLGISIMIKK 480
Cdd:cd00994    80 DPYYDSGLAVMVKA 93
PBP2_GluR0 cd00997
Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate ...
367-740 5.46e-12

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: 66.21  E-value: 5.46e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 367 KTVVVTTILESPYVMmkknhemlEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDgkygardadtkiWNGMVGELVYGKA 446
Cdd:cd00997     3 QTLTVATVPRPPFVF--------YNDGELTGFSIDLWRAIAERLGWETEYVRVDS------------VSALLAAVAEGEA 62
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 447 DIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKskpgvfsfldplayeiwmcivfayigvsvvlflvsrfspyewh 526
Cdd:cd00997    63 DIAIAAISITAEREAEFDFSQPIFESGLQILVPNTPL------------------------------------------- 99
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 527 teefedgretqssestnefgiFNslwfslgafmqqgcdiSPRSLSGRIVGgvwwfftliIISSYTAnlAAFLTvERMVSP 606
Cdd:cd00997   100 ---------------------IN----------------SVNDLYGKRVA---------TVAGSTA--ADYLR-RHDIDV 130
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 607 IESAEdlskqTEIAYGTLDSGSTkeffrrsKIAVFDkmwtymrSAEPSVFVRTTAEGVARVrkskgkyayllestmneyi 686
Cdd:cd00997   131 VEVPN-----LEAAYTALQDKDA-------DAVVFD-------APVLRYYAAHDGNGKAEV------------------- 172
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1825730066 687 eqrkpcdtmkVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKW 740
Cdd:cd00997   173 ----------TGSVFLEENYGIVFPTGSPLRKPINQALLNLREDGTYDELYEKW 216
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
387-480 4.28e-11

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: 63.28  E-value: 4.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFS 466
Cdd:cd13624    14 EFVDENGKIVGFDIDLIKAIAKEAGFEVEFKNMA-------------FDGLIPALQSGKIDIIISGMTITEERKKSVDFS 80
                          90
                  ....*....|....
gi 1825730066 467 KPFMSLGISIMIKK 480
Cdd:cd13624    81 DPYYEAGQAIVVRK 94
PBP2_BsGlnH cd13689
Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 ...
390-480 6.65e-11

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


Pssm-ID: 270407 [Multi-domain]  Cd Length: 229  Bit Score: 63.02  E-value: 6.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 390 EGNERYEGYCVDLAAEIAKHCGFKYKLTIVgdgkygarDADTKIwngmvGELVYGKADIAIAPLTITLVREEVIDFSKPF 469
Cdd:cd13689    26 PKTREIVGFDVDLCKAIAKKLGVKLELKPV--------NPAARI-----PELQNGRVDLVAANLTYTPERAEQIDFSDPY 92
                          90
                  ....*....|.
gi 1825730066 470 MSLGISIMIKK 480
Cdd:cd13689    93 FVTGQKLLVKK 103
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
378-480 2.26e-10

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 61.19  E-value: 2.26e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  378 PYVMMKKNHEmlegnerYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITL 457
Cdd:smart00062  12 PFSFADEDGE-------LTGFDVDLAKAIAKELGLKVEFVEVS-------------FDSLLTALKSGKIDVVAAGMTITP 71
                           90       100
                   ....*....|....*....|...
gi 1825730066  458 VREEVIDFSKPFMSLGISIMIKK 480
Cdd:smart00062  72 ERAKQVDFSDPYYRSGQVILVRK 94
PBP1_iGluR_delta_1 cd06392
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta1 ...
10-319 4.28e-10

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdelta1 is expressed in many areas in the developing CNS, including the hippocampus and the caudate putamen. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans.


Pssm-ID: 380615  Cd Length: 402  Bit Score: 62.72  E-value: 4.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  10 RLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKG-- 87
Cdd:cd06392    35 KITYSIKVIEANNPFQAVQEACDLMTQGILALVTSTGCASANALQSLTDAMHIPHLFVQRNSGGSPRTACHLNPSPEGee 114
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  88 -------------ALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVG-NINndkkdEMYRSLFQDL- 152
Cdd:cd06392   115 ytlaarppvrlndVMLKLVTELRWQKFIVFYDSEYDIRGLQSFLDQASRLGLDVSLQKVDrNIS-----RVFTNLFTTMk 189
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 153 --ELKKE----RRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKI---QFGGANV--SGFQIVDYDDS 221
Cdd:cd06392   190 teELNRYrdtlRRAILLLSPRGAQSFINEAVETNLASKDSHWVFVNEEISDPEILELvhsALGRMTVirQIFPLSKDNNQ 269
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 222 LVSKFIERWSTLEEKEYPGaHTTTIKYTSALTYDAVQVMTEAF-RNLRKQRIEISRRGNagdCLANPAVPWGQGVEIERA 300
Cdd:cd06392   270 RCMRNNHRISSLLCDPQEG-YLQMLQVSNLYLYDSVLMLANAFhRKLEDRKWHSMASLN---CIRKSTKPWNGGRSMLDT 345
                         330
                  ....*....|....*....
gi 1825730066 301 LKQVQVEGLSGNIKFDQNG 319
Cdd:cd06392   346 IKKGHITGLTGVMEFREDG 364
PBP2_GltS cd13620
Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 ...
386-485 5.62e-10

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: 60.43  E-value: 5.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 386 HEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDF 465
Cdd:cd13620    20 QKMKDGKNQVVGADIDIAKAIAKELGVKLEIKSMD-------------FDNLLASLQSGKVDMAISGMTPTPERKKSVDF 86
                          90       100
                  ....*....|....*....|
gi 1825730066 466 SKPFMSLGISIMIKKPQKSK 485
Cdd:cd13620    87 SDVYYEAKQSLLVKKADLDK 106
PBP2_Cystine_like cd13626
Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein ...
385-480 3.80e-09

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: 57.71  E-value: 3.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 385 NHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVID 464
Cdd:cd13626    12 PFTFKDEDGKLTGFDVEVGREIAKRLGLKVEFKATE-------------WDGLLPGLNSGKFDVIANQVTITPEREEKYL 78
                          90
                  ....*....|....*.
gi 1825730066 465 FSKPFMSLGISIMIKK 480
Cdd:cd13626    79 FSDPYLVSGAQIIVKK 94
PBP2_GlnP cd13619
Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold ...
387-484 8.38e-09

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: 56.56  E-value: 8.38e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFS 466
Cdd:cd13619    14 EFQNDDGKYVGIDVDLLNAIAKDQGFKVELKPMG-------------FDAAIQAVQSGQADGVIAGMSITDERKKTFDFS 80
                          90
                  ....*....|....*...
gi 1825730066 467 KPFMSLGISIMIKKPQKS 484
Cdd:cd13619    81 DPYYDSGLVIAVKKDNTS 98
PBP2_Dsm1740 cd13629
Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily ...
387-493 5.27e-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: 54.50  E-value: 5.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNERYEGYCVDLAAEIAKHCGfkYKLTIVgdgkygardaDTKiWNGMVGELVYGKADIAIAPLTITLVREEVIDFS 466
Cdd:cd13629    14 EMTDKKGELIGFDVDLAKALAKDLG--VKVEFV----------NTA-WDGLIPALQTGKFDLIISGMTITPERNLKVNFS 80
                          90       100
                  ....*....|....*....|....*..
gi 1825730066 467 KPFMSLGISIMIKKPQKSKPGVFSFLD 493
Cdd:cd13629    81 NPYLVSGQTLLVNKKSAAGIKSLEDLN 107
PBP2_Cysteine cd13694
Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein ...
391-480 6.51e-08

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


Pssm-ID: 270412 [Multi-domain]  Cd Length: 229  Bit Score: 54.28  E-value: 6.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 391 GNERYEGYCVDLAAEIAKHC---GFKYKLTIVgdgkygarDADTKIwngmvGELVYGKADIAIAPLTITLVREEVIDFSK 467
Cdd:cd13694    26 ENGKFQGFDIDLAKQIAKDLfgsGVKVEFVLV--------EAANRV-----PYLTSGKVDLILANFTVTPERAEVVDFAN 92
                          90
                  ....*....|...
gi 1825730066 468 PFMSLGISIMIKK 480
Cdd:cd13694    93 PYMKVALGVVSPK 105
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
397-485 1.07e-07

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: 53.40  E-value: 1.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSkPFMSLGISI 476
Cdd:cd01004    26 GFDVDLAKAIAKRLGLKVEIVNVS-------------FDGLIPALQSGRYDIIMSGITDTPERAKQVDFV-DYMKDGLGV 91
                          90
                  ....*....|.
gi 1825730066 477 MIKK--PQKSK 485
Cdd:cd01004    92 LVAKgnPKKIK 102
PRK11260 PRK11260
cystine ABC transporter substrate-binding protein;
397-501 1.51e-07

cystine ABC transporter substrate-binding protein;


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 53.57  E-value: 1.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTivgdgkygardaDTKiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISI 476
Cdd:PRK11260   65 GFEVEFAEALAKHLGVKASLK------------PTK-WDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQA 131
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1825730066 477 MIKkpqKSKPGVFSFLDPLA-----------YEIWM 501
Cdd:PRK11260  132 LVK---KGNEGTIKTAADLKgkkvgvglgtnYEQWL 164
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
390-480 2.14e-07

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: 52.29  E-value: 2.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 390 EGNErYEGYCVDLAAEIAKHCGFKykLTIVgdgkygardadTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPF 469
Cdd:cd13713    18 EDNQ-LVGFDVDVAKAIAKRLGVK--VEPV-----------TTAWDGIIAGLWAGRYDIIIGSMTITEERLKVVDFSNPY 83
                          90
                  ....*....|.
gi 1825730066 470 MSLGISIMIKK 480
Cdd:cd13713    84 YYSGAQIFVRK 94
PBP2_FliY cd13712
Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic ...
397-486 2.62e-07

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: 52.39  E-value: 2.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTivgdgkygardadTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISI 476
Cdd:cd13712    24 GFEVDVAKALAAKLGVKPEFV-------------TTEWSGILAGLQAGKYDVIINQVGITPERQKKFDFSQPYTYSGIQL 90
                          90
                  ....*....|
gi 1825730066 477 MIKKPQKSKP 486
Cdd:cd13712    91 IVRKNDTRTF 100
glnH PRK09495
glutamine ABC transporter periplasmic protein; Reviewed
387-479 3.22e-07

glutamine ABC transporter periplasmic protein; Reviewed


Pssm-ID: 236540 [Multi-domain]  Cd Length: 247  Bit Score: 52.44  E-value: 3.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNeRYEGYCVDLAAEIAKHCGFKYKLtivgdgkygaRDADtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFS 466
Cdd:PRK09495   39 EFKQGD-KYVGFDIDLWAAIAKELKLDYTL----------KPMD---FSGIIPALQTKNVDLALAGITITDERKKAIDFS 104
                          90
                  ....*....|...
gi 1825730066 467 KPFMSLGISIMIK 479
Cdd:PRK09495  105 DGYYKSGLLVMVK 117
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
397-469 3.56e-07

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: 51.70  E-value: 3.56e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTiVGDgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPF 469
Cdd:cd13628    25 GFDIELAKTIAKKLGLKLQIQ-EYD------------FNGLIPALASGQADLALAGITPTPERKKVVDFSEPY 84
PBP2_GltI_DEBP cd13688
Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic ...
389-480 2.06e-06

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


Pssm-ID: 270406 [Multi-domain]  Cd Length: 238  Bit Score: 49.94  E-value: 2.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 389 LEGNERYEGYCVDLAAEIAKHCGFKYKLTIVgDGKYGARDADTKIwngmvgELVY-GKADIAIAPLTITLVREEVIDFSK 467
Cdd:cd13688    24 LDDNGKPVGYSVDLCNAIADALKKKLALPDL-KVRYVPVTPQDRI------PALTsGTIDLECGATTNTLERRKLVDFSI 96
                          90
                  ....*....|...
gi 1825730066 468 PFMSLGISIMIKK 480
Cdd:cd13688    97 PIFVAGTRLLVRK 109
PBP2_HisJ_LAO_like cd01001
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and ...
396-493 5.15e-06

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


Pssm-ID: 270222 [Multi-domain]  Cd Length: 228  Bit Score: 48.44  E-value: 5.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 396 EGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGIS 475
Cdd:cd01001    25 VGFDIDLANALCKRMKVKCEIVTQP-------------WDGLIPALKAGKYDAIIASMSITDKRRQQIDFTDPYYRTPSR 91
                          90
                  ....*....|....*...
gi 1825730066 476 IMIKKPQKSKPGVFSFLD 493
Cdd:cd01001    92 FVARKDSPITDTTPAKLK 109
PBP2_Peb1a_like cd13691
Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 ...
394-485 5.65e-06

Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 periplasmic-binding protein fold; This group includes periplasmic aspartate/glutamate binding domain Peb1a and its closely related protein. The Peb1a is an important virulence factor in the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonization. The Peb1a domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270409 [Multi-domain]  Cd Length: 228  Bit Score: 48.22  E-value: 5.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 394 RYEGYCVDLAAEIAK-HCGFKYKLTIVgdgkygarDADTKiwngmvGELV-YGKADIAIAPLTITLVREEVIDFSKPFMS 471
Cdd:cd13691    30 KYEGMEVDLARKLAKkGDGVKVEFTPV--------TAKTR------GPLLdNGDVDAVIATFTITPERKKSYDFSTPYYT 95
                          90
                  ....*....|....
gi 1825730066 472 LGISIMIKKPQKSK 485
Cdd:cd13691    96 DAIGVLVEKSSGIK 109
PBP2_YfhD_N cd01009
The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold ...
390-471 7.55e-06

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


Pssm-ID: 270230 [Multi-domain]  Cd Length: 223  Bit Score: 47.98  E-value: 7.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 390 EGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPF 469
Cdd:cd01009    16 IDRGGPRGFEYELAKAFADYLGVELEIVPADN------------LEELLEALEEGKGDLAAAGLTITPERKKKVDFSFPY 83

                  ..
gi 1825730066 470 MS 471
Cdd:cd01009    84 YY 85
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
387-488 8.47e-06

The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding fold protein; This subfamily includes the periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space through their function as an initial high-affinity binding component. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270422 [Multi-domain]  Cd Length: 220  Bit Score: 47.58  E-value: 8.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNERYEGYCVDLAAEIAKHCGFkyKLTIVgdgkygardadTKIWNGMVGELVYGKADIaIAPLTITLVREEVIDFS 466
Cdd:cd13704    16 EFLDENGNPTGFNVDLLRAIAEEMGL--KVEIR-----------LGPWSEVLQALENGEIDV-LIGMAYSEERAKLFDFS 81
                          90       100
                  ....*....|....*....|..
gi 1825730066 467 KPFMSLGISIMIKKPQKSKPGV 488
Cdd:cd13704    82 DPYLEVSVSIFVRKGSSIINSL 103
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
387-493 8.70e-06

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: 47.53  E-value: 8.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDgkygardadtkiWNGMVGELVYGKADIaIAPLTITLVREEVIDFS 466
Cdd:cd01007    16 EFIDEGGEPQGIAADYLKLIAKKLGLKFEYVPGDS------------WSELLEALKAGEIDL-LSSVSKTPEREKYLLFT 82
                          90       100
                  ....*....|....*....|....*..
gi 1825730066 467 KPFMSLGISIMIKkpqKSKPGVFSFLD 493
Cdd:cd01007    83 KPYLSSPLVIVTR---KDAPFINSLSD 106
PBP2_YxeM cd13709
Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein ...
392-488 9.00e-06

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


Pssm-ID: 270427 [Multi-domain]  Cd Length: 227  Bit Score: 47.73  E-value: 9.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 392 NERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMS 471
Cdd:cd13709    19 NGKLKGFEVDVWNAIGKRTGYKVEFVTAD-------------FSGLFGMLDSGKVDTIANQITITPERQEKYDFSEPYVY 85
                          90
                  ....*....|....*..
gi 1825730066 472 LGISIMIKKPQKSKPGV 488
Cdd:cd13709    86 DGAQIVVKKDNNSIKSL 102
MltF COG4623
Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, ...
390-471 9.60e-06

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


Pssm-ID: 443662 [Multi-domain]  Cd Length: 421  Bit Score: 48.90  E-value: 9.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 390 EGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPF 469
Cdd:COG4623    37 IYRGGPMGFEYELAKAFADYLGVKLEIIVPDN------------LDELLPALNAGEGDIAAAGLTITPERKKQVRFSPPY 104

                  ..
gi 1825730066 470 MS 471
Cdd:COG4623   105 YS 106
PBP1_GABAb_receptor cd06366
ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for ...
250-342 1.00e-05

ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA); Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb receptor or GABAbR). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha-i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.


Pssm-ID: 380589 [Multi-domain]  Cd Length: 404  Bit Score: 48.78  E-value: 1.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 250 SALTYDAVQVMTEAFRNLRKQRIEiSRRGNAGDCLANPAVpwgqGVEIERALKQVQVEGLSGNIKFDQNGKRInYTINIM 329
Cdd:cd06366   299 APFAYDAVWAIALALNKTIEKLAE-YNKTLEDFTYNDKEM----ADLFLEAMNSTSFEGVSGPVSFDSKGDRL-GTVDIE 372
                          90
                  ....*....|...
gi 1825730066 330 ELKTNGPRKIGYW 342
Cdd:cd06366   373 QLQGGSYVKVGLY 385
PBP2_AA_binding_like_2 cd13627
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
382-485 2.35e-05

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


Pssm-ID: 270345 [Multi-domain]  Cd Length: 243  Bit Score: 46.63  E-value: 2.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 382 MKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKykLTIVgdgkygardadtKI-WNGMVGELVYGKADIAIAPLTITLVRE 460
Cdd:cd13627    22 EYAIPIINGQGGYADGYDVQIAKKLAEKLDMK--LVIK------------KIeWNGLIPALNSGDIDLIIAGMSKTPERE 87
                          90       100
                  ....*....|....*....|....*
gi 1825730066 461 EVIDFSKPFMSLGISIMIKKPQKSK 485
Cdd:cd13627    88 KTIDFSDPYYISNIVMVVKKDSAYA 112
LivK COG0683
ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid ...
37-335 2.86e-05

ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid transport and metabolism];


Pssm-ID: 440447 [Multi-domain]  Cd Length: 314  Bit Score: 46.85  E-value: 2.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  37 GVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTD-----GTHPFVIQMRPDLKGALLSLIEY----YQWDKFAYLYDS 107
Cdd:COG0683    71 KVDAIVGPLSSGVALAVAPVAEEAGVPLISPSATAPaltgpECSPYVFRTAPSDAQQAEALADYlakkLGAKKVALLYDD 150
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 108 DR-GLSTLQAVLDSAAEKKWQVTAINVgnINNDKKDemYRSLFQDLELKKerrvildcerdkvndiVDQVITIGkhvkgy 186
Cdd:COG0683   151 YAyGQGLAAAFKAALKAAGGEVVGEEY--YPPGTTD--FSAQLTKIKAAG----------------PDAVFLAG------ 204
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 187 hyiianlgfTDGDLLKIqfgganVSGFQIVDYDDSLVSKFIERWstleEKEYpGAHTTTIkytSALTYDAVQVMTEAFRN 266
Cdd:COG0683   205 ---------YGGDAALF------IKQAREAGLKGPLNKAFVKAY----KAKY-GREPSSY---AAAGYDAALLLAEAIEK 261
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1825730066 267 lrkqrieisrrgnAGDclANPAvpwgqgvEIERALKQVQVEGLSGNIKFDQNGKRINyTINIMELKTNG 335
Cdd:COG0683   262 -------------AGS--TDRE-------AVRDALEGLKFDGVTGPITFDPDGQGVQ-PVYIVQVKADG 307
PBP2_Cys_DEBP_like cd01000
Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 ...
395-480 3.23e-05

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


Pssm-ID: 270221 [Multi-domain]  Cd Length: 228  Bit Score: 46.15  E-value: 3.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 395 YEGYCVDLAAEIAKhcgfkyklTIVGDG---KYGARDADTKIWNgmvgeLVYGKADIAIAPLTITLVREEVIDFSKPFMS 471
Cdd:cd01000    30 IQGFDVDVAKALAK--------DLLGDPvkvKFVPVTSANRIPA-----LQSGKVDLIIATMTITPERAKEVDFSVPYYA 96

                  ....*....
gi 1825730066 472 LGISIMIKK 480
Cdd:cd01000    97 DGQGLLVRK 105
Periplasmic_Binding_Protein_Type_2 cd00648
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
395-489 3.51e-05

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.


Pssm-ID: 270214 [Multi-domain]  Cd Length: 196  Bit Score: 45.64  E-value: 3.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 395 YEGYCVDLAAEIAKHCGFKYKLTIVGDgkygardadtkiWNGMVGELVYGKADIAIAPLTITL------VREEVIDFSKP 468
Cdd:cd00648    12 YAGFAEDAAKQLAKETGIKVELVPGSS------------IGTLIEALAAGDADVAVGPIAPALeaaadkLAPGGLYIVPE 79
                          90       100
                  ....*....|....*....|.
gi 1825730066 469 FMSLGISIMIKKPQKSKPGVF 489
Cdd:cd00648    80 LYVGGYVLVVRKGSSIKGLLA 100
PBP1_GABAb_receptor_plant cd19990
periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close ...
62-343 6.20e-05

periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close homologs in other plants; This group includes the ligand-binding domain of Arabidopsis thaliana glutamate receptors, which have sequence similarity with animal ionotropic glutamate receptor and its close homologs in other plants. The ligand-binding domain of GABAb receptors are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb receptor or GABAbR). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha-i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.


Pssm-ID: 380645 [Multi-domain]  Cd Length: 373  Bit Score: 46.07  E-value: 6.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  62 VSF-ITPSFPTDGTHPFVIQMRPDLKG---ALLSLIEYYQWDKFAYLY-DSDRGLSTLQAVLDSAAEKKWQV---TAINV 133
Cdd:cd19990    92 ISFsATSPTLSSLRWPFFIRMTHNDSSqmkAIAAIVQSYGWRRVVLIYeDDDYGSGIIPYLSDALQEVGSRIeyrVALPP 171
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 134 gninNDKKDEMYRSLfqdLELKKER-RVIldcerdkvndIVDQVITIGKHV-----------KGYHYIIanlgfTDG--D 199
Cdd:cd19990   172 ----SSPEDSIEEEL---IKLKSMQsRVF----------VVHMSSLLASRLfqeakklgmmeKGYVWIV-----TDGitN 229
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 200 LLKIqFGGANVSGFQIV-----DYDDSL-VSKFIERWSTLEEKEYPGAHTTTIKYTSALTYDAVQVMTEAFRNLRKQRIE 273
Cdd:cd19990   230 LLDS-LDSSTISSMQGVigiktYIPESSeFQDFKARFRKKFRSEYPEEENAEPNIYALRAYDAIWALAHAVEKLNSSGGN 308
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1825730066 274 ISRRGNagdclanpavpwgqGVEIERALKQVQVEGLSGNIKFDqNGKRINYT----INIMElktNGPRKIGYWS 343
Cdd:cd19990   309 ISVSDS--------------GKKLLEEILSTKFKGLSGEVQFV-DGQLAPPPafeiVNVIG---KGYRELGFWS 364
glnH PRK09495
glutamine ABC transporter periplasmic protein; Reviewed
697-741 6.31e-05

glutamine ABC transporter periplasmic protein; Reviewed


Pssm-ID: 236540 [Multi-domain]  Cd Length: 247  Bit Score: 45.51  E-value: 6.31e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1825730066 697 VGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWW 741
Cdd:PRK09495  198 VGDSLEAQQYGIAFPKGSELREKVNGALKTLKENGTYAEIYKKWF 242
PBP2_OccT_like cd13699
Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding ...
434-478 7.11e-05

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


Pssm-ID: 270417 [Multi-domain]  Cd Length: 211  Bit Score: 44.67  E-value: 7.11e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1825730066 434 WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMI 478
Cdd:cd13699    50 WDGMIPALNAGKFDVIMDAMSITAERKKVIDFSTPYAATPNSFAV 94
PBP2_AA_binding_like_1 cd13625
Substrate-binding domain of putative amino acid-binding protein; the type 2 ...
392-468 8.42e-05

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


Pssm-ID: 270343 [Multi-domain]  Cd Length: 230  Bit Score: 44.67  E-value: 8.42e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1825730066 392 NERYEGYCVDLAAEIAKHCGFKYKLTIVGdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKP 468
Cdd:cd13625    23 NGKIVGFDRDLLDEMAKKLGVKVEQQDLP-------------WSGILPGLLAGKFDMVATSVTITKERAKRFAFTLP 86
PBP2_Arg_3 cd13622
Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding ...
387-470 8.63e-05

Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding fold; This subgroup is similar to the HisJ-like family that comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270340 [Multi-domain]  Cd Length: 222  Bit Score: 44.60  E-value: 8.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 387 EMLEGNERYEGYCVDLAAEIAK--HCGFKYKLTIvgdgkygardadtkiWNGMVGELVYGKADIAIAPLTITLVREEVID 464
Cdd:cd13622    16 EMQGTNNELFGFDIDLMNEICKriQRTCQYKPMR---------------FDDLLAALNNGKVDVAISSISITPERSKNFI 80

                  ....*.
gi 1825730066 465 FSKPFM 470
Cdd:cd13622    81 FSLPYL 86
PBP2_PheC cd01069
Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein ...
389-473 1.31e-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: 44.25  E-value: 1.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 389 LEGNERYEGYCVDLAAEIAKHCGFKykLTIVgdgkygardadTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKP 468
Cdd:cd01069    26 RDNQGQYEGYDIDMAEALAKSLGVK--VEFV-----------PTSWPTLMDDLAADKFDIAMGGISITLERQRQAFFSAP 92

                  ....*
gi 1825730066 469 FMSLG 473
Cdd:cd01069    93 YLRFG 97
PBP2_polar_AA cd13693
Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic ...
397-483 1.61e-04

Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of putative polar amino acid ABC transporter. The polar amino-acid 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: 270411 [Multi-domain]  Cd Length: 228  Bit Score: 43.84  E-value: 1.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTIVgdgKYGARdadtkiwngmVGELVYGKADIAIAPLTITLVREEVIDFSKP-FMSLGIS 475
Cdd:cd13693    32 GFEVDLAKDIAKRLGVKLELVPV---TPSNR----------IQFLQQGKVDLLIATMGDTPERRKVVDFVEPyYYRSGGA 98

                  ....*...
gi 1825730066 476 IMIKKPQK 483
Cdd:cd13693    99 LLAAKDSG 106
PBP2_Atu4678_like cd13696
The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ...
396-480 1.68e-04

The substrate binding domain of putative amino acid transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Agrobacterium tumefaciens and its related proteins. The putative Atu4678-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270414 [Multi-domain]  Cd Length: 227  Bit Score: 43.91  E-value: 1.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 396 EGYCVDLAAEIAKHCGFKYKLTIVgdgkygarDADTKIWNgmvgeLVYGKADIAIAPLTITLVREEVIDFSKPFMSLGIS 475
Cdd:cd13696    31 VGYDVDYAKDLAKALGVKPEIVET--------PSPNRIPA-----LVSGRVDVVVANTTRTLERAKTVAFSIPYVVAGMV 97

                  ....*
gi 1825730066 476 IMIKK 480
Cdd:cd13696    98 VLTRK 102
PBP2_Ala cd13628
Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 ...
675-740 3.36e-04

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: 42.84  E-value: 3.36e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1825730066 675 AYLLESTMNEYIEQRKPCDTMK--VGGNLDskGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKW 740
Cdd:cd13628   154 AAIVEDIVAETFAQKKN*LLESryIPKEAD--GSAIAFPKGSPLRDDFNRWLKEMGDSGELELMVRRW 219
PBP1_glutamate_receptors-like cd06269
ligand-binding domain of family C G-protein couples receptors (GPCRs), membrane bound guanylyl ...
35-257 4.46e-04

ligand-binding domain of family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as natriuretic peptide receptors (NPRs), and N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of ionotropic glutamate rece; This CD represents the ligand-binding domain of the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the ionotropic glutamate receptors, all of which are structurally similar and related to the periplasmic-binding fold type 1 family. The family C GPCRs consists of metabotropic glutamate receptor (mGluR), a calcium-sensing receptor (CaSR), gamma-aminobutyric acid receptor (GABAbR), the promiscuous L-alpha-amino acid receptor GPR6A, families of taste and pheromone receptors, and orphan receptors. Truncated splicing variants of the orphan receptors are not included in this CD. The family C GPCRs are activated by endogenous agonists such as amino acids, ions, and sugar based molecules. Their amino terminal ligand-binding region is homologous to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). The ionotropic glutamate receptors (iGluRs) have an integral ion channel and are subdivided into three major groups based on their pharmacology and structural similarities: NMDA receptors, AMPA receptors, and kainate receptors. The family of membrane bound guanylyl cyclases is further divided into three subfamilies: the ANP receptor (GC-A)/C-type natriuretic peptide receptor (GC-B), the heat-stable enterotoxin receptor (GC-C)/sensory organ specific membrane GCs such as retinal receptors (GC-E, GC-F), and olfactory receptors (GC-D and GC-G).


Pssm-ID: 380493 [Multi-domain]  Cd Length: 332  Bit Score: 43.17  E-value: 4.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  35 SRGVYAIFGFYDKKSVNTITSFCGTLHVSFIT-----PSFPTDGTHPFVIQMRPD---LKGALLSLIEYYQWDKFAYLYD 106
Cdd:cd06269    65 AAKVVAILGPGCSASAAPVANLARHWDIPVLSygataPGLSDKSRYAYFLRTVPPdskQADAMLALVRRLGWNKVVLIYS 144
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 107 SDR-GLSTLQAVLDSAAEKKWQVTAIN--VGNINNDKKDEMYRslFQDLElkkERRVILDCERDKVNDIVDQVITIGKHV 183
Cdd:cd06269   145 DDEyGEFGLEGLEELFQEKGGLITSRQsfDENKDDDLTKLLRN--LRDTE---ARVIILLASPDTARSLMLEAKRLDMTS 219
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 184 KGYHYIIANlGFTD-----GDLLKIQFGG--------ANVSGFQivDYDDSLVSKFIERWSTLEEKEYpgahtttIKYTS 250
Cdd:cd06269   220 KDYVWFVID-GEASssdehGDEARQAAEGaitvtlifPVVKEFL--KFSMELKLKSSKRKQGLNEEYE-------LNNFA 289

                  ....*..
gi 1825730066 251 ALTYDAV 257
Cdd:cd06269   290 AFFYDAV 296
PBP1_ABC_HAAT-like cd06349
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ...
58-332 5.10e-04

type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally.


Pssm-ID: 380572 [Multi-domain]  Cd Length: 338  Bit Score: 42.94  E-value: 5.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066  58 GTLHVSFIT--PSFPTDGTHPFVIQMRPDLKGALLSLIEYYQWD--KFAYLY-DSDRGLSTLQAVLDSAAEKKWQVTAIN 132
Cdd:cd06349    91 GLVQISPTAshPDFTKGGDYVFRNSPTQAVEAPFLADYAVKKLGakKIAIIYlNTDWGVSAADAFKKAAKALGGEIVATE 170
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 133 vgNINNDKKDemYRSLFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKgyhyIIANLGFTDGDLLKIqfGGANVSG 212
Cdd:cd06349   171 --AYLPGTKD--FSAQITKIKNANPDAIYLAAYYNDAALIAKQARQLGWDVQ----IFGSSSLYSPEFIEL--AGDAAEG 240
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 213 FQIV-----DYDDSLVSKFIERWstleEKEY---PGAHTttikytsALTYDAVQVMTEAFRNlrkqrieisrrgnAGdcl 284
Cdd:cd06349   241 VYLSspffpESPDPEVKEFVKAY----KAKYgedPDDFA-------ARAYDAVNILAEAIEK-------------AG--- 293
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1825730066 285 anpavpwGQGVEIERALKQVQ-VEGLSGNIKFDQNGkRINYTINIMELK 332
Cdd:cd06349   294 -------TDREAIRDALANIKdFSGLTGTITFDENG-DVLKSLTILVVK 334
GluR_Plant cd13686
Plant glutamate receptor domain; the type 2 periplasmic binding protein fold; This subfamily ...
695-740 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: 41.35  E-value: 1.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1825730066 695 MKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKW 740
Cdd:cd13686   186 TMVGPTYKTGGFGFAFPKGSPLVADVSRAILKVTEGGKLQQIENKW 231
PBP2_mlr5654_like cd13702
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
434-480 1.81e-03

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


Pssm-ID: 270420 [Multi-domain]  Cd Length: 223  Bit Score: 40.77  E-value: 1.81e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1825730066 434 WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKK 480
Cdd:cd13702    50 WDGIIPALQAKKFDAIIASMSITPERKKQVDFTDPYYTNPLVFVAPK 96
PBP2_GluB cd13690
Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein ...
394-480 2.16e-03

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: 40.71  E-value: 2.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 394 RYEGYCVDLAAEIAKHCGF---KYKLTIVGdgkYGARDAdtKIWNGMVgelvygkaDIAIAPLTITLVREEVIDFSKPFM 470
Cdd:cd13690    30 EFEGFDVDIARAVARAIGGdepKVEFREVT---SAEREA--LLQNGTV--------DLVVATYSITPERRKQVDFAGPYY 96
                          90
                  ....*....|
gi 1825730066 471 SLGISIMIKK 480
Cdd:cd13690    97 TAGQRLLVRA 106
PBP1_iGluR_NMDA_NR1 cd06379
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR1, an ...
255-331 2.65e-03

N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site


Pssm-ID: 380602  Cd Length: 364  Bit Score: 40.78  E-value: 2.65e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1825730066 255 DAVQVMTEAFRNLRKQRIEISRRGNagDCLANPAVpWGQGVEIERALKQVQVE-GLSGNIKFDQNGKRINYTINIMEL 331
Cdd:cd06379   256 DSVSVVAQAIRELFRSSENITDPPV--DCRDDTNI-WKSGQKFFRVLKSVKLSdGRTGRVEFNDKGDRIGAEYDIINV 330
PBP1_ABC_LivK_ligand_binding-like cd06347
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ...
189-319 2.93e-03

type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally.


Pssm-ID: 380570 [Multi-domain]  Cd Length: 334  Bit Score: 40.60  E-value: 2.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 189 IIANLGFTDGDLLKIqfGGANVSGFQIV-----DYDDSLVSKFIERWstleEKEY---PGAHtttikytSALTYDAVQVM 260
Cdd:cd06347   220 ILGGDGWDSPELLEL--GGDAVEGVYFTthfspDDPSPEVQEFVKAY----KAKYgepPNAF-------AALGYDAVMLL 286
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 261 TEAfrnlrkqrIEisrrgNAGDCLanpavpwgqGVEIERAL-KQVQVEGLSGNIKFDQNG 319
Cdd:cd06347   287 ADA--------IK-----RAGSTD---------PEAIRDALaKTKDFEGVTGTITFDPNG 324
PBP2_ml15202_like cd13701
Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the ...
434-486 4.38e-03

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


Pssm-ID: 270419 [Multi-domain]  Cd Length: 227  Bit Score: 39.75  E-value: 4.38e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1825730066 434 WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKP 486
Cdd:cd13701    51 WDGIIPALQSGKIDMIWNSMSITDERKKVIDFSDPYYETPTAIVGAKSDDRRV 103
PBP2_ArtJ_like cd13697
Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding ...
396-480 4.65e-03

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


Pssm-ID: 270415 [Multi-domain]  Cd Length: 228  Bit Score: 39.44  E-value: 4.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 396 EGYCVDLAAEIAKHCGFKYKLTIVGDgkygardadtkiwNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGIS 475
Cdd:cd13697    31 EGFDVDVAKKLADRLGVKLELVPVSS-------------ADRVPFLMAGKIDAVLGGLTRTPDRAKVIDFSDPVNTEVLG 97

                  ....*
gi 1825730066 476 IMIKK 480
Cdd:cd13697    98 ILTTA 102
PBP2_Ngo0372_TcyA cd13711
Substrate binding domain of ABC transporters involved in cystine import; the type 2 ...
397-480 8.25e-03

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


Pssm-ID: 270429 [Multi-domain]  Cd Length: 222  Bit Score: 38.82  E-value: 8.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1825730066 397 GYCVDLAAEIAKHCGFKYKLTivgdgkygardaDTKiWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISI 476
Cdd:cd13711    25 GFDVEVARAVAKKLGVKVEFV------------ETQ-WDSMIAGLDAGRFDVVANQVGITDERKKKYDFSTPYIYSRAVL 91

                  ....
gi 1825730066 477 MIKK 480
Cdd:cd13711    92 IVRK 95
 
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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