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Conserved domains on  [gi|17531183|ref|NP_495716|]
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AcetylCholine Receptor [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Neur_chan_LBD pfam02931
Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ...
21-258 6.30e-81

Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.


:

Pssm-ID: 460752 [Multi-domain]  Cd Length: 215  Bit Score: 250.65  E-value: 6.30e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183    21 EYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:pfam02931   1 EERLLDDLLSGYDKLVRPVANGSDPVTVSIGLYLQQIIDVDEKNQDLTTNVWLRQTWTDPRLAWNPEDYGGITSLRLPSD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   101 ddasfKLWRPDVLLFNSVSESFDST-YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYIN 179
Cdd:pfam02931  81 -----KIWKPDIVLYNKADGIHEVTtPNTNVRVYYDGTVLWSPPAIYKSSCSIDVTYFPFDEQNCSLKFGSWTYNGEEVD 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   180 LDFLLTQIIglhgipivvepersstnyasyFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRRR 257
Cdd:pfam02931 156 LRWDDDPPV---------------------VELEEIDLSDFWLNGEWDIVDVPAKRREYPYGcySELTGDVTFYFTLRRK 214

                  .
gi 17531183   258 T 258
Cdd:pfam02931 215 P 215
Neur_chan_memb super family cl47784
Neurotransmitter-gated ion-channel transmembrane region; This family includes the four ...
265-491 1.10e-26

Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.


The actual alignment was detected with superfamily member pfam02932:

Pssm-ID: 460753 [Multi-domain]  Cd Length: 232  Bit Score: 107.74  E-value: 1.10e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   265 LIIPSLVISMMTILGFTLPPDAC-EKITLETTVLLSVIFFLQMVSSTSPPQSQSVPILAAFFSCCLMLVACSCVFTVLTL 343
Cdd:pfam02932   1 LIIPCVLISFLSWLVFWLPADAVgEKVTLGITVLLTMTVFLLLIRESLPKTSYVVPLIGKYLLFCMVFVFLSLVETVFVL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   344 SLHHRKPETHEMSPTMRKIFIDWLPYILCMCKPDHPKTPKPKVLGKSIAPIHrlstipMLNLPRvSQTTFPDKNVFVYHE 423
Cdd:pfam02932  81 NVHHRSPSTHKMPPWVRKIFLEKLPRLLGMKRPPEAPPPPASPGYGSKAEEY------ILRKPR-SELPFEKQSERHGLG 153
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183   424 VPAVIKNTS---RICAELLIIERDIEKMLDK-------IEEDTKEDMLRSEWRFAAMAVDRLCLYVFsafitMITCGL 491
Cdd:pfam02932 154 RETTCSYGCslgNGSSQPRELSPELKKAVEGvnfiakhLRSQDEYISVKEDWKYVAMVIDRLSRWIF-----PIAFVL 226
 
Name Accession Description Interval E-value
Neur_chan_LBD pfam02931
Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ...
21-258 6.30e-81

Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.


Pssm-ID: 460752 [Multi-domain]  Cd Length: 215  Bit Score: 250.65  E-value: 6.30e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183    21 EYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:pfam02931   1 EERLLDDLLSGYDKLVRPVANGSDPVTVSIGLYLQQIIDVDEKNQDLTTNVWLRQTWTDPRLAWNPEDYGGITSLRLPSD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   101 ddasfKLWRPDVLLFNSVSESFDST-YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYIN 179
Cdd:pfam02931  81 -----KIWKPDIVLYNKADGIHEVTtPNTNVRVYYDGTVLWSPPAIYKSSCSIDVTYFPFDEQNCSLKFGSWTYNGEEVD 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   180 LDFLLTQIIglhgipivvepersstnyasyFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRRR 257
Cdd:pfam02931 156 LRWDDDPPV---------------------VELEEIDLSDFWLNGEWDIVDVPAKRREYPYGcySELTGDVTFYFTLRRK 214

                  .
gi 17531183   258 T 258
Cdd:pfam02931 215 P 215
LGIC_ECD_nAChR cd18997
extracellular domain of nicotinic acetylcholine receptor; This family contains the ...
46-257 2.88e-77

extracellular domain of nicotinic acetylcholine receptor; This family contains the extracellular domain of nicotinic acetylcholine receptor (nAChR), a member of the pentameric "Cys-loop" superfamily of transmitter-gated ion channels. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits, and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Among subtypes of muscle nAChRs, the heteromeric subunits (alpha1)2, beta, gamma, and delta in fetal muscle, and the gamma subunit replaced by epsilon in adult muscle have been implicated in congenital myasthenic syndromes and multiple pterygium syndromes due to various mutations. This family also includes alpha- and beta-like nAChRs found in protostomia.


Pssm-ID: 349798  Cd Length: 181  Bit Score: 240.08  E-value: 2.88e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDST 125
Cdd:cd18997   1 VNVTFGLTLRQIIDVDEKNQVLTTNVWLRQEWNDERLTWNPSDYGGITSIRVPSD-----KIWLPDIVLYNNADGDFDSS 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFLltqiiglhgipivvepersstn 205
Cdd:cd18997  76 YKTNVIVYSDGTVTWLPPAIFKSSCKIDVTYFPFDEQNCTLKFGSWTYDGSELDLQLK---------------------- 133
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 17531183 206 yasyfvNESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRRR 257
Cdd:cd18997 134 ------SDTVDLSDYIENGEWDLLGAPAKRNVVKYSccPEPYPDVTFTIHIRRK 181
LIC TIGR00860
Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of ...
21-483 1.84e-65

Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- orhomopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits arehomologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution.The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cationselective while glycine receptors are anion selective). [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273305 [Multi-domain]  Cd Length: 459  Bit Score: 218.81  E-value: 1.84e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183    21 EYRLLQYLKENYDSFERPVENSsAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:TIGR00860  31 ERKLLDELLKNYDARVRPVFGG-PPVTVSFNLFLRSIMDVDEKNMDYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDD 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   101 ddasfKLWRPDVLLFNSVSESFDSTYSSRFIV--SSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYI 178
Cdd:TIGR00860 110 -----SIWVPDIFFYNEKDARFHGITMTNVLVriHPNGSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDI 184
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   179 NLDFLLTqiiglhgipivvEPERSstnyasyfvnesiDLQVYLQNGEWDLEGTPGKRV-VQKFGTDEYHELYFYIHIRRR 257
Cdd:TIGR00860 185 KLEWKEQ------------GAVQV-------------DDSLFISLPEFELLGVYGTRYcTSETNTGEYPCLTFSFVLRRR 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   258 TLAYGINLIIPSLVISMMTILGFTLPPDAC-EKITLETTVLLSVIFFLQMVsSTSPPQSQSVPILAAFFSCCLMLVACSC 336
Cdd:TIGR00860 240 PLYYLLQLYIPSILIVILSWVSFWLPADASgARVSLGITTLLTMTTFSSGV-RESLPAVSYVKAIDVYFAVCMAFVFLAL 318
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   337 VFTVLTLSLHHRKPETHEmsptmRKIFIDWLPYILCMCKPDHPKTPkPKVLGKSIAPIHrLSTIPMLNLPrvSQTTFPDK 416
Cdd:TIGR00860 319 LETAFVNYVHHKDPAQGK-----RHLLLERCAWRLCKQEPGEDYRR-PALDHASLSSVE-MRAKDGGRGL--ESPTERQR 389
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17531183   417 NVFVYHevPAVIKNTSRICAELLIIERDIEKMlDKIEEdtkedmLRSEWRFAAMAVDRLCLYVFSAF 483
Cdd:TIGR00860 390 LLHSPP--PAEGDLDLAGILEEVRIAHRFRKR-DESEE------VVRDWKFRAKVIDKLSRMAFPLA 447
Neur_chan_memb pfam02932
Neurotransmitter-gated ion-channel transmembrane region; This family includes the four ...
265-491 1.10e-26

Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.


Pssm-ID: 460753 [Multi-domain]  Cd Length: 232  Bit Score: 107.74  E-value: 1.10e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   265 LIIPSLVISMMTILGFTLPPDAC-EKITLETTVLLSVIFFLQMVSSTSPPQSQSVPILAAFFSCCLMLVACSCVFTVLTL 343
Cdd:pfam02932   1 LIIPCVLISFLSWLVFWLPADAVgEKVTLGITVLLTMTVFLLLIRESLPKTSYVVPLIGKYLLFCMVFVFLSLVETVFVL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   344 SLHHRKPETHEMSPTMRKIFIDWLPYILCMCKPDHPKTPKPKVLGKSIAPIHrlstipMLNLPRvSQTTFPDKNVFVYHE 423
Cdd:pfam02932  81 NVHHRSPSTHKMPPWVRKIFLEKLPRLLGMKRPPEAPPPPASPGYGSKAEEY------ILRKPR-SELPFEKQSERHGLG 153
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183   424 VPAVIKNTS---RICAELLIIERDIEKMLDK-------IEEDTKEDMLRSEWRFAAMAVDRLCLYVFsafitMITCGL 491
Cdd:pfam02932 154 RETTCSYGCslgNGSSQPRELSPELKKAVEGvnfiakhLRSQDEYISVKEDWKYVAMVIDRLSRWIF-----PIAFVL 226
LGIC_TM_cation cd19051
transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, ...
261-348 3.74e-24

transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, and ZAC; This superfamily contains the transmembrane (TM) domain of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The ligand-gated ion channels (LGICs) in this family are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown.


Pssm-ID: 349853 [Multi-domain]  Cd Length: 112  Bit Score: 96.66  E-value: 3.74e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 261 YGINLIIPSLVISMMTILGFTLPPDACEKITLETTVLLSVIFFLQMVSSTSPPQSQSVPILAAFFSCCLMLVACSCVFTV 340
Cdd:cd19051   3 YVFNLILPCVLLSVLALLVFLLPPDSGEKVSLGITVLLSLTVFLLLVSESLPPTSDSVPLIGIYLLATMVLSALSTVLTV 82

                ....*...
gi 17531183 341 LTLSLHHR 348
Cdd:cd19051  83 IVLNLHHV 90
 
Name Accession Description Interval E-value
Neur_chan_LBD pfam02931
Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ...
21-258 6.30e-81

Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.


Pssm-ID: 460752 [Multi-domain]  Cd Length: 215  Bit Score: 250.65  E-value: 6.30e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183    21 EYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:pfam02931   1 EERLLDDLLSGYDKLVRPVANGSDPVTVSIGLYLQQIIDVDEKNQDLTTNVWLRQTWTDPRLAWNPEDYGGITSLRLPSD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   101 ddasfKLWRPDVLLFNSVSESFDST-YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYIN 179
Cdd:pfam02931  81 -----KIWKPDIVLYNKADGIHEVTtPNTNVRVYYDGTVLWSPPAIYKSSCSIDVTYFPFDEQNCSLKFGSWTYNGEEVD 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   180 LDFLLTQIIglhgipivvepersstnyasyFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRRR 257
Cdd:pfam02931 156 LRWDDDPPV---------------------VELEEIDLSDFWLNGEWDIVDVPAKRREYPYGcySELTGDVTFYFTLRRK 214

                  .
gi 17531183   258 T 258
Cdd:pfam02931 215 P 215
LGIC_ECD_nAChR cd18997
extracellular domain of nicotinic acetylcholine receptor; This family contains the ...
46-257 2.88e-77

extracellular domain of nicotinic acetylcholine receptor; This family contains the extracellular domain of nicotinic acetylcholine receptor (nAChR), a member of the pentameric "Cys-loop" superfamily of transmitter-gated ion channels. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits, and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Among subtypes of muscle nAChRs, the heteromeric subunits (alpha1)2, beta, gamma, and delta in fetal muscle, and the gamma subunit replaced by epsilon in adult muscle have been implicated in congenital myasthenic syndromes and multiple pterygium syndromes due to various mutations. This family also includes alpha- and beta-like nAChRs found in protostomia.


Pssm-ID: 349798  Cd Length: 181  Bit Score: 240.08  E-value: 2.88e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDST 125
Cdd:cd18997   1 VNVTFGLTLRQIIDVDEKNQVLTTNVWLRQEWNDERLTWNPSDYGGITSIRVPSD-----KIWLPDIVLYNNADGDFDSS 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFLltqiiglhgipivvepersstn 205
Cdd:cd18997  76 YKTNVIVYSDGTVTWLPPAIFKSSCKIDVTYFPFDEQNCTLKFGSWTYDGSELDLQLK---------------------- 133
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 17531183 206 yasyfvNESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRRR 257
Cdd:cd18997 134 ------SDTVDLSDYIENGEWDLLGAPAKRNVVKYSccPEPYPDVTFTIHIRRK 181
LIC TIGR00860
Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of ...
21-483 1.84e-65

Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- orhomopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits arehomologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution.The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cationselective while glycine receptors are anion selective). [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273305 [Multi-domain]  Cd Length: 459  Bit Score: 218.81  E-value: 1.84e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183    21 EYRLLQYLKENYDSFERPVENSsAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:TIGR00860  31 ERKLLDELLKNYDARVRPVFGG-PPVTVSFNLFLRSIMDVDEKNMDYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDD 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   101 ddasfKLWRPDVLLFNSVSESFDSTYSSRFIV--SSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYI 178
Cdd:TIGR00860 110 -----SIWVPDIFFYNEKDARFHGITMTNVLVriHPNGSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDI 184
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   179 NLDFLLTqiiglhgipivvEPERSstnyasyfvnesiDLQVYLQNGEWDLEGTPGKRV-VQKFGTDEYHELYFYIHIRRR 257
Cdd:TIGR00860 185 KLEWKEQ------------GAVQV-------------DDSLFISLPEFELLGVYGTRYcTSETNTGEYPCLTFSFVLRRR 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   258 TLAYGINLIIPSLVISMMTILGFTLPPDAC-EKITLETTVLLSVIFFLQMVsSTSPPQSQSVPILAAFFSCCLMLVACSC 336
Cdd:TIGR00860 240 PLYYLLQLYIPSILIVILSWVSFWLPADASgARVSLGITTLLTMTTFSSGV-RESLPAVSYVKAIDVYFAVCMAFVFLAL 318
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   337 VFTVLTLSLHHRKPETHEmsptmRKIFIDWLPYILCMCKPDHPKTPkPKVLGKSIAPIHrLSTIPMLNLPrvSQTTFPDK 416
Cdd:TIGR00860 319 LETAFVNYVHHKDPAQGK-----RHLLLERCAWRLCKQEPGEDYRR-PALDHASLSSVE-MRAKDGGRGL--ESPTERQR 389
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17531183   417 NVFVYHevPAVIKNTSRICAELLIIERDIEKMlDKIEEdtkedmLRSEWRFAAMAVDRLCLYVFSAF 483
Cdd:TIGR00860 390 LLHSPP--PAEGDLDLAGILEEVRIAHRFRKR-DESEE------VVRDWKFRAKVIDKLSRMAFPLA 447
LGIC_ECD_nAChR_proto_beta-like cd19032
extracellular domain of nicotinic acetylcholine receptor subunit beta-like found in ...
20-258 6.07e-59

extracellular domain of nicotinic acetylcholine receptor subunit beta-like found in protostomia; This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta-like in organisms that include arthropods, mollusks, annelid worms, and flat worms, and have their cholinergic system limited to the central nervous system. C. elegans genome encodes 29 acetylcholine receptor subunits, of which the levamisole-sensitive receptor alpha-subunits (L-AChR), UNC-38, UNC-63, and LEV-8, form heteromers with the two non-alpha (also known as beta-like) subunits, UNC-29 and LEV-1 found in this subfamily. This receptor functions as the main excitatory postsynaptic receptor at neuromuscular junctions, indicating that many are expressed in neurons. In insects, the receptors supply fast synaptic excitatory transmission and represent a major target for several insecticides. In Drosophila, ten exclusively neuronal nAChR subunits have been identified, Dalpha1-Dalpha7 and Dbeta1-Dbeta3, and various combinations of these subunits and mutations are key to nAChR function. Dbeta1 subunits in dopaminergic neurons play a role in acute locomotor hyperactivity caused by nicotine in male Drosophila. Mutations of Dbeta2 or Dalpha1 nAChR subunits in Drosophila strains have significantly lower neonicotinoid-stimulated release, but no changes in nicotine-stimulated release; they are highly resistant to the neonicotinoids nitenpyram and imidacloprid. This family also includes a novel nAChR found in Aplysia bag cell neurons (neuroendocrine cells that control reproduction) which is a cholinergic ionotropic receptor that is both, nicotine insensitive and acetylcholine sensitive.


Pssm-ID: 349833 [Multi-domain]  Cd Length: 208  Bit Score: 193.31  E-value: 6.07e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  20 DEYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSG 99
Cdd:cd19032   1 DEERLVRDLFRGYNYLIRPVRNMSEPVEVNFGLALIQLINVDEKNQIMKTNVWLTMYWNDYQLKWDPADYGGIKVIRVPP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 100 DddasfKLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYIN 179
Cdd:cd19032  81 D-----KVWKPDIVLFNNADGNYEVSYKSNVLIYSTGEVLWVPPAIYKSSCTIDVEYFPFDQQECEMKFGSWTFNGDEVS 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17531183 180 LDFlltqiiglhgipivvepersstnyasYFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRRRT 258
Cdd:cd19032 156 LDL--------------------------YNNKKFVDLSDYWKSGTWDIIDVPGQLVNKDDAGPTETDIIFKIKIRRKT 208
LGIC_ECD_cation cd18989
extracellular domain (LBD) of cationic Cys-loop neurotransmitter-gated ion channels; This ...
46-257 2.54e-55

extracellular domain (LBD) of cationic Cys-loop neurotransmitter-gated ion channels; This superfamily contains the extracellular domain (ECD) of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown.


Pssm-ID: 349790 [Multi-domain]  Cd Length: 180  Bit Score: 182.95  E-value: 2.54e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSgdddaSFKLWRPDVLLFNSV-SESFDS 124
Cdd:cd18989   1 VNVNVSFSLYSILDLDEVEQTLTLSGWLTLTWTDERLTWNPSDYGGITSIVVP-----SSEIWTPDIVLYNSVdSLDLLG 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 125 TYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLdflltqiiglhgipivvepersst 204
Cdd:cd18989  76 DSNTLVRVSSDGTVTWVPPGVLTTSCDIDVTYFPFDTQTCSLRFGSWSYTTDEINL------------------------ 131
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|...
gi 17531183 205 nyasYFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRRR 257
Cdd:cd18989 132 ----TPSSNGVDLEDYEENGEWELLSTSVSREEDKYCNETYSELTFTITLKRR 180
LGIC_ECD_nAChR_proto_alpha-like cd19031
extracellular domain of nicotinic acetylcholine receptor subunit alpha-like found in ...
20-259 2.13e-53

extracellular domain of nicotinic acetylcholine receptor subunit alpha-like found in protostomia; This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha-like in organisms that include arthropods, mollusks, annelid worms, and flat worms, and have their cholinergic system limited to the central nervous system. C. elegans genome encodes 29 acetylcholine receptor subunits, of which the levamisole-sensitive receptor (L-AChR) alpha-subunits, UNC-38, UNC-63, and LEV-8, included in this subfamily, form heteromers with the two non-alpha (also known as beta-like) subunits, UNC-29 and LEV-1. This receptor functions as the main excitatory postsynaptic receptor at neuromuscular junctions, indicating that many are expressed in neurons. Also included is the nicotinic alpha subunit MARA1 (Manduca ACh Receptor Alpha 1) which is expressed in Ca2+ responding neurons and contributes to the nicotinic responses in the neurons. In insects, the receptors supply fast synaptic excitatory transmission and represent a major target for several insecticides. In Drosophila, ten exclusively neuronal nAChRs have been identified, Dalpha1-Dalpha7 and Dbeta1-Dbeta3, and various combinations of these subunits and mutations are key to nAChR function. Alpha5 subunit is involved in alpha-bungarotoxin sensitivity while the alpha6 subunit is essential for the insecticidal effect of spinosad. nAChR agonists acetylcholine, nicotine, and neonicotinoids stimulate dopamine release in Drosophila larval ventral nerve cord and mutations in nAChR subunits affect how insecticides stimulate dopamine release.


Pssm-ID: 349832  Cd Length: 222  Bit Score: 179.40  E-value: 2.13e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  20 DEYRLLQYLKENYDSFERP-VENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFS 98
Cdd:cd19031   1 DAKRLYDDLLSNYNYNRRPrVTNDSDTLTVKLGLKLSQLIDVDEKNQIMTTNVWLEQEWYDYKLVWDPAEYGGVEMLYVP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  99 GDDdasfkLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYI 178
Cdd:cd19031  81 SED-----IWLPDIVLYNNADGNYEVTLMTKATLHYNGTVRWEPPAIYKSSCEIDVEYFPFDEQTCFMKFGSWTYDGFEV 155
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 179 NLDFLLTQiiglhgipivVEPERsstnyasYFVNESIDLQVYLQNGEWDLEGTPGKRVVQKF--GTDEYHELYFYIHIRR 256
Cdd:cd19031 156 DLRHVDQK----------YGSED-------EVIDVGIDLSEFYPSVEWDLLEVPARRNEKYYpcCDEPYPDITFNITLRR 218

                ...
gi 17531183 257 RTL 259
Cdd:cd19031 219 KTL 221
LGIC_ECD_nAChR_A7 cd19020
extracellular domain of neuronal acetylcholine receptor subunit alpha 7 (CHRNA7); This ...
45-257 6.91e-47

extracellular domain of neuronal acetylcholine receptor subunit alpha 7 (CHRNA7); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 7 (alpha7), encoded by the CHRNA7 gene. Alpha7 subunits form a homo-pentameric channel, displays marked permeability to calcium ions and is a major component of brain nicotinic receptors that are blocked by, and highly sensitive to, alpha-bungarotoxin. This protein is ubiquitously expressed in both the central nervous system and in the periphery, in several tissues, including adrenal, small intestine, testis, and stomach. CHRNA7 is located in a region identified as a major susceptibility locus for juvenile myoclonic epilepsy and a chromosomal location involved in the genetic transmission of schizophrenia. It is also genetically linked to other disorders with cognitive deficits, including bipolar disorder, ADHD, Alzheimer's disease, and Rett syndrome. An evolutionarily recent partial duplication of CHRNA7 on chromosome 15 forms a new gene, CHRFAM7A or FAM7A, which encodes the protein dup-alpha7. This protein assembles with alpha7 subunits, results in fewer binding sites and is a dominant negative regulator of alpha7 nAChR function.


Pssm-ID: 349821 [Multi-domain]  Cd Length: 180  Bit Score: 160.93  E-value: 6.91e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDS 124
Cdd:cd19020   1 PLTVYFSLSLMQIMDVDEKNQVLTTNIWLQMYWTDHYLQWNASEYPGVKNVRFPDG-----QIWKPDILLYNSADERFDA 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 125 TYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFLLTQIIGlhgipivvepersst 204
Cdd:cd19020  76 TFHTNVLVNSSGHCQYLPPGIFKSSCYIDVRWFPFDVQKCNLKFGSWTYGGWSLDLQMQEADISG--------------- 140
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 17531183 205 nyasyfvnesidlqvYLQNGEWDLEGTPGKRvVQKF---GTDEYHELYFYIHIRRR 257
Cdd:cd19020 141 ---------------YISNGEWDLVGVPGKR-NEKFyecCKEPYPDVTFTVTMRRR 180
LGIC_ECD_nAChR_proto-like cd19033
nicotinic acetylcholine receptor (nAChR) subunit extracellular domain in molluscs and annelids; ...
48-257 1.27e-46

nicotinic acetylcholine receptor (nAChR) subunit extracellular domain in molluscs and annelids; This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit found in molluscs, including several Lymnaea nAChRs, and annelids that are mostly uncharacterized. To date, 12 Lymnaea nAChRs have been identified which can be subdivided in two subtypes according to the residues that may be contributing to the selectivity of ion conductance. Phylogenetic analysis of the nAChR gene sequences suggests that anionic nAChRs in molluscs probably evolved from cationic ancestors through amino acid substitutions in the ion channel pore which is a mechanism different from acetylcholine-gated channels in other invertebrates.


Pssm-ID: 349834  Cd Length: 183  Bit Score: 160.14  E-value: 1.27e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  48 VKVRFLLN--QIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDST 125
Cdd:cd19033   1 VTVEFGLQliQILDLDENNQVLTTNVWSRYRWTDYHLRWNPEDYGGVTHVRIPPD-----KIWTPDIKLYNYADERLEER 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFlltqiiglhgipivvepersstn 205
Cdd:cd19033  76 REAMVVVYSTGTVLWMPQAIYKSTCEIDIKYFPFDTQTCYLKFGSWTYDGTRLDITF----------------------- 132
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 17531183 206 yasYFVNESIDLQVYLQNGEWDLEGTPGKRVVQKF--GTDEYHELYFYIHIRRR 257
Cdd:cd19033 133 ---YDNEEEIDLTDYIESNEWEILAYPAVKNVKYYpcCPEPYPDLTFFLVIKRR 183
LGIC_ECD_nAChR_A2 cd19015
extracellular domain of nicotinic acetylcholine receptor subunit alpha 2 (CHRNA2); This ...
21-256 4.80e-46

extracellular domain of nicotinic acetylcholine receptor subunit alpha 2 (CHRNA2); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 2 (alpha2), encoded by the CHRNA2 gene. It is specifically expressed in medial subpallium-derived amygdalar nuclei from early developmental stages to adult. This subunit is incorporated in heteropentameric neuronal nAChRs mainly with beta2 or beta4 subunits and, along with the alpha4 and alpha7, is one of the main nAChR subunits expressed in primate brain. In Xenopus laevis oocytes, when alpha2 is co-expressed with the beta2 subunit, two subtypes of alpha2beta2 nAChR are formed with either low or high ACh sensitivity. Mouse mutation studies show that alpha2 subunits in the nAChRs influence hippocampus-dependent learning and memory as well as CA1 synaptic plasticity in adolescent mice.


Pssm-ID: 349816 [Multi-domain]  Cd Length: 207  Bit Score: 159.83  E-value: 4.80e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  21 EYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:cd19015   1 EDRLFKHLFTGYNRWSRPVPNTSDVVIVKFGLSIAQLIDVDEKNQMMTTNVWLKQEWSDYKLRWNPTDFDNVTSIRVPSE 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 101 ddasfKLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd19015  81 -----MIWIPDIVLYNNADGEFAVTHMTKAHLFSTGKVKWVPPAIYKSSCSIDVTFFPFDQQNCKMKFGSWTYDKAKIDL 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183 181 DFLltqiiglhgipivvepersstnyasyfvNESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRR 256
Cdd:cd19015 156 EQM----------------------------EQTVDLKDYWESGEWAIVNATGTYNSKKYDccTEIYPDITYYFVIRR 205
LGIC_ECD_nAChR_A3 cd19016
extracellular domain of nicotinic acetylcholine receptor subunit alpha 3 (CHRNA3); This ...
21-256 2.48e-45

extracellular domain of nicotinic acetylcholine receptor subunit alpha 3 (CHRNA3); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 3 (alpha3), encoded by the CHRNA3 gene, and likely plays a role in neurotransmission. The alpha3 subunit is expressed in the aorta and macrophages, and may play a regulatory role in the process of vascular inflammation. One of the most broadly expressed subtype is the alpha3beta4 nAChR, also known as the ganglion-type nicotinic receptor, located in the autonomic ganglia and adrenal medulla, where activation yields post- and/or presynaptic excitation, mainly by increased Na+ and K+ permeability. The exact pentameric stochiometry of alpha3beta4 receptor is not known and functional assemblies with varying subunit stoichiometries are possible. Alpha4 plays a pivotal role in regulating the inflammatory responses in endothelial cells and macrophages, via mechanisms involving the modulations of multiple cell signaling pathways. Polymorphisms in this gene (CHRNA3) have been associated with an increased risk of smoking initiation and an increased susceptibility to lung cancer.


Pssm-ID: 349817 [Multi-domain]  Cd Length: 207  Bit Score: 157.79  E-value: 2.48e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  21 EYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSgd 100
Cdd:cd19016   1 EHRLFERLFEDYNEIIRPVANVSDPVIIQFEVSMSQLVKVDEVNQIMETNLWLKHIWNDYKLKWNPSDYGGAEFMRVP-- 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 101 ddaSFKLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd19016  79 ---AEKIWKPDIVLYNNAVGDFQVDDKTKALLKYTGEVTWIPPAIFKSSCKIDVTYFPFDYQNCTMKFGSWSYDKAKIDL 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183 181 dflltqiiglhgipivvepersstnyasYFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFGTDE--YHELYFYIHIRR 256
Cdd:cd19016 156 ----------------------------VLIGSSMNLKDYWESGEWAIIKAPGYKHDIKYNCCEeiYPDITYSLYIRR 205
LGIC_ECD_nAChR_B1 cd19024
extracellular domain of nicotinic acetylcholine receptor subunit beta 1 (CHRNB1); This ...
21-257 2.25e-43

extracellular domain of nicotinic acetylcholine receptor subunit beta 1 (CHRNB1); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta 1 (beta1), encoded by the CHRNB1 gene. It is a muscle type subunit found predominantly in the neuromuscular junction (NMJ), but also in other tissues and cell lines such as adrenal glands, carcinomas, brain, and lung. Simultaneous mRNA and protein expression of beta1 nAChR subunit is present in human placenta and skeletal muscle. The beta1 nAChR subunit forms a heteropentamer with either (alpha1)2, gamma and delta subunits in embryonic type or (alpha1)2, epsilon and delta subunits in adult type receptors. nAChRs containing beta1 subunits have been attributed to efficient clustering and anchoring of the receptors to the cytoskeleton which is important for formation of synapses in the NMJ. Mutations in the transmembrane domain region of this gene are associated with slow-channel congenital myasthenic syndrome (CMS).


Pssm-ID: 349825  Cd Length: 213  Bit Score: 152.67  E-value: 2.25e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  21 EYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:cd19024   1 EGQLLEKLFENYNPKVRPARTVGDRVVVSVGLTLAQLISLNEKNEEMTTKVYLDLEWTDYRLSWDPAEYDGIDSLRITSD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 101 DdasfkLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd19024  81 S-----VWLPDIVLMNNNDGNFDVALDVNVLVSSDGSVRWHPPAIYRSSCSIEVTYFPFDWQNCSMVFRSYTYDSSEVSL 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17531183 181 DflltqiiglHGIpivvEPERSSTNYAsyfvneSIDLQVYLQNGEWDLEGTPGKRVVQKfGTDEYHELYFYIHIRRR 257
Cdd:cd19024 156 Q---------HGL----DPDGKELQEI------VIHENTFIENGQWSIEHKPSRKNQLP-GDPLYEDITFYLIIRRK 212
LGIC_ECD_nAChR_A9 cd19022
extracellular domain of neuronal acetylcholine receptor subunit alpha 9 (CHRNA9); This ...
23-258 9.01e-43

extracellular domain of neuronal acetylcholine receptor subunit alpha 9 (CHRNA9); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 9 (alpha9), encoded by the CHRNA9 gene. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea as well as in keratinocytes, the pituitary gland, B-cells, and T-cells. Mammalian alpha9 subunits can form functional homomeric alpha9 receptors as well as the heteromeric alpha9alpha10 receptors, the latter being atypical since the heteromeric alpha9alpha10 receptor is composed only of alpha subunits compared to nAChRs typically assembled from alpha and beta subunits. A stoichiometry of (alpha9)2(alpha10)3 has been determined for the rat recombinant receptor. The alpha9alpha10 nAChR is an important therapeutic target for pain; selective block of alpha9alpha10 nicotinic acetylcholine receptors by the conotoxin RgIA has been shown to be analgesic in an animal model of nerve injury pain, and accelerates recovery of nerve function after injury, possibly through immune/inflammatory-mediated mechanisms. CHRNA9 polymorphisms are associated with non-small cell lung cancer, and effect of a particular SNP (rs73229797) and passive smoking exposure on risk of breast malignancy has been observed.


Pssm-ID: 349823  Cd Length: 207  Bit Score: 150.97  E-value: 9.01e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  23 RLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDdd 102
Cdd:cd19022   3 KLFNDLFEDYSNALRPVEDTDKVLNVTLQITLSQIKDMDERNQILTAYLWIRQSWYDAYLKWDRDEYDGLDSIRIPSN-- 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 103 asfKLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLdf 182
Cdd:cd19022  81 ---LVWRPDIVLYNKADDEFSEPVNTNVVLRYDGKITWDAPAITKSSCVVDVSYFPFDNQQCNLTFGSWTYNGNQVDI-- 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183 183 lltqIIGLhgipivvepersstnyasyfvnESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRRRT 258
Cdd:cd19022 156 ----INAL----------------------DSGDLSDFVEDVEWEVHGMPAVKNVITYGccSEPYPDVTFTLILKRRS 207
LGIC_ECD_nAChR_A5 cd19018
extracellular domain of nicotinic acetylcholine receptor subunit alpha 5 (CHRNA5); This ...
21-259 3.60e-41

extracellular domain of nicotinic acetylcholine receptor subunit alpha 5 (CHRNA5); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 5 (alpha5), encoded by the CHRNA5 gene, which is part of the CHRNA5/A3/B4 gene cluster. Polymorphisms in this gene cluster have been identified as risk factors for nicotine dependence, lung cancer, chronic obstructive pulmonary disease, alcoholism, and peripheral arterial disease. A loss-of-function polymorphism in CHRNA5 is strongly linked to nicotine abuse and schizophrenia; the alpha5 nAChR subunit is strategically situated in the prefrontal cortex (PFC), where a loss-of-function in this subunit may contribute to cognitive disruptions in both disorders. Alpha5 forms heteropentamers with alpha3beta2 or alpha3beta4 nAChRs which increases the calcium permeability of the resulting receptors possibly playing significant roles in the initiation of ACh-induced signaling cascades under normal and pathological condition. Acetylcholine (ACh) release and signaling via alpha4/beta2 nAChR subunits plays a central role in the control of attention, but a subset of these oligomers also contains alpha5 subunit. A strong association is seen between a CHRNA5 polymorphism and the risk of lung cancer, especially in smokers.


Pssm-ID: 349819 [Multi-domain]  Cd Length: 207  Bit Score: 146.65  E-value: 3.60e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  21 EYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:cd19018   3 EDRLFKHLFQDYQRWVRPVEHLNDTIKIKFGLAISQLVDVDEKNQLMTTNVWLKQEWIDVKLRWNPDDYAGITSIRVPSD 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 101 ddasfKLWRPDVLLFNSVSESFDSTySSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINl 180
Cdd:cd19018  83 -----SIWIPDIVLYDNADGRFEGT-STKTVVRYDGTITWTPPANYKSSCTIDVTFFPFDLQNCSMKFGSWTYDGSQVD- 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17531183 181 dflltqiiglhgipIVVEpersstnyasyfvNESIDLQVYLQNGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRRRTL 259
Cdd:cd19018 156 --------------IILE-------------DYDVDKRDFFDNGEWEIVSATGSKGNRTDGCCWYPFITYSFIIRRLPL 207
LGIC_ECD_nAChR_B3 cd19026
extracellular domain of nicotinic acetylcholine receptor subunit beta 3 (CHRNB3); This ...
48-256 2.18e-39

extracellular domain of nicotinic acetylcholine receptor subunit beta 3 (CHRNB3); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta 3 (beta3), encoded by the CHRNB3 gene. CHRNB3 polymorphisms have been reported to potentially affect nicotine-induced upregulation of nicotinic and to be associated with disorders such as schizophrenia, autism, and cancer. Beta3 subunit is depleted in the striatum of Parkinson's disease patients. Rare variants in CHRNB3 are also implicated in risk for alcohol and cocaine dependence and independently associated with bipolar disorder. Human alpha6beta2beta3* (* indicating possible additional assembly partners) nAChRs on dopaminergic neurons are important targets for drugs to treat nicotine addiction and Parkinson's disease; (alpha6beta2)(alpha4beta2)beta3 nAChR is essential for addiction to nicotine and a target for drug development for smoking cessation.


Pssm-ID: 349827  Cd Length: 179  Bit Score: 140.88  E-value: 2.18e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  48 VKVRFLL--NQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSgdddaSFKLWRPDVLLFNSVSESFDST 125
Cdd:cd19026   1 IKVLFGLkiSQLVDVDEKNQLMTTNVWLKQEWMDHKLRWNPEDYGGITSIRVP-----SESLWLPDIVLFENADGRFEGS 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLdflltqiiglhgipivvepersstn 205
Cdd:cd19026  76 LMTKAIVKYNGTVTWTPPASYKSSCTMDVTFFPFDRQNCSMKFGSWTYDGNMVDL------------------------- 130
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 17531183 206 yasYFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRR 256
Cdd:cd19026 131 ---ILIDENVDRKDFFDNGEWEILNAKGMKGNRKDGLYSYPFITYSFVLRR 178
LGIC_ECD_nAChR_A7L cd19021
extracellular domain of neuronal acetylcholine receptor subunit alpha-7-like; This family ...
46-257 2.63e-39

extracellular domain of neuronal acetylcholine receptor subunit alpha-7-like; This family contains the extracellular domain of nicotinic acetylcholine receptor (nAChR), a member of the pentameric "Cys-loop" superfamily of transmitter-gated ion channels. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease.


Pssm-ID: 349822 [Multi-domain]  Cd Length: 179  Bit Score: 140.56  E-value: 2.63e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDST 125
Cdd:cd19021   1 IVVELQLSLLQIIDVDEKNQVLITNAWLQMYWVDIYLSWDQYEYPGVQNLRFPSD-----QIWVPDILLYNSADERFDAT 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFLltqiiglhgipivvepersstn 205
Cdd:cd19021  76 FHTNVLVNYSGSCQYIPPGILKSTCYIDVRWFPFDVQKCDLKFGSWTHSGWLIDLQML---------------------- 133
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 17531183 206 yasyfvneSIDLQVYLQNGEWDLEGTPGKR--VVQKFGTDEYHELYFYIHIRRR 257
Cdd:cd19021 134 --------EADISNYISNGEWDLVGVPGKRneLYYECCKEPYPDVTYTITMRRR 179
LGIC_ECD_nAChR_A10 cd19023
extracellular domain of neuronal acetylcholine receptor subunit alpha 10 (CHRNA10); This ...
46-257 1.41e-37

extracellular domain of neuronal acetylcholine receptor subunit alpha 10 (CHRNA10); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 10 (alpha10), encoded by the CHRNA10 gene. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea as well as in keratinocytes, the pituitary gland, B-cells, and T-cells. Unlike alpha9 nAChR subunits, alpha10 subunits do not generate functional channels when expressed heterologously, suggesting that alpha10 might serve as a structural subunit, much like a beta subunit of heteromeric receptors, providing only complementary components to the agonist binding site. Mammalian alpha10 subunits can form functional heteromeric alpha9alpha10 receptors, an atypical heteromeric receptor since it is composed only of alpha subunits compared to nAChRs typically assembled from alpha and beta subunits. A stoichiometry of (alpha9)2(alpha10)3 has been determined for the rat recombinant receptor. The alpha9alpha10 nAChR is an important therapeutic target for pain; selective block of alpha9alpha10 nicotinic acetylcholine receptors by the conotoxin RgIA has been shown to be analgesic in an animal model of nerve injury pain, and accelerates recovery of nerve function after injury, possibly through immune/inflammatory-mediated mechanisms.


Pssm-ID: 349824  Cd Length: 181  Bit Score: 136.27  E-value: 1.41e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDST 125
Cdd:cd19023   1 LNVTLQITLSQIIDMDERNQILTAYLWIRQVWLDAYLAWNKEAYDGLDTIRIPSS-----YVWRPDIVLYNNADDRFTGS 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFLLtqiiglhgipivvepersstn 205
Cdd:cd19023  76 METNVVIRSDGQIMWDSPAITKSSCKVDVSFFPFDGQQCRLTFGSWTYNGNQIDILNLL--------------------- 134
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 17531183 206 yasyfvnESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRRR 257
Cdd:cd19023 135 -------DTGDLTDFVENVEWEVLGMPAKRNVITYGccSEPYPDVTYTLLLKRR 181
LGIC_ECD_nAChR_A1 cd19014
extracellular domain of nicotinic acetylcholine receptor subunit alpha 1 (CHRNA1); This ...
20-226 3.20e-36

extracellular domain of nicotinic acetylcholine receptor subunit alpha 1 (CHRNA1); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 1 (alpha1), encoded by the CHRNA1 gene. These muscle type nicotinic subunits form heteropentamers with other nAChR subunits, most broadly expressed as combination of two alpha1, beta1, delta, and epsilon subunits in mature muscles, and of two alpha1, beta1, delta, and gamma in embryonic cells. The alpha1 subunit in human nAChR is the primary target of Myasthenia gravis antibodies that disrupt communication between the nervous system and the muscle, causing chronic muscle weakness.


Pssm-ID: 349815  Cd Length: 210  Bit Score: 133.44  E-value: 3.20e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  20 DEYRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSG 99
Cdd:cd19014   2 HETRLVADLFKNYNKVVRPVEHHKDFVVVTVGLQLIQLINVDEVNQIVTTNVRLKQQWIDVNLKWNPDDYGGIKKIRIPS 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 100 DDdasfkLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYin 179
Cdd:cd19014  82 SD-----IWRPDLVLYNNADGDFAIVKETKVLLEYTGKITWTPPAIFKSYCEIIVTHFPFDQQNCSMKLGTWTYDGTL-- 154
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 17531183 180 ldflltqiiglhgipIVVEPErsstnyasyfvNESIDLQVYLQNGEW 226
Cdd:cd19014 155 ---------------VVINPE-----------SDRPDLSNFMESGEW 175
LGIC_ECD_nAChR_B2 cd19025
extracellular domain of nicotinic acetylcholine receptor subunit beta 2 (CHRNB2); This ...
23-235 6.85e-36

extracellular domain of nicotinic acetylcholine receptor subunit beta 2 (CHRNB2); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta 2 (beta2), encoded by the CHRNB2 gene. The most abundant nicotinic subtype in the human brain is alpha4beta2 receptor which is known to assemble in two functional subunit stoichiometries, (alpha4)3(beta2)2 and (alpha4)2(beta2)3, the latter having a much higher affinity for both acetylcholine and nicotine. This subtype is implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism, and neurodegenerative disorders such as Parkinson's disease and Alzheimer's disease. Thus, pharmacological ligands targeting this subtype have been researched and developed as a treatment approach implicated in these diseases. They include agonists such as varenicline and cytisine used as smoking cessation aids, as well as positive allosteric modulators (PAMs) such as desformylflustrabromine (dFBr), which are ligands that bind to nicotinic receptors at sites other than the orthosteric site where acetylcholine binds, and are not able to act as agonists on nAChR.


Pssm-ID: 349826  Cd Length: 204  Bit Score: 132.43  E-value: 6.85e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  23 RLLQYL--KENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSgd 100
Cdd:cd19025   1 RLVEHLlgPSRYNKLIRPATNGSQLVTVQLMVSLAQLISVHEREQIMTTNVWLTQEWEDYRLTWDPAEFDNMKKVRLP-- 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 101 ddaSFKLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd19025  79 ---SKHIWLPDVVLYNNADGMYEVSFYSNAVVSYDGSIFWLPPAIYKSACKIEVKHFPFDQQNCTLKFRSWTYDRTEIDL 155
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 17531183 181 dflltqiiglhgipiVVEPERSStnyasyfvnesidLQVYLQNGEWDLEGTPGKR 235
Cdd:cd19025 156 ---------------VLRSDVAS-------------LDDFTPSGEWDIVALPGRR 182
LGIC_ECD_nAChR_B4 cd19027
extracellular domain of nicotinic acetylcholine receptor subunit beta 4 (CHRNB4); This ...
46-237 1.49e-33

extracellular domain of nicotinic acetylcholine receptor subunit beta 4 (CHRNB4); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta 4 (beta4), encoded by the CHRNB4 gene and ubiquitously expressed on lung epithelial cells. The cluster of human neuronal nicotinic receptor gene CHRNA5-CHRNA3-CHRNB4 is related to drug-related behaviors and the development of lung cancer. One of the most broadly expressed subtype is the alpha-3 beta-4 nAChR, also known as the ganglion-type nicotinic receptor, located in the autonomic ganglia and adrenal medulla, where activation yields post- and/or pre-synaptic excitation, mainly by increased Na+ and K+ permeability. Beta4 forms heteromeric nAchRs to modulate receptor affinity for nicotine, but the exact pentameric stochiometry of alpha3beta4 receptor is not known; functional assemblies with varying subunit stoichiometries are possible.


Pssm-ID: 349828  Cd Length: 178  Bit Score: 125.11  E-value: 1.49e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSgdddaSFKLWRPDVLLFNSVSESFDST 125
Cdd:cd19027   1 VSIKLQLSLAQLISVNEREQIMTTNVWLNQEWTDYRLTWNPSDYEGINKLRIP-----AKHIWLPDIVLYNNADGTYEVS 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNgqYINLDFLLtqiiglhgipivvepersSTN 205
Cdd:cd19027  76 VYTNAIVQNNGSVAWLPPAIYKSACKIEVKHFPFDQQNCTLKFRSWTYD--HTEIDMVL------------------KTP 135
                       170       180       190
                ....*....|....*....|....*....|..
gi 17531183 206 YASyfvnesidLQVYLQNGEWDLEGTPGKRVV 237
Cdd:cd19027 136 TAS--------MDDFTPSGEWDIVALPGRRTV 159
LGIC_ECD cd03558
extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ...
46-256 3.24e-33

extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC)); This superfamily contains the extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), type-A gamma-aminobutyric acid receptor (GABAAR) and glycine receptor (GlyR). These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. GABAAR and GlyR are anionic channels, both mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. These ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on the inhibitory half of the Cys-loop receptor family. The ECD contains the ligand binding sites for these receptors.


Pssm-ID: 349787  Cd Length: 179  Bit Score: 124.07  E-value: 3.24e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDDdasfkLWRPDVLLFNSVSESFDST 125
Cdd:cd03558   1 VTVTVNISLAQLISVDEVNMDYTTNVFLRQSWIDKRLAYSPADYGGVDSLRLPSEQ-----IWLPDLVFYNNKDADFVTT 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLdflltqiiglhgipiVVEPERSStn 205
Cdd:cd03558  76 DNVLIRLSPDGTVLYSPRAILKSACPMDLKRFPFDQQNCTMKLESWTYDTTDIEL---------------VWDSERPD-- 138
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 17531183 206 yasyfVNESIDLqvylqnGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRR 256
Cdd:cd03558 139 -----QADFLEL------PEWDIVEKRGRYCTVVYNTGIYSDITYRFRLKR 178
LGIC_ECD_nAChR_D cd19028
extracellular domain of nicotinic acetylcholine receptor subunit delta (CHRND); This subfamily ...
23-257 1.22e-32

extracellular domain of nicotinic acetylcholine receptor subunit delta (CHRND); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit delta (delta), encoded by the CHRND gene and found in the muscle. Delta nAChR subunit forms a heteropentamer with either (alpha1)2, beta and gamma subunits in embryonic type or (alpha1)2, beta and epsilon subunits in adult type receptors. Defects in this gene are a cause of multiple pterygium syndrome lethal type (MUPSL), congenital myasthenic syndrome slow-channel type (SCCMS), and congenital myasthenic syndrome fast-channel type (FCCMS). The slow-channel congenital myasthenic syndromes (SCCMS) are caused by prolonged opening episodes of AChR due to dominant gain-of-function mutations in the transmembrane regions of the heteropentamer. These mutations produce an increase in the channel opening rate, a decrease in the channel closing rate, or an increase in the affinity of ACh for the AChR, resulting in the stabilization of the open state or the destabilization of the closed state of the AChR.


Pssm-ID: 349829  Cd Length: 221  Bit Score: 124.14  E-value: 1.22e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  23 RLLQYL--KENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGD 100
Cdd:cd19028   2 RLINHLfiERGYNKELRPVAHKDEVVNVALALTLSNLISLKEVDETLTTNVWVEHGWYDHRLTWNASEYGNISILRLPPE 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 101 ddasfKLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd19028  82 -----MVWLPEIVLENNNDGQFEVAYYCNVLVYSDGFVYWLPPAIFRSSCPINVNYFPFDWQNCSLKFSSLNYNAKEINL 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 181 DflltqiiglhgipIVVEPERSSTNYASYFVnesIDLQVYLQNGEWDLEGTPGKRVVQK---FGTDEYHELYFYIHIRRR 257
Cdd:cd19028 157 D-------------LKTDTDDGKTYPVEWII---IDPEGFTENGEWEIVHKPAKKNIDPskpPESTKYQDITFYLIIKRK 220
LGIC_ECD_nAChR_A6 cd19019
extracellular domain of nicotinic acetylcholine receptor subunit alpha 6 (CHRNA6); This ...
48-256 1.52e-32

extracellular domain of nicotinic acetylcholine receptor subunit alpha 6 (CHRNA6); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 6 (alpha6), encoded by the CHRNA6 gene. Human (alpha6beta2)(alpha4beta2)3 nicotinic acetylcholine receptors (AChRs) are essential for addiction to nicotine and a target for drug development for smoking cessation. In xenopus oocytes, data show efficient expression of (alpha6beta2)2beta3 AChR subunits with only small changes in alpha6 subunits, while not altering AChR pharmacology or channel structure. Alternatively spliced transcript variants have been observed for this gene. Single nucleotide polymorphisms in this gene have been associated with both nicotine and alcohol dependence. CHRNA6 has a cellular expression signature for retinal ganglion cells with high correlation to Thy1, a known marker, and is preferentially expressed by retinal ganglion cells (RGCs) in the young and adult mouse retina and expression is reduced in glaucoma. A genetic variant in CHRNB3#CHRNA6 cluster is associated with esophageal adenocarcinoma.


Pssm-ID: 349820 [Multi-domain]  Cd Length: 181  Bit Score: 122.44  E-value: 1.52e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  48 VKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDSTYS 127
Cdd:cd19019   3 VHFEVAITQLVNVDEVNQIMETNLWLRHIWNDYKLRWDPREYDGIEFMRVPAD-----KIWKPDIVLYNNAVGDFQVEGK 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 128 SRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLdflltQIIGlhgipivvepersstnya 207
Cdd:cd19019  78 TKALLKYNGMITWTPPAIFKSSCPMDITFFPFDHQNCSLKFGSWTYDKAKIDL-----LIIG------------------ 134
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 17531183 208 syfvnESIDLQVYLQNGEWDLEGTPGKRVVQKFGTDE--YHELYFYIHIRR 256
Cdd:cd19019 135 -----SKVDMNDFWENSEWEIVDASGYKHDIKYNCCEeiYTDITYSFYIRR 180
LGIC_ECD_nAChR_G cd19029
extracellular domain of nicotinic acetylcholine receptor subunit gamma (CHRNG); This subfamily ...
47-257 3.13e-32

extracellular domain of nicotinic acetylcholine receptor subunit gamma (CHRNG); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit gamma (gamma), encoded by the CHRNG gene expressed during early fetal development, and replaced by the epsilon subunit in the adult. The gamma subunit forms a heteropentamer with (alpha1)2, beta, and delta and plays a role in neuromuscular organogenesis and ligand binding. Disruption of gamma subunit expression prevents the correct localization of the receptor in cell membranes. Mutations in CHRNG may cause the non-lethal Escobar variant (EVMPS) and lethal form (LMPS) of multiple pterygium syndrome (MPS), a condition characterized by prenatal growth failure with pterygium and akinesia leading to muscle weakness and severe congenital contractures, as well as scoliosis. Muscle-type acetylcholine receptor is the major antigen in the autoimmune disease myasthenia gravis.


Pssm-ID: 349830  Cd Length: 193  Bit Score: 121.80  E-value: 3.13e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  47 DVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSgdddaSFKLWRPDVLLFNSVSESFDSTY 126
Cdd:cd19029   4 DVTLKLTLTNLISLNEKEEALTTNVWIEIQWNDYRLRWNPSEYEGIWVLRVP-----STMVWLPDIVLENNIDGQFEVAY 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 127 SSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLdfLLTQIIGLHGIPIVVEPErsstny 206
Cdd:cd19029  79 YANVLVYPDGSMYWLPPAIYRSTCPIEVTYFPFDWQNCSLVFQSQTYSANEINL--QLSVEEGTTIEWIDIDPE------ 150
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 17531183 207 asyfvnesidlqVYLQNGEWDLEGTPGKRVV-QKFGTD--EYHELYFYIHIRRR 257
Cdd:cd19029 151 ------------AFTENGEWAIRHRPAKKILnPQLPKDdlGYQEIVFYLIIQRK 192
LGIC_ECD_nAChR_A4 cd19017
extracellular domain of neuronal acetylcholine receptor subunit alpha 4 (CHRNA4); This ...
48-180 4.82e-30

extracellular domain of neuronal acetylcholine receptor subunit alpha 4 (CHRNA4); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 4 (alpha4), encoded by the CHRNA4 gene. Alpha4 forms a functional nAChR by interacting with either nAChR beta2 or beta4 subunits. Alpha4beta2, the major heteropentameric nAChR in the brain, exists in two isoforms, (alpha4)3(beta2)2 and (alpha4)2(beta2)3, with the latter believed to constitute the majority of alpha4beta2 nAChR in the cortex. Both isoforms contain two canonical alpha4:beta2 ACh-binding sites with either low or high ACh sensitivity. This protein is an integral membrane receptor subunit that can interact with either nAChR beta-2 or nAChR beta-4 to form a functional receptor. Mutations in this gene (CHRNA4) cause nocturnal frontal lobe epilepsy type 1. Polymorphisms in this gene may provide protection against nicotine addiction.


Pssm-ID: 349818  Cd Length: 181  Bit Score: 115.53  E-value: 4.82e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  48 VKVRFLLN--QIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDST 125
Cdd:cd19017   1 VLVRFGLSiaQLIDVDEKNQMMTTNVWVKQEWHDYKLRWDPADYENVTSIRIPSE-----LIWRPDIVLYNNADGDFAVT 75
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 17531183 126 YSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd19017  76 HLTKAHLFHDGRVQWTPPAIYKSSCSIDVTFFPFDQQNCTMKFGSWTYDKAKIDL 130
LGIC_AChBP cd18995
acetylcholine binding protein (AChBP); This family contains acetylcholine binding protein ...
48-257 4.79e-29

acetylcholine binding protein (AChBP); This family contains acetylcholine binding protein (AChBP) which is a soluble extracellular domain homolog secreted by protostomia, and has been widely recognized as a surrogate for the ligand binding domain of nicotinic acetylcholine receptors (nAChRs). AChBP forms a pentameric structure where the interfaces between the subunits provide an acetylcholine (ACh) binding pocket homologous to the binding pocket of nAChRs. Thus far, AChBPs have been characterized only in aquatic mollusks, which have shown low sensitivity to neonicotinoids, the insecticides targeting insect nAChRs. Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) which has been found in glial cells as a water-soluble protein modulating synaptic ACh concentration has its the binding pocket show better resemblance as it contains all the five aromatic residues fully conserved in nAChR. Five AChBP subunits have been characterized in Pardosa pseudoannulata, a predator enemy against rice insect pests, and share higher sequence similarities with nAChR subunits of both insects and mammals compared with mollusk AChBP subunits.


Pssm-ID: 349796  Cd Length: 180  Bit Score: 112.84  E-value: 4.79e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  48 VKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVS--ESFDSt 125
Cdd:cd18995   3 VSLSLTLQDILSVDEETNEVDLVGWLQMTWKDPRLTWDPAEYGNLKNLRLPSS-----KIWTPDIAVYNSIGapSVLFS- 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 ySSRFIVSSNGDVQQNPPGIFRFVCQIDVTyYPFDKQTCFLKLGSWTYNGQYINLDflltqiiglhgipivvePErsstn 205
Cdd:cd18995  77 -PQLVLVSSDGTVLWVPPIRIRFSCDLDNV-DPEDGATCRLKIGSWTYSGREIDLN-----------------TG----- 132
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 17531183 206 yasyfvNESIDLQVYLQNGEWDLEGTPGKRVVQKFG--TDEYHELYFYIHIRRR 257
Cdd:cd18995 133 ------TDVDLDSYYNQSSKWELLSATQKREVKTYSccPEPYPDIEFVFTFKKR 180
LGIC_ECD_5-HT3A cd19011
extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit A ...
23-257 2.75e-28

extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit A (5HT3A); This subfamily contains extracellular domain of subunit A of serotonin 5-HT3 receptor (5-HT3AR), encoded by the HTR3A gene. 5-HT3A subunit forms a homopentameric complex or a heterologous combination with other subunits (B-E). Heteromeric combination of A and B subunits provides the full functional features of this receptor, since either subunit alone results in receptors with very low conductance and response amplitude. 5-HT3A receptors are located in the dorsal vagal complex of the brainstem and in the gastrointestinal (GI) tract, and form a channel circuit that controls gut motility, secretion, visceral perception, and the emesis reflex. These receptors are implicated in several GI and psychiatric disorder conditions including anxiety, depression, bipolar disorder, and irritable bowel syndrome (IBS). Several 5-HT3AR antagonists, such as the isoquinoline Palonosetron, are in clinical use to control emetic reflexes associated with gastrointestinal pathologies and cancer therapies. SNPs in the 5-HT3A serotonin receptor gene are associated with psychiatric disorders.


Pssm-ID: 349812  Cd Length: 208  Bit Score: 111.47  E-value: 2.75e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  23 RLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDdd 102
Cdd:cd19011   3 RLSDHLLEGYKKGVRPVRDWRKPTTVSIDVMVYAILNVDEKNQVLTTYIWYRQYWTDEFLQWNPEDFDNVTQLSIPTD-- 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 103 asfKLWRPDVLL--FNSVSESFDSTYssrFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd19011  81 ---SIWVPDILIneFVDVGKSPEIPY---VYVNHEGEVQNYKPIQVVTACSLDIYNFPFDVQNCSLTFTSWLHTIQDINI 154
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183 181 DFLLTqiiglhgiPIVVEPERSstnyasyfvnesidlqVYLQNGEWDLEGT-PGKRVVQKFGTDEYHELYFYIHIRRR 257
Cdd:cd19011 155 SLWRS--------PEEVKSDKS----------------VFMNQGEWELLGVlPQYREFSIDISDSYAEMKFYVVIRRR 208
Neur_chan_memb pfam02932
Neurotransmitter-gated ion-channel transmembrane region; This family includes the four ...
265-491 1.10e-26

Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.


Pssm-ID: 460753 [Multi-domain]  Cd Length: 232  Bit Score: 107.74  E-value: 1.10e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   265 LIIPSLVISMMTILGFTLPPDAC-EKITLETTVLLSVIFFLQMVSSTSPPQSQSVPILAAFFSCCLMLVACSCVFTVLTL 343
Cdd:pfam02932   1 LIIPCVLISFLSWLVFWLPADAVgEKVTLGITVLLTMTVFLLLIRESLPKTSYVVPLIGKYLLFCMVFVFLSLVETVFVL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183   344 SLHHRKPETHEMSPTMRKIFIDWLPYILCMCKPDHPKTPKPKVLGKSIAPIHrlstipMLNLPRvSQTTFPDKNVFVYHE 423
Cdd:pfam02932  81 NVHHRSPSTHKMPPWVRKIFLEKLPRLLGMKRPPEAPPPPASPGYGSKAEEY------ILRKPR-SELPFEKQSERHGLG 153
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183   424 VPAVIKNTS---RICAELLIIERDIEKMLDK-------IEEDTKEDMLRSEWRFAAMAVDRLCLYVFsafitMITCGL 491
Cdd:pfam02932 154 RETTCSYGCslgNGSSQPRELSPELKKAVEGvnfiakhLRSQDEYISVKEDWKYVAMVIDRLSRWIF-----PIAFVL 226
LGIC_ECD_5-HT3 cd18996
extracellular domain of serotonin 5-HT3 receptor; This family contains extracellular domain of ...
22-257 1.21e-25

extracellular domain of serotonin 5-HT3 receptor; This family contains extracellular domain of serotonin 5-HT3 receptor which belongs to the Cys-loop superfamily of ligand-gated ion channels (LGICs). This ion channel is cation-selective and mediates neuronal depolarization and excitation within the central and peripheral nervous systems. Like other ligand gated ion channels, the 5-HT3 receptor consists of five subunits arranged around a central ion conducting pore, which is permeable to Na+, K+, and Ca2+ ions. Binding of the neurotransmitter 5-hydroxytryptamine (serotonin) to the 5-HT3 receptor opens the channel, which then leads to an excitatory response in neurons, and the rapidly activating, desensitizing, inward current is predominantly carried by Na+ and K+ ions. This receptor is most closely related by homology to the nicotinic acetylcholine receptor (nAChR). Five subunits have been identified for this family: 5-HT3A, 5-HT3B, 5-HT3C, 5-HT3D, and 5-HT3E, encoded by HTR3A-E genes. Only 5-HT3A subunits are able to form functional homomeric receptors, whereas the 5-HT3B, C, D, and E subunits form heteromeric receptors with 5-HT3A. Different receptor subtypes are important mediators of nausea and vomiting during chemotherapy, pregnancy, and following surgery, while some contribute to neuro-gastroenterologic disorders such irritable bowel syndrome (IBS) and eating disorders as well as co-morbid psychiatric conditions. 5-HT3 receptor antagonists are established treatments for emesis and IBS, and are beneficial in the treatment of psychiatric diseases.


Pssm-ID: 349797  Cd Length: 215  Bit Score: 104.38  E-value: 1.21e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  22 YRLLQYLKENYDS----FERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRF 97
Cdd:cd18996   5 YDVLKALNKTFNSlhltYTRPVKNWTPPTTVYLDLTLYAILDVDEKLQTLTTYIWLEMVWFNEFLSWNPEQFCGISKVSV 84
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  98 SGDddasfKLWRPDVLLFNSVSE--SFDSTYSSrfiVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNG 175
Cdd:cd18996  85 PED-----TLWKPDILIYEMTDKdkSPKIPYVY---VSNNGTVRNYKPLQVVSTCSLDIYKFPFDTQNCNLTFSSFLHTV 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 176 QYINLDflltqiiglhgipivvePERSSTNyasyfVNESidLQVYLQN-GEWDLEG-TPGKRVVQKFGtDEYHELYFYIH 253
Cdd:cd18996 157 NDIILN-----------------PGSNSEE-----ITSE--SKEIFQTqGEWELLNiKVSDEKLSLLG-NSFDQIVYQIT 211

                ....
gi 17531183 254 IRRR 257
Cdd:cd18996 212 IKRR 215
LGIC_ECD_nAChR_E cd19030
extracellular domain of nicotinic acetylcholine receptor subunit epsilon (CHRNE); This ...
48-233 1.22e-25

extracellular domain of nicotinic acetylcholine receptor subunit epsilon (CHRNE); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit epsilon (epsilon), encoded by the CHRNE gene and found in adult skeletal muscle. Epsilon subunit forms a heteropentamer with (alpha1)2, beta and delta after birth, replacing the gamma subunit seen in embryonic receptors. The adult-type epsilon-AChR has a higher conductance and a shorter open time compared to embryonic gamma-AChR and the open channel is non-selectively cation permeable. Mutations of the CHRNE gene are the most common causes of congenital myasthenic syndrome (CMS), most of which are autosomal recessive loss-of-function mutations, resulting in endplate AChR deficiency. A highly fatal fast-channel syndrome is caused by AChR epsilon subunit mutation (Trp to Arg; changing environment from anionic to cationic) at the agonist binding site at the alpha/epsilon interface of the receptor, thus disrupting agonist binding affinity and gating efficiency.


Pssm-ID: 349831  Cd Length: 191  Bit Score: 103.55  E-value: 1.22e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  48 VKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDddasfKLWRPDVLLFNSVSESFDSTYS 127
Cdd:cd19030   3 ISLKVTLTNLISLNEKEETLTTSVWIGIDWQDYRLNYSKDDFGGVETLRVPSE-----LVWLPEIVLENNIDGQFGVAYD 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 128 SRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFlltqiiglhgipiVVEPERSSTNYA 207
Cdd:cd19030  78 ANVLVYEGGSVSWLPPAIYRSTCAVEVTYFPFDWQNCSLIFRSQTYNAEEVEFTF-------------AVDDDGKTINKI 144
                       170       180
                ....*....|....*....|....*.
gi 17531183 208 syfvneSIDLQVYLQNGEWDLEGTPG 233
Cdd:cd19030 145 ------DIDTEAYTENGEWAIDFCPG 164
LGIC_TM_cation cd19051
transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, ...
261-348 3.74e-24

transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, and ZAC; This superfamily contains the transmembrane (TM) domain of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The ligand-gated ion channels (LGICs) in this family are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown.


Pssm-ID: 349853 [Multi-domain]  Cd Length: 112  Bit Score: 96.66  E-value: 3.74e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 261 YGINLIIPSLVISMMTILGFTLPPDACEKITLETTVLLSVIFFLQMVSSTSPPQSQSVPILAAFFSCCLMLVACSCVFTV 340
Cdd:cd19051   3 YVFNLILPCVLLSVLALLVFLLPPDSGEKVSLGITVLLSLTVFLLLVSESLPPTSDSVPLIGIYLLATMVLSALSTVLTV 82

                ....*...
gi 17531183 341 LTLSLHHR 348
Cdd:cd19051  83 IVLNLHHV 90
LGIC_ECD_5-HT3C_E cd19013
extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit E ...
31-257 1.12e-23

extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit E (5HT3E); may include subunits C and D (5-HT3C,D); This subfamily contains extracellular domain of subunit E of serotonin 5-HT3 receptor (5-HT3ER), encoded by the HTR3E gene, and may also contain subunits C and D, all three encoding genes forming a cluster on chromosome 3. Data show that 5-HT3C, 5-HT3D, and 5-HT3E subunits are co-expressed with 5-HT3A in cell bodies of myenteric neurons, and that 5-HT3A and 5-HT3D are expressed in submucosal plexus of the human large intestine while HTR3E is restricted to the colon, intestine, and stomach. None of these subunits can form functional homopentamers, but, upon co-expression with the 5-HT3A subunit, they give rise to functional receptors that differ in maximal responses to 5-HT, and thus modulate 5-HT3 receptor's pharmacological profile. HTR3A and HTR3E polymorphisms have been shown to remarkably up-regulate the expression of 5-HT3 receptors, which have been proved to cause the gastric functional disorders including emesis, eating disorders and IBS-D.


Pssm-ID: 349814  Cd Length: 215  Bit Score: 99.01  E-value: 1.12e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  31 NYDSFeRPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDDdasfkLWRP 110
Cdd:cd19013  19 DRKAF-RPVMNLSTPTNVNISFTLYAILGVNEKAQLLTTFLWLRLVWDNEFLSWDPEECEGVTKISVPREN-----LWVP 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 111 DVLLFNSVSEsfDSTYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFLLTqiig 189
Cdd:cd19013  93 DIFINEFMDE--DKSPKVPYVyVSHTGRVRDDKPVRVVSSCNLDIFTFPFDIQNCTLTFGSYLHTVDDIKLFLLLS---- 166
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183 190 lhgipiVVEPERSSTNYASyfvnesidlqvylQNGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRRR 257
Cdd:cd19013 167 ------VEEILKNSRKVLT-------------TQGEWELVDIKAAKAKLSFGEELYDEITFYVIIRRR 215
LGIC_ECD_5-HT3B cd19012
extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit B ...
22-257 3.77e-22

extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit B (5HT3B); This subfamily contains extracellular domain of subunit B of serotonin 5-HT3 receptor (5-HT3BR), encoded by the HTR3B gene. 5-HT3B is not functional as a homopentameric complex and is co-expression with the 5-HT3A subunit, resulting in heteromeric 5-HT3AB receptors that are functionally distinct from homomeric 5-HT3A receptors. This receptor causes fast, depolarizing responses in neurons after activation, with affinities of competitive ligands at the two receptor subtypes extracellular domains mostly similar. HTR3B gene variants may contribute to variability in severity of and response to anti-emetic therapy for nausea and vomiting in pregnancy, as well as efficacy of ondansetron in cancer chemotherapy, radiation therapy, or surgery. 5-HT3B subunit affects high-potency inhibition of 5-HT3 receptors by morphine by reducing its affinity at its high-affinity, non-competitive site.


Pssm-ID: 349813  Cd Length: 210  Bit Score: 94.59  E-value: 3.77e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  22 YRLLQYLKENYDSFERPVENSSAPLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGDd 101
Cdd:cd19012   5 NQLTRTLLRKYDKGVRPVLNWTDATTVYIDLFVHAVLDVDGQNQKLTTSIWYRQIWKDEFLVWNSSDFDGINEISLPLS- 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 102 dasfKLWRPDVLL--FNSVSESFDSTYssrFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYIN 179
Cdd:cd19012  84 ----AIWVPDIVIneFVDVGRYPDLPY---VYVNSSGTIKNYKPIQVVSACDLETYAFPFDRQNCSLTFRSWLHTVGDVD 156
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17531183 180 LDFLltqiiglhgipivvepeRSSTNYASyfvnesiDLQVYLQNGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRRR 257
Cdd:cd19012 157 LALW-----------------RSPEEIAN-------DKREFLNDGEWELLSVPSRYRILHMEDQDFAQIQFNVVIRRR 210
LGIC_TM_nAChR cd19064
transmembrane domain of nicotinic acetylcholine receptor (nAChR); This family contains ...
259-348 3.21e-17

transmembrane domain of nicotinic acetylcholine receptor (nAChR); This family contains transmembrane (TM) domain of the nicotinic acetylcholine receptor (nAChR). The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Among subtypes of muscle nAChRs, the heteromeric subunits (alpha1)2, beta, gamma, and delta in fetal muscle, and the gamma subunit replaced by epsilon in adult muscle have been implicated in congenital myasthenic syndromes and multiple pterygium syndromes due to various mutations. This family also includes alpha- and beta-like nAChRs found in protostomia.


Pssm-ID: 349866 [Multi-domain]  Cd Length: 113  Bit Score: 77.17  E-value: 3.21e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 259 LAYGINLIIPSLVISMMTILGFTLPPDACEKITLETTVLLSVIFFLQMVSSTSPPQSQSVPILAAFFSCCLMLVACSCVF 338
Cdd:cd19064   1 LFYTVNLIIPCVLISFLTVLVFYLPADSGEKITLSISVLLALTVFLLLIAEIIPPTSLVVPLIGKYLLFTMILVTLSIIV 80
                        90
                ....*....|
gi 17531183 339 TVLTLSLHHR 348
Cdd:cd19064  81 TVIVLNVHHR 90
LGIC_ECD_anion cd18987
extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels; This ...
46-180 3.60e-16

extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels; This family contains the extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels which include type-A gamma-aminobutyric acid receptor (GABAAR), glycine receptor (GlyR), invertebrate glutamate-gated chloride channel (GluCl), and histimine-gated chloride channel (HisCl). These neurotransmitter receptors directly mediate chloride permeability and constitute one half of the Cys-loop receptor family. Receptors in this family are composed of five either identical or homologous subunits, which generate diversity in functional profiles and pharmacological preferences. GABAAR and GlyR, both mediate fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. GluCl channels are found only in protostomia, but are closely related to mammalian glycine receptors (GlyRs). They have several roles in these invertebrates, including controlling locomotion and feeding, and mediating sensory inputs into behavior. Ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on this inhibitory half of the Cys-loop receptor family. Many of the therapeutically useful compounds acting at Cys-loop receptors target an allosteric site. The sites in Cys-loop receptors at which these allosteric ligands bind and their structure-based mechanisms of action are largely unresolved.


Pssm-ID: 349788 [Multi-domain]  Cd Length: 185  Bit Score: 76.56  E-value: 3.60e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPklFGGIRDVRfsGDDDASFKLWRPDVLLFNSVSESF-DS 124
Cdd:cd18987   1 TNVKVSIYIESISSIDEQTMDFTVDMYLRQRWTDPRLAYPD--RNGTDPIL--LPSDKFDKIWLPDLYFRNEKSSSFhDV 76
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 17531183 125 TYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd18987  77 TTPNVLVrIFPNGTVLYSQRLTLTLSCPMNLQKFPFDTQVCTLRLESYGYTTDQVVL 133
LGIC_ECD_GABAAR cd18990
gamma-aminobutyric acid receptor extracellular domain; This family contains extracellular ...
46-174 2.10e-11

gamma-aminobutyric acid receptor extracellular domain; This family contains extracellular domain (ECD) of type-A gamma-aminobutyric acid receptor (GABAAR), a member of the pentameric "Cys-loop" superfamily of transmitter-gated ion channels. This family includes 19 isoforms in human; six alpha, 3 beta, 3 gamma, one of delta, epsilon, pi, and theta, known to form heteropentameric GABAARs, and 3 rho subunits that only form homopentameric channels (also known as GABAA rho or GABAC receptor) or pseudoheteromeric if consisting of different rho subunits. The majority of GABAA receptor pentamers contain two alpha subunits, two beta subunits, and a gamma subunit, with different isoforms affecting potency of the neurotransmitter. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to its site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. Benzodiazepine and barbiturates each bind to their own distinct sites on the ECD. The channels have to contain the gamma subunit and alpha subunits in order to respond to benzodiazepines. Specific combinations of alpha, beta, and gamma subunits exhibit ethanol sensitivity. All these major classes of drugs favor channel-opening. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy.


Pssm-ID: 349791 [Multi-domain]  Cd Length: 184  Bit Score: 62.57  E-value: 2.10e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNqvmsilayMDY--------HWNDYKLTWDPKLFGGIrdVRFSGDDDAsfKLWRPDVLLFNS 117
Cdd:cd18990   1 VVVTVEIWVQSIGSISEIN--------MDFtldiyfrqYWRDPRLAFDHNGCNKN--LTLSGEMLS--KIWTPDTFFVNS 68
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17531183 118 VSESF-DSTYSSRFI-VSSNGDVQQNppgiFRFV----CQIDVTYYPFDKQTCFLKLGSWTYN 174
Cdd:cd18990  69 KKAKFhDVTTPNILLrIYPNGTVLYS----YRLTvtapCSMDLRKFPMDTQTCSLVFESYGYT 127
LGIC_ECD_bact cd18988
extracellular domain of prokaryotic pentameric ligand-gated ion channels (pLGIC); This family ...
45-182 3.49e-11

extracellular domain of prokaryotic pentameric ligand-gated ion channels (pLGIC); This family contains extracellular domain (ECD) of bacterial pentameric ligand-gated ion channels (pLGICs), including ones from Gloebacter violaceus (GLIC) and Erwinia chrysanthemi (ELIC). These prokaryotic homologs of Cys-loop receptors have been useful in understanding their eukaryotic counterparts. The largely beta-sheet ECD in this family is similar to other pLGICs, but lacks the cysteine loop and an intracellular domain. While most pLGICs undergo desensitization on prolonged exposure to the agonist, GLIC is activated by protons, but does not desensitize, even at proton concentrations eliciting maximal electrophysiological response (pH 4.5). Studies show that GLIC activation is inhibited by most general anaesthetics at clinical concentrations, including xenon which has been used in clinical practice as a potent gaseous anesthetic for decades. Xenon binding sites have been identified in three distinct regions of the TMD: in a large intra-subunit cavity, in the pore, and at the interface between adjacent subunits.


Pssm-ID: 349789  Cd Length: 182  Bit Score: 61.92  E-value: 3.49e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPklfggiRDVRFSGDDDASFKL---WRPDVLLFNSVSES 121
Cdd:cd18988   1 PTEVSVGIYLIDIYGIDEVNETFEADGYLRLRWQDPRLAFDP------AAGKEYRLGEAEKQLdeiWNPQIEFINQRGLR 74
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17531183 122 FdsTYSSRFIVSSNGDVQQNPpgifRFVCQI----DVTYYPFDKQTCFLKLGSWTYNGQYINLDF 182
Cdd:cd18988  75 D--TLNRRLRVFPDGTVTYRQ----RFTGTFstpmDLRRFPFDRQTLTIELESFSYDPDEVVLVV 133
LGIC_ECD_GABAAR_pi cd19004
extracellular domain of gamma-aminobutyric acid receptor subunit pi (GABRP); This family ...
45-176 1.16e-10

extracellular domain of gamma-aminobutyric acid receptor subunit pi (GABRP); This family contains extracellular domain of pi subunit of type-A gamma-aminobutyric acid receptor (GABAAR). GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GABRP is expressed mainly in non-neuronal tissues such as the mammary gland, prostate gland, lung, thymus, and uterus. It is also highly expressed in certain types of cancer such as basal-like breast cancer and pancreatic ductal adenocarcinoma. GABRP is involved in inhibitory synaptic transmission in the central nervous system. Its assembly with other GABAAR subunits alters the sensitivity of recombinant receptors to modulatory agents such as pregnanolone. Studies suggest that polymorphisms in the GABRP gene may be associated with the susceptibility to systematic lupus erythematosus (SLE).


Pssm-ID: 349805  Cd Length: 182  Bit Score: 60.77  E-value: 1.16e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPklfggirDVRFSGDDDASFKLWRPDVLLFNSvSESF-- 122
Cdd:cd19004   1 PVTVGMSLDIASIDTISEINMDYTATIFLRQRWTDERLCFEG-------NKSLSLDGRLVELLWVPDTFIVDS-KKSFlh 72
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 17531183 123 DSTYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQ 176
Cdd:cd19004  73 DITVENRLIrIFPNGTVLYALRITTTVACSMDLTKYPMDKQTCTLQLESWGYNIN 127
LGIC_ECD_GABAAR_delta cd19001
extracellular domain of gamma-aminobutyric acid receptor subunit delta; This family contains ...
45-218 9.82e-10

extracellular domain of gamma-aminobutyric acid receptor subunit delta; This family contains extracellular domain of delta subunit of type-A gamma-aminobutyric acid receptor (GABAAR). GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. Receptors containing the delta subunit (GABRD) are expressed exclusively extra-synaptically (in the cortex, hippocampus, thalamus, striatum, and cerebellum) and mediate tonic inhibition. Studies suggest that delta subunits form heteropentamers in similar stoichiometry and arrangement as alpha/beta/gamma receptors, with the delta subunit replacing the gamma subunit (2alpha:2beta:1delta), although other stoichiometries have also been detected. The delta subunit is flexible in its positioning in the pentameric complex, producing receptors with diverse pharmacological properties. Mutations in GABRD have been associated with susceptibility to generalized epilepsy with febrile seizures, type 5. GABRD gene may also be associated with childhood-onset mood disorders.


Pssm-ID: 349802  Cd Length: 184  Bit Score: 57.77  E-value: 9.82e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWD--PKLFGgiRDVRFSGdddasfKLWRPDVLLFNSVSESF 122
Cdd:cd19001   1 PVNVALAIEVASIDHISEVNMEYTMTVFLHQSWRDERLSYNhtNETLG--LDSRFVD------KLWLPDTFIVNAKSAWF 72
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 123 -DSTYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFLLTQiIGLHGIPIVVEPE 200
Cdd:cd19001  73 hDVTVENKLIrLQPDGVILYSSRITSTVACDMDLTKYPMDEQECMLDLESYGYSSEDIVYHWSENQ-EHIHGLDKLELAQ 151
                       170
                ....*....|....*...
gi 17531183 201 RSSTNYAsyFVNESIDLQ 218
Cdd:cd19001 152 FTITNYR--FTTEMMNFK 167
LGIC_TM_5-HT3 cd19063
transmembrane domain of 5-hydroxytryptamine 3 (5-HT3) receptor; This family contains ...
259-347 1.53e-08

transmembrane domain of 5-hydroxytryptamine 3 (5-HT3) receptor; This family contains transmembrane (TM) domain of the serotonin 5-HT3 receptors. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The 5-HT3 channel is cation-selective and mediates neuronal depolarization and excitation within the central and peripheral nervous systems. Like other ligand gated ion channels, the 5-HT3 receptor consists of five subunits arranged around a central ion conducting pore, which is permeable to Na+, K+, and Ca2+ ions. Binding of the neurotransmitter 5-hydroxytryptamine (serotonin) to the 5-HT3 receptor opens the channel, which then leads to an excitatory response in neurons, and the rapidly activating, desensitizing, inward current is predominantly carried by Na+ and K+ ions. This receptor is most closely related by homology to the nicotinic acetylcholine receptor (nAChR). Five subunits have been identified for this family: 5-HT3A, 5-HT3B, 5-HT3C, 5-HT3D, and 5-HT3E, encoded by HTR3A-E genes. Only 5-HT3A subunits are able to form functional homomeric receptors, whereas the 5-HT3B, C, D, and E subunits form heteromeric receptors with 5-HT3A. Different receptor subtypes are important mediators of nausea and vomiting during chemotherapy, pregnancy, and following surgery, while some contribute to neuro-gastroenterologic disorders such irritable bowel syndrome (IBS) and eating disorders as well as co-morbid psychiatric conditions. 5-HT3 receptor antagonists are established treatments for emesis and IBS, and are beneficial in the treatment of psychiatric diseases.


Pssm-ID: 349865  Cd Length: 121  Bit Score: 53.01  E-value: 1.53e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 259 LAYGINLIIPSLVISMMTILGFTLPPDACEKITLETTVLLSVIFFLQMVSSTSPPQSQSVPILAAFFSCCLMLVACSCVF 338
Cdd:cd19063   1 LLYVVNLLIPSIFLMLVDLASFYLPPNSGERLGFKVTLLLGYSVFLLILNDLLPATAIGTPLIGVYFVVCLALMVLSLLE 80

                ....*....
gi 17531183 339 TVLTLSLHH 347
Cdd:cd19063  81 TILIVKLLH 89
LGIC_ECD_GABAAR_theta cd19003
extracellular domain of gamma-aminobutyric acid receptor subunit theta (GABRQ); This family ...
45-173 8.45e-07

extracellular domain of gamma-aminobutyric acid receptor subunit theta (GABRQ); This family contains extracellular domain (ECD) of the theta subunit of type-A gamma-aminobutyric acid receptor (GABAAR), and encoded by the GABRQ gene, which is mapped to chromosome Xq28 in a cluster of genes that also that encode the alpha 3 and epsilon subunits. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GABA stimulates human hepatocellular carcinoma growth through overexpressed GABAAR theta subunit. Also, two autism spectrum disorder (ASD)-associated protein truncation variants have been identified in alpha 3 (GABRA3) and theta (GABRQ) genes.


Pssm-ID: 349804  Cd Length: 183  Bit Score: 49.22  E-value: 8.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFGGIRDVRFSGdddasfKLWRPDVLLFNSvSESF-- 122
Cdd:cd19003   1 PVPVRISIYVSSIEQISEMNMDYTITMFFHQTWKDSRLAYYETTLNLTLDYRMHE------KLWVPDCYFLNS-KDAFvh 73
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 17531183 123 DSTYSSRFIvssngdvQQNPPGIFRF--------VCQIDVTYYPFDKQTCFLKLGSWTY 173
Cdd:cd19003  74 DVTVENRVF-------QLHPDGTVRYgirltttaACSLDLHKFPMDKQACKLEVESYGY 125
LGIC_ECD_GlyR_beta cd19010
extracellular domain of glycine receptor beta subunit; This subfamily contains extracellular ...
45-173 1.81e-06

extracellular domain of glycine receptor beta subunit; This subfamily contains extracellular domain of glycine receptor (GlyR or GLR) beta subunit of the amino acid neurotransmitter glycine encoded by GLRB gene. These subunits form heteropentamers with a combination of alpha and beta subunits, either a 2alpha-3beta or 3alpha-2beta stoichiometry. While the alpha subunits contain binding sites for agonists and antagonists and are responsible for ion channel formation, the beta subunit displays structural and regulatory functions, such as GlyR clustering in synaptic locations by interaction between intracellular loop domains with the scaffolding protein gephyrin, and control of pharmacologic responses to agonist or allosteric modulators due in part to the presence of interfaces alpha/beta and beta/beta. GLRB gene mutations are associated with the neurological disorder hyperekplexia, a rare neurological disorder characterized by neonatal hypertonia and exaggerated startle responses to unexpected stimuli, as well as agoraphobic cognitions.


Pssm-ID: 349811  Cd Length: 187  Bit Score: 48.48  E-value: 1.81e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLtwdpKLFGGIRDVRFSGDDDASFK-LWRPDVLLFNSVSESFD 123
Cdd:cd19010   1 PVDVVVNIFINSFGSIQETTMDYRVNIFLRQKWNDPRL----KLPNDFRGSDALTVDPTMFKcLWKPDLFFANEKSANFH 76
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 17531183 124 STYSSRFI--VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTY 173
Cdd:cd19010  77 DVTQENILlfIFRDGDVLVSMRLSITLSCPLDLTLFPMDTQRCKMQLESFGY 128
LGIC_ECD_GlyR_alpha cd19009
extracellular domain of glycine receptor alpha subunit; This subfamily contains extracellular ...
45-174 2.17e-06

extracellular domain of glycine receptor alpha subunit; This subfamily contains extracellular domain of glycine receptor (GlyR or GLR) alpha subunits of the amino acid neurotransmitter glycine. GlyR has four known isoforms of alpha-subunit (alpha1-4, encoded by GLRA1, GLRA2, GLRA3, GLRA4) that are essential to bind ligands, and, along with the GlyR beta subunit, have been described to have a regionally and temporally controlled expression during development and maturation of the central nervous system (CNS). These alpha subunits are highly homologous, but differ in their kinetic properties, temporal and regional expression and physiological functions. They can form functional chloride-permeable GlyR ion channels by forming homopentamers with 5 alpha subunits or heteropentamers with a combination of alpha and beta subunits, either a 2alpha-3beta or 3alpha-2beta stoichiometry. In human, mutations in glycine receptor alpha subunits cause disruption of GlyR surface expression or reduced ability of expressed GlyRs to conduct chloride ions. Mutations in GlyR alpha1 subunit leads to hyperekplexia, a rare neurological disorder characterized by neonatal hypertonia and exaggerated startle responses to unexpected stimuli, while mutations in GlyR alpha2 are known to cause cortical neuronal migration/autism spectrum disorder and in GlyR alpha3 to cause inflammatory pain sensitization/rhythmic breathing. GlyR alpha1 and alpha2 subunits have an important role in regulation of the excitatory-inhibitory balance, control of motor actions, modulation of sedative ethanol effects and probably regulation ethanol preference and consumption.


Pssm-ID: 349810  Cd Length: 184  Bit Score: 48.05  E-value: 2.17e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTwdpklFGGIRDVRFSGDDDASFKLWRPDVLLFNSVSESFD- 123
Cdd:cd19009   1 PVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLA-----YSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHe 75
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 17531183 124 -STYSSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYN 174
Cdd:cd19009  76 vTTDNKLLRISKNGNVLYSIRLTLTLACPMDLKNFPMDVQTCIMQLESFGYT 127
LGIC_ECD_GABAAR_rho cd19005
extracellular domain of gamma-aminobutyric acid receptor subunit rho; This family contains ...
45-174 3.70e-06

extracellular domain of gamma-aminobutyric acid receptor subunit rho; This family contains extracellular domain of rho subunits (rho1, rho2, and rho3, encoded by GABRR1, GABRR2, and GABRR3, respectively) of type-A gamma-aminobutyric acid receptor (GABAAR). These subunits homo-oligomerize to form GABAA-rho receptors (formerly classified as GABA-rho or GABAC receptor), but do not co-assemble with any of the classical GABAA subunits. They are especially high expression in the retina and their distinctive pharmacological properties are unique; they are not modulated by many GABAA receptor modulators such as barbiturates, benzodiazepines, and neuroactive steroids. In humans, mutations in the GABRR1 and GABRR2 genes may be responsible for some cases of autosomal recessive retinitis pigmentosa. Variation in GABRR1 is also associated with susceptibility to bipolar schizoaffective disorder while a SNP in GABRR2 has been reported to show association with autism.


Pssm-ID: 349806  Cd Length: 186  Bit Score: 47.31  E-value: 3.70e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTwdpklFGGIRDVRFSGDDDASFKLWRPDVLLFNSvSESF-- 122
Cdd:cd19005   1 AIPVGVDVQVESLDSISEVDMDFTMTLYLRHYWKDERLS-----FPSTANKSMTFDGRLVKKIWVPDVFFVHS-KRSFih 74
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 17531183 123 DSTYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYN 174
Cdd:cd19005  75 DTTTDNIMLrVFPDGHVLYSLRITVTAMCNMDFSRFPLDTQTCSLELESYAYT 127
LGIC_ECD_GluCl cd18993
glutamate-gated chloride channel (GluCl) extracellular domain; This subfamily contains ...
45-173 1.68e-05

glutamate-gated chloride channel (GluCl) extracellular domain; This subfamily contains extracellular domain of glutamate-gated chloride channel (GluCl) found only in protostomia, but are closely related to mammalian glycine receptors. They have several roles in these invertebrates, including controlling locomotion and feeding, and mediating sensory inputs into behavior. Comparison of the GluCl gene families between organisms shows that insect gene family is relatively simple, while that found in nematodes tends to be larger and more diverse. Glutamate is an inhibitory neurotransmitter that shapes the responses of projection neurons to olfactory stimuli in the Drosophila. GluCls are targeted by the macrocyclic lactone family of anthelmintics and pesticides in arthropods and nematodes, thus making the GluCls of considerable medical and economic importance. In Drosophila melanogaster, GluCl mediates sensitivity to the antiparasitic agents ivermectin and nodulisporic acid, suggesting that their drug target is the same throughout the Ecdysozoa.


Pssm-ID: 349794  Cd Length: 183  Bit Score: 45.28  E-value: 1.68e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPkLFGGIRDVRFSGDDdasfKLWRPDVLLFNSVSESFDS 124
Cdd:cd18993   1 PVIVKVNIYVRSISKIDDVKMEYSVQLTFRQEWYDPRLRYDD-TGGKPEYLTLTDDS----KIWKPDTFFQNEKEGHFHN 75
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 17531183 125 TYS-SRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTY 173
Cdd:cd18993  76 IDKpNVYLrIYPDGKVLYSVRISLTLSCPMDLQYYPFDKQTCSIDLASYGY 126
LGIC_ECD_GABAAR_rho3 cd19048
extracellular domain of gamma-aminobutyric acid receptor subunit rho-3 (GABAA-rho3); This ...
45-174 5.89e-05

extracellular domain of gamma-aminobutyric acid receptor subunit rho-3 (GABAA-rho3); This family contains extracellular domain (ECD) of the rho subunit 3 of type-A gamma-aminobutyric acid receptor (GABAAR), encoded by the GABRR3 gene which maps to a different chromosome to that of GABRR1 and GABRR2. While close proximity of the rho1 and rho2 subunit genes suggests that they emerged via a local duplication event, GABRR3 may have arisen by duplication of a GABRR1/GABRR2 progenitor. This subunit homo-oligomerizes to form GABAA-rho receptors (formerly classified as GABA-rho or GABAc receptor), but does not co-assemble with any of the classical GABAAR subunits. In humans, some individuals contain a variant that is predicted to inactivate this gene product.


Pssm-ID: 349849  Cd Length: 186  Bit Score: 43.87  E-value: 5.89e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTwdpklFGGIRDVRFSGDDDASFKLWRPDVLLFNSvSESF-- 122
Cdd:cd19048   1 PIPVGIDVQVESIDSISEVDMDFTMTLYLRHYWKDERLS-----FPSTKNKSMTFDGRLIKKIWVPDVFFVHS-KRSFih 74
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 17531183 123 DSTYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYN 174
Cdd:cd19048  75 DTTMENVMLrVYPDGNVLFSLRITVSAMCFMDFSRFPLDTQNCSLELESYAYN 127
LGIC_ECD_GABAAR_rho2 cd19047
extracellular domain of gamma-aminobutyric acid receptor subunit rho-2 (GABA-rho2 or GABRR2); ...
46-180 9.16e-05

extracellular domain of gamma-aminobutyric acid receptor subunit rho-2 (GABA-rho2 or GABRR2); This family contains extracellular domain (ECD) of the rho subunit 2 of type-A gamma-aminobutyric acid receptor (GABAAR), encoded by the GABRR2 gene which exists next to GABRR1 (encoding rho subunit 1) on the chromosome region thought to be associated with susceptibility for psychiatric disorders and epilepsy. Close proximity of the rho1 and rho2 subunit genes suggests that they emerged via a local duplication event. Rho1 is expressed in many areas of the brain, but especially high in the retina. This subunit homo-oligomerizes to form GABAA-rho receptors (formerly classified as GABA-rho or GABAc receptor), but does not co-assemble with any of the classical GABAAR subunits. In humans, mutations in the GABRR2 gene may be responsible for some cases of autosomal recessive retinitis pigmentosa. Variation in GABRR2 is also associated with susceptibility to bipolar schizoaffective disorder, as well as alcohol dependence and general cognitive ability. GABA-rho2 receptors expressed pre-synaptically in the spinal dorsal horn have been implicated in pain perception and identified as a novel target for analgesia.


Pssm-ID: 349848  Cd Length: 186  Bit Score: 43.55  E-value: 9.16e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLlNQIMDVDEKnqvMSILAYMDYHWNDYKLTwdpklFGGIRDVRFSGDDDASFKLWRPDVLLFNSV-SESFDS 124
Cdd:cd19047   6 VDVQVESL-DSISEVDMD---FTMTLYLRHYWKDERLS-----FPSTTNKSMTFDGRLVKKIWVPDVFFVHSKrSFIHDT 76
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 17531183 125 TYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINL 180
Cdd:cd19047  77 TTDNIMLrVFPDGHVLYSMRITVTAMCNMDFSRFPLDSQTCSLELESYAYTDEDLML 133
LGIC_ECD_GABAAR_LCCH3-like cd19006
gamma-aminobutyric acid receptor subunit beta-like extracellular domain in protostomia, such ...
45-189 1.31e-04

gamma-aminobutyric acid receptor subunit beta-like extracellular domain in protostomia, such as LCCH3 (ligand-gated chloride channel homolog 3); This family contains extracellular domain of beta-like subunits of type-A gamma-aminobutyric acid receptor (GABAAR) found in protostomia, similar to Drosophila melanogaster ligand-gated chloride channel homolog 3 (LCCH3) subunits. Drosophila melanogaster expresses three GABA-receptor subunit orthologs: (RDL, resistant to dieldrin; GRD, GABA/glycine-like receptor of Drosophila; LCCH3, ligand-gated chloride channel homolog 3), and may possibly form homo- and/or heteropentameric associations. LCCH3 has been shown to combine with subunit GRD to form cation-selective GABA-gated ion channels when coexpressed in Xenopus laevis oocytes. GABAARs are known to be the molecular targets of a class of insecticides. The resulting pentameric receptors in this family have been shown to be activated by insect GABA-receptor agonists muscimol and CACA, and blocked by antagonists fipronil, dieldrin, and picrotoxin, but not bicuculline. GABAARs are abundant in the CNS, where their physiological role is to mediate fast inhibitory neurotransmission. In insects, this inhibitory transmission plays a crucial role in olfactory information processing.


Pssm-ID: 349807  Cd Length: 183  Bit Score: 42.83  E-value: 1.31e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKlfGGIRDVRFSGDddASFKLWRPDVLLFNSvSESF-- 122
Cdd:cd19006   1 PLLVGMDLTIASFDSISEVNMDYTITMYLNQYWKDERLAFSID--NESDVLTLSGD--FAEKIWVPDTFFAND-KNSFlh 75
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17531183 123 DSTYSSRFI-VSSNGDVQQNppgiFRFV----CQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDFLLTQIIG 189
Cdd:cd19006  76 DVTERNKMVrLNGDGSITYG----MRFTttlaCMMDLHYYPLDSQNCTVEIESYGYTVSDVVMYWKNTPVRG 143
LGIC_ECD_GlyR cd18991
extracellular domain of glycine receptor (GlyR); This subfamily contains extracellular domain ...
45-182 1.45e-04

extracellular domain of glycine receptor (GlyR); This subfamily contains extracellular domain of glycine receptor (GlyR or GLR) of the amino acid neurotransmitter glycine. GlyR has four known isoforms of the alpha-subunit (alpha1-4, encoded by GLRA1, GLRA2, GLRA3, GLRA4) that are essential to bind ligands and a single beta-subunit (encoded by GLRB), all of which have been described to have a regionally and temporally controlled expression during development and maturation of the central nervous system (CNS). Functional chloride-permeable GlyR ion channels are formed by 5 alpha subunit homopentamers or by alpha and beta subunit heteropentamers, which form complexes with either a 2alpha-3beta or 3alpha-2beta stoichiometry. The receptor can be activated by glycine as well as beta-alanine and taurine, and can be selectively blocked by the high-affinity competitive antagonist strychnine. Caffeine is also a competitive antagonist of GlyR. In human, glycine receptor alpha1 and beta subunits are the major targets of mutations that cause disruption of GlyR surface expression or reduced ability of expressed GlyRs to conduct chloride ions, leading to hyperekplexia, a rare neurological disorder characterized by neonatal hypertonia and exaggerated startle responses to unexpected stimuli. Mutations in GlyR alpha2 are known to cause cortical neuronal migration/autism spectrum disorder and in GlyR alpha3 to cause inflammatory pain sensitization/rhythmic breathing.


Pssm-ID: 349792  Cd Length: 185  Bit Score: 42.58  E-value: 1.45e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNqvmsilayMDYHWNDY-KLTW-DPKLfggirdvRFSGDDDASF---------KLWRPDVL 113
Cdd:cd18991   1 PTNVSVQIYINSIDSINEAT--------MDYSVNIFlRQRWnDPRL-------NFTKLSNIDYleldpkmidKIWVPDLF 65
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17531183 114 LFNSVSESF-DSTYSSRFI-VSSNGDVqqnppgIF------RFVCQIDVTYYPFDKQTCFLKLGSWTYNGQYINLDF 182
Cdd:cd18991  66 FPNEKKANFhDVTVPNKLLrIYPNGTV------YYsmrlslTLSCPMDLHKYPLDTQTCPIQIESFGYTTENLIFKW 136
LGIC_ECD_GABAR_GRD-like cd19007
gamma-aminobutyric acid receptor subunit alpha-like extracellular domain in protostomia, such ...
45-174 1.58e-04

gamma-aminobutyric acid receptor subunit alpha-like extracellular domain in protostomia, such as GRD (GABA/glycine-like receptor of Drosophila); This family contains extracellular domain of alpha-like subunits of type-A gamma-aminobutyric acid receptor (GABAAR) found in protostomia, similar to Drosophila melanogaster GABA/ glycine-like receptor of Drosophila (GRD) subunits. Drosophila melanogaster expresses three GABA-receptor subunit orthologs: (RDL, resistant to dieldrin; GRD, GABA/glycine-like receptor of Drosophila; LCCH3, ligand-gated chloride channel homolog 3), and may possibly form homo- and/or heteropentameric associations. LCCH3 has been shown to combine with subunit GRD to form cation-selective GABA-gated ion channels when co-expressed in Xenopus laevis oocytes. GABAARs are known to be the molecular targets of a class of insecticides. The resulting pentameric receptors in this family have been shown to be activated by insect GABA-receptor agonists muscimol and CACA, and blocked by antagonists fipronil, dieldrin, and picrotoxin, but not bicuculline. GABAARs are abundant in the CNS, where their physiological role is to mediate fast inhibitory neurotransmission. In insects, this inhibitory transmission plays a crucial role in olfactory information processing.


Pssm-ID: 349808  Cd Length: 183  Bit Score: 42.61  E-value: 1.58e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLtwdpklfggirdvRFSGDDDASF--------KLWRPDVLLFN 116
Cdd:cd19007   1 PTTVETDILIRSMGPISELDMTYSMDCYFRQSWQDRRL-------------AFNGPSIDTLslsikmldRIWKPDTYFYN 67
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17531183 117 SvSESF--DSTYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYN 174
Cdd:cd19007  68 G-KKSYlhTITTPNKLVrLRQDGRILYSMRLTIKASCPMNLEKFPMDTQSCPLIIGSYGYT 127
LGIC_ECD_ZAC cd18994
extracellular domain of zinc-activated ligand-gated ion channel; This family is the ...
46-176 1.73e-04

extracellular domain of zinc-activated ligand-gated ion channel; This family is the extracellular domain of zinc-activated ligand-gated ion channel (ZAC), a cationic ion channel belonging to the superfamily of Cys-loop receptors, which consists of pentameric ligand-gated ion channels. ZAC displays low sequence similarity to other members in the superfamily, with closest matches to the human serotonin 5-HT3 receptor (5-HT3R) subunits 5-HT3A and 5-HT3B, and nAChR alpha7 subunits that exhibit approximately 15% amino acid sequence identity to ZAC. Expression of ZAC has been detected in human fetal whole brain, spinal cord, pancreas, placenta, prostate, thyroid, trachea, and stomach, as well as in adult hippocampus, striatum, amygdala, and thalamus. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+, and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling is as yet unknown.


Pssm-ID: 349795  Cd Length: 170  Bit Score: 42.46  E-value: 1.73e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTWDPKLFggirdvRFSGDDDASFKLWRPDVllfnSVSESFDST 125
Cdd:cd18994   1 LLVDVTVFVSNVFNVDILEYTMSSRLLLNLSWLDPRLAWNENIS------PMSAVTLPWDSLWTPGL----TIQEALWVT 70
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 17531183 126 Y---SSRFIVSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTYNGQ 176
Cdd:cd18994  71 WrpqSPDARVTRDGHVELYLALTTETNCDFELFHFPRDTSDCPLSFFALSNTVL 124
LGIC_ECD_GABAAR_rho1 cd19046
extracellular domain of gamma-aminobutyric acid receptor subunit rho-1 (GABA-rho1 or GABRR1); ...
46-173 2.38e-04

extracellular domain of gamma-aminobutyric acid receptor subunit rho-1 (GABA-rho1 or GABRR1); This family contains extracellular domain (ECD) of the rho subunit 1 of type-A gamma-aminobutyric acid receptor (GABAAR), encoded by the GABRR1 gene, expressed in many areas of the brain, but especially high in the retina. GABRR1 exists next to GABRR2 (encoding rho subunit 2) on the chromosome region thought to be associated with susceptibility for psychiatric disorders and epilepsy. Close proximity of the rho1 and rho2 subunit genes suggests that they emerged via a local duplication event. This subunit homo-oligomerizes to form GABAA-rho receptors (formerly classified as GABA-rho or GABAc receptor), but does not co-assemble with any of the classical GABAAR subunits. In humans, mutations in the GABRR1 gene may be responsible for some cases of autosomal recessive retinitis pigmentosa. Variation in GABRR1 is also associated with susceptibility to bipolar schizoaffective disorder, and may be associated with alcohol dependency.


Pssm-ID: 349847  Cd Length: 186  Bit Score: 42.01  E-value: 2.38e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLlNQIMDVDEKnqvMSILAYMDYHWNDYKLTwdpklFGGIRDVRFSGDDDASFKLWRPDVLLFNSVSESFDST 125
Cdd:cd19046   6 VDVQVESL-DSISEVDMD---FTMTLYLRHYWKDERLS-----FPSTNNQSMTFDGRLVKKIWVPDMFFVHSKRSFIHDT 76
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 17531183 126 YSSRFI--VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTY 173
Cdd:cd19046  77 TTDNVMlrVQPDGKVLYSLRVTVTAMCNMDFSRFPLDTQTCSLEIESYAY 126
LGIC_ECD_GABAAR_B1 cd19040
extracellular domain of gamma-aminobutyric acid receptor subunit beta-1 (GABAAR-B1 or GABRB1); ...
46-173 2.63e-04

extracellular domain of gamma-aminobutyric acid receptor subunit beta-1 (GABAAR-B1 or GABRB1); This family contains extracellular domain (ECD) of gamma-aminobutyric acid receptor beta-1 subunit, a protein that is encoded by the GABRB1 gene. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The beta-1 subunit forms heteropentamers with other GABAAR subunits, likely expressed as alpha-beta1-gamma/delta, mainly found in the brain. It is clustered on the chromosome with genes encoding alpha 4, alpha 2, and gamma 1 subunits of the GABAAR. GABRB1 expression is altered significantly in the lateral cerebellum of subjects with schizophrenia, major depression, and bipolar disorder. Mutations in the GABRB1 gene promote alcohol consumption through increased tonic inhibition. Epigenetic control of gene expression may affect the expression of GABRB1 and disrupt inhibitory synaptic transmission during embryonic development. The GABRB1 gene is also associated with thalamus volume and modulates the association between thalamus volume and intelligence.


Pssm-ID: 349841  Cd Length: 182  Bit Score: 41.93  E-value: 2.63e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTwdpklFGGIrDVRFSGDDDASFKLWRPDVLLFNSvSESF--D 123
Cdd:cd19040   1 VDVGMRIDVASIDMVSEVNMDYTLTMYFQQSWRDKRLS-----YSGI-PLNLTLDNRVADQLWVPDTYFLND-KKSFvhG 73
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 17531183 124 STYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTY 173
Cdd:cd19040  74 VTVKNRMIrLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGY 124
LGIC_ECD_GABAAR_B cd18999
extracellular domain of gamma-aminobutyric acid receptor subunit beta (GABAAR-B or GABRB); ...
46-173 7.76e-04

extracellular domain of gamma-aminobutyric acid receptor subunit beta (GABAAR-B or GABRB); This family contains extracellular domain (ECD) of beta subunits of type-A gamma-aminobutyric acid receptor (GABAAR), which include beta1-beta4 in vertebrates. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. Benzodiazepine and barbiturates each bind to their own distinct sites on the LBD. The channels must contain the gamma subunit and alpha subunits in order to respond to benzodiazepines. Specific combinations of alpha, beta, and gamma subunits exhibit ethanol sensitivity. All these major classes of drugs favor channel-opening. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. Mutations or genetic variations of the genes encoding the GABRB2 and GABRB3 have been associated with human epilepsy, both with and without febrile seizures. Mutations in GABRB2, and GABRB3 have been associated with infantile spasms and Lennox-Gastaut syndrome. A de novo missense mutation of GABRB2 causes early myoclonic encephalopathy, a disease with a devastating prognosis, characterized by neonatal onset of seizures. Another de novo heterozygous missense variant in exon 4 of GABRB2 is associated with intellectual disability and epilepsy. Mutations in the GABRB1 gene promote alcohol consumption through increased tonic inhibition.


Pssm-ID: 349800  Cd Length: 182  Bit Score: 40.72  E-value: 7.76e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  46 LDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTwdpklFGGIrDVRFSGDDDASFKLWRPDVLLFNSvSESF--D 123
Cdd:cd18999   1 VTVGMSIDIASIDMVSEVNMDYTLTMYFQQSWRDKRLA-----YNGI-PLNLTLDNRVADQLWVPDTYFLND-KKSFvhG 73
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 17531183 124 STYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTY 173
Cdd:cd18999  74 VTVKNRMIrLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGY 124
LGIC_TM_ZAC cd19065
transmembrane domain of zinc-activated ligand-gated ion channel; This family contains ...
263-358 9.88e-04

transmembrane domain of zinc-activated ligand-gated ion channel; This family contains transmembrane (TM) domain of zinc-activated ligand-gated ion channel (ZAC). The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. ZAC displays low sequence similarity to other members in the superfamily, with closest matches to the human serotonin 5-HT3 receptor (5-HT3R) subunits 5-HT3A and 5-HT3B, and nAChR alpha7 subunits that exhibit approximately 15% amino acid sequence identity to ZAC. Expression of ZAC has been detected in human fetal whole brain, spinal cord, pancreas, placenta, prostate, thyroid, trachea, and stomach, as well as in adult hippocampus, striatum, amygdala, and thalamus. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+, and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling is as yet unknown.


Pssm-ID: 349867  Cd Length: 176  Bit Score: 39.96  E-value: 9.88e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183 263 INLIIPSLVISMMTILGFTLPPDACEKITLETTVLLSVIFFLQMVSSTSPPQSQSVPILAAFFSCCLMLVACSCVFTVLT 342
Cdd:cd19065   5 IALLVPGEALLLADVCGGLLPLRATERIAYKVTLLLSYLVFHSSLVQALPSSSSCNPLLIYYFTVLLLLLFLSTIETVLL 84
                        90
                ....*....|....*.
gi 17531183 343 LSLHHRKPETHEMSPT 358
Cdd:cd19065  85 AGLLARGNLGAKSSPS 100
LGIC_ECD_GABAAR_B3 cd19042
extracellular domain of gamma-aminobutyric acid receptor subunit beta-3 (GABAAR-B3 or GABRB3); ...
45-173 3.22e-03

extracellular domain of gamma-aminobutyric acid receptor subunit beta-3 (GABAAR-B3 or GABRB3); This family contains extracellular domain (ECD) of gamma-aminobutyric acid receptor beta-3 subunit, a protein that is encoded by the GABRB3 gene. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The beta-3 subunit forms heteropentamers with other GABAAR subunits, with alpha2-beta3-gamma2 and alpha3-beta3-gamma2 subtypes highly enriched in hippocampal pyramidal neurons and cholinergic neurons of the basal forebrain, respectively. Other heteromers include alpha1-beta3-gamma2 and alpha5-beta3-gamma2. GABRB3 mutations are likely associated with a broad phenotypic spectrum of epilepsies and that reduced receptor function causing GABAergic disinhibition represents the relevant disease mechanism. GABRB3 might be associated with heroin dependence, and increased expression possibly contributing to the pathogenesis of heroin dependence. This gene may also be associated with the pathogenesis of other disorders such as Angelman syndrome, Prader-Willi syndrome, nonsyndromic orofacial clefts, schizophrenia, and autism.


Pssm-ID: 349843  Cd Length: 183  Bit Score: 38.85  E-value: 3.22e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17531183  45 PLDVKVRFLLNQIMDVDEKNQVMSILAYMDYHWNDYKLTwdpklFGGIrDVRFSGDDDASFKLWRPDVLLFNSvSESF-- 122
Cdd:cd19042   1 PVCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLA-----YSGI-PLNLTLDNRVADQLWVPDTYFLND-KKSFvh 73
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 17531183 123 DSTYSSRFI-VSSNGDVQQNPPGIFRFVCQIDVTYYPFDKQTCFLKLGSWTY 173
Cdd:cd19042  74 GVTVKNRMIrLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGY 125
 
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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