RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17441
(458 letters)
>gnl|CDD|107374 cd06379, PBP1_iGluR_NMDA_NR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. The ionotropic N-methyl-d-asparate
(NMDA) subtype of glutamate receptor serves critical
functions in neuronal development, functioning, and
degeneration in the mammalian central nervous system.
The functional NMDA receptor is a heterotetramer
ccomposed of two NR1 and two NR2 (A, B, C, and D) or of
NR3 (A and B) subunits. The receptor controls a cation
channel that is highly permeable to monovalent ions and
calcium and exhibits voltage-dependent inhibition by
magnesium. Dual agonists, glutamate and glycine, are
required for efficient activation of the NMDA receptor.
When co-expressed with NR1, the NR3 subunits form
receptors that are activated by glycine alone and
therefore can be classified as excitatory glycine
receptors. NR1/NR3 receptors are calcium-impermeable and
unaffected by ligands acting at the NR2
glutamate-binding site.
Length = 377
Score = 367 bits (945), Expect = e-125
Identities = 148/277 (53%), Positives = 199/277 (71%), Gaps = 5/277 (1%)
Query: 4 HINFDIQYVNKGVTFSATGIQMDPNPILTALSVCKFLISERVYAVIVSHPLTGD--LSPA 61
N + ++ ++ + +AT I DPNPI TALSVC+ LIS +VYAVIVSHP T + L+P
Sbjct: 41 AANVE-RHGSRKIKLNATTITHDPNPIQTALSVCEQLISNQVYAVIVSHPPTSNDHLTPT 99
Query: 62 AVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIF 121
+VSYT+GFY IPV+GIS+RDS FSDKNIH+SFLRTVPPYSHQADVW+E+L+ F + KVI
Sbjct: 100 SVSYTAGFYRIPVVGISTRDSIFSDKNIHLSFLRTVPPYSHQADVWLEMLRSFKWNKVIL 159
Query: 122 IHSSDTDGRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQARVY 181
+ S D +GRA RF+T + +E + +IK VE V+EFEPG L E K +RV
Sbjct: 160 LVSDDHEGRAAQKRFETLLEEREIEFKIK--VEKVVEFEPGEKNVTSLLQEAKELTSRVI 217
Query: 182 LMYASKQDAEIIFKDAQYLNMTETGYVWIVTEQALTAKNVPVGIIGLKLVNATNEDAHIR 241
L+ AS+ DA +I+++A LNMT GYVWIV+EQA A+N P G++GL+L+N NE +HIR
Sbjct: 218 LLSASEDDAAVIYRNAGMLNMTGEGYVWIVSEQAGAARNAPDGVLGLQLINGKNESSHIR 277
Query: 242 DSIYVLTSALKEMNQSAVITEAPQDCDNSGSIWETGK 278
D++ VL SA++E+ + ITE P++C + IWETG
Sbjct: 278 DAVAVLASAIQELFEKENITEPPRECVGNTVIWETGP 314
>gnl|CDD|107362 cd06367, PBP1_iGluR_NMDA, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. While this N-terminal
domain belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. The function
of the NMDA subtype receptor serves critical functions
in neuronal development, functioning, and degeneration
in the mammalian central nervous system. The functional
NMDA receptor is a heterotetramer comprising two NR1 and
two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The
receptor controls a cation channel that is highly
permeable to monovalent ions and calcium and exhibits
voltage-dependent inhibition by magnesium. Dual
agonists, glutamate and glycine, are required for
efficient activation of the NMDA receptor. Among NMDA
receptor subtypes, the NR2B subunit containing receptors
appear particularly important for pain perception; thus
NR2B-selective antagonists may be useful in the
treatment of chronic pain.
Length = 362
Score = 247 bits (634), Expect = 2e-78
Identities = 85/269 (31%), Positives = 143/269 (53%), Gaps = 11/269 (4%)
Query: 15 GVTFSATGIQMDPNPILTALSVCKFLISERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPV 74
++ A + D +PI LSVC L+ + V V+ S P + + +TS IPV
Sbjct: 34 NLSLEAVAVSNDTDPISLLLSVCDLLVVQVVAGVVFSDPTDEEAVAQILDFTSAQTRIPV 93
Query: 75 IGISSRDSAF-SDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDTDGRALL 133
+GIS R+S F SDKNIH FL+T P QADV +E+L+ +++ + + S D R L
Sbjct: 94 VGISGRESIFMSDKNIHSLFLQTGPSLEQQADVMLEILEEYDWHQFSVVTSRDPGYRDFL 153
Query: 134 GRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQL-YEMKNAQARVYLMYASKQDAEI 192
R +TT + + + + V+ + +L ++K ++RV L+Y SK++AE
Sbjct: 154 DRVETTLEES----FVGWEFQLVLTLDLSDDDGDARLLRQLKKLESRVILLYCSKEEAER 209
Query: 193 IFKDAQYLNMTETGYVWIVTEQA----LTAKNVPVGIIGLKLVNATNEDAHIRDSIYVLT 248
IF+ A L +T GYVWIV E A L + +PVG++G+ L + +A +RD++ ++
Sbjct: 210 IFEAAASLGLTGPGYVWIVGELALGSGLAPEGLPVGLLGVGLDTWYSLEARVRDAVAIVA 269
Query: 249 SALKEM-NQSAVITEAPQDCDNSGSIWET 276
A + + + E P +C ++ + E+
Sbjct: 270 RAAESLLRDKGALPEPPVNCYDTANKRES 298
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 143 bits (363), Expect = 9e-40
Identities = 51/169 (30%), Positives = 92/169 (54%), Gaps = 14/169 (8%)
Query: 295 TLWILVMVSVHVVALVLYLLDRFSPFGRFRLSNSDNTEEDALNLSSAIWFAWGVLLNSGI 354
+W+ ++ + +V +VL+LL+RFSP+ E + LS+++WF++G L+ G
Sbjct: 1 EVWLCILAAYLLVGVVLFLLERFSPYEWRGPP----EEPNQFTLSNSLWFSFGALVQQG- 55
Query: 355 GEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLERPKTKLTGINDARLRNTMENL 414
PRS S R+L VW FA+I+++SYTANLAAFL +ER ++ + + D +N +
Sbjct: 56 HRELPRSLSGRILVGVWWFFALILLSSYTANLAAFLTVERMQSPIQSLEDLAKQNKIGY- 114
Query: 415 TCATVKGSAVDMYFRR--QVELSNMYRTMEA----NNYDTAEDAIADVK 457
T++G + +F+ M+ M + N ++ E+ + V+
Sbjct: 115 --GTLRGGSTFEFFKESKNPTYRRMWEYMISFKGEVNVESYEEGVQRVR 161
>gnl|CDD|153137 cd06269, PBP1_glutamate_receptors_like, Family C G-protein couples
receptors (GPCRs), membrane bound guanylyl cyclases such
as the family of natriuretic peptide receptors (NPRs),
and the N-terminal leucine/isoleucine/valine- binding
protein (LIVBP)-like domain of the ionotropic glutamate
receptors. This CD represents the ligand-binding domain
of the family C G-protein couples receptors (GPCRs),
membrane bound guanylyl cyclases such as the family of
natriuretic peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domain of the ionotropic glutamate receptors, all of
which are structurally similar and related to the
periplasmic-binding fold type I family. The family C
GPCRs consist of metabotropic glutamate receptor (mGluR)
receptors, a calcium-sensing receptor (CaSR),
gamma-aminobutyric receptors (GABAb), the promiscuous
L-alpha-amino acid receptor GPR6A, families of taste and
pheromone receptors, and orphan receptors. Truncated
splicing variants of the orphan receptors are not
included in this CD. The family C GPCRs are activated by
endogenous agonists such as amino acids, ions, and sugar
based molecules. Their amino terminal ligand-binding
region is homologous to the bacterial
leucine-isoleucine-valine binding protein (LIVBP) and a
leucine binding protein (LBP). The ionotropic glutamate
receptors (iGluRs) have an integral ion channel and are
subdivided into three major groups based on their
pharmacology and structural similarities: NMDA
receptors, AMPA receptors, and kainate receptors. The
family of membrane bound guanylyl cyclases is further
divided into three subfamilies: the ANP receptor
(GC-A)/C-type natriuretic peptide receptor (GC-B), the
heat-stable enterotoxin receptor (GC-C)/sensory organ
specific membrane GCs such as retinal receptors (GC-E,
GC-F), and olfactory receptors (GC-D and GC-G).
Length = 298
Score = 131 bits (332), Expect = 5e-35
Identities = 65/210 (30%), Positives = 98/210 (46%), Gaps = 16/210 (7%)
Query: 26 DPNPILTALSVCKFLISERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFS 85
+ AL +C L R ++ + S AV+ G HIP I S+ S
Sbjct: 52 PSDAFSAALDLCSLLEKSRGVVAVIGP--SSSSSAEAVASLLGALHIPQISYSATSPLLS 109
Query: 86 DKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQNQED 145
DK SFLRTVP S QA V+LLKHF + V ++S D GR LL + +
Sbjct: 110 DKEQFPSFLRTVPSDSSQAQAIVDLLKHFGWTWVGLVYSDDDYGRRLLELLEEELE---- 165
Query: 146 DVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQARVYLMYASKQDAEIIFKDAQYLNMTET 205
+ + V V G + L E+K++ ARV ++++S++DA + ++A L M T
Sbjct: 166 --KNGICVAFVESIPDGSEDIRRLLKELKSSTARVIVVFSSEEDALRLLEEAVELGMM-T 222
Query: 206 GYVWIVTEQALTA-------KNVPVGIIGL 228
GY WI+T+ LT+ + P + G
Sbjct: 223 GYHWIITDLWLTSCLDLELLEYFPGNLTGF 252
>gnl|CDD|107346 cd06351, PBP1_iGluR_N_LIVBP_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). While this
N-terminal domain belongs to the periplasmic-binding
fold type I superfamily, the glutamate-binding domain of
the iGluR is structurally homologous to the
periplasmic-binding fold type II. The LIVBP-like domain
of iGluRs is thought to play a role in the initial
assembly of iGluR subunits, but it is not well
understood how this domain is arranged and functions in
intact iGluR. Glutamate mediates the majority of
excitatory synaptic transmission in the central nervous
system via two broad classes of ionotropic receptors
characterized by their response to glutamate agonists:
N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA
receptors have intrinsically slow kinetics, are highly
permeable to Ca2+, and are blocked by extracellular Mg2+
in a voltage-dependent manner. On the other hand,
non-NMDA receptors have faster kinetics, are weakly
permeable to Ca2+, and are not blocked by extracellular
Mg2+. While non-NMDA receptors typically mediate
excitatory synaptic responses at resting membrane
potentials, NMDA receptors contribute to several forms
of synaptic plasticity and are suggested to play an
important role in the development of synaptic pathways.
Length = 328
Score = 123 bits (309), Expect = 1e-31
Identities = 58/245 (23%), Positives = 102/245 (41%), Gaps = 20/245 (8%)
Query: 26 DPNPILTALSVCKFLISERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFS 85
+P +VC L+ + A I T S +AV IP I IS S
Sbjct: 45 TNDPFSLLRAVCD-LLVSQGVAAIFGP--TSSESASAVQSICDALEIPHISISGGSEGLS 101
Query: 86 DKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQNQED 145
DK + L+ P AD ++LL+++N+ K I+ SD L + ++
Sbjct: 102 DKEESSTTLQLYPSLEDLADALLDLLEYYNWTKFAIIYDSD---EGLSRLQELLDESGIK 158
Query: 146 DVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQA-RVYLMYASKQDAEIIFKDAQYLNMTE 204
+++ V + ++ L E+K +++ R+ L +S+++A+ I + A L M
Sbjct: 159 GIQVT-----VRRLDLDDDNYRQLLKELKRSESRRIILDCSSEEEAKEILEQAVELGMMG 213
Query: 205 TGYVWIVTEQALT------AKNVPVGIIGLKLVNATNEDAHIRDSIYVLTSALKEMNQSA 258
GY WI+T L+ + P I G +LV+ + D + + +N A
Sbjct: 214 YGYHWILTNLDLSDIDLEPFQYGPANITGFRLVDPDSPD--VSQFLQRWLEESPGVNLRA 271
Query: 259 VITEA 263
I +A
Sbjct: 272 PIYDA 276
>gnl|CDD|216296 pfam01094, ANF_receptor, Receptor family ligand binding region.
This family includes extracellular ligand binding
domains of a wide range of receptors. This family also
includes the bacterial amino acid binding proteins of
known structure.
Length = 343
Score = 109 bits (274), Expect = 1e-26
Identities = 68/294 (23%), Positives = 112/294 (38%), Gaps = 48/294 (16%)
Query: 5 INFDIQYVNK------GVTFSATGIQMDPNPILTALSVCKFLISERVYAVIVSHPLTGDL 58
+ I+ +N G+T + A + C L S+ V AVI P +
Sbjct: 6 MRLAIEDINADGGLLPGITLGYEDDDTCDDSFAVAAAAC-LLKSKGVVAVIG--PSCSSV 62
Query: 59 SPAAVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMK 118
+ A G + IP+I + SDK + +F RTVP S QA ++LKHF + +
Sbjct: 63 AIAVARLA-GAFGIPMISYGATSPELSDKTRYPTFARTVPSDSKQARAIADILKHFGWKR 121
Query: 119 VIFIHSSDTDGRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQA 178
V I+ D G L + +E + + VI + T +L ++K ++A
Sbjct: 122 VAVIYDDDDYGEGGLEALEDAL--REAGLNVVAVASEVIASDDDFTALLKELKDIK-SKA 178
Query: 179 RVYLMYASKQDAEIIFKDAQYLNMTETGYVWIVTE--------QALTAKNVPVGIIGLKL 230
RV ++ S D I + A+ L + GYVWI+T+ A+ G++G L
Sbjct: 179 RVIVVCGSSDDLRQILRQARELGLMSGGYVWILTDLWSDSLDIDNDKAREAAKGVLGFTL 238
Query: 231 VNATNED---------------------------AHIRDSIYVLTSALKEMNQS 257
+ D++Y+L AL E +
Sbjct: 239 KPPDSPGFQEFVERLKKLANRCTPALDTEPNGYALLAYDAVYLLAHALNEALRD 292
>gnl|CDD|107261 cd04509, PBP1_ABC_transporter_GCPR_C_like, Family C of G-protein
coupled receptors and their close homologs, the type I
periplasmic-binding proteins of ATP-binding cassette
transporter-like systems. This CD includes members of
the family C of G-protein coupled receptors and their
close homologs, the type I periplasmic-binding proteins
of ATP-binding cassette transporter-like systems. The
family C GPCR includes glutamate/glycine-gated ion
channels such as the NMDA receptor, G-protein-coupled
receptors, metabotropic glutamate, GABA-B, calcium
sensing, phermone receptors, and atrial natriuretic
peptide-guanylate cyclase receptors. The glutamate
receptors that form cation-selective ion channels,
iGluR, can be classified into three different subgroups
according to their binding-affinity for the agonists
NMDA (N-methyl-D-asparate), AMPA
(alpha-amino-3-dihydro-5-methyl-3-oxo-4-
isoxazolepropionic acid), and kainate. L-glutamate is a
major neurotransmitter in the brain of vertebrates and
acts through either mGluRs or iGluRs. mGluRs subunits
possess seven transmembrane segments and a large
N-terminal extracellular domain. ABC-type
leucine-isoleucine-valine-binding protein (LIVBP) is a
bacterial periplasmic binding protein that has homology
with the amino-terminal domain of the glutamate-receptor
ion channels (iGluRs). The extracellular regions of
iGluRs are made of two PBP-like domains in tandem, a
LIVBP-like domain that constitutes the N terminus -
which is included in this CD - followed by a domain
related to lysine-arginine-ornithine-binding protein
(LAOBP) that belongs to the type II periplasmic binding
fold protein superfamily. The uncharacterized
periplasmic components of various ABC-type transport
systems are included in this group.
Length = 299
Score = 99.9 bits (249), Expect = 2e-23
Identities = 47/194 (24%), Positives = 79/194 (40%), Gaps = 9/194 (4%)
Query: 32 TALSVCKFLISERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFSDKNIHV 91
AL+ + L + +V +G AV+ + IP+I + +DK +
Sbjct: 54 RALAAARRLCQQEGVDALVGPVSSG--VALAVAPVAEALKIPLISPGATAPGLTDKKGYP 111
Query: 92 SFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQNQEDDVEIKV 151
RT P QA+ + +K +N+ KV ++ D+ GR LL F+ + V
Sbjct: 112 YLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAAFK----KKGGTV 167
Query: 152 QVEAVIEFEPGLTTFKDQLYEMKNAQARVYLMYASKQDAEIIFKDAQYLNMTETGYVWIV 211
E + G T F L ++K A+ V ++ S +DA I K A +T GY +
Sbjct: 168 VGE--EYYPLGTTDFTSLLQKLKAAKPDVIVLCGSGEDAATILKQAAEAGLTG-GYPILG 224
Query: 212 TEQALTAKNVPVGI 225
L+ + G
Sbjct: 225 ITLGLSDVLLEAGG 238
>gnl|CDD|153138 cd06350, PBP1_GPCR_family_C_like, Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). The metabotropic glutamate
receptors (mGluR) are key receptors in the modulation of
excitatory synaptic transmission in the central nervous
system. The mGluRs are coupled to G proteins and are
thus distinct from the iGluRs which internally contain
ligand-gated ion channels. The mGluR structure is
divided into three regions: the extracellular region,
the seven-spanning transmembrane region and the
cytoplasmic region. The extracellular region is further
devided into the ligand-binding domain (LBD) and the
cysteine-rich domain. The LBD has sequence similarity to
the LIVBP, which is a bacterial periplasmic protein
(PBP), as well as to the extracellular region of both
iGluR and the gamma-aminobutyric acid (GABA)b receptor.
iGluRs are divided into three main subtypes based on
pharmacological profile: NMDA, AMPA, and kainate
receptors. All family C GPCRs have a large extracellular
N terminus that contain a domain with homology to
bacterial periplasmic amino acid-binding proteins.
Length = 348
Score = 94.4 bits (235), Expect = 3e-21
Identities = 54/181 (29%), Positives = 82/181 (45%), Gaps = 9/181 (4%)
Query: 42 SERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYS 101
+V AVI P + +S AV+ G + IP I + SDK SF RTVP +
Sbjct: 89 QPKVVAVI--GPGSSSVS-MAVAELLGLFKIPQISYGATSPLLSDKLQFPSFFRTVPSDT 145
Query: 102 HQADVWVELLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEP 161
QA V LLKHF + V ++S D GR+ L + + I + I
Sbjct: 146 SQALAIVALLKHFGWTWVGLVYSDDDYGRSGLSDLEEELEKN----GICIAFVEAIPPSS 201
Query: 162 GLTTFKDQLYEMKNAQARVYLMYASKQDAEIIFKDAQYLNMTETGYVWIVTEQALTAKNV 221
K L ++K++ ARV +++ + DA +F +A L M TG WI++ T+ +
Sbjct: 202 TEEDIKRILKKLKSSTARVIVVFGDEDDALRLFCEAYKLGM--TGKYWIISTDWDTSTCL 259
Query: 222 P 222
Sbjct: 260 L 260
>gnl|CDD|107361 cd06366, PBP1_GABAb_receptor, Ligand-binding domain of GABAb
receptors, which are metabotropic transmembrane
receptors for gamma-aminobutyric acid (GABA).
Ligand-binding domain of GABAb receptors, which are
metabotropic transmembrane receptors for
gamma-aminobutyric acid (GABA). GABA is the major
inhibitory neurotransmitter in the mammalian CNS and,
like glutamate and other transmitters, acts via both
ligand gated ion channels (GABAa receptors) and
G-protein coupled receptors (GABAb). GABAa receptors are
members of the ionotropic receptor superfamily which
includes alpha-adrenergic and glycine receptors. The
GABAb receptor is a member of a receptor superfamily
which includes the mGlu receptors. The GABAb receptor is
coupled to G alpha_i proteins, and activation causes a
decrease in calcium, an increase in potassium membrane
conductance, and inhibition of cAMP formation. The
response is thus inhibitory and leads to
hyperpolarization and decreased neurotransmitter
release, for example.
Length = 350
Score = 86.5 bits (215), Expect = 1e-18
Identities = 39/155 (25%), Positives = 67/155 (43%), Gaps = 12/155 (7%)
Query: 63 VSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFI 122
V+ + +++PV+ ++ + S + + F RT P S Q LLK F + +V I
Sbjct: 82 VAEVANEWNVPVLSFAATSPSLSSRLQYPYFFRTTPSDSSQNPAIAALLKKFGWRRVATI 141
Query: 123 HSSDTDGR----ALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQA 178
+ D G L+ Q + I++ A D L ++K +
Sbjct: 142 YEDDDYGSGGLPDLVDALQ--------EAGIEISYRAAFPPSANDDDITDALKKLKEKDS 193
Query: 179 RVYLMYASKQDAEIIFKDAQYLNMTETGYVWIVTE 213
RV +++ S A +F +A L M GYVWI+T+
Sbjct: 194 RVIVVHFSPDLARRVFCEAYKLGMMGKGYVWILTD 228
>gnl|CDD|107358 cd06363, PBP1_Taste_receptor, Ligand-binding domain of the T1R
taste receptor. Ligand-binding domain of the T1R taste
receptor. The T1R is a member of the family C receptors
within the G-protein coupled receptor superfamily, which
also includes the metabotropic glutamate receptors,
GABAb receptors, the calcium-sensing receptor (CaSR),
the V2R pheromone receptors, and a small group of
uncharacterized orphan receptors.
Length = 410
Score = 83.1 bits (206), Expect = 3e-17
Identities = 54/180 (30%), Positives = 81/180 (45%), Gaps = 10/180 (5%)
Query: 44 RVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQ 103
RV AVI T L+ A + F+ IP I + S+K ++ SFLRTVP Q
Sbjct: 107 RVVAVIGPDSSTLALTVAPLF---SFFLIPQISYGASSEVLSNKELYPSFLRTVPSDKDQ 163
Query: 104 ADVWVELLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQNQEDDVEIKVQVEAVIEF-EPG 162
+ V+LL+ F + V F+ S D GR L F N I + + +I
Sbjct: 164 IEAMVQLLQEFGWNWVAFLGSDDEYGRDGLQLFSELIANT----GICIAYQGLIPLDTDP 219
Query: 163 LTTFKDQLYEMKNAQARVYLMYASKQDAEIIFKDAQYLNMTETGYVWIVTEQALTAKNVP 222
T ++ L ++ + V +++AS+Q AE F N+ TG VWI +E +P
Sbjct: 220 ETDYQQILKQINQTKVNVIVVFASRQPAEAFFNSVIQQNL--TGKVWIASEAWSLNDELP 277
>gnl|CDD|107373 cd06378, PBP1_iGluR_NMDA_NR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR2 subunit of NMDA receptor family.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the NR2 subunit of NMDA receptor
family. The ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptor serves critical functions
in neuronal development, functioning, and degeneration
in the mammalian central nervous system. The functional
NMDA receptor is a heterotetramer composed of two NR1
and two NR2 (A, B, C, and D) or of NR3 (A and B)
subunits. The receptor controls a cation channel that is
highly permeable to monovalent ions and calcium and
exhibits voltage-dependent inhibition by magnesium. Dual
agonists, glutamate and glycine, are required for
efficient activation of the NMDA receptor. Among NMDA
receptor subtypes, the NR2B subunit containing receptors
appear particularly important for pain perception; thus
NR2B-selective antagonists may be useful in the
treatment of chronic pain.
Length = 362
Score = 71.6 bits (176), Expect = 1e-13
Identities = 62/261 (23%), Positives = 114/261 (43%), Gaps = 15/261 (5%)
Query: 24 QMDPNPILTALSVCKFLISERVYAVIVSHPLTGDLSPAAV-SYTSGFYHIPVIGISSRDS 82
+ DP ILT +C L + +V+ +V T + A + + S +P++GI S
Sbjct: 44 ETDPKSILT--QLCDLLSTTKVHG-VVFEDDTDQEAVAQILDFISAQTFLPILGIHGGSS 100
Query: 83 -AFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQ 141
+ K+ +FL+ P QA V +++++ +++ + S + +TT
Sbjct: 101 MIMAAKDSGSTFLQFGPSIEQQAAVMLKIMEEYDWHAFSVVTSRFPGYDDFVSAVRTTVD 160
Query: 142 NQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQARVYLMYASKQDAEIIFKDAQYLN 201
N E++ + + + G + Q ++K +++V L+Y SK++AE IF+ A+
Sbjct: 161 NSFVGWELQSVLTLDMSDDDGDA--RTQR-QLKKLESQVILLYCSKEEAEYIFRAARSAG 217
Query: 202 MTETGYVWIVTEQAL-----TAKNVPVGIIGLKLVNATNE-DAHIRDSIYVLTSALKEM- 254
+T GYVWIV L PVG+I + A +RD + ++ + M
Sbjct: 218 LTGPGYVWIVPSLVLGNTDLGPSEFPVGLISVSYDGWRYSLRARVRDGVAIIATGASAML 277
Query: 255 NQSAVITEAPQDCDNSGSIWE 275
Q I EA C +
Sbjct: 278 RQHGFIPEAKGSCYGQAEKRD 298
>gnl|CDD|107359 cd06364, PBP1_CaSR, Ligand-binding domain of the CaSR
calcium-sensing receptor, which is a member of the
family C receptors within the G-protein coupled receptor
superfamily. Ligand-binding domain of the CaSR
calcium-sensing receptor, which is a member of the
family C receptors within the G-protein coupled receptor
superfamily. CaSR provides feedback control of
extracellular calcium homeostasis by responding
sensitively to acute fluctuations in extracellular
ionized Ca2+ concentration. This ligand-binding domain
has homology to the bacterial leucine-isoleucine-valine
binding protein (LIVBP) and a leucine binding protein
(LBP). CaSR is widely expressed in mammalian tissues and
is active in tissues that are not directly involved in
extracellular calcium homeostasis. Moreover, CaSR
responds to aromatic, aliphatic, and polar amino acids,
but not to positively charged or branched chain amino
acids, which suggests that changes in plasma amino acid
levels are likely to modulate whole body calcium
metabolism. Additionally, the family C GPCRs includes at
least two receptors with broad-spectrum amino
acid-sensing properties: GPRC6A which recognizes basic
and various aliphatic amino acids, its gold-fish homolog
the 5.24 chemoreceptor, and a specific taste receptor
(T1R) which responds to aliphatic, polar, charged, and
branched amino acids, but not to aromatic amino acids.
Length = 510
Score = 68.5 bits (167), Expect = 2e-12
Identities = 48/178 (26%), Positives = 90/178 (50%), Gaps = 18/178 (10%)
Query: 42 SERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYS 101
SE + + I TG AV+ G ++IP + +S S+KN SFLRT+P
Sbjct: 113 SEHIPSTIAVVGATGSGVSTAVANLLGLFYIPQVSYASSSRLLSNKNQFKSFLRTIPNDE 172
Query: 102 HQADVWVELLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEP 161
HQA +++++F + V I + D GR + +F+ + +E D+ I+F
Sbjct: 173 HQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFR--EEAEERDI--------CIDFSE 222
Query: 162 GLTTFKD-----QLYE-MKNAQARVYLMYASKQDAEIIFKDAQYLNMTETGYVWIVTE 213
++ + D ++ E ++N+ A+V ++++S D E + K+ N+ TG +W+ +E
Sbjct: 223 LISQYSDEEEIQRVVEVIQNSTAKVIVVFSSGPDLEPLIKEIVRRNI--TGKIWLASE 278
>gnl|CDD|107347 cd06352, PBP1_NPR_GC_like, Ligand-binding domain of membrane
guanylyl-cyclase receptors. Ligand-binding domain of
membrane guanylyl-cyclase receptors. Membrane guanylyl
cyclases (GC) have a single membrane-spanning region and
are activated by endogenous and exogenous peptides. This
family can be divided into three major subfamilies: the
natriuretic peptide receptors (NPRs), sensory
organ-specific membrane GCs, and the
enterotoxin/guanylin receptors. The binding of peptide
ligands to the receptor results in the activation of the
cytosolic catalytic domain. Three types of NPRs have
been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/
GC-B, and NPR-C. In addition, two of the GCs, GC-D and
GC-G, appear to be pseudogenes in humans. Atrial
natriuretic peptide (ANP) and brain natriuretic peptide
(BNP) are produced in the heart, and both bind to the
NPR-A. NPR-C, also termed the clearance receptor, binds
each of the natriuretic peptides and can alter
circulating levels of these peptides. The ligand binding
domain of the NPRs exhibits strong structural similarity
to the type I periplasmic binding fold protein family.
Length = 389
Score = 61.9 bits (151), Expect = 2e-10
Identities = 34/151 (22%), Positives = 68/151 (45%), Gaps = 6/151 (3%)
Query: 61 AAVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVI 120
A V+ + ++IP+I + SDK+ + + RT+PP + + LL+ FN+ +
Sbjct: 82 APVARLAAHWNIPMISWGCVALSLSDKSEYPTLTRTLPPARKLGEAVLALLRWFNWHVAV 141
Query: 121 FIHSSDTDG-RALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQAR 179
++S D++ L + + + V +E G + L ++K ++R
Sbjct: 142 VVYSDDSENCFFTLEALEAALREF----NLTVSHVVFMEDNSGAEDLLEILQDIKR-RSR 196
Query: 180 VYLMYASKQDAEIIFKDAQYLNMTETGYVWI 210
+ +M S +D + A L +T YV+I
Sbjct: 197 IIIMCGSSEDVRELLLAAHDLGLTSGDYVFI 227
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 60.7 bits (147), Expect = 2e-10
Identities = 40/213 (18%), Positives = 68/213 (31%), Gaps = 15/213 (7%)
Query: 1 MFQHINFDIQYVNKGVTFSATGIQMDPNPILTALSVCKFLISERVYAVIVSHPLTGDLSP 60
+ I + + +G+ Q DP L AL + LI + V +I S
Sbjct: 18 LLAGIELAAEEIGRGLEVILADSQSDPERALEAL---RDLIQQGVDGIIGP---PSSSSA 71
Query: 61 AAVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVI 120
AV + IPV+ + D+ D + R P + E L + +V
Sbjct: 72 LAVVELAAAAGIPVVSL---DATAPDLTGYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVA 128
Query: 121 FIHSSDTD-GRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQAR 179
I+ D GR L F+ ++ +E+ ++ E G L +
Sbjct: 129 LIYGDDGAYGRERLEGFKAAL--KKAGIEVVAIEYGDLDTEKGFQALLQLL--KAAPKPD 184
Query: 180 VYLMYASKQDAEIIFKDAQYLNMTETGYVWIVT 212
+ A K A+ +T I
Sbjct: 185 AIFACND-EMAAGALKAAREAGLTPGDISIIGF 216
>gnl|CDD|107357 cd06362, PBP1_mGluR, Ligand binding domain of the metabotropic
glutamate receptors (mGluR). Ligand binding domain of
the metabotropic glutamate receptors (mGluR), which are
members of the family C of G-protein-coupled receptors
that transduce extracellular signals into G-protein
activation and ultimately into cellular responses.
mGluRs bind to glutamate and function as an excitatory
neurotransmitter; they are involved in learning, memory,
anxiety, and the perception of pain. Eight subtypes of
mGluRs have been cloned so far, and are classified into
three groups according to their sequence similarities,
transduction mechanisms, and pharmacological profiles.
Group I is composed of mGlu1R and mGlu5R that both
stimulate PLC hydrolysis. Group II includes mGlu2R and
mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R,
mGlu6R, mGlu7R, and mGlu8R, which form group III.
Length = 452
Score = 56.1 bits (136), Expect = 2e-08
Identities = 22/59 (37%), Positives = 30/59 (50%)
Query: 68 GFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSD 126
+ IP I +S SDK + F RTVPP S QA V+++K FN+ V + S
Sbjct: 124 RLFKIPQISYASTSPELSDKTRYDYFSRTVPPDSFQAQAMVDIVKAFNWTYVSTVASEG 182
>gnl|CDD|107263 cd06268, PBP1_ABC_transporter_LIVBP_like, Periplasmic binding
domain of ATP-binding cassette transporter-like systems
that belong to the type I periplasmic binding fold
protein superfamily. Periplasmic binding domain of
ATP-binding cassette transporter-like systems that
belong to the type I periplasmic binding fold protein
superfamily. They are mostly present in archaea and
eubacteria, and are primarily involved in scavenging
solutes from the environment. ABC-type transporters
couple ATP hydrolysis with the uptake and efflux of a
wide range of substrates across bacterial membranes,
including amino acids, peptides, lipids and sterols, and
various drugs. These systems are comprised of
transmembrane domains, nucleotide binding domains, and
in most bacterial uptake systems, periplasmic binding
proteins (PBPs) which transfer the ligand to the
extracellular gate of the transmembrane domains. These
PBPs bind their substrates selectively and with high
affinity. Members of this group include ABC-type
Leucine-Isoleucine-Valine-Binding Proteins (LIVBP),
which are homologous to the aliphatic amidase
transcriptional repressor, AmiC, of Pseudomonas
aeruginosa. The uncharacterized periplasmic components
of various ABC-type transport systems are included in
this group.
Length = 298
Score = 54.3 bits (131), Expect = 3e-08
Identities = 40/168 (23%), Positives = 66/168 (39%), Gaps = 11/168 (6%)
Query: 32 TALSVCKFLISERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFSDKNIHV 91
A + + L+ + V AVI PL+ ++ AA +P+I + A + K
Sbjct: 54 AAAAAARELVDDGVDAVIG--PLSSGVALAAAPVAEE-AGVPLISPGATSPALTGKGNPY 110
Query: 92 SFLRTVPPYSHQADVWVELLK-HFNYMKVIFIHSSDTDGRALLGRFQTTSQNQEDDVEIK 150
F RT P + QA + L KV I+ GR L F+ + ++
Sbjct: 111 VF-RTAPSDAQQAAALADYLAEKGKVKKVAIIYDDYAYGRGLAAAFREALK------KLG 163
Query: 151 VQVEAVIEFEPGLTTFKDQLYEMKNAQARVYLMYASKQDAEIIFKDAQ 198
+V A + PG T F + ++K A + DA + K A+
Sbjct: 164 GEVVAEETYPPGATDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAR 211
>gnl|CDD|107370 cd06375, PBP1_mGluR_groupII, Ligand binding domain of the group II
metabotropic glutamate receptor. Ligand binding domain
of the group II metabotropic glutamate receptor, a
family that contains mGlu2R and mGlu3R, all of which
inhibit adenylyl cyclase. The metabotropic glutamate
receptor is a member of the family C of
G-protein-coupled receptors that transduce extracellular
signals into G-protein activation and ultimately into
intracellular responses. The mGluRs are classified into
three groups which comprise eight subtypes.
Length = 458
Score = 54.8 bits (132), Expect = 5e-08
Identities = 36/152 (23%), Positives = 68/152 (44%), Gaps = 18/152 (11%)
Query: 68 GFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDT 127
+ IP I +S + SDK+ + F RTVPP +QA E+L+ FN+ V + S
Sbjct: 126 RLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGD 185
Query: 128 DGRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYE------MKNAQARVY 181
G + F+ + + ++ I A E + + Y+ ++ ARV
Sbjct: 186 YGETGIEAFE--QEARLRNICI-----ATSEKVG--RSADRKSYDSVIRKLLQKPNARVV 236
Query: 182 LMYASKQDAEIIFKDAQYLNMTETGYVWIVTE 213
+++ +DA + A+ LN + + W+ ++
Sbjct: 237 VLFTRSEDARELLAAAKRLNAS---FTWVASD 265
>gnl|CDD|107356 cd06361, PBP1_GPC6A_like, Ligand-binding domain of the promiscuous
L-alpha-amino acid receptor GPRC6A which is a
broad-spectrum amino acid-sensing receptor. This family
includes the ligand-binding domain of the promiscuous
L-alpha-amino acid receptor GPRC6A which is a
broad-spectrum amino acid-sensing receptor, and its fish
homolog, the 5.24 chemoreceptor. GPRC6A is a member of
the family C of G-protein-coupled receptors that
transduce extracellular signals into G-protein
activation and ultimately into cellular responses.
Length = 403
Score = 50.3 bits (120), Expect = 1e-06
Identities = 40/161 (24%), Positives = 67/161 (41%), Gaps = 4/161 (2%)
Query: 62 AVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIF 121
AVS IP + +S SDK SFLRTVP +Q L+K + V
Sbjct: 118 AVSRMLNLQLIPQVSYASTAEILSDKIRFPSFLRTVPSDFYQTKAMAHLIKKSGWNWVGI 177
Query: 122 IHSSDTDGRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEM-KNAQARV 180
I + D GR+ L F ++ + K + A + L ++ + + V
Sbjct: 178 IITDDDYGRSALETFIIQAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNV 237
Query: 181 YLMYASKQDAEIIFKDAQYLNMTETGYVWIVTEQALTAKNV 221
+++A + ++F A N+ + VWI ++ TAK +
Sbjct: 238 IVVFARQFHVFLLFNKAIERNINK---VWIASDNWSTAKKI 275
>gnl|CDD|107369 cd06374, PBP1_mGluR_groupI, Ligand binding domain of the group I
metabotropic glutamate receptor. Ligand binding domain
of the group I metabotropic glutamate receptor, a family
containing mGlu1R and mGlu5R, all of which stimulate
phospholipase C (PLC) hydrolysis. The metabotropic
glutamate receptor is a member of the family C of
G-protein-coupled receptors that transduce extracellular
signals into G-protein activation and ultimately into
intracellular responses. The mGluRs are classified into
three groups which comprise eight subtypes.
Length = 472
Score = 44.5 bits (105), Expect = 8e-05
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 51 SHPLTGDLSPAAVSYTSG------FYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQA 104
P+ G + P + S ++IP I S+ SDK + FLR VP + QA
Sbjct: 115 KKPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSIDLSDKTLFKYFLRVVPSDTLQA 174
Query: 105 DVWVELLKHFNYMKVIFIHSSDTDG 129
++++K +N+ V +H+ G
Sbjct: 175 RAMLDIVKRYNWTYVSAVHTEGNYG 199
>gnl|CDD|107365 cd06370, PBP1_Speract_GC_like, Ligand-binding domain of membrane
bound guanylyl cyclases. Ligand-binding domain of
membrane bound guanylyl cyclases (GCs), which are known
to be activated by sperm-activating peptides (SAPs),
such as speract or resact. These ligand peptides are
released by a range of invertebrates to stimulate the
metabolism and motility of spermatozoa and are also
potent chemoattractants. These GCs contain a single
transmembrane segment, an extracellular ligand binding
domain, and intracellular protein kinase-like and
cyclase catalytic domains. GCs of insect and nematodes,
which exhibit high sequence similarity to the speract
receptor are also included in this model.
Length = 404
Score = 43.5 bits (103), Expect = 1e-04
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 72 IPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDTDGRA 131
+P+I + SDK+ + +F RTVPP + LLKHFN+ K ++ +D+ +
Sbjct: 92 LPMISYKCDEEPVSDKSKYPTFARTVPPSIQVVKSVIALLKHFNWNKFSVVYENDSKYSS 151
Query: 132 LLGRFQTTSQNQEDDVEI 149
+ + ++ + ++ I
Sbjct: 152 VFETLKEEAELR--NITI 167
>gnl|CDD|107363 cd06368, PBP1_iGluR_non_NMDA_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the non-NMDA (N-methyl-d-asparate) subtypes of
ionotropic glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the non-NMDA (N-methyl-d-asparate) subtypes of
ionotropic glutamate receptors. While this N-terminal
domain belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. Glutamate
mediates the majority of excitatory synaptic
transmission in the central nervous system via two broad
classes of ionotropic receptors, characterized by their
response to glutamate agonists: N-methyl-d -aspartate
(NMDA) and non-NMDA receptors. NMDA receptors have
intrinsically slow kinetics, are highly permeable to
Ca2+, and are blocked by extracellular Mg2+ in a
voltage-dependent manner. Non-NMDA receptors have faster
kinetics, are most often only weakly permeable to Ca2+,
and are not blocked by extracellular Mg2+. While
non-NMDA receptors typically mediate excitatory synaptic
responses at resting membrane potentials, NMDA receptors
contribute several forms of synaptic plasticity and are
thought to play an important role in the development of
synaptic pathways. Non-NMDA receptors include
alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate
(AMPA) and kainate receptors.
Length = 324
Score = 43.0 bits (102), Expect = 2e-04
Identities = 40/214 (18%), Positives = 79/214 (36%), Gaps = 36/214 (16%)
Query: 3 QHINFDIQYVNKGVTFSATGIQMDPNPILTALSVCKFLISERVYAVIVSHPLTGDLSPAA 62
+ DI +N +F T C L+S+ V A+ G S ++
Sbjct: 34 FTLVPDIDELNTNDSFELTNK------------ACD-LLSQGVAAIF------GPSSSSS 74
Query: 63 VSYTSGF---YHIPVIGIS-SRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMK 118
+ IP I S S + I++ P +D ++L+K+F + K
Sbjct: 75 ANTVQSICDALEIPHITTSWSPNPKPRQFTINL-----YPSMRDLSDALLDLIKYFGWRK 129
Query: 119 VIFIHSSDTDGRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQA 178
++I+ SD LL + +++ V+ + ++ L E+K +
Sbjct: 130 FVYIYDSD---EGLLRLQELLDALSPKGIQVTVR-----RLDDDTDMYRPLLKEIKREKE 181
Query: 179 RVYLMYASKQDAEIIFKDAQYLNMTETGYVWIVT 212
R ++ S + + + A + M Y +I+T
Sbjct: 182 RRIILDCSPERLKEFLEQAVEVGMMSEYYHYILT 215
>gnl|CDD|197504 smart00079, PBPe, Eukaryotic homologues of bacterial periplasmic
substrate binding proteins. Prokaryotic homologues are
represented by a separate alignment: PBPb.
Length = 133
Score = 39.2 bits (92), Expect = 9e-04
Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 7/63 (11%)
Query: 399 LTGINDARLRNTMENLTCATVKGSAVDMYFRRQVEL--SNMYRTM--EANNYDTAEDAIA 454
+T + D + +E T GS+ +F+R S M+ M + + +
Sbjct: 2 ITSVEDLAKQTKIE---YGTQDGSSTLAFFKRSGNPEYSRMWPYMKSPEVFVKSYAEGVQ 58
Query: 455 DVK 457
V+
Sbjct: 59 RVR 61
>gnl|CDD|223755 COG0683, LivK, ABC-type branched-chain amino acid transport
systems, periplasmic component [Amino acid transport and
metabolism].
Length = 366
Score = 40.9 bits (96), Expect = 0.001
Identities = 27/142 (19%), Positives = 50/142 (35%), Gaps = 10/142 (7%)
Query: 38 KFLISERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTV 97
K + + V +V +G A+ +P+I S+ + + + + RT
Sbjct: 72 KLITQDGV-DAVVGPTTSGVALAASPVAEE--AGVPLISPSATAPQLTGRGLKPNVFRTG 128
Query: 98 PPYSHQADVWVE-LLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQNQEDDVEIKVQVEAV 156
P + QA + L+K +V I G L F+ + +V
Sbjct: 129 PTDNQQAAAAADYLVKKGGKKRVAIIGDDYAYGEGLADAFKAALKAL------GGEVVVE 182
Query: 157 IEFEPGLTTFKDQLYEMKNAQA 178
+ PG T F + ++K A
Sbjct: 183 EVYAPGDTDFSALVAKIKAAGP 204
>gnl|CDD|107381 cd06386, PBP1_NPR_C_like, Ligand-binding domain of type C
natriuretic peptide receptor. Ligand-binding domain of
type C natriuretic peptide receptor (NPR-C). NPR-C is
found in atrial, mesentery, placenta, lung, kidney,
venous tissue, aortic smooth muscle, and aortic
endothelial cells. The affinity of NPR-C for natriuretic
peptides is ANP>CNP>BNP. The extracellular domain of
NPR-C is about 30% identical to NPR-A and NPR-B.
However, unlike the cyclase-linked receptors, it
contains only 37 intracellular amino acids and no
guanylyl cyclase activity. Major function of NPR-C is to
clear natriuretic peptides from the circulation or
extracellular surroundings through constitutive
receptor-mediated internalization and degradation.
Length = 387
Score = 39.8 bits (93), Expect = 0.002
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 61 AAVSYTSGFYHIPVIGISSRDSAFSDKNIHVSFL-RTVPPYSHQADVWVELLKHFNYMKV 119
A V+ + ++IP+I + + FS K S L R P Y + + L + F++
Sbjct: 81 APVARLASHWNIPMISAGALAAGFSHKKSEYSHLTRVAPSYVKMGETFSALFERFHWRSA 140
Query: 120 IFIHSSDTDGR 130
+ ++ D R
Sbjct: 141 LLVYEDDKQER 151
>gnl|CDD|107367 cd06372, PBP1_GC_G_like, Ligand-binding domain of membrane guanylyl
cyclase G. This group includes the ligand-binding
domain of membrane guanylyl cyclase G (GC-G) which is a
sperm surface receptor and might function, similar to
its sea urchin counterpart, in the early signaling event
that regulates the Ca2+ influx/efflux and subsequent
motility response in sperm. GC-G appears to be a
pseudogene in human. Furthermore, in contrast to the
other orphan receptor GCs, GC-G has a broad tissue
distribution in rat, including lung, intestine, kidney,
and skeletal muscle.
Length = 391
Score = 39.8 bits (93), Expect = 0.003
Identities = 27/146 (18%), Positives = 68/146 (46%), Gaps = 4/146 (2%)
Query: 70 YHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKV-IFIHSSDTD 128
++IP+ G + + ++ ++ ++++ VPP +V + L+HF + + +F SS
Sbjct: 91 WNIPMFGFVGQTAKLDNRFLYDTYVKLVPPKQKIGEVLQKSLQHFGWKHIGLFGGSSRDS 150
Query: 129 GRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQARVYLMYASKQ 188
+ +NQ ++ + A + + + ++ ARV ++ S +
Sbjct: 151 SWDEVDELWKAVENQ---LKFHFNITATVRYSSSNPDLLQEKLRYISSVARVIILICSSE 207
Query: 189 DAEIIFKDAQYLNMTETGYVWIVTEQ 214
DA+ I + A+ L + + +V+ + +Q
Sbjct: 208 DAKAILQAAEKLGLMKGKFVFFLLQQ 233
>gnl|CDD|107371 cd06376, PBP1_mGluR_groupIII, Ligand-binding domain of the group
III metabotropic glutamate receptor. Ligand-binding
domain of the group III metabotropic glutamate receptor,
a family which contains mGlu4R, mGluR6R, mGluR7, and
mGluR8; all of which inhibit adenylyl cyclase. The
metabotropic glutamate receptor is a member of the
family C of G-protein-coupled receptors that transduce
extracellular signals into G-protein activation and
ultimately into intracellular responses. The mGluRs are
classified into three groups which comprise eight
subtypes.
Length = 463
Score = 37.9 bits (88), Expect = 0.011
Identities = 41/158 (25%), Positives = 69/158 (43%), Gaps = 10/158 (6%)
Query: 69 FYHIPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDTD 128
+ IP I +S SD + F R VPP S QA V+++K + V + S
Sbjct: 125 LFQIPQISYASTAPELSDDRRYDFFSRVVPPDSFQAQAMVDIVKALGWNYVSTLASEGNY 184
Query: 129 GRALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKD---QLYEMKNAQARVYLMYA 185
G + + F S+ + V I ++ I EP F +L E NA+A + ++A
Sbjct: 185 GESGVEAFTQISR-EAGGVCIAQSIK--IPREPRPGEFDKIIKRLLETPNARAVI--IFA 239
Query: 186 SKQDAEIIFKDAQYLNMTETGYVWIVTEQALTAKNVPV 223
++ D + + A+ N + G+ V + AK P+
Sbjct: 240 NEDDIRRVLEAAKRAN--QVGHFLWVGSDSWGAKISPI 275
>gnl|CDD|107368 cd06373, PBP1_NPR_like, Ligand binding domain of natriuretic
peptide receptor (NPR) family. Ligand binding domain of
natriuretic peptide receptor (NPR) family which consists
of three different subtypes: type A natriuretic peptide
receptor (NPR-A, or GC-A), type B natriuretic peptide
receptors (NPR-B, or GC-B), and type C natriuretic
peptide receptor (NPR-C). There are three types of
natriuretic peptide (NP) ligands specific to the
receptors: atrial NP (ANP), brain or B-type NP (BNP),
and C-type NP (CNP). The NP family is thought to have
arisen through gene duplication during evolution and
plays an essential role in cardiovascular and body fluid
homeostasis. ANP and BNP bind mainly to NPR-A, while CNP
binds specifically to NPR-B. Both NPR-A and NPR-B have
guanylyl cyclase catalytic activity and produces
intracellular secondary messenger cGMP in response to
peptide-ligand binding. Consequently, the NPR-A
activation results in vasodilation and inhibition of
vascular smooth muscle cell proliferation. NPR-C acts as
the receptor for all the three members of NP family, and
functions as a clearance receptor. Unlike NPR-A and -B,
NPR-C lacks an intracellular guanylyl cyclase domain and
is thought to exert biological actions by sequestration
of released natriuretic peptides and/or inhibition of
adenylyl cyclase.
Length = 396
Score = 36.1 bits (84), Expect = 0.038
Identities = 36/144 (25%), Positives = 61/144 (42%), Gaps = 12/144 (8%)
Query: 72 IPVIGISSRDSAFSDKNIHVSFLRTVPPYSHQADVWVELLKHFNYMKVIFI-HSSDTDGR 130
+PV+ + + FSDK+ + + RT P Y+ + + L +HFN+ + + H D R
Sbjct: 98 VPVLTAGAPAAGFSDKSEYSTLTRTGPSYTKLGEFVLALHEHFNWSRAALLYHDDKNDDR 157
Query: 131 ----ALLGRFQTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQARVYLMYAS 186
L G + + I V E + L +K+ L ++ + RV +M AS
Sbjct: 158 PCYFTLEGVY-----TVLKEENITVSDFPFDEDKE-LDDYKELLRDISK-KGRVVIMCAS 210
Query: 187 KQDAEIIFKDAQYLNMTETGYVWI 210
I A L +T YV+
Sbjct: 211 PDTVREIMLAAHRLGLTSGEYVFF 234
>gnl|CDD|107372 cd06377, PBP1_iGluR_NMDA_NR3, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR3 subunit of NMDA receptor family.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the NR3 subunit of NMDA receptor
family. The ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptor serves critical functions
in neuronal development, functioning, and degeneration
in the mammalian central nervous system. The functional
NMDA receptor is a heterotetramer composed of two NR1
and two NR2 (A, B, C, and D) or of NR3 (A and B)
subunits. The receptor controls a cation channel that is
highly permeable to monovalent ions and calcium and
exhibits voltage-dependent inhibition by magnesium. Dual
agonists, glutamate and glycine, are required for
efficient activation of the NMDA receptor. Among NMDA
receptor subtypes, the NR2B subunit containing receptors
appear particularly important for pain perception; thus
NR2B-selective antagonists may be useful in the
treatment of chronic pain.
Length = 382
Score = 35.5 bits (82), Expect = 0.055
Identities = 50/274 (18%), Positives = 105/274 (38%), Gaps = 34/274 (12%)
Query: 35 SVCKFLISERVYAVIVSHPLTGDLSPAAVSYTSGFYHIPVIGISSRDSAFSDKN-IHVSF 93
SVC+ ++ + V A++ +L + + S IPV+ I R+ +N H+
Sbjct: 72 SVCQTVVVQGVSALLAFPQTRPEL--VQLDFVSAALEIPVVSIVRREFPRGSQNPFHLQ- 128
Query: 94 LRTVPPYSHQADVWVELLKHFNYMKVIFIHSSDTDGRALLGRFQTTSQNQEDDVEIKVQV 153
+ P S DV + +L+ + V + + D N + +
Sbjct: 129 MSWASPLSTLLDVLLSVLQRNGWEDVSLVLCRERD----PTGLLLLWTNHA-----RFHL 179
Query: 154 EAVIEFEPGLTTFKDQLYEMKNAQARVYLMYASKQDAEIIF-----KDAQYLNMTETGYV 208
+V+ + D L + +A++ L+ A ++F + + L +T G
Sbjct: 180 GSVLNLSRNDPSTADLLDFL---RAQLELLKDPPGPAVVLFGCDVARARRVLELTPPGPH 236
Query: 209 WIVTE----QALTAKNVPVGIIGLKLVNATNEDAHIRDSIYVLTSALKEMNQ---SAVIT 261
WI+ + +AL + +P G++ +A+++D++ ++ A+ +
Sbjct: 237 WILGDPLPPEALRTEGLPPGLLAHGETTQPPLEAYVQDALELVARAVGSATLVQPELALI 296
Query: 262 EAPQDCDNSGSIWETGKPSRSSTLVSFLQPFSNT 295
A +C + G S L FL +NT
Sbjct: 297 PATVNCMDLP---TKGNESSGQYLARFL---ANT 324
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the two
membrane helix type ion channels found in bacteria.
Length = 74
Score = 31.4 bits (72), Expect = 0.11
Identities = 10/56 (17%), Positives = 25/56 (44%)
Query: 332 EEDALNLSSAIWFAWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLA 387
E + A++F++ L G G+ P + + R+ +++ + + + A L
Sbjct: 19 EGWGWDFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYILIGIPLFLLFLAVLG 74
>gnl|CDD|216852 pfam02028, BCCT, BCCT family transporter.
Length = 484
Score = 31.3 bits (72), Expect = 0.99
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 14/83 (16%)
Query: 279 PSRSSTLVSFLQPFSNT----LWILVMVSVHVVALVLYLLDRFSPFGRFRLSNSDNTEED 334
P +S +++ L + ++L+++ V L L FS +G RL D E
Sbjct: 20 PEAASAVINTLFDWITNNFGWFYLLLVLFFLVFLLYLA----FSRYGNIRLGGDDEKPE- 74
Query: 335 ALNLSSAIWFAWGVLLNSGIGEG 357
S+ WFA +L +G+G G
Sbjct: 75 ---FSTFSWFA--MLFAAGMGIG 92
>gnl|CDD|232969 TIGR00422, valS, valyl-tRNA synthetase. The valyl-tRNA synthetase
(ValS) is a class I amino acyl-tRNA ligase and is
particularly closely related to the isoleucyl tRNA
synthetase [Protein synthesis, tRNA aminoacylation].
Length = 861
Score = 30.0 bits (68), Expect = 3.3
Identities = 23/107 (21%), Positives = 39/107 (36%), Gaps = 8/107 (7%)
Query: 142 NQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQARVYLMYASKQDAEIIFKDAQYL- 200
+ D E + E + E + K + NA +V L+Y + AE + +A +
Sbjct: 715 AEFVDEEAEKAFELLKEIIVSIRNLKAESNIPPNAPLKVLLIYTEAETAERLKLNAVDIK 774
Query: 201 NMTETGYVWIVTE-----QALTAKNVPVGIIGLK--LVNATNEDAHI 240
V +V E +A+ II L+N E A +
Sbjct: 775 GAINFSEVEVVIEKPEVTEAVVELVPGFEIIIPVKGLINKAKELARL 821
>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional.
Length = 191
Score = 28.8 bits (65), Expect = 3.8
Identities = 8/45 (17%), Positives = 21/45 (46%)
Query: 137 QTTSQNQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNAQARVY 181
+ +E+ VE + + E + E + + + +L E++ R+
Sbjct: 20 AVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEERYLRLQ 64
>gnl|CDD|107377 cd06382, PBP1_iGluR_Kainate, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the kainate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the kainate receptors, non-NMDA ionotropic
receptors which respond to the neurotransmitter
glutamate. While this N-terminal domain belongs to the
periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. Kainate receptors have five
subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are
structurally similar to AMPA and NMDA subunits of
ionotropic glutamate receptors. KA1 and KA2 subunits can
only form functional receptors with one of the GluR5-7
subunits. Moreover, GluR5-7 can also form functional
homomeric receptor channels activated by kainate and
glutamate when expressed in heterologous systems.
Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMAP receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 327
Score = 29.2 bits (66), Expect = 4.4
Identities = 44/216 (20%), Positives = 78/216 (36%), Gaps = 40/216 (18%)
Query: 3 QHINFDIQYVNKGVTFSATGIQMDPNPILTALSVCKFLISERVYAVIVSHPLTGDLSPAA 62
+ +DI+ V +F T VC L+ + V A+ P + + S +
Sbjct: 35 TTLEYDIKRVKPDDSFETTKK------------VCD-LLQQGVAAIF--GPSSSEAS-SI 78
Query: 63 VSYTSGFYHIPVI--GISSRDSAFSDKNIHVSFLRTVPPYSHQADV---WVELLKHFNYM 117
V IP I + I++ Y AD+ + +++K FN+
Sbjct: 79 VQSICDAKEIPHIQTRWDPEPKSNRQFTINL--------YPSNADLSRAYADIVKSFNWK 130
Query: 118 KVIFIHSSDTDGRALLGRFQTTSQ-NQEDDVEIKVQVEAVIEFEPGLTTFKDQLYEMKNA 176
I+ S L R Q Q + I V+ + + L ++ L E+KN+
Sbjct: 131 SFTIIYESAEG----LLRLQELLQAFGISGITITVR-----QLDDDLD-YRPLLKEIKNS 180
Query: 177 QARVYLMYASKQDAEIIFKDAQYLNMTETGYVWIVT 212
++ S + K AQ + M Y +I+T
Sbjct: 181 GDNRIIIDCSADILIELLKQAQQVGMMSEYYHYIIT 216
>gnl|CDD|107375 cd06380, PBP1_iGluR_AMPA, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the AMPA receptor. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor, a member of the glutamate-receptor ion
channels (iGluRs). AMPA receptors are the major
mediators of excitatory synaptic transmission in the
central nervous system. While this N-terminal domain
belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. AMPA
receptors consist of four types of subunits (GluR1,
GluR2, GluR3, and GluR4) which combine to form a
tetramer and play an important roles in mediating the
rapid excitatory synaptic current.
Length = 382
Score = 29.2 bits (66), Expect = 4.6
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 16/89 (17%)
Query: 42 SERVYAVIVSHPLTGDLSPAAV----SYTSGFYHIPVIGISSRDSAFSDKNIHVSFLRTV 97
S V+A+ G ++V SY+ H+P I S + D N V +R
Sbjct: 60 SRGVFAIF------GSYDKSSVNTLTSYSDAL-HVPFITPSFPTNDLDDGNQFVLQMR-- 110
Query: 98 PPYSHQADVWVELLKHFNYMKVIFIHSSD 126
P V+L++H+ + KV++++ SD
Sbjct: 111 PSLI---QALVDLIEHYGWRKVVYLYDSD 136
>gnl|CDD|237974 PRK15489, nfrB, bacteriophage N4 adsorption protein B; Provisional.
Length = 703
Score = 29.3 bits (66), Expect = 5.4
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 286 VSFLQPFSNTLWILVMVSVHVVALVLYLLDRF 317
+SF F W+ +++ + VAL L RF
Sbjct: 393 MSFPSLFVTGGWMQYLLAANAVALANRLAQRF 424
>gnl|CDD|220378 pfam09749, HVSL, Uncharacterized conserved protein. This entry is
of proteins of approximately 300 residues conserved from
plants to humans. It contains two conserved motifs, HxSL
and FHVSL. The function is unknown.
Length = 238
Score = 28.1 bits (63), Expect = 9.4
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 90 HVSFLRTVPPYSHQADVWVELLK 112
H+S RTV +HQ D +V+ L+
Sbjct: 90 HISLSRTVVLRTHQIDPFVDSLR 112
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.133 0.386
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,029,246
Number of extensions: 2219855
Number of successful extensions: 2003
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1972
Number of HSP's successfully gapped: 64
Length of query: 458
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 358
Effective length of database: 6,502,202
Effective search space: 2327788316
Effective search space used: 2327788316
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.3 bits)