RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2801
(126 letters)
>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 = 115 bits (289), Expect = 9e-32
Identities = 34/86 (39%), Positives = 53/86 (61%), Gaps = 3/86 (3%)
Query: 10 VCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYAISMRP 69
+C+Q SRGVF++ G+ S +T SYS+ +PFITP FP L + + MRP
Sbjct: 55 ICSQLSRGVFAIFGSYDKSSVNTLTSYSDALHVPFITPSFPTNDL---DDGNQFVLQMRP 111
Query: 70 DYHQAIIDTVKYYGWKNIIYMYDSHD 95
QA++D +++YGW+ ++Y+YDS
Sbjct: 112 SLIQALVDLIEHYGWRKVVYLYDSDR 137
>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 = 83.5 bits (207), Expect = 2e-20
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 2/86 (2%)
Query: 10 VCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYAISMRP 69
C+ S+GV ++ G S S +T S + ++P IT + ++ SMR
Sbjct: 55 ACDLLSQGVAAIFGPSSSSSANTVQSICDALEIPHITTSWSPNPKPRQFT-INLYPSMR- 112
Query: 70 DYHQAIIDTVKYYGWKNIIYMYDSHD 95
D A++D +KY+GW+ +Y+YDS +
Sbjct: 113 DLSDALLDLIKYFGWRKFVYIYDSDE 138
>gnl|CDD|107384 cd06389, PBP1_iGluR_AMPA_GluR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR2 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR2 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 370
Score = 71.2 bits (174), Expect = 1e-15
Identities = 35/94 (37%), Positives = 51/94 (54%), Gaps = 8/94 (8%)
Query: 2 IQNVFFVS--VCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSG 59
+ N F V+ C+QFSRGV+++ G S +T S+ T + FITP F P+ G
Sbjct: 40 VANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSF------PTDG 93
Query: 60 FLDYAISMRPDYHQAIIDTVKYYGWKNIIYMYDS 93
+ I MRPD A++ ++YY W Y+YDS
Sbjct: 94 THPFVIQMRPDLKGALLSLIEYYQWDKFAYLYDS 127
>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 = 61.8 bits (150), Expect = 2e-12
Identities = 25/91 (27%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 9 SVCNQF-SRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLA---PSSGFLDYA 64
+VC+ S+GV ++ G S +S S + ++P I+ + L+ SS L
Sbjct: 54 AVCDLLVSQGVAAIFGPTSSESASAVQSICDALEIPHISISGGSEGLSDKEESSTTLQLY 113
Query: 65 ISMRPDYHQAIIDTVKYYGWKNIIYMYDSHD 95
S+ D A++D ++YY W +YDS +
Sbjct: 114 PSLE-DLADALLDLLEYYNWTKFAIIYDSDE 143
>gnl|CDD|107385 cd06390, PBP1_iGluR_AMPA_GluR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR1 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR1 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 364
Score = 61.5 bits (149), Expect = 3e-12
Identities = 25/83 (30%), Positives = 48/83 (57%), Gaps = 6/83 (7%)
Query: 11 CNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYAISMRPD 70
C+QFS+GV+++ G + + S+ + FITP FP + S+ F+ + +RP+
Sbjct: 50 CSQFSKGVYAIFGFYDRKTVNMLTSFCGALHVCFITPSFP---VDTSNQFV---LQLRPE 103
Query: 71 YHQAIIDTVKYYGWKNIIYMYDS 93
A+I +++Y W+ +Y+YD+
Sbjct: 104 LQDALISVIEHYKWQKFVYIYDA 126
>gnl|CDD|107382 cd06387, PBP1_iGluR_AMPA_GluR3, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR3 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR3 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 372
Score = 60.4 bits (146), Expect = 8e-12
Identities = 28/85 (32%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 9 SVCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYAISMR 68
+ C+QFSRGV+++ G S +T S+ FITP F P+ + + I MR
Sbjct: 55 AFCSQFSRGVYAIFGFYDQMSMNTLTSFCGALHTSFITPSF------PTDADVQFVIQMR 108
Query: 69 PDYHQAIIDTVKYYGWKNIIYMYDS 93
P AI+ + +Y W+ +Y+YD+
Sbjct: 109 PALKGAILSLLAHYKWEKFVYLYDT 133
>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 = 59.0 bits (143), Expect = 2e-11
Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 4/89 (4%)
Query: 10 VCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYAISMRP 69
C S+GV +++G + F +P I+ L+ + + P
Sbjct: 43 ACLLKSKGVVAVIGPSCSSVAIAVARLAGAFGIPMISYGATSPELSDKTRY-PTFARTVP 101
Query: 70 DYH---QAIIDTVKYYGWKNIIYMYDSHD 95
+AI D +K++GWK + +YD D
Sbjct: 102 SDSKQARAIADILKHFGWKRVAVIYDDDD 130
>gnl|CDD|107383 cd06388, PBP1_iGluR_AMPA_GluR4, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR4 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR4 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 371
Score = 58.1 bits (140), Expect = 4e-11
Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 8/92 (8%)
Query: 4 NVFFVS--VCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFL 61
N F V+ C+Q+SRGVF++ G S T S+ + + ITP F P+ G
Sbjct: 48 NSFAVTNAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSF------PTEGES 101
Query: 62 DYAISMRPDYHQAIIDTVKYYGWKNIIYMYDS 93
+ + +RP A++ + +Y W +++YD+
Sbjct: 102 QFVLQLRPSLRGALLSLLDHYEWNRFVFLYDT 133
>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 = 48.7 bits (116), Expect = 1e-07
Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 6/94 (6%)
Query: 7 FVSVCNQF--SRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYA 64
+ +C+ SRGV +++G S S + S +P I+ +L+ F
Sbjct: 59 ALDLCSLLEKSRGVVAVIGPSSSSSAEAVASLLGALHIPQISYSATSPLLSDKEQF-PSF 117
Query: 65 ISMRP---DYHQAIIDTVKYYGWKNIIYMYDSHD 95
+ P QAI+D +K++GW + +Y D
Sbjct: 118 LRTVPSDSSQAQAIVDLLKHFGWTWVGLVYSDDD 151
>gnl|CDD|107388 cd06393, PBP1_iGluR_Kainate_GluR5_7, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR5-7 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR5-7 subunits of Kainate
receptor. 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. There are five types of
kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2,
which are structurally similar to AMPA and NMDA subunits
of ionotropic glutamate receptors. KA1 and KA2 subunits
can only form functional receptors with one of the
GluR5-7 subunits. Moreover, GluR5-7 can also form
functional homomeric receptor channels activated by
kainate and glutamate when expressed in heterologous
systems. Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMAP receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 384
Score = 40.8 bits (95), Expect = 5e-05
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 11 CNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYAISMRPD 70
C+Q + GV ++ G + S N ++P I + L F +++ PD
Sbjct: 66 CDQLALGVVAIFGPSQGSCTNAVQSICNALEVPHIQLRWKHHPLDNKDTFY---VNLYPD 122
Query: 71 Y---HQAIIDTVKYYGWKNIIYMYD 92
Y AI+D V+Y W++ +YD
Sbjct: 123 YASLSHAILDLVQYLKWRSATVVYD 147
>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 = 40.6 bits (95), Expect = 7e-05
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 6/90 (6%)
Query: 7 FVSVCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYAIS 66
+C Q GV +++G VS + ++P I+P L G+ Y
Sbjct: 59 ARRLCQQE--GVDALVGPVSSGVALAVAPVAEALKIPLISPGATAPGLTDKKGY-PYLFR 115
Query: 67 -MRPDYHQ--AIIDTVKYYGWKNIIYMYDS 93
D Q A+ D +K Y WK + +YD
Sbjct: 116 TGPSDEQQAEALADYIKEYNWKKVAILYDD 145
>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 = 37.6 bits (88), Expect = 6e-04
Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 19/97 (19%)
Query: 10 VCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFI-TPWFPEKV--------LAPSSGF 60
VC+ +GV ++ G S ++ S + ++P I T W PE L PS+
Sbjct: 56 VCDLLQQGVAAIFGPSSSEASSIVQSICDAKEIPHIQTRWDPEPKSNRQFTINLYPSNAD 115
Query: 61 LDYAISMRPDYHQAIIDTVKYYGWKNIIYMYDSHDEM 97
L A + D VK + WK+ +Y+S + +
Sbjct: 116 LSRAYA----------DIVKSFNWKSFTIIYESAEGL 142
>gnl|CDD|107376 cd06381, PBP1_iGluR_delta_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of an orphan family of delta receptors,
GluRdelta1 and GluRdelta2. This CD represents the
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of an orphan family of delta
receptors, GluRdelta1 and GluRdelta2. While this
N-terminal domain belongs to the periplasmic-binding
fold type 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. Although the delta receptors are a member
of the ionotropic glutamate receptor family, they cannot
be activated by AMPA, kainate, NMDA, glutamate, or any
other ligands. Phylogenetic analysis shows that both
GluRdelta1 and GluRalpha2 are more homologous to
non-NMDA receptors. GluRdelta2 was shown to function as
an AMPA-like receptor by mutation analysis. Moreover,
targeted disruption of GluRdelta2 gene caused motor
coordination impairment, Purkinje cell maturation, and
long-term depression of synaptic transmission. It has
been suggested that GluRdelta2 is the receptor for
cerebellin 1, a glycoprotein of the Clq, and the tumor
necrosis factor family which is secreted from cerebellar
granule cells. Furthermore, recent studies have shown
that the orphan GluRdelta1 plays an essential role in
high-frequency hearing and ionic homeostasis in the
basal cochlea and that the locus encoding GluRdelta1 may
be involved in congenial or acquired high-frequency
hearing loss in humans.
Length = 363
Score = 37.5 bits (87), Expect = 8e-04
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 54 LAPSSGFLDYAISMRP--DYHQAIIDTVKYYGWKNIIYMYDSHD 95
L PS Y +++RP + ++ V + W+ +Y YD+
Sbjct: 106 LNPSPRGQQYTLALRPPVRLNDVMLRLVTEWRWQKFVYFYDNDY 149
>gnl|CDD|107386 cd06391, PBP1_iGluR_delta_2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the delta2 receptor of an orphan glutamate
receptor family. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the delta2 receptor of an orphan glutamate
receptor family. While this N-terminal domain belongs to
the periplasmic-binding fold type 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. Although the delta receptors
are a member of the ionotropic glutamate receptor
family, they cannot be activated by AMPA, kainate, NMDA,
glutamate, or any other ligands. Phylogenetic analysis
shows that both GluRdelta1 and GluRalpha2 are closer
related to non-NMDA receptors. GluRdelta2 was shown to
function as an AMPA-like receptor by mutation analysis.
Moreover, targeted disruption of GluRdelta2 gene caused
motor coordination impairment, Purkinje cell maturation,
and long-term depression of synaptic transmission. It
has been suggested that GluRdelta2 is the receptor for
cerebellin 1, a glycoprotein of the Clq and tumor
necrosis factor family that is secreted from cerebellar
granule cells.
Length = 400
Score = 35.8 bits (82), Expect = 0.003
Identities = 25/117 (21%), Positives = 52/117 (44%), Gaps = 11/117 (9%)
Query: 11 CNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMP--FI---TPWFPEKVLAPSSGFL--DY 63
C ++G+ +++ ++ S + S ++ +P FI T P + DY
Sbjct: 56 CELMNQGILALVSSIGCTSAGSLQSLADAMHIPHLFIQRSTAGTPRSSCGLTRSNRNDDY 115
Query: 64 AISMRPD--YHQAIIDTVKYYGWKNIIYMYDSHDEMFYEGSPEFLRVFCHEKLNISV 118
+S+RP + I+ V Y W+ I YD+ ++ G EFL + +++++
Sbjct: 116 TLSVRPPVYLNDVILRVVTEYAWQKFIIFYDTDYDI--RGIQEFLDKVSQQGMDVAL 170
>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 = 34.1 bits (78), Expect = 0.011
Identities = 11/81 (13%), Positives = 23/81 (28%), Gaps = 5/81 (6%)
Query: 15 SRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFLDYAISMRPDYHQA 74
+GV ++G S S + +P ++ L +
Sbjct: 56 QQGVDGIIGPPSSSSALAVVELAAAAGIPVVSLDATAPDLTGYPYVFRVGP---DNEQAG 112
Query: 75 --IIDTVKYYGWKNIIYMYDS 93
+ + GWK + +Y
Sbjct: 113 EAAAEYLAEKGWKRVALIYGD 133
>gnl|CDD|107378 cd06383, PBP1_iGluR_AMPA_Like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of uncharacterized AMPA-like receptors.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of uncharacterized AMPA-like
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. 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 = 368
Score = 33.2 bits (76), Expect = 0.020
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 62 DYAISMRPDYH---QAIIDTVKYYGWKNIIYMYD 92
Y I + P +AI D V YY N +YD
Sbjct: 108 PYLIQLMPPADDIVEAIRDIVSYYNITNAAILYD 141
>gnl|CDD|219999 pfam08743, Nse4, Nse4. Nse4 is a component of the Smc5/6 DNA
repair complex. It forms interactions with Smc5 and
Nse1.
Length = 305
Score = 29.7 bits (67), Expect = 0.37
Identities = 6/29 (20%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 70 DYHQAIIDTVKYYGWKNIIYMYDSHDEMF 98
+QA++ + Y W++I+ Y+ + +
Sbjct: 275 ARNQAVLS-LDYETWEDIVDAYNIKEPLI 302
>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 = 28.6 bits (64), Expect = 0.79
Identities = 12/47 (25%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 40 FQMPFITPWFPEKVLAPSSGFLDYAISMRPDYHQ--AIIDTVKYYGW 84
FQ+P I+ L+ S + +A ++ PD++Q A+ + ++++ W
Sbjct: 128 FQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNW 174
>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 = 28.0 bits (63), Expect = 1.5
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 66 SMRPDYHQ--AIIDTVKYYGWKNIIYMYDSHD 95
+ D Q AI +K +GW+ + +Y+ D
Sbjct: 115 TTPSDSSQNPAIAALLKKFGWRRVATIYEDDD 146
>gnl|CDD|165250 PHA02940, PHA02940, hypothetical protein; Provisional.
Length = 315
Score = 26.8 bits (59), Expect = 3.6
Identities = 7/50 (14%), Positives = 19/50 (38%)
Query: 74 AIIDTVKYYGWKNIIYMYDSHDEMFYEGSPEFLRVFCHEKLNISVWNRNL 123
+D +K + WK I ++ + + + + +++ NL
Sbjct: 212 RALDLMKEHYWKGIRLANEAKAMIKRDAYDADEEEYKPKNVDMRKIAWNL 261
>gnl|CDD|227279 COG4943, COG4943, Predicted signal transduction protein containing
sensor and EAL domains [Signal transduction mechanisms].
Length = 524
Score = 25.9 bits (57), Expect = 7.1
Identities = 18/76 (23%), Positives = 25/76 (32%), Gaps = 7/76 (9%)
Query: 1 MIQNVFFVSVCNQFSRGVFSMLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGF 60
+I + F V G + + V+ +T S S I P L +
Sbjct: 157 VIDPLSFSDV---IPTGAWGIYATVT----NTVFSLSGEASPAIIPPLIKPADLTVENNG 209
Query: 61 LDYAISMRPDYHQAII 76
YAI P AII
Sbjct: 210 YLYAIVPSPKRPIAII 225
>gnl|CDD|147812 pfam05858, BIV_Env, Bovine immunodeficiency virus surface protein
(SU). The bovine lentivirus also known as the bovine
immunodeficiency-like virus (BIV) has conserved and
hypervariable regions in the surface envelope gene. This
family corresponds to the SU surface protein.
Length = 548
Score = 25.8 bits (56), Expect = 8.8
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 11 CNQFSRGVFS----MLGAVSPDSFDTFHSYSNTFQMPFITPWFPEKVLAPSSGFL 61
C F FS +L + TF+S S++F T W KV PS GF+
Sbjct: 488 CLNFGNRAFSTNSLILCQHNSTQNKTFYSLSHSFSKQASTRWILVKV--PSYGFV 540
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
0.327 0.140 0.462
Gapped
Lambda K H
0.267 0.0640 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,600,165
Number of extensions: 579005
Number of successful extensions: 674
Number of sequences better than 10.0: 1
Number of HSP's gapped: 661
Number of HSP's successfully gapped: 35
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.4 bits)