RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18065
(149 letters)
>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 = 160 bits (408), Expect = 2e-49
Identities = 52/149 (34%), Positives = 82/149 (55%), Gaps = 2/149 (1%)
Query: 2 AEATMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKE-FSVNLYP 60
+C LQ GV A+FGPS + VQSIC+A ++PH+++R D E S F++NLYP
Sbjct: 52 TTKKVCDLLQQGVAAIFGPSSSEASSIVQSICDAKEIPHIQTRWDPEPKSNRQFTINLYP 111
Query: 61 SQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIR-HANPSTYR 119
S L+ A+ D+++ NW I+YE GL +LQEL++ + +R + YR
Sbjct: 112 SNADLSRAYADIVKSFNWKSFTIIYESAEGLLRLQELLQAFGISGITITVRQLDDDLDYR 171
Query: 120 NVLREIRQKEIFNLIIDTSTTHISQFFRA 148
+L+EI+ +IID S + + +
Sbjct: 172 PLLKEIKNSGDNRIIIDCSADILIELLKQ 200
>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 = 141 bits (357), Expect = 6e-42
Identities = 48/147 (32%), Positives = 82/147 (55%), Gaps = 2/147 (1%)
Query: 5 TMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKL 64
C L GV A+FGPS + VQSIC+AL++PH+ + ++F++NLYPS +
Sbjct: 54 KACDLLSQGVAAIFGPSSSSSANTVQSICDALEIPHITTSWSPNPKPRQFTINLYPSMRD 113
Query: 65 LNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIR--HANPSTYRNVL 122
L+ A D+I++ W K +Y+ D GL +LQEL+ ++ +R + YR +L
Sbjct: 114 LSDALLDLIKYFGWRKFVYIYDSDEGLLRLQELLDALSPKGIQVTVRRLDDDTDMYRPLL 173
Query: 123 REIRQKEIFNLIIDTSTTHISQFFRAV 149
+EI++++ +I+D S + +F
Sbjct: 174 KEIKREKERRIILDCSPERLKEFLEQA 200
>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 = 100 bits (251), Expect = 4e-26
Identities = 55/153 (35%), Positives = 79/153 (51%), Gaps = 10/153 (6%)
Query: 2 AEATMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESR-----LDLELNSKEFSV 56
A C QL GV A+FGPS VQSIC AL+VPH++ R LD N F V
Sbjct: 61 ATKKACDQLALGVVAIFGPSQGSCTNAVQSICNALEVPHIQLRWKHHPLD---NKDTFYV 117
Query: 57 NLYPSQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIRHANPS 116
NLYP L+ A D++++L W +VY++ GL +LQEL+ P + IR
Sbjct: 118 NLYPDYASLSHAILDLVQYLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPTD 177
Query: 117 T--YRNVLREIRQKEIFNLIIDTSTTHISQFFR 147
+ R +L+E+++ F +I D S +Q +
Sbjct: 178 SDDARPLLKEMKRGREFRIIFDCSHQMAAQILK 210
>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 = 99.1 bits (247), Expect = 1e-25
Identities = 48/152 (31%), Positives = 76/152 (50%), Gaps = 8/152 (5%)
Query: 6 MCRQLQN-GVQALFGPSDALLGPHVQSICEALDVPH----MESRLDLELNSKEFSVNLYP 60
+C L + GV A+FGP+ + VQSIC+AL++PH S + ++ LYP
Sbjct: 55 VCDLLVSQGVAAIFGPTSSESASAVQSICDALEIPHISISGGSEGLSDKEESSTTLQLYP 114
Query: 61 SQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTP-PTLKTEMYIRHANP-STY 118
S + L A D++ + NWTK AI+Y+ D GL +LQEL+ R Y
Sbjct: 115 SLEDLADALLDLLEYYNWTKFAIIYDSDEGLSRLQELLDESGIKGIQVTVRRLDLDDDNY 174
Query: 119 RNVLREIRQKEIFNLIIDTSTT-HISQFFRAV 149
R +L+E+++ E +I+D S+ +
Sbjct: 175 RQLLKELKRSESRRIILDCSSEEEAKEILEQA 206
>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 = 69.1 bits (169), Expect = 9e-15
Identities = 37/161 (22%), Positives = 62/161 (38%), Gaps = 24/161 (14%)
Query: 6 MCRQL--QNGVQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKE---FSVNLY 59
+C L GV A+ GPS + V S+ AL +P + S L+ KE +
Sbjct: 62 LCSLLEKSRGVVAVIGPSSSSSAEAVASLLGALHIPQISYSATSPLLSDKEQFPSFLRTV 121
Query: 60 PSQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIRH------- 112
PS A D+++ WT V +VY +D+ +L EL L+ E+
Sbjct: 122 PSDSSQAQAIVDLLKHFGWTWVGLVYSDDDYGRRLLEL------LEEELEKNGICVAFVE 175
Query: 113 ---ANPSTYRNVLREIRQKEIFNLIID-TSTTHISQFFRAV 149
R +L+E++ +I+ +S +
Sbjct: 176 SIPDGSEDIRRLLKELKSSTA-RVIVVFSSEEDALRLLEEA 215
>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 = 69.0 bits (169), Expect = 1e-14
Identities = 33/158 (20%), Positives = 64/158 (40%), Gaps = 15/158 (9%)
Query: 4 ATMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKE---FSVNLY 59
A C GV A+ GPS + + V + A +P + EL+ K
Sbjct: 41 AAACLLKSKGVVAVIGPSCSSVAIAVARLAGAFGIPMISYGATSPELSDKTRYPTFARTV 100
Query: 60 PSQKLLNAAFKDVIRFLNWTKVAIVYEED----NGLFKLQELVKT---PPTLKTEMYIRH 112
PS A D+++ W +VA++Y++D GL L++ ++ I
Sbjct: 101 PSDSKQARAIADILKHFGWKRVAVIYDDDDYGEGGLEALEDALREAGLNVVAVASEVI-- 158
Query: 113 ANPSTYRNVLREIRQ--KEIFNLIIDTSTTHISQFFRA 148
A+ + +L+E++ + +++ S+ + Q R
Sbjct: 159 ASDDDFTALLKELKDIKSKARVIVVCGSSDDLRQILRQ 196
>gnl|CDD|107389 cd06394, PBP1_iGluR_Kainate_KA1_2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the KA1 and KA2 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the KA1 and KA2 subunits of
Kainate receptor. While this N-terminal domain belongs
to the periplasmic-binding fold type 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 AMPA receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 333
Score = 58.7 bits (142), Expect = 5e-11
Identities = 39/145 (26%), Positives = 71/145 (48%), Gaps = 13/145 (8%)
Query: 5 TMCRQLQNGVQALFGPSDA-LLGPHVQSICEALDVPHM----ESRLDLELNSKEFSVNLY 59
TMC+ L GV ++ GPS + V IC ++PH E L+ + SVNL+
Sbjct: 57 TMCQILPKGVVSVLGPSSSPASSSIVSHICGEKEIPHFKVGPEETPKLQY-LRFASVNLH 115
Query: 60 PSQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVK----TPPTLKTEMYIRHANP 115
PS + ++ A ++ N+ +++ + L +L+EL++ + TL M +P
Sbjct: 116 PSNEDISVAVAGILNSFNYPTASLICAKAECLLRLEELLRQFLISKETLSVRMLDDSRDP 175
Query: 116 STYRNVLREIRQKEIFNLIIDTSTT 140
+ +L+EIR + +IID + +
Sbjct: 176 TP---LLKEIRDDKTATIIIDANAS 197
>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 = 57.1 bits (138), Expect = 2e-10
Identities = 34/149 (22%), Positives = 64/149 (42%), Gaps = 12/149 (8%)
Query: 11 QNGVQALFGPSDALLGPHVQSICEALDVPHME--SRLDLELNSKEFS--VNLYPSQKLLN 66
Q GV AL GP + + V + EAL +P + + + K + PS +
Sbjct: 65 QEGVDALVGPVSSGVALAVAPVAEALKIPLISPGATAPGLTDKKGYPYLFRTGPSDEQQA 124
Query: 67 AAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTP-----PTLKTEMYIRHANPSTYRNV 121
A D I+ NW KVAI+Y++D+ L E K T+ E Y + + ++
Sbjct: 125 EALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAAFKKKGGTVVGEEYY-PLGTTDFTSL 183
Query: 122 LREIRQKEIFNLIIDTST-THISQFFRAV 149
L++++ + ++I+ + + +
Sbjct: 184 LQKLKAAK-PDVIVLCGSGEDAATILKQA 211
>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 = 53.9 bits (130), Expect = 3e-09
Identities = 35/143 (24%), Positives = 61/143 (42%), Gaps = 15/143 (10%)
Query: 7 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPH----MESRLDLELNSKEFSVNLYPSQ 62
C QL GV A+FG D + S +AL VP + + N F + + PS
Sbjct: 56 CSQLSRGVFAIFGSYDKSSVNTLTSYSDALHVPFITPSFPTNDLDDGNQ--FVLQMRPS- 112
Query: 63 KLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQ---ELVKTPPTLKTEMYIRHANPST-- 117
L A D+I W KV +Y+ D GL +LQ + ++ R N +
Sbjct: 113 --LIQALVDLIEHYGWRKVVYLYDSDRGLLRLQQLLDYLREKDNKWQVTARRVDNVTDEE 170
Query: 118 -YRNVLREIRQKEIFNLIIDTST 139
+ +L ++ +++ +++D +
Sbjct: 171 EFLRLLEDLDRRKEKRIVLDCES 193
>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 = 47.7 bits (113), Expect = 4e-07
Identities = 34/137 (24%), Positives = 58/137 (42%), Gaps = 11/137 (8%)
Query: 7 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLLN 66
C Q GV A+FG D + S C L V + + F + + P L
Sbjct: 51 CSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT-HPFVIQMRPD---LK 106
Query: 67 AAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLK---TEMYIRHAN----PSTYR 119
A +I + W K A +Y+ D GL LQ ++ + K T + + + N YR
Sbjct: 107 GALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDRKDEAYR 166
Query: 120 NVLREIRQKEIFNLIID 136
++ +++ K+ +I+D
Sbjct: 167 SLFQDLENKKERRVILD 183
>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 = 47.6 bits (113), Expect = 4e-07
Identities = 37/135 (27%), Positives = 59/135 (43%), Gaps = 7/135 (5%)
Query: 5 TMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKL 64
T C Q GV A+FG D + S C AL V + ++ S +F + L P
Sbjct: 48 TFCSQFSKGVYAIFGFYDRKTVNMLTSFCGALHVCFITPSFPVD-TSNQFVLQLRPE--- 103
Query: 65 LNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLK---TEMYIRHANPSTYRNV 121
L A VI W K +Y+ D GL LQ+++ T T + I YR +
Sbjct: 104 LQDALISVIEHYKWQKFVYIYDADRGLSVLQKVLDTAAEKNWQVTAVNILTTTEEGYRKL 163
Query: 122 LREIRQKEIFNLIID 136
+++ +K+ +++D
Sbjct: 164 FQDLDKKKERLIVVD 178
>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 = 44.9 bits (106), Expect = 3e-06
Identities = 22/149 (14%), Positives = 50/149 (33%), Gaps = 7/149 (4%)
Query: 8 RQLQNGVQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKEFSVNLYPSQKLLN 66
+Q GV + GP + V + A +P + +L + + P +
Sbjct: 53 DLIQQGVDGIIGPPSSSSALAVVELAAAAGIPVVSLDATAPDLTGYPYVFRVGPDNEQAG 112
Query: 67 AAFKDVIRFLNWTKVAIVYEED-NGLFKLQELVKT-----PPTLKTEMYIRHANPSTYRN 120
A + + W +VA++Y +D + E K + Y ++
Sbjct: 113 EAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIEVVAIEYGDLDTEKGFQA 172
Query: 121 VLREIRQKEIFNLIIDTSTTHISQFFRAV 149
+L+ ++ + I + + +A
Sbjct: 173 LLQLLKAAPKPDAIFACNDEMAAGALKAA 201
>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 = 42.5 bits (100), Expect = 2e-05
Identities = 16/83 (19%), Positives = 38/83 (45%)
Query: 53 EFSVNLYPSQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIRH 112
+ + L P + A +D++ + N T AI+Y++D + + + + + I +
Sbjct: 108 PYLIQLMPPADDIVEAIRDIVSYYNITNAAILYDDDFVMDHKYKSLLQNWPTRHVITIIN 167
Query: 113 ANPSTYRNVLREIRQKEIFNLII 135
+ R ++ +R +I N+ I
Sbjct: 168 SIIDEVREQIKRLRNLDIKNIFI 190
>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 = 40.4 bits (94), Expect = 1e-04
Identities = 32/133 (24%), Positives = 59/133 (44%), Gaps = 7/133 (5%)
Query: 7 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLLN 66
C Q GV A+FG D + S C AL + + E S +F + L PS L
Sbjct: 57 CSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGES-QFVLQLRPS---LR 112
Query: 67 AAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPT---LKTEMYIRHANPSTYRNVLR 123
A ++ W + +Y+ D G LQ +++ + + + + N ++YR +L
Sbjct: 113 GALLSLLDHYEWNRFVFLYDTDRGYSILQAIMEKAGQNGWQVSAICVENFNDASYRRLLE 172
Query: 124 EIRQKEIFNLIID 136
++ +++ +ID
Sbjct: 173 DLDRRQEKKFVID 185
>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 = 40.2 bits (94), Expect = 1e-04
Identities = 21/103 (20%), Positives = 41/103 (39%), Gaps = 13/103 (12%)
Query: 7 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPHM------------ESRLDLELNSKEF 54
C + G+ AL + +QS+ +A+ +PH+ L+ +++
Sbjct: 56 CDLMNQGILALVTSTGCASAIALQSLTDAMHIPHLFIQRGYGGSPRTACGLNPSPRGQQY 115
Query: 55 SVNLYPSQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQEL 97
++ L P + LN ++ W K Y+ D + LQE
Sbjct: 116 TLALRPPVR-LNDVMLRLVTEWRWQKFVYFYDNDYDIRGLQEF 157
>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 = 40.0 bits (93), Expect = 1e-04
Identities = 29/147 (19%), Positives = 59/147 (40%), Gaps = 8/147 (5%)
Query: 7 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLLN 66
C Q GV A+FG D + + S C AL + + + +F + + P+ L
Sbjct: 57 CSQFSRGVYAIFGFYDQMSMNTLTSFCGALHTSFITPSFPTDADV-QFVIQMRPA---LK 112
Query: 67 AAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIRHA----NPSTYRNVL 122
A ++ W K +Y+ + G LQ +++ ++ R + +R ++
Sbjct: 113 GAILSLLAHYKWEKFVYLYDTERGFSILQAIMEAAVQNNWQVTARSVGNIKDVQEFRRII 172
Query: 123 REIRQKEIFNLIIDTSTTHISQFFRAV 149
E+ +++ +ID I+ V
Sbjct: 173 EEMDRRQEKRYLIDCEVERINTILEQV 199
>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 = 38.7 bits (90), Expect = 4e-04
Identities = 29/130 (22%), Positives = 59/130 (45%), Gaps = 20/130 (15%)
Query: 14 VQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKE---FSVNLYPSQKLLNAAF 69
+ + GP + + VQ++ + ++P + S ++L+ K + + + PS L A
Sbjct: 118 IVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSIDLSDKTLFKYFLRVVPSDTLQARAM 177
Query: 70 KDVIRFLNWTKVAIVYEEDN----GLFKLQELVKTPPTLKTEMYIRH-------ANPSTY 118
D+++ NWT V+ V+ E N G+ +EL + I H A ++
Sbjct: 178 LDIVKRYNWTYVSAVHTEGNYGESGMEAFKELAA-----HEGLCIAHSDKIYSNAGEQSF 232
Query: 119 RNVLREIRQK 128
+LR++R +
Sbjct: 233 DRLLRKLRSR 242
>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 = 34.1 bits (79), Expect = 0.017
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 14/68 (20%)
Query: 71 DVIRFLNWTKVAIVYEEDN-GLFKLQELVKTPPTLKTEMYI---------RHANPSTYRN 120
D+++ NWT V+ V E N G ++ K L E I A + N
Sbjct: 165 DIVKAFNWTYVSTVASEGNYGEKGIEAFEK----LAAERGICIAGSEKIPSSATEEEFDN 220
Query: 121 VLREIRQK 128
++R++ K
Sbjct: 221 IIRKLLSK 228
>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 = 33.2 bits (76), Expect = 0.037
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 68 AFKDVIRFLNWTKVAIVYEE-DNG-----LFKLQELVKTPPTLKTEMYIRHANPSTYRNV 121
A +++RF NWT V+ V E D G F+ + ++ +E R A+ +Y +V
Sbjct: 164 AMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATSEKVGRSADRKSYDSV 223
Query: 122 LREIRQK 128
+R++ QK
Sbjct: 224 IRKLLQK 230
>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 = 32.3 bits (74), Expect = 0.066
Identities = 17/103 (16%), Positives = 37/103 (35%), Gaps = 20/103 (19%)
Query: 60 PSQKLLNAAFKDVIRFLNWTKVAIVYEED----NGLFKLQELVKTPPTLK-------TEM 108
PS A +++ WT V +VY +D +GL L+E ++ K E
Sbjct: 142 PSDTSQALAIVALLKHFGWTWVGLVYSDDDYGRSGLSDLEEELE-----KNGICIAFVEA 196
Query: 109 YIRHANPSTYRNVLREIRQKE--IFNLIIDTSTTHISQFFRAV 149
+ + +L++++ + ++ + F
Sbjct: 197 IPPSSTEEDIKRILKKLKSSTARVI--VVFGDEDDALRLFCEA 237
>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 = 32.2 bits (74), Expect = 0.074
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 60 PSQKLLNAAFKDVIRFLNWTKVAIVYEEDN 89
PS N A +++ W +VA +YE+D+
Sbjct: 117 PSDSSQNPAIAALLKKFGWRRVATIYEDDD 146
>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 = 31.1 bits (71), Expect = 0.18
Identities = 27/140 (19%), Positives = 53/140 (37%), Gaps = 15/140 (10%)
Query: 8 RQLQNGVQALFGPSDALLGPHVQSICEALDVPHMES--RLDLELNSK-EFS--VNLYPSQ 62
++ V A GP V + ++P M S + L L+ K E+ P
Sbjct: 63 LYWEHNVDAFIGPGCPYACAPVARLAAHWNIP-MISWGCVALSLSDKSEYPTLTRTLPPA 121
Query: 63 KLLNAAFKDVIRFLNWTKVAIVYEEDNGL-FKLQELVKTP------PTLKTEMYIRHANP 115
+ L A ++R+ NW +VY +D+ F E ++ ++
Sbjct: 122 RKLGEAVLALLRWFNWHVAVVVYSDDSENCFFTLEALEAALREFNLTVSHVVFMEDNSGA 181
Query: 116 STYRNVLREIRQKEIFNLII 135
+L++I+++ +II
Sbjct: 182 EDLLEILQDIKRRS--RIII 199
>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 = 30.3 bits (69), Expect = 0.38
Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 15/91 (16%)
Query: 52 KEFS--VNLYPSQKLLNAAFKDVIRFLNWTKVAIVYEEDN-----------GLFKLQELV 98
E+S PS L + NW++ A++Y +D G++ L
Sbjct: 114 SEYSTLTRTGPSYTKLGEFVLALHEHFNWSRAALLYHDDKNDDRPCYFTLEGVY--TVLK 171
Query: 99 KTPPTLKTEMYIRHANPSTYRNVLREIRQKE 129
+ T+ + Y+ +LR+I +K
Sbjct: 172 EENITVSDFPFDEDKELDDYKELLRDISKKG 202
>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 = 29.0 bits (65), Expect = 0.89
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 20/83 (24%)
Query: 22 DALLGPHVQSICE--ALDVPHMESRLDLELNS------------KEFS--VNLYPSQKLL 65
D +LGP +CE A V + S ++ + S E+S + PS +
Sbjct: 69 DLILGP----VCEYAAAPVARLASHWNIPMISAGALAAGFSHKKSEYSHLTRVAPSYVKM 124
Query: 66 NAAFKDVIRFLNWTKVAIVYEED 88
F + +W +VYE+D
Sbjct: 125 GETFSALFERFHWRSALLVYEDD 147
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It is an essential yeast protein involved in pre-rRNA
processing and ribosome assembly, and is speculated to
be required for correct assembly of rpS27 into the
pre-ribosomal particle. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain. .
Length = 96
Score = 27.4 bits (61), Expect = 1.2
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 130 IFNLIIDTSTTHISQFFRA 148
+ NL +DT+ H+ + F +
Sbjct: 5 LVNLPVDTTERHLRKLFGS 23
>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 = 28.2 bits (63), Expect = 1.8
Identities = 22/89 (24%), Positives = 33/89 (37%), Gaps = 9/89 (10%)
Query: 8 RQL-QNGVQALFGP--SDALLGPHVQSICEALDVPHM---ESRLDLELNSKEFSVNLYPS 61
R+L +GV A+ GP S L + E VP + + L + PS
Sbjct: 60 RELVDDGVDAVIGPLSSGVALA--AAPVAEEAGVPLISPGATSPALTGKGNPYVFRTAPS 117
Query: 62 QKLLNAAF-KDVIRFLNWTKVAIVYEEDN 89
AA + KVAI+Y++
Sbjct: 118 DAQQAAALADYLAEKGKVKKVAIIYDDYA 146
>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 = 27.7 bits (62), Expect = 2.9
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 2/71 (2%)
Query: 77 NWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIRHANPSTYRNVLREIRQKEIFNLIID 136
NW K ++VYE D+ + E +K L+ + I H I ++I
Sbjct: 135 NWNKFSVVYENDSKYSSVFETLKEEAELR-NITISHVEYYADFYPPDPIMDNPFEDIIQR 193
Query: 137 T-STTHISQFF 146
T TT I F
Sbjct: 194 TKETTRIYVFI 204
>gnl|CDD|218763 pfam05817, Ribophorin_II, Oligosaccharyltransferase subunit
Ribophorin II. This family contains eukaryotic
Ribophorin II (RPN2) proteins. The mammalian
oligosaccharyltransferase (OST) is a protein complex
that effects the cotranslational N-glycosylation of
newly synthesised polypeptides, and is composed of the
following proteins: ribophorins I and II (RI and RII),
OST48, and Dadl, N33/IAP, OST4, STT3. The family also
includes the SWP1 protein from yeast. In yeast the
oligosaccharyltransferase complex is composed 7 or 8
subunits, SWP1, being one of them.
Length = 636
Score = 27.4 bits (61), Expect = 3.3
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 89 NGLFKLQELVKTPPTLKTEMYIRHANPSTYRNVLREIRQKEIFNLI 134
G +KL + V T P +K E ++ AN R ++ K+ F+L+
Sbjct: 218 RGAYKLADHVSTEPPIKEEQIVKLANYFLSRKSVQSA--KDAFSLL 261
>gnl|CDD|218327 pfam04916, Phospholip_B, Phospholipase B. Phospholipase B (PLB)
catalyzes the hydrolytic cleavage of both acylester
bonds of glycerophospholipids. This family of PLB
enzymes has been identified in mammals, flies and
nematodes but not in yeast. In Drosophila this protein
was named LAMA for laminin ancestor since it is
expressed in the neuronal and glial precursors that
surround the lamina.
Length = 563
Score = 26.7 bits (59), Expect = 5.6
Identities = 25/110 (22%), Positives = 43/110 (39%), Gaps = 20/110 (18%)
Query: 42 ESRLDLELNSKEFSVNLYPSQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQE----- 96
+ +D EL +N D+++ L+ T+ + D+ +F+ E
Sbjct: 174 AAEIDFELFHPILMMNA-------AGDIGDLVKSLSKTE-----DPDDQMFEWPEGGHCS 221
Query: 97 -LVKTPPTLKTEMYIRHANPSTYRNVLREIRQKEIFNLIIDTSTTHISQF 145
LVK P + ++Y H S+Y +LR I + F T I F
Sbjct: 222 ALVKVVPGNE-DLYFGHVTWSSYSTMLR-IYKTYKFGYDFSTVPGRIVTF 269
>gnl|CDD|227071 COG4727, COG4727, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 287
Score = 26.5 bits (58), Expect = 5.9
Identities = 9/42 (21%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 71 DVIRF-LNWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIR 111
D+ RF L ++ AI + G ++++ L+ ++ +Y +
Sbjct: 70 DLSRFRLRYSHAAIAWRSPAGAWRVRHLLNACDEGRSRLYDQ 111
>gnl|CDD|107387 cd06392, PBP1_iGluR_delta_1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the delta1 receptor of an orphan glutamate
receptor family. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the delta1 receptor of an orphan glutamate
receptor family. While this N-terminal domain belongs to
the periplasmic-binding fold type 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 may be closer
related to non-NMDA receptors. In contrast to
GluRdelta2, GluRdelta1 is expressed in many areas in the
developing CNS, including the hippocampus and the
caudate putamen. Furthermore, recent studies have shown
that the orphan GluRdelta1 plays an essential role in
high-frequency hearing and ionic homeostasis in the
basal cochlea and that the locus encoding GluRdelta1 may
be involved in congenial or acquired high-frequency
hearing loss in humans.
Length = 400
Score = 26.5 bits (58), Expect = 6.4
Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 13/101 (12%)
Query: 7 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPHM------------ESRLDLELNSKEF 54
C + G+ AL + +QS+ +A+ +PH+ L+ +E+
Sbjct: 56 CDLMTQGILALVTSTGCASANALQSLTDAMHIPHLFVQRNSGGSPRTACHLNPSPEGEEY 115
Query: 55 SVNLYPSQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQ 95
++ P +L + K V L W K + Y+ + + LQ
Sbjct: 116 TLAARPPVRLNDVMLKLVTE-LRWQKFIVFYDSEYDIRGLQ 155
>gnl|CDD|133037 cd04194, GT8_A4GalT_like, A4GalT_like proteins catalyze the
addition of galactose or glucose residues to the
lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of
the bacterial cell surface. The members of this family
of glycosyltransferases catalyze the addition of
galactose or glucose residues to the lipooligosaccharide
(LOS) or lipopolysaccharide (LPS) of the bacterial cell
surface. The enzymes exhibit broad substrate
specificities. The known functions found in this family
include: Alpha-1,4-galactosyltransferase,
LOS-alpha-1,3-D-galactosyltransferase,
UDP-glucose:(galactosyl) LPS
alpha1,2-glucosyltransferase, UDP-galactose: (glucosyl)
LPS alpha1,2-galactosyltransferase, and
UDP-glucose:(glucosyl) LPS alpha1,2-glucosyltransferase.
Alpha-1,4-galactosyltransferase from N. meningitidis
adds an alpha-galactose from UDP-Gal (the donor) to a
terminal lactose (the acceptor) of the LOS structure of
outer membrane. LOSs are virulence factors that enable
the organism to evade the immune system of host cells.
In E. coli, the three alpha-1,2-glycosyltransferases,
that are involved in the synthesis of the outer core
region of the LPS, are all members of this family. The
three enzymes share 40 % of sequence identity, but have
different sugar donor or acceptor specificities,
representing the structural diversity of LPS.
Length = 248
Score = 26.4 bits (59), Expect = 6.6
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 40 HMESRLDLELNSKEFSVNLYPSQKLLNAAFKDVIRFLN 77
++ +L LEL + +YP Q +LNA KD I +L
Sbjct: 168 NITEKL-LELIKEYGGRLIYPDQDILNAVLKDKILYLP 204
>gnl|CDD|235450 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
Length = 288
Score = 26.2 bits (59), Expect = 7.3
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 119 RNVLREIRQKEIFNLIIDTSTTHISQ 144
R +L +R E +L+IDTS + Q
Sbjct: 126 RELLAPLR--ERADLVIDTSELSVHQ 149
>gnl|CDD|132527 TIGR03488, cas_Cas5p, CRISPR-associated protein Cas5, subtype
PGING. CC Members of this protein family are cas, or
CRISPR-associated, proteins. The two sequences in the
alignment seed are found within cas gene clusters that
are adjacent to CRISPR DNA repeats in two members of the
order Bacteroidales, Porphyromonas gingivalis W83 and
Bacteroides forsythus ATCC 43037. This cas protein
family is unique to the Pgingi (Porphyromonas
gingivalis) subtype, but shows some sequence similarity
to genes of the Cas5 type (see TIGR02593).
Length = 237
Score = 26.1 bits (57), Expect = 8.3
Identities = 12/69 (17%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 39 PHMESRLDLELNSKEFSVNLYPSQKLLNAAFKDVIRF-LNWTKVAIVYEEDNGLFKLQEL 97
PH + EL + L P + ++ F++V+ + + + ++ + K Q+
Sbjct: 22 PHAPISMVSELPGSFYKALLVPDKHIICGLFENVLGWHFDRKDREAIQKDIEKIRKKQKK 81
Query: 98 VKTPPTLKT 106
P T+ +
Sbjct: 82 GHIPNTIGS 90
>gnl|CDD|226373 COG3855, Fbp, Uncharacterized protein conserved in bacteria
[Carbohydrate transport and metabolism].
Length = 648
Score = 26.2 bits (58), Expect = 8.5
Identities = 19/87 (21%), Positives = 32/87 (36%), Gaps = 16/87 (18%)
Query: 59 YPSQKLLNAAFKDVIRFLNWTKVAIVYEEDNGLFKLQELVKTPPTLKTEMYIRHANPSTY 118
YP +KL +W + + L EL K + T +R A P +
Sbjct: 90 YPEEKLDLIKQDFEENIDDWYRTTLYR--------LIELCKYVSSKYTRSKVRKALPKDF 141
Query: 119 RNVLREI--------RQKEIFNLIIDT 137
+L E+ +KE ++ I+D
Sbjct: 142 AYILEELLYEVDETTDKKEYYDEILDQ 168
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
0.321 0.135 0.388
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,513,666
Number of extensions: 670998
Number of successful extensions: 622
Number of sequences better than 10.0: 1
Number of HSP's gapped: 603
Number of HSP's successfully gapped: 49
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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 (21.9 bits)
S2: 54 (24.6 bits)