RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15460
(123 letters)
>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 = 123 bits (310), Expect = 2e-34
Identities = 40/85 (47%), Positives = 59/85 (69%)
Query: 22 GVIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWSARGLVSDGSEAEVEGTLSLQPQAN 81
V++F + ++ G++ A +R+NA G+F W+ SDGW AR V +G E EG ++++ Q+
Sbjct: 233 VVVLFCREDDIRGLLAAAKRLNAEGHFQWIASDGWGARNSVVEGLEDVAEGAITIELQSA 292
Query: 82 PVRGFDEYFLNLTVENNRRDPWFIE 106
V GFDEYFL+LT ENN R+PWF E
Sbjct: 293 EVPGFDEYFLSLTPENNSRNPWFRE 317
>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 = 87.6 bits (217), Expect = 2e-21
Identities = 36/87 (41%), Positives = 52/87 (59%)
Query: 23 VIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWSARGLVSDGSEAEVEGTLSLQPQANP 82
V+ F V G++ A+RR+ G F +GSDGW+ R V +G E E EG ++++ Q+
Sbjct: 249 VVCFCEGMTVRGLLMAMRRLGVGGEFQLIGSDGWADRDDVVEGYEEEAEGGITIKLQSPE 308
Query: 83 VRGFDEYFLNLTVENNRRDPWFIEAKQ 109
V FD+Y+L L E N R+PWF E Q
Sbjct: 309 VPSFDDYYLKLRPETNTRNPWFREFWQ 335
>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 = 84.4 bits (209), Expect = 3e-20
Identities = 32/85 (37%), Positives = 54/85 (63%), Gaps = 2/85 (2%)
Query: 22 GVIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWSARGLVSDGSEAEVEGTLSLQPQAN 81
V++F ++ ++ A +R+NA+ F+WV SDGW A+ + GSE EG ++++ ++
Sbjct: 235 VVVLFTRSEDARELLAAAKRLNAS--FTWVASDGWGAQESIVKGSEDVAEGAITIELASH 292
Query: 82 PVRGFDEYFLNLTVENNRRDPWFIE 106
P+ FD YF +LT E N R+PWF +
Sbjct: 293 PIPDFDRYFQSLTPETNTRNPWFKD 317
>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 = 82.2 bits (203), Expect = 2e-19
Identities = 38/103 (36%), Positives = 57/103 (55%), Gaps = 4/103 (3%)
Query: 4 DKCIYDVFPTTNLLLLIPGVIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWSARGLVS 63
DK I + T N VI+F ++ ++ ++ A +R N G+F WVGSD W A+
Sbjct: 220 DKIIKRLLETPN----ARAVIIFANEDDIRRVLEAAKRANQVGHFLWVGSDSWGAKISPI 275
Query: 64 DGSEAEVEGTLSLQPQANPVRGFDEYFLNLTVENNRRDPWFIE 106
E EG +++ P+ + GFD YF + T+ENNRR+ WF E
Sbjct: 276 LQQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRNVWFAE 318
>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 = 44.0 bits (104), Expect = 3e-06
Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 1/77 (1%)
Query: 23 VIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWSARGLVSDGSEAEVEGTLSLQPQANP 82
+++ GS ++ A +++ TG + +G + L+ G EA EG L+ P
Sbjct: 195 IVLCGSGEDAATILKQAAEAGLTGGYPILGITLGLSDVLLEAGGEA-AEGVLTGTPYFPG 253
Query: 83 VRGFDEYFLNLTVENNR 99
+ +F +
Sbjct: 254 DPPPESFFFVRAAAREK 270
>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 = 39.8 bits (93), Expect = 1e-04
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 23 VIVFGSDQEVAGMMRAVRRMN-ATGNFSWVGSDGWS-ARGLVSDGSEAEVEGTLSLQPQA 80
++V GS ++ ++R R + +G + W+ +D WS + + +D + +G L +
Sbjct: 181 IVVCGSSDDLRQILRQARELGLMSGGYVWILTDLWSDSLDIDNDKAREAAKGVLGFTLKP 240
Query: 81 NPVRGFDEYFLNLTVENNRRDP 102
GF E+ L NR P
Sbjct: 241 PDSPGFQEFVERLKKLANRCTP 262
>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 = 38.5 bits (90), Expect = 3e-04
Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 4/75 (5%)
Query: 23 VIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWSARGLVSDGSEAEVEGTLSL---QPQ 79
++VFG + + + ++ TG + W+ S W + + +G L P+
Sbjct: 221 IVVFGDEDDALRLFCEAYKLGMTGKY-WIISTDWDTSTCLLLFTLDAFQGVLGFSGHAPR 279
Query: 80 ANPVRGFDEYFLNLT 94
+ + GF ++
Sbjct: 280 SGEIPGFKDFLRKYA 294
>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 = 35.2 bits (81), Expect = 0.004
Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 4/62 (6%)
Query: 23 VIVFGSDQEVAGMMRAVRRMNATG-NFSWVGSDGWSARGLVSDGSEAEVEGTLSLQPQAN 81
I +D+ AG ++A R T + S +G DG A + G ++
Sbjct: 185 AIFACNDEMAAGALKAAREAGLTPGDISIIGFDGSPA---ALLAAGEAGPGLTTVAQPFP 241
Query: 82 PV 83
Sbjct: 242 GD 243
>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 = 33.8 bits (78), Expect = 0.012
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 23 VIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWSARGLVSDGSEAEVEGT-LSLQPQAN 81
++VF S Q +V + N TG W+ S+ WS + GT L + Q
Sbjct: 238 IVVFASRQPAEAFFNSVIQQNLTGKV-WIASEAWSLNDELPSLPGIRNIGTVLGVAQQTV 296
Query: 82 PVRGFDEY 89
+ GF ++
Sbjct: 297 TIPGFSDF 304
>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 = 29.0 bits (65), Expect = 0.51
Identities = 6/35 (17%), Positives = 17/35 (48%)
Query: 23 VIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWS 57
++VF S+++ ++ + + W+ +D W
Sbjct: 199 IVVFSSEEDALRLLEEAVELGMMTGYHWIITDLWL 233
>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 = 27.1 bits (60), Expect = 2.9
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 23 VIVFGSDQEVAGMMRAVRRMNATGNFSWVGSDGWS-ARGLVSDGSEAEVEGTLSLQPQAN 81
++VF V + N N W+ SD WS A+ +++D + ++ + ++
Sbjct: 238 IVVFARQFHVFLLFNKAIERNI--NKVWIASDNWSTAKKILTDPNVKKIGKVVGFTFKSG 295
Query: 82 PVRGFDEYFLNLTV 95
+ F ++ NL +
Sbjct: 296 NISSFHQFLKNLLI 309
>gnl|CDD|201239 pfam00455, DeoRC, DeoR C terminal sensor domain. The sensor
domains of the DeoR are catalytically inactive versions
of the ISOCOT fold, but retain the substrate binding
site. DeorC senses diverse sugar derivatives such as
deoxyribose nucleoside (DeoR), tagatose phosphate
(LacR), galactosamine (AgaR), myo-inositol (Bacillus
IolR) and L-ascorbate (UlaR).
Length = 162
Score = 25.9 bits (58), Expect = 4.9
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 17 LLLIPGVIVFGSDQEVAGMM--RAVRRMNATGNFSWVGSDGWSARGLVSDGSEAEVE 71
++L+ G V G + +R+ N + +++G++G G ++ E E E
Sbjct: 66 VILLGGE-VRPKTGSFVGPLAEEFLRQFNV--DKAFIGANGIDLEGGLTTSDEEEAE 119
>gnl|CDD|211807 TIGR03323, alt_F1F0_F1_gam, alternate F1F0 ATPase, F1 subunit
gamma. A small number of taxonomically diverse
prokaryotic species, including Methanosarcina barkeri,
have what appears to be a second ATP synthase, in
addition to the normal F1F0 ATPase in bacteria and A1A0
ATPase in archaea. These enzymes use ion gradients to
synthesize ATP, and in principle may run in either
direction. This model represents the F1 gamma subunit
of this apparent second ATP synthase.
Length = 285
Score = 25.9 bits (57), Expect = 5.7
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 22 GVIVFGSDQEVAG 34
G IVFGSDQ + G
Sbjct: 73 GAIVFGSDQGLVG 85
>gnl|CDD|240171 cd05150, APH, Aminoglycoside 3'-phosphotransferase (APH). The APH
subfamily is part of a larger superfamily that includes
the catalytic domains of other kinases, such as the
typical serine/threonine/tyrosine protein kinases
(PKs), RIO kinases, actin-fragmin kinase (AFK), and
phosphoinositide 3-kinase (PI3K). APH catalyzes the
transfer of the gamma-phosphoryl group from ATP to
aminoglycoside antibiotics such as kanamycin,
streptomycin, neomycin, and gentamicin, among others.
The aminoglycoside antibiotics target the 30S ribosome
and promote miscoding, leading to the production of
defective proteins which insert into the bacterial
membrane, resulting in membrane damage and the ultimate
demise of the bacterium. Phosphorylation of the
aminoglycoside antibiotics results in their
inactivation, leading to bacterial antibiotic
resistance. The APH gene is found on transposons and
plasmids and is thought to have originated as a
self-defense mechanism used by microorganisms that
produce the antibiotics.
Length = 244
Score = 25.7 bits (57), Expect = 8.2
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 18 LLIPGVIVFGSDQEVAGM-MRAVRRMNA 44
L +P VI +GSD A + AV + A
Sbjct: 52 LPVPEVIDYGSDDGRAWLLTSAVPGVPA 79
>gnl|CDD|179287 PRK01371, PRK01371, sec-independent translocase; Provisional.
Length = 137
Score = 25.1 bits (55), Expect = 9.7
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 6/33 (18%)
Query: 16 LLLLIPGVIVFGSD------QEVAGMMRAVRRM 42
++L++ V+VFG D ++ +R +R M
Sbjct: 10 VVLVVLAVLVFGPDKLPKAARDAGRTLRQLREM 42
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
0.318 0.136 0.410
Gapped
Lambda K H
0.267 0.0674 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,244,849
Number of extensions: 535989
Number of successful extensions: 517
Number of sequences better than 10.0: 1
Number of HSP's gapped: 512
Number of HSP's successfully gapped: 25
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)