RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2803
(141 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 = 58.5 bits (142), Expect = 5e-11
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 18 LGAIFEQGTDEVQSAFKFAMLTHN-QNTTTRRFELQAYVDVINTADAFKLSRL 69
+G +F+ D+ SAF+FA+ HN +T F+L +VD ++T+D+F L+
Sbjct: 2 IGGLFDVDEDQEYSAFRFAISQHNTNPNSTAPFKLLPHVDNLDTSDSFALTNA 54
>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 = 45.7 bits (109), Expect = 1e-06
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 18 LGAIFEQGTDEVQSAFKFAMLTHNQN-TTTRRFELQAYVDVINTADAFKLSR 68
+GAIF++ + + AF+FA+ N N +F L +D +NT D+F+L+
Sbjct: 2 IGAIFDEDARQEELAFRFAIDRINTNEEILAKFTLVPDIDELNTNDSFELTN 53
>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 = 37.3 bits (86), Expect = 0.001
Identities = 18/52 (34%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 18 LGAIFEQGTDEVQSAFKFA--MLTHNQNTTTRRFELQAYVDVINTADAFKLS 67
+G +F + T + SAF+FA + NQNTT + F L +VD ++++++F ++
Sbjct: 2 IGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVT 53
>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 = 37.3 bits (86), Expect = 0.001
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 18 LGAIFEQGTDEVQSAFKFAMLTHNQ--NTTTRRFELQAYVDVINTADAFKLS 67
+G +F + TD+ +AF+ A+ HN N + F L +VD I TA++F ++
Sbjct: 2 IGGLFIRNTDQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVT 53
>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 = 35.2 bits (81), Expect = 0.006
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 18 LGAIFEQGTDEVQSAFKFAMLTHNQN-TTTRRFELQAYVDVINTADAFKLSR 68
+GAIF++ + + AF+ A+ N +L V +NT D F L R
Sbjct: 2 IGAIFDRDARKEELAFRAAIDALNTENLNALPTKLSVEVVEVNTNDPFSLLR 53
>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 = 31.1 bits (70), Expect = 0.17
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 18 LGAIFEQGTDEVQSAFKFAMLTHNQNTTTRRFELQAYVDVINTADAFKLS 67
+G +F +G D+ SAF+ M+ +T F L ++D + A++F ++
Sbjct: 2 IGGLFPRGADQEYSAFRVGMVQF----STSEFRLTPHIDNLEVANSFAVT 47
>gnl|CDD|176014 cd04049, C2_putative_Elicitor-responsive_gene, C2 domain present in
the putative elicitor-responsive gene. In plants
elicitor-responsive proteins are triggered in response
to specific elicitor molecules such as glycolproteins,
peptides, carbohydrates and lipids. A host of defensive
responses are also triggered resulting in localized cell
death. Antimicrobial secondary metabolites, such as
phytoalexins, or defense-related proteins, including
pathogenesis-related (PR) proteins are also produced.
There is a single C2 domain present here. C2 domains
fold into an 8-standed beta-sandwich that can adopt 2
structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. Members have a type-II
topology.
Length = 124
Score = 28.8 bits (65), Expect = 0.59
Identities = 17/45 (37%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 96 GFEPKFTESFGVFCPEPQSKFDLSLILRQSIIMVDLKLFSQSDCI 140
G P++ E F P D LILR IM D FS D I
Sbjct: 44 GRNPEWNEKFKFTVEYPGWGGDTKLILR---IM-DKDNFSDDDFI 84
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 28.2 bits (63), Expect = 1.8
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 50 ELQAYVDVINTADAFKLSRLSIRKMLVTNLMSLHSSPNLI 89
+ A+ D T DA L IR+M + L S+H P I
Sbjct: 337 AVSAWADTYETCDALTLY---IREMYLLRLRSMHLDPAQI 373
>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 = 27.2 bits (60), Expect = 2.9
Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 18 LGAIFEQGTDEVQSAFKFAMLTHNQNTTTRRFELQAYVDVINTADAFKLS 67
+G +F + +AF+FA+ + +L +D++N +D+F+++
Sbjct: 2 IGGLFPNQQSQEHAAFRFALSQLTEPP-----KLLPQIDIVNISDSFEMT 46
>gnl|CDD|99962 cd03786, GT1_UDP-GlcNAc_2-Epimerase, Bacterial members of the
UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are
known to catalyze the reversible interconversion of
UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The
enzyme serves to produce an activated form of ManNAc
residues (UDP-ManNAc) for use in the biosynthesis of a
variety of cell surface polysaccharides; The mammalian
enzyme is bifunctional, catalyzing both the inversion of
stereochemistry at C-2 and the hydrolysis of the
UDP-sugar linkage to generate free ManNAc. It also
catalyzes the phosphorylation of ManNAc to generate
ManNAc 6-phosphate, a precursor to salic acids. In
mammals, sialic acids are found at the termini of
oligosaccharides in a large variety of cell surface
glycoconjugates and are key mediators of cell-cell
recognition events. Mutations in human members of this
family have been associated with Sialuria, a rare
disease caused by the disorders of sialic acid
metabolism. This family belongs to the GT-B structural
superfamily of glycoslytransferases, which have
characteristic N- and C-terminal domains each containing
a typical Rossmann fold. The two domains have high
structural homology despite minimal sequence homology.
The large cleft that separates the two domains includes
the catalytic center and permits a high degree of
flexibility.
Length = 363
Score = 26.7 bits (60), Expect = 4.4
Identities = 8/64 (12%), Positives = 19/64 (29%), Gaps = 5/64 (7%)
Query: 66 LSRLSIRKMLVTNLMSLHSSPNLINFMTRLGFEPKFTESFGVFCPEPQSKFDLSLILRQS 125
L+ L+ + V + P + V P L+L+ +
Sbjct: 224 LAELAEEDVPVVFPNHPRTRPRIREAGLEFLGHHPN-----VLLISPLGYLYFLLLLKNA 278
Query: 126 IIMV 129
+++
Sbjct: 279 DLVL 282
>gnl|CDD|182523 PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase;
Provisional.
Length = 272
Score = 25.8 bits (57), Expect = 9.3
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 22 FEQGTDEVQSAFKFAMLTHNQNTTTRRFELQ 52
Q +V + +KFA LTH + F
Sbjct: 145 LAQAARQVNAIWKFA-LTHEDLPQLQHFAKH 174
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
0.326 0.137 0.389
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,812,663
Number of extensions: 581302
Number of successful extensions: 582
Number of sequences better than 10.0: 1
Number of HSP's gapped: 577
Number of HSP's successfully gapped: 19
Length of query: 141
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 54
Effective length of database: 7,078,804
Effective search space: 382255416
Effective search space used: 382255416
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: 54 (24.7 bits)