RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3581
(146 letters)
>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 = 89.6 bits (223), Expect = 4e-22
Identities = 37/109 (33%), Positives = 64/109 (58%), Gaps = 6/109 (5%)
Query: 18 EMLDSGIDVMVSHSFS-----DEISTALAKLKETDVRIILGNFNEFWAKMIFCEAYRIGM 72
+ ++GI++ +F D+I+ AL KLKE D R+I+ +F+ A+ +FCEAY++GM
Sbjct: 158 ALQEAGIEISYRAAFPPSANDDDITDALKKLKEKDSRVIVVHFSPDLARRVFCEAYKLGM 217
Query: 73 IGRKYQWLIIGMYSESWWNGSLPCPIEELVTALDGCILTDLLPLSTSGE 121
+G+ Y W++ S +WW+ S C EE++ A+ G I ++S
Sbjct: 218 MGKGYVWILTDWLSSNWWS-SSDCTDEEMLEAMQGVIGVRSYVPNSSMT 265
>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 = 47.8 bits (114), Expect = 3e-07
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 11/82 (13%)
Query: 13 NKLLAEMLDSGIDVMVSHSFS-----DEISTALAKLKETDVRIILGNFNEFWAKMIFCEA 67
+ L E+ +GI + + ++I L KLK + R+I+ +E A +FCEA
Sbjct: 178 SDLEEELEKNGICIAFVEAIPPSSTEEDIKRILKKLKSSTARVIVVFGDEDDALRLFCEA 237
Query: 68 YRIGMIGRKYQWLIIGMYSESW 89
Y++GM G+ W+I S W
Sbjct: 238 YKLGMTGK--YWII----STDW 253
>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 = 41.7 bits (98), Expect = 4e-05
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 10 RAHNKLLAEMLDSGIDVMVSHSFSDE---ISTALAKLKETDVRIILGNFNEFWAKMIFCE 66
R L E+ +GI V S D I L +LK + R+I+ +E A + E
Sbjct: 155 RLLELLEEELEKNGICVAFVESIPDGSEDIRRLLKELKSSTARVIVVFSSEEDALRLLEE 214
Query: 67 AYRIGMIGRKYQWLI 81
A +GM+ + +
Sbjct: 215 AVELGMMTGYHWIIT 229
>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 = 39.0 bits (91), Expect = 4e-04
Identities = 13/66 (19%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 26 VMVSHSFSDEISTALAKLKET--DVRIILGNFNEFWAKMIFCEAYRIGMIGRKYQWLIIG 83
+ D+ + L +LK+ R+I+ + + I +A +G++ Y W++
Sbjct: 154 ASEVIASDDDFTALLKELKDIKSKARVIVVCGSSDDLRQILRQARELGLMSGGYVWILTD 213
Query: 84 MYSESW 89
++S+S
Sbjct: 214 LWSDSL 219
>gnl|CDD|217821 pfam03969, AFG1_ATPase, AFG1-like ATPase. This family of proteins
contains a P-loop motif and are predicted to be ATPases.
Length = 361
Score = 29.7 bits (67), Expect = 0.45
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 102 VTALDGCILTDLLPLSTSGEITVSGIVSTVLLSSVPGGTRTS 143
+ D C L P S + ++ STV L+ VP TR S
Sbjct: 263 FSFADLC----LAPRHPSDYLALAERFSTVFLTDVPPMTRCS 300
>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 = 29.4 bits (66), Expect = 0.64
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 34 DEISTALAKLKETDVR--IILGNFNEFWAKMIFCEAYRIGMIGRKYQWLIIGMY 85
DE+ + +L+ D++ ILG+ E + + +A G +GRKY W +
Sbjct: 171 DEVREQIKRLRNLDIKNIFILGSTEEI-IRYVLDQALAEGFMGRKYAWFLGNPD 223
>gnl|CDD|234413 TIGR03952, metzin_BF0631, zinc-dependent metalloproteinase
lipoprotein, BF0631 family. Members of this protein
family are zinc-dependent metalloproteinases, related
to ulilysin and other members of the pappalysin family.
Members occur as predicted lipoproteins and occur
mostly in the genera Bacteriodes and Prevotella
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 351
Score = 29.0 bits (65), Expect = 0.96
Identities = 10/40 (25%), Positives = 17/40 (42%)
Query: 28 VSHSFSDEISTALAKLKETDVRIILGNFNEFWAKMIFCEA 67
V H F + + + T +R IL N NE + + +
Sbjct: 51 VFHVFYQDSTDETQYVPATRLREILDNVNELYQGNTYSNS 90
>gnl|CDD|116688 pfam08083, PROCN, PROCN (NUC071) domain. The PROCN domain is the
central domain in pre-mRNA splicing factors of PRO8
family.
Length = 408
Score = 27.4 bits (61), Expect = 3.1
Identities = 9/41 (21%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 20 LDSGIDVMVSHSFSDEISTAL-AKLKETDVRIILGNFNEFW 59
++S D+ + + +I + L++ R IL + +E W
Sbjct: 284 VESYYDLELRAAVMKDILDMIPEGLRQNKARTILQHLSEAW 324
>gnl|CDD|107374 cd06379, PBP1_iGluR_NMDA_NR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. The ionotropic N-methyl-d-asparate
(NMDA) subtype of glutamate receptor serves critical
functions in neuronal development, functioning, and
degeneration in the mammalian central nervous system.
The functional NMDA receptor is a heterotetramer
ccomposed of two NR1 and two NR2 (A, B, C, and D) or of
NR3 (A and B) subunits. The receptor controls a cation
channel that is highly permeable to monovalent ions and
calcium and exhibits voltage-dependent inhibition by
magnesium. Dual agonists, glutamate and glycine, are
required for efficient activation of the NMDA receptor.
When co-expressed with NR1, the NR3 subunits form
receptors that are activated by glycine alone and
therefore can be classified as excitatory glycine
receptors. NR1/NR3 receptors are calcium-impermeable and
unaffected by ligands acting at the NR2
glutamate-binding site.
Length = 377
Score = 27.4 bits (61), Expect = 3.1
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 37 STALAKLKETDVRIILGNFNEFWAKMIFCEAYRIGMIGRKYQWLI 81
++ L + KE R+IL + +E A +I+ A + M G Y W++
Sbjct: 203 TSLLQEAKELTSRVILLSASEDDAAVIYRNAGMLNMTGEGYVWIV 247
>gnl|CDD|107252 cd01539, PBP1_GGBP, Periplasmic glucose/galactose-binding protein
(GGBP) involved in chemotaxis towards, and active
transport of, glucose and galactose in various
bacterial species. Periplasmic
glucose/galactose-binding protein (GGBP) involved in
chemotaxis towards, and active transport of, glucose
and galactose in various bacterial species. GGBP is a
member of the pentose/hexose sugar-binding protein
family of the type I periplasmic binding protein
superfamily which consists of two alpha/beta globular
domains connected by a three-stranded hinge. This Venus
flytrap-like domain undergoes transition from an open
to a closed conformational state upon ligand binding.
Moreover, the periplasmic GGBP is homologous to the
ligand-binding domain of eukaryotic receptors such as
glutamate receptor (GluR) and DNA-binding
transcriptional repressors such as LacI and GalR.
Length = 303
Score = 27.2 bits (61), Expect = 3.3
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 4 IRILMYRA------HNKLLAEMLDSGIDVMVSHSFS-DEISTALAKLKETDVRIILGNFN 56
+ Y A N+ + L G+D++ + T + K K+ ++ +I FN
Sbjct: 32 VEFTFYDAKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINKAKQKNIPVIF--FN 89
>gnl|CDD|203016 pfam04446, Thg1, tRNAHis guanylyltransferase. The Thg1 protein
from Saccharomyces cerevisiae is responsible for adding
a GMP residue to the 5' end of tRNA His. The catalytic
domain Thg1 contains a RRM (ferredoxin) fold palm
domain, just like the viral RNA-dependent RNA
polymerases, reverse transcriptases, family A and B DNA
polymerases, adenylyl cyclases, diguanylate cyclases
(GGDEF domain) and the predicted polymerase of the
CRISPR system. Thg1 possesses an active site with three
acidic residues that chelate Mg++ cations. Thg1
catalyzes polymerization similar to the 5'-3'
polymerases.
Length = 131
Score = 26.4 bits (59), Expect = 3.7
Identities = 9/31 (29%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 10 RAHNKLLA---EMLDSGIDVMVSHSFSDEIS 37
RA + + A +++ D+++++ SDEIS
Sbjct: 45 RALDLMNAAAKALMEEFPDIVLAYGQSDEIS 75
>gnl|CDD|233316 TIGR01217, ac_ac_CoA_syn, acetoacetyl-CoA synthase. This enzyme
catalyzes the first step of the mevalonate pathway of
IPP biosynthesis. Most bacteria do not use this pathway,
but rather the deoxyxylulose pathway [Central
intermediary metabolism, Other].
Length = 652
Score = 27.2 bits (60), Expect = 4.2
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 108 CILTDLLPLSTSG-EITVSGIVSTVLLSSVPGGT 140
C+ + PL G I + V L+S+ GGT
Sbjct: 388 CVASTGSPLPPDGFRWVYDEIKADVWLASISGGT 421
>gnl|CDD|107362 cd06367, PBP1_iGluR_NMDA, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. While this N-terminal
domain belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. The function
of the NMDA subtype receptor serves critical functions
in neuronal development, functioning, and degeneration
in the mammalian central nervous system. The functional
NMDA receptor is a heterotetramer comprising two NR1 and
two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The
receptor controls a cation channel that is highly
permeable to monovalent ions and calcium and exhibits
voltage-dependent inhibition by magnesium. Dual
agonists, glutamate and glycine, are required for
efficient activation of the NMDA receptor. Among NMDA
receptor subtypes, the NR2B subunit containing receptors
appear particularly important for pain perception; thus
NR2B-selective antagonists may be useful in the
treatment of chronic pain.
Length = 362
Score = 26.9 bits (60), Expect = 4.7
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 10/61 (16%)
Query: 26 VMVSHSFSDEISTALAKLKETDVRIILGNFNEFWAKM-----IFCEAYRIGMIGRKYQWL 80
+ + S D + L +LK+ + R+IL + IF A +G+ G Y W+
Sbjct: 173 LTLDLSDDDGDARLLRQLKKLESRVIL-----LYCSKEEAERIFEAAASLGLTGPGYVWI 227
Query: 81 I 81
+
Sbjct: 228 V 228
>gnl|CDD|218048 pfam04371, PAD_porph, Porphyromonas-type peptidyl-arginine
deiminase. Peptidyl-arginine deiminase (PAD) enzymes
catalyze the deimination of the guanidino group from
carboxy-terminal arginine residues of various peptides
to produce ammonia. PAD from Porphyromonas gingivalis
(PPAD) appears to be evolutionarily unrelated to
mammalian PAD (pfam03068), which is a metalloenzyme.
PPAD is thought to belong to the same superfamily as
aminotransferase and arginine deiminase, and to form an
alpha/beta propeller structure. This family has
previously been named PPADH (Porphyromonas
peptidyl-arginine deiminase homologues). The predicted
catalytic residues in PPAD are Asp130, Asp187, His236,
Asp238 and Cys351. These are absolutely conserved with
the exception of Asp187 which is absent in two family
members. PPAD is also able to catalyze the deimination
of free L-arginine, but has primarily peptidyl-arginine
specificity. It may have a FMN cofactor.
Length = 329
Score = 26.5 bits (59), Expect = 5.9
Identities = 10/36 (27%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 26 VMVSHSFSDEISTALAKLKETDVRIILGNFNEFWAK 61
V VS ++ + A A+L + +VR + + N+ W +
Sbjct: 50 VCVSD---EQYANARARLADVNVRFVEISTNDAWLR 82
>gnl|CDD|169387 PRK08335, PRK08335, translation initiation factor IF-2B subunit
alpha; Validated.
Length = 275
Score = 26.3 bits (58), Expect = 6.5
Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 5/39 (12%)
Query: 17 AEMLDSGIDVMVSHSFSD---EISTALAKLKETDVRIIL 52
+E++D G DV+++HSFS EI AK K ++IL
Sbjct: 104 SELIDDG-DVIITHSFSSAVLEILKT-AKRKGKRFKVIL 140
>gnl|CDD|197310 cd09076, L1-EN, Endonuclease domain (L1-EN) of the non-LTR
retrotransposon LINE-1 (L1), and related domains. This
family contains the endonuclease domain (L1-EN) of the
non-LTR retrotransposon LINE-1 (L1), and related
domains, including the endonuclease of Xenopus laevis
Tx1. These retrotranspons belong to the subtype 2,
L1-clade. LINES can be classified into two subtypes.
Subtype 2 has two ORFs: the second (ORF2) encodes a
modular protein consisting of an N-terminal
apurine/apyrimidine endonuclease domain (EN), a central
reverse transcriptase, and a zinc-finger-like domain at
the C-terminus. LINE-1/L1 elements (full length and
truncated) comprise about 17% of the human genome. This
endonuclease nicks the genomic DNA at the consensus
target sequence 5'TTTT-AA3' producing a ribose
3'-hydroxyl end as a primer for reverse transcription of
associated template RNA. This subgroup also includes the
endonuclease of Xenopus laevis Tx1, another member of
the L1-clade. This family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 236
Score = 26.2 bits (58), Expect = 6.9
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 32 FSDEISTALAKLKETDVRIILGNFN 56
F D++ L K+ D II G+FN
Sbjct: 119 FYDQLQDVLDKVPRHDTLIIGGDFN 143
>gnl|CDD|216842 pfam02009, Rifin_STEVOR, Rifin/stevor family. Several multicopy
gene families have been described in Plasmodium
falciparum, including the stevor family of subtelomeric
open reading frames and the rif interspersed repetitive
elements. Both families contain three predicted
transmembrane segments. It has been proposed that stevor
and rif are members of a larger superfamily that code
for variant surface antigens.
Length = 290
Score = 26.2 bits (58), Expect = 7.9
Identities = 8/37 (21%), Positives = 15/37 (40%)
Query: 36 ISTALAKLKETDVRIILGNFNEFWAKMIFCEAYRIGM 72
I+ L KLK +++ N + +I Y +
Sbjct: 139 IAAGLKKLKGLGKYVVILKLNRCTSGIINASNYSAPL 175
>gnl|CDD|236762 PRK10796, PRK10796, LPS-assembly lipoprotein RlpB; Provisional.
Length = 188
Score = 25.8 bits (57), Expect = 7.9
Identities = 12/25 (48%), Positives = 13/25 (52%)
Query: 24 IDVMVSHSFSDEISTALAKLKETDV 48
I V V SF D ALAK E D+
Sbjct: 117 ISVKVFRSFFDNPLMALAKDAEQDM 141
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
0.323 0.138 0.420
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,508,907
Number of extensions: 685860
Number of successful extensions: 673
Number of sequences better than 10.0: 1
Number of HSP's gapped: 672
Number of HSP's successfully gapped: 28
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (24.5 bits)