RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13438
(154 letters)
>gnl|CDD|204533 pfam10613, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called the
S1 domain, is the luminal domain just upstream of the
first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan,
pfam00060.
Length = 65
Score = 53.8 bits (130), Expect = 1e-10
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 118 CCSGFCIDLLGKFAEELGFTYELVRVEDGKWGTQED 153
G+CIDLL + A+ LGF YE+ V DGK+G+++
Sbjct: 17 RFEGYCIDLLDELAKILGFNYEIYLVPDGKYGSEDK 52
>gnl|CDD|214911 smart00918, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called the
S1 domain, is the luminal domain just upstream of the
first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan.
Length = 62
Score = 53.0 bits (128), Expect = 2e-10
Identities = 18/36 (50%), Positives = 26/36 (72%)
Query: 118 CCSGFCIDLLGKFAEELGFTYELVRVEDGKWGTQED 153
G+CIDLL + A++LGFTYE++ V DGK+G +
Sbjct: 15 RFEGYCIDLLKELAKKLGFTYEIILVPDGKYGARLP 50
>gnl|CDD|107373 cd06378, PBP1_iGluR_NMDA_NR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR2 subunit of NMDA receptor family.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the NR2 subunit of NMDA receptor
family. 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 composed 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. 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 = 31.5 bits (72), Expect = 0.12
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 32 SWEKEGLDIKDIVWPG 47
WE L +K VWP
Sbjct: 347 KWENGSLRLKYPVWPR 362
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 29.2 bits (66), Expect = 0.66
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 120 SGFCIDLLGKFAEELGFTYELVRVE 144
GF +DL A+ LG E V V
Sbjct: 22 VGFDVDLAKAIAKRLGVKVEFVPVS 46
>gnl|CDD|163655 cd07412, MPP_YhcR_N, Bacillus subtilis YhcR endonuclease and
related proteins, N-terminal metallophosphatase domain.
YhcR is a Bacillus subtilis sugar-nonspecific
endonuclease. It cleaves endonucleolytically to yield
nucleotide 3'-monophosphate products, similar to
Staphylococcus aureus micrococcal nuclease. YhcR appears
to be located in the cell wall, and is thought to be a
substrate for a Bacillus subtilis sortase. YhcR is the
major calcium-activated nuclease of B. subtilis. The
N-terminal metallophosphatase domain belongs to a large
superfamily of distantly related metallophosphatases
(MPPs) that includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 288
Score = 29.2 bits (66), Expect = 0.74
Identities = 10/41 (24%), Positives = 13/41 (31%), Gaps = 1/41 (2%)
Query: 78 PDPVTGKCNMNRGVICRVAGDADMDKIDVAMAHHNESFYQC 118
C+ G I + D +DV A H Y C
Sbjct: 205 TKGGDDTCSAASGPIADIVNRLD-PDVDVVFAGHTHQAYNC 244
>gnl|CDD|238078 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins (PBPs)
to transport a wide variety of substrates, such as,
amino acids, peptides, sugars, vitamins and inorganic
ions. PBPs have two cell-membrane translocation
functions: bind substrate, and interact with the
membrane bound complex. A diverse group of periplasmic
transport receptors for lysine/arginine/ornithine (LAO),
glutamine, histidine, sulfate, phosphate, molybdate, and
methanol are included in the PBPb CD.
Length = 218
Score = 28.9 bits (65), Expect = 0.88
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 121 GFCIDLLGKFAEELGFTYELVRVE 144
GF +DL A+ELG + V V+
Sbjct: 23 GFDVDLAKAIAKELGVKVKFVEVD 46
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 28.8 bits (65), Expect = 1.0
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 121 GFCIDLLGKFAEELGFTYELVRVE 144
GF +DL A+ELG E V V
Sbjct: 24 GFDVDLAKAIAKELGLKVEFVEVS 47
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 27.1 bits (60), Expect = 3.7
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 33 WEKEGLDIKDIVWPGNSHTPPQGVPEKFHLKITFLEEAPYIQMSPPDPVTG 83
W G+ + I PG + TP PE H F E+ P +M+ D + G
Sbjct: 178 WVGRGIRVNSIS-PGYTATPMNTRPEMVHQTKLFEEQTPMQRMAKVDEMVG 227
>gnl|CDD|219959 pfam08661, Rep_fac-A_3, Replication factor A protein 3.
Replication factor A is involved in eukaryotic DNA
replication, recombination and repair.
Length = 111
Score = 26.5 bits (59), Expect = 4.0
Identities = 8/42 (19%), Positives = 14/42 (33%), Gaps = 10/42 (23%)
Query: 75 MSPPDPVTGKCNMNRG----------VICRVAGDADMDKIDV 106
+S D ++N VI +V+ D + I
Sbjct: 41 LSSTDGGNVTVSLNSPLDLEISGWVEVIGKVSPDGTIGSIRA 82
>gnl|CDD|178566 PLN02985, PLN02985, squalene monooxygenase.
Length = 514
Score = 27.2 bits (60), Expect = 4.4
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 53 PQGVPEKFHLKITFL---EEAPYIQMSPPDPVTGKCNMNRGVICRVAGDA 99
PQ VP K L+ FL +E +I++ P ++ + +GVI V GDA
Sbjct: 290 PQ-VPPK--LRKIFLKGIDEGAHIKVVPTKRMSATLSDKKGVI--VLGDA 334
>gnl|CDD|107329 cd06334, PBP1_ABC_ligand_binding_like_1, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 351
Score = 26.8 bits (60), Expect = 5.7
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 12/59 (20%)
Query: 97 GDADMDKIDVAMAHHNESFYQCCSGFC---IDLLGKFAEELGFTYELVRVEDGKWGTQE 152
+ +A+ +H+ S F I+ L AE+LGF E+V G +
Sbjct: 134 EGGKLKGKKIALVYHD-------SPFGKEPIEALKALAEKLGF--EVVLEPVPPPGPND 183
>gnl|CDD|119436 cd05177, PI3Kc_C2_gamma, Phosphoinositide 3-kinase (PI3K), class
II, gamma isoform, catalytic domain; The PI3K catalytic
domain family is part of a larger superfamily that
includes the catalytic domains of other kinases such as
the typical serine/threonine/tyrosine protein kinases
(PKs), aminoglycoside phosphotransferase, choline
kinase, and RIO kinases. PI3Ks catalyze the transfer of
the gamma-phosphoryl group from ATP to the 3-hydroxyl of
the inositol ring of D-myo-phosphatidylinositol (PtdIns)
or its derivatives. PI3Ks play an important role in a
variety of fundamental cellular processes, including
cell motility, the Ras pathway, vesicle trafficking and
secretion, immune cell activation and apoptosis. They
can be divided into three main classes (I, II, and III),
defined by their substrate specificity, regulation, and
domain structure. Class II PI3Ks preferentially use
PtdIns as a substrate to produce PtdIns(3)P, but can
also phosphorylate PtdIns(4)P. They function as monomers
and do not associate with any regulatory subunits. Class
II enzymes contain an N-terminal Ras binding domain, a
lipid binding C2 domain, a PI3K homology domain of
unknown function, an ATP-binding cataytic domain, a Phox
homology (PX) domain, and a second C2 domain at the
C-terminus. The class II gamma isoform, PI3K-C2gamma, is
expressed in the liver, breast, and prostate. It's
biological function remains unknown.
Length = 354
Score = 26.8 bits (59), Expect = 5.9
Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 30/102 (29%)
Query: 33 WEKEGLDIKDIVWPGNSHTPPQGVPEKFHLKITFLEEAPYIQMSPPDPVTGKCNMNRGVI 92
W +EGLD++ I++ S QG+ +QM P K + G+I
Sbjct: 119 WLQEGLDMQMIIYRCLSTGKTQGL----------------VQMVPDAVTLAKIHRESGLI 162
Query: 93 CRVAGDADMDKIDVAMAHHNE----------SFYQCCSGFCI 124
G + I+ HN+ +F+ C+G+C+
Sbjct: 163 ----GPLKENTIEKWFHMHNKLKEDYDKAVRNFFHSCAGWCV 200
>gnl|CDD|193533 cd05657, M42_glucanase_like, M42 Peptidase, Endoglucanase-like
subfamily. Peptidase M42 family, glucanase (endo-1
4-beta-glucanase or endoglucanase)-like subfamily.
Proteins in this subfamily are co-catalytic
metallopeptidases, found in archaea and bacteria. They
show similarity to cellulase and endo-1,4-beta-glucanase
(endoglucanase) which typically bind two zinc or cobalt
atoms. Some of the enzymes exhibit typical
aminopeptidase specificity, whereas others are also
capable of N-terminal deblocking activity, i.e.
hydrolyzing acylated N-terminal residues. Many of these
enzymes are assembled either as tetrahedral dodecamers
or as octahedral tetracosameric structures, with the
active site located on the inside such that substrate
sizes are limited, indicating function as possible
peptide scavengers.
Length = 336
Score = 26.7 bits (60), Expect = 5.9
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 120 SGFC---IDLLGKFAEELGFTYELVR 142
SG+ ++ + K E LG+ EL
Sbjct: 16 SGYTDEAVEYVEKELEALGYEPELTN 41
>gnl|CDD|133054 cd06432, GT8_HUGT1_C_like, The C-terminal domain of HUGT1-like is
highly homologous to the GT 8 family. C-terminal domain
of glycoprotein glucosyltransferase (UGT). UGT is a
large glycoprotein whose C-terminus contains the
catalytic activity. This catalytic C-terminal domain is
highly homologous to Glycosyltransferase Family 8 (GT 8)
and contains the DXD motif that coordinates donor sugar
binding, characteristic for Family 8
glycosyltransferases. GT 8 proteins are retaining
enzymes based on the relative anomeric stereochemistry
of the substrate and product in the reaction catalyzed.
The non-catalytic N-terminal portion of the human UTG1
(HUGT1) has been shown to monitor the protein folding
status and activate its glucosyltransferase activity.
Length = 248
Score = 26.6 bits (59), Expect = 6.0
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 3/24 (12%)
Query: 125 DLLGKFAEELGFTYELVRVEDGKW 148
+ L + A+E GF YELV KW
Sbjct: 46 EFLPEMAKEYGFEYELVTY---KW 66
>gnl|CDD|238319 cd00570, GST_N_family, Glutathione S-transferase (GST) family,
N-terminal domain; a large, diverse group of cytosolic
dimeric proteins involved in cellular detoxification by
catalyzing the conjugation of glutathione (GSH) with a
wide range of endogenous and xenobiotic alkylating
agents, including carcinogens, therapeutic drugs,
environmental toxins and products of oxidative stress.
In addition, GSTs also show GSH peroxidase activity and
are involved in the synthesis of prostaglandins and
leukotrienes. This family, also referred to as soluble
GSTs, is the largest family of GSH transferases and is
only distantly related to the mitochondrial GSTs (GSTK
subfamily, a member of the DsbA family). Soluble GSTs
bear no structural similarity to microsomal GSTs (MAPEG
family) and display additional activities unique to
their group, such as catalyzing thiolysis, reduction
and isomerization of certain compounds. The GST fold
contains an N-terminal TRX-fold domain and a C-terminal
alpha helical domain, with an active site located in a
cleft between the two domains. Based on sequence
similarity, different classes of GSTs have been
identified, which display varying tissue distribution,
substrate specificities and additional specific
activities. In humans, GSTs display polymorphisms which
may influence individual susceptibility to diseases such
as cancer, arthritis, allergy and sclerosis. Some GST
family members with non-GST functions include
glutaredoxin 2, the CLIC subfamily of anion channels,
prion protein Ure2p, crystallins, metaxin 2 and
stringent starvation protein A.
Length = 71
Score = 24.8 bits (55), Expect = 7.2
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 130 FAEELGFTYELVRVEDGKWGTQE 152
EE G YELV V+ G+ +E
Sbjct: 18 ALEEKGLPYELVPVDLGEGEQEE 40
>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 = 26.1 bits (58), Expect = 9.3
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 32 SWEKEGLDIKDIVWP 46
SWE L ++ IVWP
Sbjct: 348 SWENGKLVMRYIVWP 362
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
0.322 0.141 0.460
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,152,440
Number of extensions: 736702
Number of successful extensions: 586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 586
Number of HSP's successfully gapped: 22
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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: 55 (24.9 bits)