RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy227
(139 letters)
>gnl|CDD|215724 pfam00110, wnt, wnt family. Wnt genes have been identified in
vertebrates and invertebrates but not in plants,
unicellular eukaryotes or prokaryotes. In humans, 19 WNT
proteins are known. Because of their insolubility little
is known about Wnt protein structure, but all have 23 or
24 Cys residues whose spacing is highly conserved.
Signal transduction by Wnt proteins (including the
Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity
pathway) is mediated by receptors of the Frizzled and
LDL-receptor-related protein (LRP) families.
Length = 308
Score = 101 bits (254), Expect = 5e-27
Identities = 38/116 (32%), Positives = 57/116 (49%), Gaps = 26/116 (22%)
Query: 18 GTREQGIVYALGSAAITYTLARGCADGTIFHCSCATPSKKATAKAIKNSFQWGGCGDNVR 77
GTRE VYA+ SA + + + R C++G + C C + ++ ++WGGC DN++
Sbjct: 64 GTRETAFVYAISSAGVVHAVTRACSEGNLESCGC---DRSRRGRSGPGGWEWGGCSDNIK 120
Query: 78 WGAQFARSFTDILENERDIQTQRNLRLIDAAMFDEKNNRNYMLNVMNLHNNKAGRK 133
+G +F+R F D E RD + MNLHNN+AGRK
Sbjct: 121 FGIRFSREFLDARERGRDARAL-----------------------MNLHNNEAGRK 153
>gnl|CDD|128408 smart00097, WNT1, found in Wnt-1.
Length = 305
Score = 92.8 bits (231), Expect = 1e-23
Identities = 39/116 (33%), Positives = 56/116 (48%), Gaps = 26/116 (22%)
Query: 18 GTREQGIVYALGSAAITYTLARGCADGTIFHCSCATPSKKATAKAIKNSFQWGGCGDNVR 77
GTRE VYA+ SA + + + R C++G + C C + +A ++WGGC DN+
Sbjct: 61 GTRETAFVYAISSAGVAHAVTRACSEGELDSCGC---DYRKRGRAGGRGWKWGGCSDNID 117
Query: 78 WGAQFARSFTDILENERDIQTQRNLRLIDAAMFDEKNNRNYMLNVMNLHNNKAGRK 133
+G +F+R F D E +D R L MNLHNN+AGR
Sbjct: 118 FGIRFSREFVDARERGKDA---RAL--------------------MNLHNNEAGRL 150
>gnl|CDD|239669 cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II
of the eukaryotic class II release factor (eRF3). In
eukaryotes, translation termination is mediated by two
interacting release factors, eRF1 and eRF3, which act
as class I and II factors, respectively. eRF1 functions
as an omnipotent release factor, decoding all three
stop codons and triggering the release of the nascent
peptide catalyzed by the ribsome. eRF3 is a GTPase,
which enhances the termination efficiency by
stimulating the eRF1 activity in a GTP-dependent
manner. Sequence comparison of class II release factors
with elongation factors shows that eRF3 is more similar
to eEF1alpha whereas prokaryote RF3 is more similar to
EF-G, implying that their precise function may differ.
Only eukaryote RF3s are found in this group.
Saccharomyces cerevisiae eRF3 (Sup35p) is a translation
termination factor which is divided into three regions
N, M and a C-terminal eEF1a-like region essential for
translation termination. Sup35NM is a non-pathogenic
prion-like protein with the property of aggregating
into polymer-like fibrils. This group also contains
proteins similar to S. cerevisiae Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation and, to associate with Dom34. It has been
speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 83
Score = 26.3 bits (59), Expect = 2.6
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 4/28 (14%)
Query: 54 PSK-KATAKAI---KNSFQWGGCGDNVR 77
PSK K+I + G+NVR
Sbjct: 37 PSKESVEVKSIYVDDEEVDYAVAGENVR 64
>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 = 26.9 bits (60), Expect = 4.2
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 110 FDEKNNR-NYMLNVMNLHNNKAGRKIDTYQP 139
FDE R NY L+V+ L RK+ +
Sbjct: 348 FDEFGQRTNYTLDVVELKTRGL-RKVGYWNE 377
>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 = 25.9 bits (57), Expect = 7.4
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 104 LIDAAM-------FDEKNNR-NYMLNVMNLHNNKAGRKIDTYQP 139
L DA + FDE R N+ L+++ L+ ++ RK+ T+
Sbjct: 279 LYDAVLLLTGTVSFDEDGVRSNFTLDIIELNRSRGWRKVGTWNG 322
>gnl|CDD|200369 TIGR04118, Cxxx_AC3_0185, modification target Cys-rich peptide,
AC3_0185 family. Radical SAM enzyme family TIGR04115
is paired with a number of short peptides with multiple
tandem repeats of Cys-Xaa-Xaa-Xaa (see TIGR04114). This
family represent a peptide family with a TIGR04114-like
region, although the repeat region is relatively short
in this group.
Length = 46
Score = 24.1 bits (52), Expect = 8.7
Identities = 9/41 (21%), Positives = 15/41 (36%)
Query: 10 RRLFFRLNGTREQGIVYALGSAAITYTLARGCADGTIFHCS 50
+ LF ++ V + + T GCA+ HC
Sbjct: 2 KHLFSAKKISKVNKDVQGYMCSDCSGTCINGCANLCTSHCG 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
0.323 0.134 0.413
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,776,378
Number of extensions: 568507
Number of successful extensions: 471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 467
Number of HSP's successfully gapped: 10
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
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 (24.6 bits)