RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13804
(129 letters)
>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 51.9 bits (125), Expect = 6e-09
Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 3/83 (3%)
Query: 29 GHPGQLGLGHGPPGGTLENTINGRSTDEEANAPPGPGGGAHLIHPGKDINKL---YGITP 85
G G P G R + E A G A + + +++ +
Sbjct: 146 GVGGPETSSGLPGGSGSGLGSPFRLSPELKKALEGVRFIAEHLRSRDEFDEVKEDWKYVA 205
Query: 86 SDIDKYSRIVFPVCFVCFNLMYW 108
ID+ SR +FP+ FV L+YW
Sbjct: 206 MVIDRLSRWIFPIAFVLGTLVYW 228
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The best
characterized are the nicotinic acetyl-choline receptors
which are pentameric channels of a2bgd subunit
composition. All subunits arehomologous. The three
dimensional structures of the protein complex in both
the open and closed configurations have been solved at
0.9 nm resolution.The channel protein complexes of the
LIC family preferentially transport cations or anions
depending on the channel (e.g., the acetylcholine
receptors are cationselective while glycine receptors
are anion selective) [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 459
Score = 45.1 bits (107), Expect = 2e-06
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 88 IDKYSRIVFPVCFVCFNLMYWIIY 111
IDK SR+ FP+ F+ FN+ YW+ Y
Sbjct: 436 IDKLSRMAFPLAFLLFNIGYWMSY 459
>gnl|CDD|234256 TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1.
The Pfam domain family pfam00296 is named for
luciferase-like monooxygenases, but the family also
contains several coenzyme F420-dependent enzymes. This
protein family represents a well-resolved clade within
family pfam00296 and shows no restriction to coenzyme
F420-positive species, unlike some other clades within
pfam00296 [Unknown function, Enzymes of unknown
specificity].
Length = 323
Score = 31.7 bits (73), Expect = 0.064
Identities = 18/34 (52%), Positives = 21/34 (61%), Gaps = 5/34 (14%)
Query: 17 KVAEQKKTIEATGHPGQ--LGLGHGPPGGTLENT 48
KVAEQ T+EA +PG+ LGLG P GT T
Sbjct: 83 KVAEQFGTLEAL-YPGRIDLGLGRAP--GTDPLT 113
>gnl|CDD|197204 cd09105, PLDc_vPLD1_2_like_2, Catalytic domain, repeat 2, of
vertebrate phospholipases, PLD1 and PLD2, and similar
proteins. Catalytic domain, repeat 2, of phospholipase
D (PLD, EC 3.1.4.4) found in yeast, plants, and
vertebrates, and their bacterial homologs. PLDs are
involved in signal transduction, vesicle formation,
protein transport, and mitosis by participating in
phospholipid metabolism. They hydrolyze the terminal
phosphodiester bond of phospholipids resulting in the
formation of phosphatidic acid and alcohols.
Phosphatidic acid is an essential compound involved in
signal transduction. PLDs also catalyze the
transphosphatidylation of phospholipids to acceptor
alcohols, by which various phospholipids can be
synthesized. Both prokaryotic and eukaryotic PLDs have
two HKD motifs (H-x-K-x(4)-D, where x represents any
amino acid residue) that characterizes the phospholipase
D (PLD) superfamily. PLDs are active as bi-lobed
monomers. Each monomer contains two domains, each of
which carries one copy of the HKD motif. Two HKD motifs
from two domains form a single active site. PLDs utilize
a common two-step ping-pong catalytic mechanism
involving an enzyme-substrate intermediate to cleave
phosphodiester bonds. The two histidine residues from
the two HKD motifs play key roles in the catalysis. Upon
substrate binding, a histidine residue from one HKD
motif could function as the nucleophile, attacking the
phosphodiester bond to create a covalent
phosphohistidine intermediate, while the other histidine
residue from the second HKD motif could serve as a
general acid, stabilizing the leaving group.
Length = 146
Score = 26.9 bits (60), Expect = 2.2
Identities = 14/64 (21%), Positives = 20/64 (31%), Gaps = 4/64 (6%)
Query: 61 PPGPGGGAHLIHPGKDINK---LYGITPSDIDKYSRIVFPVCFVCFNLMYWIIYLHISDV 117
P P A G D L + + D+ + L IY+H V
Sbjct: 57 PALPDAVAFGADDGLDALALLALLLLADAAPDRV-AVFSLATHRRGLLGGPPIYVHSKVV 115
Query: 118 VADD 121
+ DD
Sbjct: 116 IVDD 119
>gnl|CDD|221747 pfam12740, Chlorophyllase2, Chlorophyllase enzyme. This family
consists of several chlorophyllase and chlorophyllase-2
(EC:3.1.1.14) enzymes. Chlorophyllase (Chlase) is the
first enzyme involved in chlorophyll (Chl) degradation
and catalyzes the hydrolysis of an ester bond to yield
chlorophyllide and phytol. The family includes both
plant and Amphioxus members.
Length = 258
Score = 27.0 bits (60), Expect = 3.2
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 83 ITPSDIDKYSRIVFPVCFVCFNLMYWIIYLHISD----VVADDLVLL 125
TPS+ Y ++F ++ N Y + HI+ VVA L +
Sbjct: 9 ATPSEKGTYPVLLFLHGYLLSNSFYSQLLEHIASHGYIVVAPQLYTI 55
>gnl|CDD|216888 pfam02127, Peptidase_M18, Aminopeptidase I zinc metalloprotease
(M18).
Length = 425
Score = 26.6 bits (59), Expect = 3.9
Identities = 7/37 (18%), Positives = 9/37 (24%)
Query: 62 PGPGGGAHLIHPGKDINKLYGITPSDIDKYSRIVFPV 98
G H I + GI D I+
Sbjct: 176 SGEEKNKHKPALLGLIAEELGIEEEDFVSMELILVDA 212
>gnl|CDD|221477 pfam12235, FXR1P_C, Fragile X-related 1 protein C terminal. This
domain family is found in eukaryotes, and is typically
between 126 and 160 amino acids in length. The family
is found in association with pfam05641, pfam00013. This
family is the C terminal region of the fragile X
related 1 protein FXR1P. FXR1P contains two KH domains
and a RGG box that are characteristic motifs in
RNA-binding proteins as well as nuclear localization
and export signals. FXR1P is thought to regulate mRNA
transport and translation.
Length = 79
Score = 25.5 bits (56), Expect = 4.4
Identities = 11/34 (32%), Positives = 14/34 (41%)
Query: 33 QLGLGHGPPGGTLENTINGRSTDEEANAPPGPGG 66
Q+G G PP + G TD+ G GG
Sbjct: 17 QIGAGSRPPPSRPGDKEKGYLTDDSGGRGRGGGG 50
>gnl|CDD|165195 PHA02859, PHA02859, ankyrin repeat protein; Provisional.
Length = 209
Score = 25.9 bits (57), Expect = 6.4
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 70 LIHPGKDINKL--YGITPSDIDKYSRIVF 96
L G DIN+ G D+ K+ + F
Sbjct: 178 LTSLGIDINETNKSGYNCYDLIKFRNLFF 206
>gnl|CDD|218635 pfam05556, Calsarcin, Calcineurin-binding protein (Calsarcin).
This family consists of several mammalian
calcineurin-binding proteins. The calcium- and
calmodulin-dependent protein phosphatase calcineurin has
been implicated in the transduction of signals that
control the hypertrophy of cardiac muscle and slow fibre
gene expression in skeletal muscle. Calsarcin-1 and
calsarcin-2 are expressed in developing cardiac and
skeletal muscle during embryogenesis, but calsarcin-1 is
expressed specifically in adult cardiac and slow-twitch
skeletal muscle, whereas calsarcin-2 is restricted to
fast skeletal muscle. Calsarcins represent a novel
family of sarcomeric proteins that link calcineurin with
the contractile apparatus, thereby potentially coupling
muscle activity to calcineurin activation. Calsarcin-3,
is expressed specifically in skeletal muscle and is
enriched in fast-twitch muscle fibres. Like calsarcin-1
and calsarcin-2, calsarcin-3 interacts with calcineurin,
and the Z-disc proteins alpha-actinin, gamma-filamin,
and telethonin.
Length = 273
Score = 25.9 bits (57), Expect = 6.6
Identities = 13/39 (33%), Positives = 14/39 (35%)
Query: 37 GHGPPGGTLENTINGRSTDEEANAPPGPGGGAHLIHPGK 75
PG T NT + S PG GG I P K
Sbjct: 111 DSHQPGQTQPNTPDLGSVYNPEAIAPGYGGPLKEIPPEK 149
>gnl|CDD|217381 pfam03134, TB2_DP1_HVA22, TB2/DP1, HVA22 family. This family
includes members from a wide variety of eukaryotes. It
includes the TB2/DP1 (deleted in polyposis) protein,
which in humans is deleted in severe forms of familial
adenomatous polyposis, an autosomal dominant oncological
inherited disease. The family also includes the plant
protein of known similarity to TB2/DP1, the HVA22
abscisic acid-induced protein, which is thought to be a
regulatory protein.
Length = 94
Score = 24.8 bits (55), Expect = 7.9
Identities = 6/21 (28%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 105 LMYWIIY--LHISDVVADDLV 123
L YW++Y L + + +D ++
Sbjct: 37 LTYWVVYSFLTLFESFSDIIL 57
>gnl|CDD|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional.
Length = 367
Score = 25.6 bits (57), Expect = 8.3
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 79 KLYGITPSDIDKYSR 93
K G+TPSDI +Y R
Sbjct: 281 KFIGVTPSDIVEYER 295
>gnl|CDD|217991 pfam04258, Peptidase_A22B, Signal peptide peptidase. The members
of this family are membrane proteins. In some proteins
this region is found associated with pfam02225. This
family corresponds with Merops subfamily A22B, the type
example of which is signal peptide peptidase. There is a
sequence-similarity relationship with pfam01080.
Length = 291
Score = 25.4 bits (56), Expect = 9.5
Identities = 9/41 (21%), Positives = 14/41 (34%), Gaps = 3/41 (7%)
Query: 87 DIDKYSRIVFPV--CFVCFNLMYWIIYLHISDVVADDLVLL 125
ID I+FP+ +Y + + LVL
Sbjct: 8 TIDSRHAIIFPISASCTLL-GLYLFFKSLSKEYINSVLVLT 47
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
0.319 0.141 0.432
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,966,558
Number of extensions: 629305
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: 20
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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 (21.7 bits)
S2: 53 (24.3 bits)