RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15038
(67 letters)
>gnl|CDD|191111 pfam04849, HAP1_N, HAP1 N-terminal conserved region. This family
represents an N-terminal conserved region found in
several huntingtin-associated protein 1 (HAP1)
homologues. HAP1 binds to huntingtin in a polyglutamine
repeat-length-dependent manner. However, its possible
role in the pathogenesis of Huntington's disease is
unclear. This family also includes a similar N-terminal
conserved region from hypothetical protein products of
ALS2CR3 genes found in the human juvenile amyotrophic
lateral sclerosis critical region 2q33-2q34.
Length = 307
Score = 44.0 bits (104), Expect = 5e-07
Identities = 24/53 (45%), Positives = 30/53 (56%), Gaps = 6/53 (11%)
Query: 16 LEEQLPQYKLRADTLTEFIGYENQDWFVPCPLQADDPT-ALTPDQIRETLNYF 67
LEEQLP Y +RADTL GY++ DW P + D L+ +Q ETL Y
Sbjct: 1 LEEQLPPYSIRADTLG---GYDDDDWKT--PRASPDARLDLSTEQRAETLKYL 48
>gnl|CDD|206765 cd11305, alpha_DG_C, C-terminal domain of alpha dystroglycan.
Dystroglycan is a glycoprotein widely distributed in
skeletal muscle and other tissues; the pre-protein is
cleaved into two subunits (alpha and beta) that form a
complex which links the extracellular matrix to the
cytoskeleton. This C-terminal domain of the
alpha-subunit appears to contact neighboring
cadherin-like repeats of alpha dystroglycan, and may
also be involved in interactions with other components
of the dystrophin-dystroglycan-complex (DGC). DGC has
been shown to interact with extracellular matrix
components such as laminin, perlecan and m-agrin,
suggesting that the complex may play various different
roles depending on the extracellular ligand.
Length = 124
Score = 28.8 bits (65), Expect = 0.10
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 1 VCCGGDLPEVEIISLLEEQLPQYKLRADTLTEFIGYENQDWFV 43
V CGGDL + ++S LEEQ + TL E +G W V
Sbjct: 82 VGCGGDLNHLPLVSQLEEQ-----AKDGTLAEVLGLPVIGWHV 119
>gnl|CDD|225322 COG2602, COG2602, Beta-lactamase class D [Defense mechanisms].
Length = 254
Score = 27.3 bits (61), Expect = 0.41
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 14 SLLEEQLPQYKLRADTLTEFIGYENQDWFV 43
++ E+ P ++L T T + +N WFV
Sbjct: 182 IMILERGPNWELHGKTGTGIVNTKNLGWFV 211
>gnl|CDD|215100 PLN00198, PLN00198, anthocyanidin reductase; Provisional.
Length = 338
Score = 27.2 bits (60), Expect = 0.54
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 1 VCCGGDLPEVEIISLLEEQLPQYKLRAD 28
+CC + E+ L ++ PQY++ D
Sbjct: 264 ICCAANTSVPELAKFLIKRYPQYQVPTD 291
>gnl|CDD|187536 cd05193, AR_like_SDR_e, aldehyde reductase, flavonoid reductase,
and related proteins, extended (e) SDRs. This subgroup
contains aldehyde reductase and flavonoid reductase of
the extended SDR-type and related proteins. Proteins in
this subgroup have a complete SDR-type active site
tetrad and a close match to the canonical extended SDR
NADP-binding motif. Aldehyde reductase I (aka carbonyl
reductase) is an NADP-binding SDR; it catalyzes the
NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 295
Score = 25.7 bits (56), Expect = 2.0
Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 5/40 (12%)
Query: 1 VCCGGDLPEVEIISLLEEQLPQYKLRADTLTEFIGYENQD 40
+C G+ ++ L ++ P Y D + QD
Sbjct: 249 ICTAGNFDWNTLLKTLRKKYPSYTFPTD-----FPDQGQD 283
>gnl|CDD|220205 pfam09363, XFP_C, XFP C-terminal domain. Bacterial enzyme splits
fructose-6-P and/or xylulose-5-P with the aid of
inorganic phosphate into either acetyl-P and
erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P
EC:4.1.2.9, EC:4.1.2.22.
Length = 203
Score = 25.5 bits (57), Expect = 2.1
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 3 CGGDLPEVEI---ISLLEEQLPQYKLR 26
C GD+P +E + LL E P K+R
Sbjct: 41 CAGDVPTLETLAAVDLLREHFPDLKIR 67
>gnl|CDD|216414 pfam01288, HPPK,
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
(HPPK).
Length = 127
Score = 24.7 bits (55), Expect = 2.9
Identities = 8/36 (22%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 31 TEFIGYENQDWFVPCPLQADDPTALTPDQIRETLNY 66
T +G+ +Q F+ ++ + T L+P+++ L
Sbjct: 39 TAPVGFTDQPDFLNAVVELE--TTLSPEELLALLQA 72
>gnl|CDD|185256 PRK15358, PRK15358, pathogenicity island 2 effector protein SseF;
Provisional.
Length = 239
Score = 25.0 bits (54), Expect = 2.9
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 43 VPCPLQADDPTALTPDQIRETLNY 66
+P P P LTP+QIR+ +Y
Sbjct: 13 IPAPGTPAAPVLLTPEQIRQQRDY 36
>gnl|CDD|239399 cd03125, alpha_CA_VI, Carbonic anhydrase alpha, isozyme VI.
Carbonic anhydrases (CAs) are zinc-containing enzymes
that catalyze the reversible hydration of carbon dioxide
in a two-step mechanism: a nucleophilic attack of a
zinc-bound hydroxide ion on carbon dioxide, followed by
the regeneration of the active site by ionization of the
zinc-bound water molecule and removal of a proton from
the active site. They are ubiquitous enzymes involved in
fundamental processes like photosynthesis, respiration,
pH homeostasis and ion transport. There are three
evolutionary distinct groups - alpha, beta and gamma
carbonic anhydrases - which show no significant sequence
identity or structural similarity. Most alpha CAs are
monomeric enzymes. The zinc ion is complexed by three
histidine residues. This sub-family comprises the
secreted CA VI, which is found in saliva.
Length = 249
Score = 25.1 bits (55), Expect = 3.2
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 7 LPEVEIISLLEEQLPQYKLRADTLTEFIGYENQDWFVPCPLQADDPTALTPDQIR 61
L +++ +L E L Y +LT EN WFV DDP L+ QI
Sbjct: 166 LTSLDVRDMLPENLHHYYTYQGSLTTPPCTENVLWFV-----FDDPVTLSKTQIV 215
>gnl|CDD|213023 cd10918, CE4_NodB_like_5s_6s, Putative catalytic NodB homology
domain of PgaB, IcaB, and similar proteins which
consist of a deformed (beta/alpha)8 barrel fold with 5-
or 6-strands. This family belongs to the large and
functionally diverse carbohydrate esterase 4 (CE4)
superfamily, whose members show strong sequence
similarity with some variability due to their distinct
carbohydrate substrates. It includes bacterial
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
PgaB, hemin storage system HmsF protein in
gram-negative species, intercellular adhesion proteins
IcaB, and many uncharacterized prokaryotic
polysaccharide deacetylases. It also includes a
putative polysaccharide deacetylase YxkH encoded by the
Bacillus subtilis yxkH gene, which is one of six
polysaccharide deacetylase gene homologs present in the
Bacillus subtilis genome. Sequence comparison shows all
family members contain a conserved domain similar to
the catalytic NodB homology domain of rhizobial
NodB-like proteins, which consists of a deformed
(beta/alpha)8 barrel fold with 6 or 7 strands. However,
in this family, most proteins have 5 strands and some
have 6 strands. Moreover, long insertions are found in
many family members, whose function remains unknown.
Length = 157
Score = 24.5 bits (54), Expect = 4.9
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 8/44 (18%)
Query: 22 QYKLRADTL---TEFIGYENQDWFVPCPLQADDPTALTPDQIRE 62
+Y L A T T +IG N W P P LT DQ+RE
Sbjct: 23 KYGLPA-TFFVITGYIGGGNPWWAPAPP----RPPYLTWDQLRE 61
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
0.320 0.142 0.450
Gapped
Lambda K H
0.267 0.0844 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,550,595
Number of extensions: 260919
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 304
Number of HSP's successfully gapped: 11
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
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 (24.0 bits)