RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1336
(96 letters)
>gnl|CDD|200466 cd11327, AmyAc_Glg_debranch_2, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities, 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. The catalytic triad (DED),
which is highly conserved in other debranching enzymes,
is not present in this group. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 478
Score = 95.0 bits (237), Expect = 1e-24
Identities = 30/61 (49%), Positives = 42/61 (68%)
Query: 10 ELGGSNSCYSLSSQLDLNPLFSTPEHKLSWDDVIAFTEKMRTEWQMLSLCDIVLNHTANE 69
ELG SNS YS++ QL+LNP F K +++DV +K+ EW +LS+ D+VLNHTAN
Sbjct: 60 ELGESNSPYSIADQLELNPDFFPDGKKKTFEDVEELVKKLEKEWGLLSITDVVLNHTANN 119
Query: 70 T 70
+
Sbjct: 120 S 120
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 79.5 bits (196), Expect = 6e-19
Identities = 33/61 (54%), Positives = 40/61 (65%), Gaps = 2/61 (3%)
Query: 10 ELGGSNSCYSLSSQLDLNPLFSTPEHKLSWDDVIAFTEKMRTEWQMLSLCDIVLNHTANE 69
ELGGSNSCYSL QL LN F + K +DV A EK+ +W +LS+ DIV NHTAN
Sbjct: 156 ELGGSNSCYSLYDQLQLNQHFKSQ--KDGKNDVQALVEKLHRDWNVLSITDIVFNHTANN 213
Query: 70 T 70
+
Sbjct: 214 S 214
>gnl|CDD|200463 cd11324, AmyAc_Amylosucrase, Alpha amylase catalytic domain found
in Amylosucrase. Amylosucrase is a glucosyltransferase
that catalyzes the transfer of a D-glucopyranosyl moiety
from sucrose onto an acceptor molecule. When the
acceptor is another saccharide, only alpha-1,4 linkages
are produced. Unlike most amylopolysaccharide synthases,
it does not require any alpha-D-glucosyl nucleoside
diphosphate substrate. In the presence of glycogen it
catalyzes the transfer of a D-glucose moiety onto a
glycogen branch, but in its absence, it hydrolyzes
sucrose and synthesizes polymers, smaller
maltosaccharides, and sucrose isoforms. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 536
Score = 30.2 bits (69), Expect = 0.10
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 40 DDVIAFTEKMRTEWQMLSLC-DIVLNHTANE 69
+D+ A ++R +SL D VLNHTA+E
Sbjct: 136 EDLRALAAELRER--GISLVLDFVLNHTADE 164
Score = 28.7 bits (65), Expect = 0.46
Identities = 10/14 (71%), Positives = 11/14 (78%), Gaps = 1/14 (7%)
Query: 78 SLC-DIVLNHTANE 90
SL D VLNHTA+E
Sbjct: 151 SLVLDFVLNHTADE 164
>gnl|CDD|236759 PRK10785, PRK10785, maltodextrin glucosidase; Provisional.
Length = 598
Score = 26.9 bits (60), Expect = 1.7
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 13/56 (23%)
Query: 24 LDLNPLFSTPE-HKLSWDDVIAFTEKMRTEWQMLSLC------------DIVLNHT 66
L LNP+F+ P HK +D ++ + +L L D V NHT
Sbjct: 196 LYLNPIFTAPSVHKYDTEDYRHVDPQLGGDAALLRLRHATQQRGMRLVLDGVFNHT 251
>gnl|CDD|218747 pfam05786, Cnd2, Condensin complex subunit 2. This family consists
of several Barren protein homologues from several
eukaryotic organisms. In Drosophila Barren (barr) is
required for sister-chromatid segregation in mitosis.
barr encodes a novel protein that is present in
proliferating cells and has homologues in yeast and
human. Mitotic defects in barr embryos become apparent
during cycle 16, resulting in a loss of PNS and CNS
neurons. Centromeres move apart at the
metaphase-anaphase transition and Cyclin B is degraded,
but sister chromatids remain connected, resulting in
chromatin bridging. Barren protein localises to
chromatin throughout mitosis. Colocalisation and
biochemical experiments indicate that Barren associates
with Topoisomerase II throughout mitosis and alters the
activity of Topoisomerase II. It has been suggested that
this association is required for proper chromosomal
segregation by facilitating the decatenation of
chromatids at anaphase. This family forms one of the
three non-structural maintenance of chromosomes (SMC)
subunits of the mitotic condensation complex along with
Cnd1 and Cnd3.
Length = 719
Score = 26.6 bits (59), Expect = 1.9
Identities = 19/68 (27%), Positives = 26/68 (38%), Gaps = 10/68 (14%)
Query: 18 YSLSSQLDLNPLFSTPEHKLSWDDVIAFTEKMRTEWQML----------SLCDIVLNHTA 67
L S D + E + ++ +FT+ MR+ L SL I L H A
Sbjct: 639 ERLESTADFESIPPEEEEESESEEEKSFTQLMRSLPDRLPAEMAQDISTSLAFICLLHLA 698
Query: 68 NETYLSLN 75
NE L L
Sbjct: 699 NEKGLRLI 706
>gnl|CDD|198289 cd03180, GST_C_2, C-terminal, alpha helical domain of an unknown
subfamily 2 of Glutathione S-transferases. Glutathione
S-transferase (GST) C-terminal domain family, unknown
subfamily 2; composed of uncharacterized bacterial
proteins, with similarity to GSTs. GSTs are 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.
GSTs also show GSH peroxidase activity and are involved
in the synthesis of prostaglandins and leukotrienes.
The GST fold contains an N-terminal thioredoxin-fold
domain and a C-terminal alpha helical domain, with an
active site located in a cleft between the two domains.
GSH binds to the N-terminal domain while the
hydrophobic substrate occupies a pocket in the
C-terminal domain.
Length = 110
Score = 26.1 bits (58), Expect = 2.4
Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 14/81 (17%)
Query: 22 SQLDLNPLFS--------TPEHKLSWDDVIAFTEKMRTEWQMLSLCDIVLNHTANETYLS 73
LNP F TP + + A +L D L A + YL+
Sbjct: 13 QTSTLNPAFRYAFWGLVRTPPEQRDPAAIAASLAACNKLMAIL---DAQL---ARQAYLA 66
Query: 74 LNMLSLCDIVLNHTANETFDL 94
+ +L DI L + +L
Sbjct: 67 GDRFTLADIALGCSVYRWLEL 87
>gnl|CDD|200454 cd11315, AmyAc_bac1_AmyA, Alpha amylase catalytic domain found in
bacterial Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes Firmicutes, Proteobacteria, Actinobacteria,
and Cyanobacteria. The Alpha-amylase family comprises
the largest family of glycoside hydrolases (GH), with
the majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains:
A, B, C. A is a (beta/alpha) 8-barrel; B is a loop
between the beta 3 strand and alpha 3 helix of A; C is
the C-terminal extension characterized by a Greek key.
The majority of the enzymes have an active site cleft
found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc,
or only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 352
Score = 26.1 bits (58), Expect = 2.8
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 59 CDIVLNHTANET 70
D+V NH ANE
Sbjct: 86 VDVVFNHMANEG 97
Score = 26.1 bits (58), Expect = 2.8
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 80 CDIVLNHTANET 91
D+V NH ANE
Sbjct: 86 VDVVFNHMANEG 97
>gnl|CDD|236691 PRK10426, PRK10426, alpha-glucosidase; Provisional.
Length = 635
Score = 26.1 bits (58), Expect = 3.4
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 32 TPEHKLSWDDVIAFTEKMRT 51
T E L W + AFT MRT
Sbjct: 472 TKELLLRWCEFSAFTPVMRT 491
>gnl|CDD|177736 PLN00124, PLN00124, succinyl-CoA ligase [GDP-forming] subunit beta;
Provisional.
Length = 422
Score = 25.9 bits (57), Expect = 3.4
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 11/49 (22%)
Query: 17 CYSLSSQLDLNPLFSTPEH-------KLSWDDVIAFTEK----MRTEWQ 54
C + +++NPL T + KL++DD AF +K +R Q
Sbjct: 224 CKCDCTMVEINPLAETADGQLVAADAKLNFDDNAAFRQKEIFALRDTSQ 272
>gnl|CDD|198308 cd03199, GST_C_GRX2, C-terminal, alpha helical domain of
Glutaredoxin 2. Glutathione S-transferase (GST)
C-terminal domain family, Glutaredoxin 2 (GRX2)
subfamily; composed of Escherichia coli GRX2 and
similar proteins. Escherichia coli GRX2 is an atypical
GRX with a molecular mass of about 24kD (most GRXs
range from 9-12kD). It adopts a GST fold containing an
N-terminal thioredoxin-fold domain and a C-terminal
alpha helical domain. It contains a redox active CXXC
motif located in the N-terminal domain, but is not able
to reduce ribonucleotide reductase like other GRXs.
However, it catalyzes GSH-dependent protein disulfide
reduction of other substrates efficiently. GRX2 is
thought to function primarily in catalyzing the
reversible glutathionylation of proteins in cellular
redox regulation including stress responses.
Length = 128
Score = 25.2 bits (56), Expect = 4.1
Identities = 9/24 (37%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 25 DLNPLFSTPEH---KLSWDDVIAF 45
L+PL + + +LS+DD+I F
Sbjct: 71 ALDPLILSSDAVNGELSYDDIILF 94
>gnl|CDD|241278 cd01247, PH_FAPP1_FAPP2, Four phosphate adaptor protein 1 and 2
Pleckstrin homology (PH) domain. Human FAPP1 (also
called PLEKHA3/Pleckstrin homology domain-containing,
family A member 3) regulates secretory transport from
the trans-Golgi network to the plasma membrane. It is
recruited through binding of PH domain to
phosphatidylinositol 4-phosphate (PtdIns(4)P) and a
small GTPase ADP-ribosylation factor 1 (ARF1). These
two binding sites have little overlap the FAPP1 PH
domain to associate with both ligands simultaneously
and independently. FAPP1 has a N-terminal PH domain
followed by a short proline-rich region. FAPP1 is a
member of the oxysterol binding protein (OSBP) family
which includes OSBP, OSBP-related proteins (ORP), and
Goodpasture antigen binding protein (GPBP). They have a
wide range of purported functions including sterol
transport, cell cycle control, pollen development and
vessicle transport from Golgi recognize both PI lipids
and ARF proteins. FAPP2 (also called PLEKHA8/Pleckstrin
homology domain-containing, family A member 8), a
member of the Glycolipid lipid transfer protein(GLTP)
family has an N-terminal PH domain that targets the TGN
and C-terminal GLTP domain. FAPP2 functions to traffic
glucosylceramide (GlcCer) which is made in the Golgi.
It's interaction with vesicle-associated membrane
protein-associated protein (VAP) could be a means of
regulation. Some FAPP2s share the FFAT-like motifs
found in GLTP. PH domains have diverse functions, but
in general are involved in targeting proteins to the
appropriate cellular location or in the interaction
with a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 100
Score = 25.0 bits (55), Expect = 4.3
Identities = 10/24 (41%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 73 SLNMLSLCDIVLNHTANETFDLIV 96
S+ M S+C+I+++ T N DLI+
Sbjct: 43 SIKM-SVCEIIVHPTDNTRMDLII 65
>gnl|CDD|235502 PRK05560, PRK05560, DNA gyrase subunit A; Validated.
Length = 805
Score = 25.8 bits (58), Expect = 4.4
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 60 DIVLN----HTANETYLSLNMLSLCD 81
++VLN HT +T +NML+L D
Sbjct: 309 EVVLNNLYKHTQLQTSFGINMLALVD 334
>gnl|CDD|200453 cd11314, AmyAc_arch_bac_plant_AmyA, Alpha amylase catalytic
domain found in archaeal, bacterial, and plant
Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes AmyA from bacteria, archaea, water fleas, and
plants. The Alpha-amylase family comprises the largest
family of glycoside hydrolases (GH), with the majority
of enzymes acting on starch, glycogen, and related
oligo- and polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 302
Score = 25.3 bits (56), Expect = 5.4
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 66 TANETYLSLNMLSLCDIVLNH 86
+ + + + DIV+NH
Sbjct: 71 SLIAALHAKGIKVIADIVINH 91
>gnl|CDD|236937 PRK11617, PRK11617, endonuclease V; Provisional.
Length = 224
Score = 25.3 bits (56), Expect = 5.7
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 27 NPLFSTPEHKLSWDDVIAFTEK 48
NPLF + H++S D +A+ ++
Sbjct: 171 NPLFISTGHRVSLDSALAWVQR 192
>gnl|CDD|214758 smart00642, Aamy, Alpha-amylase domain.
Length = 166
Score = 25.0 bits (55), Expect = 6.0
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 14/76 (18%)
Query: 26 LNPLFSTPEHKLSWD--DVIAFTEKMR---TEWQMLSLCDIVLNHTANETYLSLNMLSLC 80
L+P+F +P+ S+ D+ + + T L D A+ + +
Sbjct: 38 LSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVD-----AAHA----RGIKVIL 88
Query: 81 DIVLNHTANETFDLIV 96
D+V+NHT++ F L
Sbjct: 89 DVVINHTSDGGFRLDA 104
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
0.321 0.134 0.402
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,631,323
Number of extensions: 356688
Number of successful extensions: 353
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 27
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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: 53 (24.2 bits)