RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9007
(132 letters)
>gnl|CDD|215519 PLN02960, PLN02960, alpha-amylase.
Length = 897
Score = 83.0 bits (205), Expect = 1e-19
Identities = 33/82 (40%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 20 PISRLSPWATYVTEPPVVGHAYEQRIWNPKPQDKHKWTSSKPKKPENLKIYESHVGICTQ 79
P+ R+ WATYV P G + W P P++ +KW +PK P++L+IYE HVGI
Sbjct: 350 PLERVPAWATYV-LPDPDGKQWYAIHWEPPPEEAYKWKFERPKVPKSLRIYECHVGISGS 408
Query: 80 EQKCASYEDFVRVVIPRIVKQG 101
E K +S+++F + V+P + K G
Sbjct: 409 EPKISSFKEFTQKVLPHVKKAG 430
Score = 26.7 bits (59), Expect = 4.3
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 5/30 (16%)
Query: 101 GDFNNWN-REEFAYKKL----DFGKWELVL 125
GDFNNW+ E A + DFG W ++L
Sbjct: 146 GDFNNWSPTENRAREGYFGHDDFGYWFIIL 175
>gnl|CDD|200460 cd11321, AmyAc_bac_euk_BE, Alpha amylase catalytic domain found in
bacterial and eukaryotic branching enzymes. Branching
enzymes (BEs) catalyze the formation of alpha-1,6 branch
points in either glycogen or starch by cleavage of the
alpha-1,4 glucosidic linkage yielding a non-reducing end
oligosaccharide chain, and subsequent attachment to the
alpha-1,6 position. By increasing the number of
non-reducing ends, glycogen is more reactive to
synthesis and digestion as well as being more soluble.
This group includes bacterial and eukaryotic proteins.
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 = 406
Score = 73.4 bits (181), Expect = 2e-16
Identities = 23/52 (44%), Positives = 36/52 (69%)
Query: 50 PQDKHKWTSSKPKKPENLKIYESHVGICTQEQKCASYEDFVRVVIPRIVKQG 101
P++ +++ +P KP L+IYE+HVG+ ++E K ASY +F V+PRI K G
Sbjct: 1 PEEPYQFKHPRPPKPRALRIYEAHVGMSSEEPKVASYREFTDNVLPRIKKLG 52
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 73.6 bits (181), Expect = 3e-16
Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 20 PISRLSPWATYVT-EPPVVGHAYEQRIWNPKPQDKHKWTSSKPKKPENLKIYESHVGICT 78
+ R+ W Y P +G Y W+P ++K+ + +P +P L+IYE+HVG+ +
Sbjct: 182 WVDRIPAWIKYAVQAPGEIGAPYNGVYWDPPEEEKYVFKHPRPPRPAALRIYEAHVGMSS 241
Query: 79 QEQKCASYEDFVRVVIPRIVKQG 101
+E K SY +F V+PRI G
Sbjct: 242 EEPKVNSYREFADDVLPRIKALG 264
Score = 44.7 bits (106), Expect = 3e-06
Identities = 17/32 (53%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 101 GDFNNWNREEFAYKKLDFGKWELVLPPNPDGS 132
GDFNNWN K +FG WE+ L P+ DGS
Sbjct: 132 GDFNNWNPNAHWMTKNEFGVWEIFL-PDADGS 162
>gnl|CDD|178782 PLN03244, PLN03244, alpha-amylase; Provisional.
Length = 872
Score = 72.7 bits (178), Expect = 6e-16
Identities = 34/74 (45%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 20 PISRLSPWATYVTEPPVVGHAYEQRIWNPKPQDKHKWTSSKPKKPENLKIYESHVGICTQ 79
P+ R+ WATYV P G W P P+ HKW + KPK PE+L+IYE HVGI
Sbjct: 355 PLERIPAWATYV-LPDDDGKQAFAIHWEPPPEAAHKWKNMKPKVPESLRIYECHVGISGS 413
Query: 80 EQKCASYEDFVRVV 93
E K +S+E+F V
Sbjct: 414 EPKISSFEEFTEKV 427
>gnl|CDD|199884 cd02854, E_set_GBE_euk_N, N-terminal Early set domain associated
with the catalytic domain of eukaryotic glycogen
branching enzyme (also called 1,4 alpha glucan branching
enzyme). This subfamily is composed of predominantly
eukaryotic 1,4 alpha glucan branching enzymes, also
called glycogen branching enzymes or starch binding
enzymes in plants. E or "early" set domains are
associated with the catalytic domain of the 1,4 alpha
glucan branching enzymes at the N-terminal end. These
enzymes catalyze the formation of alpha-1,6 branch
points in either glycogen or starch by cleavage of the
alpha-1,4 glucosidic linkage, yielding a non-reducing
end oligosaccharide chain, as well as the subsequent
attachment of short glucosyl chains to the alpha-1,6
position. Starch is composed of two types of glucan
polymer: amylose and amylopectin. Amylose is mainly
composed of linear chains of alpha-1,4 linked glucose
residues and amylopectin consists of shorter alpha-1,4
linked chains connected by alpha-1,6 linkages.
Amylopectin is synthesized from linear chains by starch
branching enzyme. The N-terminal domains of the
branching enzyme proteins may be related to the
immunoglobulin and/or fibronectin type III
superfamilies. These domains are associated with
different types of catalytic domains at either the
N-terminal or C-terminal end and may be involved in
homodimeric/tetrameric/dodecameric interactions. Members
of this family include members of the alpha amylase
family, sialidase, galactose oxidase, cellulase,
cellulose, hyaluronate lyase, chitobiase, and chitinase,
among others.
Length = 95
Score = 56.0 bits (136), Expect = 2e-11
Identities = 19/29 (65%), Positives = 21/29 (72%)
Query: 101 GDFNNWNREEFAYKKLDFGKWELVLPPNP 129
GDFNNWNRE K+ +FGKWEL LPP
Sbjct: 20 GDFNNWNRESHPLKRDEFGKWELFLPPKE 48
Score = 29.4 bits (67), Expect = 0.21
Identities = 6/24 (25%), Positives = 10/24 (41%), Gaps = 1/24 (4%)
Query: 23 RLSPWATYVTEPPVVGHAYEQRIW 46
R+ WA V + P ++ W
Sbjct: 73 RIPAWAKRVVQDP-ETKIFDGVFW 95
>gnl|CDD|217288 pfam02922, CBM_48, Carbohydrate-binding module 48 (Isoamylase
N-terminal domain). This domain is found in a range of
enzymes that act on branched substrates - isoamylase,
pullulanase and branching enzyme. This family also
contains the beta subunit of 5' AMP activated kinase.
Length = 83
Score = 34.3 bits (79), Expect = 0.003
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 101 GDFNNWNREEFAYKKL-DFGKWELVLPPNPDG 131
DFNNW+ EE ++ + G WE+ LP +
Sbjct: 29 LDFNNWDGEEHPMERKREGGVWEVFLPGDLPH 60
>gnl|CDD|223373 COG0296, GlgB, 1,4-alpha-glucan branching enzyme [Carbohydrate
transport and metabolism].
Length = 628
Score = 33.4 bits (77), Expect = 0.021
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 8/79 (10%)
Query: 26 PWATYVTEPPVVGHAYEQRIWNPKPQ--DKHKWTSSKPKKP-ENLKIYESHVGICTQEQK 82
P+A E + + + +W + + E + IYE HVG T + +
Sbjct: 105 PYARR-QEVGPHTASQ---VVDLPDYEWQDERWDRAWRGRFWEPIVIYELHVGSFTPD-R 159
Query: 83 CASYEDFVRVVIPRIVKQG 101
Y + ++P + + G
Sbjct: 160 FLGYFELAIELLPYLKELG 178
Score = 32.7 bits (75), Expect = 0.037
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 84 ASYEDFVRVVIPRIVKQGDFNNWN-REEFAYKKLDFGKWELVLPPNPDGS 132
A V +V GDFN+W+ R + + G WEL +P P G+
Sbjct: 44 APNARRVSLV-------GDFNDWDGRRMPMRDRKESGIWELFVPGAPPGT 86
>gnl|CDD|237795 PRK14706, PRK14706, glycogen branching enzyme; Provisional.
Length = 639
Score = 33.0 bits (75), Expect = 0.032
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 101 GDFNNWNREEFAYKKLDFGKWELVLP 126
GDFN+WN + ++LDFG W +P
Sbjct: 56 GDFNDWNGFDHPMQRLDFGFWGAFVP 81
>gnl|CDD|199885 cd02855, E_set_GBE_prok_N, N-terminal Early set domain associated
with the catalytic domain of prokaryotic glycogen
branching enzyme. This subfamily is composed of
predominantly prokaryotic 1,4 alpha glucan branching
enzymes, also called glycogen branching enzymes. E or
"early" set domains are associated with the catalytic
domain of glycogen branching enzymes at the N-terminal
end. Glycogen branching enzyme catalyzes the formation
of alpha-1,6 branch points in either glycogen or starch
by cleavage of the alpha-1,4 glucosidic linkage,
yielding a non-reducing end oligosaccharide chain, as
well as the subsequent attachment of short glucosyl
chains to the alpha-1,6 position. By increasing the
number of non-reducing ends, glycogen is more reactive
to synthesis and digestion as well as being more
soluble. The N-terminal domain of the 1,4 alpha glucan
branching enzyme may be related to the immunoglobulin
and/or fibronectin type III superfamilies. These domains
are associated with different types of catalytic domains
at either the N-terminal or C-terminal end and may be
involved in homodimeric/tetrameric/dodecameric
interactions. Members of this family include members of
the alpha amylase family, sialidase, galactose oxidase,
cellulase, cellulose, hyaluronate lyase, chitobiase, and
chitinase, among others.
Length = 105
Score = 31.3 bits (72), Expect = 0.044
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 90 VRVVIPRIVKQGDFNNWNREEFAYKKL-DFGKWELVLP 126
V VV GDFN+W+ +++ D G WEL +P
Sbjct: 33 VSVV-------GDFNDWDGRAHPMRRIGDSGVWELFIP 63
>gnl|CDD|235445 PRK05402, PRK05402, glycogen branching enzyme; Provisional.
Length = 726
Score = 31.3 bits (72), Expect = 0.12
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 90 VRVVIPRIVKQGDFNNWNREEFAYKKL-DFGKWELVLPPNPDG 131
V VV GDFN W+ + + G WEL +P +G
Sbjct: 145 VSVV-------GDFNGWDGRRHPMRLRGESGVWELFIPGLGEG 180
>gnl|CDD|199892 cd07184, E_set_Isoamylase_like_N, N-terminal Early set domain
associated with the catalytic domain of isoamylase-like
(also called glycogen 6-glucanohydrolase) proteins. E
or "early" set domains are associated with the catalytic
domain of isoamylase-like proteins at the N-terminal
end. Isoamylase is one of the starch-debranching enzymes
that catalyze the hydrolysis of alpha-1,6-glucosidic
linkages specific in alpha-glucans such as amylopectin
or glycogen. Isoamylase contains a bound calcium ion,
but this is not in the same position as the conserved
calcium ion that has been reported in other
alpha-amylase family enzymes. The N-terminal domain of
isoamylase may be related to the immunoglobulin and/or
fibronectin type III superfamilies. These domains are
associated with different types of catalytic domains at
either the N-terminal or C-terminal end and may be
involved in homodimeric/tetrameric/dodecameric
interactions. Members of this family include members of
the alpha amylase family, sialidase, galactose oxidase,
cellulase, cellulose, hyaluronate lyase, chitobiase, and
chitinase. This domain is also a member of the CBM48
(Carbohydrate Binding Module 48) family whose members
include pullulanase, maltooligosyl trehalose synthase,
starch branching enzyme, glycogen branching enzyme,
glycogen debranching enzyme, and the beta subunit of
AMP-activated protein kinase.
Length = 86
Score = 29.9 bits (68), Expect = 0.12
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 101 GDFNNWNREEFAYKKLDFGKW--ELVLPPN 128
GDFN+W+ + KKL G + L LP
Sbjct: 20 GDFNDWDPQATPMKKLKNGTFSATLDLPAG 49
>gnl|CDD|237052 PRK12313, PRK12313, glycogen branching enzyme; Provisional.
Length = 633
Score = 30.3 bits (69), Expect = 0.28
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 101 GDFNNWNREEFAYKKLDFGKWELVLP 126
GDFN+W + + G WE +P
Sbjct: 56 GDFNDWRGNAHPLVRRESGVWEGFIP 81
>gnl|CDD|227513 COG5186, PAP1, Poly(A) polymerase [RNA processing and
modification].
Length = 552
Score = 29.5 bits (66), Expect = 0.44
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 27 WATYVTEPPVVGHAYEQRIWNPK--PQDK-HKWTSSKPKKP 64
W V P+ + R+WNPK P DK H+ P P
Sbjct: 268 WPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYP 308
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 29.5 bits (66), Expect = 0.54
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 96 RIVKQGDFNNWNREEFAYKKLDFGKWELVLP 126
R+ GDFN W+ ++ G WEL LP
Sbjct: 151 RVAVVGDFNGWDVRRHPMRQRIGGFWELFLP 181
>gnl|CDD|188150 TIGR01515, branching_enzym, alpha-1,4-glucan:alpha-1,4-glucan
6-glycosyltransferase. This model describes the
glycogen branching enzymes which are responsible for the
transfer of chains of approx. 7 alpha(1--4)-linked
glucosyl residues to other similar chains (in new
alpha(1--6) linkages) in the biosynthesis of glycogen.
This enzyme is a member of the broader amylase family of
starch hydrolases which fold as (beta/alpha)8 barrels,
the so-called TIM-barrel structure. All of the sequences
comprising the seed of this model have been
experimentally characterized. (For instance,). This
model encompasses both bacterial and eukaryotic species.
No archaea have this enzyme, although Aquifex aolicus
does. Two species, Bacillus thuringiensis and
Clostridium perfringens have two sequences each which
are annotated as amylases. These annotations are
aparrently in error. GP|18143720 from C. perfringens,
for instance, contains the note "674 aa, similar to
gp:A14658_1 amylase (1,4-alpha-glucan branching enzyme
(EC 2.4.1.18) ) from Bacillus thuringiensis (648 aa);
51.1% identity in 632 aa overlap." A branching enzyme
from Porphyromonas gingivales, OMNI|PG1793, appears to
be more closely related to the eukaryotic species
(across a deep phylogenetic split) and may represent an
instance of lateral transfer from this species' host. A
sequence from Arabidopsis thaliana, GP|9294564, scores
just above trusted, but appears either to contain
corrupt sequence or, more likely, to be a pseudogene as
some of the conserved catalytic residues common to the
alpha amylase family are not conserved here [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 618
Score = 28.6 bits (64), Expect = 0.89
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 101 GDFNNWNREEFAYKKL-DFGKWELVLP 126
GDFN W+ E ++ D G WEL +P
Sbjct: 46 GDFNYWDGREHPMRRRNDNGIWELFIP 72
>gnl|CDD|131396 TIGR02343, chap_CCT_epsi, T-complex protein 1, epsilon subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
epsilon chain (part of a paralogous family) from
animals, plants, fungi, and other eukaryotes.
Length = 532
Score = 27.8 bits (62), Expect = 1.8
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 48 PKPQDKHKWTSSKPKKPENLKIYE 71
PKP+ KHK S ++ + L+ YE
Sbjct: 253 PKPKTKHKLDISSVEEYKKLQKYE 276
>gnl|CDD|237794 PRK14705, PRK14705, glycogen branching enzyme; Provisional.
Length = 1224
Score = 27.7 bits (61), Expect = 2.3
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 100 QGDFNNWNREEFAYKKL-DFGKWELVLP 126
+GDFN W+ E + + L G WEL +P
Sbjct: 655 KGDFNGWDGREHSMRSLGSSGVWELFIP 682
>gnl|CDD|200464 cd11325, AmyAc_GTHase, Alpha amylase catalytic domain found in
Glycosyltrehalose trehalohydrolase (also called
Maltooligosyl trehalose Trehalohydrolase).
Glycosyltrehalose trehalohydrolase (GTHase) was
discovered as part of a coupled system for the
production of trehalose from soluble starch. In the
first half of the reaction, glycosyltrehalose synthase
(GTSase), an intramolecular glycosyl transferase,
converts the glycosidic bond between the last two
glucose residues of amylose from an alpha-1,4 bond to
an alpha-1,1 bond, making a non-reducing glycosyl
trehaloside. In the second half of the reaction, GTHase
cleaves the alpha-1,4 glycosidic bond adjacent to the
trehalose moiety to release trehalose and
malto-oligosaccharide. Like isoamylase and other
glycosidases that recognize branched oligosaccharides,
GTHase contains an N-terminal extension and does not
have the conserved calcium ion present in other alpha
amylase family enzymes. 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.
Glycosyltrehalose Trehalohydrolase
Maltooligosyltrehalose Trehalohydrolase.
Length = 436
Score = 27.5 bits (62), Expect = 2.3
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 26 PWATYVTEPPVVGHAYEQRIWNPKPQDKHKWTSSKPKKP--ENLKIYESHVGICTQE 80
P + + E V G + + +P WT + + P E L IYE HVG T E
Sbjct: 2 PASRFQPEG-VHGPS---VVVDP---SAFWWTDAGWRGPPLEELVIYELHVGTFTPE 51
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 26.5 bits (59), Expect = 4.0
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 107 NREEFAYKKLDFGKWEL 123
N EE YK + F W++
Sbjct: 50 NVEEIVYKNIRFLMWDI 66
>gnl|CDD|199839 cd00596, Peptidase_M14_like, M14 family of metallocarboxypeptidases
and related proteins. The M14 family of
metallocarboxypeptidases (MCPs), also known as
funnelins, are zinc-binding carboxypeptidases (CPs)
which hydrolyze single, C-terminal amino acids from
polypeptide chains, and have a recognition site for the
free C-terminal carboxyl group, which is a key
determinant of specificity. Two major subfamilies of the
M14 family, defined based on sequence and structural
homology, are the A/B and N/E subfamilies. Enzymes
belonging to the A/B subfamily are normally synthesized
as inactive precursors containing preceding signal
peptide, followed by an N-terminal pro-region linked to
the enzyme; these proenzymes are called
procarboxypeptidases. The A/B enzymes can be further
divided based on their substrate specificity;
Carboxypeptidase A-like (CPA-like) enzymes favor
hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavage.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on their
involvement in specific physiological processes; the
pancreatic MCPs participate only in alimentary digestion
and include carboxypeptidase A and B (A/B subfamily),
while others, namely regulatory MCPs or the N/E
subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily, is
that of succinylglutamate desuccinylase /aspartoacylase,
which hydrolyzes N-acetyl-L-aspartate (NAA), and
deficiency in which is the established cause of Canavan
disease. Another subfamily (referred to as subfamily C)
includes an exceptional type of activity in the MCP
family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 211
Score = 26.3 bits (58), Expect = 5.6
Identities = 9/69 (13%), Positives = 18/69 (26%), Gaps = 8/69 (11%)
Query: 39 HAYEQRIWNPKPQDKHKWTSSKPKKPENLKIYESHVGICTQEQKCASYEDFVRVVIPRIV 98
H+ I P P++ + ++ V ++
Sbjct: 115 HSGSLAILYPY--------GHSDNDPDDFSNPKEIAQSLAIAADKHGGKEGVGFIVQEKA 166
Query: 99 KQGDFNNWN 107
QG F +W
Sbjct: 167 TQGGFEDWA 175
>gnl|CDD|233850 TIGR02402, trehalose_TreZ, malto-oligosyltrehalose
trehalohydrolase. Members of this family are the
trehalose biosynthetic enzyme malto-oligosyltrehalose
trehalohydrolase, formally known as
4-alpha-D-{(1->4)-alpha-D-glucano}trehalose
trehalohydrolase (EC 3.2.1.141). It is the TreZ protein
of the TreYZ pathway for trehalose biosynthesis, and
alternative to the OtsAB system [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 544
Score = 26.5 bits (59), Expect = 5.7
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 44 RIWNPKPQDKHKWTSS--KPKKPENLKIYESHVGICTQE 80
++ +P D++ W + + + E IYE HVG T E
Sbjct: 72 QVVDP---DRYAWQDTGWRGRPLEEAVIYELHVGTFTPE 107
>gnl|CDD|183463 PRK12351, PRK12351, methylcitrate synthase; Provisional.
Length = 378
Score = 26.0 bits (58), Expect = 6.5
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 9/36 (25%)
Query: 12 TLIFRYLLPISRLSPWATYVTEPPVVGHAYEQRIWN 47
T +F L ISR + WA H EQR N
Sbjct: 329 TAMFTPLFVISRTTGWA---------AHVIEQRQDN 355
>gnl|CDD|217033 pfam02438, Adeno_100, Late 100kD protein. The late 100kD protein
is a non-structural viral protein involved in the
transport of hexon from the cytoplasm to the nucleus.
Length = 583
Score = 26.1 bits (58), Expect = 7.5
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 37 VGHAYEQRIWNPKPQDKHK 55
+ A E+ ++NPK + +
Sbjct: 31 LSRALERFLFNPKVPPERQ 49
>gnl|CDD|201432 pfam00764, Arginosuc_synth, Arginosuccinate synthase. This family
contains a PP-loop motif.
Length = 387
Score = 25.8 bits (57), Expect = 7.9
Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 10/58 (17%)
Query: 19 LPISRLSPWATYVTEPPVVGHAYE----QRIWNPKPQDKHKWTSS---KPKKPENLKI 69
+P+++ P++ + + G + E + WN P+D ++WT P +PE ++I
Sbjct: 160 IPVTKKKPYSI---DENLWGRSIEGGILEDPWNAPPEDIYEWTKDPAKAPDEPEVVEI 214
>gnl|CDD|234293 TIGR03648, Na_symport_lg, probable sodium:solute symporter, VC_2705
subfamily. This family belongs to a larger family of
transporters of the sodium:solute symporter superfamily,
TC 2.A.21. Members of this strictly bacterial protein
subfamily are found almost invariably immediately
downstream from a member of family TIGR03647.
Occasionally, the two genes are fused.
Length = 552
Score = 26.1 bits (58), Expect = 8.0
Identities = 12/30 (40%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 5 VPQYITRTLIFRYLLPISRLSPWATYVTEP 34
V QYI LI YL+P +S T P
Sbjct: 173 VAQYIV--LIVAYLVPAIFISLKLTGNPVP 200
>gnl|CDD|189040 cd09870, PIN_YEN1, PIN domain of Yeast Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and fungal homologs. Yeast Endonuclease 1
(YEN1) is a Holliday junction resolvase which promotes
reciprocal exchange during mitotic recombination to
maintain genome integrity in budding yeast. YEN1 is a
member of the structure-specific, 5' nuclease family
that catalyzes hydrolysis of DNA duplex-containing
nucleic acid structures during DNA replication, repair,
and recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 15 - 50
residues in YEN1 PIN domains) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 239
Score = 25.7 bits (57), Expect = 8.3
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 87 EDFVRVVIPRIVKQGDFNNWNREEFAYKKL 116
ED V V ++ +W +KL
Sbjct: 188 EDHVTVYDLDEIRNTTSTSWTGSLDDLEKL 217
>gnl|CDD|215148 PLN02264, PLN02264, lipoxygenase.
Length = 919
Score = 26.0 bits (57), Expect = 8.9
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 8 YITRTLIFRYLLPISRLSPWATYVTEPPVVGHAYEQRIWNPKPQDKHKWT 57
Y TRT+ F L + L P A ++ PP ++ +R+ P W
Sbjct: 510 YATRTIFF--LTRLGTLKPIAIELSLPPSGPNSRSKRVVTPPVDATSNWM 557
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 0.138 0.454
Gapped
Lambda K H
0.267 0.0595 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,033,837
Number of extensions: 592327
Number of successful extensions: 467
Number of sequences better than 10.0: 1
Number of HSP's gapped: 464
Number of HSP's successfully gapped: 39
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (24.5 bits)