RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14038
(131 letters)
>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 = 154 bits (391), Expect = 2e-46
Identities = 52/83 (62%), Positives = 67/83 (80%)
Query: 49 PQDKHKWTSSKPKKPDNLKIYESHVGICTQEQKCASYEDFVRVVIPRIVKQGYNAVQLMA 108
P++ +++ +P KP L+IYE+HVG+ ++E K ASY +F V+PRI K GYNA+QLMA
Sbjct: 1 PEEPYQFKHPRPPKPRALRIYEAHVGMSSEEPKVASYREFTDNVLPRIKKLGYNAIQLMA 60
Query: 109 IMEHAYYASFGYQVTSFFAASSR 131
IMEHAYYASFGYQVT+FFAASSR
Sbjct: 61 IMEHAYYASFGYQVTNFFAASSR 83
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 148 bits (376), Expect = 9e-43
Identities = 54/111 (48%), Positives = 71/111 (63%), Gaps = 1/111 (0%)
Query: 22 RLSPWATYVT-EPPVVGHAYEQRIWNPKPQDKHKWTSSKPKKPDNLKIYESHVGICTQEQ 80
R+ W Y P +G Y W+P ++K+ + +P +P L+IYE+HVG+ ++E
Sbjct: 185 RIPAWIKYAVQAPGEIGAPYNGVYWDPPEEEKYVFKHPRPPRPAALRIYEAHVGMSSEEP 244
Query: 81 KCASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGYQVTSFFAASSR 131
K SY +F V+PRI GYNAVQLMAI EHAYY SFGY VT+FFA SSR
Sbjct: 245 KVNSYREFADDVLPRIKALGYNAVQLMAIQEHAYYGSFGYHVTNFFAVSSR 295
>gnl|CDD|215519 PLN02960, PLN02960, alpha-amylase.
Length = 897
Score = 129 bits (325), Expect = 9e-36
Identities = 51/110 (46%), Positives = 72/110 (65%), Gaps = 1/110 (0%)
Query: 22 RLSPWATYVTEPPVVGHAYEQRIWNPKPQDKHKWTSSKPKKPDNLKIYESHVGICTQEQK 81
R+ WATYV P G + W P P++ +KW +PK P +L+IYE HVGI E K
Sbjct: 353 RVPAWATYV-LPDPDGKQWYAIHWEPPPEEAYKWKFERPKVPKSLRIYECHVGISGSEPK 411
Query: 82 CASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGYQVTSFFAASSR 131
+S+++F + V+P + K GYNA+QL+ + EH Y+S GY+VT+FFA SSR
Sbjct: 412 ISSFKEFTQKVLPHVKKAGYNAIQLIGVQEHKDYSSVGYKVTNFFAVSSR 461
>gnl|CDD|223373 COG0296, GlgB, 1,4-alpha-glucan branching enzyme [Carbohydrate
transport and metabolism].
Length = 628
Score = 83.5 bits (207), Expect = 8e-20
Identities = 26/110 (23%), Positives = 48/110 (43%), Gaps = 8/110 (7%)
Query: 25 PWATYVTEPPVVGHAYEQRIWNPKPQ--DKHKWTSSKPKKPDN-LKIYESHVGICTQEQK 81
P+A E + + + +W + + + IYE HVG T + +
Sbjct: 105 PYARR-QEVGPHTASQ---VVDLPDYEWQDERWDRAWRGRFWEPIVIYELHVGSFTPD-R 159
Query: 82 CASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGYQVTSFFAASSR 131
Y + ++P + + G ++LM + EH S+GYQ T ++A +SR
Sbjct: 160 FLGYFELAIELLPYLKELGITHIELMPVAEHPGDRSWGYQGTGYYAPTSR 209
>gnl|CDD|178782 PLN03244, PLN03244, alpha-amylase; Provisional.
Length = 872
Score = 69.6 bits (170), Expect = 6e-15
Identities = 40/110 (36%), Positives = 51/110 (46%), Gaps = 31/110 (28%)
Query: 22 RLSPWATYVTEPPVVGHAYEQRIWNPKPQDKHKWTSSKPKKPDNLKIYESHVGICTQEQK 81
R+ WATYV P G W P P+ HKW + KPK P++L+IYE HVGI E K
Sbjct: 358 RIPAWATYV-LPDDDGKQAFAIHWEPPPEAAHKWKNMKPKVPESLRIYECHVGISGSEPK 416
Query: 82 CASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGYQVTSFFAASSR 131
+S+E+F +VT+FFAASSR
Sbjct: 417 ISSFEEFTE------------------------------KVTNFFAASSR 436
>gnl|CDD|200461 cd11322, AmyAc_Glg_BE, Alpha amylase catalytic domain found in the
Glycogen branching enzyme (also called 1,4-alpha-glucan
branching enzyme). The glycogen branching enzyme
catalyzes the third step of glycogen biosynthesis by the
cleavage of an alpha-(1,4)-glucosidic linkage and the
formation a new alpha-(1,6)-branch by subsequent
transfer of cleaved oligosaccharide. They are part of a
group called branching enzymes which catalyze the
formation of alpha-1,6 branch points in either glycogen
or starch. This group includes proteins from bacteria,
eukaryotes, and archaea. 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 = 402
Score = 67.2 bits (165), Expect = 4e-14
Identities = 34/90 (37%), Positives = 50/90 (55%), Gaps = 4/90 (4%)
Query: 44 IWNPKPQDKHKWTSSKPKKPDNLKIYESHVG--ICTQEQKCASYEDFVRVVIPRIVKQGY 101
W K K + +K KP N IYE H+G ++ + SY + +IP + + GY
Sbjct: 16 KWTDKKWMKKRKRKNKKNKPMN--IYEVHLGSWKRKEDGRFLSYRELADELIPYVKEMGY 73
Query: 102 NAVQLMAIMEHAYYASFGYQVTSFFAASSR 131
V+LM +MEH + S+GYQVT +FA +SR
Sbjct: 74 THVELMPVMEHPFDGSWGYQVTGYFAPTSR 103
>gnl|CDD|237052 PRK12313, PRK12313, glycogen branching enzyme; Provisional.
Length = 633
Score = 66.1 bits (162), Expect = 9e-14
Identities = 36/124 (29%), Positives = 60/124 (48%), Gaps = 17/124 (13%)
Query: 18 YSILRLSPWATYVTEPPVVGHAYEQRIWNPKPQDKHKW------TSSKPKKPDN--LKIY 69
Y + ++ P+A Y P G A +W+ ++KW K + + IY
Sbjct: 99 YQVEKIDPFAFYFEARP--GTA--SIVWDL---PEYKWKDGLWLARRKRWNALDRPISIY 151
Query: 70 ESHVG--ICTQEQKCASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGYQVTSFFA 127
E H+G ++ + SY + +IP + + GY V+ M +MEH S+GYQ+T +FA
Sbjct: 152 EVHLGSWKRNEDGRPLSYRELADELIPYVKEMGYTHVEFMPLMEHPLDGSWGYQLTGYFA 211
Query: 128 ASSR 131
+SR
Sbjct: 212 PTSR 215
>gnl|CDD|235445 PRK05402, PRK05402, glycogen branching enzyme; Provisional.
Length = 726
Score = 59.4 bits (145), Expect = 2e-11
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 68 IYESHVGI---CTQEQKCASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGYQVTS 124
IYE H+G + SY + +IP + + G+ V+L+ I EH + S+GYQ T
Sbjct: 244 IYEVHLGSWRRHEDGGRFLSYRELADQLIPYVKEMGFTHVELLPIAEHPFDGSWGYQPTG 303
Query: 125 FFAASSR 131
++A +SR
Sbjct: 304 YYAPTSR 310
>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 = 53.3 bits (128), Expect = 3e-09
Identities = 31/118 (26%), Positives = 56/118 (47%), Gaps = 11/118 (9%)
Query: 21 LRLSPWATYVTEPP-----VVGHAYEQRIWNPKPQDKHKWTSSKPKKPDNLKIYESHVG- 74
L+ P+A Y P V W + + + + +KP + IYE H+G
Sbjct: 93 LKADPYAFYAEVRPNTASLVYNLEGYS--WQDQKWQEKRKAKTPYEKP--VSIYELHLGS 148
Query: 75 -ICTQEQKCASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGYQVTSFFAASSR 131
+ + SY + +IP + + G+ ++L+ + EH + S+GYQVT ++A +SR
Sbjct: 149 WRKHSDGRHLSYRELADQLIPYVKELGFTHIELLPVAEHPFDGSWGYQVTGYYAPTSR 206
>gnl|CDD|237795 PRK14706, PRK14706, glycogen branching enzyme; Provisional.
Length = 639
Score = 48.8 bits (116), Expect = 1e-07
Identities = 31/109 (28%), Positives = 51/109 (46%), Gaps = 18/109 (16%)
Query: 37 GHAYEQR------IWNPKPQDKHKWTSSK------PKKPDNLKIYESHVGICTQEQK--C 82
G +E R IW +D+ +WT ++ + IYE HVG +
Sbjct: 108 GSFFEVRPNTASIIW----EDRFEWTDTRWMSSRTAGFDQPISIYEVHVGSWARRDDGWF 163
Query: 83 ASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGYQVTSFFAASSR 131
+Y + + + GY V+L+ +MEH + S+GYQVT ++A +SR
Sbjct: 164 LNYRELAHRLGEYVTYMGYTHVELLGVMEHPFDGSWGYQVTGYYAPTSR 212
>gnl|CDD|237794 PRK14705, PRK14705, glycogen branching enzyme; Provisional.
Length = 1224
Score = 48.1 bits (114), Expect = 2e-07
Identities = 25/81 (30%), Positives = 46/81 (56%), Gaps = 6/81 (7%)
Query: 54 KWTSSKPKK-PDN--LKIYESHVGICTQEQKCASYEDFVRVVIPRIVKQGYNAVQLMAIM 110
+W S++ ++ P N + +YE H+G + Y + + ++ + G+ V+ M +
Sbjct: 733 EWMSARAERDPHNSPMSVYEVHLG---SWRLGLGYRELAKELVDYVKWLGFTHVEFMPVA 789
Query: 111 EHAYYASFGYQVTSFFAASSR 131
EH + S+GYQVTS+FA +SR
Sbjct: 790 EHPFGGSWGYQVTSYFAPTSR 810
>gnl|CDD|224440 COG1523, PulA, Type II secretory pathway, pullulanase PulA and
related glycosidases [Carbohydrate transport and
metabolism].
Length = 697
Score = 38.9 bits (91), Expect = 3e-04
Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 22/101 (21%)
Query: 51 DKHKWTSSKPK--KPDNLKIYESHVGICTQ------EQKCASYEDFVR-VVIPRIVKQGY 101
W + KP ++ IYE+HV TQ E+ +Y V+I + G
Sbjct: 155 PLFDWENDKPPRIPWEDTVIYEAHVRDFTQLHPGVPEELRGTYLGLAEPVIIDYLKDLGV 214
Query: 102 NAVQLMAIMEH-----------AYYASFGYQVTSFFAASSR 131
AV+L+ + + +GY +FFA R
Sbjct: 215 TAVELLPVFDFYDEPHLDKSGLNNN--WGYDPLNFFAPEGR 253
>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 = 37.1 bits (87), Expect = 0.001
Identities = 28/108 (25%), Positives = 44/108 (40%), Gaps = 19/108 (17%)
Query: 25 PWATYVTEPPVVGHAYEQRIWNPKPQDKHKWTSSKPKKPD--NLKIYESHVGICTQEQKC 82
P + + E V G + + +P WT + + P L IYE HVG T E
Sbjct: 2 PASRFQPEG-VHGPS---VVVDP---SAFWWTDAGWRGPPLEELVIYELHVGTFTPE--- 51
Query: 83 ASYEDFVRVVIPR---IVKQGYNAVQLMAIMEHAYYASFGYQVTSFFA 127
+++ I R + G A++LM + E ++GY FA
Sbjct: 52 GTFDA----AIERLDYLADLGVTAIELMPVAEFPGERNWGYDGVLPFA 95
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 36.1 bits (83), Expect = 0.003
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 63 PDNLKIYESHVGICTQE--QKCASYEDFVRVVIPRIVKQGYNAVQLMAIMEHAYYASFGY 120
P L IYE H ++ + + +IP + + G+ ++L+ I EH + S+GY
Sbjct: 244 PAPLSIYEVHAASWRRDGHNQPLDWPTLAEQLIPYVQQLGFTHIELLPITEHPFGGSWGY 303
Query: 121 QVTSFFAASSR 131
Q +A ++R
Sbjct: 304 QPLGLYAPTAR 314
>gnl|CDD|200465 cd11326, AmyAc_Glg_debranch, 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. In Escherichia coli, GlgX is
the debranching enzyme and malQ is the
4-alpha-glucanotransferase. TreX, an archaeal
glycogen-debranching enzyme has dual activities like
mammals and yeast, but is structurally similar to GlgX.
TreX exists in two oligomeric states, a dimer and
tetramer. Isoamylase (EC 3.2.1.68) is one of the
starch-debranching enzymes that catalyzes the hydrolysis
of alpha-1,6-glucosidic linkages specific in
alpha-glucans such as amylopectin or glycogen and their
beta-limit dextrins. 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 = 433
Score = 34.4 bits (80), Expect = 0.010
Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 23/97 (23%)
Query: 55 WTSSKPKKP-DNLKIYESHVGICTQ------EQKCASYEDFVR-VVIPRIVKQGYNAVQL 106
++P+ P ++ IYE HV T+ E+ +Y IP + + G AV+L
Sbjct: 4 EGDARPRIPWEDTVIYEMHVRGFTKLHPDVPEELRGTYAGLAEPAKIPYLKELGVTAVEL 63
Query: 107 MAIMEHA------------YYASFGYQVTSFFAASSR 131
+ + Y+ GY +FFA R
Sbjct: 64 LPVHAFDDEEHLVERGLTNYW---GYNTLNFFAPDPR 97
>gnl|CDD|227513 COG5186, PAP1, Poly(A) polymerase [RNA processing and
modification].
Length = 552
Score = 33.0 bits (75), Expect = 0.031
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 17 FYSILRLSPWATYVTEPPVVGHAYEQRIWNPK--PQDK-HKWTSSKPKKP 63
F+ IL W V P+ + R+WNPK P DK H+ P P
Sbjct: 259 FFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYP 308
>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 = 31.0 bits (71), Expect = 0.056
Identities = 6/24 (25%), Positives = 10/24 (41%), Gaps = 1/24 (4%)
Query: 22 RLSPWATYVTEPPVVGHAYEQRIW 45
R+ WA V + P ++ W
Sbjct: 73 RIPAWAKRVVQDP-ETKIFDGVFW 95
>gnl|CDD|200488 cd11350, AmyAc_4, Alpha amylase catalytic domain found in an
uncharacterized protein family. 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
(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 = 390
Score = 31.5 bits (72), Expect = 0.11
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 20/77 (25%)
Query: 59 KPKKPDNLKIYESHVGICTQEQKCASYEDFV-----RVVIPRI---VKQGYNAVQLMAIM 110
+ ++L IYE V DF + VI ++ G NA++LM +
Sbjct: 9 ELPAKEDLVIYELLVR------------DFTERGDFKGVIDKLDYLQDLGVNAIELMPVQ 56
Query: 111 EHAYYASFGYQVTSFFA 127
E S+GY +FA
Sbjct: 57 EFPGNDSWGYNPRHYFA 73
>gnl|CDD|214758 smart00642, Aamy, Alpha-amylase domain.
Length = 166
Score = 30.4 bits (69), Expect = 0.16
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 100 GYNAVQLMAIMEH--AYYASFGYQVTSFFAASSR 131
G A+ L I E Y + GY ++ + R
Sbjct: 32 GVTAIWLSPIFESPQGYPSYHGYDISDYKQIDPR 65
>gnl|CDD|239528 cd03444, Thioesterase_II_repeat1, Thioesterase II (TEII) is
thought to regenerate misprimed nonribosomal peptide
synthetases (NRPSs) as well as modular polyketide
synthases (PKSs) by hydrolyzing acetyl groups bound to
the peptidyl carrier protein (PCP) and acyl carrier
protein (ACP) domains, respectively. TEII has two
tandem asymmetric hot dog folds that are structurally
similar to one found in PaaI thioesterase,
4-hydroxybenzoyl-CoA thioesterase (4HBT) and
beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII
monomer is equivalent to the homodimeric form of the
latter three enzymes. Human TEII is expressed in T
cells and has been shown to bind the product of the
HIV-1 Nef gene.
Length = 104
Score = 27.6 bits (62), Expect = 1.0
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 3/51 (5%)
Query: 1 TLYFILFYSILFYSVLFYSILRLSPWATYVTEPPVVGHA---YEQRIWNPK 48
L+ + L +++ F+ R W Y P G+ E RI+
Sbjct: 41 PLFDASASASLDHAIWFHRPFRADDWLLYEQRSPRAGNGRGLVEGRIFTRD 91
>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 = 28.5 bits (64), Expect = 1.1
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 10/63 (15%)
Query: 68 IYESHVGICTQEQKCASYEDFVRVVIPR---IVKQGYNAVQLMAIMEHAYYASFGYQVTS 124
IYE HVG T E F I + + G A++LM + + +GY
Sbjct: 96 IYELHVGTFTPEG------TF-DAAIEKLPYLADLGITAIELMPVAQFPGTRGWGYDGVL 148
Query: 125 FFA 127
+A
Sbjct: 149 PYA 151
>gnl|CDD|200451 cd00551, AmyAc_family, Alpha amylase catalytic domain family. 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; and 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 this 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 = 260
Score = 27.1 bits (60), Expect = 2.4
Identities = 6/32 (18%), Positives = 10/32 (31%)
Query: 93 IPRIVKQGYNAVQLMAIMEHAYYASFGYQVTS 124
+ + G A+ L I E Y +
Sbjct: 31 LDYLKDLGVTAIWLTPIFESPEYDGYDKDDGY 62
>gnl|CDD|165129 PHA02764, PHA02764, hypothetical protein; Provisional.
Length = 399
Score = 26.8 bits (59), Expect = 3.3
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 13 YSVLFYSILRLSPWATYVTEPPVVG 37
+S FY+I +S W TYV P++G
Sbjct: 87 FSSKFYTIFGISLWLTYVLSQPILG 111
>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 = 26.7 bits (59), Expect = 4.2
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 47 PKPQDKHKWTSSKPKKPDNLKIYE 70
PKP+ KHK S ++ L+ YE
Sbjct: 253 PKPKTKHKLDISSVEEYKKLQKYE 276
>gnl|CDD|239506 cd03413, CbiK_C, Anaerobic cobalamin biosynthetic cobalt chelatase
(CbiK), C-terminal domain. CbiK is part of the
cobalt-early path for cobalamin biosynthesis. It
catalyzes the insertion of cobalt into the oxidized form
of precorrin-2, factor II (sirohydrochlorin), the second
step of the anaerobic branch of vitamin B12
biosynthesis. CbiK belongs to the class II family of
chelatases, and is a homomeric enzyme that does not
require ATP for its enzymatic activity.
Length = 103
Score = 25.7 bits (57), Expect = 4.6
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 92 VIPRIVKQGYNAVQLMAIM----EHA 113
V+ ++ K G V LM +M +HA
Sbjct: 47 VLAKLKKAGIKKVTLMPLMLVAGDHA 72
>gnl|CDD|218315 pfam04892, VanZ, VanZ like family. This family contains several
examples of the VanZ protein, but also contains
examples of phosphotransbutyrylases.
Length = 132
Score = 25.8 bits (57), Expect = 5.2
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 4 FILFYSILFYSVLFYSILRLSPWATYVTEPP 34
F+++ +L +SV+F L++ WA
Sbjct: 2 FLVYLILLVWSVIFALSLQVLAWAFVSAVRS 32
>gnl|CDD|214459 MTH00211, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 597
Score = 26.5 bits (59), Expect = 5.6
Identities = 13/23 (56%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 7 FYSILFYSVLFY---SILRLSPW 26
FYSI F SV Y SIL S W
Sbjct: 79 FYSIFFTSVALYVTWSILEFSLW 101
>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 = 26.5 bits (59), Expect = 5.8
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 36 VGHAYEQRIWNPKPQDKHK 54
+ A E+ ++NPK + +
Sbjct: 31 LSRALERFLFNPKVPPERQ 49
>gnl|CDD|197331 cd09097, Deadenylase_CCR4, C-terminal deadenylase domain of CCR4
and related domains. This subfamily contains the
C-terminal catalytic domain of the deadenylases,
Saccharomyces cerevisiae Ccr4p and two vertebrate
homologs (CCR4a and CCR4b), and related domains. CCR4
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. CCR4 is the major deadenylase subunit of the
CCR4-NOT transcription complex, which contains two
deadenylase subunits and several noncatalytic subunits.
The other deadenylase subunit, Caf1 (called Pop2 in
yeast), is a DEDD-type protein and does not belong in
this superfamily. Saccharomyces cerevisiae CCR4 (or
Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It
is the catalytic subunit of the yeast mRNA deadenylase
(Ccr4p/Pop2p/Not complex). This complex participates in
various ways in mRNA metabolism, including transcription
initiation and elongation, and mRNA degradation. Ccr4p
degrades both poly(A) and single-stranded DNA. There are
two vertebrate homologs of Ccr4p, CCR4a (also called
CCR4-NOT transcription complex subunit 6 or CNOT6) and
CCR4b (also called CNOT6-like or CNOT6L), which
independently associate with other components to form
distinct CCR4-NOT multisubunit complexes. The nuclease
domain of CNOT6 and CNOT6L exhibits Mg2+-dependent
deadenylase activity, with specificity for poly (A) RNA
as substrate. CCR4a is a component of P-bodies and is
necessary for foci formation. CCR4b regulates p27/Kip1
mRNA levels, thereby influencing cell cycle progression.
They both contribute to the prevention of cell death by
regulating insulin-like growth factor-binding protein 5.
Length = 329
Score = 25.7 bits (57), Expect = 9.2
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 75 ICTQEQKCASYEDFVRVVIPRIVKQGYNAV 104
+C QE + YEDF +P + + GY+ V
Sbjct: 46 LCLQEVETDQYEDF---FLPELKQHGYDGV 72
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
0.324 0.136 0.429
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: 6,679,370
Number of extensions: 558949
Number of successful extensions: 840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 830
Number of HSP's successfully gapped: 46
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (24.2 bits)