RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8670
(224 letters)
>gnl|CDD|200467 cd11328, AmyAc_maltase, Alpha amylase catalytic domain found in
maltase (also known as alpha glucosidase) and related
proteins. Maltase (EC 3.2.1.20) hydrolyzes the
terminal, non-reducing (1->4)-linked alpha-D-glucose
residues in maltose, releasing alpha-D-glucose. In most
cases, maltase is equivalent to alpha-glucosidase, but
the term "maltase" emphasizes the disaccharide nature of
the substrate from which glucose is cleaved, and the
term "alpha-glucosidase" emphasizes the bond, whether
the substrate is a disaccharide or polysaccharide. 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 = 470
Score = 230 bits (589), Expect = 9e-74
Identities = 71/122 (58%), Positives = 96/122 (78%), Gaps = 1/122 (0%)
Query: 34 PLEWWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMAD 93
+WW+ +VFY +YPRSFKDS+GDG+GDLKG+ EKL + D+G+ A+W+SPIFKSPM D
Sbjct: 1 DKDWWENAVFYQIYPRSFKDSDGDGIGDLKGITEKLD-YFKDIGIDAIWLSPIFKSPMVD 59
Query: 94 FGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANIPP 153
FGYDISD+ +P+FG ++DFE L LG+K++LDFVPNH+S++HEWF+KS+ P
Sbjct: 60 FGYDISDFTDIDPIFGTMEDFEELIAEAKKLGLKVILDFVPNHSSDEHEWFQKSVKRDEP 119
Query: 154 YK 155
YK
Sbjct: 120 YK 121
>gnl|CDD|200472 cd11333, AmyAc_SI_OligoGlu_DGase, Alpha amylase catalytic domain
found in Sucrose isomerases, oligo-1,6-glucosidase (also
called isomaltase; sucrase-isomaltase; alpha-limit
dextrinase), dextran glucosidase (also called glucan
1,6-alpha-glucosidase), and related proteins. The
sucrose isomerases (SIs) Isomaltulose synthase (EC
5.4.99.11) and Trehalose synthase (EC 5.4.99.16)
catalyze the isomerization of sucrose and maltose to
produce isomaltulose and trehalulose, respectively.
Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the
alpha-1,6-glucosidic linkage of
isomaltooligosaccharides, pannose, and dextran. Unlike
alpha-1,4-glucosidases (EC 3.2.1.20), it fails to
hydrolyze the alpha-1,4-glucosidic bonds of
maltosaccharides. Dextran glucosidase (DGase, EC
3.2.1.70) hydrolyzes alpha-1,6-glucosidic linkages at
the non-reducing end of panose, isomaltooligosaccharides
and dextran to produce alpha-glucose.The common reaction
chemistry of the alpha-amylase family enzymes is based
on a two-step acid catalytic mechanism that requires two
critical carboxylates: one acting as a general acid/base
(Glu) and the other as a nucleophile (Asp). Both
hydrolysis and transglycosylation proceed via the
nucleophilic substitution reaction between the anomeric
carbon, C1 and a nucleophile. Both enzymes contain the
three catalytic residues (Asp, Glu and Asp) common to
the alpha-amylase family as well as two histidine
residues which are predicted to be critical to binding
the glucose residue adjacent to the scissile bond in the
substrates. 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 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 = 428
Score = 203 bits (520), Expect = 8e-64
Identities = 64/117 (54%), Positives = 87/117 (74%), Gaps = 2/117 (1%)
Query: 39 QTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDI 98
+ +V Y +YPRSFKDSNGDG+GDL G+I KL +L DLGV A+W+SPI+ SP D GYDI
Sbjct: 1 KEAVVYQIYPRSFKDSNGDGIGDLPGIISKLD-YLKDLGVDAIWLSPIYPSPQVDNGYDI 59
Query: 99 SDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANI-PPY 154
SDY + +P FG ++DF+ L + H GIKI++D V NHTS++H WF++S ++ PY
Sbjct: 60 SDYRAIDPEFGTMEDFDELIKEAHKRGIKIIMDLVVNHTSDEHPWFQESRSSRDNPY 116
Score = 106 bits (268), Expect = 4e-27
Identities = 35/84 (41%), Positives = 46/84 (54%), Gaps = 23/84 (27%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLRI----------------------KILLDF 200
L DLGV A+W+SPI+ SP D GYDISDY I KI++D
Sbjct: 34 LKDLGVDAIWLSPIYPSPQVDNGYDISDYRAIDPEFGTMEDFDELIKEAHKRGIKIIMDL 93
Query: 201 VPNHTSNQHEWFKKSLANI-PPYS 223
V NHTS++H WF++S ++ PY
Sbjct: 94 VVNHTSDEHPWFQESRSSRDNPYR 117
>gnl|CDD|200470 cd11331, AmyAc_OligoGlu_like, Alpha amylase catalytic domain found
in oligo-1,6-glucosidase (also called isomaltase;
sucrase-isomaltase; alpha-limit dextrinase) and related
proteins. Oligo-1,6-glucosidase (EC 3.2.1.10)
hydrolyzes the alpha-1,6-glucosidic linkage of
isomalto-oligosaccharides, pannose, and dextran. Unlike
alpha-1,4-glucosidases (EC 3.2.1.20), it fails to
hydrolyze the alpha-1,4-glucosidic bonds of
maltosaccharides. 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 = 450
Score = 200 bits (511), Expect = 2e-62
Identities = 73/115 (63%), Positives = 92/115 (80%), Gaps = 1/115 (0%)
Query: 36 EWWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFG 95
WWQT V Y +YPRSF+DSNGDGVGDL+G+I +L +L DLGV AVW+SPI+ SPMADFG
Sbjct: 1 LWWQTGVIYQIYPRSFQDSNGDGVGDLRGIISRLD-YLSDLGVDAVWLSPIYPSPMADFG 59
Query: 96 YDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLAN 150
YD+SDY +PLFG L+DF+ L HA G+K++LDFVPNHTS+QH WF +S ++
Sbjct: 60 YDVSDYCGIDPLFGTLEDFDRLVAEAHARGLKVILDFVPNHTSDQHPWFLESRSS 114
Score = 100 bits (250), Expect = 1e-24
Identities = 38/78 (48%), Positives = 48/78 (61%), Gaps = 22/78 (28%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDY----------------------LRIKILLDF 200
L DLGV AVW+SPI+ SPMADFGYD+SDY +K++LDF
Sbjct: 37 LSDLGVDAVWLSPIYPSPMADFGYDVSDYCGIDPLFGTLEDFDRLVAEAHARGLKVILDF 96
Query: 201 VPNHTSNQHEWFKKSLAN 218
VPNHTS+QH WF +S ++
Sbjct: 97 VPNHTSDQHPWFLESRSS 114
>gnl|CDD|200469 cd11330, AmyAc_OligoGlu, Alpha amylase catalytic domain found in
oligo-1,6-glucosidase (also called isomaltase;
sucrase-isomaltase; alpha-limit dextrinase) and related
proteins. Oligo-1,6-glucosidase (EC 3.2.1.10)
hydrolyzes the alpha-1,6-glucosidic linkage of
isomalto-oligosaccharides, pannose, and dextran. Unlike
alpha-1,4-glucosidases (EC 3.2.1.20), it fails to
hydrolyze the alpha-1,4-glucosidic bonds of
maltosaccharides. 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 = 472
Score = 199 bits (507), Expect = 2e-61
Identities = 66/115 (57%), Positives = 88/115 (76%), Gaps = 1/115 (0%)
Query: 36 EWWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFG 95
WW+ +V Y +YPRSF DSNGDG+GDL G+ EKL ++ LGV A+W+SP FKSPM DFG
Sbjct: 1 PWWRGAVIYQIYPRSFLDSNGDGIGDLPGITEKLD-YIASLGVDAIWLSPFFKSPMKDFG 59
Query: 96 YDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLAN 150
YD+SDY + +PLFG L DF+ L R HALG+K+++D V +HTS+QH WF++S +
Sbjct: 60 YDVSDYCAVDPLFGTLDDFDRLVARAHALGLKVMIDQVLSHTSDQHPWFEESRQS 114
Score = 93.1 bits (232), Expect = 5e-22
Identities = 32/76 (42%), Positives = 44/76 (57%), Gaps = 22/76 (28%)
Query: 165 DLGVGAVWISPIFKSPMADFGYDISDY----------------------LRIKILLDFVP 202
LGV A+W+SP FKSPM DFGYD+SDY L +K+++D V
Sbjct: 39 SLGVDAIWLSPFFKSPMKDFGYDVSDYCAVDPLFGTLDDFDRLVARAHALGLKVMIDQVL 98
Query: 203 NHTSNQHEWFKKSLAN 218
+HTS+QH WF++S +
Sbjct: 99 SHTSDQHPWFEESRQS 114
>gnl|CDD|200494 cd11359, AmyAc_SLC3A1, Alpha amylase catalytic domain found in
Solute Carrier family 3 member 1 proteins. SLC3A1, also
called Neutral and basic amino acid transport protein
rBAT or NBAT, plays a role in amino acid and cystine
absorption. Mutations in the gene encoding SLC3A1 causes
cystinuria, an autosomal recessive disorder
characterized by the failure of proximal tubules to
reabsorb filtered cystine and dibasic amino acids. 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 = 456
Score = 193 bits (493), Expect = 1e-59
Identities = 72/119 (60%), Positives = 93/119 (78%), Gaps = 1/119 (0%)
Query: 37 WWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGY 96
WWQTSV Y +YPRSFKDSNGDG GDLKG+ EKL ++L LGV VW+SPI+KSPM DFGY
Sbjct: 2 WWQTSVIYQIYPRSFKDSNGDGNGDLKGIREKL-DYLKYLGVKTVWLSPIYKSPMKDFGY 60
Query: 97 DISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANIPPYK 155
D+SD+ +P+FG ++DFE L +H G+K+++DFVPNHTS++HEWF+ S + PY
Sbjct: 61 DVSDFTDIDPMFGTMEDFERLLAAMHDRGMKLIMDFVPNHTSDKHEWFQLSRNSTNPYT 119
Score = 94.0 bits (234), Expect = 2e-22
Identities = 37/82 (45%), Positives = 48/82 (58%), Gaps = 22/82 (26%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLRI----------------------KILLDF 200
L LGV VW+SPI+KSPM DFGYD+SD+ I K+++DF
Sbjct: 37 LKYLGVKTVWLSPIYKSPMKDFGYDVSDFTDIDPMFGTMEDFERLLAAMHDRGMKLIMDF 96
Query: 201 VPNHTSNQHEWFKKSLANIPPY 222
VPNHTS++HEWF+ S + PY
Sbjct: 97 VPNHTSDKHEWFQLSRNSTNPY 118
>gnl|CDD|200471 cd11332, AmyAc_OligoGlu_TS, Alpha amylase catalytic domain found in
oligo-1,6-glucosidase (also called isomaltase;
sucrase-isomaltase; alpha-limit dextrinase), trehalose
synthase (also called maltose
alpha-D-glucosyltransferase), and related proteins.
Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the
alpha-1,6-glucosidic linkage of
isomaltooligosaccharides, pannose, and dextran. Unlike
alpha-1,4-glucosidases (EC 3.2.1.20), it fails to
hydrolyze the alpha-1,4-glucosidic bonds of
maltosaccharides. Trehalose synthase (EC 5.4.99.16)
catalyzes the isomerization of maltose to produce
trehalulose. 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 = 481
Score = 187 bits (476), Expect = 7e-57
Identities = 63/117 (53%), Positives = 86/117 (73%), Gaps = 1/117 (0%)
Query: 36 EWWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFG 95
WW+ +V Y +YPRSF D+NGDG+GDL G+ +LP +L LGV A+W+SP + SPMAD G
Sbjct: 1 PWWRDAVVYQVYPRSFADANGDGIGDLAGIRARLP-YLAALGVDAIWLSPFYPSPMADGG 59
Query: 96 YDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANIP 152
YD++DY +PLFG L DF+ L H LG+++++D VPNHTS+QH WF+ +LA P
Sbjct: 60 YDVADYRDVDPLFGTLADFDALVAAAHELGLRVIVDIVPNHTSDQHPWFQAALAAGP 116
Score = 89.6 bits (223), Expect = 8e-21
Identities = 33/80 (41%), Positives = 46/80 (57%), Gaps = 22/80 (27%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDY----------------------LRIKILLDF 200
L LGV A+W+SP + SPMAD GYD++DY L +++++D
Sbjct: 37 LAALGVDAIWLSPFYPSPMADGGYDVADYRDVDPLFGTLADFDALVAAAHELGLRVIVDI 96
Query: 201 VPNHTSNQHEWFKKSLANIP 220
VPNHTS+QH WF+ +LA P
Sbjct: 97 VPNHTSDQHPWFQAALAAGP 116
>gnl|CDD|233851 TIGR02403, trehalose_treC, alpha,alpha-phosphotrehalase. Trehalose
is a glucose disaccharide that serves in many biological
systems as a compatible solute for protection against
hyperosmotic and thermal stress. This family describes
trehalose-6-phosphate hydrolase, product of the treC (or
treA) gene, which is often found together with a
trehalose uptake transporter and a trehalose operon
repressor.
Length = 543
Score = 179 bits (455), Expect = 2e-53
Identities = 65/119 (54%), Positives = 82/119 (68%), Gaps = 1/119 (0%)
Query: 37 WWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGY 96
WWQ V Y +YP+SF DS GDG GDL+G+IEKL ++L LGV +W++P + SP D GY
Sbjct: 1 WWQKKVIYQIYPKSFYDSTGDGTGDLRGIIEKL-DYLKKLGVDYIWLNPFYVSPQKDNGY 59
Query: 97 DISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANIPPYK 155
D+SDY + PLFG + DFE L IKI+LD V NHTS +HEWFKK+LA PY+
Sbjct: 60 DVSDYYAINPLFGTMADFEELVSEAKKRNIKIMLDMVFNHTSTEHEWFKKALAGDSPYR 118
Score = 90.9 bits (226), Expect = 3e-21
Identities = 35/82 (42%), Positives = 43/82 (52%), Gaps = 22/82 (26%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLRI----------------------KILLDF 200
L LGV +W++P + SP D GYD+SDY I KI+LD
Sbjct: 36 LKKLGVDYIWLNPFYVSPQKDNGYDVSDYYAINPLFGTMADFEELVSEAKKRNIKIMLDM 95
Query: 201 VPNHTSNQHEWFKKSLANIPPY 222
V NHTS +HEWFKK+LA PY
Sbjct: 96 VFNHTSTEHEWFKKALAGDSPY 117
>gnl|CDD|200473 cd11334, AmyAc_TreS, Alpha amylase catalytic domain found in
Trehalose synthetase. Trehalose synthetase (TreS)
catalyzes the reversible interconversion of trehalose
and maltose. The enzyme catalyzes the reaction in both
directions, but the preferred substrate is maltose.
Glucose is formed as a by-product of this reaction. It
is believed that the catalytic mechanism may involve the
cutting of the incoming disaccharide and transfer of a
glucose to an enzyme-bound glucose. This enzyme also
catalyzes production of a glucosamine disaccharide from
maltose and glucosamine. 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 = 447
Score = 163 bits (416), Expect = 2e-48
Identities = 52/111 (46%), Positives = 73/111 (65%), Gaps = 1/111 (0%)
Query: 37 WWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGY 96
W++ +V Y L R+F DSNGDG+GD +G+ EKL +L LGV A+W+ P + SP+ D GY
Sbjct: 1 WYKNAVIYQLDVRTFMDSNGDGIGDFRGLTEKLD-YLQWLGVTAIWLLPFYPSPLRDDGY 59
Query: 97 DISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKS 147
DI+DY +P G L DF H GI++++D V NHTS+QH WF+ +
Sbjct: 60 DIADYYGVDPRLGTLGDFVEFLREAHERGIRVIIDLVVNHTSDQHPWFQAA 110
Score = 78.4 bits (194), Expect = 7e-17
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 22/75 (29%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLR----------------------IKILLDF 200
L LGV A+W+ P + SP+ D GYDI+DY I++++D
Sbjct: 36 LQWLGVTAIWLLPFYPSPLRDDGYDIADYYGVDPRLGTLGDFVEFLREAHERGIRVIIDL 95
Query: 201 VPNHTSNQHEWFKKS 215
V NHTS+QH WF+ +
Sbjct: 96 VVNHTSDQHPWFQAA 110
>gnl|CDD|200455 cd11316, AmyAc_bac2_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 Chloroflexi, Dictyoglomi, and Fusobacteria. 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 = 403
Score = 159 bits (405), Expect = 4e-47
Identities = 56/114 (49%), Positives = 82/114 (71%), Gaps = 3/114 (2%)
Query: 42 VFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDY 101
VFY ++ RSF DS+GDG+GDL G+ EKL +L+DLGV +W+ PIF SP + GYD++DY
Sbjct: 2 VFYEIFVRSFYDSDGDGIGDLNGLTEKLD-YLNDLGVNGIWLMPIFPSP-SYHGYDVTDY 59
Query: 102 LSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANI-PPY 154
+ EP +G ++DFE L H GIK+++D V NHTS++H WF+++ ++ PY
Sbjct: 60 YAIEPDYGTMEDFERLIAEAHKRGIKVIIDLVINHTSSEHPWFQEAASSPDSPY 113
Score = 78.0 bits (193), Expect = 8e-17
Identities = 29/83 (34%), Positives = 45/83 (54%), Gaps = 24/83 (28%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLR----------------------IKILLDF 200
L+DLGV +W+ PIF SP + GYD++DY IK+++D
Sbjct: 32 LNDLGVNGIWLMPIFPSP-SYHGYDVTDYYAIEPDYGTMEDFERLIAEAHKRGIKVIIDL 90
Query: 201 VPNHTSNQHEWFKKSLANI-PPY 222
V NHTS++H WF+++ ++ PY
Sbjct: 91 VINHTSSEHPWFQEAASSPDSPY 113
>gnl|CDD|200486 cd11348, AmyAc_2, 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
residues (GH31). The catalytic triad (DED) is not
present here. 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 = 429
Score = 148 bits (377), Expect = 7e-43
Identities = 54/106 (50%), Positives = 73/106 (68%), Gaps = 1/106 (0%)
Query: 42 VFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDY 101
VFY +YP+SF DSNGDG+GDL+G+I KL +++ LG A+W++P F SP D GYD+ DY
Sbjct: 1 VFYEIYPQSFYDSNGDGIGDLQGIISKL-DYIKSLGCNAIWLNPCFDSPFKDAGYDVRDY 59
Query: 102 LSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKS 147
P +G +D L + H GI +LLD VP HTS++H WFK+S
Sbjct: 60 YKVAPRYGTNEDLVRLFDEAHKRGIHVLLDLVPGHTSDEHPWFKES 105
Score = 75.4 bits (186), Expect = 7e-16
Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 22/75 (29%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLR----------------------IKILLDF 200
+ LG A+W++P F SP D GYD+ DY + I +LLD
Sbjct: 31 IKSLGCNAIWLNPCFDSPFKDAGYDVRDYYKVAPRYGTNEDLVRLFDEAHKRGIHVLLDL 90
Query: 201 VPNHTSNQHEWFKKS 215
VP HTS++H WFK+S
Sbjct: 91 VPGHTSDEHPWFKES 105
>gnl|CDD|182849 PRK10933, PRK10933, trehalose-6-phosphate hydrolase; Provisional.
Length = 551
Score = 147 bits (373), Expect = 2e-41
Identities = 54/122 (44%), Positives = 83/122 (68%), Gaps = 1/122 (0%)
Query: 34 PLEWWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMAD 93
WWQ V Y +YP+SF+D+ G G GDL+G+ ++L ++L LGV A+W++P + SP D
Sbjct: 4 LPHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVTQRL-DYLQKLGVDAIWLTPFYVSPQVD 62
Query: 94 FGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANIPP 153
GYD+++Y + +P +G L DF+ L + + GI+I+LD V NHTS QH WF+++L P
Sbjct: 63 NGYDVANYTAIDPTYGTLDDFDELVAQAKSRGIRIILDMVFNHTSTQHAWFREALNKESP 122
Query: 154 YK 155
Y+
Sbjct: 123 YR 124
Score = 70.2 bits (172), Expect = 4e-14
Identities = 30/82 (36%), Positives = 42/82 (51%), Gaps = 22/82 (26%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYL----------------------RIKILLDF 200
L LGV A+W++P + SP D GYD+++Y I+I+LD
Sbjct: 42 LQKLGVDAIWLTPFYVSPQVDNGYDVANYTAIDPTYGTLDDFDELVAQAKSRGIRIILDM 101
Query: 201 VPNHTSNQHEWFKKSLANIPPY 222
V NHTS QH WF+++L PY
Sbjct: 102 VFNHTSTQHAWFREALNKESPY 123
>gnl|CDD|223443 COG0366, AmyA, Glycosidases [Carbohydrate transport and
metabolism].
Length = 505
Score = 144 bits (364), Expect = 1e-40
Identities = 63/121 (52%), Positives = 83/121 (68%), Gaps = 7/121 (5%)
Query: 41 SVFYHLYPRSFKDSNG------DGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADF 94
+V Y +YP F DSNG DG GDLKG+ EKL +L +LGV A+W+SPIF+SP AD
Sbjct: 1 AVIYQIYPDRFADSNGSNGPDYDGGGDLKGITEKLD-YLKELGVDAIWLSPIFESPQADH 59
Query: 95 GYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANIPPY 154
GYD+SDY +P FG +DF+ L E H GIK++LD V NHTS++H WFK++ ++ P
Sbjct: 60 GYDVSDYTKVDPHFGTEEDFKELVEEAHKRGIKVILDLVFNHTSDEHPWFKEARSSKPNP 119
Query: 155 K 155
K
Sbjct: 120 K 120
Score = 78.1 bits (192), Expect = 9e-17
Identities = 35/85 (41%), Positives = 49/85 (57%), Gaps = 22/85 (25%)
Query: 160 LARLHDLGVGAVWISPIFKSPMADFGYDISDYLR----------------------IKIL 197
L L +LGV A+W+SPIF+SP AD GYD+SDY + IK++
Sbjct: 35 LDYLKELGVDAIWLSPIFESPQADHGYDVSDYTKVDPHFGTEEDFKELVEEAHKRGIKVI 94
Query: 198 LDFVPNHTSNQHEWFKKSLANIPPY 222
LD V NHTS++H WFK++ ++ P
Sbjct: 95 LDLVFNHTSDEHPWFKEARSSKPNP 119
>gnl|CDD|233874 TIGR02456, treS_nterm, trehalose synthase. Trehalose synthase
interconverts maltose and alpha, alpha-trehalose by
transglucosylation. This is one of at least three
mechanisms for biosynthesis of trehalose, an important
and widespread compatible solute. However, it is not
driven by phosphate activation of sugars and its
physiological role may tend toward trehalose
degradation. This view is accentuated by numerous
examples of fusion to a probable maltokinase domain. The
sequence region described by this model is found both as
the whole of a trehalose synthase and as the N-terminal
region of a larger fusion protein that includes
trehalose synthase activity. Several of these fused
trehalose synthases have a domain homologous to proteins
with maltokinase activity from Actinoplanes
missouriensis and Streptomyces coelicolor
(PMID:15378530) [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 539
Score = 141 bits (358), Expect = 2e-39
Identities = 54/116 (46%), Positives = 81/116 (69%), Gaps = 1/116 (0%)
Query: 36 EWWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFG 95
W++ +VFY ++ RSF DSNGDG+GD G+ KL +L LGV A+W+ P F+SP+ D G
Sbjct: 1 LWYKDAVFYEVHVRSFFDSNGDGIGDFPGLTSKLD-YLKWLGVDALWLLPFFQSPLRDDG 59
Query: 96 YDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANI 151
YD+SDY + P FG + DF+ + HA G+++++D V NHTS+QH WF+++ +N
Sbjct: 60 YDVSDYRAILPEFGTIDDFKDFVDEAHARGMRVIIDLVLNHTSDQHPWFQEARSNP 115
Score = 66.3 bits (162), Expect = 9e-13
Identities = 31/84 (36%), Positives = 45/84 (53%), Gaps = 22/84 (26%)
Query: 158 SLLARLHDLGVGAVWISPIFKSPMADFGYDISDYLRI----------------------K 195
S L L LGV A+W+ P F+SP+ D GYD+SDY I +
Sbjct: 32 SKLDYLKWLGVDALWLLPFFQSPLRDDGYDVSDYRAILPEFGTIDDFKDFVDEAHARGMR 91
Query: 196 ILLDFVPNHTSNQHEWFKKSLANI 219
+++D V NHTS+QH WF+++ +N
Sbjct: 92 VIIDLVLNHTSDQHPWFQEARSNP 115
>gnl|CDD|214758 smart00642, Aamy, Alpha-amylase domain.
Length = 166
Score = 132 bits (335), Expect = 3e-39
Identities = 54/96 (56%), Positives = 70/96 (72%), Gaps = 4/96 (4%)
Query: 47 YPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPM---ADFGYDISDYLS 103
YP F D NGDG GDL+G+IEKL ++L DLGV A+W+SPIF+SP + GYDISDY
Sbjct: 3 YPDRFADGNGDGGGDLQGIIEKL-DYLKDLGVTAIWLSPIFESPQGYPSYHGYDISDYKQ 61
Query: 104 FEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSN 139
+P FG ++DF+ L + HA GIK++LD V NHTS+
Sbjct: 62 IDPRFGTMEDFKELVDAAHARGIKVILDVVINHTSD 97
Score = 63.9 bits (156), Expect = 6e-13
Identities = 29/70 (41%), Positives = 37/70 (52%), Gaps = 25/70 (35%)
Query: 163 LHDLGVGAVWISPIFKSPM---ADFGYDISDYLR----------------------IKIL 197
L DLGV A+W+SPIF+SP + GYDISDY + IK++
Sbjct: 28 LKDLGVTAIWLSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHARGIKVI 87
Query: 198 LDFVPNHTSN 207
LD V NHTS+
Sbjct: 88 LDVVINHTSD 97
>gnl|CDD|215737 pfam00128, Alpha-amylase, Alpha amylase, catalytic domain. Alpha
amylase is classified as family 13 of the glycosyl
hydrolases. The structure is an 8 stranded alpha/beta
barrel containing the active site, interrupted by a ~70
a.a. calcium-binding domain protruding between beta
strand 3 and alpha helix 3, and a carboxyl-terminal
Greek key beta-barrel domain.
Length = 314
Score = 135 bits (342), Expect = 1e-38
Identities = 50/97 (51%), Positives = 72/97 (74%), Gaps = 2/97 (2%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLKDFETLKE 119
GDL+G+I+KL +L DLGV A+W+SPIF SP + GYDI+DY +P FG + DF+ L +
Sbjct: 1 GDLQGIIDKLD-YLKDLGVTAIWLSPIFDSPQSYHGYDITDYYKIDPHFGTMDDFKELID 59
Query: 120 RLHALGIKILLDFVPNHTSNQHEWFKKSLANI-PPYK 155
+ H GIK++LD VPNHTS++H WF++S ++ PY+
Sbjct: 60 KAHERGIKVILDLVPNHTSDEHAWFQESRSSKDNPYR 96
Score = 86.2 bits (214), Expect = 5e-20
Identities = 35/84 (41%), Positives = 48/84 (57%), Gaps = 23/84 (27%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLR----------------------IKILLDF 200
L DLGV A+W+SPIF SP + GYDI+DY + IK++LD
Sbjct: 13 LKDLGVTAIWLSPIFDSPQSYHGYDITDYYKIDPHFGTMDDFKELIDKAHERGIKVILDL 72
Query: 201 VPNHTSNQHEWFKKSLANI-PPYS 223
VPNHTS++H WF++S ++ PY
Sbjct: 73 VPNHTSDEHAWFQESRSSKDNPYR 96
>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 = 113 bits (283), Expect = 1e-30
Identities = 46/101 (45%), Positives = 61/101 (60%), Gaps = 7/101 (6%)
Query: 42 VFYHLYPRSFKDSN---GDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDI 98
V Y L+P F D + GDG GDLKG+I+KL +L DLGV A+W++PIF+SP D
Sbjct: 1 VIYQLFPDRFTDGDSSGGDGGGDLKGIIDKLD-YLKDLGVTAIWLTPIFESPEYDGYDKD 59
Query: 99 S---DYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNH 136
DY +P G +DF+ L + H GIK++LD V NH
Sbjct: 60 DGYLDYYEIDPRLGTEEDFKELVKAAHKRGIKVILDLVFNH 100
Score = 44.5 bits (105), Expect = 2e-05
Identities = 22/68 (32%), Positives = 28/68 (41%), Gaps = 25/68 (36%)
Query: 162 RLHDLGVGAVWISPIFKSPMADFGYDISDYLR-------------------------IKI 196
L DLGV A+W++PIF+SP D YL IK+
Sbjct: 33 YLKDLGVTAIWLTPIFESPEYDGYDKDDGYLDYYEIDPRLGTEEDFKELVKAAHKRGIKV 92
Query: 197 LLDFVPNH 204
+LD V NH
Sbjct: 93 ILDLVFNH 100
>gnl|CDD|200477 cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in
cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase
(NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC
3.2.1.133) catalyze the hydrolysis of alpha-(1,4)
glycosidic linkages on a number of substrates including
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. Since these
proteins are nearly indistinguishable from each other,
they are referred to as cyclomaltodextrinases (CMDs).
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 = 389
Score = 111 bits (279), Expect = 8e-29
Identities = 39/91 (42%), Positives = 60/91 (65%), Gaps = 2/91 (2%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLKDFETLKE 119
GDL+G+IEKL +L DLGV A++++PIF++P ++ YD +DY +P G +DF+ L E
Sbjct: 53 GDLQGIIEKLD-YLKDLGVNAIYLNPIFEAP-SNHKYDTADYFKIDPHLGTEEDFKELVE 110
Query: 120 RLHALGIKILLDFVPNHTSNQHEWFKKSLAN 150
H GI+++LD V NHT + +F+ L
Sbjct: 111 EAHKRGIRVILDGVFNHTGDDSPYFQDVLKY 141
Score = 58.6 bits (143), Expect = 3e-10
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 23/78 (29%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLRI----------------------KILLDF 200
L DLGV A++++PIF++P ++ YD +DY +I +++LD
Sbjct: 65 LKDLGVNAIYLNPIFEAP-SNHKYDTADYFKIDPHLGTEEDFKELVEEAHKRGIRVILDG 123
Query: 201 VPNHTSNQHEWFKKSLAN 218
V NHT + +F+ L
Sbjct: 124 VFNHTGDDSPYFQDVLKY 141
>gnl|CDD|200452 cd11313, AmyAc_arch_bac_AmyA, Alpha amylase catalytic domain found
in archaeal and 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, bacteroidetes, and proteobacteria.
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 = 336
Score = 102 bits (257), Expect = 5e-26
Identities = 36/116 (31%), Positives = 57/116 (49%), Gaps = 12/116 (10%)
Query: 37 WWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIF------KSP 90
W + +V Y + R F G K + + LP L DLGV +W+ PI +
Sbjct: 1 WLRDAVIYEVNVRQFTPE-----GTFKAVTKDLP-RLKDLGVDILWLMPIHPIGEKNRKG 54
Query: 91 MADFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKK 146
Y + DY + P +G L+DF+ L + H G+K++LD+V NHT+ H ++
Sbjct: 55 SLGSPYAVKDYRAVNPEYGTLEDFKALVDEAHDRGMKVILDWVANHTAWDHPLVEE 110
>gnl|CDD|236759 PRK10785, PRK10785, maltodextrin glucosidase; Provisional.
Length = 598
Score = 95.8 bits (239), Expect = 7e-23
Identities = 49/153 (32%), Positives = 67/153 (43%), Gaps = 38/153 (24%)
Query: 27 VDVPIQEPLEWWQTSVFYHLYPRSFKDSNG-----DGV---------------------- 59
VDVP Q P +W VFY ++P F S D V
Sbjct: 109 VDVPDQGP-QWVADQVFYQIFPDRFARSLPREAVQDHVYYHHAAGQEIILRDWDEPVTAQ 167
Query: 60 --------GDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDL 111
GDL G+ EKLP +L LGV A++++PIF +P + YD DY +P G
Sbjct: 168 AGGSTFYGGDLDGISEKLP-YLKKLGVTALYLNPIFTAP-SVHKYDTEDYRHVDPQLGGD 225
Query: 112 KDFETLKERLHALGIKILLDFVPNHTSNQHEWF 144
L+ G++++LD V NHT + H WF
Sbjct: 226 AALLRLRHATQQRGMRLVLDGVFNHTGDSHPWF 258
Score = 52.7 bits (127), Expect = 4e-08
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 23/72 (31%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLRI----------------------KILLDF 200
L LGV A++++PIF +P + YD DY + +++LD
Sbjct: 188 LKKLGVTALYLNPIFTAP-SVHKYDTEDYRHVDPQLGGDAALLRLRHATQQRGMRLVLDG 246
Query: 201 VPNHTSNQHEWF 212
V NHT + H WF
Sbjct: 247 VFNHTGDSHPWF 258
>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 = 94.9 bits (237), Expect = 1e-22
Identities = 42/97 (43%), Positives = 60/97 (61%), Gaps = 3/97 (3%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMA--DFGYDISDYLSFEPLFGDLKDFETL 117
GDLKG+ EK+P +L +LGV + + P+ K P D GY +SDY +P G ++D L
Sbjct: 83 GDLKGLAEKIP-YLKELGVTYLHLMPLLKPPEGDNDGGYAVSDYREVDPRLGTMEDLRAL 141
Query: 118 KERLHALGIKILLDFVPNHTSNQHEWFKKSLANIPPY 154
L GI ++LDFV NHT+++HEW +K+ A P Y
Sbjct: 142 AAELRERGISLVLDFVLNHTADEHEWAQKARAGDPEY 178
Score = 51.0 bits (123), Expect = 1e-07
Identities = 30/84 (35%), Positives = 42/84 (50%), Gaps = 24/84 (28%)
Query: 163 LHDLGVGAVWISPIFKSPMA--DFGYDISDY-------------------LR---IKILL 198
L +LGV + + P+ K P D GY +SDY LR I ++L
Sbjct: 95 LKELGVTYLHLMPLLKPPEGDNDGGYAVSDYREVDPRLGTMEDLRALAAELRERGISLVL 154
Query: 199 DFVPNHTSNQHEWFKKSLANIPPY 222
DFV NHT+++HEW +K+ A P Y
Sbjct: 155 DFVLNHTADEHEWAQKARAGDPEY 178
>gnl|CDD|200459 cd11320, AmyAc_AmyMalt_CGTase_like, Alpha amylase catalytic domain
found in maltogenic amylases, cyclodextrin
glycosyltransferase, and related proteins. Enzymes such
as amylases, cyclomaltodextrinase (CDase), and
cyclodextrin glycosyltransferase (CGTase) degrade starch
to smaller oligosaccharides by hydrolyzing the
alpha-D-(1,4) linkages between glucose residues. In the
case of CGTases, an additional cyclization reaction is
catalyzed yielding mixtures of cyclic oligosaccharides
which are referred to as alpha-, beta-, or
gamma-cyclodextrins (CDs), consisting of six, seven, or
eight glucose residues, respectively. CGTases are
characterized depending on the major product of the
cyclization reaction. Besides having similar catalytic
site residues, amylases and CGTases contain carbohydrate
binding domains that are distant from the active site
and are implicated in attaching the enzyme to raw starch
granules and in guiding the amylose chain into the
active site. The maltogenic alpha-amylase from Bacillus
is a five-domain structure, unlike most alpha-amylases,
but similar to that of cyclodextrin glycosyltransferase.
In addition to the A, B, and C domains, they have a
domain D and a starch-binding domain E. Maltogenic
amylase is an endo-acting amylase that has activity on
cyclodextrins, terminally modified linear maltodextrins,
and amylose. 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 = 389
Score = 88.9 bits (221), Expect = 9e-21
Identities = 39/88 (44%), Positives = 54/88 (61%), Gaps = 10/88 (11%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFK---SPMADF------GYDISDYLSFEPLFGD 110
GD +G+I+KLP +L DLGV A+WISP + SP+ GY D+ FG
Sbjct: 44 GDWQGIIDKLP-YLKDLGVTAIWISPPVENINSPIEGGGNTGYHGYWARDFKRTNEHFGT 102
Query: 111 LKDFETLKERLHALGIKILLDFVPNHTS 138
+DF+ L + HA GIK+++DFVPNH+S
Sbjct: 103 WEDFDELVDAAHANGIKVIIDFVPNHSS 130
Score = 43.8 bits (104), Expect = 3e-05
Identities = 25/75 (33%), Positives = 33/75 (44%), Gaps = 31/75 (41%)
Query: 163 LHDLGVGAVWISPIFK---SPMADF------GYDISDYLR-------------------- 193
L DLGV A+WISP + SP+ GY D+ R
Sbjct: 56 LKDLGVTAIWISPPVENINSPIEGGGNTGYHGYWARDFKRTNEHFGTWEDFDELVDAAHA 115
Query: 194 --IKILLDFVPNHTS 206
IK+++DFVPNH+S
Sbjct: 116 NGIKVIIDFVPNHSS 130
>gnl|CDD|200479 cd11340, AmyAc_bac_CMD_like_3, Alpha amylase catalytic domain found
in bacterial cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54),
neopullulanase (NPase; EC 3.2.1.135), and maltogenic
amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of
alpha-(1,4) glycosidic linkages on a number of
substrates including cyclomaltodextrins (CDs), pullulan,
and starch. These enzymes hydrolyze CDs and starch to
maltose and pullulan to panose by cleavage of alpha-1,4
glycosidic bonds whereas alpha-amylases essentially lack
activity on CDs and pullulan. They also catalyze
transglycosylation of oligosaccharides to the C3-, C4-
or C6-hydroxyl groups of various acceptor sugar
molecules. Since these proteins are nearly
indistinguishable from each other, they are referred to
as cyclomaltodextrinases (CMDs). This group of CMDs is
bacterial. 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 = 407
Score = 85.3 bits (212), Expect = 2e-19
Identities = 34/89 (38%), Positives = 60/89 (67%), Gaps = 4/89 (4%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADF---GYDISDYLSFEPLFGDLKDFET 116
GD++G+I+ L ++L DLGV A+W++P+ ++ M + GY +D+ +P FG +D++
Sbjct: 42 GDIQGIIDHL-DYLQDLGVTAIWLTPLLENDMPSYSYHGYAATDFYRIDPRFGSNEDYKE 100
Query: 117 LKERLHALGIKILLDFVPNHTSNQHEWFK 145
L + HA G+K+++D VPNH ++H W K
Sbjct: 101 LVSKAHARGMKLIMDMVPNHCGSEHWWMK 129
Score = 46.1 bits (110), Expect = 6e-06
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 25/76 (32%)
Query: 163 LHDLGVGAVWISPIFKSPMADF---GYDISDYLRI----------------------KIL 197
L DLGV A+W++P+ ++ M + GY +D+ RI K++
Sbjct: 54 LQDLGVTAIWLTPLLENDMPSYSYHGYAATDFYRIDPRFGSNEDYKELVSKAHARGMKLI 113
Query: 198 LDFVPNHTSNQHEWFK 213
+D VPNH ++H W K
Sbjct: 114 MDMVPNHCGSEHWWMK 129
>gnl|CDD|200478 cd11339, AmyAc_bac_CMD_like_2, Alpha amylase catalytic domain found
in bacterial cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54),
neopullulanase (NPase; EC 3.2.1.135), and maltogenic
amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of
alpha-(1,4) glycosidic linkages on a number of
substrates including cyclomaltodextrins (CDs), pullulan,
and starch. These enzymes hydrolyze CDs and starch to
maltose and pullulan to panose by cleavage of alpha-1,4
glycosidic bonds whereas alpha-amylases essentially lack
activity on CDs and pullulan. They also catalyze
transglycosylation of oligosaccharides to the C3-, C4-
or C6-hydroxyl groups of various acceptor sugar
molecules. Since these proteins are nearly
indistinguishable from each other, they are referred to
as cyclomaltodextrinases (CMDs). This group of CMDs is
bacterial. 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 = 344
Score = 81.5 bits (202), Expect = 3e-18
Identities = 34/86 (39%), Positives = 50/86 (58%), Gaps = 7/86 (8%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFKSPM-----ADF-GYDISDYLSFEPLFGDLKD 113
GD KG+I+KL ++ DLG A+WI+P+ K+ A + GY D+ +P G D
Sbjct: 42 GDFKGLIDKLD-YIKDLGFTAIWITPVVKNRSVQAGSAGYHGYWGYDFYRIDPHLGTDAD 100
Query: 114 FETLKERLHALGIKILLDFVPNHTSN 139
+ L + HA GIK++LD V NHT +
Sbjct: 101 LQDLIDAAHARGIKVILDIVVNHTGD 126
Score = 42.6 bits (101), Expect = 7e-05
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 28/71 (39%)
Query: 165 DLGVGAVWISPIFKSPM-----ADF-GYDISDYLR----------------------IKI 196
DLG A+WI+P+ K+ A + GY D+ R IK+
Sbjct: 56 DLGFTAIWITPVVKNRSVQAGSAGYHGYWGYDFYRIDPHLGTDADLQDLIDAAHARGIKV 115
Query: 197 LLDFVPNHTSN 207
+LD V NHT +
Sbjct: 116 ILDIVVNHTGD 126
>gnl|CDD|200476 cd11337, AmyAc_CMD_like, Alpha amylase catalytic domain found in
cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase
(NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC
3.2.1.133) catalyze the hydrolysis of alpha-(1,4)
glycosidic linkages on a number of substrates including
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. Since these
proteins are nearly indistinguishable from each other,
they are referred to as cyclomaltodextrinases (CMDs).
This group of CMDs is mainly bacterial. 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 = 328
Score = 77.6 bits (192), Expect = 6e-17
Identities = 38/108 (35%), Positives = 55/108 (50%), Gaps = 9/108 (8%)
Query: 42 VFYHLYPRSF------KDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFG 95
+FYH+YP F D +G L + + LP HL +LG A+++ P+F+S G
Sbjct: 1 IFYHIYPLGFCGAPIRNDFDGPPEHRLLKLEDWLP-HLKELGCNALYLGPVFES--DSHG 57
Query: 96 YDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEW 143
YD DY + G +DF+ L LH GI+++LD V NH W
Sbjct: 58 YDTRDYYRIDRRLGTNEDFKALVAALHERGIRVVLDGVFNHVGRDFFW 105
Score = 43.7 bits (104), Expect = 3e-05
Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 24/74 (32%)
Query: 160 LARLHDLGVGAVWISPIFKSPMADFGYDISDYLR----------------------IKIL 197
L L +LG A+++ P+F+S GYD DY R I+++
Sbjct: 34 LPHLKELGCNALYLGPVFES--DSHGYDTRDYYRIDRRLGTNEDFKALVAALHERGIRVV 91
Query: 198 LDFVPNHTSNQHEW 211
LD V NH W
Sbjct: 92 LDGVFNHVGRDFFW 105
>gnl|CDD|200490 cd11353, AmyAc_euk_bac_CMD_like, Alpha amylase catalytic domain
found in eukaryotic and bacterial cyclomaltodextrinases
and related proteins. Cyclomaltodextrinase (CDase;
EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and
maltogenic amylase (MA; EC 3.2.1.133) catalyze the
hydrolysis of alpha-(1,4) glycosidic linkages on a
number of substrates including cyclomaltodextrins (CDs),
pullulan, and starch. These enzymes hydrolyze CDs and
starch to maltose and pullulan to panose by cleavage of
alpha-1,4 glycosidic bonds whereas alpha-amylases
essentially lack activity on CDs and pullulan. They also
catalyze transglycosylation of oligosaccharides to the
C3-, C4- or C6-hydroxyl groups of various acceptor sugar
molecules. Since these proteins are nearly
indistinguishable from each other, they are referred to
as cyclomaltodextrinases (CMDs). This group of CMDs is
mainly bacterial. 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 = 366
Score = 74.9 bits (185), Expect = 6e-16
Identities = 39/104 (37%), Positives = 59/104 (56%), Gaps = 11/104 (10%)
Query: 41 SVFYHLYPRSF----KDSNGDGVGDLKGMIEKLPE---HLHDLGVGAVWISPIFKSPMAD 93
+VFYH+YP F K+++ DG + I KL + HL LG+ A++ P+F+S
Sbjct: 2 AVFYHIYPLGFCGAPKENDFDGE--TEHRILKLEDWIPHLKKLGINAIYFGPVFES--DS 57
Query: 94 FGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHT 137
GYD DY + G +DF+ + ++LH GIK++LD V NH
Sbjct: 58 HGYDTRDYYKIDRRLGTNEDFKAVCKKLHENGIKVVLDGVFNHV 101
Score = 39.1 bits (92), Expect = 0.001
Identities = 19/65 (29%), Positives = 27/65 (41%), Gaps = 24/65 (36%)
Query: 163 LHDLGVGAVWISPIFKSPMADFGYDISDYLR----------------------IKILLDF 200
L LG+ A++ P+F+S GYD DY + IK++LD
Sbjct: 39 LKKLGINAIYFGPVFES--DSHGYDTRDYYKIDRRLGTNEDFKAVCKKLHENGIKVVLDG 96
Query: 201 VPNHT 205
V NH
Sbjct: 97 VFNHV 101
>gnl|CDD|200489 cd11352, AmyAc_5, 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
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 = 443
Score = 73.5 bits (181), Expect = 3e-15
Identities = 33/83 (39%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMAD---FGYDISDYLSFEPLFGDLKDFET 116
G LKG+ KL +L LGV A+W+SP+FK GY I ++L +P FG +D
Sbjct: 47 GTLKGVRSKL-GYLKRLGVTALWLSPVFKQRPELETYHGYGIQNFLDVDPRFGTREDLRD 105
Query: 117 LKERLHALGIKILLDFVPNHTSN 139
L + HA GI ++LD + NH+ +
Sbjct: 106 LVDAAHARGIYVILDIILNHSGD 128
Score = 39.2 bits (92), Expect = 9e-04
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 25/70 (35%)
Query: 163 LHDLGVGAVWISPIFKSPMAD---FGYDISDYLR----------------------IKIL 197
L LGV A+W+SP+FK GY I ++L I ++
Sbjct: 59 LKRLGVTALWLSPVFKQRPELETYHGYGIQNFLDVDPRFGTREDLRDLVDAAHARGIYVI 118
Query: 198 LDFVPNHTSN 207
LD + NH+ +
Sbjct: 119 LDIILNHSGD 128
>gnl|CDD|200475 cd11336, AmyAc_MTSase, Alpha amylase catalytic domain found in
maltooligosyl trehalose synthase (MTSase).
Maltooligosyl trehalose synthase (MTSase) domain. MTSase
and maltooligosyl trehalose trehalohydrolase (MTHase)
work together to produce trehalose. MTSase is
responsible for converting the alpha-1,4-glucosidic
linkage to an alpha,alpha-1,1-glucosidic linkage at the
reducing end of the maltooligosaccharide through an
intramolecular transglucosylation reaction, while MTHase
hydrolyzes the penultimate alpha-1,4 linkage of the
reducing end, resulting in the release of trehalose. 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 = 660
Score = 70.2 bits (173), Expect = 4e-14
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 72 HLHDLGVGAVWISPIFKS-PMADFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILL 130
+L DLG+ ++ SPI + P + GYD+ D+ P G + L L A G+ ++L
Sbjct: 22 YLADLGISHLYASPILTARPGSTHGYDVVDHTRINPELGGEEGLRRLAAALRAHGMGLIL 81
Query: 131 DFVPNH 136
D VPNH
Sbjct: 82 DIVPNH 87
Score = 46.3 bits (111), Expect = 5e-06
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 23/71 (32%)
Query: 157 ASLLARLHDLGVGAVWISPIFKS-PMADFGYDISDYLRI--------------------- 194
A+L+ L DLG+ ++ SPI + P + GYD+ D+ RI
Sbjct: 17 AALVPYLADLGISHLYASPILTARPGSTHGYDVVDHTRINPELGGEEGLRRLAAALRAHG 76
Query: 195 -KILLDFVPNH 204
++LD VPNH
Sbjct: 77 MGLILDIVPNH 87
>gnl|CDD|237737 PRK14507, PRK14507, putative bifunctional
4-alpha-glucanotransferase/malto-oligosyltrehalose
synthase; Provisional.
Length = 1693
Score = 67.4 bits (165), Expect = 5e-13
Identities = 35/98 (35%), Positives = 45/98 (45%), Gaps = 5/98 (5%)
Query: 65 MIEKLPEHLHDLGVGAVWISPIFKS-PMADFGYDISDYLSFEPLFGDLKDFETLKERLHA 123
LP +L LG+ V+ SPI K+ P + GYDI D+ P G + FE L A
Sbjct: 760 AEAILP-YLAALGISHVYASPILKARPGSTHGYDIVDHSQINPEIGGEEGFERFCAALKA 818
Query: 124 LGIKILLDFVPNH---TSNQHEWFKKSLANIPPYKCAS 158
G+ LLD VPNH + W+ L N P A
Sbjct: 819 HGLGQLLDIVPNHMGVGGADNPWWLDVLENGPASPAAD 856
Score = 37.8 bits (88), Expect = 0.004
Identities = 23/69 (33%), Positives = 30/69 (43%), Gaps = 23/69 (33%)
Query: 159 LLARLHDLGVGAVWISPIFKS-PMADFGYDISDYLRI----------------------K 195
+L L LG+ V+ SPI K+ P + GYDI D+ +I
Sbjct: 763 ILPYLAALGISHVYASPILKARPGSTHGYDIVDHSQINPEIGGEEGFERFCAALKAHGLG 822
Query: 196 ILLDFVPNH 204
LLD VPNH
Sbjct: 823 QLLDIVPNH 831
>gnl|CDD|237739 PRK14510, PRK14510, putative bifunctional
4-alpha-glucanotransferase/glycogen debranching enzyme;
Provisional.
Length = 1221
Score = 66.8 bits (163), Expect = 8e-13
Identities = 41/171 (23%), Positives = 64/171 (37%), Gaps = 28/171 (16%)
Query: 38 WQTSVFYHLYPRSFKDSNGDGVG-DLKGMIEKLPE-----HLHDLGVGAVWISPIFKS-- 89
W S Y + R F D +L+G KL +L LGV V ++PIF S
Sbjct: 156 WDDSPLYEMNVRGFT-LRHDFFPGNLRGTFAKLAAPEAISYLKKLGVSIVELNPIFASVD 214
Query: 90 --------PMADFGYDISDYLSFEPLFG--DLKDFETLKERLHALGIKILLDFVPNHT-S 138
+GY+ +L+ +P ++F + + GI ++LD V NHT
Sbjct: 215 EHHLPQLGLSNYWGYNTVAFLAPDPRLAPGGEEEFAQAIKEAQSAGIAVILDVVFNHTGE 274
Query: 139 NQHE---WFKKSLANIPPYKCASLLARLH--DLGVG---AVWISPIFKSPM 181
+ H N P Y+ + + G G + I + PM
Sbjct: 275 SNHYGPTLSAYGSDNSPYYRLEPGNPKEYENWWGCGNLPNLERPFILRLPM 325
>gnl|CDD|200491 cd11354, AmyAc_bac_CMD_like, Alpha amylase catalytic domain found
in bacterial cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54),
neopullulanase (NPase; EC 3.2.1.135), and maltogenic
amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of
alpha-(1,4) glycosidic linkages on a number of
substrates including cyclomaltodextrins (CDs), pullulan,
and starch. These enzymes hydrolyze CDs and starch to
maltose and pullulan to panose by cleavage of alpha-1,4
glycosidic bonds whereas alpha-amylases essentially lack
activity on CDs and pullulan. They also catalyze
transglycosylation of oligosaccharides to the C3-, C4-
or C6-hydroxyl groups of various acceptor sugar
molecules. Since these proteins are nearly
indistinguishable from each other, they are referred to
as cyclomaltodextrinases (CMDs). This group of CMDs is
bacterial. 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 = 357
Score = 63.9 bits (156), Expect = 5e-12
Identities = 35/124 (28%), Positives = 55/124 (44%), Gaps = 16/124 (12%)
Query: 37 WWQTSVFYHLYPRSF-------KDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKS 89
WW H+YP F ++ L + L + +LG + + P+F+S
Sbjct: 4 WW------HVYPLGFVGAPIRPREPEAAVEHRLDRLEPWLD-YAVELGCNGLLLGPVFES 56
Query: 90 PMADFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLA 149
A GYD D+ +P GD +DF+ L H G+++LLD V NH H ++L
Sbjct: 57 --ASHGYDTLDHYRIDPRLGDDEDFDALIAAAHERGLRVLLDGVFNHVGRSHPAVAQALE 114
Query: 150 NIPP 153
+ P
Sbjct: 115 DGPG 118
Score = 39.2 bits (92), Expect = 8e-04
Identities = 24/91 (26%), Positives = 35/91 (38%), Gaps = 31/91 (34%)
Query: 160 LARLH-------DLGVGAVWISPIFKSPMADFGYDISDYLRI------------------ 194
L RL +LG + + P+F+S A GYD D+ RI
Sbjct: 30 LDRLEPWLDYAVELGCNGLLLGPVFES--ASHGYDTLDHYRIDPRLGDDEDFDALIAAAH 87
Query: 195 ----KILLDFVPNHTSNQHEWFKKSLANIPP 221
++LLD V NH H ++L + P
Sbjct: 88 ERGLRVLLDGVFNHVGRSHPAVAQALEDGPG 118
>gnl|CDD|200481 cd11343, AmyAc_Sucrose_phosphorylase-like, Alpha amylase catalytic
domain found in sucrose phosphorylase (also called
sucrose glucosyltransferase, disaccharide
glucosyltransferase, and sucrose-phosphate alpha-D
glucosyltransferase). Sucrose phosphorylase is a
bacterial enzyme that catalyzes the phosphorolysis of
sucrose to yield glucose-1-phosphate and fructose. These
enzymes do 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.
Length = 445
Score = 64.1 bits (157), Expect = 5e-12
Identities = 37/109 (33%), Positives = 49/109 (44%), Gaps = 10/109 (9%)
Query: 47 YPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEP 106
Y S +G LK + + L EHL +G V I P F +D G+ + DY +P
Sbjct: 9 YGDSLGR---EGEKPLKTLNKFLDEHLKGA-IGGVHILPFFPY-SSDDGFSVIDYTEVDP 63
Query: 107 LFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANIPPYK 155
GD D E L E ++ D V NH S+Q WF+ LA P K
Sbjct: 64 RLGDWDDIEALAEDY-----DLMFDLVINHISSQSPWFQDFLAGGDPSK 107
Score = 42.1 bits (100), Expect = 1e-04
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 19/78 (24%)
Query: 162 RLHDLGVGAVWISPIFKSPMADFGYDISDYLRI-----------------KILLDFVPNH 204
L +G V I P F +D G+ + DY + ++ D V NH
Sbjct: 31 HLKGA-IGGVHILPFFPY-SSDDGFSVIDYTEVDPRLGDWDDIEALAEDYDLMFDLVINH 88
Query: 205 TSNQHEWFKKSLANIPPY 222
S+Q WF+ LA P
Sbjct: 89 ISSQSPWFQDFLAGGDPS 106
>gnl|CDD|237740 PRK14511, PRK14511, maltooligosyl trehalose synthase; Provisional.
Length = 879
Score = 63.1 bits (154), Expect = 1e-11
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 66 IEKLPEHLHDLGVGAVWISPIFKS-PMADFGYDISDYLSFEPLFGDLKDFETLKERLHAL 124
E +P + DLGV +++SPI + P + GYD+ D+ P G + L L A
Sbjct: 23 AELVP-YFADLGVSHLYLSPILAARPGSTHGYDVVDHTRINPELGGEEGLRRLAAALRAH 81
Query: 125 GIKILLDFVPNH 136
G+ ++LD VPNH
Sbjct: 82 GMGLILDIVPNH 93
Score = 44.6 bits (106), Expect = 2e-05
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 23/71 (32%)
Query: 157 ASLLARLHDLGVGAVWISPIFKS-PMADFGYDISDYLRIK-------------------- 195
A L+ DLGV +++SPI + P + GYD+ D+ RI
Sbjct: 23 AELVPYFADLGVSHLYLSPILAARPGSTHGYDVVDHTRINPELGGEEGLRRLAAALRAHG 82
Query: 196 --ILLDFVPNH 204
++LD VPNH
Sbjct: 83 MGLILDIVPNH 93
>gnl|CDD|236543 PRK09505, malS, alpha-amylase; Reviewed.
Length = 683
Score = 62.4 bits (152), Expect = 2e-11
Identities = 34/93 (36%), Positives = 44/93 (47%), Gaps = 15/93 (16%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFKS--------PMADF------GYDISDYLSFE 105
GDL+G+ EKL ++L LGV A+WIS + DF GY D+ +
Sbjct: 227 GDLRGLTEKL-DYLQQLGVNALWISSPLEQIHGWVGGGTKGDFPHYAYHGYYTLDWTKLD 285
Query: 106 PLFGDLKDFETLKERLHALGIKILLDFVPNHTS 138
G D TL + H GI+IL D V NHT
Sbjct: 286 ANMGTEADLRTLVDEAHQRGIRILFDVVMNHTG 318
>gnl|CDD|225819 COG3280, TreY, Maltooligosyl trehalose synthase [Carbohydrate
transport and metabolism].
Length = 889
Score = 62.5 bits (152), Expect = 2e-11
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 66 IEKLPEHLHDLGVGAVWISPIFKS-PMADFGYDISDYLSFEPLFGDLKDFETLKERLHAL 124
L +L DLG+ +++SPIF + P + GYD+ D P G + E L L +
Sbjct: 22 RALLD-YLADLGISHLYLSPIFTARPGSTHGYDVVDPTEINPELGGEEGLERLVAALKSR 80
Query: 125 GIKILLDFVPNH 136
G+ +++D VPNH
Sbjct: 81 GLGLIVDIVPNH 92
Score = 42.1 bits (99), Expect = 2e-04
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 23/74 (31%)
Query: 154 YKCASLLARLHDLGVGAVWISPIFKS-PMADFGYDISDYLRIK----------------- 195
+LL L DLG+ +++SPIF + P + GYD+ D I
Sbjct: 19 ADARALLDYLADLGISHLYLSPIFTARPGSTHGYDVVDPTEINPELGGEEGLERLVAALK 78
Query: 196 -----ILLDFVPNH 204
+++D VPNH
Sbjct: 79 SRGLGLIVDIVPNH 92
>gnl|CDD|233849 TIGR02401, trehalose_TreY, malto-oligosyltrehalose synthase. This
enzyme, formally named (1->4)-alpha-D-glucan
1-alpha-D-glucosylmutase, is the TreY enzyme of the
TreYZ pathway of trehalose biosynthesis, an alternative
to the OtsAB pathway. Trehalose may be incorporated into
more complex compounds but is best known as compatible
solute. It is one of the most effective osmoprotectants,
and unlike the various betaines does not require
nitrogen for its synthesis [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 825
Score = 62.0 bits (151), Expect = 3e-11
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 67 EKLPEHLHDLGVGAVWISPIFKS-PMADFGYDISDYLSFEPLFGDLKDFETLKERLHALG 125
L +L LGV +++SPI + P + GYD+ D+ P G + L E A G
Sbjct: 19 AALLPYLKSLGVSHLYLSPILTAVPGSTHGYDVVDHSEINPELGGEEGLRRLSEAARARG 78
Query: 126 IKILLDFVPNH 136
+ +++D VPNH
Sbjct: 79 LGLIVDIVPNH 89
Score = 42.4 bits (100), Expect = 1e-04
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 23/74 (31%)
Query: 154 YKCASLLARLHDLGVGAVWISPIFKS-PMADFGYDISDYLRIK----------------- 195
A+LL L LGV +++SPI + P + GYD+ D+ I
Sbjct: 16 DDAAALLPYLKSLGVSHLYLSPILTAVPGSTHGYDVVDHSEINPELGGEEGLRRLSEAAR 75
Query: 196 -----ILLDFVPNH 204
+++D VPNH
Sbjct: 76 ARGLGLIVDIVPNH 89
>gnl|CDD|200485 cd11347, AmyAc_1, 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
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 = 391
Score = 57.6 bits (140), Expect = 7e-10
Identities = 23/48 (47%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 96 YDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEW 143
Y I+DY + P G D L+ERL A G+K++LDFVPNH + H W
Sbjct: 87 YAITDY-TVNPDLGGEDDLAALRERLAARGLKLMLDFVPNHVALDHPW 133
Score = 34.9 bits (81), Expect = 0.022
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 194 IKILLDFVPNHTSNQHEW 211
+K++LDFVPNH + H W
Sbjct: 116 LKLMLDFVPNHVALDHPW 133
>gnl|CDD|200468 cd11329, AmyAc_maltase-like, Alpha amylase catalytic domain family
found in maltase. Maltase (EC 3.2.1.20) hydrolyzes the
terminal, non-reducing (1->4)-linked alpha-D-glucose
residues in maltose, releasing alpha-D-glucose. The
catalytic triad (DED) which is highly conserved in the
other maltase group is not present in this subfamily.
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 = 477
Score = 57.0 bits (138), Expect = 1e-09
Identities = 36/129 (27%), Positives = 50/129 (38%), Gaps = 33/129 (25%)
Query: 33 EPLEWWQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFK---S 89
PL+WWQ L SF + V A+
Sbjct: 61 VPLKWWQKGPLVELDTESF---------------------FKEEHVEAISKLGAKGVIYE 99
Query: 90 PMADFGYDISDYLSFEPLFGDLKDF-ETLKERLHALGIKILLDFVPNHTSNQHEWFKKSL 148
AD Y + Y + DLK+ +T K++ IK++LD PNH+S QH FK S+
Sbjct: 100 LPADETYLNNSY----GVESDLKELVKTAKQK----DIKVILDLTPNHSSKQHPLFKDSV 151
Query: 149 ANIPPYKCA 157
PPY+ A
Sbjct: 152 LKEPPYRSA 160
Score = 42.4 bits (100), Expect = 1e-04
Identities = 16/30 (53%), Positives = 20/30 (66%)
Query: 194 IKILLDFVPNHTSNQHEWFKKSLANIPPYS 223
IK++LD PNH+S QH FK S+ PPY
Sbjct: 129 IKVILDLTPNHSSKQHPLFKDSVLKEPPYR 158
>gnl|CDD|200493 cd11356, AmyAc_Sucrose_phosphorylase-like_1, Alpha amylase
catalytic domain found in sucrose phosphorylase-like
proteins (also called sucrose glucosyltransferase,
disaccharide glucosyltransferase, and sucrose-phosphate
alpha-D glucosyltransferase). Sucrose phosphorylase is
a bacterial enzyme that catalyzes the phosphorolysis of
sucrose to yield glucose-1-phosphate and fructose. These
enzymes do 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.
Length = 458
Score = 56.4 bits (137), Expect = 2e-09
Identities = 32/87 (36%), Positives = 44/87 (50%), Gaps = 7/87 (8%)
Query: 69 LPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKI 128
L EHL D + V I P F +D G+ + DY P GD +D E L + ++
Sbjct: 30 LKEHLKDT-ISGVHILPFFPYS-SDDGFSVIDYRQVNPELGDWEDIEALAKDF-----RL 82
Query: 129 LLDFVPNHTSNQHEWFKKSLANIPPYK 155
+ D V NH S+ WF++ LA PPYK
Sbjct: 83 MFDLVINHVSSSSPWFQQFLAGEPPYK 109
Score = 41.3 bits (98), Expect = 2e-04
Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 19/81 (23%)
Query: 159 LLARLHDLGVGAVWISPIFKSPMADFGYDISDYLRI-----------------KILLDFV 201
L L D + V I P F +D G+ + DY ++ +++ D V
Sbjct: 30 LKEHLKDT-ISGVHILPFFPYS-SDDGFSVIDYRQVNPELGDWEDIEALAKDFRLMFDLV 87
Query: 202 PNHTSNQHEWFKKSLANIPPY 222
NH S+ WF++ LA PPY
Sbjct: 88 INHVSSSSPWFQQFLAGEPPY 108
>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 = 55.7 bits (135), Expect = 3e-09
Identities = 35/101 (34%), Positives = 52/101 (51%), Gaps = 7/101 (6%)
Query: 42 VFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMA-DFGYDISD 100
V Y L R F GD KG+I+KL +L DLGV A+ + P+ + P +GY+
Sbjct: 17 VIYELLVRDF-----TERGDFKGVIDKLD-YLQDLGVNAIELMPVQEFPGNDSWGYNPRH 70
Query: 101 YLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQH 141
Y + + +G +D + L + H GI ++LD V NH Q
Sbjct: 71 YFALDKAYGTPEDLKRLVDECHQRGIAVILDVVYNHAEGQS 111
>gnl|CDD|200483 cd11345, AmyAc_SLC3A2, Alpha amylase catalytic domain found in
solute carrier family 3 member 2 proteins. 4F2
cell-surface antigen heavy chain (hc) is a protein that
in humans is encoded by the SLC3A2 gene. 4F2hc is a
multifunctional type II membrane glycoprotein involved
in amino acid transport and cell fusion, adhesion, and
transformation. It is related to bacterial
alpha-glycosidases, but lacks alpha-glycosidase
activity. 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 = 326
Score = 54.8 bits (132), Expect = 5e-09
Identities = 34/123 (27%), Positives = 53/123 (43%), Gaps = 11/123 (8%)
Query: 30 PIQEPLEWWQTSVFYHLY-PRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFK 88
PI E + WW Y + ++F ++ G LKG+ KL ++L L V + + PI
Sbjct: 6 PIPE-MNWWNEGPLYQIGDLQAFSEAGG-----LKGVEGKL-DYLSQLKVKGLVLGPIHV 58
Query: 89 SPMADFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSL 148
G + +P G L+DF +L H GI ++LD PN+ W
Sbjct: 59 VQADQPG--ELNLTEIDPDLGTLEDFTSLLTAAHKKGISVVLDLTPNYRGES-SWAFSDA 115
Query: 149 ANI 151
N+
Sbjct: 116 ENV 118
>gnl|CDD|200492 cd11355, AmyAc_Sucrose_phosphorylase, Alpha amylase catalytic
domain found in sucrose phosphorylase (also called
sucrose glucosyltransferase, disaccharide
glucosyltransferase, and sucrose-phosphate alpha-D
glucosyltransferase). Sucrose phosphorylase is a
bacterial enzyme that catalyzes the phosphorolysis of
sucrose to yield glucose-1-phosphate and fructose. These
enzymes do 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.
Length = 433
Score = 53.0 bits (128), Expect = 2e-08
Identities = 29/91 (31%), Positives = 40/91 (43%), Gaps = 7/91 (7%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLKDFETLKE 119
G+LK + L + + G V I P F D G+D DY +P FG D E L E
Sbjct: 15 GNLKDLNTVLDTYFKGV-FGGVHILPFF-PSSDDRGFDPIDYTEVDPRFGTWDDIEALGE 72
Query: 120 RLHALGIKILLDFVPNHTSNQHEWFKKSLAN 150
++ D + NH S Q +F+ LA
Sbjct: 73 DYE-----LMADLMVNHISAQSPYFQDFLAK 98
Score = 29.5 bits (67), Expect = 1.4
Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 18/68 (26%)
Query: 168 VGAVWISPIFKSPMADFGYDISDYLRI-----------------KILLDFVPNHTSNQHE 210
G V I P F D G+D DY + +++ D + NH S Q
Sbjct: 32 FGGVHILPFF-PSSDDRGFDPIDYTEVDPRFGTWDDIEALGEDYELMADLMVNHISAQSP 90
Query: 211 WFKKSLAN 218
+F+ LA
Sbjct: 91 YFQDFLAK 98
>gnl|CDD|200458 cd11319, AmyAc_euk_AmyA, Alpha amylase catalytic domain found in
eukaryotic 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 eukaryotic alpha-amylases including proteins
from fungi, sponges, and protozoans. 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 = 375
Score = 53.0 bits (128), Expect = 3e-08
Identities = 31/84 (36%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIFK-------SPMADFGYDISDYLSFEPLFGDLK 112
G KG+I KL +++ +G A+WISPI K A GY D S P FG
Sbjct: 40 GTWKGIINKL-DYIQGMGFDAIWISPIVKNIEGNTAYGEAYHGYWAQDLYSLNPHFGTAD 98
Query: 113 DFETLKERLHALGIKILLDFVPNH 136
D + L + LH G+ +++D V NH
Sbjct: 99 DLKALSKALHKRGMYLMVDVVVNH 122
Score = 27.5 bits (62), Expect = 6.6
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 165 DLGVGAVWISPIFK 178
+G A+WISPI K
Sbjct: 54 GMGFDAIWISPIVK 67
>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 = 51.4 bits (124), Expect = 8e-08
Identities = 32/108 (29%), Positives = 47/108 (43%), Gaps = 23/108 (21%)
Query: 38 WQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADF--- 94
+ V Y L+ +F G IE+L +L DLGV A+ + P+ A+F
Sbjct: 35 LEELVIYELHVGTF-----TPEGTFDAAIERLD-YLADLGVTAIELMPV-----AEFPGE 83
Query: 95 ---GYDISDYLSFEPLFG---DLKDFETLKERLHALGIKILLDFVPNH 136
GYD + E +G DLK + H G+ ++LD V NH
Sbjct: 84 RNWGYDGVLPFAPESSYGGPDDLKRL--VDA-AHRRGLAVILDVVYNH 128
>gnl|CDD|236518 PRK09441, PRK09441, cytoplasmic alpha-amylase; Reviewed.
Length = 479
Score = 51.4 bits (124), Expect = 8e-08
Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 14/92 (15%)
Query: 67 EKLPEHLHDLGVGAVWISPIFK--SPMADFGYDISDYLSF---------EPLFGDLKDFE 115
E+ P L + G+ AVW+ P +K S D GY + D +G ++
Sbjct: 26 ERAP-ELAEAGITAVWLPPAYKGTSGGYDVGYGVYDLFDLGEFDQKGTVRTKYGTKEELL 84
Query: 116 TLKERLHALGIKILLDFVPNHTSN--QHEWFK 145
+ LH GIK+ D V NH + + E F+
Sbjct: 85 NAIDALHENGIKVYADVVLNHKAGADEKETFR 116
Score = 34.1 bits (79), Expect = 0.050
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 163 LHDLGVGAVWISPIFK--SPMADFGYDISDY 191
L + G+ AVW+ P +K S D GY + D
Sbjct: 31 LAEAGITAVWLPPAYKGTSGGYDVGYGVYDL 61
>gnl|CDD|200487 cd11349, AmyAc_3, 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
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 = 456
Score = 51.1 bits (123), Expect = 1e-07
Identities = 41/136 (30%), Positives = 59/136 (43%), Gaps = 39/136 (28%)
Query: 42 VFYHLYPRSFKDSNG----------DGVGDLKGMIEKLPEHLHDLGVGAVW--------- 82
+ Y L PR F + N +GVG + + + LG VW
Sbjct: 2 IIYQLLPRLFGNKNTTNIPNGTIEENGVGKFNDFDDTALKEIKSLGFTHVWYTGVIRHAT 61
Query: 83 --------ISP----IFK----SPMA--DFGYDISDYLSFEPLFGDLKDFETLKERLHAL 124
I P I K SP A D+ YD+ L+ +P +++FE L ER HA
Sbjct: 62 QTDYSAYGIPPDDPDIVKGRAGSPYAIKDY-YDVDPDLATDPT-NRMEEFEALVERTHAA 119
Query: 125 GIKILLDFVPNHTSNQ 140
G+K+++DFVPNH + Q
Sbjct: 120 GLKVIIDFVPNHVARQ 135
Score = 27.3 bits (61), Expect = 8.2
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 195 KILLDFVPNHTSNQ 208
K+++DFVPNH + Q
Sbjct: 122 KVIIDFVPNHVARQ 135
>gnl|CDD|223373 COG0296, GlgB, 1,4-alpha-glucan branching enzyme [Carbohydrate
transport and metabolism].
Length = 628
Score = 51.2 bits (123), Expect = 1e-07
Identities = 32/102 (31%), Positives = 53/102 (51%), Gaps = 4/102 (3%)
Query: 38 WQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPM-ADFGY 96
W+ V Y L+ SF +G + IE LP +L +LG+ + + P+ + P +GY
Sbjct: 142 WEPIVIYELHVGSFTP--DRFLGYFELAIELLP-YLKELGITHIELMPVAEHPGDRSWGY 198
Query: 97 DISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTS 138
+ Y + +G +DF+ L + H GI ++LD+VPNH
Sbjct: 199 QGTGYYAPTSRYGTPEDFKALVDAAHQAGIGVILDWVPNHFP 240
>gnl|CDD|237052 PRK12313, PRK12313, glycogen branching enzyme; Provisional.
Length = 633
Score = 50.3 bits (121), Expect = 2e-07
Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 65 MIEKLPEHLHDLGVGAVWISPIFKSPM-ADFGYDISDYLSFEPLFGDLKDFETLKERLHA 123
+ ++L ++ ++G V P+ + P+ +GY ++ Y + +G +DF L + LH
Sbjct: 172 LADELIPYVKEMGYTHVEFMPLMEHPLDGSWGYQLTGYFAPTSRYGTPEDFMYLVDALHQ 231
Query: 124 LGIKILLDFVPNH-TSNQH 141
GI ++LD+VP H +
Sbjct: 232 NGIGVILDWVPGHFPKDDD 250
>gnl|CDD|131155 TIGR02100, glgX_debranch, glycogen debranching enzyme GlgX. This
family consists of the GlgX protein from the E. coli
glycogen operon and probable equivalogs from other
prokaryotic species. GlgX is not required for glycogen
biosynthesis, but instead acts as a debranching enzyme
for glycogen catabolism. This model distinguishes GlgX
from pullanases and other related proteins that also
operate on alpha-1,6-glycosidic linkages. In the wide
band between the trusted and noise cutoffs are
functionally similar enzymes, mostly from plants, that
act similarly but usually are termed isoamylase [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 688
Score = 50.0 bits (120), Expect = 3e-07
Identities = 31/118 (26%), Positives = 54/118 (45%), Gaps = 18/118 (15%)
Query: 38 WQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLP-----EHLHDLGVGAVWISPIFKSPMA 92
W+ ++ Y + + F + D +L+G L ++L LGV AV + P+
Sbjct: 153 WEDTIIYEAHVKGFTQLHPDIPEELRGTYAGLAHPAMIDYLKKLGVTAVELLPVHAFIDD 212
Query: 93 DF----------GYDISDYLSFEPLF---GDLKDFETLKERLHALGIKILLDFVPNHT 137
GY+ + + EP + G + +F+T+ LH GI+++LD V NHT
Sbjct: 213 RHLLEKGLRNYWGYNTLGFFAPEPRYLASGQVAEFKTMVRALHDAGIEVILDVVYNHT 270
>gnl|CDD|163564 TIGR03852, sucrose_gtfA, sucrose phosphorylase. In the forward
direction, this enzyme uses phosphate to cleave sucrose
into D-fructose + alpha-D-glucose 1-phosphate.
Characterized representatives from Streptococcus mutans
and Bifidobacterium adolescentis represent
well-separated branches of a molecular phylogenetic
tree. In S. mutans, the region including this gene has
been associated with neighboring transporter genes and
multiple sugar metabolism.
Length = 470
Score = 49.3 bits (118), Expect = 5e-07
Identities = 32/101 (31%), Positives = 50/101 (49%), Gaps = 10/101 (9%)
Query: 50 SFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFG 109
++ DS G + +L ++E + D VG V + P F S D G+ DY +P FG
Sbjct: 7 TYADSLGKNLKELNKVLEN---YFKD-AVGGVHLLPFFPST-GDRGFAPMDYTEVDPAFG 61
Query: 110 DLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLAN 150
D D E L E+ + ++ DF+ NH S Q E+++ L
Sbjct: 62 DWSDVEALSEKYY-----LMFDFMINHISRQSEYYQDFLEK 97
Score = 27.8 bits (62), Expect = 5.9
Identities = 21/68 (30%), Positives = 29/68 (42%), Gaps = 18/68 (26%)
Query: 168 VGAVWISPIFKS-------PM------ADFGYDISDYLRIK----ILLDFVPNHTSNQHE 210
VG V + P F S PM FG D SD + ++ DF+ NH S Q E
Sbjct: 31 VGGVHLLPFFPSTGDRGFAPMDYTEVDPAFG-DWSDVEALSEKYYLMFDFMINHISRQSE 89
Query: 211 WFKKSLAN 218
+++ L
Sbjct: 90 YYQDFLEK 97
>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 = 48.9 bits (117), Expect = 7e-07
Identities = 34/101 (33%), Positives = 51/101 (50%), Gaps = 9/101 (8%)
Query: 38 WQTSVFYHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMA-DFGY 96
+ +V Y L+ +F G IEKLP +L DLG+ A+ + P+ + P +GY
Sbjct: 91 LEEAVIYELHVGTFTPE-----GTFDAAIEKLP-YLADLGITAIELMPVAQFPGTRGWGY 144
Query: 97 D-ISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNH 136
D + Y E +G D + L + H LG+ +LLD V NH
Sbjct: 145 DGVLPYAPHEA-YGGPDDLKALVDAAHGLGLGVLLDVVYNH 184
>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 = 46.7 bits (112), Expect = 3e-06
Identities = 22/94 (23%), Positives = 46/94 (48%), Gaps = 1/94 (1%)
Query: 44 YHLYPRSFKDSNGDGVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPM-ADFGYDISDYL 102
Y ++ S+K + + ++L ++ ++G V + P+ + P +GY ++ Y
Sbjct: 39 YEVHLGSWKRKEDGRFLSYRELADELIPYVKEMGYTHVELMPVMEHPFDGSWGYQVTGYF 98
Query: 103 SFEPLFGDLKDFETLKERLHALGIKILLDFVPNH 136
+ +G DF+ + H GI ++LD+VP H
Sbjct: 99 APTSRYGTPDDFKYFVDACHQAGIGVILDWVPGH 132
>gnl|CDD|200474 cd11335, AmyAc_MTase_N, Alpha amylase catalytic domain found in
maltosyltransferase. Maltosyltransferase (MTase), a
maltodextrin glycosyltransferase, acts on starch and
maltooligosaccharides. It catalyzes the transfer of
maltosyl units from alpha-1,4-linked glucans or
maltooligosaccharides to other alpha-1,4-linked glucans,
maltooligosaccharides or glucose. MTase is a homodimer.
The catalytic core domain has the (beta/alpha) 8 barrel
fold with the active-site cleft formed at the C-terminal
end of the barrel. Substrate binding experiments have
led to the location of two distinct maltose-binding
sites: one lies in the active-site cleft and the other
is located in a pocket adjacent to the active-site
cleft. It is a member of the alpha-amylase family, but
unlike typical alpha-amylases, MTase does not require
calcium for activity and lacks two histidine residues
which are predicted to be critical for binding the
glucose residue adjacent to the scissile bond in the
substrates. The common reaction chemistry of the
alpha-amylase family of enzymes is based on a two-step
acid catalytic mechanism that requires two critical
carboxylates: one acting as a general acid/base (Glu)
and the other as a nucleophile (Asp). Both hydrolysis
and transglycosylation proceed via the nucleophilic
substitution reaction between the anomeric carbon, C1
and a nucleophile. 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 = 538
Score = 46.1 bits (110), Expect = 6e-06
Identities = 49/166 (29%), Positives = 74/166 (44%), Gaps = 46/166 (27%)
Query: 36 EWWQTSVFYHLYPR---SFKDSNGDGV------------GDLKGMIEKLPEHLHDLGVGA 80
+W ++S Y L+ R ++ D +GDG G MI LP +L +G+
Sbjct: 41 DWIKSSSVYSLFVRTTTAW-DHDGDGALEPENLYGFRETGTFLKMIALLP-YLKRMGINT 98
Query: 81 VWISPIFK-----------SPMA--DFGYDISDYLSFEPLFGDLK---DFETLKERLHAL 124
+++ PI K SP A +F ++I L +PL GDL +F+ E H L
Sbjct: 99 IYLLPITKISKKFKKGELGSPYAVKNF-FEIDPLLH-DPLLGDLSVEEEFKAFVEACHML 156
Query: 125 GIKILLDFVPNHTSN------QH-EWF----KKSLANIPPYKCASL 159
GI+++LDF+P + +H EWF L N P K L
Sbjct: 157 GIRVVLDFIPRTAARDSDLILEHPEWFYWIKVDELNNYHPPKVPGL 202
>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 = 45.7 bits (109), Expect = 6e-06
Identities = 28/85 (32%), Positives = 36/85 (42%), Gaps = 18/85 (21%)
Query: 67 EKLPEHLHDLGVGAVWISPIFKS-PMADFG-----------YDISDYLSFEPLFGDLKDF 114
E LPE + G A+ SP KS + G Y I + L G DF
Sbjct: 17 ENLPE-IAAAGYTAIQTSPPQKSKEGGNEGGNWWYRYQPTDYRIGNN----QL-GTEDDF 70
Query: 115 ETLKERLHALGIKILLDFVPNHTSN 139
+ L H GIKI++D V NH +N
Sbjct: 71 KALCAAAHKYGIKIIVDVVFNHMAN 95
>gnl|CDD|200484 cd11346, AmyAc_plant_IsoA, Alpha amylase catalytic domain family
found in plant isoamylases. Two types of debranching
enzymes exist in plants: isoamylase-type (EC 3.2.1.68)
and a pullulanase-type (EC 3.2.1.41, also known as
limit-dextrinase). These efficiently hydrolyze
alpha-(1,6)-linkages in amylopectin and pullulan. This
group does not contain the conserved catalytic triad
present in other alpha-amylase-like 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 = 347
Score = 44.0 bits (104), Expect = 2e-05
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWISPIF---KSPMADFGYD----ISDYLSFEPLFGDLK 112
G G++EK+ HL LGV V + PIF + + Y + +
Sbjct: 29 GTFLGVLEKVD-HLKSLGVNTVLLQPIFAFARVKGPYYPPSFFSAPDPYGAGDSSLSASA 87
Query: 113 DFETLKERLHALGIKILLDFVPNHTS 138
+ + + LH+ GI++LL+ V HT+
Sbjct: 88 ELRAMVKGLHSNGIEVLLEVVLTHTA 113
>gnl|CDD|200457 cd11318, AmyAc_bac_fung_AmyA, Alpha amylase catalytic domain found
in bacterial and fungal 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 bacterial and fungal 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 = 391
Score = 43.3 bits (103), Expect = 5e-05
Identities = 26/89 (29%), Positives = 38/89 (42%), Gaps = 25/89 (28%)
Query: 66 IEKLPEHLHDLGVGAVWISPIFK--SPMADFGYDISDYLSFEPLFGDLKDF--------- 114
+ + L +LG+ AVW+ P +K S D GYD+ D L+ DL +F
Sbjct: 22 LAEDAPELAELGITAVWLPPAYKGASGTEDVGYDVYD------LY-DLGEFDQKGTVRTK 74
Query: 115 -------ETLKERLHALGIKILLDFVPNH 136
+ LH GI++ D V NH
Sbjct: 75 YGTKEELLEAIKALHENGIQVYADAVLNH 103
Score = 37.1 bits (87), Expect = 0.005
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 155 KCASLLARLHDLGVGAVWISPIFK--SPMADFGYDISD 190
+ A L +LG+ AVW+ P +K S D GYD+ D
Sbjct: 21 RLAEDAPELAELGITAVWLPPAYKGASGTEDVGYDVYD 58
>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 = 42.8 bits (102), Expect = 7e-05
Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 22/94 (23%)
Query: 64 GMIE--KLPEHLHDLGVGAVWISPIFK------------------SPMADFGYDISDYLS 103
G+ E K+P +L +LGV AV + P+ + + F D Y S
Sbjct: 43 GLAEPAKIP-YLKELGVTAVELLPVHAFDDEEHLVERGLTNYWGYNTLNFFAPD-PRYAS 100
Query: 104 FEPLFGDLKDFETLKERLHALGIKILLDFVPNHT 137
+ G + +F+ + + LH GI+++LD V NHT
Sbjct: 101 DDAPGGPVDEFKAMVKALHKAGIEVILDVVYNHT 134
>gnl|CDD|237794 PRK14705, PRK14705, glycogen branching enzyme; Provisional.
Length = 1224
Score = 42.7 bits (100), Expect = 1e-04
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 63 KGMIEKLPEHLHDLGVGAVWISPIFKSPMA-DFGYDISDYLSFEPLFGDLKDFETLKERL 121
+ + ++L +++ LG V P+ + P +GY ++ Y + FG +F L + L
Sbjct: 765 RELAKELVDYVKWLGFTHVEFMPVAEHPFGGSWGYQVTSYFAPTSRFGHPDEFRFLVDSL 824
Query: 122 HALGIKILLDFVPNH 136
H GI +LLD+VP H
Sbjct: 825 HQAGIGVLLDWVPAH 839
>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 = 41.4 bits (98), Expect = 2e-04
Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 65 MIEKLPEHLHDLGVGAVWISPIFKS----PMADFGYDISDYLSFEPLFGDLKDFETLKER 120
+ K PE L G A+W+ P KS M GYD D +G + +L
Sbjct: 20 LESKAPE-LAAAGFTAIWLPPPSKSVSGSSM---GYDPGDLYDLNSRYGSEAELRSLIAA 75
Query: 121 LHALGIKILLDFVPNH 136
LHA GIK++ D V NH
Sbjct: 76 LHAKGIKVIADIVINH 91
>gnl|CDD|224440 COG1523, PulA, Type II secretory pathway, pullulanase PulA and
related glycosidases [Carbohydrate transport and
metabolism].
Length = 697
Score = 41.2 bits (97), Expect = 3e-04
Identities = 36/123 (29%), Positives = 61/123 (49%), Gaps = 24/123 (19%)
Query: 38 WQTSVFYHLYPRSFKDSNGDGVGDLK-----GMIEKLP-EHLHDLGVGAVWISPIF---- 87
W+ +V Y + R F + GV + G+ E + ++L DLGV AV + P+F
Sbjct: 169 WEDTVIYEAHVRDFTQLH-PGVPEELRGTYLGLAEPVIIDYLKDLGVTAVELLPVFDFYD 227
Query: 88 -----KSPMADF-GYDISDYLSFEPLF-------GDLKDFETLKERLHALGIKILLDFVP 134
KS + + GYD ++ + E + +K+F+ + + LH GI+++LD V
Sbjct: 228 EPHLDKSGLNNNWGYDPLNFFAPEGRYASNPEPATRIKEFKDMVKALHKAGIEVILDVVF 287
Query: 135 NHT 137
NHT
Sbjct: 288 NHT 290
>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 = 40.6 bits (95), Expect = 4e-04
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 63 KGMIEKLPEHLHDLGVGAVWISPIFKSPM-ADFGYDISDYLSFEPLFGDLKDFETLKERL 121
+ + ++L ++ +LG + + P+ + P +GY ++ Y + FG DF +
Sbjct: 161 RELADQLIPYVKELGFTHIELLPVAEHPFDGSWGYQVTGYYAPTSRFGTPDDFMYFVDAC 220
Query: 122 HALGIKILLDFVPNH 136
H GI ++LD+VP H
Sbjct: 221 HQAGIGVILDWVPGH 235
>gnl|CDD|237528 PRK13840, PRK13840, sucrose phosphorylase; Provisional.
Length = 495
Score = 40.0 bits (94), Expect = 6e-04
Identities = 31/95 (32%), Positives = 42/95 (44%), Gaps = 9/95 (9%)
Query: 58 GVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPM--ADFGYDISDYLSFEPLFGDLKDFE 115
G G LK + L L L G V I P F P+ AD G+D D+ +P GD D +
Sbjct: 15 GDGGLKSLTALLDGRLDGL-FGGVHILPFF-YPIDGADAGFDPIDHTKVDPRLGDWDDVK 72
Query: 116 TLKERLHALGIKILLDFVPNHTSNQHEWFKKSLAN 150
L + I+ D + NH S + F+ LA
Sbjct: 73 ALGK-----THDIMADLIVNHMSAESPQFQDVLAK 102
>gnl|CDD|237795 PRK14706, PRK14706, glycogen branching enzyme; Provisional.
Length = 639
Score = 39.6 bits (92), Expect = 8e-04
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 68 KLPEHLHDLGVGAVWISPIFKSPM-ADFGYDISDYLSFEPLFGDLKDFETLKERLHALGI 126
+L E++ +G V + + + P +GY ++ Y + G +DF+ L LH LGI
Sbjct: 172 RLGEYVTYMGYTHVELLGVMEHPFDGSWGYQVTGYYAPTSRLGTPEDFKYLVNHLHGLGI 231
Query: 127 KILLDFVPNH 136
++LD+VP H
Sbjct: 232 GVILDWVPGH 241
>gnl|CDD|200482 cd11344, AmyAc_GlgE_like, Alpha amylase catalytic domain found in
GlgE-like proteins. GlgE is a
(1,4)-a-D-glucan:phosphate a-D-maltosyltransferase,
involved in a-glucan biosynthesis in bacteria. It is
also an anti-tuberculosis drug target. GlgE isoform I
from Streptomyces coelicolor has the same catalytic and
very similar kinetic properties to GlgE from
Mycobacterium tuberculosis. GlgE from Streptomyces
coelicolor forms a homodimer with each subunit
comprising five domains (A, B, C, N, and S) and 2
inserts. Domain A is a catalytic alpha-amylase-type
domain that along with domain N, which has a
beta-sandwich fold and forms the core of the dimer
interface, binds cyclodextrins. Domain A, B, and the 2
inserts define a well conserved donor pocket that binds
maltose. Cyclodextrins competitively inhibit the binding
of maltooligosaccharides to the S. coelicolor enzyme,
indicating that the hydrophobic patch overlaps with the
acceptor binding site. This is not the case in M.
tuberculosis GlgE because cyclodextrins do not inhibit
this enzyme, despite acceptor length specificity being
conserved. Domain C is hypothesized to help stabilize
domain A and could be involved in substrate binding.
Domain S is a helix bundle that is inserted within the N
domain and it plays a role in the dimer interface and
interacts directly with domain B. 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 = 355
Score = 38.0 bits (89), Expect = 0.002
Identities = 33/139 (23%), Positives = 51/139 (36%), Gaps = 40/139 (28%)
Query: 40 TSVFYHLYPRSFKDSNGDGV-GDLKGMIEKLPEHLHDLGVGAVWISPIFK---------- 88
S +Y +PRS G G + +LP + +G +++ PI
Sbjct: 1 FSAWYEFFPRSA--GADPGRHGTFRDAEARLPR-IAAMGFDVLYLPPIHPIGRTNRKGKN 57
Query: 89 -----------SPMA----DFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFV 133
SP A + G+D + P G L+DF+ L LGI++ LD
Sbjct: 58 NALVAGPGDPGSPWAIGSEEGGHD-----AIHPELGTLEDFDRLVAEARELGIEVALDIA 112
Query: 134 ----PNH--TSNQHEWFKK 146
P+H EWF+
Sbjct: 113 LQCSPDHPYVKEHPEWFRH 131
>gnl|CDD|233728 TIGR02102, pullulan_Gpos, pullulanase, extracellular,
Gram-positive. Pullulan is an unusual, industrially
important polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. In
contrast, a glycogen debranching enzyme such GlgX,
homologous to this family, can release glucose at
alpha,1-6 linkages from glycogen first subjected to
limit degradation by phosphorylase. Characterized
members of this family include a surface-located
pullulanase from Streptococcus pneumoniae
(PMID:11083842) and an extracellular bifunctional
amylase/pullulanase with C-terminal pullulanase activity
(PMID:8798645).
Length = 1111
Score = 36.8 bits (85), Expect = 0.007
Identities = 32/136 (23%), Positives = 57/136 (41%), Gaps = 34/136 (25%)
Query: 39 QTSVFYHLYPRSF-KDSNGDG-----VGDLKGMIEKLPEHLHDLGVGAVWISPIF----- 87
+ ++ Y + R F D G G +EKL ++L DLGV + + P+
Sbjct: 450 EDAIIYEAHVRDFTSDPAIAGDLTAQFGTFAAFVEKL-DYLQDLGVTHIQLLPVLSYFFV 508
Query: 88 -----KSPMADF---------GYDISDYLSFEPLFGD--------LKDFETLKERLHALG 125
K M D+ GYD +Y + ++ + + +F+ L +H G
Sbjct: 509 NEFKNKERMLDYASSNTNYNWGYDPQNYFALSGMYSEDPKDPELRIAEFKNLINEIHKRG 568
Query: 126 IKILLDFVPNHTSNQH 141
+ ++LD V NHT+ +
Sbjct: 569 MGVILDVVYNHTAKVY 584
>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 = 36.7 bits (85), Expect = 0.007
Identities = 25/108 (23%), Positives = 42/108 (38%), Gaps = 11/108 (10%)
Query: 67 EKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLK----DFETLKERLH 122
E + G + +P+ + ++ Y + D L F K D + L E+LH
Sbjct: 135 EPRLRVAKEKGYNMIHFTPLQELGGSNSCYSLYDQLQLNQHFKSQKDGKNDVQALVEKLH 194
Query: 123 -ALGIKILLDFVPNHTSNQHEWFKK------SLANIPPYKCASLLARL 163
+ + D V NHT+N W + + P + A +L RL
Sbjct: 195 RDWNVLSITDIVFNHTANNSPWLLEHPEAAYNCITSPHLRPAIVLDRL 242
>gnl|CDD|215419 PLN02784, PLN02784, alpha-amylase.
Length = 894
Score = 36.1 bits (83), Expect = 0.014
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 67 EKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLKDFETLKERLHALGI 126
EK E L LG VW+ P +S ++ GY D + +G + + + L + H +GI
Sbjct: 525 EKAAE-LSSLGFTVVWLPPPTES-VSPEGYMPKDLYNLNSRYGTIDELKDLVKSFHEVGI 582
Query: 127 KILLDFVPNH 136
K+L D V NH
Sbjct: 583 KVLGDAVLNH 592
>gnl|CDD|200462 cd11323, AmyAc_AGS, Alpha amylase catalytic domain found in Alpha
1,3-glucan synthase (also called uridine
diphosphoglucose-1,3-alpha-glucan glucosyltransferase
and 1,3-alpha-D-glucan synthase). Alpha 1,3-glucan
synthase (AGS, EC 2.4.1.183) is an enzyme that catalyzes
the reversible chemical reaction of UDP-glucose and
[alpha-D-glucosyl-(1-3)]n to form UDP and
[alpha-D-glucosyl-(1-3)]n+1. AGS is a component of
fungal cell walls. The cell wall of filamentous fungi is
composed of 10-15% chitin and 10-35% alpha-1,3-glucan.
AGS is triggered in fungi as a response to cell wall
stress and elongates the glucan chains in cell wall
synthesis. This group includes proteins from Ascomycetes
and Basidomycetes. 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 = 569
Score = 35.7 bits (83), Expect = 0.014
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 60 GDLKGMIEKLPEHLHDLGVGAVWI--SPIFKSPMADFGYDISDYLSFEPLFGDLKDFETL 117
GD+ G+++ L ++L +G+ ++I +P P GY D+ + FG + D+
Sbjct: 94 GDIVGLVDSL-DYLQGMGIKGIYIAGTPFINMPWGADGYSPLDFTLLDHHFGTIADWRAA 152
Query: 118 KERLHALGIKILLDF 132
+ +H G+ ++LD
Sbjct: 153 IDEIHRRGMYVVLDN 167
>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 = 34.9 bits (81), Expect = 0.025
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 92 ADFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSN 139
A FGY ++++ + FG +D + L + H +GI +LLD V +H S
Sbjct: 68 ASFGYQVTNFFAASSRFGTPEDLKYLIDTAHGMGIAVLLDVVHSHASK 115
>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 = 34.5 bits (80), Expect = 0.038
Identities = 25/86 (29%), Positives = 36/86 (41%), Gaps = 14/86 (16%)
Query: 96 YDISDYLSFEPLF------GDLKDFETLKERLHA-LGIKILLDFVPNHTSNQHEWFKK-- 146
Y I+D L P F +D E L ++L G+ + D V NHT+N W +
Sbjct: 68 YSIADQLELNPDFFPDGKKKTFEDVEELVKKLEKEWGLLSITDVVLNHTANNSPWLLEHP 127
Query: 147 ----SLANIPPYKCASLLAR-LHDLG 167
+L N P + A L R L +
Sbjct: 128 EAGYNLENSPHLRPAYELDRALLEFS 153
>gnl|CDD|235445 PRK05402, PRK05402, glycogen branching enzyme; Provisional.
Length = 726
Score = 34.0 bits (79), Expect = 0.048
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 108 FGDLKDFETLKERLHALGIKILLDFVPNH 136
FG DF + H GI ++LD+VP H
Sbjct: 311 FGTPDDFRYFVDACHQAGIGVILDWVPAH 339
>gnl|CDD|233730 TIGR02104, pulA_typeI, pullulanase, type I. Pullulan is an
unusual, industrially important polysaccharide in which
short alpha-1,4 chains (maltotriose) are connected in
alpha-1,6 linkages. Enzymes that cleave alpha-1,6
linkages in pullulan and release maltotriose are called
pullulanases although pullulan itself may not be the
natural substrate. This family consists of pullulanases
related to the subfamilies described in TIGR02102 and
TIGR02103 but having a different domain architecture
with shorter sequences. Members are called type I
pullulanases.
Length = 605
Score = 33.8 bits (78), Expect = 0.059
Identities = 35/148 (23%), Positives = 65/148 (43%), Gaps = 34/148 (22%)
Query: 22 GFKEDVDVPIQEPLEWWQTSVFYHLYPRSFKDSNGDGV---GDLKGMIE---KLPE---- 71
G+++D ++ P + ++ Y L+ R F GV G G+ E K P
Sbjct: 113 GWEKDHGPRLENP----EDAIIYELHIRDFSIHENSGVKNKGKYLGLTETGTKGPNGVST 168
Query: 72 ---HLHDLGVGAVWISPIF---------KSPMADFGYDISDYLSFEPLFGD--------L 111
+L +LGV V + P+F + ++GYD +Y E + +
Sbjct: 169 GLDYLKELGVTHVQLLPVFDFAGVDEEDPNNAYNWGYDPLNYNVPEGSYSTNPYDPATRI 228
Query: 112 KDFETLKERLHALGIKILLDFVPNHTSN 139
++ + + + LH GI++++D V NHT +
Sbjct: 229 RELKQMIQALHENGIRVIMDVVYNHTYS 256
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 33.5 bits (77), Expect = 0.094
Identities = 14/48 (29%), Positives = 29/48 (60%)
Query: 92 ADFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSN 139
FGY ++++ + G +D + L ++ H+LG+++L+D V +H S
Sbjct: 280 GSFGYHVTNFFAVSSRSGTPEDLKYLIDKAHSLGLRVLMDVVHSHASK 327
>gnl|CDD|215519 PLN02960, PLN02960, alpha-amylase.
Length = 897
Score = 33.3 bits (76), Expect = 0.096
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 95 GYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTS 138
GY ++++ + FG DF+ L + H LG+ + LD V ++ +
Sbjct: 449 GYKVTNFFAVSSRFGTPDDFKRLVDEAHGLGLLVFLDIVHSYAA 492
>gnl|CDD|233264 TIGR01082, murC, UDP-N-acetylmuramate--alanine ligase. This model
describes the MurC protein in bacterial peptidoglycan
(murein) biosynthesis. In a few species (Mycobacterium
leprae, the Chlamydia), the amino acid may be L-serine
or glycine instead of L-alanine. A related protein,
UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-
diaminopimelate ligase (murein tripeptide ligase) is
described by model TIGR01081 [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 448
Score = 31.9 bits (73), Expect = 0.25
Identities = 26/115 (22%), Positives = 42/115 (36%), Gaps = 29/115 (25%)
Query: 72 HLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFG-DLKDFETLKERLHALGIKILL 130
+H +G+G + +S I + + + GY +S G D+ + T K RL ALGI I +
Sbjct: 1 KIHFVGIGGIGMSGIAEI-LLNRGYQVS---------GSDIAENATTK-RLEALGIPIYI 49
Query: 131 DFVPNHTSNQ-----HEWFKKSL--------ANIP--PYK--CASLLARLHDLGV 168
+ + K IP A L+ H + V
Sbjct: 50 GHSAENLDDADVVVVSAAIKDDNPEIVEAKERGIPVIRRAEMLAELMRFRHSIAV 104
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 30.9 bits (71), Expect = 0.44
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 98 ISDYLSFEPLFGDLKDFETLKERLHALGIKILLDF 132
+ DYL E + FE LKE L ALGI ++D
Sbjct: 220 LLDYLDEE----SKEHFEELKELLDALGIPYVIDP 250
>gnl|CDD|227018 COG4672, gp18, Phage-related protein [Function unknown].
Length = 231
Score = 30.1 bits (68), Expect = 0.81
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 15/60 (25%)
Query: 32 QEPLEWWQTSVFYHLYP---RSFKDSNGDG--------VGDLKGMIEKLPEHLHDLGVGA 80
EP+ WQ Y YP F + NG G V +L G++ + E L L VGA
Sbjct: 45 GEPV-TWQ-GREYQAYPIDGSGF-EMNGKGSSARPSLTVSNLFGLVTGMAEDLQSL-VGA 100
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 29.5 bits (67), Expect = 1.4
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 98 ISDYLSFEPLFGDLKDFETLKERLHALGIKILLDF 132
+ DYL E L+ E L L ALGI +D
Sbjct: 232 LLDYLDEE----SLEHLEELLALLDALGISYEIDP 262
>gnl|CDD|233729 TIGR02103, pullul_strch, alpha-1,6-glucosidases, pullulanase-type.
Members of this protein family include secreted (or
membrane-anchored) pullulanases of Gram-negative
bacteria and pullulanase-type starch debranching enzymes
of plants. Both enzymes hydrolyze alpha-1,6 glycosidic
linkages. Pullulan is an unusual, industrially important
polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. This
family is closely homologous to, but architecturally
different from, the Gram-positive pullulanases of
Gram-positive bacteria (TIGR02102) [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 898
Score = 29.8 bits (67), Expect = 1.5
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 111 LKDFETLKERLHALGIKILLDFVPNHT--SNQHEWFKKSLANIPP 153
+K+F + + L+ G+ +++D V NHT S ++ + L I P
Sbjct: 403 IKEFREMVQALNKTGLNVVMDVVYNHTNASGPND--RSVLDKIVP 445
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 29.4 bits (67), Expect = 1.7
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 98 ISDYLSFEPLFGDLKDFETLKERLHALGIKILLDF 132
I D+L E FE LKE L ALGI ++D
Sbjct: 219 ILDFLDEE----SRAHFEELKELLDALGIPYVIDP 249
>gnl|CDD|165762 PLN00196, PLN00196, alpha-amylase; Provisional.
Length = 428
Score = 29.1 bits (65), Expect = 1.8
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 16/74 (21%)
Query: 77 GVGAVWISPIFKSPMADFGY--------DISDYLSFEPLFGDLKDFETLKERLHALGIKI 128
G+ VW+ P S +++ GY D S Y G+ ++L E H G+++
Sbjct: 57 GITHVWLPPPSHS-VSEQGYMPGRLYDLDASKY-------GNEAQLKSLIEAFHGKGVQV 108
Query: 129 LLDFVPNHTSNQHE 142
+ D V NH + +H+
Sbjct: 109 IADIVINHRTAEHK 122
>gnl|CDD|235152 PRK03705, PRK03705, glycogen debranching enzyme; Provisional.
Length = 658
Score = 29.2 bits (66), Expect = 1.8
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 90 PMADFGYDISDYLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHT 137
P+A F D Y S L +F + LH GI+++LD V NH+
Sbjct: 223 PLAMFALD-PAYASGPE--TALDEFRDAVKALHKAGIEVILDVVFNHS 267
>gnl|CDD|232840 TIGR00129, fdhD_narQ, formate dehydrogenase family accessory
protein FdhD. FdhD in E. coli and NarQ in B. subtilis
are required for the activity of formate dehydrogenase.
The gene name in B. subtilis reflects the requirement of
the neighboring gene narA for nitrate assimilation, for
which NarQ is not required. In some species, the gene is
associated not with a known formate dehydrogenase but
with a related putative molybdopterin-binding
oxidoreductase. A reasonable hypothesis is that this
protein helps prepare a required cofactor for assembly
into the holoenzyme [Energy metabolism, Anaerobic,
Energy metabolism, Electron transport].
Length = 237
Score = 29.0 bits (65), Expect = 2.0
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 70 PEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLKD--FETLKER 120
P++L + VG + I SP G +I D ++ E + DL F LKE
Sbjct: 27 PKNLEEFAVGFLLSEGIINSPDDIEGIEIDDNINIE-VQIDLSSRRFMILKEN 78
>gnl|CDD|234367 TIGR03828, pfkB, 1-phosphofructokinase. This enzyme acts in
concert with the fructose-specific phosphotransferase
system (PTS) which imports fructose as
fructose-1-phosphate. The action of
1-phosphofructokinase results in
beta-D-fructose-1,6-bisphosphate and is an entry point
into glycolysis (GenProp0688).
Length = 304
Score = 28.7 bits (65), Expect = 2.2
Identities = 18/80 (22%), Positives = 24/80 (30%), Gaps = 25/80 (31%)
Query: 114 FETLKERLHALGIKILLD--------------FV--PNHTSNQHE---WFKKSLANIPPY 154
+ L G K++LD F+ PN E F + L
Sbjct: 146 YAELIALAREKGAKVILDTSGEALRDGLKAKPFLIKPND----EELEELFGRELKT--LE 199
Query: 155 KCASLLARLHDLGVGAVWIS 174
+ L DLG V IS
Sbjct: 200 EIIEAARELLDLGAENVLIS 219
>gnl|CDD|234133 TIGR03168, 1-PFK, hexose kinase, 1-phosphofructokinase family.
This family consists largely of 1-phosphofructokinases,
but also includes tagatose-6-kinases and
6-phosphofructokinases.
Length = 303
Score = 28.7 bits (65), Expect = 2.4
Identities = 16/81 (19%), Positives = 22/81 (27%), Gaps = 27/81 (33%)
Query: 114 FETLKERLHALGIKILLDFVPNHTS-----------------NQHE---WFKKSLANIPP 153
+ L G K++LD TS N E F + L
Sbjct: 146 YAQLIAIARKRGAKVILD-----TSGEALREALAAKPFLIKPNHEELEELFGRELKT--E 198
Query: 154 YKCASLLARLHDLGVGAVWIS 174
+ L D G V +S
Sbjct: 199 EEIIEAARELLDRGAENVLVS 219
>gnl|CDD|183150 PRK11468, PRK11468, dihydroxyacetone kinase subunit DhaK;
Provisional.
Length = 356
Score = 28.8 bits (65), Expect = 2.4
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 109 GDLKDFETLKERLHALGIK---ILLD 131
GD+ +FET E LH G+K +L+D
Sbjct: 108 GDVLNFETATELLHDSGVKVTTVLID 133
>gnl|CDD|133121 cd06589, GH31, The enzymes of glycosyl hydrolase family 31 (GH31)
occur in prokaryotes, eukaryotes, and archaea with a
wide range of hydrolytic activities, including
alpha-glucosidase (glucoamylase and sucrase-isomaltase),
alpha-xylosidase, 6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein. In most cases, the pyranose
moiety recognized in subsite -1 of the substrate binding
site is an alpha-D-glucose, though some GH31 family
members show a preference for alpha-D-xylose. Several
GH31 enzymes can accommodate both glucose and xylose and
different levels of discrimination between the two have
been observed. Most characterized GH31 enzymes are
alpha-glucosidases. In mammals, GH31 members with
alpha-glucosidase activity are implicated in at least
three distinct biological processes. The lysosomal acid
alpha-glucosidase (GAA) is essential for glycogen
degradation and a deficiency or malfunction of this
enzyme causes glycogen storage disease II, also known as
pompe disease. In the endoplasmic reticulum,
alpha-glucosidase II catalyzes the second step in the
N-linked oligosaccharide processing pathway that
constitutes part of the quality control system for
glycoprotein folding and maturation. The intestinal
enzymes sucrase-isomaltase (SI) and maltase-glucoamylase
(MGAM) play key roles in the final stage of carbohydrate
digestion, making alpha-glucosidase inhibitors useful in
the treatment of type 2 diabetes. GH31
alpha-glycosidases are retaining enzymes that cleave
their substrates via an acid/base-catalyzed,
double-displacement mechanism involving a covalent
glycosyl-enzyme intermediate. Two aspartic acid residues
have been identified as the catalytic nucleophile and
the acid/base, respectively.
Length = 265
Score = 28.5 bits (64), Expect = 2.6
Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 18/85 (21%)
Query: 91 MADFGYDISD-YLSFEPLFGDLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLA 149
+ D Y +F+ G + +++ + LH G+K+ V EW+ +
Sbjct: 44 VLDDDYTDGYGDFTFDWDAGKFPNPKSMIDELHDNGVKL----VLWIDPYIREWWAE--- 96
Query: 150 NIPPYKCASLLARLH-DLGVGAVWI 173
++ +L LGV W
Sbjct: 97 ---------VVKKLLVSLGVDGFWT 112
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 28.9 bits (66), Expect = 2.6
Identities = 19/57 (33%), Positives = 21/57 (36%), Gaps = 27/57 (47%)
Query: 96 YDISDYLSFEPL--------------------FGD---LKDFETLKERLHALGIKIL 129
YD SD L FEPL FG LK L + L A G+ IL
Sbjct: 605 YDTSDRLYFEPLTLEDVLEIIEKEKPKGVIVQFGGQTPLK----LAKALEAAGVPIL 657
>gnl|CDD|217983 pfam04241, DUF423, Protein of unknown function (DUF423). This
family of proteins with unknown function is a possible
integral membrane protein from Caenorhabditis elegans.
This family of proteins has GO references indicating
the protein is involved in nematode larval development
and is a positive regulator of growth rate.
Length = 89
Score = 26.7 bits (60), Expect = 3.1
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 32 QEPLEWWQTSVFYHLY 47
E LE ++T+V Y LY
Sbjct: 16 PEQLEAFETAVQYQLY 31
>gnl|CDD|99965 cd03791, GT1_Glycogen_synthase_DULL1_like, This family is most
closely related to the GT1 family of
glycosyltransferases. Glycogen synthase catalyzes the
formation and elongation of the alpha-1,4-glucose
backbone using ADP-glucose, the second and key step of
glycogen biosynthesis. This family includes starch
synthases of plants, such as DULL1 in Zea mays and
glycogen synthases of various organisms.
Length = 476
Score = 28.3 bits (64), Expect = 3.4
Identities = 14/73 (19%), Positives = 24/73 (32%), Gaps = 4/73 (5%)
Query: 58 GVGDLKGMIEKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLKDFETL 117
G+GD ++ LP+ L LG I P + + D L + +
Sbjct: 17 GLGD---VVGALPKALAKLGHDVRVIMPKYGR-ILDELRGQLLVLRLFGVPVGGRPEYVG 72
Query: 118 KERLHALGIKILL 130
L G+ +
Sbjct: 73 VFELPVDGVPVYF 85
>gnl|CDD|216656 pfam01709, Transcrip_reg, Transcriptional regulator. This is a
family of transcriptional regulators. In mammals, it
activates the transcription of mitochondrially-encoded
COX1. In bacteria, it negatively regulates the
quorum-sensing response regulator by binding to its
promoter region.
Length = 234
Score = 27.8 bits (63), Expect = 3.5
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 103 SFEPLFGDLKDFETLKERLHALGIKIL---LDFVPNHT 137
S E + D DFE +K+ L G++I + +P +T
Sbjct: 166 SIE-VITDPTDFEAVKKALEEAGLEIESAEITMIPQNT 202
>gnl|CDD|239063 cd02150, NADPH_oxidoreductase_1, NAD(P)H:flavin oxidoreductase-like
family 1. A subfamily of the nitroreductase family
containing uncharacterized proteins that are similar to
nitroreductase. Nitroreductase catalyzes the reduction
of nitroaromatic compounds such as nitrotoluenes,
nitrofurans and nitroimidazoles. This process requires
NAD(P)H as electron donor in an obligatory two-electron
transfer and uses FMN as cofactor. The enzyme is
typically a homodimer. Members of this family are also
called NADH dehydrogenase, oxygen-insensitive NAD(P)H
nitrogenase or dihydropteridine reductase.
Length = 166
Score = 27.6 bits (62), Expect = 3.8
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 159 LLARLHDLGVGAVWI-SPIFKSPMA 182
LLA H LG+GAVW+ F+ +
Sbjct: 100 LLA-AHALGLGAVWLGVYPFEERVE 123
>gnl|CDD|219550 pfam07745, Glyco_hydro_53, Glycosyl hydrolase family 53. This
domain belongs to family 53 of the glycosyl hydrolase
classification. These enzymes are enzymes are endo-1,4-
beta-galactanases (EC:3.2.1.89). The structure of this
domain is known and has a TIM barrel fold.
Length = 332
Score = 27.7 bits (62), Expect = 5.1
Identities = 26/87 (29%), Positives = 36/87 (41%), Gaps = 30/87 (34%)
Query: 50 SFKDSNGDGVGDLKGMIEKLPEHLHDLGVGA----VWISPIFKSPMADFGYDISDYLSFE 105
S+K+ NG DL + L D GV + VW++P D G
Sbjct: 18 SYKNENGQ-TQDL----FTI---LKDAGVNSIRLRVWVNP------YDTGN--------- 54
Query: 106 PLFGDLKDFETLKERLHALGIKILLDF 132
DL D + +R A G+K+LLDF
Sbjct: 55 ---NDLDDVIEIAKRAKAAGMKVLLDF 78
>gnl|CDD|172200 PRK13652, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 277
Score = 27.5 bits (61), Expect = 5.3
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 113 DFETLKER----LHALGIKILLDFVPNHTS 138
D ET+ R LH LG++ L D VP+H S
Sbjct: 110 DEETVAHRVSSALHMLGLEELRDRVPHHLS 139
>gnl|CDD|153111 cd01052, DPSL, DPS-like protein, ferritin-like diiron-binding
domain. DPSL (DPS-like). DPSL is a phylogenetically
distinct class within the ferritin-like superfamily, and
similar in many ways to the DPS (DNA Protecting protein
under Starved conditions) proteins. Like DPS, these
proteins are expressed in response to oxidative stress,
form dodecameric cage-like particles, preferentially
utilize hydrogen peroxide in the controlled oxidation of
iron, and possess a short N-terminal extension
implicated in stabilizing cellular DNA. This domain is
a member of a broad superfamily of ferritin-like
diiron-carboxylate proteins. These proteins are
distantly related to bacterial ferritins which assemble
24 monomers, each of which have a four-helix bundle
with a fifth shorter helix at the C terminus and a
diiron (ferroxidase) center. Ferritins contain a center
where oxidation of ferrous iron by molecular oxygen
occurs, facilitating the detoxification of iron,
protection against dioxygen and radical products, and
storage of iron in the ferric form. Many of the
conserved residues of a diiron center are present in
this domain.
Length = 148
Score = 26.9 bits (60), Expect = 5.4
Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 8/45 (17%)
Query: 110 DLKDFETLKERLHALGIKILLDFVPNHTSNQHEWFKKSLANIPPY 154
+L E L ER++ LG D +W++ S
Sbjct: 51 ELNHAELLAERIYELGGTPPRDP--------KDWYEISGCKCGYL 87
>gnl|CDD|238570 cd01164, FruK_PfkB_like, 1-phosphofructokinase (FruK), minor
6-phosphofructokinase (pfkB) and related sugar kinases.
FruK plays an important role in the predominant pathway
for fructose utilisation.This group also contains
tagatose-6-phophate kinase, an enzyme of the tagatose
6-phosphate pathway, which responsible for breakdown of
the galactose moiety during lactose metabolism by
bacteria such as L. lactis.
Length = 289
Score = 27.5 bits (62), Expect = 5.5
Identities = 14/82 (17%), Positives = 25/82 (30%), Gaps = 27/82 (32%)
Query: 113 DFETLKERLHALGIKILLDFVPNHTS-----------------NQHE---WFKKSLANIP 152
+ L G +++LD TS N+ E F + L +
Sbjct: 146 FYAELVRLAREKGARVILD-----TSGEALLAALAAKPFLIKPNREELEELFGRPLGDEE 200
Query: 153 PYKCASLLARLHDLGVGAVWIS 174
+ +L + G V +S
Sbjct: 201 DVI--AAARKLIERGAENVLVS 220
>gnl|CDD|233599 TIGR01853, lipid_A_lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine
N-acyltransferase. This model describes LpxD, an enzyme
for the biosynthesis of lipid A, a component
oflipopolysaccharide (LPS) in the outer membrane outer
leaflet of most Gram-negative bacteria. Some differences
are found between lipid A of different species. This
protein represents the third step from
UDP-N-acetyl-D-glucosamine. The group added at this step
generally is 14:0(3-OH) (myristate) but may vary; in
Aquifex it appears to be 16:0(3-OH) (palmitate) [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 324
Score = 27.3 bits (61), Expect = 6.4
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 67 EKLPEHLHDLGVGAVWISPIFKSPMADFGYDISD--YLSFEPL 107
K +HL GAV +SP + A + YL+F +
Sbjct: 38 PKYLKHLKSSQAGAVIVSPDDQGLPAKCAALVVKDPYLAFAKV 80
>gnl|CDD|177990 PLN02361, PLN02361, alpha-amylase.
Length = 401
Score = 27.5 bits (61), Expect = 7.0
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 67 EKLPEHLHDLGVGAVWISPIFKSPMADFGYDISDYLSFEPLFGDLKDFETLKERLHALGI 126
K+P+ L G + W+ P +S +A GY + S +G ++L ++ +
Sbjct: 33 GKVPD-LAKSGFTSAWLPPPSQS-LAPEGYLPQNLYSLNSAYGSEHLLKSLLRKMKQYNV 90
Query: 127 KILLDFVPNH 136
+ + D V NH
Sbjct: 91 RAMADIVINH 100
>gnl|CDD|178296 PLN02693, PLN02693, IAA-amino acid hydrolase.
Length = 437
Score = 27.3 bits (60), Expect = 7.9
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 21 VGFKEDVD-VPIQEPLEWWQTSVFYHLYPRSFKDSNGDG-VGDLKGMIEKLPEHLHDL 76
V + D+D +PIQE +EW S P DG V L G + L EH H L
Sbjct: 105 VALRADMDALPIQEAVEWEHKSKI----PGKMHACGHDGHVAMLLGAAKILQEHRHHL 158
>gnl|CDD|147930 pfam06035, BTLCP, Bacterial transglutaminase-like cysteine
proteinase BTLCP. Members of this family are predicted
to be bacterial transglutaminase-like cysteine
proteinases. They contain a conserved Cys-His-Asp
catalytic triad. Their structure is predicted to be
similar to that of Salmonella typhimurium
N-hydroxyarylamine O-acetyltransferase, in pfam00797,
however they lack the sub-domain which is important for
arylamine recognition.
Length = 169
Score = 26.4 bits (59), Expect = 8.6
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 90 PMADF-GYDISDYLSFEPLFGDLKDFETLKER-LHALGI 126
PM D Y + + ++ GD +D+ LK + L GI
Sbjct: 57 PMTDMEIYGVEERWAYPTGAGDCEDYALLKRKMLIEAGI 95
>gnl|CDD|216321 pfam01136, Peptidase_U32, Peptidase family U32.
Length = 232
Score = 26.9 bits (60), Expect = 9.0
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 65 MIEKLPEHLHDLGVGAVWISPIFKSP 90
+IE+LPE L + GV ++ I KSP
Sbjct: 158 LIEELPE-LLEAGVDSLKIEGRMKSP 182
>gnl|CDD|200480 cd11341, AmyAc_Pullulanase_LD-like, Alpha amylase catalytic domain
found in Pullulanase (also called dextrinase;
alpha-dextrin endo-1,6-alpha glucosidase), limit
dextrinase, and related proteins. Pullulanase is an
enzyme with action similar to that of isoamylase; it
cleaves 1,6-alpha-glucosidic linkages in pullulan,
amylopectin, and glycogen, and in alpha-and beta-amylase
limit-dextrins of amylopectin and glycogen. Pullulanases
are very similar to limit dextrinases, although they
differ in their action on glycogen and the rate of
hydrolysis of 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 = 406
Score = 27.1 bits (61), Expect = 9.1
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 112 KDFETLKERLHALGIKILLDFVPNHT 137
K+F+ + + LH GI++++D V NHT
Sbjct: 107 KEFKEMVQALHKNGIRVIMDVVYNHT 132
>gnl|CDD|163566 TIGR03854, F420_MSMEG_3544, probable F420-dependent oxidoreductase,
MSMEG_3544 family. Coenzyme F420 has a limited
phylogenetic distribution, including methanogenic
archaea, Mycobacterium tuberculosis and related species,
Colwellia psychrerythraea 34H, Rhodopseudomonas
palustris HaA2, and others. Partial phylogenetic
profiling identifies protein subfamilies, within the
larger family called luciferase-like monooxygenanases
(pfam00296), that appear only in F420-positive genomes
and are likely to be F420-dependent. This model
describes a small family, closely related to other such
families in the putative F420-binding region,
exemplified by MSMEG_3544 in Mycobacterium smegmatis
[Unknown function, Enzymes of unknown specificity].
Length = 290
Score = 26.7 bits (59), Expect = 9.9
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 149 ANIPPYKCASLLARLHDLGVGAVWISPIFKSPMAD 183
A++ P + +++ RL GV ++W+S + SP D
Sbjct: 8 ADVAPAELPAIVDRLESTGVDSLWLSELVYSPAVD 42
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
0.323 0.142 0.457
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: 12,077,320
Number of extensions: 1166330
Number of successful extensions: 1603
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1494
Number of HSP's successfully gapped: 165
Length of query: 224
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 131
Effective length of database: 6,812,680
Effective search space: 892461080
Effective search space used: 892461080
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: 57 (25.8 bits)