RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9004
(237 letters)
>gnl|CDD|200460 cd11321, AmyAc_bac_euk_BE, Alpha amylase catalytic domain found in
bacterial and eukaryotic branching enzymes. Branching
enzymes (BEs) catalyze the formation of alpha-1,6 branch
points in either glycogen or starch by cleavage of the
alpha-1,4 glucosidic linkage yielding a non-reducing end
oligosaccharide chain, and subsequent attachment to the
alpha-1,6 position. By increasing the number of
non-reducing ends, glycogen is more reactive to
synthesis and digestion as well as being more soluble.
This group includes bacterial and eukaryotic proteins.
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 406
Score = 356 bits (917), Expect = e-124
Identities = 135/174 (77%), Positives = 147/174 (84%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLW 103
FGTPE LKYL+D H G+ VLLDVVHSHASKNVLDGLN FDGT C+FH+G RG HPLW
Sbjct: 84 FGTPEDLKYLIDTAHGMGIAVLLDVVHSHASKNVLDGLNMFDGTDGCYFHEGERGNHPLW 143
Query: 104 DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYFG 163
DSRLFNY + EVLRFLLSNLRW+LEEY+FDGFRFDGVTSMLYH+HG G GFSG Y EYFG
Sbjct: 144 DSRLFNYGKWEVLRFLLSNLRWWLEEYRFDGFRFDGVTSMLYHHHGLGTGFSGDYGEYFG 203
Query: 164 LNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDYRLG 217
LNVD DAL+YLM+AN LH+ YP ITIAEDVSGMP CRPV+EGG GFDYRL
Sbjct: 204 LNVDEDALVYLMLANDLLHELYPNAITIAEDVSGMPGLCRPVSEGGIGFDYRLA 257
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 325 bits (835), Expect = e-107
Identities = 125/173 (72%), Positives = 140/173 (80%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLW 103
GTPE LKYL+D+ H GL VL+DVVHSHASKN LDGLN FDGT +FH GPRG H LW
Sbjct: 296 SGTPEDLKYLIDKAHSLGLRVLMDVVHSHASKNTLDGLNGFDGTDGSYFHSGPRGYHWLW 355
Query: 104 DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYFG 163
DSRLFNY EVLRFLLSNLRW+LEEY+FDGFRFDGVTSMLYH+HG F+G+Y+EYFG
Sbjct: 356 DSRLFNYGNWEVLRFLLSNLRWWLEEYKFDGFRFDGVTSMLYHHHGLQMAFTGNYNEYFG 415
Query: 164 LNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDYRL 216
+ D DA++YLM+AN LH YPE +TIAEDVSGMP CRPV EGG GFDYRL
Sbjct: 416 MATDVDAVVYLMLANDLLHGLYPEAVTIAEDVSGMPTLCRPVQEGGVGFDYRL 468
>gnl|CDD|215519 PLN02960, PLN02960, alpha-amylase.
Length = 897
Score = 216 bits (552), Expect = 3e-65
Identities = 90/171 (52%), Positives = 117/171 (68%), Gaps = 1/171 (0%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLW 103
FGTP+ K LVDE H GL V LD+VHS+A+ + + GL+ FDG+ C+FH G RG H W
Sbjct: 462 FGTPDDFKRLVDEAHGLGLLVFLDIVHSYAAADEMVGLSLFDGSNDCYFHSGKRGHHKRW 521
Query: 104 DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYFG 163
+R+F Y + EVL FLLSNL W++ EY+ DGF+F + SMLY ++G F+G DEY
Sbjct: 522 GTRMFKYGDHEVLHFLLSNLNWWVTEYRVDGFQFHSLGSMLYTHNGFAS-FTGDLDEYCN 580
Query: 164 LNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDY 214
VD DALIYL++AN+ LH +P IITIAED + P C P ++GG GFDY
Sbjct: 581 QYVDRDALIYLILANEMLHQLHPNIITIAEDATFYPGLCEPTSQGGLGFDY 631
>gnl|CDD|178782 PLN03244, PLN03244, alpha-amylase; Provisional.
Length = 872
Score = 191 bits (486), Expect = 4e-56
Identities = 94/213 (44%), Positives = 136/213 (63%), Gaps = 11/213 (5%)
Query: 9 PEQLKYLVDECHKAGLFGTPEQLKYLVDECHK-------AGLFGTPEQLKYLVDECHKAG 61
PE L+ + ECH G+ G+ ++ + K + +GTP+ K LVDE H G
Sbjct: 398 PESLR--IYECH-VGISGSEPKISSFEEFTEKVTNFFAASSRYGTPDDFKRLVDEAHGLG 454
Query: 62 LYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLWDSRLFNYSEIEVLRFLLS 121
L V LD+VHS+A+ + + GL+ FDG+ C+FH G RG H W +R+F Y +++VL FL+S
Sbjct: 455 LLVFLDIVHSYAAADEMVGLSLFDGSNDCYFHTGKRGHHKHWGTRMFKYGDLDVLHFLIS 514
Query: 122 NLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYFGLNVDTDALIYLMVANKFL 181
NL W++ EYQ DGF+F + SM+Y ++G F+G D+Y VD DAL+YL++AN+ L
Sbjct: 515 NLNWWITEYQIDGFQFHSLASMIYTHNGFAS-FNGDLDDYCNQYVDKDALMYLILANEIL 573
Query: 182 HDKYPEIITIAEDVSGMPASCRPVTEGGTGFDY 214
H +P+IITIAED + P C P ++GG GFDY
Sbjct: 574 HALHPKIITIAEDATYYPGLCEPTSQGGLGFDY 606
>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 = 154 bits (391), Expect = 7e-45
Identities = 73/172 (42%), Positives = 101/172 (58%), Gaps = 5/172 (2%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPR-GTHPL 102
+GTP+ KY VD CH+AG+ V+LD V H K+ GL FDGT + + PR G HP
Sbjct: 104 YGTPDDFKYFVDACHQAGIGVILDWVPGHFPKD-DHGLARFDGT-PLYEYPDPRKGEHPD 161
Query: 103 WDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYF 162
W + F+Y EV FL+SN ++LEEY DG R D V+SMLY ++ G G +
Sbjct: 162 WGTLNFDYGRNEVRSFLISNALYWLEEYHIDGLRVDAVSSMLYLDYDRGPGEWIPNI--Y 219
Query: 163 GLNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDY 214
G N + +A+ +L N +H ++P ++TIAE+ + P PV EGG GFDY
Sbjct: 220 GGNENLEAIEFLKELNTVIHKRHPGVLTIAEESTAWPGVTAPVEEGGLGFDY 271
>gnl|CDD|223373 COG0296, GlgB, 1,4-alpha-glucan branching enzyme [Carbohydrate
transport and metabolism].
Length = 628
Score = 155 bits (395), Expect = 5e-44
Identities = 68/172 (39%), Positives = 91/172 (52%), Gaps = 3/172 (1%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLW 103
+GTPE K LVD H+AG+ V+LD V +H + + L FDGT D RG H W
Sbjct: 210 YGTPEDFKALVDAAHQAGIGVILDWVPNHFPPDG-NYLARFDGTFLYEHEDPRRGEHTDW 268
Query: 104 DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYFG 163
+ +FNY EV FLL+N ++LEEY DG R D V SMLY +EY G
Sbjct: 269 GTAIFNYGRNEVRNFLLANALYWLEEYHIDGLRVDAVASMLY-LDYSRAEGEWVPNEY-G 326
Query: 164 LNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDYR 215
+ +A +L N +H++ P +TIAE+ + P PV GG GF Y+
Sbjct: 327 GRENLEAAEFLRNLNSLIHEEEPGAMTIAEESTDDPHVTLPVAIGGLGFGYK 378
>gnl|CDD|237052 PRK12313, PRK12313, glycogen branching enzyme; Provisional.
Length = 633
Score = 144 bits (366), Expect = 5e-40
Identities = 64/180 (35%), Positives = 99/180 (55%), Gaps = 20/180 (11%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGP-RGTHPL 102
+GTPE YLVD H+ G+ V+LD V H K+ DGL FDGT + + P R +P
Sbjct: 216 YGTPEDFMYLVDALHQNGIGVILDWVPGHFPKDD-DGLAYFDGT-PLYEYQDPRRAENPD 273
Query: 103 WDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEY- 161
W + F+ + EV FL+S+ ++L+EY DG R D V++MLY + YDE
Sbjct: 274 WGALNFDLGKNEVRSFLISSALFWLDEYHLDGLRVDAVSNMLYLD----------YDEEG 323
Query: 162 ------FGLNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDYR 215
+G + +A+ +L N+ ++ ++P+++ IAE+ + P PV GG GFDY+
Sbjct: 324 EWTPNKYGGRENLEAIYFLQKLNEVVYLEHPDVLMIAEESTAWPKVTGPVEVGGLGFDYK 383
>gnl|CDD|235445 PRK05402, PRK05402, glycogen branching enzyme; Provisional.
Length = 726
Score = 131 bits (333), Expect = 3e-35
Identities = 74/178 (41%), Positives = 103/178 (57%), Gaps = 17/178 (9%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLD--GLNEFDGTQACFFHDGPR-GTH 100
FGTP+ +Y VD CH+AG+ V+LD V +H K D GL FDGT A + H PR G H
Sbjct: 311 FGTPDDFRYFVDACHQAGIGVILDWVPAHFPK---DAHGLARFDGT-ALYEHADPREGEH 366
Query: 101 PLWDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDE 160
P W + +FNY EV FL++N ++LEE+ DG R D V SMLY ++ EG E
Sbjct: 367 PDWGTLIFNYGRNEVRNFLVANALYWLEEFHIDGLRVDAVASMLYLDYSRKEG------E 420
Query: 161 Y----FGLNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDY 214
+ +G + +A+ +L N +H+++P +TIAE+ + P RP EGG GF Y
Sbjct: 421 WIPNIYGGRENLEAIDFLRELNAVVHEEFPGALTIAEESTAWPGVTRPTEEGGLGFGY 478
>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 = 126 bits (319), Expect = 1e-33
Identities = 66/172 (38%), Positives = 94/172 (54%), Gaps = 3/172 (1%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLW 103
FGTP+ Y VD CH+AG+ V+LD V H K+ GL EFDGT D G H W
Sbjct: 207 FGTPDDFMYFVDACHQAGIGVILDWVPGHFPKDDH-GLAEFDGTPLYEHKDPRDGEHWDW 265
Query: 104 DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYFG 163
+ +F+Y EV FL++N ++ E Y DG R D V SMLY ++ EG G
Sbjct: 266 GTLIFDYGRPEVRNFLVANALYWAEFYHIDGLRVDAVASMLYLDYSRDEG--EWSPNEDG 323
Query: 164 LNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDYR 215
+ +A+ +L N+ +++ +P ++TIAE+ + P RP EGG GF Y+
Sbjct: 324 GRENLEAVEFLRKLNQTVYEAFPGVVTIAEESTEWPGVTRPTDEGGLGFHYK 375
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 110 bits (277), Expect = 6e-28
Identities = 61/176 (34%), Positives = 98/176 (55%), Gaps = 13/176 (7%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPR-GTHPLW 103
G+P+ VD CH+AG+ V+LD V +H + GL +FDG A + H PR G H W
Sbjct: 316 GSPDGFAQFVDACHRAGIGVILDWVSAHFPDDA-HGLAQFDGA-ALYEHADPREGMHRDW 373
Query: 104 DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYF- 162
++ ++NY EV +LL + ++E Y DG R D V SMLY ++G EG E+
Sbjct: 374 NTLIYNYGRPEVTAYLLGSALEWIEHYHLDGLRVDAVASMLYRDYGRAEG------EWVP 427
Query: 163 ---GLNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDYR 215
G + +A+ +L N+ + ++P ++TIAE+ + P P+++GG GF ++
Sbjct: 428 NAHGGRENLEAVAFLRQLNREIASQFPGVLTIAEESTAWPGVTAPISDGGLGFTHK 483
>gnl|CDD|237794 PRK14705, PRK14705, glycogen branching enzyme; Provisional.
Length = 1224
Score = 110 bits (277), Expect = 8e-28
Identities = 61/170 (35%), Positives = 94/170 (55%), Gaps = 5/170 (2%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPR-GTHPL 102
FG P++ ++LVD H+AG+ VLLD V +H K+ L +FDG Q + H P G HP
Sbjct: 811 FGHPDEFRFLVDSLHQAGIGVLLDWVPAHFPKDSW-ALAQFDG-QPLYEHADPALGEHPD 868
Query: 103 WDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYF 162
W + +F++ EV FL++N ++L+E+ DG R D V SMLY ++ EG F
Sbjct: 869 WGTLIFDFGRTEVRNFLVANALYWLDEFHIDGLRVDAVASMLYLDYSREEG--QWRPNRF 926
Query: 163 GLNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGF 212
G + +A+ +L N ++ +P + IAE+ + P P + GG GF
Sbjct: 927 GGRENLEAISFLQEVNATVYKTHPGAVMIAEESTAFPGVTAPTSHGGLGF 976
>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 = 97.2 bits (243), Expect = 2e-23
Identities = 55/175 (31%), Positives = 74/175 (42%), Gaps = 36/175 (20%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDG--LNEFDGTQACFFHDGPRGTHP 101
+G P+ LK LVD H+ GL V+LDVV++H DG L +F G +F D + P
Sbjct: 100 YGGPDDLKRLVDAAHRRGLAVILDVVYNHFGP---DGNYLWQFAGP---YFTD--DYSTP 151
Query: 102 LW-DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHN--HGCGEGFSGHY 158
W D+ F+ EV +F + N ++L EY DG R D V ++ + H E
Sbjct: 152 -WGDAINFDGPGDEVRQFFIDNALYWLREYHVDGLRLDAVHAIRDDSGWHFLQE------ 204
Query: 159 DEYFGLNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFD 213
L + A IAED P RP GG GFD
Sbjct: 205 -----LAREVRA-----------AAAGRPAHLIAEDDRNDPRLVRPPELGGAGFD 243
>gnl|CDD|237795 PRK14706, PRK14706, glycogen branching enzyme; Provisional.
Length = 639
Score = 92.0 bits (228), Expect = 2e-21
Identities = 60/184 (32%), Positives = 90/184 (48%), Gaps = 8/184 (4%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLW 103
GTPE KYLV+ H G+ V+LD V H + GL FDG + D +G H W
Sbjct: 213 LGTPEDFKYLVNHLHGLGIGVILDWVPGHFPTDES-GLAHFDGGPLYEYADPRKGYHYDW 271
Query: 104 DSRLFNYSEIEVLRFLL-SNLRWYLEEYQFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYF 162
++ +F+Y EV+ FL+ S L+W L+++ DG R D V SMLY + E +
Sbjct: 272 NTYIFDYGRNEVVMFLIGSALKW-LQDFHVDGLRVDAVASMLYLDFSRTEWVPNIH---- 326
Query: 163 GLNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVTEGGTGFDYRLGRPGLD 222
G + +A+ +L N+ H P + IAE+ + P P G GFDY+ ++
Sbjct: 327 GGRENLEAIAFLKRLNEVTHHMAPGCMMIAEESTSFPGVTVPTPY-GLGFDYKWAMGWMN 385
Query: 223 KSFY 226
+
Sbjct: 386 DTLA 389
>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 = 72.4 bits (178), Expect = 1e-14
Identities = 38/105 (36%), Positives = 53/105 (50%), Gaps = 16/105 (15%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSH--ASKNVLDGLNEFDGTQACFFHDGPRGTHP 101
+G P+ LK LVD H GL VLLDVV++H N L A +F D R + P
Sbjct: 156 YGGPDDLKALVDAAHGLGLGVLLDVVYNHFGPEGNYLPRF-------APYFTD--RYSTP 206
Query: 102 LWDSRLFNYSE---IEVLRFLLSNLRWYLEEYQFDGFRFDGVTSM 143
+ N+ EV R+++ N ++L EY FDG R D V ++
Sbjct: 207 WGAA--INFDGPGSDEVRRYIIDNALYWLREYHFDGLRLDAVHAI 249
>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 = 68.8 bits (169), Expect = 1e-13
Identities = 40/104 (38%), Positives = 53/104 (50%), Gaps = 14/104 (13%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEF-----DGTQACFFHDGPR- 97
+GTPE LK LVDECH+ G+ V+LDVV++HA +G + D D P
Sbjct: 78 YGTPEDLKRLVDECHQRGIAVILDVVYNHA-----EGQSPLARLYWDYWYNPPPADPPWF 132
Query: 98 ---GTHPLWDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
G H + FN+ F+ R++LEEY DGFRFD
Sbjct: 133 NVWGPHFYYVGYDFNHESPPTRDFVDDVNRYWLEEYHIDGFRFD 176
>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 = 61.4 bits (150), Expect = 4e-11
Identities = 27/100 (27%), Positives = 50/100 (50%), Gaps = 10/100 (10%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRG--THP 101
+GT E K LVDE H G+ V+LD V +H + + + ++ G T+
Sbjct: 72 YGTLEDFKALVDEAHDRGMKVILDWVANHTAWD-----HPLVEEHPEWYLRDSDGNITNK 126
Query: 102 LWDSRL---FNYSEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
++D +YS E+ +++ +++++ E+ DGFR D
Sbjct: 127 VFDWTDVADLDYSNPELRDYMIDAMKYWVREFDVDGFRCD 166
>gnl|CDD|224440 COG1523, PulA, Type II secretory pathway, pullulanase PulA and
related glycosidases [Carbohydrate transport and
metabolism].
Length = 697
Score = 53.5 bits (129), Expect = 3e-08
Identities = 32/101 (31%), Positives = 46/101 (45%), Gaps = 20/101 (19%)
Query: 50 LKYLVDECHKAGLYVLLDVVHSH-ASKNVLDGLNEFDGT--QACFFHDGPRGTHPLWDSR 106
K +V HKAG+ V+LDVV +H A N L F G + D D
Sbjct: 267 FKDMVKALHKAGIEVILDVVFNHTAEGNELGPTLSFRGIDPNYYYRLDP--------DGY 318
Query: 107 LFNYS----EIE-----VLRFLLSNLRWYLEEYQFDGFRFD 138
N + + V + ++ +LR+++EEY DGFRFD
Sbjct: 319 YSNGTGCGNTLNTEHPMVRKLIVDSLRYWVEEYHVDGFRFD 359
>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 = 52.5 bits (127), Expect = 4e-08
Identities = 33/120 (27%), Positives = 47/120 (39%), Gaps = 17/120 (14%)
Query: 43 LFGTPEQLKYLVDECHKAGLYVLLDVVHSHAS-------KNVLDG-----LNEFDGTQAC 90
GT E K LV+E HK G+ V+LD V +H + G + F
Sbjct: 98 HLGTEEDFKELVEEAHKRGIRVILDGVFNHTGDDSPYFQDVLKYGESSAYQDWFSIYYFW 157
Query: 91 FFHDGPRGTHPLW--DSRL--FNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYH 146
+ + W L N EV +L S R++L+E DG+R D V + H
Sbjct: 158 PYFTDEPPNYESWWGVPSLPKLNTENPEVREYLDSVARYWLKEGDIDGWRLD-VADEVPH 216
>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 = 51.7 bits (125), Expect = 9e-08
Identities = 32/111 (28%), Positives = 46/111 (41%), Gaps = 35/111 (31%)
Query: 48 EQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGP----RG----- 98
++ K +V HKAG+ V+LDVV++H + E GP RG
Sbjct: 109 DEFKAMVKALHKAGIEVILDVVYNHTA--------EGG-------ELGPTLSFRGLDNAS 153
Query: 99 --THPLWDSRLFNYS---------EIEVLRFLLSNLRWYLEEYQFDGFRFD 138
NY+ VLR +L +LR+++ E DGFRFD
Sbjct: 154 YYRLDPDGPYYLNYTGCGNTLNTNHPVVLRLILDSLRYWVTEMHVDGFRFD 204
>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 = 50.3 bits (121), Expect = 2e-07
Identities = 27/127 (21%), Positives = 44/127 (34%), Gaps = 42/127 (33%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSH-ASKNVLDGLNEFDGT---------QACFFH 93
FGT + LK L HK G+Y+++DVV +H AS ++ C+
Sbjct: 94 FGTADDLKALSKALHKRGMYLMVDVVVNHMASAGPGSDVDYSSFVPFNDSSYYHPYCWIT 153
Query: 94 DGPRGTHPLWDSRLFNYSEIE--------------------VLRFLLSNLRWYLEEYQFD 133
D ++ N + +E V+ L ++ + Y D
Sbjct: 154 D--------YN----NQTSVEDCWLGDDVVALPDLNTENPFVVSTLNDWIKNLVSNYSID 201
Query: 134 GFRFDGV 140
G R D
Sbjct: 202 GLRIDTA 208
>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 = 50.6 bits (121), Expect = 2e-07
Identities = 33/100 (33%), Positives = 53/100 (53%), Gaps = 23/100 (23%)
Query: 49 QLKYLVDECHKAGLYVLLDVVHSHASK---------NVLDGLNEFDGTQACFFHDGPRG- 98
+ K L++E HK G+ V+LDVV++H +K N ++ DGT F G G
Sbjct: 556 EFKNLINEIHKRGMGVILDVVYNHTAKVYIFEDLEPNYYHFMDA-DGTPRTSFGGGRLGT 614
Query: 99 THPLWDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
TH + SR R L+ ++++ ++E++ DGFRFD
Sbjct: 615 THEM--SR----------RILVDSIKYLVDEFKVDGFRFD 642
>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 = 47.3 bits (113), Expect = 2e-06
Identities = 27/94 (28%), Positives = 52/94 (55%), Gaps = 8/94 (8%)
Query: 49 QLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGT-QACFFHDGPRGTHPLWDSRL 107
+LK ++ H+ G+ V++DVV++H + F+ T ++ GT + +
Sbjct: 230 ELKQMIQALHENGIRVIMDVVYNHTYSRE---ESPFEKTVPGYYYRYNEDGT-LSNGTGV 285
Query: 108 FN--YSEIEVLR-FLLSNLRWYLEEYQFDGFRFD 138
N SE E++R F++ ++ ++++EY DGFRFD
Sbjct: 286 GNDTASEREMMRKFIVDSVLYWVKEYNIDGFRFD 319
>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 = 44.9 bits (106), Expect = 1e-05
Identities = 23/97 (23%), Positives = 30/97 (30%), Gaps = 49/97 (50%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLW 103
GT E K LV HK G+ V+LD+V +H
Sbjct: 72 LGTEEDFKELVKAAHKRGIKVILDLVFNH------------------------------- 100
Query: 104 DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGV 140
++LRF L + DGFR D
Sbjct: 101 ----------DILRFWL--------DEGVDGFRLDAA 119
Score = 31.4 bits (71), Expect = 0.37
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 6 FGTPEQLKYLVDECHKAGL 24
GT E K LV HK G+
Sbjct: 72 LGTEEDFKELVKAAHKRGI 90
>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 = 44.2 bits (105), Expect = 2e-05
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKN 76
FGT E L+ LVD H G+YV+LD++ +H+
Sbjct: 97 FGTREDLRDLVDAAHARGIYVILDIILNHSGDV 129
Score = 27.3 bits (61), Expect = 7.5
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 6 FGTPEQLKYLVDECHKAGL 24
FGT E L+ LVD H G+
Sbjct: 97 FGTREDLRDLVDAAHARGI 115
>gnl|CDD|214758 smart00642, Aamy, Alpha-amylase domain.
Length = 166
Score = 42.7 bits (101), Expect = 3e-05
Identities = 17/31 (54%), Positives = 20/31 (64%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
FGT E K LVD H G+ V+LDVV +H S
Sbjct: 66 FGTMEDFKELVDAAHARGIKVILDVVINHTS 96
Score = 34.6 bits (80), Expect = 0.019
Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 9/66 (13%)
Query: 25 FGTPEQLKYLVDECHKAGLFGTPEQLKYLVDEC--HKAGLYVLLDVVHSHASKNVLDGLN 82
FGT E K LVD H G +K ++D H + LD + + L+
Sbjct: 66 FGTMEDFKELVDAAHARG-------IKVILDVVINHTSDGGFRLDAAKFPLNGSAFSLLD 118
Query: 83 EFDGTQ 88
F
Sbjct: 119 FFALAL 124
Score = 30.8 bits (70), Expect = 0.33
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 6 FGTPEQLKYLVDECHKAGL 24
FGT E K LVD H G+
Sbjct: 66 FGTMEDFKELVDAAHARGI 84
>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 = 43.9 bits (104), Expect = 4e-05
Identities = 32/116 (27%), Positives = 45/116 (38%), Gaps = 38/116 (32%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSH-ASKNVLDGLNEFDGTQACFFHDGP----RG- 98
G + K +V H AG+ V+LDVV++H A N GP RG
Sbjct: 242 GQVAEFKTMVRALHDAGIEVILDVVYNHTAEGN----------------ELGPTLSFRGI 285
Query: 99 -------THPLWDSRLFNY---------SEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
P N S VL+ ++ +LR+++ E DGFRFD
Sbjct: 286 DNASYYRLQPDDKRYYINDTGTGNTLNLSHPRVLQMVMDSLRYWVTEMHVDGFRFD 341
>gnl|CDD|236543 PRK09505, malS, alpha-amylase; Reviewed.
Length = 683
Score = 42.7 bits (101), Expect = 8e-05
Identities = 17/41 (41%), Positives = 23/41 (56%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEF 84
GT L+ LVDE H+ G+ +L DVV +H L + EF
Sbjct: 288 MGTEADLRTLVDEAHQRGIRILFDVVMNHTGYATLADMQEF 328
Score = 27.7 bits (62), Expect = 6.8
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 6 FGTPEQLKYLVDECHKAGL 24
GT L+ LVDE H+ G+
Sbjct: 288 MGTEADLRTLVDEAHQRGI 306
>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 = 41.9 bits (99), Expect = 1e-04
Identities = 26/115 (22%), Positives = 41/115 (35%), Gaps = 27/115 (23%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSH--ASKNVLDGLNE--FDGTQACFFHDGPRGTH 100
GT + K L HK G+ +++DVV +H + ++ L D G
Sbjct: 65 GTEDDFKALCAAAHKYGIKIIVDVVFNHMANEGSAIEDLWYPSADIELFSPEDFHGNGGI 124
Query: 101 PLWDSRLFNYSEIEVLRFLLSNL------RWYLEEYQ-----------FDGFRFD 138
W+ R +V + L L +++ Q DGFRFD
Sbjct: 125 SNWNDRW------QVTQGRLGGLPDLNTENPAVQQQQKAYLKALVALGVDGFRFD 173
>gnl|CDD|235152 PRK03705, PRK03705, glycogen debranching enzyme; Provisional.
Length = 658
Score = 41.6 bits (98), Expect = 2e-04
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 54 VDECHKAGLYVLLDVVHSHASKNVLDG----LNEFDGTQACFFHDGPRGTHPLWDS--RL 107
V HKAG+ V+LDVV +H+++ LDG L D ++ G + W
Sbjct: 248 VKALHKAGIEVILDVVFNHSAELDLDGPTLSLRGID--NRSYYWIREDGDYHNWTGCGNT 305
Query: 108 FNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSM 143
N S V+ + + LR+++E DGFRFD T +
Sbjct: 306 LNLSHPAVVDWAIDCLRYWVETCHVDGFRFDLATVL 341
>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 = 41.1 bits (97), Expect = 3e-04
Identities = 17/31 (54%), Positives = 21/31 (67%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
+GT E L L DE HK G++VLLD+V H S
Sbjct: 66 YGTNEDLVRLFDEAHKRGIHVLLDLVPGHTS 96
Score = 27.3 bits (61), Expect = 7.3
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 6 FGTPEQLKYLVDECHKAGL 24
+GT E L L DE HK G+
Sbjct: 66 YGTNEDLVRLFDEAHKRGI 84
>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 = 41.0 bits (97), Expect = 3e-04
Identities = 26/100 (26%), Positives = 48/100 (48%), Gaps = 22/100 (22%)
Query: 50 LKYLVDECHKAGLYVLLDVVHSH---ASKNVLDGL--------NEFDGTQACFFHDGPRG 98
K +V HK G+ V++DVV++H + + + + N DG F +G
Sbjct: 109 FKEMVQALHKNGIRVIMDVVYNHTYDSENSPFEKIVPGYYYRYNA-DGG----FSNGSGC 163
Query: 99 THPLWDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
+ R V ++++ +L+++ +EY+ DGFRFD
Sbjct: 164 GNDTASERPM------VRKYIIDSLKYWAKEYKIDGFRFD 197
>gnl|CDD|223443 COG0366, AmyA, Glycosidases [Carbohydrate transport and
metabolism].
Length = 505
Score = 41.1 bits (96), Expect = 3e-04
Identities = 40/185 (21%), Positives = 66/185 (35%), Gaps = 50/185 (27%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFH---------- 93
FGT E K LV+E HK G+ V+LD+V +H S + E ++
Sbjct: 73 FGTEEDFKELVEEAHKRGIKVILDLVFNHTS-DEHPWFKEARSSKPNPKRSDYYIWRDPD 131
Query: 94 -------------DGPRGTHPLWDSRL----------FNYSEIEVLRFLLSNLRWYLEEY 130
G T N+ EV LL ++++L +
Sbjct: 132 PDGTPPNNWFSVFGGDAWTWGNTGEYYLHLFSSEQPDLNWENPEVREELLDVVKFWL-DK 190
Query: 131 QFDGFRFDGVTSMLYHNHGCGEGFSGHYDEYFGLNVDTDALIYLMVANKFLHDKYPEIIT 190
DGFR D H + FGL + L +L +++L ++ P+++
Sbjct: 191 GVDGFRLDAAK---------------HISKDFGLPPSEENLTFLEEIHEYLREENPDVLI 235
Query: 191 IAEDV 195
E +
Sbjct: 236 YGEAI 240
>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 = 40.7 bits (96), Expect = 3e-04
Identities = 26/97 (26%), Positives = 43/97 (44%), Gaps = 20/97 (20%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLW 103
+G+ +L+ L+ H G+ V+ D+V +H ++ D G F P
Sbjct: 63 YGSEAELRSLIAALHAKGIKVIADIVINH--RSGPD-----TGE---DFGGAP------- 105
Query: 104 DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGV 140
D +++ EV L + L W + FDG+RFD V
Sbjct: 106 D---LDHTNPEVQNDLKAWLNWLKNDIGFDGWRFDFV 139
>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 = 41.0 bits (97), Expect = 3e-04
Identities = 27/131 (20%), Positives = 47/131 (35%), Gaps = 27/131 (20%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKN---VLDGLNEFDGTQACF--FHDGPRG 98
+GT E + L+ E HK G+ V++D+V +H S + + D + + D G
Sbjct: 66 YGTMEDFERLIAEAHKRGIKVIIDLVINHTSSEHPWFQEAASSPDSPYRDYYIWADDDPG 125
Query: 99 THPLWDSRL--------------------FNYSEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
W + N V + +++L++ DGFR D
Sbjct: 126 GWSSWGGNVWHKAGDGGYYYGAFWSGMPDLNLDNPAVREEIKKIAKFWLDK-GVDGFRLD 184
Query: 139 GVTSMLYHNHG 149
+Y N
Sbjct: 185 AAK-HIYENGE 194
>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 = 39.5 bits (93), Expect = 0.001
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSH 72
FG+ E K LV + H G+ +++D+V +H
Sbjct: 92 FGSNEDYKELVSKAHARGMKLIMDMVPNH 120
>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 = 39.2 bits (92), Expect = 0.001
Identities = 36/140 (25%), Positives = 49/140 (35%), Gaps = 43/140 (30%)
Query: 43 LFGTPEQLKYLVDECHKAGLYVLLDVVHSHAS-------KNVLDGLNEF----------- 84
LFGT + LV H GL V++D V SH S ++ N
Sbjct: 71 LFGTLDDFDRLVARAHALGLKVMIDQVLSHTSDQHPWFEESRQSRDNPKADWYVWADPKP 130
Query: 85 DGT-----QACFFHDGPRGTHPLWDSRL--------------FNYSEIEVLRFLLSNLRW 125
DG+ + F G WD R N+ EV LL R+
Sbjct: 131 DGSPPNNWLSVF--GGSAWQ---WDPRRGQYYLHNFLPSQPDLNFHNPEVQDALLDVARF 185
Query: 126 YLEEYQFDGFRFDGVTSMLY 145
+L+ DGFR D V ++
Sbjct: 186 WLDR-GVDGFRLDAVNFYMH 204
>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 = 38.8 bits (91), Expect = 0.002
Identities = 36/135 (26%), Positives = 46/135 (34%), Gaps = 40/135 (29%)
Query: 43 LFGTPEQLKYLVDECHKAGLYVLLDVVHSHAS------KNVLDGLNEFDGTQACFFHDG- 95
LFGT LV H+ GL V++D+V +H S + L F DG
Sbjct: 71 LFGTLADFDALVAAAHELGLRVIVDIVPNHTSDQHPWFQAALAAGPGSPERARYIFRDGR 130
Query: 96 -PRGTHPL--WDSR----------------------LF-------NYSEIEVLRFLLSNL 123
P G P W S LF N+ EV L
Sbjct: 131 GPDGELPPNNWQSVFGGPAWTRVTEPDGTDGQWYLHLFAPEQPDLNWDNPEVRAEFEDVL 190
Query: 124 RWYLEEYQFDGFRFD 138
R++L+ DGFR D
Sbjct: 191 RFWLDR-GVDGFRID 204
>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 = 38.1 bits (89), Expect = 0.003
Identities = 17/32 (53%), Positives = 19/32 (59%)
Query: 43 LFGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
LFGT E LV E H GL V+LD V +H S
Sbjct: 71 LFGTLEDFDRLVAEAHARGLKVILDFVPNHTS 102
>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 = 37.7 bits (88), Expect = 0.003
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSHASKN---VLDGLNEFDGTQACFFHDGPRGTHP 101
G E L+ H+ GL VLLD V +H ++ V L + G++ +H G P
Sbjct: 74 GDDEDFDALIAAAHERGLRVLLDGVFNHVGRSHPAVAQALEDGPGSEEDRWHGHAGGGTP 133
>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 = 37.9 bits (88), Expect = 0.004
Identities = 30/110 (27%), Positives = 50/110 (45%), Gaps = 33/110 (30%)
Query: 53 LVDECHKAGLYVLLDVV--HSHAS----KNVLDG--------LNEFDG--TQACFFHDGP 96
+V +K GL V++DVV H++AS ++VLD LNE G C +
Sbjct: 409 MVQALNKTGLNVVMDVVYNHTNASGPNDRSVLDKIVPGYYHRLNEDGGVENSTCCSNTAT 468
Query: 97 RGTHPLWDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYH 146
+ R+ + ++ +L + ++Y+ DGFRFD M +H
Sbjct: 469 -------EHRMMA-------KLIVDSLVVWAKDYKVDGFRFD---LMGHH 501
>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 = 37.2 bits (87), Expect = 0.005
Identities = 35/115 (30%), Positives = 53/115 (46%), Gaps = 25/115 (21%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSH------ASKNVL------------DGLNEFDG 86
GT E K + + H+ G+ V+LD V +H A K+V G+N FDG
Sbjct: 73 GTNEDFKAVCKKLHENGIKVVLDGVFNHVGRDFFAFKDVQENRENSPYKDWFKGVN-FDG 131
Query: 87 TQAC---FFHDGPRGTHPLWDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
F ++G G + L L N EV+ +L +R+++EE+ DG R D
Sbjct: 132 NSPYNDGFSYEGWEGHYELVKLNLHNP---EVVDYLFDAVRFWIEEFDIDGLRLD 183
>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 = 37.2 bits (87), Expect = 0.006
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 43 LFGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
+FGT E + L+ E K GL V+LD V +H+S
Sbjct: 73 IFGTMEDFEELIAEAKKLGLKVILDFVPNHSS 104
>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 = 36.7 bits (86), Expect = 0.008
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 43 LFGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
FGT E L+ E HK G+ +++D+V +H S
Sbjct: 68 EFGTMEDFDELIKEAHKRGIKIIMDLVVNHTS 99
>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 = 36.1 bits (84), Expect = 0.010
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
FGT + K L+D+ H+ G+ V+LD+V +H S
Sbjct: 48 FGTMDDFKELIDKAHERGIKVILDLVPNHTS 78
>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 = 35.9 bits (83), Expect = 0.011
Identities = 26/116 (22%), Positives = 46/116 (39%), Gaps = 10/116 (8%)
Query: 42 GLFGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNV-----LDGLNEFDGTQACFFHDGP 96
+L+ +V H G+ VLL+VV +H ++ + L D A ++ G
Sbjct: 81 SSLSASAELRAMVKGLHSNGIEVLLEVVLTHTAEGTDESPESESLRGIDA--ASYYILGK 138
Query: 97 RGTHPLWD---SRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSMLYHNHG 149
G + + N + +L +LR + E+ DGF F ++ HG
Sbjct: 139 SGVLENSGVPGAAVLNCNHPVTQSLILDSLRHWATEFGVDGFCFINAEGLVRGPHG 194
>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 = 35.6 bits (83), Expect = 0.016
Identities = 28/94 (29%), Positives = 43/94 (45%), Gaps = 20/94 (21%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTHPLWD 104
GT E K LV H+ G+ V+LD V +H ++ FF +G H +D
Sbjct: 71 GTNEDFKALVAALHERGIRVVLDGVFNHVGRD--------------FFWEG----H--YD 110
Query: 105 SRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
N V+ +L +R+++EE+ DG R D
Sbjct: 111 LVKLNLDNPAVVDYLFDVVRFWIEEFDIDGLRLD 144
>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 = 34.6 bits (80), Expect = 0.042
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 43 LFGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
LFGT + LV E K + ++LD+V +H S
Sbjct: 70 LFGTMADFEELVSEAKKRNIKIMLDMVFNHTS 101
>gnl|CDD|236518 PRK09441, PRK09441, cytoplasmic alpha-amylase; Reviewed.
Length = 479
Score = 34.1 bits (79), Expect = 0.053
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSH 72
+GT E+L +D H+ G+ V DVV +H
Sbjct: 77 YGTKEELLNAIDALHENGIKVYADVVLNH 105
Score = 32.9 bits (76), Expect = 0.13
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 124 RWYLEEYQFDGFRFDGV 140
+WY+E FDGFR D V
Sbjct: 219 KWYMETTGFDGFRLDAV 235
>gnl|CDD|238624 cd01299, Met_dep_hydrolase_A, Metallo-dependent hydrolases,
subgroup A is part of the superfamily of
metallo-dependent hydrolases, a large group of proteins
that show conservation in their 3-dimensional fold (TIM
barrel) and in details of their active site. The vast
majority of the members have a conserved metal binding
site, involving four histidines and one aspartic acid
residue. In the common reaction mechanism, the metal ion
(or ions) deprotonate a water molecule for a
nucleophilic attack on the substrate. The function of
this subgroup is unknown.
Length = 342
Score = 33.8 bits (78), Expect = 0.061
Identities = 13/33 (39%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 46 TPEQLKYLVDECHKAGLYVLLDVVHSHASKNVL 78
+ E+L+ +VDE HKAGLYV H++ ++ +
Sbjct: 158 SEEELRAIVDEAHKAGLYV---AAHAYGAEAIR 187
>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 = 32.9 bits (76), Expect = 0.11
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 110 YSEIEVLRFLLSNLRWYLEEYQFDGFRFDGV 140
YS EV L +WY+ DGFR D V
Sbjct: 203 YSNPEVREELKRWGKWYINTTGLDGFRLDAV 233
Score = 30.9 bits (71), Expect = 0.57
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSH 72
GT E+L + H+ G+ V D V +H
Sbjct: 76 GTKEELLEAIKALHENGIQVYADAVLNH 103
>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 = 32.6 bits (75), Expect = 0.14
Identities = 37/158 (23%), Positives = 55/158 (34%), Gaps = 35/158 (22%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNE-----------FDGTQACFF 92
FGT E LVD H G+ V++D V +H+S + F
Sbjct: 100 FGTWEDFDELVDAAHANGIKVIIDFVPNHSSPADYAEDGALYDNGTLVGDYPNDDNGWFH 159
Query: 93 HDGPRGT---------HPLWDSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDGVTSM 143
H+G L+D N S V ++L ++++L ++ DG R D V M
Sbjct: 160 HNGGIDDWSDREQVRYKNLFDLADLNQSNPWVDQYLKDAIKFWL-DHGIDGIRVDAVKHM 218
Query: 144 -----------LYHNHGC---GEGFSGHYDEYFGLNVD 167
+Y GE F G D + V
Sbjct: 219 PPGWQKSFADAIYSKKPVFTFGEWFLGSPDPGYEDYVK 256
>gnl|CDD|237739 PRK14510, PRK14510, putative bifunctional
4-alpha-glucanotransferase/glycogen debranching enzyme;
Provisional.
Length = 1221
Score = 32.9 bits (75), Expect = 0.16
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 7/97 (7%)
Query: 48 EQLKYLVDECHKAGLYVLLDVVHSHASKNVLDG--LNEFDGTQACFFHDGPRGTHPLWD- 104
E+ + E AG+ V+LDVV +H ++ G L+ + + ++ P +
Sbjct: 247 EEFAQAIKEAQSAGIAVILDVVFNHTGESNHYGPTLSAYGSDNSPYYRLEPGNPKEYENW 306
Query: 105 ---SRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFD 138
L N +LR + LR + DGFR D
Sbjct: 307 WGCGNLPNLERPFILRLPMDVLR-SWAKRGVDGFRLD 342
>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 = 32.2 bits (74), Expect = 0.17
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHAS------KNVLDGL 81
GT L+ L+D H G+ V+LD+V +H V+D L
Sbjct: 95 LGTDADLQDLIDAAHARGIKVILDIVVNHTGDLNTENPEVVDYL 138
>gnl|CDD|215419 PLN02784, PLN02784, alpha-amylase.
Length = 894
Score = 31.9 bits (72), Expect = 0.30
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSH 72
+GT ++LK LV H+ G+ VL D V +H
Sbjct: 564 YGTIDELKDLVKSFHEVGIKVLGDAVLNH 592
>gnl|CDD|182252 PRK10122, PRK10122, GalU regulator GalF; Provisional.
Length = 297
Score = 31.4 bits (71), Expect = 0.31
Identities = 15/38 (39%), Positives = 25/38 (65%), Gaps = 4/38 (10%)
Query: 50 LKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGT 87
++Y+VDE AG+ ++ V +HASKN ++ N FD +
Sbjct: 37 IQYIVDEIVAAGIKEIVLV--THASKNAVE--NHFDTS 70
>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 = 31.5 bits (72), Expect = 0.32
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 48 EQLKYLVDECHKAGLYVLLDVVHSHASKN 76
E+ + LV+ H AGL V++D V +H ++
Sbjct: 107 EEFEALVERTHAAGLKVIIDFVPNHVARQ 135
>gnl|CDD|200456 cd11317, AmyAc_bac_euk_AmyA, Alpha amylase catalytic domain found
in bacterial and 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 AmyA proteins from bacteria, fungi, mammals,
insects, mollusks, and nematodes. 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 = 329
Score = 31.4 bits (72), Expect = 0.34
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSH 72
GT + + +V+ C+ AG+ V +D V +H
Sbjct: 62 SGTEAEFRDMVNRCNAAGVRVYVDAVINH 90
>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 = 31.6 bits (72), Expect = 0.36
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 14/75 (18%)
Query: 6 FGTPEQLKYLVDECHKAGLFGT----PEQLKYLVDECHKAGLFGTPEQLKYLVDECHKAG 61
F E ++ + K G G P YL + G+ LK LV +
Sbjct: 79 FFKEEHVEAI----SKLGAKGVIYELPADETYLN---NSYGVE---SDLKELVKTAKQKD 128
Query: 62 LYVLLDVVHSHASKN 76
+ V+LD+ +H+SK
Sbjct: 129 IKVILDLTPNHSSKQ 143
>gnl|CDD|237740 PRK14511, PRK14511, maltooligosyl trehalose synthase;
Provisional.
Length = 879
Score = 31.5 bits (72), Expect = 0.38
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSH 72
G E L+ L G+ ++LD+V +H
Sbjct: 66 GGEEGLRRLAAALRAHGMGLILDIVPNH 93
>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 = 31.0 bits (71), Expect = 0.51
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASK 75
GT E L+ L E + G+ ++LD V +H +
Sbjct: 132 LGTMEDLRALAAELRERGISLVLDFVLNHTAD 163
>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 = 30.9 bits (70), Expect = 0.67
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
FGT + K VDE H G+ V++D+V +H S
Sbjct: 72 FGTIDDFKDFVDEAHARGMRVIIDLVLNHTS 102
>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 = 30.5 bits (69), Expect = 0.71
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLD 67
GT E L+ HK G+ V+LD
Sbjct: 76 LGTLEDFTSLLTAAHKKGISVVLD 99
>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 = 30.6 bits (70), Expect = 0.75
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
GT + E H+ G+ V++D+V +H S
Sbjct: 71 LGTLGDFVEFLREAHERGIRVIIDLVVNHTS 101
>gnl|CDD|216395 pfam01261, AP_endonuc_2, Xylose isomerase-like TIM barrel. This
TIM alpha/beta barrel structure is found in xylose
isomerase and in endonuclease IV (EC:3.1.21.2). This
domain is also found in the N termini of bacterial
myo-inositol catabolism proteins. These are involved in
the myo-inositol catabolism pathway, and is required for
growth on myo-inositol in Rhizobium leguminosarum bv.
viciae.
Length = 202
Score = 30.0 bits (68), Expect = 0.75
Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 14/72 (19%)
Query: 29 EQLKYLVDECHKAGL-------------FGTPEQLKYLVDECHKAGLYVLLDVVHSHASK 75
E L L + + G+ G E+ L+DE + + LD H+ A+
Sbjct: 103 ESLNELAELAEEYGVKLALENHPGTGVELGYFEEALRLIDEVDSPNVGLCLDTGHAFAAG 162
Query: 76 -NVLDGLNEFDG 86
+ + L
Sbjct: 163 GDPEELLRRLGD 174
>gnl|CDD|182849 PRK10933, PRK10933, trehalose-6-phosphate hydrolase; Provisional.
Length = 551
Score = 30.5 bits (69), Expect = 0.79
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
+GT + LV + G+ ++LD+V +H S
Sbjct: 77 YGTLDDFDELVAQAKSRGIRIILDMVFNHTS 107
>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 = 30.3 bits (69), Expect = 0.93
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLD 67
FGT + +DE H+ G+YV+LD
Sbjct: 143 FGTIADWRAAIDEIHRRGMYVVLD 166
>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 = 30.2 bits (69), Expect = 1.1
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 45 GTPEQLKYLVDECHKAGLYVLLDVVHSH 72
G E L+ L G+ ++LD+V +H
Sbjct: 60 GGEEGLRRLAAALRAHGMGLILDIVPNH 87
>gnl|CDD|218799 pfam05893, LuxC, Acyl-CoA reductase (LuxC). This family consists
of several bacterial Acyl-CoA reductase (LuxC)
proteins. The channelling of fatty acids into the fatty
aldehyde substrate for the bacterial bioluminescence
reaction is catalyzed by a fatty acid reductase
multienzyme complex, which channels fatty acids through
the thioesterase (LuxD), synthetase (LuxE) and
reductase (LuxC) components.
Length = 400
Score = 29.2 bits (66), Expect = 1.6
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 48 EQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRG 98
+ LK L+ C K LY L+ ++LD E+ Q + PRG
Sbjct: 45 KALKALMLLCSKDALYDKLE--RELGQPHILD---EWLPRQDSYEKAQPRG 90
>gnl|CDD|184021 PRK13389, PRK13389, UTP--glucose-1-phosphate uridylyltransferase
subunit GalU; Provisional.
Length = 302
Score = 29.1 bits (65), Expect = 1.7
Identities = 15/36 (41%), Positives = 24/36 (66%), Gaps = 4/36 (11%)
Query: 50 LKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFD 85
++Y+V+EC AG+ ++ V HS SKN ++ N FD
Sbjct: 42 IQYVVNECIAAGITEIVLVTHS--SKNSIE--NHFD 73
>gnl|CDD|165762 PLN00196, PLN00196, alpha-amylase; Provisional.
Length = 428
Score = 29.5 bits (66), Expect = 1.7
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 11/67 (16%)
Query: 41 AGLFGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFHDGPRGTH 100
A +G QLK L++ H G+ V+ D+V +H + DG + C F G
Sbjct: 85 ASKYGNEAQLKSLIEAFHGKGVQVIADIVINHRTAEHKDGRGIY-----CLFEGGTP--- 136
Query: 101 PLWDSRL 107
DSRL
Sbjct: 137 ---DSRL 140
>gnl|CDD|188634 cd00945, Aldolase_Class_I, Class I aldolases. Class I aldolases.
The class I aldolases use an active-site lysine which
stabilizes a reaction intermediates via Schiff base
formation, and have TIM beta/alpha barrel fold. The
members of this family include
2-keto-3-deoxy-6-phosphogluconate (KDPG) and
2-keto-4-hydroxyglutarate (KHG) aldolases,
transaldolase, dihydrodipicolinate synthase sub-family,
Type I 3-dehydroquinate dehydratase, DeoC and DhnA
proteins, and metal-independent
fructose-1,6-bisphosphate aldolase. Although
structurally similar, the class II aldolases use a
different mechanism and are believed to have an
independent evolutionary origin.
Length = 201
Score = 28.8 bits (65), Expect = 1.8
Identities = 17/80 (21%), Positives = 26/80 (32%), Gaps = 15/80 (18%)
Query: 4 NGFGTPEQLKYLVDECHKAGLFG---TPEQLKYLVDECHKAGL-------FGTP----EQ 49
+ T E + L DE + G P ++ D + + F T E
Sbjct: 7 HPDATLEDIAKLCDEAIEYGFAAVCVNPGYVRLAADALAGSDVPVIVVVGFPTGLTTTEV 66
Query: 50 LKYLVDECHKAGLYVLLDVV 69
V+E G +DVV
Sbjct: 67 KVAEVEEAIDLGA-DEIDVV 85
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 29.2 bits (66), Expect = 2.1
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 28 PEQLKYLVDECHKA-------GLFGTPEQLKYLVDECHKAGLYVLLDVVHS 71
+ L+ L+ K + GT +K + + H+ G VL+D +
Sbjct: 152 LDALEKLITPKTKLVALSHVSNVTGTVNPVKEIAELAHEHGALVLVDAAQA 202
>gnl|CDD|177598 PHA03360, PHA03360, tegument protein; Provisional.
Length = 442
Score = 28.7 bits (64), Expect = 3.0
Identities = 10/42 (23%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 164 LNVDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPV 205
+ D D++I +V +H + ++ + + + G P S RP
Sbjct: 98 FHFDIDSVILKLVYPHLVHREI--VLRLYDLICGRPRSQRPS 137
>gnl|CDD|216307 pfam01120, Alpha_L_fucos, Alpha-L-fucosidase.
Length = 320
Score = 28.4 bits (64), Expect = 3.1
Identities = 18/91 (19%), Positives = 27/91 (29%), Gaps = 22/91 (24%)
Query: 50 LKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQACFFH-DGPRGTHPLWDSRLF 108
+ L C K G+ +S + H D D L+
Sbjct: 117 VGELAKACRKNGI--KFGFYYSLLD----------------WHHPDYKVDKEGQEDKGLW 158
Query: 109 NYSEIEVLRFLLSNLRWYLEEYQFDGFRFDG 139
N V F + L+ + Y+ D FDG
Sbjct: 159 NQY---VKEFTFNQLKELVTNYKPDILWFDG 186
>gnl|CDD|220525 pfam10022, DUF2264, Uncharacterized protein conserved in bacteria
(DUF2264). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 361
Score = 28.3 bits (64), Expect = 3.5
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 114 EVLRFLLSNLRWYLEEYQFDGFRFDGVTSM--LYHNHGCGEGFSG 156
+V LL LRW+L+ Q F DG ++ N E ++
Sbjct: 288 QVRGALLRVLRWWLD--QPGIFDEDGWLTIGFAGPNPRMAENYNS 330
>gnl|CDD|236759 PRK10785, PRK10785, maltodextrin glucosidase; Provisional.
Length = 598
Score = 28.4 bits (64), Expect = 3.6
Identities = 33/134 (24%), Positives = 49/134 (36%), Gaps = 36/134 (26%)
Query: 44 FGTPEQLKYLVDECHKAGLYVLLDVVHSHASKNVLDGLNEFDGTQ-----AC-------- 90
G L L + G+ ++LD V +H D FD AC
Sbjct: 222 LGGDAALLRLRHATQQRGMRLVLDGVFNHTG----DSHPWFDRHNRGTGGACHHPDSPWR 277
Query: 91 -FFHDGPRGTHPLW---DS--RLFNYSEIEVLRFLL----SNLRWYLEE-YQFDGFRFDG 139
++ G W S +L ++ EV+ + S +R +L+ Y DG+R D
Sbjct: 278 DWYSFSDDGRALDWLGYASLPKL-DFQSEEVVNEIYRGEDSIVRHWLKAPYNIDGWRLD- 335
Query: 140 VTSMLYHNHGCGEG 153
V ML GEG
Sbjct: 336 VVHML------GEG 343
>gnl|CDD|166421 PLN02780, PLN02780, ketoreductase/ oxidoreductase.
Length = 320
Score = 28.3 bits (63), Expect = 3.7
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 99 THPLWDSRLFNYSEIEVLRFLLSNLRWY 126
+ PLW LF + +L+F + L W
Sbjct: 11 SQPLWLLVLFVLGSLSILKFFFTILNWV 38
>gnl|CDD|238625 cd01300, YtcJ_like, YtcJ_like metal dependent amidohydrolases. YtcJ
is a Bacillus subtilis ORF of unknown function. The
Arabidopsis homolog LAF3 has been identified as a factor
required for photochrome A signalling.
Length = 479
Score = 28.4 bits (64), Expect = 3.8
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 33 YLVDECHKAGLFGTPEQLKYLVDECHKAGLYVLLDVVHSH---ASKNVLDGL 81
YL L +PE+L+ LV +AGL V +H+ A VLD L
Sbjct: 280 YLDSPGTGGLLLISPEELEELVRAADEAGLQV---AIHAIGDRAVDTVLDAL 328
>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 = 28.5 bits (64), Expect = 3.8
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 43 LFGTPEQLKYLVDECHKAGLYVLLDVVHSHAS 74
+FGT E + L+ H G+ +++D V +H S
Sbjct: 71 MFGTMEDFERLLAAMHDRGMKLIMDFVPNHTS 102
>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 = 28.4 bits (64), Expect = 4.1
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 21 KAGLFGTPEQLK--YLVDECHK---AGLFGTPEQLKYLVDECHKAGLYVLLDVVHSHASK 75
K G G+P +K + +D G E+ K V+ CH G+ V+LD + A++
Sbjct: 112 KKGELGSPYAVKNFFEIDPLLHDPLLGDLSVEEEFKAFVEACHMLGIRVVLDFIPRTAAR 171
Query: 76 N 76
+
Sbjct: 172 D 172
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 28.1 bits (63), Expect = 4.2
Identities = 6/27 (22%), Positives = 15/27 (55%)
Query: 46 TPEQLKYLVDECHKAGLYVLLDVVHSH 72
+ E+L+ L + K G+ ++ D ++
Sbjct: 150 SEEELEELAELAKKHGILIISDEAYAE 176
>gnl|CDD|133128 cd06597, GH31_transferase_CtsY, CtsY (cyclic
tetrasaccharide-synthesizing enzyme Y) is a bacterial
3-alpha-isomaltosyltransferase, first identified in
Arthrobacter globiformis, that produces cyclic
tetrasaccharides together with a closely related enzyme
CtsZ. CtsY and CtsZ both have a glycosyl hydrolase
family 31 (GH31) catalytic domain. 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.
Length = 340
Score = 27.5 bits (61), Expect = 6.3
Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 9/98 (9%)
Query: 51 KYLVDECHKAGLYVLL--DVVHSHASKNVLDGLNEFDGTQACFF----HDGPRGTHPLW- 103
K ++DE H+ G+ VLL + N+ D A + G P
Sbjct: 88 KGMIDELHEQGVKVLLWQIPIIKLRPHPHGQADNDEDYAVAQNYLVQRGVGKPYRIPGQW 147
Query: 104 --DSRLFNYSEIEVLRFLLSNLRWYLEEYQFDGFRFDG 139
DS + +++ E ++ + R+ ++E DGF+ DG
Sbjct: 148 FPDSLMLDFTNPEAAQWWMEKRRYLVDELGIDGFKTDG 185
>gnl|CDD|224101 COG1180, PflA, Pyruvate-formate lyase-activating enzyme
[Posttranslational modification, protein turnover,
chaperones].
Length = 260
Score = 27.3 bits (61), Expect = 6.8
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 1 MRTNGFGTPEQLKYLVDECHKAGLFGTPEQLKYLVDECHK----AGLFGTPEQLKYLVDE 56
+ TNGF PE L+ L+ L LK DE ++ A E L+ L D
Sbjct: 117 LDTNGFLPPEALEELLPLLDAVLL-----DLKAFDDELYRKLTGADNEPVLENLELLADL 171
>gnl|CDD|234710 PRK00278, trpC, indole-3-glycerol-phosphate synthase; Reviewed.
Length = 260
Score = 27.4 bits (62), Expect = 6.9
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 46 TPEQLKYLVDECHKAGLYVLLDVVHSHA 73
EQLK L+D H GL VL++ VH
Sbjct: 145 DDEQLKELLDYAHSLGLDVLVE-VHDEE 171
>gnl|CDD|216595 pfam01595, DUF21, Domain of unknown function DUF21. This
transmembrane region has no known function. Many of the
sequences in this family are annotated as hemolysins,
however this is due to a similarity to Treponema
hyodysenteriae hemolysin C that does not contain this
domain. This domain is found in the N-terminus of the
proteins adjacent to two intracellular CBS domains
pfam00571.
Length = 182
Score = 26.8 bits (60), Expect = 7.3
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 20 HKAGLFGTPEQLKYLVDECHKAGLF 44
G T E+L+ LVDE + G+
Sbjct: 154 KPEGPAVTEEELRALVDEGEEEGVI 178
>gnl|CDD|224761 COG1848, COG1848, Predicted nucleic acid-binding protein, contains
PIN domain [General function prediction only].
Length = 140
Score = 26.7 bits (59), Expect = 7.5
Identities = 9/41 (21%), Positives = 18/41 (43%)
Query: 166 VDTDALIYLMVANKFLHDKYPEIITIAEDVSGMPASCRPVT 206
+DT+ L+Y + + HD+ E++ E + V
Sbjct: 4 IDTNVLVYALFRDHPHHDRARELLERLEAGDIRVYTPELVL 44
>gnl|CDD|99739 cd00615, Orn_deC_like, Ornithine decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD corresponds to ornithine decarboxylase (ODC),
arginine decarboxylase (ADC) and lysine decarboxylase
(LDC). ODC is a dodecamer composed of six homodimers and
catalyzes the decarboxylation of tryptophan. ADC
catalyzes the decarboxylation of arginine and LDC
catalyzes the decarboxylation of lysine. Members of this
family are widely found in all three forms of life.
Length = 294
Score = 27.2 bits (61), Expect = 7.6
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 50 LKYLVDECHKAGLYVLLDVVH 70
L+ +V+E H GL VL+D H
Sbjct: 172 LRKIVEEAHHRGLPVLVDEAH 192
>gnl|CDD|238203 cd00331, IGPS, Indole-3-glycerol phosphate synthase (IGPS); an
enzyme in the tryptophan biosynthetic pathway,
catalyzing the ring closure reaction of
1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate
(CdRP) to indole-3-glycerol phosphate (IGP), accompanied
by the release of carbon dioxide and water. IGPS is
active as a separate monomer in most organisms, but is
also found fused to other enzymes as part of a
bifunctional or multifunctional enzyme involved in
tryptophan biosynthesis.
Length = 217
Score = 27.0 bits (61), Expect = 8.2
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 46 TPEQLKYLVDECHKAGLYVLLDV 68
EQLK L + + G+ VL++V
Sbjct: 106 DDEQLKELYELARELGMEVLVEV 128
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 27.3 bits (61), Expect = 8.4
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 8/37 (21%)
Query: 15 LVDECHKAGLFGTPEQLKYLVDECH----KAGLFGTP 47
+VDECH T + L ++ + K GL G+
Sbjct: 227 IVDECHLF----TGKSLTSIITKLDNCKFKFGLTGSL 259
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 27.4 bits (61), Expect = 8.9
Identities = 13/26 (50%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 187 EIITIAEDVSGMPASCRPV-TEGGTG 211
E IAED+ P RP T GGTG
Sbjct: 170 ECFEIAEDIGEFPLIIRPAFTLGGTG 195
>gnl|CDD|133123 cd06592, GH31_glucosidase_KIAA1161, KIAA1161 is an uncharacterized
Homo sapiens protein with a glycosyl hydrolase family 31
(GH31) domain that is homologous to the Escherichia coli
YihQ glucosidase. Orthologs of KIA1161 are found in
eukaryotes and prokaryotes. In bacteria, YihQ (along
with YihO) is important for bacterial O-antigen capsule
assembly and translocation. Enzymes of the GH31 family
possess a wide range of different 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.
Length = 303
Score = 27.2 bits (61), Expect = 9.0
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 114 EVLRFLLSNLRWYLEEYQFDGFRFDG 139
E + + LS L+ E+Y D F+FD
Sbjct: 138 EAVDWFLSRLKSLQEKYGIDSFKFDA 163
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
0.322 0.143 0.456
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: 12,763,079
Number of extensions: 1233923
Number of successful extensions: 1524
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1478
Number of HSP's successfully gapped: 150
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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)