RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11172
(75 letters)
>gnl|CDD|212120 cd10809, GH38N_AMII_GMII_SfManIII_like, N-terminal catalytic domain
of Golgi alpha-mannosidase II, Spodoptera frugiperda Sf9
alpha-mannosidase III, and similar proteins; glycoside
hydrolase family 38 (GH38). This subfamily is
represented by Golgi alpha-mannosidase II (GMII, also
known as mannosyl-oligosaccharide 1,3- 1,6-alpha
mannosidase, EC 3.2.1.114, Man2A1), a monomeric,
membrane-anchored class II alpha-mannosidase existing in
the Golgi apparatus of eukaryotes. GMII plays a key role
in the N-glycosylation pathway. It catalyzes the
hydrolysis of the terminal both alpha-1,3-linked and
alpha-1,6-linked mannoses from the high-mannose
oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield
GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which
is the committed step of complex N-glycan synthesis.
GMII is activated by zinc or cobalt ions and is strongly
inhibited by swainsonine. Inhibition of GMII provides a
route to block cancer-induced changes in cell surface
oligosaccharide structures. GMII has a pH optimum of
5.5-6.0, which is intermediate between those of acidic
(lysosomal alpha-mannosidase) and neutral (ER/cytosolic
alpha-mannosidase) enzymes. GMII is a retaining glycosyl
hydrolase of family GH38 that employs a two-step
mechanism involving the formation of a covalent glycosyl
enzyme complex; two carboxylic acids positioned within
the active site act in concert: one as a catalytic
nucleophile and the other as a general acid/base
catalyst. This subfamily also includes human
alpha-mannosidase 2x (MX, also known as
mannosyl-oligosaccharide 1,3- 1,6-alpha mannosidase, EC
3.2.1.114, Man2A2). MX is enzymatically and functionally
very similar to GMII, and is thought to also function in
the N-glycosylation pathway. Also found in this
subfamily is class II alpha-mannosidase encoded by
Spodoptera frugiperda Sf9 cell. This alpha-mannosidase
is an integral membrane glycoprotein localized in the
Golgi apparatus. It shows high sequence homology with
mammalian Golgi alpha-mannosidase II(GMII). It can
hydrolyze p-nitrophenyl alpha-D-mannopyranoside
(pNP-alpha-Man), and it is inhibited by swainsonine.
However, the Sf9 enzyme is stimulated by cobalt and can
hydrolyze (Man)5(GlcNAc)2 to (Man)3(GlcNAc)2, but it
cannot hydrolyze GlcNAc(Man)5(GlcNAc)2, which is
distinct from that of GMII. Thus, this enzyme has been
designated as Sf9 alpha-mannosidase III (SfManIII). It
probably functions in an alternate N-glycan processing
pathway in Sf9 cells.
Length = 340
Score = 100 bits (251), Expect = 2e-27
Identities = 40/61 (65%), Positives = 46/61 (75%), Gaps = 1/61 (1%)
Query: 3 WSGEIPNHKPIV-SLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61
W P+ K V LVK+GQLEIVTGGWVMTDEANSHY++MI QL G QWL N+GVKP
Sbjct: 59 WDDASPDKKEAVKKLVKNGQLEIVTGGWVMTDEANSHYFAMIDQLIEGHQWLKENLGVKP 118
Query: 62 R 62
+
Sbjct: 119 K 119
>gnl|CDD|178304 PLN02701, PLN02701, alpha-mannosidase.
Length = 1050
Score = 85.2 bits (211), Expect = 2e-21
Identities = 34/61 (55%), Positives = 42/61 (68%), Gaps = 1/61 (1%)
Query: 3 WSGEIPNHKP-IVSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61
W P+ K LVK+GQLEIV GGWVM DEANSHY+++I+Q+T G WL IGV P
Sbjct: 97 WRDASPSKKEAFTKLVKNGQLEIVGGGWVMNDEANSHYFAIIEQITEGNMWLNDTIGVAP 156
Query: 62 R 62
+
Sbjct: 157 K 157
>gnl|CDD|212131 cd11666, GH38N_Man2A1, N-terminal catalytic domain of Golgi
alpha-mannosidase II and similar proteins; glycoside
hydrolase family 38 (GH38). This subfamily is
represented by Golgi alpha-mannosidase II (GMII, also
known as mannosyl-oligosaccharide 1,3- 1,6-alpha
mannosidase, EC 3.2.1.114, Man2A1), a monomeric,
membrane-anchored class II alpha-mannosidase existing in
the Golgi apparatus of eukaryotes. GMII plays a key role
in the N-glycosylation pathway. It catalyzes the
hydrolysis of the terminal of both alpha-1,3-linked and
alpha-1,6-linked mannoses from the high-mannose
oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield
GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which
is the committed step of complex N-glycan synthesis.
GMII is activated by zinc or cobalt ions and is strongly
inhibited by swainsonine. Inhibition of GMII provides a
route to block cancer-induced changes in cell surface
oligosaccharide structures. GMII has a pH optimum of
5.5-6.0, which is intermediate between those of acidic
(lysosomal alpha-mannosidase) and neutral (ER/cytosolic
alpha-mannosidase) enzymes. GMII is a retaining glycosyl
hydrolase of family GH38 that employs a two-step
mechanism involving the formation of a covalent glycosyl
enzyme complex; two carboxylic acids positioned within
the active site act in concert: one as a catalytic
nucleophile and the other as a general acid/base
catalyst.
Length = 344
Score = 83.1 bits (205), Expect = 7e-21
Identities = 31/61 (50%), Positives = 42/61 (68%), Gaps = 1/61 (1%)
Query: 3 WSG-EIPNHKPIVSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61
W + + L+++GQLEIVTGGWVM DEA +HY+++I QL G QWL N+GVKP
Sbjct: 59 WDIIDGQKKDAVKRLIENGQLEIVTGGWVMPDEATAHYFALIDQLIEGHQWLERNLGVKP 118
Query: 62 R 62
+
Sbjct: 119 K 119
>gnl|CDD|216284 pfam01074, Glyco_hydro_38, Glycosyl hydrolases family 38 N-terminal
domain. Glycosyl hydrolases are key enzymes of
carbohydrate metabolism.
Length = 269
Score = 79.2 bits (196), Expect = 8e-20
Identities = 22/47 (46%), Positives = 29/47 (61%)
Query: 16 LVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPR 62
LV G+LE V GGWV DE S+I+QL +GQ++ GV+PR
Sbjct: 69 LVAEGRLEPVGGGWVEPDENLPSGESLIRQLLYGQRFFKEEFGVRPR 115
>gnl|CDD|212132 cd11667, GH38N_Man2A2, N-terminal catalytic domain of Golgi
alpha-mannosidase IIx, and similar proteins; glycoside
hydrolase family 38 (GH38). This subfamily is
represented by human alpha-mannosidase 2x (MX, also
known as mannosyl-oligosaccharide 1,3- 1,6-alpha
mannosidase, EC 3.2.1.114, Man2A2). MX is enzymatically
and functionally very similar to GMII (found in another
subfamily), and as an isoenzyme of GMII. It is thought
to also function in the N-glycosylation pathway. MX
specifically hydrolyzes the same oligosaccharide
substrate as does MII. It specifically removes two
mannosyl residues from GlcNAc(Man)5(GlcNAc)2 to yield
GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine).
Length = 344
Score = 77.3 bits (190), Expect = 9e-19
Identities = 33/47 (70%), Positives = 37/47 (78%)
Query: 16 LVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPR 62
LV +GQLE+ TGGWVM DEANSHY++MI QL G QWL NIGV PR
Sbjct: 73 LVGNGQLEMATGGWVMPDEANSHYFAMIDQLIEGHQWLEKNIGVTPR 119
>gnl|CDD|212095 cd00451, GH38N_AMII_euk, N-terminal catalytic domain of eukaryotic
class II alpha-mannosidases; glycoside hydrolase family
38 (GH38). The family corresponds to a group of
eukaryotic class II alpha-mannosidases (AlphaMII), which
contain Golgi alpha-mannosidases II (GMII), the major
broad specificity lysosomal alpha-mannosidases (LAM,
MAN2B1), the noval core-specific lysosomal alpha
1,6-mannosidases (Epman, MAN2B2), and similar proteins.
GMII catalyzes the hydrolysis of the terminal both
alpha-1,3-linked and alpha-1,6-linked mannoses from the
high-mannose oligosaccharide GlcNAc(Man)5(GlcNAc)2 to
yield GlcNAc(Man)3(GlcNAc)2 (GlcNAc,
N-acetylglucosmine), which is the committed step of
complex N-glycan synthesis. LAM is a broad specificity
exoglycosidase hydrolyzing all known alpha 1,2-, alpha
1,3-, and alpha 1,6-mannosidic linkages from numerous
high mannose type oligosaccharides. Different from LAM,
Epman can efficiently cleave only the alpha 1,6-linked
mannose residue from (Man)3GlcNAc, but not
(Man)3(GlcNAc)2 or other larger high mannose
oligosaccharides, in the core of N-linked glycans.
Members in this family are retaining glycosyl hydrolases
of family GH38 that employs a two-step mechanism
involving the formation of a covalent glycosyl enzyme
complex. Two carboxylic acids positioned within the
active site act in concert: one as a catalytic
nucleophile and the other as a general acid/base
catalyst.
Length = 258
Score = 75.0 bits (185), Expect = 3e-18
Identities = 30/62 (48%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 3 WSGEIPNHKPIV-SLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61
W + + K LVK+GQLE V GGWVM DEA + Y S+I Q+T G Q+L GV+P
Sbjct: 58 WEDQGNDTKQQFKKLVKNGQLEFVGGGWVMNDEACTTYESIIDQMTEGHQFLKDTFGVRP 117
Query: 62 RY 63
R
Sbjct: 118 RV 119
>gnl|CDD|212121 cd10810, GH38N_AMII_LAM_like, N-terminal catalytic domain of
lysosomal alpha-mannosidase and similar proteins;
glycoside hydrolase family 38 (GH38). The subfamily is
represented by lysosomal alpha-mannosidase (LAM, Man2B1,
EC 3.2.1.114), which is a broad specificity
exoglycosidase hydrolyzing all known alpha 1,2-, alpha
1,3-, and alpha 1,6-mannosidic linkages from numerous
high mannose type oligosaccharides. LAM is expressed in
all tissues and in many species. In mammals, the absence
of LAM can cause the autosomal recessive disease
alpha-mannosidosis. LAM has an acidic pH optimum at
4.0-4.5. It is stimulated by zinc ion and is inhibited
by cobalt ion and plant alkaloids, such as swainsonine
(SW). LAM catalyzes hydrolysis by a double displacement
mechanism in which a glycosyl-enzyme intermediate is
formed and hydrolyzed via oxacarbenium ion-like
transition states. A carboxylic acid in the active site
acts as the catalytic nucleophile in the formation of
the covalent intermediate while a second carboxylic acid
acts as a general acid catalyst. The same residue is
thought to assist in the hydrolysis (deglycosylation)
step, this time acting as a general base.
Length = 278
Score = 71.9 bits (177), Expect = 5e-17
Identities = 25/49 (51%), Positives = 32/49 (65%), Gaps = 2/49 (4%)
Query: 16 LVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGV--KPR 62
LVK+GQLE + GGW M DEA +HY +I Q+T G Q+L G +PR
Sbjct: 80 LVKNGQLEFINGGWCMNDEATTHYEDIIDQMTLGHQFLKDTFGECARPR 128
>gnl|CDD|212098 cd10786, GH38N_AMII_like, N-terminal catalytic domain of class II
alpha-mannosidases and similar proteins; glycoside
hydrolase family 38 (GH38). Alpha-mannosidases (EC
3.2.1.24) are extensively found in eukaryotes and play
important roles in the processing of newly formed
N-glycans and in degradation of mature glycoproteins. A
deficiency of this enzyme causes the lysosomal storage
disease alpha-mannosidosis. Many bacterial and archaeal
species also possess putative alpha-mannosidases, but
their activity and specificity is largely unknown.
Based on different functional characteristics and
sequence homology, alpha-mannosidases have been
organized into two classes (class I, belonging to
glycoside hydrolase family 47, and class II, belonging
to glycoside hydrolase family 38). Members of this
family corresponds to class II alpha-mannosidases
(alphaMII), which contain intermediate Golgi
alpha-mannosidases II, acidic lysosomal
alpha-mannosidases, animal sperm and epididymal alpha
-mannosidases, neutral ER/cytosolic alpha-mannosidases,
and some putative prokaryotic alpha-mannosidases.
AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic
activity, and catalyzes the degradation of N-linked
oligosaccharides. The N-terminal catalytic domain of
alphaMII adopts a structure consisting of parallel
7-stranded beta/alpha barrel. Members in this family are
retaining glycosyl hydrolases of family GH38 that
employs a two-step mechanism involving the formation of
a covalent glycosyl enzyme complex. Two carboxylic acids
positioned within the active site act in concert: one as
a catalytic nucleophile and the other as a general
acid/base catalyst.
Length = 251
Score = 52.8 bits (127), Expect = 4e-10
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 8 PNHKPIV-SLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPR 62
P+ K + V+SG+LEI GG+VM D S+++Q+ G++WL +G +P
Sbjct: 61 PDLKAKLKQAVRSGRLEIAGGGYVMPDTNLPDGESLVRQILLGKRWLKEFLGARPP 116
>gnl|CDD|212122 cd10811, GH38N_AMII_Epman_like, N-terminal catalytic domain of
mammalian core-specific lysosomal alpha 1,6-mannosidase
and similar proteins; glycoside hydrolase family 38
(GH38). The subfamily is represented by a novel human
core-specific lysosomal alpha 1,6-mannosidase (Epman,
Man2B2) and similar proteins. Although it was previously
named as epididymal alpha-mannosidase, Epman has a
broadly distributed transcript expression profile.
Different from the major broad specificity lysosomal
alpha-mannosidases (LAM, MAN2B1), Epman is not
associated with genetic alpha-mannosidosis that is
caused by the absence of LAM. Furthermore, Epman has
unique substrate specificity. It can efficiently cleave
only the alpha 1,6-linked mannose residue from
(Man)3GlcNAc, but not (Man)3(GlcNAc)2 or other larger
high mannose oligosaccharides, in the core of N-linked
glycans. In contrast, the major LAM can cleave all of
the alpha-linked mannose residues from high mannose
oligosaccharides except the core alpha 1,6-linked
mannose residue. Moreover, it is suggested that the
catalytic activity of Epman is dependent on prior action
by di-N-acetyl-chitobiase (chitobiase), which indicates
there is a functional cooperation between these two
enzymes for the full and efficient catabolism of
mammalian lysosomal N-glycan core structures. Epman has
an acidic pH optimum. It is strongly stimulated by
cobalt or zinc ions and strongly inhibited by furanose
analogues swainsonine (SW) and
1,4-dideoxy-1,4-imino-d-mannitol (DIM).
Length = 326
Score = 49.1 bits (117), Expect = 1e-08
Identities = 22/48 (45%), Positives = 28/48 (58%)
Query: 16 LVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRY 63
L+ G+LE V GG VM DEA + I QLT G +L GV+PR+
Sbjct: 73 LLSEGRLEFVIGGQVMHDEAVTELDDQILQLTEGHGFLYETFGVRPRF 120
>gnl|CDD|212097 cd10785, GH38-57_N_LamB_YdjC_SF, Catalytic domain of glycoside
hydrolase (GH) families 38 and 57, lactam utilization
protein LamB/YcsF family proteins, YdjC-family proteins,
and similar proteins. The superfamily possesses strong
sequence similarities across a wide range of all three
kingdoms of life. It mainly includes four families,
glycoside hydrolases family 38 (GH38), heat stable
retaining glycoside hydrolases family 57 (GH57), lactam
utilization protein LamB/YcsF family, and YdjC-family.
The GH38 family corresponds to class II
alpha-mannosidases (alphaMII, EC 3.2.1.24), which
contain intermediate Golgi alpha-mannosidases II, acidic
lysosomal alpha-mannosidases, animal sperm and
epididymal alpha -mannosidases, neutral ER/cytosolic
alpha-mannosidases, and some putative prokaryotic
alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and
a-1,2 hydrolytic activity, and catalyzes the degradation
of N-linked oligosaccharides by employing a two-step
mechanism involving the formation of a covalent glycosyl
enzyme complex. GH57 is a purely prokaryotic family
with the majority of thermostable enzymes from
extremophiles (many of them are archaeal
hyperthermophiles), which exhibit the enzyme
specificities of alpha-amylase (EC 3.2.1.1),
4-alpha-glucanotransferase (EC 2.4.1.25),
amylopullulanase (EC 3.2.1.1/41), and
alpha-galactosidase (EC 3.2.1.22). This family also
includes many hypothetical proteins with uncharacterized
activity and specificity. GH57 cleaves alpha-glycosidic
bond by employing a retaining mechanism, which involves
a glycosyl-enzyme intermediate, allowing
transglycosylation. Although the exact molecular
function of LamB/YcsF family and YdjC-family remains
unclear, they show high sequence and structure homology
to the members of GH38 and GH57. Their catalytic domains
adopt a similar parallel 7-stranded beta/alpha barrel,
which is remotely related to catalytic NodB homology
domain of the carbohydrate esterase 4 superfamily.
Length = 203
Score = 42.2 bits (99), Expect = 3e-06
Identities = 23/51 (45%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 14 VSLVKSGQLEIVTGGWVMTD--EANSHYYSMIQQLTHGQQWLLTNIGVKPR 62
S+ K+GQLEI T G D EA SH ++ Q+T G WL ++GV PR
Sbjct: 67 KSIQKNGQLEIGTHGATHPDESEAQSHPENVYAQITEGITWLEKHMGVTPR 117
>gnl|CDD|212101 cd10789, GH38N_AMII_ER_cytosolic, N-terminal catalytic domain of
endoplasmic reticulum(ER)/cytosolic class II
alpha-mannosidases; glycoside hydrolase family 38
(GH38). The subfamily is represented by Saccharomyces
cerevisiae vacuolar alpha-mannosidase Ams1, rat
ER/cytosolic alpha-mannosidase Man2C1, and similar
proteins. Members in this family share high sequence
similarity. None of them have any classical signal
sequence or membrane spanning domains, which are typical
of sorting or targeting signals. Ams1 functions as a
second resident vacuolar hydrolase in S. cerevisiae. It
aids in recycling macromolecular components of the cell
through hydrolysis of terminal, non-reducing
alpha-d-mannose residues. Ams1 utilizes both the
cytoplasm to vacuole targeting (Cvt, nutrient-rich
conditions) and autophagic (starvation conditions)
pathways for biosynthetic delivery to the vacuole.
Man2C1is involved in oligosaccharide catabolism in both
the ER and cytosol. It can catalyze the cobalt-dependent
cleavage of alpha 1,2-, alpha 1,3-, and alpha 1,6-linked
mannose residues. Members in this family are retaining
glycosyl hydrolases of family GH38 that employs a
two-step mechanism involving the formation of a covalent
glycosyl-enzyme complex. Two carboxylic acids positioned
within the active site act in concert: one as a
catalytic nucleophile and the other as a general
acid/base catalyst.
Length = 252
Score = 37.5 bits (88), Expect = 1e-04
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 12/58 (20%)
Query: 13 IVSLVKSGQLEIVTGGWVMTD------EANSHYYSMIQQLTHGQQWLLTNIGVKPRYL 64
I VK G+ E V G WV D E S+++Q +GQ++ GV+ R L
Sbjct: 66 IKERVKEGRWEPVGGMWVEPDCNLPSGE------SLVRQFLYGQRYFREEFGVESRIL 117
>gnl|CDD|212124 cd10813, GH38N_AMII_Man2C1, N-terminal catalytic domain of
mammalian cytosolic alpha-mannosidase Man2C1 and similar
proteins; glycoside hydrolase family 38 (GH38). The
subfamily corresponds to cytosolic alpha-mannosidase
Man2C1 (also known as ER-mannosidase II or
neutral/cytosolic mannosidase), mainly found in various
vertebrates, and similar proteins. Man2C1 plays an
essential role in the catabolism of cytosolic free
oligomannosides derived from dolichol intermediates and
the degradation of newly synthesized glycoproteins in ER
or cytosol. It can catalyze the cleavage of alpha 1,2-,
alpha 1,3-, and alpha 1,6-linked mannose residues.
Man2C1 is a cobalt-dependent enzyme belonging to
alpha-mannosidase class II. It has a neutral pH optimum
and is strongly inhitibed by furanose analogs
swainsonine (SW) and 1,4-dideoxy-1,4-imino-D-mannitol
(DIM), moderately by deoxymannojirimycin (DMM), but not
by kifunensine (KIF). DMM and KIF, both pyranose
analogs, are normally known to inhibit class I
alpha-mannosidase.
Length = 252
Score = 31.2 bits (71), Expect = 0.022
Identities = 15/47 (31%), Positives = 23/47 (48%)
Query: 13 IVSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGV 59
I VK+G+ V G WV D SM++Q +GQ++ G+
Sbjct: 66 IQERVKNGRFIPVGGTWVEMDGNLPSGESMVRQFLYGQRFFKEEFGI 112
>gnl|CDD|130283 TIGR01216, ATP_synt_epsi, ATP synthase, F1 epsilon subunit (delta
in mitochondria). This model describes one of the five
types of subunits in the F1 part of F1/F0 ATP
synthases. Members of this family are designated
epsilon in bacterial and chloroplast systems but
designated delta in mitochondria, where the counterpart
of the bacterial delta subunit is designated OSCP. In a
few cases (Propionigenium modestum, Acetobacterium
woodii) scoring above the trusted cutoff and designated
here as exceptions, Na+ replaces H+ for translocation
[Energy metabolism, ATP-proton motive force
interconversion].
Length = 130
Score = 30.7 bits (70), Expect = 0.032
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 4 SGEI---PNHKPIVSLVKSGQLEIVTGG 28
GE+ P H P+++ +K G + I G
Sbjct: 27 EGELGILPGHAPLITALKPGVVRIRKLG 54
>gnl|CDD|212123 cd10812, GH38N_AMII_ScAms1_like, N-terminal catalytic domain of
yeast vacuolar alpha-mannosidases and similar proteins;
glycoside hydrolase family 38 (GH38). The family is
represented by Saccharomyces cerevisiae
alpha-mannosidase (Ams1) and its eukaryotic homologs.
Ams1 functions as a second resident vacuolar hydrolase
in S. cerevisiae. It aids in recycling macromolecular
components of the cell through hydrolysis of terminal,
non-reducing alpha-d-mannose residues. Ams1 forms an
oligomer in the cytoplasm and retains its oligomeric
form during the import process. It utilizes both the Cvt
(nutrient-rich conditions) and autophagic (starvation
conditions) pathways for biosynthetic delivery to the
vacuole. Mutants in either pathway are defective in Ams1
import. Members in this family show high sequence
similarity with rat ER/cytosolic alpha-mannosidase
Man2C1.
Length = 258
Score = 30.1 bits (68), Expect = 0.055
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 17 VKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVK 60
VK G+ + G WV D S+ +Q +GQ++ + G +
Sbjct: 70 VKQGRFHPIGGSWVENDTNMPSGESLARQFLYGQRYFESRFGKR 113
>gnl|CDD|223432 COG0355, AtpC, F0F1-type ATP synthase, epsilon subunit
(mitochondrial delta subunit) [Energy production and
conversion].
Length = 135
Score = 28.0 bits (63), Expect = 0.30
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 5 GEI---PNHKPIVSLVKSGQLEIVTGG 28
GE+ P H P+++ +K G + I T
Sbjct: 30 GELGILPGHAPLITALKPGVVRIKTED 56
>gnl|CDD|212105 cd10793, GH57N_TLGT_like, N-terminal catalytic domain of
4-alpha-glucanotransferase; glycoside hydrolase family
57 (GH57). 4-alpha-glucanotransferase (TLGT, EC
2.4.1.25) plays a key role in the maltose metabolism. It
catalyzes the disproportionation of amylose and the
formation of large cyclic alpha-1,4-glucan
(cycloamylose) from linear amylose. TLGT functions as a
homodimer. Each monomer is composed of two domains, an
N-terminal catalytic domain with a (beta/alpha)7 barrel
fold and a C-terminal domain with a twisted
beta-sandwich fold. Some family members have been
designated as alpha-amylases, such as the heat-stable
eubacterial amylase from Dictyoglomus thermophilum
(DtAmyA) and the extremely thermostable archaeal amylase
from Pyrococcus furiosus(PfAmyA). However, both of these
proteins are 4-alpha-glucanotransferases. DtAmyA was
shown to have transglycosylating activity and PfAmyA
exhibits 4-alpha-glucanotransferase activity.
Length = 279
Score = 27.9 bits (63), Expect = 0.32
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 20/60 (33%)
Query: 13 IVSLVKSGQLEIVTGGWVMTDEANSHYY----SMI------QQLTHGQQWLLTNIGVKPR 62
+ LV GQ+EI+ GG +Y + I Q+ +++ N G +P+
Sbjct: 65 LRKLVDRGQIEILGGG----------FYEPILASIPSEDRVGQIKKLNRFIEKNFGQRPK 114
>gnl|CDD|173197 PRK14735, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 139
Score = 27.7 bits (61), Expect = 0.35
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 5 GEIPNHKPIVSLVKSGQLEIVTGG 28
G +P H P++++++ G+L+IV G
Sbjct: 32 GILPRHAPLLTILEPGELDIVKNG 55
>gnl|CDD|139576 PRK13444, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 127
Score = 27.5 bits (61), Expect = 0.36
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 5 GEIPNHKPIVSLVKSGQLEIVTGG 28
G +PNH P+V+ + G LEI G
Sbjct: 35 GILPNHAPLVATLGIGLLEIRKGE 58
>gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed.
Length = 790
Score = 28.1 bits (62), Expect = 0.40
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 1 MSWSGEIPN--HKPIVSLVKSGQLEI---VTGGWVMTDEANS---HYYSMIQQLTHGQQW 52
++W IPN +P ++ G L + GWV ++ + Y + +QL H W
Sbjct: 442 LAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTTTSEQLAHQIHW 501
Query: 53 LLTNIGV 59
LL GV
Sbjct: 502 LLLRFGV 508
>gnl|CDD|213395 cd12152, F1-ATPase_delta, mitochondrial ATP synthase delta
subunit. The F-ATPase is found in bacterial plasma
membranes, mitochondrial inner membranes and in
chloroplast thylakoid membranes. It has also been found
in the archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain, F1, is composed of alpha, beta, gamma, delta,
and epsilon subunits with a stoichiometry of 3:3:1:1:1.
Alpha and beta subunit form the globular catalytic
moiety, a hexameric ring of alternating subunits.
Gamma, delta and epsilon subunits form a stalk,
connecting F1 to F0, the integral membrane proton
translocating domain. In bacteria, which is lacking a
eukaryotic epsilon subunit homolog, this subunit is
called the epsilon subunit.
Length = 123
Score = 27.1 bits (61), Expect = 0.50
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 4 SGEI---PNHKPIVSLVKSGQLEIVTGG 28
GE P H P+V+ +K G L I
Sbjct: 26 EGEFGILPGHAPLVTALKPGVLRIRDED 53
>gnl|CDD|184055 PRK13442, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 89
Score = 26.5 bits (59), Expect = 0.60
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 15/41 (36%)
Query: 3 WSGE---------------IPNHKPIVSLVKSGQLEIVTGG 28
WSGE +P H+P++ +++SG + +VT G
Sbjct: 18 WSGEATMVVARTTEGDIGILPGHEPLLGVLESGTVTVVTPG 58
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 27.4 bits (60), Expect = 0.63
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 23 EIVTGGWVMTDEANSHYYSMIQQLTHGQ---QWLLTNIGVKPRY 63
+ VTG ++TDE ++ ++ G+ +W+L N +P Y
Sbjct: 257 DYVTGSRIVTDETKKEMKRVLTEIQQGEFAKKWILENQAGRPTY 300
>gnl|CDD|139579 PRK13448, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 135
Score = 27.0 bits (60), Expect = 0.76
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 5 GEIPNHKPIVSLVKSGQLEIVTGG 28
G + H P+V++++ G L + GG
Sbjct: 33 GVLAGHAPVVAVIRPGILTVTAGG 56
>gnl|CDD|184056 PRK13446, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 136
Score = 26.5 bits (59), Expect = 0.90
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 5 GEIPNHKPIVSLVKSGQLEIVTGG 28
G +P H P ++ +K G+L GG
Sbjct: 34 GVLPGHAPFLTALKIGELTYKKGG 57
>gnl|CDD|217242 pfam02823, ATP-synt_DE_N, ATP synthase, Delta/Epsilon chain,
beta-sandwich domain. Part of the ATP synthase CF(1).
These subunits are part of the head unit of the ATP
synthase. The subunit is called epsilon in bacteria and
delta in mitochondria. In bacteria the delta (D)
subunit is equivalent to the mitochondrial Oligomycin
sensitive subunit, OSCP (pfam00213).
Length = 80
Score = 25.8 bits (58), Expect = 1.0
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 4 SGEI---PNHKPIVSLVKSGQLEIVTGG 28
GE P H P+++ +K G L I T
Sbjct: 26 EGEFGILPGHAPLLTALKPGVLRIKTED 53
>gnl|CDD|234796 PRK00571, atpC, F0F1 ATP synthase subunit epsilon; Validated.
Length = 135
Score = 26.3 bits (59), Expect = 1.1
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 4 SGEI---PNHKPIVSLVKSGQLEIVT--GGW 29
GE+ P H P+++ +K G + I G
Sbjct: 29 EGELGILPGHAPLLTALKPGVVRIKKDDGEE 59
>gnl|CDD|237795 PRK14706, PRK14706, glycogen branching enzyme; Provisional.
Length = 639
Score = 25.3 bits (55), Expect = 3.3
Identities = 8/35 (22%), Positives = 17/35 (48%)
Query: 29 WVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRY 63
WV D+ ++ Y+ +++ + W L + P Y
Sbjct: 524 WVSADDTDNSVYAYVRRDSESGAWSLAVANLTPVY 558
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 25.2 bits (56), Expect = 3.6
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 54 LTNIGVKPRYLHNNSRTI 71
L +G+K RYLH++ T+
Sbjct: 466 LKELGIKVRYLHSDIDTL 483
>gnl|CDD|239768 cd04235, AAK_CK, AAK_CK: Carbamate kinase (CK) catalyzes both the
ATP-phosphorylation of carbamate and carbamoyl phosphate
(CP) utilization with the production of ATP from ADP and
CP. Both CK (this CD) and nonhomologous CP synthetase
synthesize carbamoyl phosphate, an essential precursor
of arginine and pyrimidine bases, in the presence of
ATP, bicarbonate, and ammonia. CK is a homodimer of 33
kDa subunits and is a member of the Amino Acid Kinase
Superfamily (AAK).
Length = 308
Score = 24.8 bits (55), Expect = 4.1
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 6 EIPNHKPIVSLVKSGQLEIVTGG 28
+I + I +LV +G + I GG
Sbjct: 167 DIVEIEAIKTLVDNGVIVIAAGG 189
>gnl|CDD|212096 cd01022, GH57N_like, N-terminal catalytic domain of heat stable
retaining glycoside hydrolase family 57. Glycoside
hydrolase family 57(GH57) is a chiefly prokaryotic
family with the majority of thermostable enzymes coming
from extremophiles (many of these are archaeal
hyperthermophiles), which exhibit the enzyme
specificities of alpha-amylase (EC 3.2.1.1),
4-alpha-glucanotransferase (EC 2.4.1.25),
amylopullulanase (EC 3.2.1.1/41), and
alpha-galactosidase (EC 3.2.1.22). This family also
includes many hypothetical proteins with uncharacterized
activity and specificity. GH57s cleave alpha-glycosidic
bonds by employing a retaining mechanism, which involves
a glycosyl-enzyme intermediate, allowing
transglycosylation.
Length = 313
Score = 25.1 bits (55), Expect = 4.4
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 13/55 (23%)
Query: 15 SLVKSGQLEIVTGGW-------VMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPR 62
LV +GQ+E++ G+ + E Q+ G G +P+
Sbjct: 86 ELVDTGQVELLGCGYTHAYLPLLGPKEDV------RAQIEAGLDTFERLFGRRPK 134
>gnl|CDD|239124 cd02659, peptidase_C19C, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 334
Score = 24.9 bits (55), Expect = 4.5
Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 13/41 (31%)
Query: 16 LVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTN 56
LV SG GG HYYS I+ G +W N
Sbjct: 258 LVHSGDA---HGG---------HYYSYIKDRDDG-KWYKFN 285
>gnl|CDD|218291 pfam04850, Baculo_E66, Baculovirus E66 occlusion-derived virus
envelope protein.
Length = 389
Score = 24.2 bits (53), Expect = 7.4
Identities = 13/45 (28%), Positives = 16/45 (35%), Gaps = 16/45 (35%)
Query: 33 DEANSHYYS--------MIQQLTHGQQWLLTNIGVKPRYLHNNSR 69
+E N + S M Q L NI P L+NN R
Sbjct: 166 EELNLEFKSYTLYHETGMFQ--------LYDNIKALPGSLNNNGR 202
>gnl|CDD|217349 pfam03065, Glyco_hydro_57, Glycosyl hydrolase family 57. This
family includes alpha-amylase (EC:3.2.1.1),
4--glucanotransferase (EC:2.4.1.-) and amylopullulanase
enzymes.
Length = 312
Score = 23.9 bits (52), Expect = 9.0
Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 14/69 (20%)
Query: 4 SGEIPNHKPIVSLVKSGQLEIVTGG------WVMTDEANSHYYSMIQQLTHGQQWLLTNI 57
+ + L +SGQ+E++T ++ D I Q+ G++
Sbjct: 64 PEVLELFR---ELAESGQVELLTSPYYHPLLPLLPD-----KEDFIAQVEMGRELYREYF 115
Query: 58 GVKPRYLHN 66
GV+PR
Sbjct: 116 GVEPRGFWL 124
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
0.315 0.130 0.409
Gapped
Lambda K H
0.267 0.0652 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,672,709
Number of extensions: 257914
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 241
Number of HSP's successfully gapped: 35
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.4 bits)