RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4375
(62 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 = 87.3 bits (217), Expect = 1e-22
Identities = 30/43 (69%), Positives = 35/43 (81%)
Query: 5 HPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
P K+ VKKL+ G+LE+VTGGWVMTDEA SH FAM+DQLIE
Sbjct: 63 SPDKKEAVKKLVKNGQLEIVTGGWVMTDEANSHYFAMIDQLIE 105
>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 = 68.5 bits (167), Expect = 1e-15
Identities = 28/46 (60%), Positives = 38/46 (82%)
Query: 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
+I+ K++ VK+LI G+LE+VTGGWVM DEAT+H FA++DQLIE
Sbjct: 60 DIIDGQKKDAVKRLIENGQLEIVTGGWVMPDEATAHYFALIDQLIE 105
>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 = 67.6 bits (166), Expect = 1e-15
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 6/51 (11%)
Query: 6 PTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQL------IEETF 50
R VKKL+ G+LE + GGW M DEAT+H ++DQ+ +++TF
Sbjct: 71 EDTRQKVKKLVKNGQLEFINGGWCMNDEATTHYEDIIDQMTLGHQFLKDTF 121
>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 = 67.7 bits (165), Expect = 2e-15
Identities = 27/44 (61%), Positives = 34/44 (77%)
Query: 4 VHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
++ KR V++L+ G+LEM TGGWVM DEA SH FAM+DQLIE
Sbjct: 62 INAQKRAAVRRLVGNGQLEMATGGWVMPDEANSHYFAMIDQLIE 105
>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 = 65.7 bits (161), Expect = 6e-15
Identities = 19/43 (44%), Positives = 25/43 (58%)
Query: 5 HPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
P +KKL+AEGRLE V GGWV DE +++ QL+
Sbjct: 59 QPELFKKIKKLVAEGRLEPVGGGWVEPDENLPSGESLIRQLLY 101
>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 = 63.8 bits (156), Expect = 3e-14
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 6/53 (11%)
Query: 6 PTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQL------IEETFST 52
+ KKL+ G+LE V GGWVM DEA + +++DQ+ +++TF
Sbjct: 63 NDTKQQFKKLVKNGQLEFVGGGWVMNDEACTTYESIIDQMTEGHQFLKDTFGV 115
>gnl|CDD|178304 PLN02701, PLN02701, alpha-mannosidase.
Length = 1050
Score = 57.5 bits (139), Expect = 7e-12
Identities = 22/42 (52%), Positives = 31/42 (73%)
Query: 6 PTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
P+K+ KL+ G+LE+V GGWVM DEA SH FA+++Q+ E
Sbjct: 102 PSKKEAFTKLVKNGQLEIVGGGWVMNDEANSHYFAIIEQITE 143
>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 = 46.6 bits (111), Expect = 5e-08
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 4 VHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
V P + +K+ + GRLE+ GG+VM D ++V Q++
Sbjct: 59 VRPDLKAKLKQAVRSGRLEIAGGGYVMPDTNLPDGESLVRQILL 102
>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 = 43.7 bits (103), Expect = 5e-07
Identities = 21/45 (46%), Positives = 28/45 (62%), Gaps = 6/45 (13%)
Query: 12 VKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE------ETF 50
V++L++EGRLE V GG VM DEA + + + QL E ETF
Sbjct: 70 VRQLLSEGRLEFVIGGQVMHDEAVTELDDQILQLTEGHGFLYETF 114
>gnl|CDD|212125 cd10814, GH38N_AMII_SpGH38_like, N-terminal catalytic domain of
SPGH38, a putative alpha-mannosidase of Streptococcus
pyogenes, and its prokaryotic homologs; glycoside
hydrolase family 38 (GH38). The subfamily is
represented by SpGH38 of Streptococcus pyogenes, which
has been assigned as a putative alpha-mannosidase, and
is encoded by ORF spy1604. SpGH38 appears to exist as
an elongated dimer and display alpha-1,3 mannosidase
activity. It is active on disaccharides and some aryl
glycosides. SpGH38 can also effectively deglycosylate
human N-glycans in vitro. A divalent metal ion, such as
a zinc ion, is required for its activity. SpGH38 is
inhibited by swainsonine. The absence of any secretion
signal peptide suggests that SpGH38 may be
intracellular.
Length = 271
Score = 31.5 bits (72), Expect = 0.014
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 4 VHPTKRNIVKKLIAEGRLEMVTGGW-VMTDE 33
V P KR +KKLI EG+L V G W V+ DE
Sbjct: 60 VRPEKRERLKKLIREGKL--VIGPWYVLQDE 88
>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 = 29.8 bits (68), Expect = 0.056
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 12 VKKLIAEGRLEMVTGGWVMTD 32
+K+ + EGR E V G WV D
Sbjct: 66 IKERVKEGRWEPVGGMWVEPD 86
>gnl|CDD|212126 cd10815, GH38N_AMII_EcMngB_like, N-terminal catalytic domain of
Escherichia coli alpha-mannosidase MngB and its
bacterial homologs; glycoside hydrolase family 38
(GH38). The bacterial subfamily is represented by
Escherichia coli alpha-mannosidase MngB, which is
encoded by the mngB gene (previously called ybgG). MngB
exhibits alpha-mannosidase activity that converts
2-O-(6-phospho-alpha-mannosyl)-D-glycerate to
mannose-6-phosphate and glycerate in the pathway which
enables use of mannosyl-D-glycerate as a sole carbon
source. A divalent metal ion is required for its
activity.
Length = 270
Score = 29.0 bits (66), Expect = 0.092
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 4 VHPTKRNIVKKLIAEGRLEMVTGGW-VMTDE 33
V P + +KKL+ EGRL G W TDE
Sbjct: 60 VRPEDKERIKKLVKEGRL--FIGPWYTQTDE 88
>gnl|CDD|219665 pfam07959, Fucokinase, L-fucokinase. In the salvage pathway of
GDP-L-fucose, free cytosolic fucose is phosphorylated by
L-fucokinase to form L-fucose-L-phosphate, which is then
further converted to GDP-L-fucose in the reaction
catalyzed by GDP-L-fucose pyrophosphorylase.
Length = 414
Score = 28.6 bits (64), Expect = 0.15
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 6 PTKRNIVKK--LIAEGRLEMVTGGWVMTDEATSHIFAM 41
PT +V+ + +G + TG ++ EA +FAM
Sbjct: 122 PTIEELVQFNAVGRDGLFLLDTGILSLSGEAVESLFAM 159
>gnl|CDD|182093 PRK09819, PRK09819, alpha-mannosidase; Provisional.
Length = 875
Score = 26.9 bits (60), Expect = 0.52
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 4 VHPTKRNIVKKLIAEGRLEMVTGGW-VMTDE 33
V P + VKKL+ G+L + G W TD+
Sbjct: 64 VKPEDKERVKKLVQAGKL--IIGPWYTQTDQ 92
>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 753
Score = 25.4 bits (56), Expect = 1.7
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 14 KLIAEGRLEMVTGGWVMTDEATS-----HIFAM--VDQLIEETFSTFS 54
K + RL +G + E + IFA +Q IE++ STFS
Sbjct: 335 KTLGLLRLMAQSGLPIPALEGSELPVFVKIFADIGDEQSIEQSLSTFS 382
>gnl|CDD|234752 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 25.4 bits (57), Expect = 2.0
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 15/41 (36%)
Query: 36 SHIFAMVDQLIEET---------------FSTFSVQSSKRP 61
+HIF +Q+ EE F + V+ S RP
Sbjct: 384 AHIFCTPEQIEEEVKKVIDLILDVYKDFGFEDYEVKLSTRP 424
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 318
Score = 24.9 bits (55), Expect = 2.7
Identities = 11/42 (26%), Positives = 14/42 (33%), Gaps = 4/42 (9%)
Query: 4 VHPTKRNIVKKLIAEGRLEMVTGGWV----MTDEATSHIFAM 41
PT + G+L G + D A HI AM
Sbjct: 173 EGPTSTGLDVLDYLNGKLPAYPPGGTSFVDVRDVAEGHIAAM 214
>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 = 24.5 bits (53), Expect = 3.4
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 13 KKLIAEGRLEMVTGGWVMTDE 33
K + G+LE+ T G DE
Sbjct: 67 KSIQKNGQLEIGTHGATHPDE 87
>gnl|CDD|237642 PRK14224, PRK14224, camphor resistance protein CrcB; Provisional.
Length = 126
Score = 24.0 bits (52), Expect = 6.0
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 49 TFSTFSVQSSKRPP 62
TFSTF+VQS P
Sbjct: 80 TFSTFAVQSFSMPF 93
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 24.0 bits (52), Expect = 6.6
Identities = 12/33 (36%), Positives = 22/33 (66%), Gaps = 4/33 (12%)
Query: 27 GWVMTDEATSHIFAMVDQLIEET----FSTFSV 55
G+++ DEAT++I +D+ I+ T FS ++V
Sbjct: 1466 GFILMDEATANIDPALDRQIQATVMSAFSAYTV 1498
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
0.318 0.130 0.371
Gapped
Lambda K H
0.267 0.0629 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,040,602
Number of extensions: 209968
Number of successful extensions: 302
Number of sequences better than 10.0: 1
Number of HSP's gapped: 302
Number of HSP's successfully gapped: 24
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
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 (21.8 bits)
S2: 53 (24.4 bits)