RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2170
(78 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 = 117 bits (295), Expect = 9e-34
Identities = 38/58 (65%), Positives = 48/58 (82%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWER 67
VF+VPHSHNDPGW+KTFE YY QT+ IL+NMV+KL ++P M FIW+EISF +WW+
Sbjct: 4 VFVVPHSHNDPGWIKTFEEYYQDQTKHILDNMVDKLSKNPKMKFIWAEISFLERWWDD 61
>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 = 96.5 bits (241), Expect = 2e-26
Identities = 29/59 (49%), Positives = 39/59 (66%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERS 68
V L+PHSH D GWLKTF+ YY+ + IL+++V+ L P FIW+EI F +WWE
Sbjct: 3 VHLIPHSHCDVGWLKTFDEYYNGDVKSILDSVVKALNNDPERKFIWAEIGFLERWWEDQ 61
>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 = 94.3 bits (234), Expect = 5e-25
Identities = 39/57 (68%), Positives = 48/57 (84%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE 66
VF+VPHSHNDPGW+KTF+ YY+ QT+ ILN+MV KL + P FIWSEISFFS+WW+
Sbjct: 4 VFVVPHSHNDPGWIKTFDKYYYDQTQHILNSMVVKLQEDPRRRFIWSEISFFSKWWD 60
>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 = 91.6 bits (227), Expect = 6e-24
Identities = 37/57 (64%), Positives = 46/57 (80%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE 66
VF+VPHSHNDPGWLKTF+ Y+ QT+ ILNNMV KL + FIWSEIS+F++WW+
Sbjct: 4 VFVVPHSHNDPGWLKTFDDYFRDQTQHILNNMVLKLKEDSRRKFIWSEISYFAKWWD 60
>gnl|CDD|178304 PLN02701, PLN02701, alpha-mannosidase.
Length = 1050
Score = 86.4 bits (214), Expect = 1e-21
Identities = 31/56 (55%), Positives = 40/56 (71%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWW 65
VF+VPHSHNDPGW+ T E YY Q+R IL+ +VE L + P FIW E+S+ +WW
Sbjct: 42 VFVVPHSHNDPGWILTVEEYYQEQSRHILDTIVESLSKDPRRKFIWEEMSYLERWW 97
>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 = 77.6 bits (192), Expect = 4e-19
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWER 67
V LV HSH D GWL T + + + +N+++ L ++P FI SE F+ WWE
Sbjct: 2 VHLVGHSHIDVGWLWTVDET-RRKVQRTFSNVLKLLDRYPEFRFIQSEAQFYEWWWED 58
>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 = 73.4 bits (181), Expect = 2e-17
Identities = 29/66 (43%), Positives = 46/66 (69%), Gaps = 8/66 (12%)
Query: 10 VFLVPHSHNDPGWLKTFESYY--------HSQTRMILNNMVEKLVQHPNMTFIWSEISFF 61
V LVPH+H+D GWLKT + YY H+ + IL++++E+L+++P+ FI+ EI+FF
Sbjct: 3 VHLVPHTHDDVGWLKTVDQYYYGSNNSIQHAGVQYILDSVIEELLKNPDRKFIYVEIAFF 62
Query: 62 SQWWER 67
S+WW
Sbjct: 63 SRWWRE 68
>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 = 68.6 bits (168), Expect = 7e-16
Identities = 24/63 (38%), Positives = 35/63 (55%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERSR 69
V LVPHSH D GWL+TFE YY + IL+ + L +P F+ E+ ++W+
Sbjct: 2 VHLVPHSHYDVGWLQTFEQYYQINFKAILDKALRLLDANPEYKFLIEEVILLERYWDVRP 61
Query: 70 KLR 72
L+
Sbjct: 62 DLK 64
>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 = 48.3 bits (115), Expect = 2e-08
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE 66
F++PHSH D GW+ T + H+ + ++VE+L++ FI E FF WW+
Sbjct: 3 AFVIPHSHMDVGWVYTVQESMHAYAANVYTSVVEELMRGKQRRFIAVEQEFFRLWWD 59
>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 = 43.0 bits (101), Expect = 2e-06
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 11 FLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFF 61
F+ HSHN W++TFE +Y T+ ++ ++ M+F + IS+
Sbjct: 1 FINAHSHNPYVWIQTFEEWYFEATKATYIPLLMHFHRNFEMSFNIAPISYE 51
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 28.4 bits (64), Expect = 0.27
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 37 ILNNMVEKLVQHPNMTFIWSEISFFSQWWERSRKL--RIIPIVA 78
I ++ + + + HP F+ +IS S+W E K ++P+VA
Sbjct: 348 IGSDAISRFLGHPRFHFVEGDISIHSEWIEYHIKKCDVVLPLVA 391
>gnl|CDD|212102 cd10790, GH38N_AMII_1, N-terminal catalytic domain of putative
prokaryotic class II alpha-mannosidases; glycoside
hydrolase family 38 (GH38). This mainly bacterial
subfamily corresponds to a group of putative class II
alpha-mannosidases, including various proteins assigned
as alpha-mannosidases, Streptococcus pyogenes (SpGH38)
encoded by ORF spy1604. Escherichia coli MngB encoded
by the mngB/ybgG gene, and Thermotoga maritime TMM, and
similar proteins. SpGH38 targets alpha-1,3 mannosidic
linkages. 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. MngB exhibits alpha-mannosidase
activity that catalyzes the conversion of
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. TMM is a homodimeric enzyme that hydrolyzes
p-nitrophenyl-alpha-D-mannopyranoside, alpha
-1,2-mannobiose, alpha -1,3-mannobiose, alpha
-1,4-mannobiose, and alpha -1,6-mannobiose. The GH38
family contains retaining glycosyl hydrolases that
employ 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. Divalent metal ions, such
as zinc or cobalt ions, are suggested to be required
for the catalytic activities of typical class II
alpha-mannosidases. However, TMM requires the cobalt or
cadmium for its activity. The cadmium ion dependency is
unique to TMM. Moreover, TMM is inhibited by
swainsonine but not 1-deoxymannojirimycin, which is in
agreement with the features of cytosolic
alpha-mannosidase.
Length = 273
Score = 27.4 bits (61), Expect = 0.69
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 5/38 (13%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQ 47
V ++ H+H D W T E QT L N+ E+L++
Sbjct: 2 VHIISHTHWDREWFATTE-----QTHKWLINLFERLLE 34
>gnl|CDD|153234 cd03140, GATase1_PfpI_3, Type 1 glutamine amidotransferase
(GATase1)-like domain found in a subgroup of proteins
similar to PfpI from Pyrococcus furiosus. Type 1
glutamine amidotransferase (GATase1)-like domain found
in a subgroup of proteins similar to PfpI from
Pyrococcus furiosus. PfpI is an ATP-independent
intracellular proteases which may hydrolyze small
peptides to provide a nutritional source. Only Cys of
the catalytic triad typical of GATase1 domains is
conserved in this group. This Cys residue is found in
the sharp turn between a beta strand and an alpha helix
termed the nucleophile elbow.
Length = 170
Score = 26.0 bits (58), Expect = 1.7
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 13 VPHSHNDPGWLKTFESYYH 31
H+ N +LK YY
Sbjct: 113 RKHTSNSLDFLKAHAPYYG 131
>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 = 25.5 bits (57), Expect = 2.4
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 7/51 (13%)
Query: 10 VFLVPHSHNDPGWLKTFE---SYYHSQTRMILNNMVEKLVQHPNMTFIWSE 57
++ V H+H D WL +L+ M E +P+ F S+
Sbjct: 2 IYAVGHAHIDLAWLWPVRETRRKAARTFSTVLDLMEE----YPDFVFTQSQ 48
>gnl|CDD|216980 pfam02335, Cytochrom_C552, Cytochrome c552. Cytochrome c552
(cytochrome c nitrite reductase) is a crucial enzyme in
the nitrogen cycle catalyzing the reduction of nitrite
to ammonia. The crystal structure of cytochrome c552
reveals it to be a dimer, with with 10 close-packed
type c haem groups.
Length = 383
Score = 25.7 bits (57), Expect = 3.0
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 22 WLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWS 56
W KT ES + T +KL + P + +W+
Sbjct: 16 WKKTAES---TPTGYGGEEREDKLEEDPRLVILWA 47
>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 = 25.3 bits (56), Expect = 3.2
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 9 IVFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPN 50
V ++ H+H D W FE + +I + ++E L + P
Sbjct: 1 KVHIISHTHWDREWYLPFEEFRMRLIDLI-DRLLELLEEDPE 41
>gnl|CDD|232960 TIGR00406, prmA, ribosomal protein L11 methyltransferase.
Ribosomal protein L11 methyltransferase is an
S-adenosyl-L-methionine-dependent methyltransferase
required for the modification of ribosomal protein L11.
This protein is found in bacteria and (with a probable
transit peptide) in Arabidopsis [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 288
Score = 25.2 bits (55), Expect = 4.4
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 32 SQTRMILNNMVEKLVQHPNM-TFIWSEISFFSQWWERSRKLRIIPI 76
++T M + + ++ E FS+ WER+ K P+
Sbjct: 61 AETDMNNSVIPLLEAFCLDLGRNHKIEFDEFSKDWERAWKDNFHPV 106
>gnl|CDD|183375 PRK11908, PRK11908, NAD-dependent epimerase/dehydratase family
protein; Provisional.
Length = 347
Score = 25.1 bits (55), Expect = 4.7
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 39 NNMVEKLVQHPNMTFIWSEISFFSQWWE-RSRKLR-IIPIVA 78
+ + LV HP M F +I+ +W E +K I+P+VA
Sbjct: 36 TDRLGDLVNHPRMHFFEGDITINKEWIEYHVKKCDVILPLVA 77
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 24.7 bits (55), Expect = 4.8
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 30 YHSQTRMILNNMVE 43
H TR ++NNMV
Sbjct: 63 LHGTTRALINNMVI 76
>gnl|CDD|100018 cd02189, delta_tubulin, The tubulin superfamily includes five
distinct families, the alpha-, beta-, gamma-, delta-,
and epsilon-tubulins and a sixth family (zeta-tubulin)
which is present only in kinetoplastid protozoa. The
alpha- and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. Delta-tubulin plays an essential role in
forming the triplet microtubules of centrioles and basal
bodies.
Length = 446
Score = 25.0 bits (55), Expect = 5.2
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 32 SQTRMILNNMVEKLVQHPNMTFI 54
++ LN++VE L HP +
Sbjct: 247 GRSTNPLNDLVEDLCPHPAYKLL 269
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
0.326 0.136 0.446
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,048,866
Number of extensions: 299636
Number of successful extensions: 440
Number of sequences better than 10.0: 1
Number of HSP's gapped: 438
Number of HSP's successfully gapped: 29
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.5 bits)