RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7082
(528 letters)
>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 = 416 bits (1072), Expect = e-144
Identities = 140/277 (50%), Positives = 189/277 (68%), Gaps = 1/277 (0%)
Query: 64 INVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETG 123
+NVH++PH+HDD+GWLKTV++YY G + V+ I+ S + L NPDR+FI VE
Sbjct: 1 LNVHLVPHTHDDVGWLKTVDQYYYGSNNSIQHAGVQYILDSVIEELLKNPDRKFIYVEIA 60
Query: 124 FFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNET 183
FFS WW+EQ+ T++ V+KLV G+LEF G W MNDEAT HY I+D +LG + L +T
Sbjct: 61 FFSRWWREQSEDTRQKVKKLVKNGQLEFINGGWCMNDEATTHYEDIIDQMTLGHQFLKDT 120
Query: 184 FGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLWEAS 243
FG C PRVGWQIDPFGHS+ AS+FAQMG++G F R+DYQD ++R K K M+ +W S
Sbjct: 121 FGECARPRVGWQIDPFGHSRTQASLFAQMGFDGLFFGRIDYQDKAQRLKNKEMEFIWRGS 180
Query: 244 ADLGKSSHIFTEMINNVYNPPSGFCFDILCHIEFI-DDETSSGYNAPYLAKEYLKWVQEQ 302
LG + IFT ++ N Y PP GFCFDILC E I DD YN +++++ +EQ
Sbjct: 181 PSLGPDADIFTGVLYNHYGPPPGFCFDILCGDEPIQDDPNLEDYNVDERVDDFVQYAKEQ 240
Query: 303 AAQFRSNNIPALFGGDFTYQEAEYYYRSLDKMIKYVN 339
A +R+N+I G DF YQ AE +++++DK+IKYVN
Sbjct: 241 AQHYRTNHIMLTMGSDFQYQNAEMWFKNMDKLIKYVN 277
>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 = 308 bits (791), Expect = e-102
Identities = 109/277 (39%), Positives = 169/277 (61%), Gaps = 19/277 (6%)
Query: 64 INVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETG 123
+NVH+IPHSH D+GWLKT +EYY G V+ I+ S V ALN++P+R+FI E G
Sbjct: 1 LNVHLIPHSHCDVGWLKTFDEYYNG--------DVKSILDSVVKALNNDPERKFIWAEIG 52
Query: 124 FFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNET 183
F WW++Q N TK+ +KLV G+LEF GG W MNDEA Y SI+D + G + L +T
Sbjct: 53 FLERWWEDQGNDTKQQFKKLVKNGQLEFVGGGWVMNDEACTTYESIIDQMTEGHQFLKDT 112
Query: 184 FGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLWEAS 243
FG PRVGWQIDPFGHS ++F++MG++G + +R+ Y ++ + K ++ +W S
Sbjct: 113 FGV--RPRVGWQIDPFGHSSTTPTLFSKMGFKGLVINRIPYSLKAEMKDNKQLEFVWRGS 170
Query: 244 ADLGKSSHIFTEMINNVYNPPSGFCFDILCHIEFIDDETSSGYNAPYLAKEYLKWVQEQA 303
LG S IFT ++++ Y+ P F + YN A E+++++++++
Sbjct: 171 PSLGPDSEIFTHVLDDHYSYPESLDF---------GGPPITDYNIAERADEFVEYIKKRS 221
Query: 304 AQFRSNNIPALFGGDFTYQEAEYYYRSLDKMIKYVNN 340
+R+N+I G DF ++ A + ++DK+I Y+N+
Sbjct: 222 KTYRTNHILIPLGDDFRFKNASLQFSNMDKLIAYINS 258
>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 = 254 bits (652), Expect = 1e-81
Identities = 90/315 (28%), Positives = 134/315 (42%), Gaps = 47/315 (14%)
Query: 65 NVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETGF 124
VH++ HSH D+GWL TV+E V++ + + L+ P+ RFIQ E F
Sbjct: 1 KVHLVGHSHIDVGWLWTVDET---------RRKVQRTFSNVLKLLDRYPEFRFIQSEAQF 51
Query: 125 FSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNETF 184
+ WW E + ++KLV GRLE GG W DE S++ G R E F
Sbjct: 52 YE-WWWEDQPELFKKIKKLVAEGRLEPVGGGWVEPDENLPSGESLIRQLLYGQRFFKEEF 110
Query: 185 GRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLWEASA 244
G PRVGW DPFG+S + + Q G + F+ R+ + D +K ++ +W
Sbjct: 111 G--VRPRVGWLPDPFGYSATLPQILKQAGIDYFLTQRLHWNDKNKFN--PHLEFIWRGP- 165
Query: 245 DLGKSSHIFTEMINNVYNPPSGFCFDILCHIEFIDDETSSGYNAPYLAKEYLKWVQEQAA 304
S I T M+ Y P G F A L + K+ A
Sbjct: 166 ---DGSEILTHMLPFDYYPTYGAQFR-----------------ADDLLDQAKKY----AD 201
Query: 305 QFRSNNIPALFGGDFTYQEAEYYYRSLDKMIKYVNNMQINGSKVNLLYSTPSCYIKAVHN 364
+ R+N++ FG + D++++Y+N + + TPS Y A+
Sbjct: 202 KTRTNHVLWPFGDG------DGGGGPTDELLEYINRWNELPGLPKVQFGTPSDYFDALEE 255
Query: 365 SGITLPTKQDDFFPY 379
+ T PTK DF Y
Sbjct: 256 A--TWPTKSGDFPTY 268
>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 = 223 bits (571), Expect = 1e-68
Identities = 108/359 (30%), Positives = 160/359 (44%), Gaps = 53/359 (14%)
Query: 65 NVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETGF 124
V ++PHSH+D GW+KT EEYY + I+ + V L+ NP +FI E F
Sbjct: 3 KVFVVPHSHNDPGWIKTFEEYYQ--------DQTKHILDNMVDKLSKNPKMKFIWAEISF 54
Query: 125 FSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNETF 184
WW + + KE V+KLV G+LE G W M DEA +HY +++D G + L E
Sbjct: 55 LERWWDDASPDKKEAVKKLVKNGQLEIVTGGWVMTDEANSHYFAMIDQLIEGHQWLKENL 114
Query: 185 GRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDY---QDLSKRQKEKGMQMLWE 241
G P+ GW IDPFGHS M + + G++ + R+ Y + L++R K ++ +W
Sbjct: 115 GV--KPKSGWSIDPFGHSPTMPYLLKRAGFKNMVIQRIHYEVKKYLAQR---KALEFMWR 169
Query: 242 ASADLGKSSHIFTEM-------INNVYNPPSGFC--FD--------ILC-----HIEFID 279
D S+ I T M I + P C FD C D
Sbjct: 170 QYWDATGSTDILTHMMPFYSYDIPHTCGPDPAVCCQFDFKRLPGGGESCPWKKPPQPITD 229
Query: 280 DETSSGYNAPYLAKEYLKWVQEQAAQFRSNNIPALFGGDFTY---QEAEYYYRSLDKMIK 336
D + A L +Y K ++ +RSN + G DF Y +E + Y + K+
Sbjct: 230 DNVAE--RAELLLDQYRK----KSQLYRSNVVLIPLGDDFRYDSDEEWDAQYDNYQKLFD 283
Query: 337 YVNNMQINGSKVNLLYSTPSCYIKAVH----NSGITLPTKQDDFFPYGSGKHAYWTGFF 391
Y+N+ V + + T S Y A+ + PT DFF Y YW+G++
Sbjct: 284 YINSNPEL--NVEIQFGTLSDYFNALRKRTGTNTPGFPTLSGDFFTYADRDDDYWSGYY 340
>gnl|CDD|178304 PLN02701, PLN02701, alpha-mannosidase.
Length = 1050
Score = 204 bits (521), Expect = 8e-57
Identities = 136/491 (27%), Positives = 208/491 (42%), Gaps = 98/491 (19%)
Query: 66 VHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETGFF 125
V ++PHSH+D GW+ TVEEYY ++ H I+ + V +L+ +P R+FI E +
Sbjct: 42 VFVVPHSHNDPGWILTVEEYY----QEQSRH----ILDTIVESLSKDPRRKFIWEEMSYL 93
Query: 126 SMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNETFG 185
WW++ + + KE KLV G+LE GG W MNDEA +HY +I++ + G LN+T G
Sbjct: 94 ERWWRDASPSKKEAFTKLVKNGQLEIVGGGWVMNDEANSHYFAIIEQITEGNMWLNDTIG 153
Query: 186 RCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLWEASAD 245
P+ W IDPFG+S MA + +MG+E + R Y+ + + K ++ +W S D
Sbjct: 154 V--APKNSWAIDPFGYSSTMAYLLRRMGFENMLIQRTHYEVKKELAQNKNLEYIWRQSWD 211
Query: 246 LGKSSHIFTEM-------INNVYNPPSGFC--FDI---------LCHIEFIDDETSSGYN 287
+++ IF M I + P C FD LC ET+ N
Sbjct: 212 AEETTDIFVHMMPFYSYDIPHTCGPEPAICCQFDFARMRGFQYELCPWGKHPVETNDE-N 270
Query: 288 APYLAKEYLKWVQEQAAQFRSNNIPALFGGDFTY---QEAEYYYRSLDKMIKYVN----- 339
A + L ++++ +R+N + G DF Y EAE +R+ K+ Y+N
Sbjct: 271 VQERAMKLLDQYRKKSTLYRTNTLLVPLGDDFRYISIDEAEAQFRNYQKLFDYINSNPSL 330
Query: 340 NMQIN--------------GSKVNLLYSTPSCYIKAVHNSGITLPTKQDDFFPYGSGKHA 385
++ ++N YS P + P+ DFF Y +
Sbjct: 331 KAEVKFGTLEDYFSTLRDEADRIN--YSRPG---EVGSGEVPGFPSLSGDFFTYADRQQD 385
Query: 386 YWTGFFTSRPALKRYERFGHNMLQESNEAFRKQPWLSPSSIYSEDLSCEPSETWDKFAIN 445
YW+G++ SRP K +R L+ + F S Y CE K +
Sbjct: 386 YWSGYYVSRPFFKAVDRVLEQTLRAAEILF------SFLLGYCRRFQCE------KLPTS 433
Query: 446 VYNALGRTVNRYVCKQLYVLSNLKSHSSHHHEDDLNVLREAMGVLQHHDGITGTAKQHPS 505
L R + + QHHDG+TGTAK H
Sbjct: 434 FSYKLTAA------------------------------RRNLALFQHHDGVTGTAKDHVV 463
Query: 506 NNYAELIHNGL 516
+Y +H L
Sbjct: 464 VDYGTRMHTSL 474
>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 = 170 bits (433), Expect = 1e-48
Identities = 106/340 (31%), Positives = 163/340 (47%), Gaps = 36/340 (10%)
Query: 64 INVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHS-VRKIIGSTVAALNSNPDRRFIQVET 122
I +IPHSH D+GW+ TV+E + H+ + S V L RRFI VE
Sbjct: 1 IQAFVIPHSHMDVGWVYTVQE---------SMHAYAANVYTSVVEELMRGKQRRFIAVEQ 51
Query: 123 GFFSMWWKE-QNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLN 181
FF +WW + K+ VR+L++ GRLEF G M+DEA + + G L
Sbjct: 52 EFFRLWWDGVATDKQKQQVRQLLSEGRLEFVIGGQVMHDEAVTELDDQILQLTEGHGFLY 111
Query: 182 ETFGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLWE 241
ETFG PR W +DPFG S ++FA G+ + SR+DY + QK KG+Q +W
Sbjct: 112 ETFGV--RPRFSWHVDPFGASATTPTLFALAGFNAHLISRIDYDLKAAMQKAKGLQFVWR 169
Query: 242 ASADLGKSSHIFTEMINNV-YNPP--------SGFCFDILCHIEFIDDETSSGY------ 286
S L +S IFT +++ Y P SGF ++ + F D Y
Sbjct: 170 GSPSLSESQEIFTHVMDQYSYCTPSYIPFSNRSGFYWNGVA--VFPDPPKDGIYPNMSLP 227
Query: 287 ----NAPYLAKEYLKWVQEQAAQFRSNNIPALFGGDFTYQEAEYYYRSLDKMIKYVNNMQ 342
N A+ + ++++AA FR+ ++ +G D + A + ++D ++ Y+N
Sbjct: 228 VTTQNIHQYAETMVANIKQRAAWFRTPHVLWPWGCDKQFFNASVQFSNMDPLLDYINQ-H 286
Query: 343 INGSKVNLLYSTPSCYIKAVHNSGITLPTK-QDDFFPYGS 381
+ V + Y+T Y +A+HNS +T + DF PY +
Sbjct: 287 SSEFGVTVQYATLGDYFQALHNSNLTWEVRGSQDFLPYST 326
>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 = 162 bits (413), Expect = 1e-46
Identities = 73/260 (28%), Positives = 119/260 (45%), Gaps = 25/260 (9%)
Query: 65 NVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETGF 124
VH++PHSH D+GWL+T E+YY + + I+ + L++NP+ +F+ E
Sbjct: 1 TVHLVPHSHYDVGWLQTFEQYY--------QINFKAILDKALRLLDANPEYKFLIEEVIL 52
Query: 125 FSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNETF 184
+W + + K +++ V +GRLE GG + M D S++ LG R L E
Sbjct: 53 LERYWDVRPD-LKAKLKQAVRSGRLEIAGGGYVMPDTNLPDGESLVRQILLGKRWLKEFL 111
Query: 185 GRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLWEASA 244
G P V WQ D FGHS ++ + A+ G+ GF F R Y ++ + LW
Sbjct: 112 G--ARPPVMWQADVFGHSPQLPQILAKSGFTGFAFGRGPYSQKRMQRP---SEFLWRGLD 166
Query: 245 DLGKSSHIFTEMINNVYNPPSGFCFDILCHIEFIDDETSSGYNAPYLAKEYLKWVQEQAA 304
+ I T + N Y+ C + +SG NA + ++ ++ A
Sbjct: 167 ----GTRILTHWMPNGYSDGPFLCGPDI-------PGDNSGPNALASLEALVEQWKKLAE 215
Query: 305 QFRSNNIPALFGGDFTYQEA 324
+N++ GGDFT +A
Sbjct: 216 LGATNHLLMPSGGDFTIPQA 235
>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 = 162 bits (410), Expect = 3e-45
Identities = 102/355 (28%), Positives = 158/355 (44%), Gaps = 39/355 (10%)
Query: 64 INVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETG 123
+ V ++PHSH+D GWLKT ++Y+ +T H I+ + V L + R+FI E
Sbjct: 2 LQVFVVPHSHNDPGWLKTFDDYFRD----QTQH----ILNNMVLKLKEDSRRKFIWSEIS 53
Query: 124 FFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNET 183
+F+ WW + K+ V++L+ G+LE G W M DEATAHY +++D G + L
Sbjct: 54 YFAKWWDIIDGQKKDAVKRLIENGQLEIVTGGWVMPDEATAHYFALIDQLIEGHQWLERN 113
Query: 184 FGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLWEAS 243
G P+ GW +DPFGHS MA + + G + R+ Y +K ++ W +
Sbjct: 114 LGV--KPKSGWAVDPFGHSPTMAYLLKRAGLSNMLIQRVHYSVKKHFSLQKTLEFFWRQN 171
Query: 244 ADLGKSSHIFTEMIN-NVYNPPSGFCFD--ILCHIEF-------------IDDETSSGYN 287
DLG S+ I M+ Y+ P D I C +F + E N
Sbjct: 172 WDLGSSTDILCHMMPFYSYDVPHTCGPDPKICCQFDFKRLPGGRISCPWRVPPEAIHPGN 231
Query: 288 APYLAKEYLKWVQEQAAQFRSNNIPALFGGDFTYQEAEYY---YRSLDKMIKYVNNMQIN 344
A+ L ++++ FR+ + A G DF Y E + + + K+ Y+N+
Sbjct: 232 VQSRAQMLLDQYRKKSKLFRTKVLLAPLGDDFRYTEYTEWDQQFENYQKLFDYMNSHP-- 289
Query: 345 GSKVNLLYSTPSCYIKAVHNSGIT--------LPTKQDDFFPYGSGKHAYWTGFF 391
V + T S Y A+ S P DFF Y YW+G+F
Sbjct: 290 ELHVKAQFGTLSDYFDALRKSTGMDPVGGQSAFPVLSGDFFTYADRDDHYWSGYF 344
>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 = 152 bits (384), Expect = 1e-41
Identities = 101/355 (28%), Positives = 158/355 (44%), Gaps = 39/355 (10%)
Query: 64 INVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETG 123
+ V ++PHSH+D GW+KT ++YY +T H I+ S V L +P RRFI E
Sbjct: 2 LQVFVVPHSHNDPGWIKTFDKYYY----DQTQH----ILNSMVVKLQEDPRRRFIWSEIS 53
Query: 124 FFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNET 183
FFS WW N + VR+LV G+LE G W M DEA +HY +++D G + L +
Sbjct: 54 FFSKWWDNINAQKRAAVRRLVGNGQLEMATGGWVMPDEANSHYFAMIDQLIEGHQWLEKN 113
Query: 184 FGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLWEAS 243
G PR GW +DPFGHS M + + + R+ Y + ++ +W +
Sbjct: 114 IG--VTPRSGWAVDPFGHSSTMPYILRRSNLTSMLIQRVHYAIKKHFAATQSLEFMWRQT 171
Query: 244 ADLGKSSHIFTEMIN-NVYNPPSGFCFD--ILCHIEF-------------IDDETSSGYN 287
D S+ IF M+ Y+ P D I C +F + + N
Sbjct: 172 WDPDSSTDIFCHMMPFYSYDVPHTCGPDPKICCQFDFKRLPGGRINCPWKVPPRAITEAN 231
Query: 288 APYLAKEYLKWVQEQAAQFRSNNIPALFGGDFTY---QEAEYYYRSLDKMIKYVNNMQIN 344
A+ L ++++ +RS + G DF Y QE + + + ++ ++N+
Sbjct: 232 VAERAQLLLDQYRKKSKLYRSKVLLVPLGDDFRYDKPQEWDAQFLNYQRLFDFLNSHP-- 289
Query: 345 GSKVNLLYSTPSCYIKAVHNS-GIT-------LPTKQDDFFPYGSGKHAYWTGFF 391
V + T S Y A++ G+ P DFF Y + YWTG++
Sbjct: 290 ELHVQAQFGTLSDYFDALYKRTGVVPGMRPPGFPVVSGDFFSYADREDHYWTGYY 344
>gnl|CDD|214875 smart00872, Alpha-mann_mid, Alpha mannosidase, middle domain.
Members of this entry belong to the glycosyl hydrolase
family 38, This domain, which is found in the central
region adopts a structure consisting of three alpha
helices, in an immunoglobulin/albumin-binding
domain-like fold. The domain is predominantly found in
the enzyme alpha-mannosidase.
Length = 79
Score = 71.4 bits (176), Expect = 1e-15
Identities = 27/125 (21%), Positives = 43/125 (34%), Gaps = 48/125 (38%)
Query: 386 YWTGFFTSRPALKRYERFGHNMLQESNEAFRKQPWLSPSSIYSEDLSCEPSETWDKFAIN 445
Y G +TSRP LKR R ++L+
Sbjct: 1 YHRGTYTSRPYLKRLNRRAESLLRA----------------------------------- 25
Query: 446 VYNALGRTVNRYVCKQLYVLSNLKSHSSHHHEDDLNVLREAMGVLQHHDGITGTAKQHPS 505
++L L+ L S + + L L +A+ + QHHD ITGT+
Sbjct: 26 -------------AEELAALAALLSLGYKYPSEQLEELWKALLLNQHHDAITGTSIDEVY 72
Query: 506 NNYAE 510
++Y +
Sbjct: 73 DDYEK 77
>gnl|CDD|220157 pfam09261, Alpha-mann_mid, Alpha mannosidase, middle domain.
Members of this family adopt a structure consisting of
three alpha helices, in an
immunoglobulin/albumin-binding domain-like fold. They
are predominantly found in the enzyme alpha-mannosidase.
Length = 82
Score = 67.6 bits (166), Expect = 3e-14
Identities = 23/128 (17%), Positives = 44/128 (34%), Gaps = 50/128 (39%)
Query: 385 AYWTGFFTSRPALKRYERFGHNMLQESNEAFRKQPWLSPSSIYSEDLSCEPSETWDKFAI 444
Y G +TSRP +KR R ++L+
Sbjct: 1 EYHRGTYTSRPDIKRLNRKLESLLRA---------------------------------- 26
Query: 445 NVYNALGRTVNRYVCKQLYVLSNLKSHSSH--HHEDDLNVLREAMGVLQHHDGITGTAKQ 502
+ L L++L + + ++L+ L +A+ + Q HD + GT+ Q
Sbjct: 27 --------------AELLASLASLLGNKGELDDYYEELDKLWKALLLNQFHDALPGTSIQ 72
Query: 503 HPSNNYAE 510
++Y +
Sbjct: 73 EVYDDYEK 80
>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 = 69.8 bits (172), Expect = 2e-13
Identities = 44/166 (26%), Positives = 64/166 (38%), Gaps = 30/166 (18%)
Query: 66 VHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIG--STVAAL-NSNPDRRFIQVET 122
++ + H+H D+ WL V E + RK STV L PD F Q
Sbjct: 2 IYAVGHAHIDLAWLWPVRE------------TRRKAARTFSTVLDLMEEYPDFVFTQ-SQ 48
Query: 123 GFFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSL------G 176
W +E E +++ V GR E GG W D ++ G SL G
Sbjct: 49 AQLYEWLEEDYPELFERIKERVKEGRWEPVGGMWVEPD------CNLPSGESLVRQFLYG 102
Query: 177 LRLLNETFGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRM 222
R E FG R+ W D FG S + + + G + F+ ++
Sbjct: 103 QRYFREEFGV--ESRILWLPDSFGFSAALPQILKKSGIDYFVTQKL 146
>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 = 45.1 bits (107), Expect = 4e-05
Identities = 33/167 (19%), Positives = 58/167 (34%), Gaps = 35/167 (20%)
Query: 66 VHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETG-F 124
VHII H+H D W T E+ L + +R ++
Sbjct: 2 VHIISHTHWDREWFATTEQ-----------THKW---------LINLFERLLELIQKDPE 41
Query: 125 FSMWWKEQNNATKEM----------VRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFS 174
+S Q ++ +R+ + +G+L G + D SI+ F
Sbjct: 42 YSFVLDGQTAILEDYLKVFPEREKKLRQAIKSGKLII-GPYYIQIDWRITSEESIVRNFE 100
Query: 175 LGLRLLNETFGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSR 221
+G + + FG ++GW D FG ++ + + G E R
Sbjct: 101 IGKKDCDR-FGA--SMKIGWLPDSFGFISQLPQLMRKFGIEAVFLWR 144
>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 = 43.4 bits (102), Expect = 8e-05
Identities = 40/221 (18%), Positives = 72/221 (32%), Gaps = 37/221 (16%)
Query: 68 IIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETGFFSM 127
I HSH+ W++T EE+Y T + ++ + N + F + ++
Sbjct: 2 INAHSHNPYVWIQTFEEWYF----EATKATYIPLL----MHFHRNFEMSFNIAPISYEAL 53
Query: 128 WWKEQNNATKEMVRKLVNTGRLEFTGGAWAMND--EATAHYASILDGFSLGLRLLNETFG 185
++ + K ++ + G+LE D EA +H ++ + G+ L + G
Sbjct: 54 FYHDLGENIKLQMKSIQKNGQLEIGTHGATHPDESEAQSHPENVYAQITEGITWLEKHMG 113
Query: 186 RCGVPRVGWQIDPFG-----HSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEKGMQMLW 240
PR W + F S+ + + + G+ K LW
Sbjct: 114 V--TPRHIWLHECFYNQAKQLSQGIPYILQKSGFLYLFVQSRSIS-------VKKELALW 164
Query: 241 EASADLGKSSHIFTEMINNVYNPPSGFCFDILCHIEFIDDE 281
K S +FT I H EF
Sbjct: 165 RQIWYNKKDSGVFTF-------------IVIPLHDEFFGHW 192
>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 = 43.1 bits (102), Expect = 1e-04
Identities = 41/161 (25%), Positives = 59/161 (36%), Gaps = 20/161 (12%)
Query: 66 VHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALN---SNPDRRFIQVET 122
+H + H H D WL EE ++RK S V L PD F +
Sbjct: 2 IHAMGHCHIDSAWLWPYEE------------TIRKCARSWVTVLRLMEDYPDFTFACSQA 49
Query: 123 GFFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLNE 182
W K E +++ V GR GG W D S++ F G R E
Sbjct: 50 QQLE-WVKSWYPGLYEEIQERVKNGRFIPVGGTWVEMDGNLPSGESMVRQFLYGQRFFKE 108
Query: 183 TFG-RCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRM 222
FG C + W D FG+S ++ + G F+ ++
Sbjct: 109 EFGITC---KEFWLPDTFGYSAQLPQIMKGCGISRFLTQKL 146
>gnl|CDD|182093 PRK09819, PRK09819, alpha-mannosidase; Provisional.
Length = 875
Score = 43.4 bits (103), Expect = 3e-04
Identities = 40/166 (24%), Positives = 67/166 (40%), Gaps = 30/166 (18%)
Query: 65 NVHIIPHSHDDMGWLKTVEE---YYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRF---- 117
VHI+PH H D W T E +++ +I+ L + D ++
Sbjct: 5 KVHIVPHMHWDREWYFTTERSRILLV--------NNMEEIL----DRLEQDNDYKYYVLD 52
Query: 118 --IQVETGFFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSL 175
+ + + K ++ KE V+KLV G+L G + D+ SI+
Sbjct: 53 GQTSLLEDYLA--VKPED---KERVKKLVQAGKL-IIGPWYTQTDQLVVSGESIVRNLLY 106
Query: 176 GLRLLNETFGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSR 221
G+R E FG ++G+ D FG S +M ++ G +F R
Sbjct: 107 GIRDCRE-FGE--PMKIGYLPDSFGQSGQMPQIYNGFGITRTLFWR 149
>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 = 42.6 bits (101), Expect = 3e-04
Identities = 46/208 (22%), Positives = 77/208 (37%), Gaps = 43/208 (20%)
Query: 66 VHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQVETGFF 125
VHII H+H D W EE+ + +I + L +P+ F
Sbjct: 2 VHIISHTHWDREWYLPFEEFR---------MRLIDLIDRLLELLEEDPE---------FK 43
Query: 126 SMWWKEQNNA----------TKEMVRKLVNTGRLEFTGGAW-AMNDEATAHYASILDGFS 174
S Q +E ++KL+ G+L G W + DE + +
Sbjct: 44 SFHLDGQTIVLEDYLEVRPEKRERLKKLIREGKLVI--GPWYVLQDEFLTSGEANIRNLL 101
Query: 175 LGLRLLNETFGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSKRQKEK 234
+G ++ E FG ++G+ D FGH +M + G + +F R + + E
Sbjct: 102 IGKKVAEE-FG--KSMKIGYFPDTFGHIGQMPQILKGFGIDNAVFGR-GVKPTESQYSE- 156
Query: 235 GMQMLWEASADLGKSSHIFTEMINNVYN 262
WE S D S + ++ N Y+
Sbjct: 157 ---FWWE-SPD---GSRVLGILLANWYS 177
>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 = 41.7 bits (98), Expect = 5e-04
Identities = 40/169 (23%), Positives = 65/169 (38%), Gaps = 20/169 (11%)
Query: 65 NVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALN---SNPDRRFIQVE 121
NV+ I + H D WL E + +K+ S + P+ RF+ +
Sbjct: 1 NVYGIGNCHIDTAWLWPFSE------------TQQKVARSWSTQCDLMDRYPEYRFVASQ 48
Query: 122 TGFFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLN 181
F W + E V++ V GR GG+W ND S+ F G R
Sbjct: 49 AQQFK-WLETLYPDLFEKVKEYVKQGRFHPIGGSWVENDTNMPSGESLARQFLYGQRYFE 107
Query: 182 ETFG-RCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSK 229
FG RC W D FG+S ++ + G + F ++ + +++
Sbjct: 108 SRFGKRC---DTFWLPDTFGYSSQIPQLCRLAGMDYFFTQKLSWNNINS 153
>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 = 38.7 bits (91), Expect = 0.005
Identities = 40/169 (23%), Positives = 71/169 (42%), Gaps = 36/169 (21%)
Query: 65 NVHIIPHSHDDMGWLKTVEE-----YYTGGGDPKTPHSVRKIIGSTVAALNSNPD-RRFI 118
VH++PH+H D W T E+ + + L +NPD ++
Sbjct: 1 KVHVVPHTHWDREWYFTTEDSRILLVNH--------------MDEVLDELENNPDFPYYV 46
Query: 119 ---Q---VETGFFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDG 172
Q ++ + + + ++ KE ++KLV GRL F G + DE SI+
Sbjct: 47 LDGQSSILDD-YLA--VRPED---KERIKKLVKEGRL-FIGPWYTQTDELVVSGESIVRN 99
Query: 173 FSLGLRLLNETFGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSR 221
G++ + G G ++G+ D FG S +M ++ G + +F R
Sbjct: 100 LLYGIKDARK-LG--GYMKIGYLPDSFGQSAQMPQIYNGFGIDNAVFWR 145
>gnl|CDD|212103 cd10791, GH38N_AMII_like_1, N-terminal catalytic domain of mainly
uncharacterized eukaryotic proteins similar to
alpha-mannosidases; glycoside hydrolase family 38
(GH38). The subfamily of mainly uncharacterized
eukaryotic proteins shows sequence homology with class
II alpha-mannosidases (AlphaAMIIs). AlphaAMIIs possess
a-1,3, a-1,6, and a-1,2 hydrolytic activity, and
catalyze the degradation of N-linked oligosaccharides.
The N-terminal catalytic domain of alphaMII adopts a
structure consisting of parallel 7-stranded beta/alpha
barrel. This subfamily belongs to the GH38 family of
retaining glycosyl hydrolases, which 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.
Length = 254
Score = 38.1 bits (89), Expect = 0.006
Identities = 35/158 (22%), Positives = 60/158 (37%), Gaps = 19/158 (12%)
Query: 66 VHIIPHSHDDMGWLKT---VEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFI-QVE 121
VH++ HSH D+G+ V+ Y+ + + + A N D RF E
Sbjct: 2 VHVVHHSHTDIGYTDLQEKVDRYHV--------DYIPQALDLAEATKNYPEDARFRWTTE 53
Query: 122 TGF-FSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLL 180
+ + + K + +E + + V GR+ + + E + GL L
Sbjct: 54 STWLVEEYLKCASPEQRERLEQAVRRGRIGWHALPLNITTELMDE-----ELLRRGLYLS 108
Query: 181 NETFGRCGVP-RVGWQIDPFGHSKEMASMFAQMGYEGF 217
E R G+P V Q D GH+ + + A G +
Sbjct: 109 KELDRRFGLPIIVAMQTDVPGHTWGLVDVLADAGIKYL 146
>gnl|CDD|223460 COG0383, AMS1, Alpha-mannosidase [Carbohydrate transport and
metabolism].
Length = 943
Score = 33.2 bits (76), Expect = 0.37
Identities = 34/168 (20%), Positives = 62/168 (36%), Gaps = 20/168 (11%)
Query: 65 NVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRRFIQV---E 121
+ + H+H D WL ++E + ++ + + + D +Q
Sbjct: 199 EIPAVGHAHIDTAWLWPLDE-------------TERKASTSFSLVMNLMDHYPVQKFVQS 245
Query: 122 TGFFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFSLGLRLLN 181
W K R V + E GG W D T S+ F G R
Sbjct: 246 AAALYNWLKPDVPFL--FSRPAVEFEQWEIVGGMWVEEDLNTPSGESLSRQFLYGQRFFT 303
Query: 182 ETFGRCGVPRVGWQIDPFGHSKEMASMFAQMGYEGFMFSRMDYQDLSK 229
E FG R+ W+ D FG S ++ + +G + F+ +++ + D ++
Sbjct: 304 EKFG--ASSRIYWKPDSFGFSGQLPQILEPLGIDVFVTTKLAWNDTNR 349
>gnl|CDD|227097 COG4755, COG4755, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 151
Score = 29.1 bits (65), Expect = 3.0
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 437 ETWDKFAINVY-NALGRTVNRYVCKQLYVLSNLKSHSSHHH-EDDLNVLREAMGVLQH 492
ET A+ Y + + ++V Q L LKSH H D L+++ A H
Sbjct: 2 ETPTTEAVLEYLESFMERLEQWVKLQKRQLKELKSHGEHMKVADRLDLIYSARAAFGH 59
>gnl|CDD|185181 PRK15279, PRK15279, type III secretion protein SopE; Provisional.
Length = 240
Score = 29.0 bits (64), Expect = 5.0
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 360 KAVHNSGITLPTKQDDFFPYGSGKHAYWTGFFTSRPALKRYERFGHNMLQESN 412
+A N+G+ TK D F P G+G + + T +S A +Y R N Q+++
Sbjct: 146 EAAKNAGLPGTTKNDVFTPSGAGANPFITPLISS--ANSKYPRMFINQHQQAS 196
>gnl|CDD|177025 CHL00093, groEL, chaperonin GroEL.
Length = 529
Score = 29.3 bits (66), Expect = 6.2
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 218 MFSRMDYQDLSKRQKEKGMQMLWEA-SADLG 247
M ++ YQD ++R E+GM +L EA S LG
Sbjct: 1 MSKKILYQDNARRALERGMDILAEAVSVTLG 31
>gnl|CDD|222416 pfam13848, Thioredoxin_6, Thioredoxin-like domain.
Length = 183
Score = 28.5 bits (64), Expect = 6.7
Identities = 10/57 (17%), Positives = 17/57 (29%), Gaps = 6/57 (10%)
Query: 277 FIDDETSSGYNAPYLAKEYLKWVQEQAAQFRSNNIPALFGGDFTYQEAEYYYRSLDK 333
+ S ++ V+E A +F+ A G + EY S
Sbjct: 100 LFIKKDSEET------EKLKNRVEEVAKKFKGKINFATVDGKSFGRVLEYLGLSSAD 150
>gnl|CDD|221558 pfam12395, DUF3658, Protein of unknown function. This domain
family is found in bacteria, and is approximately 110
amino acids in length. The family is found in
association with pfam08874. There are two completely
conserved residues (D and R) that may be functionally
important.
Length = 111
Score = 27.6 bits (62), Expect = 7.1
Identities = 17/104 (16%), Positives = 33/104 (31%), Gaps = 37/104 (35%)
Query: 57 HPVKPDHINVHIIPHSHDDMGWLKTVEEYYTGGGDPKTPHSVRKIIGSTVAALNSNPDRR 116
V D+ + I+ + D+ + K ++IG + L
Sbjct: 42 VSVPEDYFDAFILEAATDE--FQKA-----------------ARVIGEVMGHLEQLVGDT 82
Query: 117 FIQVETGFFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMND 160
F+ ++ +R+L+ G LE G +M D
Sbjct: 83 FL---------EYR---------IRELIKQGVLELRGDLKSMRD 108
>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 = 28.9 bits (65), Expect = 7.4
Identities = 20/101 (19%), Positives = 35/101 (34%), Gaps = 16/101 (15%)
Query: 122 TGFFSMWWKEQNNATKEMVRKLVNTGRLEFTGGAWAMNDEATAHYASILDGFS------- 174
+G ++ E+ R+L +G++E +L
Sbjct: 52 SGSLLEQLEDYLPEVLELFRELAESGQVELLTSP------YYHPLLPLLPDKEDFIAQVE 105
Query: 175 LGLRLLNETFGRCGVPRVGWQIDPFGHSKEMASMFAQMGYE 215
+G L E FG PR W + +S E+ + A+ G E
Sbjct: 106 MGRELYREYFGV--EPRGFWLPE-LAYSPEIVKILAEAGIE 143
>gnl|CDD|239743 cd03774, MATH_SPOP, Speckle-type POZ protein (SPOP) family, MATH
domain; composed of proteins with similarity to human
SPOP. SPOP was isolated as a novel antigen recognized by
serum from a scleroderma patient, whose overexpression
in COS cells results in a discrete speckled pattern in
the nuclei. It contains an N-terminal MATH domain and a
C-terminal BTB (also called POZ) domain. Together with
Cul3, SPOP constitutes an ubiquitin E3 ligase which is
able to ubiquitinate the PcG protein BMI1, the variant
histone macroH2A1 and the death domain-associated
protein Daxx. Therefore, SPOP may be involved in the
regulation of these proteins and may play a role in
transcriptional regulation, apoptosis and X-chromosome
inactivation. Cul3 binds to the BTB domain of SPOP
whereas Daxx and the macroH2A1 nonhistone region have
been shown to bind to the MATH domain. Both MATH and BTB
domains are necessary for the nuclear speckled
accumulation of SPOP. There are many proteins, mostly
uncharacterized, containing both MATH and BTB domains
from C. elegans and plants which are excluded from this
family.
Length = 139
Score = 27.9 bits (62), Expect = 8.1
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 425 SIYSEDLSCEPSETWDKFAINVYNALGRTVN 455
S+Y +SC SE KF ++ NA G
Sbjct: 58 SLYLLLVSCPKSEVRAKFKFSILNAKGEETK 88
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
0.320 0.134 0.419
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,323,843
Number of extensions: 2632081
Number of successful extensions: 2435
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2391
Number of HSP's successfully gapped: 42
Length of query: 528
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 427
Effective length of database: 6,457,848
Effective search space: 2757501096
Effective search space used: 2757501096
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 (21.8 bits)
S2: 61 (27.1 bits)