RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10965
(400 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 = 400 bits (1031), Expect = e-140
Identities = 141/225 (62%), Positives = 170/225 (75%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F+YVE +FF RWW EQ+E R VK+LV G+LEF+ GGWCM+DEAT HY +IDQMTLG
Sbjct: 54 FIYVEIAFFSRWWREQSEDTRQKVKKLVKNGQLEFINGGWCMNDEATTHYEDIIDQMTLG 113
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
++L DTFGEC +PRV WQIDPFGHS A FA MGFDG+FFGRID++D A R KNK M
Sbjct: 114 HQFLKDTFGECARPRVGWQIDPFGHSRTQASLFAQMGFDGLFFGRIDYQDKAQRLKNKEM 173
Query: 121 EMVWRPDDTLGPEGDFFTGVMYNIYDPPPGFCFDTYCEDEPIMDNPKLHGVNVNARVDEF 180
E +WR +LGP+ D FTGV+YN Y PPPGFCFD C DEPI D+P L NV+ RVD+F
Sbjct: 174 EFIWRGSPSLGPDADIFTGVLYNHYGPPPGFCFDILCGDEPIQDDPNLEDYNVDERVDDF 233
Query: 181 IEVVKKYAQAYRTNNVIITMGGDFHYVVASAWFKNIDKLIKYVNA 225
++ K+ AQ YRTN++++TMG DF Y A WFKN+DKLIKYVN
Sbjct: 234 VQYAKEQAQHYRTNHIMLTMGSDFQYQNAEMWFKNMDKLIKYVNK 278
>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 = 261 bits (670), Expect = 4e-86
Identities = 100/224 (44%), Positives = 134/224 (59%), Gaps = 12/224 (5%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E F RWWE+Q + K+LV G+LEF+ GGW M+DEA Y S+IDQMT G
Sbjct: 46 FIWAEIGFLERWWEDQGNDTKQQFKKLVKNGQLEFVGGGWVMNDEACTTYESIIDQMTEG 105
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
++L DTFG +PRV WQIDPFGHS+ F+ MGF G+ RI + A K NK +
Sbjct: 106 HQFLKDTFG--VRPRVGWQIDPFGHSSTTPTLFSKMGFKGLVINRIPYSLKAEMKDNKQL 163
Query: 121 EMVWRPDDTLGPEGDFFTGVMYNIYDPPPGFCFDTYCEDEPIMDNPKLHGVNVNARVDEF 180
E VWR +LGP+ + FT V+ + Y P F PI D N+ R DEF
Sbjct: 164 EFVWRGSPSLGPDSEIFTHVLDDHYSYPESLDFGGP----PITD------YNIAERADEF 213
Query: 181 IEVVKKYAQAYRTNNVIITMGGDFHYVVASAWFKNIDKLIKYVN 224
+E +KK ++ YRTN+++I +G DF + AS F N+DKLI Y+N
Sbjct: 214 VEYIKKRSKTYRTNHILIPLGDDFRFKNASLQFSNMDKLIAYIN 257
>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 = 219 bits (560), Expect = 2e-69
Identities = 78/266 (29%), Positives = 114/266 (42%), Gaps = 44/266 (16%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F+ E F+ WWE+Q E + +K+LV +GRLE + GGW DE P SLI Q+ G
Sbjct: 44 FIQSEAQFYEWWWEDQPELFKK-IKKLVAEGRLEPVGGGWVEPDENLPSGESLIRQLLYG 102
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
++ + FG +PRV W DPFG+SA + G D R+ D K N +
Sbjct: 103 QRFFKEEFG--VRPRVGWLPDPFGYSATLPQILKQAGIDYFLTQRLHWNDK--NKFNPHL 158
Query: 121 EMVWR-PDDTLGPEGDFFTGVMYNIYDPPPGFCFDTYCEDEPIMDNPKLHGVNVNARVDE 179
E +WR PD + + T ++ Y P G F R D+
Sbjct: 159 EFIWRGPDGS-----EILTHMLPFDYYPTYGAQF----------------------RADD 191
Query: 180 FIEVVKKYAQAYRTNNVIITMGGDFHYVVASAWFKNIDKLIKYVNA--KLNSDVHVLYST 237
++ KKYA RTN+V+ G D+L++Y+N +L V + T
Sbjct: 192 LLDQAKKYADKTRTNHVLWPFGDGDG------GGGPTDELLEYINRWNELPGLPKVQFGT 245
Query: 238 PACYLQALNKENITWPSKMDDDFFPF 263
P+ Y AL + DF +
Sbjct: 246 PSDYFDALEEAT---WPTKSGDFPTY 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 = 201 bits (514), Expect = 1e-61
Identities = 96/305 (31%), Positives = 147/305 (48%), Gaps = 41/305 (13%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E SF RWW++ + + +VK+LV G+LE + GGW M+DEA HY ++IDQ+ G
Sbjct: 47 FIWAEISFLERWWDDASPDKKEAVKKLVKNGQLEIVTGGWVMTDEANSHYFAMIDQLIEG 106
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRK---KN 117
++L + G +P+ W IDPFGHS + GF + RI +E ++K +
Sbjct: 107 HQWLKENLGV--KPKSGWSIDPFGHSPTMPYLLKRAGFKNMVIQRIHYE---VKKYLAQR 161
Query: 118 KTMEMVWRPDDTLGPEGDFFTGVM-YNIYD------PPPGFC--FD--------TYCE-- 158
K +E +WR D T +M + YD P P C FD C
Sbjct: 162 KALEFMWRQYWDATGSTDILTHMMPFYSYDIPHTCGPDPAVCCQFDFKRLPGGGESCPWK 221
Query: 159 --DEPIMDNPKLHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---F 213
+PI D+ NV R + ++ +K +Q YR+N V+I +G DF Y W +
Sbjct: 222 KPPQPITDD------NVAERAELLLDQYRKKSQLYRSNVVLIPLGDDFRYDSDEEWDAQY 275
Query: 214 KNIDKLIKYVNAKLNSDVHVLYSTPACYLQALNKENITWPS---KMDDDFFPFGSDEHSY 270
N KL Y+N+ +V + + T + Y AL K T + DFF + + Y
Sbjct: 276 DNYQKLFDYINSNPELNVEIQFGTLSDYFNALRKRTGTNTPGFPTLSGDFFTYADRDDDY 335
Query: 271 WTGYF 275
W+GY+
Sbjct: 336 WSGYY 340
>gnl|CDD|178304 PLN02701, PLN02701, alpha-mannosidase.
Length = 1050
Score = 188 bits (480), Expect = 8e-53
Identities = 123/422 (29%), Positives = 190/422 (45%), Gaps = 73/422 (17%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+ RWW + + + + +LV G+LE + GGW M+DEA HY ++I+Q+T G
Sbjct: 85 FIWEEMSYLERWWRDASPSKKEAFTKLVKNGQLEIVGGGWVMNDEANSHYFAIIEQITEG 144
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKK---N 117
+LNDT G P+ +W IDPFG+S+ +A MGF+ + R +E ++K+ N
Sbjct: 145 NMWLNDTIGVA--PKNSWAIDPFGYSSTMAYLLRRMGFENMLIQRTHYE---VKKELAQN 199
Query: 118 KTMEMVWRPDDTLGPEGDFFTGVM-YNIYD------PPPGFC--FD---------TYCE- 158
K +E +WR D F +M + YD P P C FD C
Sbjct: 200 KNLEYIWRQSWDAEETTDIFVHMMPFYSYDIPHTCGPEPAICCQFDFARMRGFQYELCPW 259
Query: 159 -DEPIMDNPKLHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVV---ASAWFK 214
P+ N + NV R + ++ +K + YRTN +++ +G DF Y+ A A F+
Sbjct: 260 GKHPVETNDE----NVQERAMKLLDQYRKKSTLYRTNTLLVPLGDDFRYISIDEAEAQFR 315
Query: 215 NIDKLIKYVNAKLNSDVHVLYSTPACYLQALNKE----NITWPSKMDD-----------D 259
N KL Y+N+ + V + T Y L E N + P ++ D
Sbjct: 316 NYQKLFDYINSNPSLKAEVKFGTLEDYFSTLRDEADRINYSRPGEVGSGEVPGFPSLSGD 375
Query: 260 FFPFGSDEHSYWTGYFTSRPSFK-----------------YFVYQTNVALQMTKQLKTSL 302
FF + + YW+GY+ SRP FK F+ Q K +
Sbjct: 376 FFTYADRQQDYWSGYYVSRPFFKAVDRVLEQTLRAAEILFSFLLGYCRRFQCEKLPTSFS 435
Query: 303 PNDTLAEEQFLIQRAMGIAQHHDAVSGTERQHVTNDYSLYLYEGIQAAMKIINVAYRHLL 362
T A +R + + QHHD V+GT + HV DY ++ +Q ++ A LL
Sbjct: 436 YKLTAA------RRNLALFQHHDGVTGTAKDHVVVDYGTRMHTSLQDLQIFMSAAVEVLL 489
Query: 363 GD 364
G
Sbjct: 490 GI 491
>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 = 152 bits (385), Expect = 1e-43
Identities = 68/226 (30%), Positives = 102/226 (45%), Gaps = 20/226 (8%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F+ E R+W+ + + +A +K+ V GRLE GG+ M D P SL+ Q+ LG
Sbjct: 45 FLIEEVILLERYWDVRPDL-KAKLKQAVRSGRLEIAGGGYVMPDTNLPDGESLVRQILLG 103
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
++L + G +P V WQ D FGHS ++ A GF G FGR + ++ +
Sbjct: 104 KRWLKEFLG--ARPPVMWQADVFGHSPQLPQILAKSGFTGFAFGRGPYSQ---KRMQRPS 158
Query: 121 EMVWR-PDDTLGPEGDFFTGVMYNIYDPPPGFCFDTYCEDEPIMDNPKLHGVNVNARVDE 179
E +WR D T T M N Y P C D G N A ++
Sbjct: 159 EFLWRGLDGT-----RILTHWMPNGYSDGPFLCGPDIPGDNS--------GPNALASLEA 205
Query: 180 FIEVVKKYAQAYRTNNVIITMGGDFHYVVASAWFKNIDKLIKYVNA 225
+E KK A+ TN++++ GGDF A N +L++ N+
Sbjct: 206 LVEQWKKLAELGATNHLLMPSGGDFTIPQADPLQVNQARLVEPWNS 251
>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 = 152 bits (385), Expect = 9e-43
Identities = 93/303 (30%), Positives = 142/303 (46%), Gaps = 33/303 (10%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+F +WW+ + Q + +VK L++ G+LE + GGW M DEAT HY +LIDQ+ G
Sbjct: 47 FIWSEISYFAKWWDIIDGQKKDAVKRLIENGQLEIVTGGWVMPDEATAHYFALIDQLIEG 106
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
++L G +P+ W +DPFGHS +A G + R+ + KT+
Sbjct: 107 HQWLERNLGV--KPKSGWAVDPFGHSPTMAYLLKRAGLSNMLIQRVHYSVKKHFSLQKTL 164
Query: 121 EMVWRPDDTLGPEGDFFTGVM-YNIYD------PPPGFC--FD--------TYCEDEPIM 163
E WR + LG D +M + YD P P C FD C P
Sbjct: 165 EFFWRQNWDLGSSTDILCHMMPFYSYDVPHTCGPDPKICCQFDFKRLPGGRISC---PWR 221
Query: 164 DNPK-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNIDKL 219
P+ +H NV +R ++ +K ++ +RT ++ +G DF Y + W F+N KL
Sbjct: 222 VPPEAIHPGNVQSRAQMLLDQYRKKSKLFRTKVLLAPLGDDFRYTEYTEWDQQFENYQKL 281
Query: 220 IKYVNAKLNSDVHVLYSTPACYLQALNKENITWPSK-------MDDDFFPFGSDEHSYWT 272
Y+N+ V + T + Y AL K P + DFF + + YW+
Sbjct: 282 FDYMNSHPELHVKAQFGTLSDYFDALRKSTGMDPVGGQSAFPVLSGDFFTYADRDDHYWS 341
Query: 273 GYF 275
GYF
Sbjct: 342 GYF 344
>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 = 147 bits (372), Expect = 5e-41
Identities = 91/283 (32%), Positives = 139/283 (49%), Gaps = 20/283 (7%)
Query: 1 FVYVETSFFWRWWEE-QNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTL 59
F+ VE FF WW+ ++ + V++L+ +GRLEF++GG M DEA I Q+T
Sbjct: 46 FIAVEQEFFRLWWDGVATDKQKQQVRQLLSEGRLEFVIGGQVMHDEAVTELDDQILQLTE 105
Query: 60 GLKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKT 119
G +L +TFG +PR +W +DPFG SA FA GF+ RID++ A +K K
Sbjct: 106 GHGFLYETFGV--RPRFSWHVDPFGASATTPTLFALAGFNAHLISRIDYDLKAAMQKAKG 163
Query: 120 MEMVWRPDDTLGPEGDFFTGVMYNI-YDPPPGFCFDT----YCEDEPIMDNPKLHGV--- 171
++ VWR +L + FT VM Y P F Y + +P G+
Sbjct: 164 LQFVWRGSPSLSESQEIFTHVMDQYSYCTPSYIPFSNRSGFYWNGVAVFPDPPKDGIYPN 223
Query: 172 --------NVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAWFKNIDKLIKYV 223
N++ + + +K+ A +RT +V+ G D + AS F N+D L+ Y+
Sbjct: 224 MSLPVTTQNIHQYAETMVANIKQRAAWFRTPHVLWPWGCDKQFFNASVQFSNMDPLLDYI 283
Query: 224 NAKLNS-DVHVLYSTPACYLQALNKENITWPSKMDDDFFPFGS 265
N + V V Y+T Y QAL+ N+TW + DF P+ +
Sbjct: 284 NQHSSEFGVTVQYATLGDYFQALHNSNLTWEVRGSQDFLPYST 326
>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 = 136 bits (343), Expect = 1e-36
Identities = 91/305 (29%), Positives = 137/305 (44%), Gaps = 37/305 (12%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E SFF +WW+ N Q RA+V+ LV G+LE GGW M DEA HY ++IDQ+ G
Sbjct: 47 FIWSEISFFSKWWDNINAQKRAAVRRLVGNGQLEMATGGWVMPDEANSHYFAMIDQLIEG 106
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
++L G PR W +DPFGHS+ + + R+ + +++
Sbjct: 107 HQWLEKNIG--VTPRSGWAVDPFGHSSTMPYILRRSNLTSMLIQRVHYAIKKHFAATQSL 164
Query: 121 EMVWRPDDTLGPEG--DFFTGVM-YNIYD------PPPGFC--FD--------TYCEDEP 161
E +WR T P+ D F +M + YD P P C FD C P
Sbjct: 165 EFMWR--QTWDPDSSTDIFCHMMPFYSYDVPHTCGPDPKICCQFDFKRLPGGRINC---P 219
Query: 162 IMDNPK-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNID 217
P+ + NV R ++ +K ++ YR+ +++ +G DF Y W F N
Sbjct: 220 WKVPPRAITEANVAERAQLLLDQYRKKSKLYRSKVLLVPLGDDFRYDKPQEWDAQFLNYQ 279
Query: 218 KLIKYVNAKLNSDVHVLYSTPACYLQALNKENITWPSK-------MDDDFFPFGSDEHSY 270
+L ++N+ V + T + Y AL K P + DFF + E Y
Sbjct: 280 RLFDFLNSHPELHVQAQFGTLSDYFDALYKRTGVVPGMRPPGFPVVSGDFFSYADREDHY 339
Query: 271 WTGYF 275
WTGY+
Sbjct: 340 WTGYY 344
>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 = 77.2 bits (191), Expect = 7e-18
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 7/77 (9%)
Query: 270 YWTGYFTSRPSFKYFVYQTNVALQMTKQL-------KTSLPNDTLAEEQFLIQRAMGIAQ 322
Y G +TSRP K + L+ + L D EE + +A+ + Q
Sbjct: 2 YHRGTYTSRPDIKRLNRKLESLLRAAELLASLASLLGNKGELDDYYEELDKLWKALLLNQ 61
Query: 323 HHDAVSGTERQHVTNDY 339
HDA+ GT Q V +DY
Sbjct: 62 FHDALPGTSIQEVYDDY 78
>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 = 66.0 bits (162), Expect = 8e-14
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 270 YWTGYFTSRPSFKYFVYQTNVALQMTKQLKTSLPNDTLAEEQFLIQ-----RAMGIAQHH 324
Y G +TSRP K + L+ ++L +L + Q +A+ + QHH
Sbjct: 1 YHRGTYTSRPYLKRLNRRAESLLRAAEELAALAALLSLGYKYPSEQLEELWKALLLNQHH 60
Query: 325 DAVSGTERQHVTNDY 339
DA++GT V +DY
Sbjct: 61 DAITGTSIDEVYDDY 75
>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 = 48.2 bits (115), Expect = 2e-06
Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 10 WRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLGLKYLNDTFG 69
++W E + VKE V QGR + G W +D P SL Q G +Y FG
Sbjct: 52 FKWLETLYPDLFEKVKEYVKQGRFHPIGGSWVENDTNMPSGESLARQFLYGQRYFESRFG 111
Query: 70 ECGQPRVAWQIDPFGHSAEV 89
+ + W D FG+S+++
Sbjct: 112 K--RCDTFWLPDTFGYSSQI 129
>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 = 47.9 bits (115), Expect = 2e-06
Identities = 30/89 (33%), Positives = 43/89 (48%), Gaps = 5/89 (5%)
Query: 1 FVYV-ETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGG-WCMSDEATPHYSSLIDQMT 58
FV+ + + W EE ++ +KE V +GR E +GG W D P SL+ Q
Sbjct: 42 FVFTQSQAQLYEWLEEDYPELFERIKERVKEGRWE-PVGGMWVEPDCNLPSGESLVRQFL 100
Query: 59 LGLKYLNDTFGECGQPRVAWQIDPFGHSA 87
G +Y + FG + R+ W D FG SA
Sbjct: 101 YGQRYFREEFGV--ESRILWLPDSFGFSA 127
>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 = 44.9 bits (107), Expect = 3e-05
Identities = 49/231 (21%), Positives = 92/231 (39%), Gaps = 43/231 (18%)
Query: 21 RASVKELVDQGRLEFLLGGW-CMSDEATPHYSSLIDQMTLGLKYLNDTFGECGQPRVAWQ 79
R +K+L+ +G+L G W + DE + I + +G K + + FG+ ++ +
Sbjct: 65 RERLKKLIREGKLVI--GPWYVLQDEFLTSGEANIRNLLIGKK-VAEEFGKS--MKIGYF 119
Query: 80 IDPFGHSAEVALEFADMGFDGVFFGR-IDHEDIALRKKNKTMEMVWRPDDTLGPEGD-FF 137
D FGH ++ G D FGR + +++ E W P+G
Sbjct: 120 PDTFGHIGQMPQILKGFGIDNAVFGRGVK------PTESQYSEFWWE-----SPDGSRVL 168
Query: 138 TGVMYNIYDPPPGFCFDTYCEDEPIMDNPKLHGVNVNARVDEFIEVVKKYAQAYRTNNVI 197
++ N Y +E +D + D+ + ++YA T++++
Sbjct: 169 GILLANWY----------SNGNEIPVDEEEAK-----EFWDKKLADAERYAS---TDHLL 210
Query: 198 ITMGGDFHYVVASAWFKNIDKLIKYVNAKLNSDVHVLYSTPACYLQALNKE 248
+ G D V ++ K I+ N +L D ++S YL+AL E
Sbjct: 211 LMNGCDHQPV-----QPDLTKAIREAN-ELYPDYEFIHSNFDEYLEALKSE 255
>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 = 40.2 bits (95), Expect = 0.001
Identities = 50/244 (20%), Positives = 93/244 (38%), Gaps = 67/244 (27%)
Query: 21 RASVKELVDQGRLEFLLGGW-CMSDEATPHYSSLIDQMTLGLK------------YLNDT 67
+ +K+LV +GRL +G W +DE S++ + G+K YL D+
Sbjct: 65 KERIKKLVKEGRL--FIGPWYTQTDELVVSGESIVRNLLYGIKDARKLGGYMKIGYLPDS 122
Query: 68 FGECGQ-PRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTMEMVWRP 126
FG+ Q P QI + G D F R ++ T E +W+
Sbjct: 123 FGQSAQMP----QI------------YNGFGIDNAVFWR----GVSEDLVKST-EFIWK- 160
Query: 127 DDTLGPEGD-FFTGVMYNIYDPPPGFCFDTYCEDEPIMDNPKLHGVNVNARVDEFIEVVK 185
+G + Y G + + R+D +E ++
Sbjct: 161 ----SLDGSKVLAANIPFGYG--IGKYLPEDPDY-------------LKKRLDPILEKLE 201
Query: 186 KYAQAYRTNNVIITMGGDFHYVVASAWFKNIDKLIKYVNAKLNSDVHVLYSTPACYLQAL 245
+ A T+N+++ GGD + KN+ ++I+ +N +++ D + S+ + +AL
Sbjct: 202 RRAT---TDNILLPNGGDQMPIR-----KNLPEVIEELN-EISPDYEYVISSYEEFFKAL 252
Query: 246 NKEN 249
K
Sbjct: 253 EKNK 256
>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 = 39.8 bits (93), Expect = 0.001
Identities = 37/181 (20%), Positives = 67/181 (37%), Gaps = 32/181 (17%)
Query: 24 VKELVDQGRLEFLLGGW-CMSDEATPHYSSLIDQMTLGLKYLNDTFGECGQPRVAWQIDP 82
+++ + G+L ++G + D S++ +G K D FG ++ W D
Sbjct: 67 LRQAIKSGKL--IIGPYYIQIDWRITSEESIVRNFEIGKKDC-DRFGA--SMKIGWLPDS 121
Query: 83 FGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTMEMVWRPDDTLGPEGDFFTGVMY 142
FG +++ G + VF R I+ + +E W+ D G F G
Sbjct: 122 FGFISQLPQLMRKFGIEAVFLWR----GISPEGSSPKIEFSWQSPDGSRVLGVFLAGGYR 177
Query: 143 NIYDPPPGFCFDTYCEDEPIMDNPKLHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGG 202
N Y+ P E I R+D I ++K++ T +++ G
Sbjct: 178 NGYELP---------TTEDIARK----------RLDHEIAKLEKFS---STKEILLLNGY 215
Query: 203 D 203
D
Sbjct: 216 D 216
>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 = 35.3 bits (81), Expect = 0.031
Identities = 22/97 (22%), Positives = 40/97 (41%), Gaps = 4/97 (4%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSD--EATPHYSSLIDQMT 58
F S+ ++ + E ++ +K + G+LE G D EA H ++ Q+T
Sbjct: 43 FNIAPISYEALFYHDLGENIKLQMKSIQKNGQLEIGTHGATHPDESEAQSHPENVYAQIT 102
Query: 59 LGLKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFAD 95
G+ +L G PR W + F + A+ +
Sbjct: 103 EGITWLEKHMG--VTPRHIWLHECFYNQAKQLSQGIP 137
>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 = 34.3 bits (79), Expect = 0.090
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 11 RWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLGLKYLNDTFGE 70
W + + ++E V GR + G W D P S++ Q G ++ + FG
Sbjct: 53 EWVKSWYPGLYEEIQERVKNGRFIPVGGTWVEMDGNLPSGESMVRQFLYGQRFFKEEFGI 112
Query: 71 -CGQPRVAWQIDPFGHSAE 88
C + W D FG+SA+
Sbjct: 113 TC---KEFWLPDTFGYSAQ 128
>gnl|CDD|212042 cd10334, SLC6sbd_u1, uncharacterized bacterial and archaeal solute
carrier 6 subfamily; solute-binding domain. SLC6
proteins (also called the sodium- and chloride-dependent
neurotransmitter transporter family or Na+/Cl--dependent
transporter family) include neurotransmitter
transporters (NTTs): these are sodium- and
chloride-dependent plasma membrane transporters for the
monoamine neurotransmitters serotonin
(5-hydroxytryptamine), dopamine, and norepinephrine, and
the amino acid neurotransmitters GABA and glycine. These
NTTs are widely expressed in the mammalian brain,
involved in regulating neurotransmitter signaling and
homeostasis, and the target of a range of therapeutic
drugs for the treatment of psychiatric diseases.
Bacterial members of the SLC6 family include the LeuT
amino acid transporter.
Length = 480
Score = 34.0 bits (79), Expect = 0.13
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 15/57 (26%)
Query: 177 VDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAWFKNIDKLIKYVNAKLNSDVHV 233
VD FI NN I + G V+ W +KL +++NA SD V
Sbjct: 380 VDHFI------------NNYGIVLVG-LVEVIVVGWVFGAEKLREHLNA--VSDFKV 421
>gnl|CDD|212107 cd10795, GH57N_MJA1_like, N-terminal catalytic domain of a
thermoactive alpha-amylase from Methanococcus jannaschii
and similar proteins; glycoside hydrolase family 57
(GH57). The subfamily is represented by a thermostable
alpha-amylase (MJA1, EC 3.2.1.1) encoded from the
hyperthermophilic archaeon Methanococcus jannaschii
locus, M J1611. MJA1 has a broad pH optimum 5.0-8.0. It
exhibits extremely thermophilic alpha-amylase activity
that catalyzes the hydrolysis of large sugar polymers
with alpha-l,6 and alpha-l,4 linkages, and yields
products including glucose polymers of 1-7 units. MJ1611
also encodes another alpha-amylase with catalytic
features distinct from MJA1, which belongs to glycoside
hydrolase family 13 (GH-13), and is not included here.
This subfamily also includes many uncharacterized
proteins found in bacteria and archaea.
Length = 306
Score = 33.3 bits (77), Expect = 0.19
Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 24/101 (23%)
Query: 11 RWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSL---------IDQMTLGL 61
+ +V S +EL D G +EFL A +Y SL +Q+ +
Sbjct: 79 EKY---APEVIDSFRELADTGNVEFL---------AETYYHSLASLFDKDEFREQVKMHR 126
Query: 62 KYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVF 102
+ + + FG +P V + +S ++A DMGF +
Sbjct: 127 ELIKELFGV--KPTVFRNTE-LIYSDDIAEIAEDMGFKAIL 164
>gnl|CDD|217589 pfam03485, Arg_tRNA_synt_N, Arginyl tRNA synthetase N terminal
domain. This domain is found at the amino terminus of
Arginyl tRNA synthetase, also called additional domain 1
(Add-1). It is about 140 residues long and it has been
suggested that this domain will be involved in tRNA
recognition.
Length = 84
Score = 30.7 bits (70), Expect = 0.26
Identities = 12/25 (48%), Positives = 19/25 (76%), Gaps = 2/25 (8%)
Query: 286 YQTNVALQMTKQLKTSLPNDTLAEE 310
Y TNVA+++ K+LK + P + +AEE
Sbjct: 36 YATNVAMKLAKKLKKN-PRE-IAEE 58
>gnl|CDD|214975 smart01016, Arg_tRNA_synt_N, Arginyl tRNA synthetase N terminal
dom. This domain is found at the amino terminus of
Arginyl tRNA synthetase, also called additional domain 1
(Add-1). It is about 140 residues long and it has been
suggested that this domain will be involved in tRNA
recognition.
Length = 85
Score = 29.9 bits (68), Expect = 0.51
Identities = 13/25 (52%), Positives = 18/25 (72%), Gaps = 2/25 (8%)
Query: 286 YQTNVALQMTKQLKTSLPNDTLAEE 310
Y TNVA ++ K+LK + P + LAEE
Sbjct: 37 YATNVAFRLAKKLKKN-PRE-LAEE 59
>gnl|CDD|223460 COG0383, AMS1, Alpha-mannosidase [Carbohydrate transport and
metabolism].
Length = 943
Score = 32.0 bits (73), Expect = 0.69
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 4/78 (5%)
Query: 11 RWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLGLKYLNDTFGE 70
W + + + V+ + E + G W D TP SL Q G ++ + FG
Sbjct: 251 NWLKPDVPFL--FSRPAVEFEQWEIVGGMWVEEDLNTPSGESLSRQFLYGQRFFTEKFG- 307
Query: 71 CGQPRVAWQIDPFGHSAE 88
R+ W+ D FG S +
Sbjct: 308 -ASSRIYWKPDSFGFSGQ 324
>gnl|CDD|185019 PRK15059, PRK15059, tartronate semialdehyde reductase; Provisional.
Length = 292
Score = 31.5 bits (71), Expect = 0.73
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 276 TSRPSFKYFVYQT--NVALQMTKQLKTSLPNDTLAEEQFLIQRAMGIAQ 322
T P FK ++Q N+ALQ K L +LPN +E F A G +Q
Sbjct: 225 TFNPGFKIALHQKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQ 273
>gnl|CDD|217866 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyze diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 30.2 bits (68), Expect = 1.1
Identities = 20/114 (17%), Positives = 35/114 (30%), Gaps = 11/114 (9%)
Query: 5 ETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLGLKYL 64
+ E E++ KEL G +L G P + ++ L L
Sbjct: 18 SIRARGKGRELSPEEILEEAKELARLGVEVVILTGG------EPLLLPDLVELLERLLKL 71
Query: 65 NDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNK 118
+ G R+ + + E+ E + G D V + D + K
Sbjct: 72 REGEGI----RITLETNGTLLDEELLEELKEAGLDRVSIS-LQSGDDEVLKIIN 120
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 30.7 bits (70), Expect = 1.6
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 6/41 (14%)
Query: 216 IDKLIKYVNAKLNSDVHVLYSTPACYLQALNK---ENITWP 253
I++L+ KL ++ LY +P L+ALN + P
Sbjct: 59 INELLSLGKGKLEDGIYALYISP---LKALNNDIRRRLEEP 96
>gnl|CDD|234964 PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
Length = 507
Score = 30.1 bits (69), Expect = 2.4
Identities = 13/25 (52%), Positives = 19/25 (76%), Gaps = 2/25 (8%)
Query: 286 YQTNVALQMTKQLKTSLPNDTLAEE 310
Y TNVA+Q+ K+LK + P + +AEE
Sbjct: 41 YATNVAMQLAKKLKKN-PRE-IAEE 63
>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 = 29.7 bits (67), Expect = 2.7
Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 22/101 (21%)
Query: 12 WWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSL----------IDQMTLGL 61
E+ +V +EL + G++E L +P+Y L I Q+ +G
Sbjct: 58 QLEDYLPEVLELFRELAESGQVELL---------TSPYYHPLLPLLPDKEDFIAQVEMGR 108
Query: 62 KYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVF 102
+ + FG +PR W + +S E+ A+ G + V
Sbjct: 109 ELYREYFGV--EPRGFWLPE-LAYSPEIVKILAEAGIEYVI 146
>gnl|CDD|233893 TIGR02491, NrdG, anaerobic ribonucleoside-triphosphate reductase
activating protein. This enzyme is a member of the
radical-SAM family (pfam04055) and utilizes S-adenosyl
methionine, an iron-sulfur cluster and a reductant
(dihydroflavodoxin ) to produce a glycine-centered
radical in the class III (anaerobic) ribonucleotide
triphosphate reductase (NrdD, TIGR02487). The two
components form an alpha-2/beta-2 heterodimer [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism, Protein fate, Protein
modification and repair].
Length = 154
Score = 28.5 bits (64), Expect = 3.5
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 16/95 (16%)
Query: 150 GFCFDTYCEDEPI---MDNPKLHGVNV-------NARVDEFIEVVKKYAQAYRTNNVIIT 199
G F E E I DNP + G+ + V+E IE+VKK + ++ +
Sbjct: 43 GKEFTEALEKEIIRDLNDNPLIDGLTLSGGDPLYPRNVEELIELVKKIKAEFPEKDIWLW 102
Query: 200 MGGDFHYVVA----SAWFKNIDKLI--KYVNAKLN 228
G + ++ K ID L+ K+ +K +
Sbjct: 103 TGYTWEEILEDEKHLEVLKYIDVLVDGKFELSKKD 137
>gnl|CDD|212105 cd10793, GH57N_TLGT_like, N-terminal catalytic domain of
4-alpha-glucanotransferase; glycoside hydrolase family
57 (GH57). 4-alpha-glucanotransferase (TLGT, EC
2.4.1.25) plays a key role in the maltose metabolism.
It catalyzes the disproportionation of amylose and the
formation of large cyclic alpha-1,4-glucan
(cycloamylose) from linear amylose. TLGT functions as a
homodimer. Each monomer is composed of two domains, an
N-terminal catalytic domain with a (beta/alpha)7 barrel
fold and a C-terminal domain with a twisted
beta-sandwich fold. Some family members have been
designated as alpha-amylases, such as the heat-stable
eubacterial amylase from Dictyoglomus thermophilum
(DtAmyA) and the extremely thermostable archaeal
amylase from Pyrococcus furiosus(PfAmyA). However, both
of these proteins are 4-alpha-glucanotransferases.
DtAmyA was shown to have transglycosylating activity
and PfAmyA exhibits 4-alpha-glucanotransferase
activity.
Length = 279
Score = 29.1 bits (66), Expect = 4.1
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 10 WRWWEEQNEQVRASVKELVDQGRLEFLLGG 39
W EE + + +++LVD+G++E L GG
Sbjct: 51 LEWLEENHPEYLDLLRKLVDRGQIEILGGG 80
>gnl|CDD|197337 cd10282, DNase1, Deoxyribonuclease 1. Deoxyribonuclease 1 (DNase1,
EC 3.1.21.1), also known as DNase I, is a Ca2+,
Mg2+/Mn2+-dependent secretory endonuclease, first
isolated from bovine pancreas extracts. It cleaves DNA
preferentially at phosphodiester linkages next to a
pyrimidine nucleotide, producing 5'-phosphate terminated
polynucleotides with a free hydroxyl group on position
3'. It generally produces tetranucleotides. DNase1
substrates include single-stranded DNA, double-stranded
DNA, and chromatin. This enzyme may be responsible for
apoptotic DNA fragmentation. Other deoxyribonucleases in
this subfamily include human DNL1L (human DNase I
lysosomal-like, also known as DNASE1L1, Xib, and DNase X
), human DNASE1L2 (also known as DNAS1L2), and DNASE1L3
(also known as DNAS1L3, nhDNase, LS-DNase, DNase Y, and
DNase gamma) . DNASE1L3 is implicated in apoptotic DNA
fragmentation. DNase I is also a cytoskeletal protein
which binds actin. A recombinant form of human DNase1 is
used as a mucoactive therapy in patients with cystic
fibrosis; it hydrolyzes the extracellular DNA in sputum
and reduces its viscosity. Mutations in the gene
encoding DNase1 have been associated with Systemic Lupus
Erythematosus, a multifactorial autoimmune disease. This
subfamily belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 256
Score = 28.7 bits (65), Expect = 4.5
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 177 VDEFIEVVKKYAQAYRTNNVIITMGGDFH----YVVASAWFKNI 216
+D +V Q +R ++VI+ GDF+ YV + W K+I
Sbjct: 141 IDALYDVYDDVKQRWREDDVILL--GDFNADCSYVTSKGW-KSI 181
>gnl|CDD|200603 cd11374, CE4_u10, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. The family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups of cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 226
Score = 28.5 bits (64), Expect = 5.5
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 8 FFWRWWEEQNEQVRASVKELVDQGRLEFLLGGW 40
+ W E + + A +++ V G E +L G+
Sbjct: 41 NYHGKWLEADPEFVAWLRDRVAAGD-ELVLHGF 72
>gnl|CDD|197543 smart00148, PLCXc, Phospholipase C, catalytic domain (part); domain
X. Phosphoinositide-specific phospholipases C. These
enzymes contain 2 regions (X and Y) which together form
a TIM barrel-like structure containing the active site
residues. Phospholipase C enzymes (PI-PLC) act as signal
transducers that generate two second messengers,
inositol-1,4,5-trisphosphate and diacylglycerol. The
bacterial enzyme appears to be a homologue of the
mammalian PLCs.
Length = 143
Score = 27.6 bits (62), Expect = 5.9
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 152 CFDTYCEDEPIMDNPKLHGVNV--NARVDEFIEVVKKYAQAYRTNNVIITM 200
C + C D P + HG ++ E +E +K +A VI+++
Sbjct: 42 CVELDCWDGPDGEPVIYHGHTFTLPIKLSEVLEAIKDFAFVTSPYPVILSL 92
>gnl|CDD|225843 COG3306, COG3306, Glycosyltransferase involved in LPS biosynthesis
[Cell envelope biogenesis, outer membrane].
Length = 255
Score = 28.1 bits (63), Expect = 8.1
Identities = 19/78 (24%), Positives = 27/78 (34%), Gaps = 8/78 (10%)
Query: 247 KENITWPSK-MDDDFFPFGSDEHSYWTGYFTSRPSFKYFVYQTNVALQMTKQLKTSLPND 305
N + FP + H GY SR + K F L++T+ K LP D
Sbjct: 132 SPNPLAFNAVFIGRNFPLLNSYHLGTAGYIISRKAAKKF-------LELTESFKVVLPVD 184
Query: 306 TLAEEQFLIQRAMGIAQH 323
+FL + Q
Sbjct: 185 WFMFLEFLHGVGNKVYQP 202
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.138 0.436
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,944,441
Number of extensions: 2039605
Number of successful extensions: 2001
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1961
Number of HSP's successfully gapped: 48
Length of query: 400
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 301
Effective length of database: 6,546,556
Effective search space: 1970513356
Effective search space used: 1970513356
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (26.8 bits)