RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12962
(75 letters)
>gnl|CDD|119332 cd06562, GH20_HexA_HexB-like, Beta-N-acetylhexosaminidases catalyze
the removal of beta-1,4-linked N-acetyl-D-hexosamine
residues from the non-reducing ends of
N-acetyl-beta-D-hexosaminides including
N-acetylglucosides and N-acetylgalactosides. The hexA
and hexB genes encode the alpha- and beta-subunits of
the two major beta-N-acetylhexosaminidase isoenzymes,
N-acetyl-beta-D-hexosaminidase A (HexA) and
beta-N-acetylhexosaminidase B (HexB). Both the alpha
and the beta catalytic subunits have a TIM-barrel fold
and belong to the glycosyl hydrolase family 20 (GH20).
The HexA enzyme is a heterodimer containing one alpha
and one beta subunit while the HexB enzyme is a
homodimer containing two beta-subunits. Hexosaminidase
mutations cause an inability to properly hydrolyze
certain sphingolipids which accumulate in lysosomes
within the brain, resulting in the lipid storage
disorders Tay-Sachs and Sandhoff. Mutations in the
alpha subunit cause in a deficiency in the HexA enzyme
and result in Tay-Sachs, mutations in the beta-subunit
cause in a deficiency in both HexA and HexB enzymes and
result in Sandhoff disease. In both disorders GM(2)
gangliosides accumulate in lysosomes. The GH20
hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by solvent or the enzyme, but by the substrate
itself.
Length = 348
Score = 77.6 bits (192), Expect = 7e-19
Identities = 29/72 (40%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 4 HVWSWGYGNPNLLCKINITIPDLNTTQEYWGPIDPTKSSSYDFVRDLFTEVRSVFHDEFL 63
H SWG G P LL + G ++PT +YDF++ LF EV +F D++
Sbjct: 95 HTGSWGQGYPELLTGCYAVWRKY-CPEPPCGQLNPTNPKTYDFLKTLFKEVSELFPDKYF 153
Query: 64 HTGGDEVDFYCW 75
H GGDEV+F CW
Sbjct: 154 HLGGDEVNFNCW 165
>gnl|CDD|216086 pfam00728, Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic
domain. This domain has a TIM barrel fold.
Length = 335
Score = 52.3 bits (126), Expect = 9e-10
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 34 GPIDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEVDFYCW 75
G ++P +YDF+ + EV +F E++H GGDEV+ CW
Sbjct: 126 GTLNPGNPKTYDFLDKVLDEVAELFPSEYIHIGGDEVNKGCW 167
>gnl|CDD|119338 cd06570, GH20_chitobiase-like_1, A functionally uncharacterized
subgroup of the Glycosyl hydrolase family 20 (GH20)
catalytic domain found in proteins similar to the
chitobiase of Serratia marcescens, a
beta-N-1,4-acetylhexosaminidase that hydrolyzes the
beta-1,4-glycosidic linkages in oligomers derived from
chitin. Chitin is degraded by a two step process: i) a
chitinase hydrolyzes the chitin to oligosaccharides and
disaccharides such as di-N-acetyl-D-glucosamine and
chitobiose, ii) chitobiase then further degrades these
oligomers into monomers. This subgroup lacks the
C-terminal PKD (polycystic kidney disease I)-like domain
found in the chitobiases. The GH20 hexosaminidases are
thought to act via a catalytic mechanism in which the
catalytic nucleophile is not provided by solvent or the
enzyme, but by the substrate itself.
Length = 311
Score = 51.6 bits (124), Expect = 1e-09
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 4 HVWSWGYGNPNLLCKINITIPDLNTTQEYWG----PIDPTKSSSYDFVRDLFTEVRSVFH 59
H + P L + P + WG +DPT +Y F+ +LF E+ +F
Sbjct: 93 HASAIAVAYPELA-----SGPGPYVIERGWGVFEPLLDPTNEETYTFLDNLFGEMAELFP 147
Query: 60 DEFLHTGGDEVDFYCW 75
DE+ H GGDEVD W
Sbjct: 148 DEYFHIGGDEVDPKQW 163
>gnl|CDD|119331 cd02742, GH20_hexosaminidase, Beta-N-acetylhexosaminidases of
glycosyl hydrolase family 20 (GH20) catalyze the removal
of beta-1,4-linked N-acetyl-D-hexosamine residues from
the non-reducing ends of N-acetyl-beta-D-hexosaminides
including N-acetylglucosides and N-acetylgalactosides.
These enzymes are broadly distributed in microorganisms,
plants and animals, and play roles in various key
physiological and pathological processes. These
processes include cell structural integrity, energy
storage, cellular signaling, fertilization, pathogen
defense, viral penetration, the development of
carcinomas, inflammatory events and lysosomal storage
disorders. The GH20 enzymes include the eukaryotic
beta-N-acetylhexosaminidases A and B, the bacterial
chitobiases, dispersin B, and lacto-N-biosidase. The
GH20 hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by the solvent or the enzyme, but by the
substrate itself.
Length = 303
Score = 48.2 bits (115), Expect = 2e-08
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 1 MSWHVWSWGYGNPNLLCKINITIPDLNTTQEYWGPIDPTKSSSYDFVRDLFTEVRSVFHD 60
M H ++ P LL + + + + P+DPT YDF+ DLF E+ +F D
Sbjct: 94 MPGHSTAFVKSFPKLLTECYAGLKLRDV----FDPLDPTLPKGYDFLDDLFGEIAELFPD 149
Query: 61 EFLHTGGDEVDF 72
+LH GGDE F
Sbjct: 150 RYLHIGGDEAHF 161
>gnl|CDD|119333 cd06563, GH20_chitobiase-like, The chitobiase of Serratia
marcescens is a beta-N-1,4-acetylhexosaminidase with a
glycosyl hydrolase family 20 (GH20) domain that
hydrolyzes the beta-1,4-glycosidic linkages in oligomers
derived from chitin. Chitin is degraded by a two step
process: i) a chitinase hydrolyzes the chitin to
oligosaccharides and disaccharides such as
di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase
then further degrades these oligomers into monomers.
This GH20 domain family includes an
N-acetylglucosamidase (GlcNAcase A) from
Pseudoalteromonas piscicida and an
N-acetylhexosaminidase (SpHex) from Streptomyces
plicatus. SpHex lacks the C-terminal PKD (polycystic
kidney disease I)-like domain found in the chitobiases.
The GH20 hexosaminidases are thought to act via a
catalytic mechanism in which the catalytic nucleophile
is not provided by solvent or the enzyme, but by the
substrate itself.
Length = 357
Score = 44.1 bits (105), Expect = 6e-07
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 13 PNLLCKINITIPDLNTTQEYWG-PIDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEVD 71
P L C + + Q + P K +Y F+ D+ EV +F ++H GGDEV
Sbjct: 120 PELGC--TGGPGSVVSVQGVVSNVLCPGKPETYTFLEDVLDEVAELFPSPYIHIGGDEVP 177
Query: 72 FYCW 75
W
Sbjct: 178 KGQW 181
>gnl|CDD|119335 cd06565, GH20_GcnA-like, Glycosyl hydrolase family 20 (GH20)
catalytic domain of N-acetyl-beta-D-glucosaminidase
(GcnA, also known as BhsA) and related proteins. GcnA
is an exoglucosidase which cleaves
N-acetyl-beta-D-galactosamine (NAG) and
N-acetyl-beta-D-galactosamine residues from
4-methylumbelliferylated (4MU) substrates, as well as
cleaving NAG from chito-oligosaccharides (i.e. NAG
polymers). In contrast, sulfated forms of the substrate
are unable to be cleaved and act instead as mild
competitive inhibitors. Additionally, the enzyme is
known to be poisoned by several first-row transition
metals as well as by mercury. GcnA forms a homodimer
with subunits comprised of three domains, an N-terminal
zincin-like domain, this central catalytic GH20 domain,
and a C-terminal alpha helical domain. The GH20
hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by solvent or the enzyme, but by the substrate
itself.
Length = 301
Score = 37.6 bits (88), Expect = 1e-04
Identities = 10/46 (21%), Positives = 22/46 (47%)
Query: 25 DLNTTQEYWGPIDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEV 70
L + + P + +YDF+ ++ +V + +++H G DE
Sbjct: 97 HLREVDDPPQTLCPGEPKTYDFIEEMIRQVLELHPSKYIHIGMDEA 142
>gnl|CDD|119336 cd06568, GH20_SpHex_like, A subgroup of the Glycosyl hydrolase
family 20 (GH20) catalytic domain found in proteins
similar to the N-acetylhexosaminidase from Streptomyces
plicatus (SpHex). SpHex catalyzes the hydrolysis of
N-acetyl-beta-hexosaminides. An Asp residue within the
active site plays a critical role in substrate-assisted
catalysis by orienting the 2-acetamido group and
stabilizing the transition state. The GH20
hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by solvent or the enzyme, but by the substrate
itself. Proteins belonging to this subgroup lack the
C-terminal PKD (polycystic kidney disease I)-like domain
found in the chitobiases.
Length = 329
Score = 37.3 bits (87), Expect = 2e-04
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 10/59 (16%)
Query: 23 IPDLN----------TTQEYWGPIDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEVD 71
P+LN + + +D K ++Y+FV D+F E+ ++ ++H GGDE
Sbjct: 108 YPELNCDGKAKPLYTGIEVGFSSLDVDKPTTYEFVDDVFRELAALTPGPYIHIGGDEAH 166
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 31.4 bits (71), Expect = 0.024
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 36 IDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEV 70
++PT +Y F+ + EV +F +H GGDE
Sbjct: 403 LNPTLDPTYQFLDKVLDEVADLFPSTTIHIGGDEF 437
>gnl|CDD|119337 cd06569, GH20_Sm-chitobiase-like, The chitobiase of Serratia
marcescens is a beta-N-1,4-acetylhexosaminidase with a
glycosyl hydrolase family 20 (GH20) domain that
hydrolyzes the beta-1,4-glycosidic linkages in oligomers
derived from chitin. Chitin is degraded by a two step
process: i) a chitinase hydrolyzes the chitin to
oligosaccharides and disaccharides such as
di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase
then further degrades these oligomers into monomers. The
GH20 hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by solvent or the enzyme, but by the substrate
itself.
Length = 445
Score = 29.2 bits (66), Expect = 0.15
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 36 IDPTKSSSYDFVRDLFTEVRSVFHDEF------LHTGGDEV 70
I+P S+Y FV + E+ H E +H GGDEV
Sbjct: 171 INPCMPSTYRFVDKVIDEIA-RMHQEAGQPLTTIHFGGDEV 210
>gnl|CDD|237846 PRK14876, PRK14876, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 928
Score = 27.5 bits (61), Expect = 0.59
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 10/42 (23%)
Query: 17 CKINITIPDLNTTQEYW--GPI--------DPTKSSSYDFVR 48
C ++++P L EY GPI D TK+ S DF R
Sbjct: 519 CGTDVSVPTLEKETEYQCGGPIRCMGDDCLDLTKTQSTDFAR 560
>gnl|CDD|119334 cd06564, GH20_DspB_LnbB-like, Glycosyl hydrolase family 20 (GH20)
catalytic domain of dispersin B (DspB),
lacto-N-biosidase (LnbB) and related proteins. Dispersin
B is a soluble beta-N-acetylglucosamidase found in
bacteria that hydrolyzes the beta-1,6-linkages of PGA
(poly-beta-(1,6)-N-acetylglucosamine), a major component
of the extracellular polysaccharide matrix.
Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I
oligosaccharides at the nonreducing terminus to produce
lacto-N-biose as part of the GNB/LNB
(galacto-N-biose/lacto-N-biose I) degradation pathway.
The lacto-N-biosidase from Bifidobacterium bifidum has
this GH20 domain, a carbohydrate binding module 32, and
a bacterial immunoglobulin-like domain 2, as well as a
YSIRK signal peptide and a G5 membrane anchor at the N
and C termini, respectively. The GH20 hexosaminidases
are thought to act via a catalytic mechanism in which
the catalytic nucleophile is not provided by solvent or
the enzyme, but by the substrate itself.
Length = 326
Score = 26.5 bits (59), Expect = 1.3
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 36 IDPTKSSSYDFVRDLFTEVRSVFHD--EFLHTGGDEVD 71
+D + + FV+ LF E F+ + +H G DE
Sbjct: 132 LDISNPEAVKFVKALFDEYLDGFNPKSDTVHIGADEYA 169
>gnl|CDD|220930 pfam10994, DUF2817, Protein of unknown function (DUF2817). This
family of proteins has no known function.
Length = 341
Score = 26.1 bits (58), Expect = 1.9
Identities = 14/53 (26%), Positives = 19/53 (35%), Gaps = 4/53 (7%)
Query: 3 WHVWSWGYGNPNLLCKINITIPDLNTTQEYWGP----IDPTKSSSYDFVRDLF 51
H YG ++C P L + +WGP I S SYD +
Sbjct: 215 LHTGLGPYGYGEIICMGPDDGPALERARRWWGPDVTSIQAGSSVSYDLTGLII 267
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 25.7 bits (57), Expect = 2.3
Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 2/54 (3%)
Query: 9 GYGNPNLLCKINITIP-DLNTTQ-EYWGPIDPTKSSSYDFVRDLFTEVRSVFHD 60
G +L ++ + P +L+ Q E + + F ++++ F
Sbjct: 318 SGGRGDLYVRVKVETPKNLSDEQKELLEEFAKSLGEGPEQSPGFFDKLKNFFKG 371
>gnl|CDD|226630 COG4150, CysP, ABC-type sulfate transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 341
Score = 25.6 bits (56), Expect = 2.5
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 42 SSYDFVRDLFTEVRSVF--HDEFLHTG 66
SSYD R+LF + F + G
Sbjct: 36 SSYDVSRELFAALNPAFEAQWAKDNPG 62
>gnl|CDD|182616 PRK10647, PRK10647, ferric iron reductase involved in ferric
hydroximate transport; Provisional.
Length = 262
Score = 24.3 bits (53), Expect = 7.4
Identities = 6/26 (23%), Positives = 12/26 (46%)
Query: 35 PIDPTKSSSYDFVRDLFTEVRSVFHD 60
+ P+ + D +R+L + R D
Sbjct: 17 HLQPSDAGLADAIRELIAKTREHLLD 42
>gnl|CDD|215355 PLN02658, PLN02658, homogentisate 1,2-dioxygenase.
Length = 435
Score = 24.3 bits (53), Expect = 7.4
Identities = 12/27 (44%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 26 LNTTQEYWGPIDPTKSSSYDFVRDLFT 52
TQ W P P S DFV LFT
Sbjct: 88 TTPTQLRWRPF-PVPDSPVDFVDGLFT 113
>gnl|CDD|236831 PRK11052, malQ, 4-alpha-glucanotransferase; Provisional.
Length = 695
Score = 24.1 bits (53), Expect = 7.9
Identities = 8/14 (57%), Positives = 8/14 (57%)
Query: 62 FLHTGGDEVDFYCW 75
F DEVDFY W
Sbjct: 335 FCEEHADEVDFYLW 348
>gnl|CDD|213303 cd05937, FATP_chFAT1_like, Uncharacterized subfamily of
bifunctional fatty acid transporter/very-long-chain
acyl-CoA synthetase in fungi. Fatty acid transport
protein (FATP) transports long-chain or very-long-chain
fatty acids across the plasma membrane. FATPs also have
fatty acid CoA synthetase activity, thus playing dual
roles as fatty acid transporters and its activation
enzymes. FATPs are the key players in the trafficking of
exogenous fatty acids into the cell and in intracellular
fatty acid homeostasis. Members of this family are
fungal FATPs, including FAT1 from Cochliobolus
heterostrophus.
Length = 468
Score = 24.0 bits (52), Expect = 9.6
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 3/32 (9%)
Query: 20 NITIPDLNTTQEYWGPIDPTKSSSYDFVRDLF 51
+ + Q Y D T+S +RD+F
Sbjct: 305 RVRFKNRELFQGYLKNEDATESK---LLRDVF 333
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 0.141 0.509
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,904,052
Number of extensions: 282254
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 269
Number of HSP's successfully gapped: 21
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)