RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11379
(306 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 = 279 bits (715), Expect = 7e-93
Identities = 98/185 (52%), Positives = 125/185 (67%), Gaps = 7/185 (3%)
Query: 125 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 184
FPHRGLL+D SRH+L + +IK+ +D M+YNKLNVLHWH+ D QSFP ES +P LS KGA
Sbjct: 1 FPHRGLLLDTSRHFLSVDSIKRTIDAMAYNKLNVLHWHITDSQSFPLESPSYPELSKKGA 60
Query: 185 FGPDAIYTEKMIKSVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHCPH-----RVE 239
+ P +YT + +K ++EYARLRGIRVIPEIDTPGHT S G P++ C E
Sbjct: 61 YSPSEVYTPEDVKEIVEYARLRGIRVIPEIDTPGHTGSWGQGYPELLTGCYAVWRKYCPE 120
Query: 240 GKTFVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFMSSG 299
G L+PT T DF++ LF E+ + FP+ Y HLGGDEV+F CW NPEI+ FM
Sbjct: 121 PP--CGQLNPTNPKTYDFLKTLFKEVSELFPDKYFHLGGDEVNFNCWNSNPEIQKFMKKN 178
Query: 300 DEVDF 304
+ D+
Sbjct: 179 NGTDY 183
Score = 144 bits (366), Expect = 8e-41
Identities = 43/75 (57%), Positives = 58/75 (77%)
Query: 18 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 77
FPHRGLL+D SRH+L + +IK+ +D M+YNKLNVLHWH+ D QSFP ES +P LS KGA
Sbjct: 1 FPHRGLLLDTSRHFLSVDSIKRTIDAMAYNKLNVLHWHITDSQSFPLESPSYPELSKKGA 60
Query: 78 FGPDAIYTEKMIKKV 92
+ P +YT + +K++
Sbjct: 61 YSPSEVYTPEDVKEI 75
>gnl|CDD|216086 pfam00728, Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic
domain. This domain has a TIM barrel fold.
Length = 335
Score = 221 bits (566), Expect = 1e-70
Identities = 72/181 (39%), Positives = 107/181 (59%), Gaps = 5/181 (2%)
Query: 125 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 184
FP+RGL++D +RH+ + IK+ +D M++ KLNVLHWHL DDQ + E K +P L+ GA
Sbjct: 1 FPYRGLMLDVARHFFSVDTIKRLIDAMAFYKLNVLHWHLTDDQGWRLEIKAYPELTEVGA 60
Query: 185 FGPDAIYTEKMIKSVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHC-----PHRVE 239
+ YT++ I+ ++ YA RGI VIPEID PGH + P++ C V+
Sbjct: 61 YRGSDFYTQEDIREIVAYAAARGIEVIPEIDMPGHARAALKAYPELGCKPEDTSWYVSVQ 120
Query: 240 GKTFVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFMSSG 299
G L+P T DF+ + E+ + FP Y+H+GGDEV+ CW ++P+ +AFM
Sbjct: 121 VGPPNGTLNPGNPKTYDFLDKVLDEVAELFPSEYIHIGGDEVNKGCWLKSPKCQAFMKQE 180
Query: 300 D 300
Sbjct: 181 G 181
Score = 111 bits (280), Expect = 2e-28
Identities = 33/75 (44%), Positives = 52/75 (69%)
Query: 18 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 77
FP+RGL++D +RH+ + IK+ +D M++ KLNVLHWHL DDQ + E K +P L+ GA
Sbjct: 1 FPYRGLMLDVARHFFSVDTIKRLIDAMAFYKLNVLHWHLTDDQGWRLEIKAYPELTEVGA 60
Query: 78 FGPDAIYTEKMIKKV 92
+ YT++ I+++
Sbjct: 61 YRGSDFYTQEDIREI 75
>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 = 191 bits (486), Expect = 5e-59
Identities = 86/175 (49%), Positives = 113/175 (64%), Gaps = 5/175 (2%)
Query: 125 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 184
FP RGLL+D SRH++P+ IK+QLD M+ KLNV HWHL DDQ F ESKK+P L K +
Sbjct: 1 FPWRGLLIDVSRHFIPVAVIKRQLDAMASVKLNVFHWHLTDDQGFRIESKKYPKLQQKAS 60
Query: 185 FGPDAIYTEKMIKSVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCH-CPHRVEGK-- 241
G YT++ I+ V+ YAR RGIRV+PEID PGH ++ P++ P+ +E
Sbjct: 61 DG--LYYTQEQIREVVAYARDRGIRVVPEIDVPGHASAIAVAYPELASGPGPYVIERGWG 118
Query: 242 TFVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFM 296
F LDPT T F+ +LF E+ + FP+ Y H+GGDEVD W +NP I+AFM
Sbjct: 119 VFEPLLDPTNEETYTFLDNLFGEMAELFPDEYFHIGGDEVDPKQWNENPRIQAFM 173
Score = 95.6 bits (238), Expect = 8e-23
Identities = 41/75 (54%), Positives = 53/75 (70%), Gaps = 2/75 (2%)
Query: 18 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 77
FP RGLL+D SRH++P+ IK+QLD M+ KLNV HWHL DDQ F ESKK+P L K +
Sbjct: 1 FPWRGLLIDVSRHFIPVAVIKRQLDAMASVKLNVFHWHLTDDQGFRIESKKYPKLQQKAS 60
Query: 78 FGPDAIYTEKMIKKV 92
G YT++ I++V
Sbjct: 61 DG--LYYTQEQIREV 73
>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 = 180 bits (458), Expect = 5e-55
Identities = 71/174 (40%), Positives = 106/174 (60%), Gaps = 5/174 (2%)
Query: 127 HRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA-- 184
RG+++D SRH+L +++IK+ +D+++ K+N HWHL DDQ++ ESKKFP L+ KG
Sbjct: 1 IRGIMLDVSRHFLSVESIKRTIDVLARYKINTFHWHLTDDQAWRIESKKFPELAEKGGQI 60
Query: 185 --FGPDAIYTEKMIKSVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHCPHRVEGKT 242
P YT +K +IEYA RGI VIPEID PGH+ + P++ C ++ +
Sbjct: 61 NPRSPGGFYTYAQLKDIIEYAAARGIEVIPEIDMPGHSTAFVKSFPKLLTECYAGLKLRD 120
Query: 243 FVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFM 296
PLDPT DF+ DLF E+ + FP+ Y+H+GGDE F ++ + F+
Sbjct: 121 VFDPLDPTLPKGYDFLDDLFGEIAELFPDRYLHIGGDEAHFKQ-DRKHLMSQFI 173
Score = 90.6 bits (225), Expect = 4e-21
Identities = 28/57 (49%), Positives = 44/57 (77%)
Query: 20 HRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKG 76
RG+++D SRH+L +++IK+ +D+++ K+N HWHL DDQ++ ESKKFP L+ KG
Sbjct: 1 IRGIMLDVSRHFLSVESIKRTIDVLARYKINTFHWHLTDDQAWRIESKKFPELAEKG 57
>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 = 176 bits (450), Expect = 4e-53
Identities = 71/192 (36%), Positives = 102/192 (53%), Gaps = 21/192 (10%)
Query: 125 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 184
F RGL++D SRH+ P+ +K+ +D+M+ KLNV HWHL DDQ + E KK+P L+ GA
Sbjct: 1 FSWRGLMLDVSRHFFPVDEVKRFIDLMALYKLNVFHWHLTDDQGWRIEIKKYPKLTEVGA 60
Query: 185 FGPDAI----------------YTEKMIKSVIEYARLRGIRVIPEIDTPGHTDSMEPGMP 228
+ YT++ I+ ++ YA RGI VIPEID PGH + P
Sbjct: 61 WRGPTEIGLPQGGGDGTPYGGFYTQEEIREIVAYAAERGITVIPEIDMPGHALAALAAYP 120
Query: 229 QIHCHCPHRVEGKTFVG----PLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFF 284
++ C + G L P K T F+ D+ E+ + FP Y+H+GGDEV
Sbjct: 121 ELGC-TGGPGSVVSVQGVVSNVLCPGKPETYTFLEDVLDEVAELFPSPYIHIGGDEVPKG 179
Query: 285 CWEQNPEIKAFM 296
WE++P +A M
Sbjct: 180 QWEKSPACQARM 191
Score = 89.6 bits (223), Expect = 2e-20
Identities = 30/67 (44%), Positives = 43/67 (64%)
Query: 18 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 77
F RGL++D SRH+ P+ +K+ +D+M+ KLNV HWHL DDQ + E KK+P L+ GA
Sbjct: 1 FSWRGLMLDVSRHFFPVDEVKRFIDLMALYKLNVFHWHLTDDQGWRIEIKKYPKLTEVGA 60
Query: 78 FGPDAIY 84
+
Sbjct: 61 WRGPTEI 67
>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 = 130 bits (328), Expect = 2e-35
Identities = 64/166 (38%), Positives = 94/166 (56%), Gaps = 8/166 (4%)
Query: 125 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 184
F +RGL++D +RH+ + +K+ +D+++ KLNVLH HL DDQ + E K +P L+ G
Sbjct: 1 FAYRGLMLDVARHFFTVAEVKRYIDLLALYKLNVLHLHLTDDQGWRIEIKSWPKLTEIGG 60
Query: 185 F-----GPDAIYTEKMIKSVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCH-CPHRV 238
GP YT++ K ++ YA R I V+PEID PGHT++ P+++C +
Sbjct: 61 STEVGGGPGGYYTQEDYKDIVAYAAERHITVVPEIDMPGHTNAALAAYPELNCDGKAKPL 120
Query: 239 EGKTFVG--PLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVD 282
VG LD K T +FV D+F EL P Y+H+GGDE
Sbjct: 121 YTGIEVGFSSLDVDKPTTYEFVDDVFRELAALTPGPYIHIGGDEAH 166
Score = 62.7 bits (153), Expect = 3e-11
Identities = 24/55 (43%), Positives = 38/55 (69%)
Query: 18 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSL 72
F +RGL++D +RH+ + +K+ +D+++ KLNVLH HL DDQ + E K +P L
Sbjct: 1 FAYRGLMLDVARHFFTVAEVKRYIDLLALYKLNVLHLHLTDDQGWRIEIKSWPKL 55
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 129 bits (326), Expect = 1e-33
Identities = 69/210 (32%), Positives = 103/210 (49%), Gaps = 23/210 (10%)
Query: 118 TIEDFPQFPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFP 177
TI D P+F RGLLVD +R + +K+ +D ++ +KLNVLH HL DD+ + E K++P
Sbjct: 254 TIVDAPRFAWRGLLVDVARQFHSTDDVKRLIDQLAAHKLNVLHLHLTDDEGWRLEIKRYP 313
Query: 178 SLSLKGAF-GPDAI---------------YTEKMIKSVIEYARLRGIRVIPEIDTPGHTD 221
L+ GA+ PD YT+ I+ ++ YA R I VIPEID PGH
Sbjct: 314 KLTTIGAWRIPDEPDLPQLGYGPERMGGFYTQDDIRELVAYASARQITVIPEIDMPGHAR 373
Query: 222 SMEPGMP-----QIHCHCPHRVEGKTFVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHL 276
+ P + V+ L+PT + T F+ + E+ FP + +H+
Sbjct: 374 AAVVAYPDLNLGRADPDSYDSVQAYLN-PVLNPTLDPTYQFLDKVLDEVADLFPSTTIHI 432
Query: 277 GGDEVDFFCWE-QNPEIKAFMSSGDEVDFF 305
GGDE W+ +P ++A M D F
Sbjct: 433 GGDEFIDGQWKASSPLVQALMEKLGNKDTF 462
Score = 75.3 bits (185), Expect = 4e-15
Identities = 31/74 (41%), Positives = 45/74 (60%)
Query: 4 DEIIRVQTIEDFPQFPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFP 63
D TI D P+F RGLLVD +R + +K+ +D ++ +KLNVLH HL DD+ +
Sbjct: 247 DIRFPAVTIVDAPRFAWRGLLVDVARQFHSTDDVKRLIDQLAAHKLNVLHLHLTDDEGWR 306
Query: 64 YESKKFPSLSLKGA 77
E K++P L+ GA
Sbjct: 307 LEIKRYPKLTTIGA 320
>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 = 96.2 bits (240), Expect = 5e-23
Identities = 50/172 (29%), Positives = 74/172 (43%), Gaps = 18/172 (10%)
Query: 126 PHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSF----------PYESKK 175
RG ++D R Y + +K + MS+ K+N L HL D+ F
Sbjct: 1 EVRGFMLDVGRKYYSMDFLKDIIKTMSWYKMNDLQLHLNDNLIFNLDDMSTTVNNATYAS 60
Query: 176 FPSLSLKGAFGPDAI---YTEKMIKSVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHC 232
S + A YT++ K +I YA+ RG+ +IPEID+PGH+ + MP++
Sbjct: 61 DDVKSGNNYYNLTANDGYYTKEEFKELIAYAKDRGVNIIPEIDSPGHSLAFTKAMPELGL 120
Query: 233 HCPHRVEGKTFVGPLDPTKNVTLDFVRDLFTELGQRFPES--YVHLGGDEVD 282
P K LD + + FV+ LF E F VH+G DE
Sbjct: 121 KNPFSKYDKDT---LDISNPEAVKFVKALFDEYLDGFNPKSDTVHIGADEYA 169
Score = 41.9 bits (99), Expect = 2e-04
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 19 PHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVD 58
RG ++D R Y + +K + MS+ K+N L HL D
Sbjct: 1 EVRGFMLDVGRKYYSMDFLKDIIKTMSWYKMNDLQLHLND 40
>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 = 95.1 bits (237), Expect = 5e-22
Identities = 64/233 (27%), Positives = 94/233 (40%), Gaps = 67/233 (28%)
Query: 121 DFPQFPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLS 180
D P+F +RG+ +D +R++ + + K LD M+ KLN LH HL DD+ + E P L+
Sbjct: 1 DAPRFEYRGMHLDVARNFHSKETVLKLLDQMAAYKLNKLHLHLTDDEGWRLEIPGLPELT 60
Query: 181 LKGAF-----------------GPDAI------YTEKMIKSVIEYARLRGIRVIPEIDTP 217
GA GPD Y+ +++YA+ R I VIPEID P
Sbjct: 61 EVGAKRCHDLSETTCLLPQLGSGPDTNNSGSGYYSRADYIEILKYAKARHIEVIPEIDMP 120
Query: 218 GHT----DSMEP--------GMPQIHCHCPHRVEGKTF--VGPLDPTK------------ 251
GH +ME G P E + + P D ++
Sbjct: 121 GHARAAIKAMEARYRKLMAAGKPA---------EAEEYRLSDPADTSQYLSVQFYTDNVI 171
Query: 252 NVTLD----FVRDLFTELGQRF-----PESYVHLGGDEVDFFCWEQNPEIKAF 295
N + FV + E+ + P + +H GGDEV W +P KA
Sbjct: 172 NPCMPSTYRFVDKVIDEIARMHQEAGQPLTTIHFGGDEVPEGAWGGSPACKAQ 224
Score = 65.4 bits (160), Expect = 6e-12
Identities = 20/46 (43%), Positives = 30/46 (65%)
Query: 14 DFPQFPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDD 59
D P+F +RG+ +D +R++ + + K LD M+ KLN LH HL DD
Sbjct: 1 DAPRFEYRGMHLDVARNFHSKETVLKLLDQMAAYKLNKLHLHLTDD 46
>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 = 71.9 bits (177), Expect = 2e-14
Identities = 46/158 (29%), Positives = 77/158 (48%), Gaps = 19/158 (12%)
Query: 127 HRGLLVDGSRHYLP-IKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGAF 185
RG+ +D R+ +P + +KK L +++ N L + D +FPYE + ++GA
Sbjct: 1 FRGVHLDLKRNAVPKVSYLKKLLRLLALLGANGLLLYYED--TFPYEGEPEV-GRMRGA- 56
Query: 186 GPDAIYTEKMIKSVIEYARLRGIRVIPEIDTPGHTDSMEPGM--PQIHCHCPHRVEGKTF 243
YT++ I+ + +YA GI VIP I T GH +E + P+ H E
Sbjct: 57 -----YTKEEIREIDDYAAELGIEVIPLIQTLGH---LEFILKHPEFR----HLREVDDP 104
Query: 244 VGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEV 281
L P + T DF+ ++ ++ + P Y+H+G DE
Sbjct: 105 PQTLCPGEPKTYDFIEEMIRQVLELHPSKYIHIGMDEA 142
>gnl|CDD|99816 cd06220, DHOD_e_trans_like2, FAD/NAD binding domain in the electron
transfer subunit of dihydroorotate dehydrogenase-like
proteins. Dihydroorotate dehydrogenases (DHODs) catalyze
the only redox reaction in pyrimidine de novo
biosynthesis. They catalyze the oxidation of
(S)-dihydroorotate to orotate coupled with the reduction
of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is
co-expressed with pyrK and both gene products are
required for full activity, as well as 3 cofactors: FMN,
FAD, and an [2Fe-2S] cluster.
Length = 233
Score = 30.7 bits (70), Expect = 0.71
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 165 DDQSFPYESKKFPSLSLKGAFG--PDAIYT---EKMIKSVIEYARLRGIRV 210
DD S+ + K F + LK DAIY E M+ V+E RG+R
Sbjct: 145 DDGSYGF--KGFVTDLLKELDLEEYDAIYVCGPEIMMYKVLEILDERGVRA 193
>gnl|CDD|239677 cd03706, mtEFTU_III, Domain III of mitochondrial EF-TU (mtEF-TU).
mtEF-TU is highly conserved and is 55-60% identical to
bacterial EF-TU. The overall structure is similar to
that observed in the Escherichia coli and Thermus
aquaticus EF-TU. However, compared with that observed in
prokaryotic EF-TU the nucleotide-binding domain (domain
I) of EF-TUmt is in a different orientation relative to
the rest of the structure. Furthermore, domain III is
followed by a short 11-amino acid extension that forms
one helical turn. This extension seems to be specific to
the mitochondrial factors and has not been observed in
any of the prokaryotic factors.
Length = 93
Score = 28.8 bits (65), Expect = 1.0
Identities = 19/49 (38%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 227 MPQIHCH---CPHRV---EGKTFVGPLDPTKNVTLDFVRDLFTELGQRF 269
PQ+ C R+ GK V P + TK VTL R + E GQRF
Sbjct: 29 QPQMFSLTWDCAARIDLPPGKEMVMPGEDTK-VTLILRRPMVLEKGQRF 76
>gnl|CDD|216156 pfam00857, Isochorismatase, Isochorismatase family. This family
are hydrolase enzymes.
Length = 173
Score = 29.7 bits (67), Expect = 1.3
Identities = 14/57 (24%), Positives = 20/57 (35%)
Query: 196 IKSVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHCPHRVEGKTFVGPLDPTKN 252
I +++ AR GI VI P D+ + + P G V L P
Sbjct: 29 ISRLLKAARAAGIPVIFTRHVPEPDDADDALKDRPSGAFPPGTWGAELVPELAPLPG 85
>gnl|CDD|237889 PRK15052, PRK15052, D-tagatose-1,6-bisphosphate aldolase subunit
GatZ; Provisional.
Length = 421
Score = 30.2 bits (68), Expect = 1.5
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 256 DFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFMSSGDEV 302
+FV + ++G FP + LGGD + CW+Q P A S + V
Sbjct: 66 EFVYGIADKVG--FPRERIILGGDHLGPNCWQQEPADAAMEKSVELV 110
>gnl|CDD|176250 cd08290, ETR, 2-enoyl thioester reductase (ETR). 2-enoyl thioester
reductase (ETR) catalyzes the NADPH-dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains, at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. Candida tropicalis
enoyl thioester reductase (Etr1p) catalyzes the
NADPH-dependent reduction of trans-2-enoyl thioesters in
mitochondrial fatty acid synthesis. Etr1p forms
homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 341
Score = 28.3 bits (64), Expect = 5.5
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 197 KSVIEYARLRGIRVI 211
++VI+ A+L GI+ I
Sbjct: 161 QAVIQLAKLLGIKTI 175
>gnl|CDD|218600 pfam05476, PET122, PET122. The nuclear PET122 gene of S.
cerevisiae encodes a mitochondrial-localised protein
that activates initiation of translation of the
mitochondrial mRNA from the COX3 gene, which encodes
subunit III of cytochrome c oxidase.
Length = 267
Score = 27.9 bits (62), Expect = 7.2
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 61 SFPYESKKFPSLSLKGAFGPDAIYTEKMIKKVGLGARKMTLCNSTLVPFLFQIIRVQTIE 120
P+ + FP L+ K + D E+ G + +++ N T +P L ++ +Q
Sbjct: 162 DPPFRVRDFPHLT-KAVYQTD----EQAALLALFGDQPISVKNETSLPLLLNMVLLQ--N 214
Query: 121 DFP 123
+FP
Sbjct: 215 EFP 217
>gnl|CDD|200488 cd11350, AmyAc_4, Alpha amylase catalytic domain found in an
uncharacterized protein family. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
(GH31). The family members are quite extensive and
include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 390
Score = 28.0 bits (63), Expect = 7.7
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 185 FGPDAIY-TEKMIKSVIEYARLRGIRVI 211
F D Y T + +K +++ RGI VI
Sbjct: 72 FALDKAYGTPEDLKRLVDECHQRGIAVI 99
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 27.4 bits (61), Expect = 7.8
Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 6/74 (8%)
Query: 199 VIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHCPHRVEGKTFVGPLDPTKNVTLDFV 258
V E+ I++I D PG D G H + +D +++ D +
Sbjct: 38 VFEFGDGVDIQII---DLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASEDCVGDPL 94
Query: 259 RD---LFTELGQRF 269
D L E+ F
Sbjct: 95 EDQKTLNEEVSGSF 108
>gnl|CDD|220707 pfam10347, Fmp27_GFWDK, RNA pol II promoter Fmp27 protein domain.
Fmp27_GFWDK is a conserved domain of a family of
proteins involved in RNA polymerase II transcription
initiation. It contains characteristic GFWDK sequence
motifs. Some members are associated with domain Fmp27_SW
(pfam10305) towards the N terminus.
Length = 154
Score = 26.8 bits (60), Expect = 8.5
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 168 SFPYESKKFPSLSLKGAFGPDAIYTEKMIKSVIEYARLRGIRV 210
FP +S P+ LKG + E++++S LR I V
Sbjct: 8 HFPSQSPSLPAWHLKGDL----VIAEQLVQSPES---LRTIFV 43
>gnl|CDD|169215 PRK08091, PRK08091, ribulose-phosphate 3-epimerase; Validated.
Length = 228
Score = 27.5 bits (61), Expect = 8.8
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 39 KQLDIMSYNKLNVLHWHLVDDQSFPYES------KKFPSLSLK 75
+ L +S N+L +LH+ + D Q P+ + K+FP+ K
Sbjct: 29 ETLTTLSENQLRLLHFDIADGQFSPFFTVGAIAIKQFPTHCFK 71
Score = 27.5 bits (61), Expect = 8.8
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 146 KQLDIMSYNKLNVLHWHLVDDQSFPYES------KKFPSLSLK 182
+ L +S N+L +LH+ + D Q P+ + K+FP+ K
Sbjct: 29 ETLTTLSENQLRLLHFDIADGQFSPFFTVGAIAIKQFPTHCFK 71
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 27.6 bits (62), Expect = 9.0
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 3/25 (12%)
Query: 200 IEYARLRGIRVIPEIDTPG--HTDS 222
IE+A+ RGI V+ IDT G HTD+
Sbjct: 215 IEHAKARGIDVV-LIDTAGRMHTDA 238
>gnl|CDD|143404 cd07085, ALDH_F6_MMSDH, Methylmalonate semialdehyde dehydrogenase
and ALDH family members 6A1 and 6B2. Methylmalonate
semialdehyde dehydrogenase (MMSDH, EC=1.2.1.27)
[acylating] from Bacillus subtilis is involved in valine
metabolism and catalyses the NAD+- and CoA-dependent
oxidation of methylmalonate semialdehyde into
propionyl-CoA. Mitochondrial human MMSDH ALDH6A1 and
Arabidopsis MMSDH ALDH6B2 are also present in this CD.
Length = 478
Score = 27.5 bits (62), Expect = 9.3
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 240 GKTFVGPLDPTKNV--TLDFVRDLFTELGQRFPE---SYVHLGGDEVDFFCWEQNPEIKA 294
G TFV L P++ V + +L E G P+ + VH G + V+ +P+IKA
Sbjct: 164 GNTFV--LKPSERVPGAAMRLAELLQEAG--LPDGVLNVVHGGKEAVNALL--DHPDIKA 217
Query: 295 F 295
Sbjct: 218 V 218
>gnl|CDD|178062 PLN02443, PLN02443, acyl-coenzyme A oxidase.
Length = 664
Score = 27.5 bits (61), Expect = 9.8
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 14/76 (18%)
Query: 139 LPIKAIKKQLDIMSY-NKLNVLHWHLVDDQSFPYESKKFPSL------SLKGAFGPDAI- 190
+P K +KKQL + Y L +LH HL D S + K SL SL P+A+
Sbjct: 543 IPGKGVKKQLQNLCYIYALYLLHKHLGDFLSTGCITPKQASLANDQLRSLYSQVRPNAVA 602
Query: 191 ------YTEKMIKSVI 200
YT+ + SV+
Sbjct: 603 LVDAFNYTDHYLGSVL 618
>gnl|CDD|178095 PLN02477, PLN02477, glutamate dehydrogenase.
Length = 410
Score = 27.4 bits (61), Expect = 9.9
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 270 PESYVHLGGDEVDFFCWEQNPEIKAFMSSGDEVD 303
P+ Y + GG V +F W QN I+ FM ++V+
Sbjct: 332 PDIYANSGGVTVSYFEWVQN--IQGFMWEEEKVN 363
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
0.323 0.142 0.441
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,092,169
Number of extensions: 1552914
Number of successful extensions: 1480
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1463
Number of HSP's successfully gapped: 45
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.4 bits)