RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13745
(406 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 = 340 bits (875), Expect = e-115
Identities = 135/355 (38%), Positives = 176/355 (49%), Gaps = 81/355 (22%)
Query: 12 ILLDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYSSEK 71
+LLDT+R+F ++D+IK+TID MA NKLN HWHITDSQSFP ES YP L++ GAYS +
Sbjct: 6 LLLDTSRHFLSVDSIKRTIDAMAYNKLNVLHWHITDSQSFPLESPSYPELSKKGAYSPSE 65
Query: 72 IYSREDIREIVHYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDELLVCFKKEPWTKFCVE 131
+Y+ ED++EIV Y +RG+ VIPE+D P H G ELL W K+C E
Sbjct: 66 VYTPEDVKEIVEYARLRGIRVIPEIDTPGHTGSWGQG----YPELLTGC-YAVWRKYCPE 120
Query: 132 PPCGQLNPVSDRVYEVLGGLYEEMTDLFRTDLSGLFHMGGDEVNMNCWNHTKSITDWM-- 189
PPCGQLNP + + Y+ L L++E+++LF FH+GGDEVN NCWN I +M
Sbjct: 121 PPCGQLNPTNPKTYDFLKTLFKEVSELFPDK---YFHLGGDEVNFNCWNSNPEIQKFMKK 177
Query: 190 ---------YAKF-----GAWVGEGNNWCSPYIGWQKVYDNDPIKLLDQTSLNI-SNNPE 234
+ F G I W++V+DN L T + + + E
Sbjct: 178 NNGTDYSDLESYFIQRALDIVRSLG----KTPIVWEEVFDNGVYLLPKDTIVQVWGGSDE 233
Query: 235 LK---------------------------------------------------SLIMGQE 243
LK L++G E
Sbjct: 234 LKNVLAAGYKVILSSYDFWYLDCGFGGWVGPGNDWCDPYKNWPRIYSGTPEQKKLVLGGE 293
Query: 244 AALWSEQADAATLDGRLWPRASAMAERLWSNPASNW-RAAEYRFLHQRERLVEIG 297
A +W EQ D LD RLWPRASA+AERLWS P+ AE R + R RLV G
Sbjct: 294 ACMWGEQVDDTNLDQRLWPRASALAERLWSGPSDTNLTDAEPRLVEFRCRLVRRG 348
>gnl|CDD|216086 pfam00728, Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic
domain. This domain has a TIM barrel fold.
Length = 335
Score = 209 bits (535), Expect = 9e-65
Identities = 69/178 (38%), Positives = 100/178 (56%), Gaps = 6/178 (3%)
Query: 12 ILLDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYSSEK 71
++LD AR+F+++D IK+ ID MA KLN HWH+TD Q + E + YP LT+ GAY
Sbjct: 6 LMLDVARHFFSVDTIKRLIDAMAFYKLNVLHWHLTDDQGWRLEIKAYPELTEVGAYRGSD 65
Query: 72 IYSREDIREIVHYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDELLVCFKKEPWTKFCVE 131
Y++EDIREIV Y RG+ VIPE+D P H + + + + V
Sbjct: 66 FYTQEDIREIVAYAAARGIEVIPEIDMPGHARAALKAYPELGCKPEDT---SWYVSVQVG 122
Query: 132 PPCGQLNPVSDRVYEVLGGLYEEMTDLFRTDLSGLFHMGGDEVNMNCWNHTKSITDWM 189
PP G LNP + + Y+ L + +E+ +LF ++ H+GGDEVN CW + +M
Sbjct: 123 PPNGTLNPGNPKTYDFLDKVLDEVAELFPSE---YIHIGGDEVNKGCWLKSPKCQAFM 177
Score = 64.3 bits (157), Expect = 2e-11
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 192 KFGAWVGEGNNWCSPYIGWQKVYDNDPIKLLDQTSLNISNNPELKSLIMGQEAALWSEQA 251
+G W E + + ++ +K Y +P + P ++G EAALW E
Sbjct: 258 GYGKWPTERGYYWAGFMPLKKFYAWEPPY-------DTWGAPLEAGNVLGGEAALWGEYI 310
Query: 252 -DAATLDGRLWPRASAMAERLWSNP 275
D L+ ++PR +A+AER WS P
Sbjct: 311 RDPENLEYMVFPRLAALAERAWSPP 335
>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 = 167 bits (426), Expect = 6e-49
Identities = 104/332 (31%), Positives = 142/332 (42%), Gaps = 82/332 (24%)
Query: 12 ILLDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYSSEK 71
+L+D +R+F + IK+ +D MA KLN FHWH+TD Q F ES+KYP L Q S
Sbjct: 6 LLIDVSRHFIPVAVIKRQLDAMASVKLNVFHWHLTDDQGFRIESKKYPKLQQKA--SDGL 63
Query: 72 IYSREDIREIVHYGLVRGVHVIPELDAPAHV------------GEGWNSIEKQKDELLVC 119
Y++E IRE+V Y RG+ V+PE+D P H G G IE+
Sbjct: 64 YYTQEQIREVVAYARDRGIRVVPEIDVPGHASAIAVAYPELASGPGPYVIERG------- 116
Query: 120 FKKEPWTKFCVEPPCGQLNPVSDRVYEVLGGLYEEMTDLFRTDLSGLFHMGGDEVNMNCW 179
W F EP L+P ++ Y L L+ EM +LF + FH+GGDEV+ W
Sbjct: 117 -----WGVF--EP---LLDPTNEETYTFLDNLFGEMAELFPDE---YFHIGGDEVDPKQW 163
Query: 180 NHTKSITDWM--------YAKFGAWVGEGNNWCSPY----IGWQKVYDND-P-------- 218
N I +M A + S + IGW +V D P
Sbjct: 164 NENPRIQAFMKEHGLKDAAALQAYFNQRVEKILSKHGKKMIGWDEVLHPDLPKNVVIQSW 223
Query: 219 -----------------------IKLLDQTSLNISNNPELKSLIMGQEAALWSEQADAAT 255
I + + +P +I+G EA +W+E T
Sbjct: 224 RGHDSLGEAAKAGYQGILSTGYYIDQPQPAAYHYRVDP----MILGGEATMWAELVSEET 279
Query: 256 LDGRLWPRASAMAERLWSNPASNWRAAEYRFL 287
+D RLWPR +A+AERLWS YR L
Sbjct: 280 IDSRLWPRTAAIAERLWSAQDVRDEDDMYRRL 311
>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 = 164 bits (416), Expect = 1e-47
Identities = 87/320 (27%), Positives = 135/320 (42%), Gaps = 78/320 (24%)
Query: 12 ILLDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGA----Y 67
I+LD +R+F ++++IK+TID +A K+N FHWH+TD Q++ ES+K+P L + G
Sbjct: 4 IMLDVSRHFLSVESIKRTIDVLARYKINTFHWHLTDDQAWRIESKKFPELAEKGGQINPR 63
Query: 68 SSEKIYSREDIREIVHYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDELLVCFKKEPWTK 127
S Y+ +++I+ Y RG+ VIPE+D P H S K L+
Sbjct: 64 SPGGFYTYAQLKDIIEYAAARGIEVIPEIDMPGHSTAFVKSFPK-----LLTECYAGLKL 118
Query: 128 FCVEPPCGQLNPVSDRVYEVLGGLYEEMTDLFRTDLSGLFHMGGDEVN------------ 175
V P L+P + Y+ L L+ E+ +LF H+GGDE +
Sbjct: 119 RDVFDP---LDPTLPKGYDFLDDLFGEIAELFPDR---YLHIGGDEAHFKQDRKHLMSQF 172
Query: 176 ---------------------------------MNCWN-----HTKSITDWMYAKFGAWV 197
+ W+ + + + F +
Sbjct: 173 IQRVLDIVKKKGKKVIVWQDGFDKKMKLKEDVIVQYWDYDGDKYNVELPEAAAKGFPVIL 232
Query: 198 GEG---NNWCSPYIGWQKVYDNDPIKLLDQTSLNISNNPELKSLIMGQEAALWSEQADA- 253
G + + + +KVY NDP+ + P+ K L++G A LW E
Sbjct: 233 SNGYYLDIFIDGALDARKVYKNDPLAVP---------TPQQKDLVLGVIACLWGETVKDT 283
Query: 254 ATLDGRLWPRASAMAERLWS 273
TL R WPRA A+AER WS
Sbjct: 284 KTLQYRFWPRALAVAERSWS 303
>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 = 136 bits (345), Expect = 1e-36
Identities = 64/188 (34%), Positives = 90/188 (47%), Gaps = 30/188 (15%)
Query: 12 ILLDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYSSEK 71
++LD +R+F+ +D +K+ ID MA+ KLN FHWH+TD Q + E +KYP LT+ GA+
Sbjct: 6 LMLDVSRHFFPVDEVKRFIDLMALYKLNVFHWHLTDDQGWRIEIKKYPKLTEVGAWRGPT 65
Query: 72 I----------------YSREDIREIVHYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDE 115
Y++E+IREIV Y RG+ VIPE+D P H + E
Sbjct: 66 EIGLPQGGGDGTPYGGFYTQEEIREIVAYAAERGITVIPEIDMPGHA----LAALAAYPE 121
Query: 116 LLVCF---KKEPWTKFCVEPPCGQLNPVSDRVYEVLGGLYEEMTDLFRTDLSGLFHMGGD 172
L C + V L P Y L + +E+ +LF S H+GGD
Sbjct: 122 LG-CTGGPGSVVSVQGVVSNV---LCPGKPETYTFLEDVLDEVAELFP---SPYIHIGGD 174
Query: 173 EVNMNCWN 180
EV W
Sbjct: 175 EVPKGQWE 182
Score = 58.0 bits (141), Expect = 3e-09
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 11/88 (12%)
Query: 194 GAWVGEGNNWCSPYIGWQKVYDNDPIKLLDQTSLNISNNPELKSLIMGQEAALWSE-QAD 252
E +W + + +KVY +P+ PE I+G +A LW+E
Sbjct: 272 SKGPDEPASW-AGFNTLEKVYSFEPVPGGL--------TPEQAKRILGVQANLWTEYIPT 322
Query: 253 AATLDGRLWPRASAMAERLWSNPA-SNW 279
++ +PR A+AE W+ P +W
Sbjct: 323 PERVEYMAFPRLLALAEVAWTPPEKKDW 350
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 106 bits (265), Expect = 1e-24
Identities = 61/193 (31%), Positives = 90/193 (46%), Gaps = 43/193 (22%)
Query: 13 LLDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGA------ 66
L+D AR F++ D++K+ ID +A +KLN H H+TD + + E ++YP LT GA
Sbjct: 267 LVDVARQFHSTDDVKRLIDQLAAHKLNVLHLHLTDDEGWRLEIKRYPKLTTIGAWRIPDE 326
Query: 67 -------YSSEKI---YSREDIREIVHYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDEL 116
Y E++ Y+++DIRE+V Y R + VIPE+D P H ++ D
Sbjct: 327 PDLPQLGYGPERMGGFYTQDDIRELVAYASARQITVIPEIDMPGHARA---AVVAYPDLN 383
Query: 117 L----------VCFKKEPWTKFCVEPPCGQLNPVSDRVYEVLGGLYEEMTDLFRTDLSGL 166
L V P LNP D Y+ L + +E+ DLF +
Sbjct: 384 LGRADPDSYDSVQAYLNPV-----------LNPTLDPTYQFLDKVLDEVADLFPST---T 429
Query: 167 FHMGGDEVNMNCW 179
H+GGDE W
Sbjct: 430 IHIGGDEFIDGQW 442
Score = 39.1 bits (91), Expect = 0.004
Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 232 NPELKSLIMGQEAALWSEQADA-ATLDGRLWPRASAMAERLWSNPASN-WRAAEYRFLHQ 289
N EL I+G +AALWSE + ++PR +A AER W+ A N W R Q
Sbjct: 572 NDELAKRILGVQAALWSEHIQTRGRFEYMVFPRLAAAAERAWTPMAFNDWLYYLDRLSAQ 631
Query: 290 RERLVEIGLAA 300
LV I +
Sbjct: 632 LPLLVLISIPY 642
>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 = 81.6 bits (202), Expect = 3e-17
Identities = 52/175 (29%), Positives = 81/175 (46%), Gaps = 31/175 (17%)
Query: 14 LDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYSSEK-- 71
LD AR+F+T+ +K+ ID +A+ KLN H H+TD Q + E + +P LT+ G +
Sbjct: 8 LDVARHFFTVAEVKRYIDLLALYKLNVLHLHLTDDQGWRIEIKSWPKLTEIGGSTEVGGG 67
Query: 72 ---IYSREDIREIVHYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDELLVCFKKEP---- 124
Y++ED ++IV Y R + V+PE+D P H N+ EL K +P
Sbjct: 68 PGGYYTQEDYKDIVAYAAERHITVVPEIDMPGHT----NAALAAYPELNCDGKAKPLYTG 123
Query: 125 ----WTKFCVEPPCGQLNPVSDR-VYEVLGGLYEEMTDLFRTDLSGLFHMGGDEV 174
++ V+ P + V +V L +T H+GGDE
Sbjct: 124 IEVGFSSLDVD------KPTTYEFVDDVFREL-AALTP------GPYIHIGGDEA 165
Score = 44.6 bits (106), Expect = 5e-05
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 207 YIGWQKVYDNDPIKLLDQTSLNISNNPELKSLIMGQEAALWSEQ-ADAATLDGRLWPRAS 265
+ ++ YD DP + E I+G EA LW+E + L+ +PR +
Sbjct: 257 PVEVREAYDWDP------AAYGPGVPDEA---ILGVEAPLWTETIRNLDDLEYMAFPRLA 307
Query: 266 AMAERLWSNPAS-NWRAAEYR 285
+AE WS + +W +Y+
Sbjct: 308 GVAEIGWSPQEARDW--DDYK 326
>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 = 81.2 bits (201), Expect = 1e-16
Identities = 40/113 (35%), Positives = 53/113 (46%), Gaps = 23/113 (20%)
Query: 12 ILLDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYS--- 68
+ LD ARNF++ + + K +D MA KLN H H+TD + + E P LT+ GA
Sbjct: 10 MHLDVARNFHSKETVLKLLDQMAAYKLNKLHLHLTDDEGWRLEIPGLPELTEVGAKRCHD 69
Query: 69 -SEK-------------------IYSREDIREIVHYGLVRGVHVIPELDAPAH 101
SE YSR D EI+ Y R + VIPE+D P H
Sbjct: 70 LSETTCLLPQLGSGPDTNNSGSGYYSRADYIEILKYAKARHIEVIPEIDMPGH 122
Score = 34.2 bits (79), Expect = 0.10
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 239 IMGQEAALWSE-QADAATLDGRLWPRASAMAERLWSNPASNWRAAEYRFLHQRER 292
I+G + LWSE L+ ++PR A+AER W + A + + +
Sbjct: 381 ILGLQGQLWSETIRTDEQLEYMVFPRLLALAERAW-HKAPWEADYQDTAVRKAAL 434
>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 = 79.3 bits (196), Expect = 2e-16
Identities = 43/176 (24%), Positives = 76/176 (43%), Gaps = 29/176 (16%)
Query: 13 LLDTARNFYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYSSEKI 72
+LD R +Y++D +K I M+ K+N H+ D+ F T + Y+S+ +
Sbjct: 6 MLDVGRKYYSMDFLKDIIKTMSWYKMNDLQLHLNDN--LIFNLDDMSTTVNNATYASDDV 63
Query: 73 ---------------YSREDIREIVHYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDELL 117
Y++E+ +E++ Y RGV++IPE+D+P H + K EL
Sbjct: 64 KSGNNYYNLTANDGYYTKEEFKELIAYAKDRGVNIIPEIDSPGHSL----AFTKAMPELG 119
Query: 118 VCFKKEPWTKFCVEPPCGQLNPVSDRVYEVLGGLYEEMTDLFRTDLSGLFHMGGDE 173
+ + K L+ + + + L++E D F S H+G DE
Sbjct: 120 LKNPFSKYDK-------DTLDISNPEAVKFVKALFDEYLDGF-NPKSDTVHIGADE 167
>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 = 62.6 bits (153), Expect = 6e-11
Identities = 40/164 (24%), Positives = 67/164 (40%), Gaps = 30/164 (18%)
Query: 14 LDTARN-FYTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQS-GAYSSEK 71
LD RN + +KK + +A+ N + D+ FP+E P + + GAY+
Sbjct: 6 LDLKRNAVPKVSYLKKLLRLLALLGANGLLLYYEDT--FPYE--GEPEVGRMRGAYT--- 58
Query: 72 IYSREDIREIVHYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDELLVCFKKEPWTKFC-V 130
+E+IREI Y G+ VIP + H+ +L K + V
Sbjct: 59 ---KEEIREIDDYAAELGIEVIPLIQTLGHLE-----------FIL---KHPEFRHLREV 101
Query: 131 EPPCGQLNPVSDRVYEVLGGLYEEMTDLFRTDLSGLFHMGGDEV 174
+ P L P + Y+ + + ++ +L S H+G DE
Sbjct: 102 DDPPQTLCPGEPKTYDFIEEMIRQVLELHP---SKYIHIGMDEA 142
>gnl|CDD|111707 pfam02838, Glyco_hydro_20b, Glycosyl hydrolase family 20, domain 2.
This domain has a zincin-like fold.
Length = 131
Score = 43.9 bits (104), Expect = 1e-05
Identities = 21/43 (48%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 359 ATITANTFFGGHHGAETLSQLIVYDPYTASVVMPERVEIQDGP 401
I ANT +G G ETLSQLIVYD + V+ + V I D P
Sbjct: 91 IVIKANTVWGALRGLETLSQLIVYDSEG-TFVINQ-VSISDSP 131
>gnl|CDD|132382 TIGR03339, phn_lysR, aminoethylphosphonate catabolism associated
LysR family transcriptional regulator. This group of
sequences represents a number of related clades with
numerous examples of members adjacent to operons for the
degradation of 2-aminoethylphosphonate (AEP) in
Pseudomonas, Ralstonia, Bordetella and Burkholderia
species. These are transcriptional regulators of the
LysR family which contain a helix-turn-helix (HTH)
domain (pfam00126) and a periplasmic substrate-binding
protein-like domain (pfam03466).
Length = 279
Score = 35.1 bits (81), Expect = 0.046
Identities = 21/59 (35%), Positives = 24/59 (40%), Gaps = 15/59 (25%)
Query: 72 IYSREDIREIVHYGLVRGVHVIPELDAPAH--------VGEGWNSIEKQKDELLVCFKK 122
I SRE IRE V GL GV V+ + VG E DE L C K+
Sbjct: 214 IGSREAIREAVLAGL--GVSVVSAAEVGRDPRLRVLPIVG-----AEPTMDEYLYCLKE 265
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 33.8 bits (77), Expect = 0.18
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 10/87 (11%)
Query: 224 QTSLNISNNPELKSLIMGQEAALWSEQADAATLDGRLWPRASAMAERLWSNPASNWRAAE 283
QTS ++S +P G E L DAA G P + ERL++ P + A +
Sbjct: 371 QTSKDLSEHP-----YAGAEVTLTLVAKDAAGNQGHSEPFTIRLPERLFTKPLARAVAEQ 425
Query: 284 YRFL----HQRERLVEIGLAAESIEPE 306
R L +Q ++ + L A + PE
Sbjct: 426 RRILALDANQNSQVYDA-LDALLLAPE 451
>gnl|CDD|221307 pfam11907, DUF3427, Domain of unknown function (DUF3427). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and archaea. This domain is
typically between 243 to 275 amino acids in length. This
domain is found associated with pfam04851, pfam00271.
Length = 266
Score = 31.2 bits (71), Expect = 0.89
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 21 YTLDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYSSEKIYSREDIRE 80
Y +D ++TI +A L+ W D +P +L++ E ++++R+
Sbjct: 40 YNIDVDEETIQSVA-RMLSLSFW---DKAGYPLLELGGYSLSEEFLELLENPAFKKELRD 95
Query: 81 IVHYGLVR 88
++ YGL R
Sbjct: 96 VIEYGLER 103
>gnl|CDD|182115 PRK09855, PRK09855, PTS system N-acetylgalactosamine-specific
transporter subunit IID; Provisional.
Length = 263
Score = 30.5 bits (69), Expect = 1.5
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 210 WQKVYDNDPIKLLDQTSLN---ISNNPELKSLIMGQEAALWSEQADAATLDG 258
+K+Y +D L N I+ +P L +MG ++ + + T+ G
Sbjct: 42 LKKIYKDDKPGLSAAMKDNLEFINTHPNLVGFLMGLLISMEEKGENRDTIKG 93
>gnl|CDD|227949 COG5662, COG5662, Predicted transmembrane transcriptional regulator
(anti-sigma factor) [Transcription].
Length = 256
Score = 30.5 bits (69), Expect = 1.5
Identities = 18/66 (27%), Positives = 24/66 (36%), Gaps = 5/66 (7%)
Query: 248 SEQADAATLDGRLWP-RASAMAERLWSNPASNWRAAEYRFLHQRERLVEI--GLAAESIE 304
+E A +DG L P S + L + PA R AE+R R L E +
Sbjct: 7 TEDDLHAYVDGELPPDERSEVEAHLATCPACAARVAEWR--AMRAALRSALAPYLDEEVP 64
Query: 305 PEWCYQ 310
Q
Sbjct: 65 AAAKRQ 70
>gnl|CDD|220812 pfam10566, Glyco_hydro_97, Glycoside hydrolase 97. This is the
97th family of glycosidases, in this case bacterial. The
central part of the GH97 family protein sequences
represents a typical and complete (beta/alpha)8-barrel
or catalytic TIM-barrel type domain. The N- and
C-terminal parts of the sequences, mainly consisting of
beta-strands, most probably form two additional
non-catalytic domains with as yet unknown functions. The
non-catalytic domains of glycosidases from the
alpha-galactosidase and alpha-glucosidase superfamilies
are also predominantly composed of beta-strands, and at
least some of these domains are involved in
oligomerisation and carbohydrate binding. In all known
glycosidases with the (beta-alpha)8-barrel fold, the
amino acid residues at the active site are located on
the C-termini of the beta-strands.
Length = 621
Score = 29.4 bits (66), Expect = 3.7
Identities = 22/100 (22%), Positives = 37/100 (37%), Gaps = 19/100 (19%)
Query: 23 LDNIKKTIDGMAVNKLNYFHWHITDSQSFPFESRKYPTLTQSGAYSSEKIYSREDIREIV 82
K ID A N L Y D + + K +T K+ S D++E++
Sbjct: 287 FPTYKYYIDFAARNGLEY---ISLDEGWYTPDGGKNSDMT--------KVISELDLQELI 335
Query: 83 HYGLVRGVHVIPELDAPAHVGEGWNSIEKQKDELLVCFKK 122
YG +GV + + ++ Q DE ++K
Sbjct: 336 AYGKSKGVGI--------ILWTNQKALYAQLDEAFKLYEK 367
>gnl|CDD|184522 PRK14123, PRK14123, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 28.2 bits (63), Expect = 7.7
Identities = 24/109 (22%), Positives = 40/109 (36%), Gaps = 18/109 (16%)
Query: 291 ERLVEIGLAAESIEPEWCYQNEGLCG-SVILTPYASTYIRSY-LDCGSKGTFQSHSGSIN 348
+R V I E ++ E C + + TYIR+ D G K F +H +
Sbjct: 144 KRKVNIKDIGRISELDF---KENECHFKIRVICGKGTYIRTLATDIGVKLGFPAHMSKLT 200
Query: 349 RVYSILFQVNATIT-------------ANTFFGGHHGAETLSQLIVYDP 384
R+ S F + ++T N F +G + L + + D
Sbjct: 201 RIESGGFVLKDSLTLEQIKELHEQDSLQNKLFPLEYGLKGLPSIKIKDS 249
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
0.318 0.135 0.427
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,670,335
Number of extensions: 1959853
Number of successful extensions: 1618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1587
Number of HSP's successfully gapped: 30
Length of query: 406
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 307
Effective length of database: 6,546,556
Effective search space: 2009792692
Effective search space used: 2009792692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.9 bits)