RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13692
(592 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 = 428 bits (1103), Expect = e-147
Identities = 174/365 (47%), Positives = 224/365 (61%), Gaps = 37/365 (10%)
Query: 163 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 222
FPHRGLL+D SRH+L + +IK+ +D M+YNKLNVLHWH+ D QSFP ES +P LS KGA
Sbjct: 1 FPHRGLLLDTSRHFLSVDSIKRTIDAMAYNKLNVLHWHITDSQSFPLESPSYPELSKKGA 60
Query: 223 FGPDAIYTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHCPH-----RVE 277
+ P +YT + +K ++EYARLRGIRVIPEIDTPGHT S G P++ C E
Sbjct: 61 YSPSEVYTPEDVKEIVEYARLRGIRVIPEIDTPGHTGSWGQGYPELLTGCYAVWRKYCPE 120
Query: 278 GKTFVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFMSTR 337
G L+PT T DF++ LF E+ + FP+ Y HLGGDEV+F CW NPEI+ FM
Sbjct: 121 PP--CGQLNPTNPKTYDFLKTLFKEVSELFPDKYFHLGGDEVNFNCWNSNPEIQKFMKKN 178
Query: 338 Q-WDGPQLQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQAMSMDKDTIVQVWRG 396
D L+SY++Q L ++++ K +VWEEVF + + KDTIVQVW G
Sbjct: 179 NGTDYSDLESYFIQRALDIVRSLGKTPIVWEEVFDNG--------VYLLPKDTIVQVWGG 230
Query: 397 GGLEGASAAVKRVVSAGYKVI--NSIGWYLDNLE-QEFETYH--------GIRVGSIDLT 445
S +K V++AGYKVI + WYLD + R+ S
Sbjct: 231 ------SDELKNVLAAGYKVILSSYDFWYLDCGFGGWVGPGNDWCDPYKNWPRIYSGT-- 282
Query: 446 PEEKKLFLGGEACMWGEKVDETNIESRVWPRACAAAEHLWSSPQPSNNT--KNRITEHVC 503
PE+KKL LGGEACMWGE+VD+TN++ R+WPRA A AE LWS P +N T + R+ E C
Sbjct: 283 PEQKKLVLGGEACMWGEQVDDTNLDQRLWPRASALAERLWSGPSDTNLTDAEPRLVEFRC 342
Query: 504 RLKRR 508
RL RR
Sbjct: 343 RLVRR 347
>gnl|CDD|216086 pfam00728, Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic
domain. This domain has a TIM barrel fold.
Length = 335
Score = 328 bits (844), Expect = e-108
Identities = 124/349 (35%), Positives = 180/349 (51%), Gaps = 37/349 (10%)
Query: 163 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 222
FP+RGL++D +RH+ + IK+ +D M++ KLNVLHWHL DDQ + E K +P L+ GA
Sbjct: 1 FPYRGLMLDVARHFFSVDTIKRLIDAMAFYKLNVLHWHLTDDQGWRLEIKAYPELTEVGA 60
Query: 223 FGPDAIYTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHC-----PHRVE 277
+ YT++ I+ ++ YA RGI VIPEID PGH + P++ C V+
Sbjct: 61 YRGSDFYTQEDIREIVAYAAARGIEVIPEIDMPGHARAALKAYPELGCKPEDTSWYVSVQ 120
Query: 278 GKTFVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFMSTR 337
G L+P T DF+ + E+ + FP Y+H+GGDEV+ CW ++P+ +AFM
Sbjct: 121 VGPPNGTLNPGNPKTYDFLDKVLDEVAELFPSEYIHIGGDEVNKGCWLKSPKCQAFMKQE 180
Query: 338 QWDGPQLQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQAMSMDKDTIVQVWRGG 397
+LQSY+++ ++K +K K+ + WEE+ + + DT VQ WR G
Sbjct: 181 GLKS-ELQSYFIKRVVKIVKKRGKKPIGWEEILTGGGTL--------LPPDTTVQSWRNG 231
Query: 398 GLEGASAAVKRVVSAGYKVINSIG--WYLD---NLEQEFETYHGIRVGSIDLT------- 445
G A ++ + GYKVI S G YLD Y+ +
Sbjct: 232 G-----AQARQAANQGYKVILSPGDFLYLDHGYGKWPTERGYYWAGFMPLKKFYAWEPPY 286
Query: 446 -----PEEKKLFLGGEACMWGEKV-DETNIESRVWPRACAAAEHLWSSP 488
P E LGGEA +WGE + D N+E V+PR A AE WS P
Sbjct: 287 DTWGAPLEAGNVLGGEAALWGEYIRDPENLEYMVFPRLAALAERAWSPP 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 = 275 bits (704), Expect = 5e-88
Identities = 136/330 (41%), Positives = 183/330 (55%), Gaps = 35/330 (10%)
Query: 163 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 222
FP RGLL+D SRH++P+ IK+QLD M+ KLNV HWHL DDQ F ESKK+P L K +
Sbjct: 1 FPWRGLLIDVSRHFIPVAVIKRQLDAMASVKLNVFHWHLTDDQGFRIESKKYPKLQQKAS 60
Query: 223 FGPDAIYTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCH-CPHRVEGK-- 279
G YT++ I+ V+ YAR RGIRV+PEID PGH ++ P++ P+ +E
Sbjct: 61 DG--LYYTQEQIREVVAYARDRGIRVVPEIDVPGHASAIAVAYPELASGPGPYVIERGWG 118
Query: 280 TFVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFMSTRQW 339
F LDPT T F+ +LF E+ + FP+ Y H+GGDEVD W +NP I+AFM
Sbjct: 119 VFEPLLDPTNEETYTFLDNLFGEMAELFPDEYFHIGGDEVDPKQWNENPRIQAFMKEHGL 178
Query: 340 -DGPQLQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQAMSMDKDTIVQVWRGGG 398
D LQ+Y+ Q + K + K+ + W+EV + K+ ++Q WRG
Sbjct: 179 KDAAALQAYFNQRVEKILSKHGKKMIGWDEVLHP-----------DLPKNVVIQSWRGHD 227
Query: 399 LEGASAAVKRVVSAGYKVINSIGWYLDNLEQEFETYHGIRVGSIDLTPEEKKLFLGGEAC 458
G +A AGY+ I S G+Y+D + Y RV + LGGEA
Sbjct: 228 SLGEAA------KAGYQGILSTGYYIDQPQPAAYHY---RV---------DPMILGGEAT 269
Query: 459 MWGEKVDETNIESRVWPRACAAAEHLWSSP 488
MW E V E I+SR+WPR A AE LWS+
Sbjct: 270 MWAELVSEETIDSRLWPRTAAIAERLWSAQ 299
>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 = 255 bits (653), Expect = 1e-80
Identities = 118/329 (35%), Positives = 180/329 (54%), Gaps = 33/329 (10%)
Query: 165 HRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA-- 222
RG+++D SRH+L +++IK+ +D+++ K+N HWHL DDQ++ ESKKFP L+ KG
Sbjct: 1 IRGIMLDVSRHFLSVESIKRTIDVLARYKINTFHWHLTDDQAWRIESKKFPELAEKGGQI 60
Query: 223 --FGPDAIYTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHCPHRVEGKT 280
P YT +K++IEYA RGI VIPEID PGH+ + P++ C ++ +
Sbjct: 61 NPRSPGGFYTYAQLKDIIEYAAARGIEVIPEIDMPGHSTAFVKSFPKLLTECYAGLKLRD 120
Query: 281 FVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFMSTRQWD 340
PLDPT DF+ DLF E+ + FP+ Y+H+GGDE F +Q+ +
Sbjct: 121 VFDPLDPTLPKGYDFLDDLFGEIAELFPDRYLHIGGDEAHF---KQDRK----------- 166
Query: 341 GPQLQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQAMSMDKDTIVQVWRGGGLE 400
L S ++Q +L +K K+ +VW++ F M + +D IVQ W G +
Sbjct: 167 --HLMSQFIQRVLDIVKKKGKKVIVWQDGFDK---------KMKLKEDVIVQYWDYDG-D 214
Query: 401 GASAAVKRVVSAGYKVINSIGWYLD-NLEQEFETYHGIRVGSID-LTPEEKKLFLGGEAC 458
+ + + G+ VI S G+YLD ++ + + + TP++K L LG AC
Sbjct: 215 KYNVELPEAAAKGFPVILSNGYYLDIFIDGALDARKVYKNDPLAVPTPQQKDLVLGVIAC 274
Query: 459 MWGEKVDET-NIESRVWPRACAAAEHLWS 486
+WGE V +T ++ R WPRA A AE WS
Sbjct: 275 LWGETVKDTKTLQYRFWPRALAVAERSWS 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 = 255 bits (655), Expect = 5e-80
Identities = 115/367 (31%), Positives = 172/367 (46%), Gaps = 55/367 (14%)
Query: 163 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 222
F RGL++D SRH+ P+ +K+ +D+M+ KLNV HWHL DDQ + E KK+P L+ GA
Sbjct: 1 FSWRGLMLDVSRHFFPVDEVKRFIDLMALYKLNVFHWHLTDDQGWRIEIKKYPKLTEVGA 60
Query: 223 FGPDAI----------------YTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMP 266
+ YT++ I+ ++ YA RGI VIPEID PGH + P
Sbjct: 61 WRGPTEIGLPQGGGDGTPYGGFYTQEEIREIVAYAAERGITVIPEIDMPGHALAALAAYP 120
Query: 267 QIHCHCPHRVEGKTFVG----PLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFF 322
++ C + G L P K T F+ D+ E+ + FP Y+H+GGDEV
Sbjct: 121 ELGC-TGGPGSVVSVQGVVSNVLCPGKPETYTFLEDVLDEVAELFPSPYIHIGGDEVPKG 179
Query: 323 CWEQNPEIKAFMSTRQWDGP-QLQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQ 381
WE++P +A M +LQSY+++ + K + + K+ + W+E+ + G
Sbjct: 180 QWEKSPACQARMKEEGLKDEHELQSYFIKRVEKILASKGKKMIGWDEI------LEGGL- 232
Query: 382 AMSMDKDTIVQVWRGGGLEGASAAVKRVVSAGYKVINSIG--WYLDNLEQEFETYHGIRV 439
+ V WRG +G A K+ GY VI S G YLD + +
Sbjct: 233 ----PPNATVMSWRGE--DGGIKAAKQ----GYDVIMSPGQYLYLDYAQSKGPDEPASWA 282
Query: 440 GSIDL-------------TPEEKKLFLGGEACMWGEKV-DETNIESRVWPRACAAAEHLW 485
G L TPE+ K LG +A +W E + +E +PR A AE W
Sbjct: 283 GFNTLEKVYSFEPVPGGLTPEQAKRILGVQANLWTEYIPTPERVEYMAFPRLLALAEVAW 342
Query: 486 SSPQPSN 492
+ P+ +
Sbjct: 343 TPPEKKD 349
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 186 bits (473), Expect = 1e-50
Identities = 129/500 (25%), Positives = 203/500 (40%), Gaps = 65/500 (13%)
Query: 61 YTEILKTNWRNLTKFDSVVTAPNIVGKTIKLKIRLLNECEKYPHIDMDEKYTLEIKNSSC 120
TE L R L +P K + K P + +E Y L I + +
Sbjct: 167 ATEALNILLRELANDAEKGLSPLQADKYYPNR--------KGPTLG-EEAYRLAINDKAI 217
Query: 121 LLTSQSIWGILRGLETFSQLPIPAPNGDQ-LIIRVQTIEDFPQFPHRGLLVDGSRHYLPI 179
+T+ + G+ T QL A + + TI D P+F RGLLVD +R +
Sbjct: 218 KVTAHDLAGLFYADGTLLQLDTSADSFQGDIRFPAVTIVDAPRFAWRGLLVDVARQFHST 277
Query: 180 KAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGAF-GPDAI---------- 228
+K+ +D ++ +KLNVLH HL DD+ + E K++P L+ GA+ PD
Sbjct: 278 DDVKRLIDQLAAHKLNVLHLHLTDDEGWRLEIKRYPKLTTIGAWRIPDEPDLPQLGYGPE 337
Query: 229 -----YTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMP-----QIHCHCPHRVEG 278
YT+ I+ ++ YA R I VIPEID PGH + P + V+
Sbjct: 338 RMGGFYTQDDIRELVAYASARQITVIPEIDMPGHARAAVVAYPDLNLGRADPDSYDSVQA 397
Query: 279 KTFVGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWE-QNPEIKAFMSTR 337
L+PT + T F+ + E+ FP + +H+GGDE W+ +P ++A M
Sbjct: 398 YLN-PVLNPTLDPTYQFLDKVLDEVADLFPSTTIHIGGDEFIDGQWKASSPLVQALMEKL 456
Query: 338 QWDGP-QLQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQAMSMDKDTIVQVWRG 396
+LQSY++ + K + + +R + W+E GD ++ + V W
Sbjct: 457 GNKDTFELQSYFITQVGKTLASKGRRLIGWDEGAH-----GGDVNGTALTANVTVMSWY- 510
Query: 397 GGLEGASAAVKRVVSAGYKVINSIG--WYLDNLEQEFETYHGIRVGSID----------- 443
G + A K GY V+ + YLD L+ G +
Sbjct: 511 -GKDKAIELAK----QGYDVVLTPAQFVYLDMLQIAAPEEPGYSWATTTPLERNKYAYDF 565
Query: 444 -----LTPEEKKLFLGGEACMWGEKV-DETNIESRVWPRACAAAEHLWSSPQPSNNTKNR 497
+ E K LG +A +W E + E V+PR AAAE W +P N+
Sbjct: 566 AGKQPINDELAKRILGVQAALWSEHIQTRGRFEYMVFPRLAAAAERAW-TPMAFNDWLYY 624
Query: 498 ITEHVCRLKRRNVQAAPVYD 517
+ +L + + P
Sbjct: 625 LDRLSAQLPLLVLISIPYNA 644
>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 = 153 bits (389), Expect = 5e-42
Identities = 99/351 (28%), Positives = 152/351 (43%), Gaps = 57/351 (16%)
Query: 163 FPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGA 222
F +RGL++D +RH+ + +K+ +D+++ KLNVLH HL DDQ + E K +P L+ G
Sbjct: 1 FAYRGLMLDVARHFFTVAEVKRYIDLLALYKLNVLHLHLTDDQGWRIEIKSWPKLTEIGG 60
Query: 223 F-----GPDAIYTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCH-CPHRV 276
GP YT++ K+++ YA R I V+PEID PGHT++ P+++C +
Sbjct: 61 STEVGGGPGGYYTQEDYKDIVAYAAERHITVVPEIDMPGHTNAALAAYPELNCDGKAKPL 120
Query: 277 EGKTFVG--PLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEVDFFCWEQNPEIKAFM 334
VG LD K T +FV D+F EL P Y+H+GGDE
Sbjct: 121 YTGIEVGFSSLDVDKPTTYEFVDDVFRELAALTPGPYIHIGGDEA--------------H 166
Query: 335 STRQWDGPQLQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQAMSMDKDTIVQVW 394
ST D +Y++ + + K V W+E+ + T+ Q W
Sbjct: 167 STPHDD----YAYFVNRVRAIVAKYGKTPVGWQEI-----------ARADLPAGTVAQYW 211
Query: 395 RGGGLEGASAAVKRVVSAGYKVINSIG--WYLD---------NLE----QEFETYHGIRV 439
A + G KVI S YLD L E +
Sbjct: 212 SD---RAPDADAAAALDKGAKVILSPADKAYLDMKYDADSPLGLTWAGPVEVREAYDWDP 268
Query: 440 GSIDLTPEEKKLFLGGEACMWGEKV-DETNIESRVWPRACAAAEHLWSSPQ 489
+ ++ + LG EA +W E + + ++E +PR AE WS +
Sbjct: 269 AAYGPGVPDEAI-LGVEAPLWTETIRNLDDLEYMAFPRLAGVAEIGWSPQE 318
>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 = 123 bits (311), Expect = 3e-31
Identities = 88/354 (24%), Positives = 135/354 (38%), Gaps = 62/354 (17%)
Query: 164 PHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSF----------PYESKK 213
RG ++D R Y + +K + MS+ K+N L HL D+ F
Sbjct: 1 EVRGFMLDVGRKYYSMDFLKDIIKTMSWYKMNDLQLHLNDNLIFNLDDMSTTVNNATYAS 60
Query: 214 FPSLSLKGAFGPDAI---YTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHC 270
S + A YT++ K +I YA+ RG+ +IPEID+PGH+ + MP++
Sbjct: 61 DDVKSGNNYYNLTANDGYYTKEEFKELIAYAKDRGVNIIPEIDSPGHSLAFTKAMPELGL 120
Query: 271 HCPHRVEGKTFVGPLDPTKNVTLDFVRDLFTELGQRFPES--YVHLGGDEVDFFCWEQNP 328
P K LD + + FV+ LF E F VH+G DE +
Sbjct: 121 KNPFSKYDKDT---LDISNPEAVKFVKALFDEYLDGFNPKSDTVHIGADE--YAGDAGYA 175
Query: 329 EIKAFMSTRQWDGPQLQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQAMSMDKD 388
E AF R + + +Y+ KT R V+ D GD + KD
Sbjct: 176 E--AF---RAY-----VNDLAKYVKDKGKTPR--------VWGDGIYYKGDTT--VLSKD 215
Query: 389 TIVQVWRGGGLEGASAAVKRVVSAGYKVINSIG---WYLDNLEQEFETYHGIRV------ 439
I+ W G A K +++ GYK+IN+ + + + + +
Sbjct: 216 VIINYWSYGW-----ADPKELLNKGYKIINTNDGYLYIVPGAGYYGDYLNTEDIYNNWTP 270
Query: 440 ----GSIDLTPEEKKLFLGGEACMWGEKVDETNIESRVWPR----ACAAAEHLW 485
G+ PE LGG +W + D E ++ R A AE W
Sbjct: 271 NKFGGTNATLPEGDPQILGGMFAIWNDDSDAGISEVDIYDRIFPALPAFAEKTW 324
>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 = 122 bits (307), Expect = 8e-30
Identities = 106/428 (24%), Positives = 155/428 (36%), Gaps = 114/428 (26%)
Query: 159 DFPQFPHRGLLVDGSRHYLPIKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLS 218
D P+F +RG+ +D +R++ + + K LD M+ KLN LH HL DD+ + E P L+
Sbjct: 1 DAPRFEYRGMHLDVARNFHSKETVLKLLDQMAAYKLNKLHLHLTDDEGWRLEIPGLPELT 60
Query: 219 LKGAF-----------------GPDAI------YTEKMIKNVIEYARLRGIRVIPEIDTP 255
GA GPD Y+ +++YA+ R I VIPEID P
Sbjct: 61 EVGAKRCHDLSETTCLLPQLGSGPDTNNSGSGYYSRADYIEILKYAKARHIEVIPEIDMP 120
Query: 256 GHT----DSMEP--------GMPQIHCHCPHRVEGKTF--VGPLDPTK------------ 289
GH +ME G P E + + P D ++
Sbjct: 121 GHARAAIKAMEARYRKLMAAGKPA---------EAEEYRLSDPADTSQYLSVQFYTDNVI 171
Query: 290 NVTLD----FVRDLFTELGQRF-----PESYVHLGGDEVDFFCWEQNPEIKA--FMSTRQ 338
N + FV + E+ + P + +H GGDEV W +P KA F
Sbjct: 172 NPCMPSTYRFVDKVIDEIARMHQEAGQPLTTIHFGGDEVPEGAWGGSPACKAQLFAKEGS 231
Query: 339 WDGPQ-LQSYYMQYLLKAIKTIRKRSVVWEEVFQDWKNVNGDAQAMSMDKDTIVQVWRGG 397
+ L+ Y+ + + K +K WE+ N D A VW G
Sbjct: 232 VKDVEDLKDYFFERVSKILKAHGITLAGWEDGLLGKDTTNVDGFATPY---VWNNVWGWG 288
Query: 398 GLEGASAAVKRVVSAGYKVI--NSIGWYLD------------------------------ 425
G A K + + GY V+ N+ Y D
Sbjct: 289 YWGGEDRAYK-LANKGYDVVLSNATNLYFDFPYEKHPEERGYYWAGRFVDTKKVFSFMPD 347
Query: 426 NLEQEFETY---HGIRVGSI----DLTPEEKKLFLGGEACMWGEKV-DETNIESRVWPRA 477
NL E I ++ LT E K LG + +W E + + +E V+PR
Sbjct: 348 NLYANAEVTRDGDPIDDTALNGKVRLTLEGPKNILGLQGQLWSETIRTDEQLEYMVFPRL 407
Query: 478 CAAAEHLW 485
A AE W
Sbjct: 408 LALAERAW 415
>gnl|CDD|111707 pfam02838, Glyco_hydro_20b, Glycosyl hydrolase family 20, domain 2.
This domain has a zincin-like fold.
Length = 131
Score = 82.5 bits (204), Expect = 9e-19
Identities = 33/119 (27%), Positives = 55/119 (46%), Gaps = 13/119 (10%)
Query: 48 GKSCDILEDAILRYTEILKTNWRNLTKFDSVVTAP-----NIVGKTIKLKIRLLNECEKY 102
SC +L+ A RY ++ F + V K++ + + + + C+
Sbjct: 21 QTSCSLLKVAFARYINLIF-------GFKAWQFPSVNFRAETVIKSVLVPVVVTSPCDSL 73
Query: 103 PHIDMDEKYTLEIKNSSCLLTSQSIWGILRGLETFSQLPIPAPNGDQLIIRVQTIEDFP 161
+ DE YTL IK+ ++ + ++WG LRGLET SQL I + +I +I D P
Sbjct: 74 QSLGSDESYTLSIKSDGIVIKANTVWGALRGLETLSQL-IVYDSEGTFVINQVSISDSP 131
>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 = 73.4 bits (181), Expect = 3e-14
Identities = 46/158 (29%), Positives = 77/158 (48%), Gaps = 19/158 (12%)
Query: 165 HRGLLVDGSRHYLP-IKAIKKQLDIMSYNKLNVLHWHLVDDQSFPYESKKFPSLSLKGAF 223
RG+ +D R+ +P + +KK L +++ N L + D +FPYE + ++GA
Sbjct: 1 FRGVHLDLKRNAVPKVSYLKKLLRLLALLGANGLLLYYED--TFPYEGEPEV-GRMRGA- 56
Query: 224 GPDAIYTEKMIKNVIEYARLRGIRVIPEIDTPGHTDSMEPGM--PQIHCHCPHRVEGKTF 281
YT++ I+ + +YA GI VIP I T GH +E + P+ H E
Sbjct: 57 -----YTKEEIREIDDYAAELGIEVIPLIQTLGH---LEFILKHPEFR----HLREVDDP 104
Query: 282 VGPLDPTKNVTLDFVRDLFTELGQRFPESYVHLGGDEV 319
L P + T DF+ ++ ++ + P Y+H+G DE
Sbjct: 105 PQTLCPGEPKTYDFIEEMIRQVLELHPSKYIHIGMDEA 142
>gnl|CDD|180820 PRK07064, PRK07064, hypothetical protein; Provisional.
Length = 544
Score = 33.8 bits (78), Expect = 0.30
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 393 VWRGGGLEGASAAVKRVVSAGYKVINS 419
+W GGG A A VKR+V G+ V+ S
Sbjct: 208 LWLGGGARHAGAEVKRLVDLGFGVVTS 234
>gnl|CDD|216156 pfam00857, Isochorismatase, Isochorismatase family. This family
are hydrolase enzymes.
Length = 173
Score = 30.8 bits (70), Expect = 1.1
Identities = 14/57 (24%), Positives = 20/57 (35%)
Query: 234 IKNVIEYARLRGIRVIPEIDTPGHTDSMEPGMPQIHCHCPHRVEGKTFVGPLDPTKN 290
I +++ AR GI VI P D+ + + P G V L P
Sbjct: 29 ISRLLKAARAAGIPVIFTRHVPEPDDADDALKDRPSGAFPPGTWGAELVPELAPLPG 85
>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 = 29.2 bits (66), Expect = 1.5
Identities = 19/49 (38%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 265 MPQIHCH---CPHRV---EGKTFVGPLDPTKNVTLDFVRDLFTELGQRF 307
PQ+ C R+ GK V P + TK VTL R + E GQRF
Sbjct: 29 QPQMFSLTWDCAARIDLPPGKEMVMPGEDTK-VTLILRRPMVLEKGQRF 76
>gnl|CDD|217407 pfam03176, MMPL, MMPL family. Members of this family are putative
integral membrane proteins from bacteria. Several of the
members are mycobacterial proteins. Many of the proteins
contain two copies of this aligned region. The function
of these proteins is not known, although it has been
suggested that they may be involved in lipid transport.
Length = 332
Score = 30.7 bits (70), Expect = 2.2
Identities = 21/114 (18%), Positives = 33/114 (28%), Gaps = 21/114 (18%)
Query: 303 LGQRFPESYVHLGGDEVDFFCWEQNPEIKAFMSTRQWDGPQLQSY-YMQYLLKAIKTIRK 361
LG FP++ + +P I + L + +R
Sbjct: 16 LGAAFPQA--------------DSDPIIVVVLGEG---DQALGDAAAEAGYDTLVDALRA 58
Query: 362 RSVVWEEVFQDWKNVNGDAQAMSMD-KDTIVQVWRGGGLEGASA--AVKRVVSA 412
+ V W + + A +S D K V V G A +V V A
Sbjct: 59 DTGHVGSVQDFWGDPDTAALFVSPDGKAAYVVVTLEGDPGTTEADESVAAVRDA 112
>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 = 29.5 bits (67), Expect = 3.7
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 203 DDQSFPYESKKFPSLSLKGAFG--PDAIYT---EKMIKNVIEYARLRGIRV 248
DD S+ + K F + LK DAIY E M+ V+E RG+R
Sbjct: 145 DDGSYGF--KGFVTDLLKELDLEEYDAIYVCGPEIMMYKVLEILDERGVRA 193
>gnl|CDD|178095 PLN02477, PLN02477, glutamate dehydrogenase.
Length = 410
Score = 29.7 bits (67), Expect = 4.6
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 308 PESYVHLGGDEVDFFCWEQNPEIKAFMSTRQWDGPQLQSYYMQYLLKAIKTIR 360
P+ Y + GG V +F W QN I+ FM W+ ++ +Y+ A K ++
Sbjct: 332 PDIYANSGGVTVSYFEWVQN--IQGFM----WEEEKVNRELDRYMTDAFKALK 378
>gnl|CDD|223744 COG0672, FTR1, High-affinity Fe2+/Pb2+ permease [Inorganic ion
transport and metabolism].
Length = 383
Score = 29.3 bits (66), Expect = 6.5
Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 3/59 (5%)
Query: 379 DAQAMSM-DKDTIVQVWRGGGLEGASAAVKR--VVSAGYKVINSIGWYLDNLEQEFETY 434
Q + +QVW G L ++A + + IG Y L++ E
Sbjct: 32 LKQIGRKEEISGRLQVWAGVSLGAVLCLALGYGFLTAAGGLEDKIGGYDAALKELLEGI 90
>gnl|CDD|176229 cd08268, MDR2, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 328
Score = 28.7 bits (65), Expect = 9.9
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 136 TFSQLPIPAPNGDQLIIRVQTI 157
+LP+PAP +++IRV+ I
Sbjct: 16 RIEELPVPAPGAGEVLIRVEAI 37
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
0.319 0.136 0.419
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,353,783
Number of extensions: 2980207
Number of successful extensions: 2852
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2803
Number of HSP's successfully gapped: 30
Length of query: 592
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 490
Effective length of database: 6,413,494
Effective search space: 3142612060
Effective search space used: 3142612060
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 (21.7 bits)
S2: 62 (27.6 bits)