RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14880
(497 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 = 326 bits (838), Expect = e-108
Identities = 129/350 (36%), Positives = 171/350 (48%), Gaps = 67/350 (19%)
Query: 138 RFGAYSPAKVYTPLEVQELVHYAKLRGIRVIFELDAPAHAGNGWQWGPRYGLGDLIVCLN 197
+ GAYSP++VYTP +V+E+V YA+LRGIRVI E+D P H G+ Q P +L+
Sbjct: 57 KKGAYSPSEVYTPEDVKEIVEYARLRGIRVIPEIDTPGHTGSWGQGYP-----ELLTGCY 111
Query: 198 DPSWRANCIQPPCGQLNPINPHVYTVLKDIYGELMGMAKYGDEMFHMGADELVTLMALCR 257
WR C +PPCGQLNP NP Y LK ++ E+ + + D+ FH+G DE
Sbjct: 112 AV-WRKYCPEPPCGQLNPTNPKTYDFLKTLFKEVSEL--FPDKYFHLGGDE--------- 159
Query: 258 WQMCTRQQVPCVQPISGVDHLSPHLWTVFIKCWNNTPAIVDFMLAHGKNTTFDDYIQLWA 317
V CWN+ P I FM + DY L +
Sbjct: 160 ---------------------------VNFNCWNSNPEIQKFMKKNNGT----DYSDLES 188
Query: 318 HFQNKAAASLDEAVGHNRTKLIVWSSHLTDPEIILNYLDPKRYIIQTWVPRIDPLADLLI 377
+F +A + V IVW + YL PK I+Q W ++
Sbjct: 189 YFIQRA----LDIVRSLGKTPIVWEEVFDNG----VYLLPKDTIVQVWGG--SDELKNVL 238
Query: 378 SKGYQVIISTKDAWYLDHGFWGVT-------SYYR-WQRVYDNLLPSSPLVLGGEVAMWT 429
+ GY+VI+S+ D WYLD GF G Y+ W R+Y LVLGGE MW
Sbjct: 239 AAGYKVILSSYDFWYLDCGFGGWVGPGNDWCDPYKNWPRIYSGTPEQKKLVLGGEACMWG 298
Query: 430 EYVDDQSLDGRLWPRTAAAAERLWSNPKSSS-SEAETRFLEQRERLVEMG 478
E VDD +LD RLWPR +A AERLWS P ++ ++AE R +E R RLV G
Sbjct: 299 EQVDDTNLDQRLWPRASALAERLWSGPSDTNLTDAEPRLVEFRCRLVRRG 348
Score = 32.2 bits (74), Expect = 0.55
Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 4/45 (8%)
Query: 4 FDDYIQLWAHFQNKAAASLDEAVGHNRTKLIVWSSHLTDPEIILN 48
DY L ++F +A + V IVW + +L
Sbjct: 180 GTDYSDLESYFIQRA----LDIVRSLGKTPIVWEEVFDNGVYLLP 220
>gnl|CDD|216086 pfam00728, Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic
domain. This domain has a TIM barrel fold.
Length = 335
Score = 202 bits (515), Expect = 1e-60
Identities = 93/337 (27%), Positives = 132/337 (39%), Gaps = 74/337 (21%)
Query: 137 PRFGAYSPAKVYTPLEVQELVHYAKLRGIRVIFELDAPAHAGNGWQWGPRYGLGDLIVCL 196
GAY + YT +++E+V YA RGI VI E+D P HA + P G
Sbjct: 56 TEVGAYRGSDFYTQEDIREIVAYAAARGIEVIPEIDMPGHARAALKAYPELGCKPED--- 112
Query: 197 NDPSWRANCIQPPCGQLNPINPHVYTVLKDIYGELMGMAKYGDEMFHMGADELVTLMALC 256
+ + + PP G LNP NP Y L + E+ + + E H+G DE
Sbjct: 113 -TSWYVSVQVGPPNGTLNPGNPKTYDFLDKVLDEVAEL--FPSEYIHIGGDE-------- 161
Query: 257 RWQMCTRQQVPCVQPISGVDHLSPHLWTVFIKCWNNTPAIVDFMLAHGKNTTFDDYIQLW 316
V CW +P FM G + +L
Sbjct: 162 ----------------------------VNKGCWLKSPKCQAFMKQEGLKS------ELQ 187
Query: 317 AHFQNKAAASLDEAVGHNRTKLIVWSSHLTDPEIILNYLDPKRYIIQTWVPRIDPLADLL 376
++F + + + + K I W LT L P +Q+W A
Sbjct: 188 SYFIKRVVKIVKK---RGK-KPIGWEEILTGG----GTLLPPDTTVQSWR-NGGAQARQA 238
Query: 377 ISKGYQVIISTKDAWYLDHG----------FWGVTS----YYRWQRVYDNLLP--SSPLV 420
++GY+VI+S D YLDHG +W +Y W+ YD + V
Sbjct: 239 ANQGYKVILSPGDFLYLDHGYGKWPTERGYYWAGFMPLKKFYAWEPPYDTWGAPLEAGNV 298
Query: 421 LGGEVAMWTEYVDDQS-LDGRLWPRTAAAAERLWSNP 456
LGGE A+W EY+ D L+ ++PR AA AER WS P
Sbjct: 299 LGGEAALWGEYIRDPENLEYMVFPRLAALAERAWSPP 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 = 135 bits (341), Expect = 7e-36
Identities = 95/309 (30%), Positives = 132/309 (42%), Gaps = 74/309 (23%)
Query: 148 YTPLEVQELVHYAKLRGIRVIFELDAPAHAGNGWQWGPRYGLGDLIVCLNDPSWRANCIQ 207
YT +++E+V YA+ RGIRV+ E+D P HA P G R +
Sbjct: 65 YTQEQIREVVAYARDRGIRVVPEIDVPGHASAIAVAYPELASGPG----PYVIERGWGVF 120
Query: 208 PPCGQLNPINPHVYTVLKDIYGELMGMAKYGDEMFHMGADELVTLMALCRWQMCTRQQVP 267
P L+P N YT L +++GE+ + + DE FH+G DE+
Sbjct: 121 EPL--LDPTNEETYTFLDNLFGEMAEL--FPDEYFHIGGDEVDP---------------- 160
Query: 268 CVQPISGVDHLSPHLWTVFIKCWNNTPAIVDFMLAHGKNTTFDDYIQLWAHFQNKAAASL 327
K WN P I FM HG D L A+F + L
Sbjct: 161 --------------------KQWNENPRIQAFMKEHG----LKDAAALQAYFNQRVEKIL 196
Query: 328 DEAVGHNRTKLIVWSSHLTDPEIILNYLDPKRYIIQTWVPRIDPLADLLISKGYQVIIST 387
+ + K+I W L P++ PK +IQ+W D L + GYQ I+ST
Sbjct: 197 SK----HGKKMIGWDEVLH-PDL------PKNVVIQSWRGH-DSLGEA-AKAGYQGILST 243
Query: 388 KDAWYLDHGFWGVTSYYRWQRVYDNLLPSSPLVLGGEVAMWTEYVDDQSLDGRLWPRTAA 447
+Y+D +YR P++LGGE MW E V ++++D RLWPRTAA
Sbjct: 244 --GYYIDQPQP-AAYHYR----------VDPMILGGEATMWAELVSEETIDSRLWPRTAA 290
Query: 448 AAERLWSNP 456
AERLWS
Sbjct: 291 IAERLWSAQ 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 = 102 bits (255), Expect = 4e-24
Identities = 81/339 (23%), Positives = 113/339 (33%), Gaps = 96/339 (28%)
Query: 126 PAHAGNGWQWGPRFGAYSPAKVYTPLEVQELVHYAKLRGIRVIFELDAPAHAGNGWQWGP 185
P A G Q P SP YT ++++++ YA RGI VI E+D P H+ + P
Sbjct: 51 PELAEKGGQINP----RSPGGFYTYAQLKDIIEYAAARGIEVIPEIDMPGHSTAFVKSFP 106
Query: 186 RYGLGDLIVCLNDPSWRANCIQPPCGQLNPINPHVYTVLKDIYGELMGMAKYGDEMFHMG 245
L C R L+P P Y L D++GE+ + + D H+G
Sbjct: 107 ----KLLTECYAGLKLRDV-----FDPLDPTLPKGYDFLDDLFGEIAEL--FPDRYLHIG 155
Query: 246 ADELVTLMALCRWQMCTRQQVPCVQPISGVDHLSPHLWTVFIKCWNNTPAIVDFMLAHGK 305
DE HL FI ++D + GK
Sbjct: 156 GDE--------------------AHFKQDRKHLMSQ----FI------QRVLDIVKKKGK 185
Query: 306 NTTFDDYIQLWAHFQNKAAASLDEAVGHNRTKLIVWSSHLTDPEIILNYLDPKRYIIQTW 365
IVW + + I+Q W
Sbjct: 186 KV-------------------------------IVWQDGFDKKMKL-----KEDVIVQYW 209
Query: 366 VPRIDPLAD---LLISKGYQVIISTKDAWYLDHGFWGVTSYYRWQRVYDN------LLPS 416
D +KG+ VI+S +YLD + ++VY N
Sbjct: 210 DYDGDKYNVELPEAAAKGFPVILSN--GYYLD---IFIDGALDARKVYKNDPLAVPTPQQ 264
Query: 417 SPLVLGGEVAMWTEYV-DDQSLDGRLWPRTAAAAERLWS 454
LVLG +W E V D ++L R WPR A AER WS
Sbjct: 265 KDLVLGVIACLWGETVKDTKTLQYRFWPRALAVAERSWS 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 = 99.6 bits (249), Expect = 7e-23
Identities = 75/343 (21%), Positives = 110/343 (32%), Gaps = 112/343 (32%)
Query: 148 YTPLEVQELVHYAKLRGIRVIFELDAPAHA------------------GNGWQWGPRYGL 189
YT E++E+V YA RGI VI E+D P HA Q
Sbjct: 83 YTQEEIREIVAYAAERGITVIPEIDMPGHALAALAAYPELGCTGGPGSVVSVQGVVSN-- 140
Query: 190 GDLIVCLNDPSWRANCIQPPCGQLNPINPHVYTVLKDIYGELMGMAKYGDEMFHMGADEL 249
L P P YT L+D+ E+ + H+G DE
Sbjct: 141 ----------------------VLCPGKPETYTFLEDVLDEVAELFPS--PYIHIGGDE- 175
Query: 250 VTLMALCRWQMCTRQQVPCVQPISGVDHLSPHLWTVFIKCWNNTPAIVDFMLAHGKNTTF 309
VP Q W +PA M G
Sbjct: 176 ----------------VPKGQ-------------------WEKSPACQARMKEEG----L 196
Query: 310 DDYIQLWAHFQNKAAASLDEAVGHNRTKLIVWSSHLTDPEIILNYLDPKRYIIQTWVPRI 369
D +L ++F + L + K+I W EI+ L P + +W
Sbjct: 197 KDEHELQSYFIKRVEKILA---SKGK-KMIGWD------EILEGGL-PPNATVMSWR-GE 244
Query: 370 DPLADLLISKGYQVIISTKDAWYLDHG---FW----GVTSYYRWQRVYD-NLLPSSP--- 418
D +GY VI+S YLD+ + ++VY +P
Sbjct: 245 DGGIKAA-KQGYDVIMSPGQYLYLDYAQSKGPDEPASWAGFNTLEKVYSFEPVPGGLTPE 303
Query: 419 ---LVLGGEVAMWTEYVDDQS-LDGRLWPRTAAAAERLWSNPK 457
+LG + +WTEY+ ++ +PR A AE W+ P+
Sbjct: 304 QAKRILGVQANLWTEYIPTPERVEYMAFPRLLALAEVAWTPPE 346
>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 = 62.7 bits (153), Expect = 1e-10
Identities = 57/293 (19%), Positives = 97/293 (33%), Gaps = 76/293 (25%)
Query: 148 YTPLEVQELVHYAKLRGIRVIFELDAPAHAGNGWQWGPRYGLGDLIVCLNDPSWRANCIQ 207
YT E +EL+ YAK RG+ +I E+D+P H+ + P GL + +
Sbjct: 79 YTKEEFKELIAYAKDRGVNIIPEIDSPGHSLAFTKAMPELGLKN------------PFSK 126
Query: 208 PPCGQLNPINPHVYTVLKDIYGELMGMAKYGDEMFHMGADELVTLMALCRWQMCTRQQVP 267
L+ NP +K ++ E + + H+GADE
Sbjct: 127 YDKDTLDISNPEAVKFVKALFDEYLDGFNPKSDTVHIGADEYAGDAGYAE---------- 176
Query: 268 CVQPISGVDHLSPHL----WTVFIKCWNNTPAIVDFMLAHGKNTTFDDYIQ--LWAHFQN 321
+ V+ L+ ++ T + W D + G T + W++
Sbjct: 177 --AFRAYVNDLAKYVKDKGKTP--RVWG------DGIYYKGDTTVLSKDVIINYWSYGWA 226
Query: 322 KAAASLDEAVGHNRTKLIVWSSHLTDPEIILNYLDPKRYIIQTWVPRIDPLADLLISKGY 381
L++ G+ I+N D YI VP D L
Sbjct: 227 DPKELLNK--GY----------------KIINTNDGYLYI----VPGAGYYGDYL----- 259
Query: 382 QVIISTKDAWYLDHGFWGVTSYYRWQRVYDNLLPSSPLVLGGEVAMWTEYVDD 434
+T+D + + + + L P +LGG A+W + D
Sbjct: 260 ----NTEDIY---NNWTPNK----FGGTNATLPEGDPQILGGMFAIWNDDSDA 301
Score = 39.6 bits (93), Expect = 0.003
Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 100 YTPLEVQELVHYAKLRGVRVIFELDAPAHAG 130
YT E +EL+ YAK RGV +I E+D+P H+
Sbjct: 79 YTKEEFKELIAYAKDRGVNIIPEIDSPGHSL 109
>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 = 56.6 bits (137), Expect = 1e-08
Identities = 35/117 (29%), Positives = 46/117 (39%), Gaps = 17/117 (14%)
Query: 356 DPKRYIIQTWVPR-IDPLADLLISKGYQVIISTKDAWYLDH-------------GFWGVT 401
P + Q W R D A + KG +VI+S D YLD G V
Sbjct: 202 LPAGTVAQYWSDRAPDADAAAALDKGAKVILSPADKAYLDMKYDADSPLGLTWAGPVEVR 261
Query: 402 SYYRWQ-RVYDNLLPSSPLVLGGEVAMWTEYVDD-QSLDGRLWPRTAAAAERLWSNP 456
Y W Y +P +LG E +WTE + + L+ +PR A AE WS
Sbjct: 262 EAYDWDPAAYGPGVPDE-AILGVEAPLWTETIRNLDDLEYMAFPRLAGVAEIGWSPQ 317
Score = 39.6 bits (93), Expect = 0.002
Identities = 27/117 (23%), Positives = 42/117 (35%), Gaps = 12/117 (10%)
Query: 143 SPAKVYTPLEVQELVHYAKLRGIRVIFELDAPAHAGNGWQWGPRYGLGDLIVCLNDPSWR 202
P YT + +++V YA R I V+ E+D P H +L C
Sbjct: 67 GPGGYYTQEDYKDIVAYAAERHITVVPEIDMPGHT-----NAALAAYPEL-NCDGKAKPL 120
Query: 203 ANCIQPPCGQLNPINPHVYTVLKDIYGELMGMA--KY----GDEMFHMGADELVTLM 253
I+ L+ P Y + D++ EL + Y GDE D+ +
Sbjct: 121 YTGIEVGFSSLDVDKPTTYEFVDDVFRELAALTPGPYIHIGGDEAHSTPHDDYAYFV 177
Score = 36.2 bits (84), Expect = 0.035
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 95 SPAKVYTPLEVQELVHYAKLRGVRVIFELDAPAH 128
P YT + +++V YA R + V+ E+D P H
Sbjct: 67 GPGGYYTQEDYKDIVAYAAERHITVVPEIDMPGH 100
>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 = 48.1 bits (115), Expect = 7e-06
Identities = 77/394 (19%), Positives = 117/394 (29%), Gaps = 129/394 (32%)
Query: 130 GNGWQWGPRFGAYSPAKVYTPLEVQELVHYAKLRGIRVIFELDAPAHAGNG--------- 180
G+G Y Y+ + E++ YAK R I VI E+D P HA
Sbjct: 81 GSGPDTNNSGSGY-----YSRADYIEILKYAKARHIEVIPEIDMPGHARAAIKAMEARYR 135
Query: 181 -------WQWGPRYGLGDLIVCLNDPS-------WRANCIQPPCGQLNPINPHVYTVLKD 226
Y L D D S + N I NP P Y +
Sbjct: 136 KLMAAGKPAEAEEYRLSD----PADTSQYLSVQFYTDNVI-------NPCMPSTYRFVDK 184
Query: 227 IYGELMGMAKYGDE---MFHMGADELVTLMALCRWQMCTRQQVPCVQPISGVDHLSPHLW 283
+ E+ M + + H G DE+ P
Sbjct: 185 VIDEIARMHQEAGQPLTTIHFGGDEV------------------------------PEGA 214
Query: 284 TVFIKCWNNTPAIVDFMLAHGKNTTFDDYIQLWAHFQNKAAASLDEAVGHNRTKLIVWSS 343
W +PA + A K + D L +F + + L + L W
Sbjct: 215 ------WGGSPACKAQLFA--KEGSVKDVEDLKDYFFERVSKILKA----HGITLAGWED 262
Query: 344 HLTDPEIILNYLDPKRYI-IQTW---VPRIDPLADLLISKGYQVIISTKDAWYLDHGF-- 397
L + Y+ W + A L +KGY V++S Y D +
Sbjct: 263 GLLGKDTTNVDGFATPYVWNNVWGWGYWGGEDRAYKLANKGYDVVLSNATNLYFDFPYEK 322
Query: 398 --------WG--------VTSY-----YR--WQRVYDNLLPSSPL-------------VL 421
W V S+ Y + + + L +L
Sbjct: 323 HPEERGYYWAGRFVDTKKVFSFMPDNLYANAEVTRDGDPIDDTALNGKVRLTLEGPKNIL 382
Query: 422 GGEVAMWTEYV--DDQSLDGRLWPRTAAAAERLW 453
G + +W+E + D+Q L+ ++PR A AER W
Sbjct: 383 GLQGQLWSETIRTDEQ-LEYMVFPRLLALAERAW 415
Score = 40.7 bits (96), Expect = 0.002
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 86 CLLPRFGA--YSPAKV---YTPLEVQELVHYAKLRGVRVIFELDAPAHA 129
CLLP+ G+ + Y+ + E++ YAK R + VI E+D P HA
Sbjct: 75 CLLPQLGSGPDTNNSGSGYYSRADYIEILKYAKARHIEVIPEIDMPGHA 123
>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 = 43.3 bits (103), Expect = 1e-04
Identities = 27/123 (21%), Positives = 45/123 (36%), Gaps = 23/123 (18%)
Query: 137 PRFGAYSPAKVYTPLEVQELVHYAKLRGIRVIFELDAPAHAGNGWQWGPRYGLGDLIVCL 196
P G A YT E++E+ YA GI VI + H + L ++
Sbjct: 48 PEVGRMRGA--YTKEEIREIDDYAAELGIEVIPLIQTLGHLEFILKHPEFRHLREV---- 101
Query: 197 NDPSWRANCIQPPCGQLNPINPHVYTVLKDIYGELMGM--AKYGDEMFHMGADELVTLMA 254
P L P P Y ++++ +++ + +KY H+G DE +
Sbjct: 102 ----------DDPPQTLCPGEPKTYDFIEEMIRQVLELHPSKY----IHIGMDE-AYDLG 146
Query: 255 LCR 257
R
Sbjct: 147 RGR 149
Score = 30.6 bits (70), Expect = 1.8
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 89 PRFGAYSPAKVYTPLEVQELVHYAKLRGVRVI 120
P G A YT E++E+ YA G+ VI
Sbjct: 48 PEVGRMRGA--YTKEEIREIDDYAAELGIEVI 77
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 42.9 bits (101), Expect = 3e-04
Identities = 82/382 (21%), Positives = 129/382 (33%), Gaps = 84/382 (21%)
Query: 124 DAPAHAGNGWQWGPRFGAYSPAKV---YTPLEVQELVHYAKLRGIRVIFELDAPAHAGNG 180
A P+ G Y P ++ YT +++ELV YA R I VI E+D P HA
Sbjct: 317 TIGAWRIPDEPDLPQLG-YGPERMGGFYTQDDIRELVAYASARQITVIPEIDMPGHAR-- 373
Query: 181 WQWGPRYGLGDLIVCLNDPSWRANCIQPPCGQLNPINPHVYTVLKDIYGELMGMAKYGDE 240
DL + DP + LNP Y L + E+ +
Sbjct: 374 ---AAVVAYPDLNLGRADPDSYDSVQAYLNPVLNPTLDPTYQFLDKVLDEVADLFP--ST 428
Query: 241 MFHMGADELVTLMALCRWQMCTRQQVPCVQPISGVDHLSPHLWTVFIKCWNNTPAIVDFM 300
H+G DE +W+ ++P + M
Sbjct: 429 TIHIGGDEF----IDGQWK-------------------------------ASSPLVQALM 453
Query: 301 LAHGKNTTFDDYIQLWAHFQNKAAASLDEAVGHNRTKLIVWS--SHLTDPEIILNYLDPK 358
G D +L ++F + +L R +LI W +H D +
Sbjct: 454 EKLG----NKDTFELQSYFITQVGKTLAS---KGR-RLIGWDEGAHGGDVNGTALTANVT 505
Query: 359 RYIIQTWVPRIDPLADLLISKGYQVIISTKDAWYLDH-----------GFWGVTSYYRWQ 407
I+ L +GY V+++ YLD + T R +
Sbjct: 506 VMSWYGKDKAIE-----LAKQGYDVVLTPAQFVYLDMLQIAAPEEPGYSWATTTPLERNK 560
Query: 408 RVYDNLLPSSPL-------VLGGEVAMWTEYV-DDQSLDGRLWPRTAAAAERLWSNPKSS 459
YD P+ +LG + A+W+E++ + ++PR AAAAER W+ P +
Sbjct: 561 YAYD-FAGKQPINDELAKRILGVQAALWSEHIQTRGRFEYMVFPRLAAAAERAWT-PMAF 618
Query: 460 SSE--AETRFLEQRERLVEMGI 479
+ R Q LV + I
Sbjct: 619 NDWLYYLDRLSAQLPLLVLISI 640
Score = 36.0 bits (83), Expect = 0.053
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 86 CLLPRFGAYSPAKV---YTPLEVQELVHYAKLRGVRVIFELDAPAHAG 130
LP+ G Y P ++ YT +++ELV YA R + VI E+D P HA
Sbjct: 327 PDLPQLG-YGPERMGGFYTQDDIRELVAYASARQITVIPEIDMPGHAR 373
>gnl|CDD|223896 COG0826, COG0826, Collagenase and related proteases
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 36.9 bits (86), Expect = 0.020
Identities = 23/118 (19%), Positives = 37/118 (31%), Gaps = 9/118 (7%)
Query: 84 VPCLLPRFGAYSPAKVYTPLEVQELVHYAKLRGVRVIFELDAPAHAGNGWQWGPRFGAYS 143
V FG A ++ ++ E V A G +V ++ H
Sbjct: 30 VYIGEKEFGLRRRALNFSVEDLAEAVELAHSAGKKVYVAVNTLLHNDELETLERYLDRLV 89
Query: 144 PAKVYTPLEVQE--LVHYAKLRGIRVIFELDAPAHAGNGWQ---WGPRYGLGDLIVCL 196
V + V + L+ A+ RG + + A+ N W LG V L
Sbjct: 90 ELGVD-AVIVADPGLIMLARERGPDLPIHVSTQANVTNAETAKFWK---ELGAKRVVL 143
>gnl|CDD|198029 smart00961, RuBisCO_small, Ribulose bisphosphate carboxylase, small
chain. RuBisCO (ribulose-1,5-bisphosphate
carboxylase/oxygenase) is a bifunctional enzyme that
catalyses both the carboxylation and oxygenation of
ribulose-1,5-bisphosphate (RuBP), thus fixing carbon
dioxide as the first step of the Calvin cycle. RuBisCO
is the major protein in the stroma of chloroplasts, and
in higher plants exists as a complex of 8 large and 8
small subunits. The function of the small subunit is
unknown. While the large subunit is coded for by a
single gene, the small subunit is coded for by several
different genes, which are distributed in a tissue
specific manner. They are transcriptionally regulated by
light receptor phytochrome. which results in RuBisCO
being more abundant during the day when it is required.
Length = 96
Score = 29.4 bits (67), Expect = 1.00
Identities = 18/64 (28%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 90 RFGAYSPAKVYTPLEVQELVHYAKLRGVRVIFELDAPAHAGNG-WQWGPRFGAYSPAKVY 148
+S T E+ V Y +G + E P WQ P FGA A+V
Sbjct: 1 TQETFSYLPPLTDAEIVAQVRYLLAQGYAIGVEHADPRRFRTSSWQKLPMFGATDAAEVL 60
Query: 149 TPLE 152
LE
Sbjct: 61 AELE 64
>gnl|CDD|236869 PRK11168, glpC, sn-glycerol-3-phosphate dehydrogenase subunit C;
Provisional.
Length = 396
Score = 31.0 bits (71), Expect = 1.3
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 238 GDEMF----HMGADELVTLMALCRWQMCTRQQVPCVQPIS 273
G +F GAD +VT C+WQ+ + C PI+
Sbjct: 349 GAPLFRQIEESGADLVVTDCETCKWQIEMSTGLECEHPIT 388
>gnl|CDD|200489 cd11352, AmyAc_5, 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
residues (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 = 443
Score = 30.7 bits (70), Expect = 1.9
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 13/47 (27%)
Query: 137 PRFGAYSPAKVYTPLEVQELVHYAKLRGIRVIFE--LDAPAHAGNGW 181
PRFG T ++++LV A RGI VI + L+ H+G+ +
Sbjct: 95 PRFG--------TREDLRDLVDAAHARGIYVILDIILN---HSGDVF 130
Score = 28.4 bits (64), Expect = 9.6
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 13/47 (27%)
Query: 89 PRFGAYSPAKVYTPLEVQELVHYAKLRGVRVIFE--LDAPAHAGNGW 133
PRFG T ++++LV A RG+ VI + L+ H+G+ +
Sbjct: 95 PRFG--------TREDLRDLVDAAHARGIYVILDIILN---HSGDVF 130
>gnl|CDD|166628 PLN02987, PLN02987, Cytochrome P450, family 90, subfamily A.
Length = 472
Score = 30.3 bits (68), Expect = 2.6
Identities = 13/41 (31%), Positives = 18/41 (43%)
Query: 111 YAKLRGVRVIFELDAPAHAGNGWQWGPRFGAYSPAKVYTPL 151
+A R V + E A N W+W G P+ V+TP
Sbjct: 371 FASFRAVHLDHEYFKDARTFNPWRWQSNSGTTVPSNVFTPF 411
>gnl|CDD|213187 cd03220, ABC_KpsT_Wzt, ATP-binding cassette component of
polysaccharide transport system. The KpsT/Wzt ABC
transporter subfamily is involved in extracellular
polysaccharide export. Among the variety of
membrane-linked or extracellular polysaccharides
excreted by bacteria, only capsular polysaccharides,
lipopolysaccharides, and teichoic acids have been shown
to be exported by ABC transporters. A typical system is
made of a conserved integral membrane and an ABC. In
addition to these proteins, capsular polysaccharide
exporter systems require two 'accessory' proteins to
perform their function: a periplasmic (E.coli) or a
lipid-anchored outer membrane protein called OMA
(Neisseria meningitidis and Haemophilus influenza) and a
cytoplasmic membrane protein MPA2.
Length = 224
Score = 29.8 bits (68), Expect = 2.7
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 15/61 (24%)
Query: 296 IVDFMLAHGKNTTFDDYIQLWAHFQNKAAASLDEAVGHNRTKLIVWSSHLTDPEIILNYL 355
++D +LA G D A FQ K L E + +T ++V SH DP I
Sbjct: 165 LIDEVLAVG------D-----AAFQEKCQRRLRELLKQGKTVILV--SH--DPSSIKRLC 209
Query: 356 D 356
D
Sbjct: 210 D 210
Score = 29.0 bits (66), Expect = 4.3
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 12 AHFQNKAAASLDEAVGHNRTKLIVWSSHLTDPEIILNYLD 51
A FQ K L E + +T ++V SH DP I D
Sbjct: 175 AAFQEKCQRRLRELLKQGKTVILV--SH--DPSSIKRLCD 210
>gnl|CDD|227463 COG5134, COG5134, Uncharacterized conserved protein [Function
unknown].
Length = 272
Score = 29.7 bits (66), Expect = 3.2
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 450 ERLWSNPKSSSSEAETRFLEQRERLVEMGIRAE 482
+RLWS+P SS +F E+++ +E A+
Sbjct: 162 KRLWSDPFVSSQRLRKQFRERKK--IEKKQEAK 192
>gnl|CDD|131079 TIGR02024, FtcD, glutamate formiminotransferase. This model
represents the tetrahydrofolate (THF) dependent
glutamate formiminotransferase involved in the histidine
utilization pathway. This enzyme interconverts
L-glutamate and N-formimino-L-glutamate. The enzyme is
bifunctional as it also catalyzes the cyclodeaminase
reaction on N-formimino-THF, converting it to
5,10-methenyl-THF and releasing ammonia - part of the
process of regenerating THF. This model covers enzymes
from metazoa as well as gram-positive bacteria and
archaea. In humans, deficiency of this enzyme results in
a disease phenotype. The crystal structure of the enzyme
has been studied in the context of the catalytic
mechanism [Energy metabolism, Amino acids and amines].
Length = 298
Score = 29.0 bits (65), Expect = 5.5
Identities = 27/82 (32%), Positives = 35/82 (42%), Gaps = 13/82 (15%)
Query: 99 VYTPLEVQELVHYAKLRGVRVIFEL-DAPAHAGNGWQWGPRFGAYSPAKV--YTPLE--- 152
V T + E V A L+ + EL D H G PR GA A V + P+
Sbjct: 48 VITFVGEPECVVNAALKLAKKAAELIDMRNHKGEH----PRMGA---ADVIPFIPVRNVT 100
Query: 153 VQELVHYAKLRGIRVIFELDAP 174
++E V AK G R+ EL P
Sbjct: 101 MEECVELAKEFGKRLGEELGVP 122
>gnl|CDD|200473 cd11334, AmyAc_TreS, Alpha amylase catalytic domain found in
Trehalose synthetase. Trehalose synthetase (TreS)
catalyzes the reversible interconversion of trehalose
and maltose. The enzyme catalyzes the reaction in both
directions, but the preferred substrate is maltose.
Glucose is formed as a by-product of this reaction. It
is believed that the catalytic mechanism may involve the
cutting of the incoming disaccharide and transfer of a
glucose to an enzyme-bound glucose. This enzyme also
catalyzes production of a glucosamine disaccharide from
maltose and glucosamine. 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 residues (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 = 447
Score = 29.1 bits (66), Expect = 5.8
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 8/35 (22%)
Query: 137 PRFGAYSPAKVYTPLEVQELVHYAKLRGIRVIFEL 171
PR G T + E + A RGIRVI +L
Sbjct: 69 PRLG--------TLGDFVEFLREAHERGIRVIIDL 95
>gnl|CDD|224799 COG1887, TagB, Putative glycosyl/glycerophosphate transferases
involved in teichoic acid biosynthesis
TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer
membrane].
Length = 388
Score = 28.9 bits (65), Expect = 6.3
Identities = 21/101 (20%), Positives = 32/101 (31%), Gaps = 16/101 (15%)
Query: 275 VDHLSPHLWTVFIKCWNNTPAIVDFMLAHGKNTTFDDYIQLWAHFQNKAAASLDEAVGHN 334
L +++ W+ TP F +T ++A A H
Sbjct: 102 PSWLPKRKGQFYVQLWHGTPLKKKFGFEQPGIST------------DEAKAEFIYVRNH- 148
Query: 335 RTKLIVWSSHLTDPEII-LNYLDPKRYIIQTWVPRIDPLAD 374
LI + T I + K I++T PR D L D
Sbjct: 149 WDYLISPNPESTA--IFAEAFNIDKENILETGYPRNDKLFD 187
>gnl|CDD|132422 TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase,
anaerobic, C subunit. Members of this protein family
are the membrane-anchoring, non-catalytic C subunit,
product of the glpC gene, of a three-subunit,
FAD-dependent, anaerobic glycerol-3-phosphate
dehydrogenase. GlpC lasks classical hydrophobic
transmembrane helices; Cole, et al suggest interaction
with the membrane may involve amphipathic helices. GlcC
has conserved Cys-containing motifs suggestive of
iron-sulfur binding. This complex is found mostly in
Escherichia coli and closely related species [Energy
metabolism, Anaerobic].
Length = 397
Score = 29.0 bits (65), Expect = 6.5
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 245 GADELVTLMALCRWQMCTRQQVPCVQPIS 273
GAD ++T C+WQ+ + C+ PIS
Sbjct: 362 GADYVITDCETCKWQIEMSTSLECIHPIS 390
>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing
protein; Provisional.
Length = 697
Score = 28.7 bits (64), Expect = 9.4
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 443 PRTAAAAERLWSNPKSS-SSEAETRFLEQRERLVEMGIRAEVTTPEWCYLNDGQCR 497
PR + R P SS S + + L+ R RL IR EV+ + L+D Q R
Sbjct: 29 PRKFSLRGRRTKTPFSSISCSSVEQGLKPRPRLKPEPIRIEVSESKDARLDDTQIR 84
>gnl|CDD|215069 PLN00134, PLN00134, fumarate hydratase; Provisional.
Length = 458
Score = 28.5 bits (64), Expect = 9.6
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 184 GPRYGLGDLIVCLNDPSWRANCIQPPCGQLNPINPHVYT 222
GPR GLG+L + N+P + I P G++NP T
Sbjct: 293 GPRCGLGELNLPENEP---GSSIMP--GKVNPTQCEALT 326
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 0.137 0.460
Gapped
Lambda K H
0.267 0.0815 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,321,435
Number of extensions: 2573209
Number of successful extensions: 2471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2443
Number of HSP's successfully gapped: 63
Length of query: 497
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 396
Effective length of database: 6,457,848
Effective search space: 2557307808
Effective search space used: 2557307808
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: 61 (27.1 bits)