RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12961
(315 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 = 249 bits (637), Expect = 4e-81
Identities = 119/324 (36%), Positives = 168/324 (51%), Gaps = 66/324 (20%)
Query: 1 NKGSFHRTKAVYTIEDIKSIIEYGWQQEWQRYY--RIDPQEF--PGTPEQHSLVLGGEAC 56
KG++ ++ VYT ED+K I+EY R R+ P E PG H+
Sbjct: 57 KKGAYSPSE-VYTPEDVKEIVEYA------RLRGIRVIP-EIDTPG----HTG------- 97
Query: 57 IWGERVDESNVESRIWPRGAAIAERLWSWGYGNPNLLCKINITIPDLNTTQEYWGPIDPT 116
SWG G P LL + G ++PT
Sbjct: 98 ---------------------------SWGQGYPELLTGCYAVWRKY-CPEPPCGQLNPT 129
Query: 117 KSSSYDFVRDLFTEVRSVFHDEFLHTGGDEVDFYCWLNDPNIRQFL-ADRGWDGQQLQSY 175
+YDF++ LF EV +F D++ H GGDEV+F CW ++P I++F+ + G D L+SY
Sbjct: 130 NPKTYDFLKTLFKEVSELFPDKYFHLGGDEVNFNCWNSNPEIQKFMKKNNGTDYSDLESY 189
Query: 176 YTRRALAIAKQLGFTSIVWQEVYENWRSESRRMDPDTVVQVWYGNRNDLLNRITRDGYTA 235
+ +RAL I + LG T IVW+EV++N + DT+VQVW G +D L + GY
Sbjct: 190 FIQRALDIVRSLGKTPIVWEEVFDNG---VYLLPKDTIVQVWGG--SDELKNVLAAGYKV 244
Query: 236 ITSA--GWYLDVLDIRDGYGW---QQEWQRYYRIDPQEFPGTPEQHSLVLGGEACIWGER 290
I S+ WYLD GW +W Y+ P+ + GTPEQ LVLGGEAC+WGE+
Sbjct: 245 ILSSYDFWYLDCGF----GGWVGPGNDWCDPYKNWPRIYSGTPEQKKLVLGGEACMWGEQ 300
Query: 291 VDESNVESRIWPRGAAIAERLWSN 314
VD++N++ R+WPR +A+AERLWS
Sbjct: 301 VDDTNLDQRLWPRASALAERLWSG 324
>gnl|CDD|216086 pfam00728, Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic
domain. This domain has a TIM barrel fold.
Length = 335
Score = 161 bits (410), Expect = 2e-47
Identities = 89/318 (27%), Positives = 130/318 (40%), Gaps = 57/318 (17%)
Query: 7 RTKAVYTIEDIKSIIEYGWQQEWQRYYRIDPQ-EFPGTPEQHSLVLGGEACIWGERVDES 65
R YT EDI+ I+ Y R + P+ + PG H+ A +
Sbjct: 62 RGSDFYTQEDIREIVAYA----AARGIEVIPEIDMPG----HA----RAALKAYPELGCK 109
Query: 66 NVESRIWPRGAAIAERLWSWGYGNPNLLCKINITIPDLNTTQEYWGPIDPTKSSSYDFVR 125
++ + L P +YDF+
Sbjct: 110 PEDTSWYV---------SVQVGPPNGTLN--------------------PGNPKTYDFLD 140
Query: 126 DLFTEVRSVFHDEFLHTGGDEVDFYCWLNDPNIRQFLADRGWDGQQLQSYYTRRALAIAK 185
+ EV +F E++H GGDEV+ CWL P + F+ G +LQSY+ +R + I K
Sbjct: 141 KVLDEVAELFPSEYIHIGGDEVNKGCWLKSPKCQAFMKQEGLKS-ELQSYFIKRVVKIVK 199
Query: 186 QLGFTSIVWQEVYENWRSESRRMDPDTVVQVWYGNRNDLLNRITRDGYTAITSAG--WYL 243
+ G I W+E+ + PDT VQ W N + GY I S G YL
Sbjct: 200 KRGKKPIGWEEILTGGGTLL---PPDTTVQSWR-NGGAQARQAANQGYKVILSPGDFLYL 255
Query: 244 DVLDIRD----GYGWQ--QEWQRYYRIDPQ-EFPGTPEQHSLVLGGEACIWGERV-DESN 295
D + GY W +++Y +P + G P + VLGGEA +WGE + D N
Sbjct: 256 DHGYGKWPTERGYYWAGFMPLKKFYAWEPPYDTWGAPLEAGNVLGGEAALWGEYIRDPEN 315
Query: 296 VESRIWPRGAAIAERLWS 313
+E ++PR AA+AER WS
Sbjct: 316 LEYMVFPRLAALAERAWS 333
>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 = 150 bits (380), Expect = 4e-43
Identities = 75/202 (37%), Positives = 105/202 (51%), Gaps = 29/202 (14%)
Query: 113 IDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEVDFYCWLNDPNIRQFLADRGW-DGQQ 171
+DPT +Y F+ +LF E+ +F DE+ H GGDEVD W +P I+ F+ + G D
Sbjct: 124 LDPTNEETYTFLDNLFGEMAELFPDEYFHIGGDEVDPKQWNENPRIQAFMKEHGLKDAAA 183
Query: 172 LQSYYTRRALAIAKQLGFTSIVWQEVYENWRSESRRMDPDTVVQVWYGNRNDLLNRITRD 231
LQ+Y+ +R I + G I W EV + + V+Q W G+ D L +
Sbjct: 184 LQAYFNQRVEKILSKHGKKMIGWDEVLH------PDLPKNVVIQSWRGH--DSLGEAAKA 235
Query: 232 GYTAITSAGWYLDVLDIRDGYGWQQEWQRYYRIDPQEFPGTPEQHSLVLGGEACIWGERV 291
GY I S G+Y+D Q +YR+DP ++LGGEA +W E V
Sbjct: 236 GYQGILSTGYYIDQP---------QPAAYHYRVDP-----------MILGGEATMWAELV 275
Query: 292 DESNVESRIWPRGAAIAERLWS 313
E ++SR+WPR AAIAERLWS
Sbjct: 276 SEETIDSRLWPRTAAIAERLWS 297
Score = 69.4 bits (170), Expect = 2e-13
Identities = 27/53 (50%), Positives = 35/53 (66%), Gaps = 11/53 (20%)
Query: 32 YYRIDPQEFPGTPEQHSLVLGGEACIWGERVDESNVESRIWPRGAAIAERLWS 84
+YR+DP ++LGGEA +W E V E ++SR+WPR AAIAERLWS
Sbjct: 256 HYRVDP-----------MILGGEATMWAELVSEETIDSRLWPRTAAIAERLWS 297
>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 = 142 bits (361), Expect = 2e-40
Identities = 72/207 (34%), Positives = 101/207 (48%), Gaps = 30/207 (14%)
Query: 111 GPIDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEVDFYCWLNDPNIRQFLADRGWDGQ 170
P+DPT YDF+ DLF E+ +F D +LH GGDE F D +
Sbjct: 123 DPLDPTLPKGYDFLDDLFGEIAELFPDRYLHIGGDEAHFKQ----------------DRK 166
Query: 171 QLQSYYTRRALAIAKQLGFTSIVWQEVYENWRSESRRMDPDTVVQVW---YGNRNDLLNR 227
L S + +R L I K+ G IVWQ+ ++ ++ D +VQ W N L
Sbjct: 167 HLMSQFIQRVLDIVKKKGKKVIVWQDGFDK----KMKLKEDVIVQYWDYDGDKYNVELPE 222
Query: 228 ITRDGYTAITSAGWYLDVLDIRDGYGWQQEWQRYYRIDPQEFPGTPEQHSLVLGGEACIW 287
G+ I S G+YLD+ + ++ Y+ DP P TP+Q LVLG AC+W
Sbjct: 223 AAAKGFPVILSNGYYLDIFIDG-----ALDARKVYKNDPLAVP-TPQQKDLVLGVIACLW 276
Query: 288 GERVDES-NVESRIWPRGAAIAERLWS 313
GE V ++ ++ R WPR A+AER WS
Sbjct: 277 GETVKDTKTLQYRFWPRALAVAERSWS 303
Score = 65.1 bits (159), Expect = 4e-12
Identities = 27/60 (45%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 26 QQEWQRYYRIDPQEFPGTPEQHSLVLGGEACIWGERVDES-NVESRIWPRGAAIAERLWS 84
+ ++ Y+ DP P TP+Q LVLG AC+WGE V ++ ++ R WPR A+AER WS
Sbjct: 245 ALDARKVYKNDPLAVP-TPQQKDLVLGVIACLWGETVKDTKTLQYRFWPRALAVAERSWS 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 = 129 bits (327), Expect = 6e-35
Identities = 82/314 (26%), Positives = 122/314 (38%), Gaps = 65/314 (20%)
Query: 12 YTIEDIKSIIEYGWQQEWQRYYRIDPQ-EFPGTPEQHSLVLGGEACIWGERVDESNVESR 70
YT E+I+ I+ Y + R + P+ + PG H+L
Sbjct: 83 YTQEEIREIVAYAAE----RGITVIPEIDMPG----HAL--------------------- 113
Query: 71 IWPRGAAIAERLWSWGYGNPNLLCKINITIPDLNTTQEYWG-PIDPTKSSSYDFVRDLFT 129
AA+A Y P L C + + Q + P K +Y F+ D+
Sbjct: 114 -----AALA------AY--PELGC--TGGPGSVVSVQGVVSNVLCPGKPETYTFLEDVLD 158
Query: 130 EVRSVFHDEFLHTGGDEVDFYCWLNDPNIRQFLADRGW-DGQQLQSYYTRRALAIAKQLG 188
EV +F ++H GGDEV W P + + + G D +LQSY+ +R I G
Sbjct: 159 EVAELFPSPYIHIGGDEVPKGQWEKSPACQARMKEEGLKDEHELQSYFIKRVEKILASKG 218
Query: 189 FTSIVWQEVYENWRSESRRMDPDTVVQVWYGNRNDLLNRITRDGYTAITSAGWYLDVLDI 248
I W E+ E + P+ V W D + + GY I S G YL LD
Sbjct: 219 KKMIGWDEILE------GGLPPNATVMSW--RGEDGGIKAAKQGYDVIMSPGQYLY-LDY 269
Query: 249 RDGYGWQQE--------WQRYYRIDPQEFPGTPEQHSLVLGGEACIWGERV-DESNVESR 299
G + ++ Y +P TPEQ +LG +A +W E + VE
Sbjct: 270 AQSKGPDEPASWAGFNTLEKVYSFEPVPGGLTPEQAKRILGVQANLWTEYIPTPERVEYM 329
Query: 300 IWPRGAAIAERLWS 313
+PR A+AE W+
Sbjct: 330 AFPRLLALAEVAWT 343
>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 = 84.3 bits (209), Expect = 1e-18
Identities = 61/241 (25%), Positives = 94/241 (39%), Gaps = 58/241 (24%)
Query: 100 IPDLN----------TTQEYWGPIDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEV-- 147
P+LN + + +D K ++Y+FV D+F E+ ++ ++H GGDE
Sbjct: 108 YPELNCDGKAKPLYTGIEVGFSSLDVDKPTTYEFVDDVFRELAALTPGPYIHIGGDEAHS 167
Query: 148 ----DFYCWLNDPNIRQFLADRGWDGQQLQSYYTRRALAIAKQLGFTSIVWQEVYENWRS 203
D+ +Y+ R AI + G T + WQE+
Sbjct: 168 TPHDDY------------------------AYFVNRVRAIVAKYGKTPVGWQEI------ 197
Query: 204 ESRRMDPDTVVQVWYGNRND-LLNRITRDGYTAITSAG--WYLDV---LDIRDGYGW--Q 255
+ TV Q W D G I S YLD+ D G W
Sbjct: 198 ARADLPAGTVAQYWSDRAPDADAAAALDKGAKVILSPADKAYLDMKYDADSPLGLTWAGP 257
Query: 256 QEWQRYYRIDPQEF-PGTPEQHSLVLGGEACIWGERV-DESNVESRIWPRGAAIAERLWS 313
E + Y DP + PG P++ +LG EA +W E + + ++E +PR A +AE WS
Sbjct: 258 VEVREAYDWDPAAYGPGVPDEA--ILGVEAPLWTETIRNLDDLEYMAFPRLAGVAEIGWS 315
Query: 314 N 314
Sbjct: 316 P 316
Score = 46.6 bits (111), Expect = 8e-06
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 27 QEWQRYYRIDPQEF-PGTPEQHSLVLGGEACIWGERV-DESNVESRIWPRGAAIAERLWS 84
E + Y DP + PG P++ +LG EA +W E + + ++E +PR A +AE WS
Sbjct: 258 VEVREAYDWDPAAYGPGVPDEA--ILGVEAPLWTETIRNLDDLEYMAFPRLAGVAEIGWS 315
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 69.1 bits (169), Expect = 5e-13
Identities = 49/215 (22%), Positives = 83/215 (38%), Gaps = 17/215 (7%)
Query: 113 IDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEVDFYCWL-NDPNIRQFLADRGWDGQ- 170
++PT +Y F+ + EV +F +H GGDE W + P ++ + G
Sbjct: 403 LNPTLDPTYQFLDKVLDEVADLFPSTTIHIGGDEFIDGQWKASSPLVQALMEKLGNKDTF 462
Query: 171 QLQSYYTRRALAIAKQLGFTSIVWQEVYENWRSESRRMDPDTVVQVWYGNRNDLLNRITR 230
+LQSY+ + G I W E + + V WYG + + +
Sbjct: 463 ELQSYFITQVGKTLASKGRRLIGWDEGAHGGDVNGTALTANVTVMSWYGKDKAI--ELAK 520
Query: 231 DGYTAITSAGWYLDVLDIRDGYGWQQEWQRYYRIDPQE-----------FPGTPEQHSLV 279
GY + + ++ LD+ ++ + P E P E +
Sbjct: 521 QGYDVVLTPAQFVY-LDMLQIAAPEEPGYSWATTTPLERNKYAYDFAGKQPINDELAKRI 579
Query: 280 LGGEACIWGERV-DESNVESRIWPRGAAIAERLWS 313
LG +A +W E + E ++PR AA AER W+
Sbjct: 580 LGVQAALWSEHIQTRGRFEYMVFPRLAAAAERAWT 614
Score = 33.7 bits (77), Expect = 0.15
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 39 EFPGTPEQHSLVLGGEACIWGERV-DESNVESRIWPRGAAIAERLWS 84
+ P E +LG +A +W E + E ++PR AA AER W+
Sbjct: 568 KQPINDELAKRILGVQAALWSEHIQTRGRFEYMVFPRLAAAAERAWT 614
>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 = 52.7 bits (127), Expect = 1e-07
Identities = 56/247 (22%), Positives = 82/247 (33%), Gaps = 49/247 (19%)
Query: 113 IDPTKSSSYDFVRDLFTEVRSVFHDEF------LHTGGDEVDFYCWLNDP--NIRQFLAD 164
I+P S+Y FV + E+ H E +H GGDEV W P + F +
Sbjct: 171 INPCMPSTYRFVDKVIDEIA-RMHQEAGQPLTTIHFGGDEVPEGAWGGSPACKAQLFAKE 229
Query: 165 RGWDG-QQLQSYYTRRALAIAKQLGFTSIVWQEVYENWRSESRR--MDPDTVVQVW---Y 218
+ L+ Y+ R I K G T W++ + + P VW Y
Sbjct: 230 GSVKDVEDLKDYFFERVSKILKAHGITLAGWEDGLLGKDTTNVDGFATPYVWNNVWGWGY 289
Query: 219 GNRNDLLNRITRDGYTAITSAGWYLDVLDI-------RDGYGW----------------- 254
D ++ GY + S L D GY W
Sbjct: 290 WGGEDRAYKLANKGYDVVLSNATNL-YFDFPYEKHPEERGYYWAGRFVDTKKVFSFMPDN 348
Query: 255 --QQEWQRYYR--IDPQEFPG----TPEQHSLVLGGEACIWGERV-DESNVESRIWPRGA 305
ID G T E +LG + +W E + + +E ++PR
Sbjct: 349 LYANAEVTRDGDPIDDTALNGKVRLTLEGPKNILGLQGQLWSETIRTDEQLEYMVFPRLL 408
Query: 306 AIAERLW 312
A+AER W
Sbjct: 409 ALAERAW 415
Score = 30.3 bits (69), Expect = 1.3
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 43 TPEQHSLVLGGEACIWGERV-DESNVESRIWPRGAAIAERLW 83
T E +LG + +W E + + +E ++PR A+AER W
Sbjct: 374 TLEGPKNILGLQGQLWSETIRTDEQLEYMVFPRLLALAERAW 415
>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 = 48.4 bits (116), Expect = 2e-06
Identities = 54/218 (24%), Positives = 76/218 (34%), Gaps = 43/218 (19%)
Query: 113 IDPTKSSSYDFVRDLFTEVRSVFHD--EFLHTGGDEVDFYCWLNDPNIRQFLADRGWDGQ 170
+D + + FV+ LF E F+ + +H G DE + F A
Sbjct: 132 LDISNPEAVKFVKALFDEYLDGFNPKSDTVHIGADEYAGDAGYAE----AFRA------- 180
Query: 171 QLQSYYTRRALAIAKQLGFTSIVW--QEVYENWRSESRRMDPDTVVQVWYG---NRNDLL 225
Y K G T VW Y+ + + D ++ W + +LL
Sbjct: 181 -----YVNDLAKYVKDKGKTPRVWGDGIYYKGDTTV---LSKDVIINYWSYGWADPKELL 232
Query: 226 NRITRDGYTAI-TSAGWYLDVLDIRDGYG--WQQEWQRYYRIDPQEFPGT----PEQHSL 278
N GY I T+ G+ V YG E Y P +F GT PE
Sbjct: 233 N----KGYKIINTNDGYLYIVPG-AGYYGDYLNTEDI-YNNWTPNKFGGTNATLPEGDPQ 286
Query: 279 VLGGEACIWGERVDESNVESRIWPRG----AAIAERLW 312
+LGG IW + D E I+ R A AE+ W
Sbjct: 287 ILGGMFAIWNDDSDAGISEVDIYDRIFPALPAFAEKTW 324
Score = 32.3 bits (74), Expect = 0.27
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 44 PEQHSLVLGGEACIWGERVDESNVESRIWPRG----AAIAERLW 83
PE +LGG IW + D E I+ R A AE+ W
Sbjct: 281 PEGDPQILGGMFAIWNDDSDAGISEVDIYDRIFPALPAFAEKTW 324
>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 = 41.8 bits (99), Expect = 2e-04
Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 15/98 (15%)
Query: 102 DLNTTQEYWGPIDPTKSSSYDFVRDLFTEVRSVFHDEFLHTGGDEV-----DFYCWLNDP 156
L + + P + +YDF+ ++ +V + +++H G DE +
Sbjct: 97 HLREVDDPPQTLCPGEPKTYDFIEEMIRQVLELHPSKYIHIGMDEAYDLGRGRSLRKH-- 154
Query: 157 NIRQFLADRGWDGQQLQSYYTRRALAIAKQLGFTSIVW 194
+L + ++ L I K+ G ++W
Sbjct: 155 --------GNLGRGELYLEHLKKVLKIIKKRGPKPMMW 184
>gnl|CDD|140327 PTZ00306, PTZ00306, NADH-dependent fumarate reductase; Provisional.
Length = 1167
Score = 32.4 bits (74), Expect = 0.33
Identities = 13/22 (59%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 157 NIRQFLADRG-WDGQQLQSYYT 177
+ QF+A RG WDGQQL YY+
Sbjct: 949 TLGQFIAIRGDWDGQQLIGYYS 970
>gnl|CDD|236831 PRK11052, malQ, 4-alpha-glucanotransferase; Provisional.
Length = 695
Score = 31.8 bits (73), Expect = 0.55
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 16/50 (32%)
Query: 139 FLHTGGDEVDFYCWLNDPNIRQFLADRGWDGQQLQSYYTRRALAIAKQLG 188
F DEVDFY WL Q+LAD Q + + ++QLG
Sbjct: 335 FCEEHADEVDFYLWL------QWLAD-----SQFAACWQL-----SQQLG 368
>gnl|CDD|200572 cd10948, CE4_BsPdaA_like, Catalytic NodB homology domain of
Bacillus subtilis polysaccharide deacetylase PdaA, and
its bacterial homologs. The Bacillus subtilis genome
contains six polysaccharide deacetylase gene homologs:
pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH
and ylxY. This family is represented by Bacillus
subtilis pdaA gene encoding polysaccharide deacetylase
BsPdaA, which is a member of the carbohydrate esterase 4
(CE4) superfamily. BsPdaA deacetylates peptidoglycan
N-acetylmuramic acid (MurNAc) residues to facilitate the
formation of muramic delta-lactam, which is required for
recognition of germination lytic enzymes. BsPdaA
deficiency leads to the absence of muramic delta-lactam
residues in the spore cortex. Like other CE4 esterases,
BsPdaA consists of a single catalytic NodB homology
domain that appears to adopt a deformed (beta/alpha)8
barrel fold with a putative substrate binding groove
harboring the majority of the conserved residues. It
utilizes a general acid/base catalytic mechanism
involving a tetrahedral transition intermediate, where a
water molecule functions as the nucleophile tightly
associated to the zinc cofactor.
Length = 223
Score = 30.3 bits (69), Expect = 0.92
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 175 YYTRRALAIAKQLGFTSIVWQEVYENW 201
++ R+L I K LG+T++ W Y +W
Sbjct: 142 EFSERSLKITKDLGYTTVFWSFAYRDW 168
>gnl|CDD|131930 TIGR02884, spore_pdaA, delta-lactam-biosynthetic de-N-acetylase.
Muramic delta-lactam is an unusual constituent of
peptidoglycan, found only in bacterial spores in the
peptidoglycan wall, or spore cortex. The proteins in
this family are PdaA (yfjS), a member of a larger family
of polysaccharide deacetylases, and are specificially
involved in delta-lactam biosynthesis. PdaA acts
immediately after CwlD, an N-acetylmuramoyl-L-alanine
amidase and performs a de-N-acetylation. PdaA may also
perform the following transpeptidation for lactam ring
formation, as heterologous expression in E. coli of CwlD
and PdaA together is sufficient for delta-lactam
production [Cell envelope, Biosynthesis and degradation
of murein sacculus and peptidoglycan, Cellular
processes, Sporulation and germination].
Length = 224
Score = 30.1 bits (68), Expect = 1.3
Identities = 8/26 (30%), Positives = 17/26 (65%)
Query: 176 YTRRALAIAKQLGFTSIVWQEVYENW 201
++ R LA K+LG+ ++ W +++W
Sbjct: 140 FSERTLAYTKELGYYTVFWSLAFKDW 165
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 29.4 bits (67), Expect = 1.4
Identities = 30/114 (26%), Positives = 42/114 (36%), Gaps = 37/114 (32%)
Query: 131 VRSVFHDEFLHTGGDEVDFYCWLNDPNIRQFLADRG-------WD--GQQ-----LQSYY 176
F +++ T G VDF + D G WD GQ+ SYY
Sbjct: 21 TDGKFSEQYKSTIG--VDFK-------TKTIEVD-GKRVKLQIWDTAGQERFRSITSSYY 70
Query: 177 TRRALA------IAKQLGFTSIVWQEVYENWRSESRRMDPDTVVQVWYGNRNDL 224
R A+ I + F ++ ENW E R VV + GN++DL
Sbjct: 71 -RGAVGALLVYDITNRESFENL------ENWLKELREYASPNVVIMLVGNKSDL 117
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 30.1 bits (68), Expect = 1.7
Identities = 27/101 (26%), Positives = 38/101 (37%), Gaps = 17/101 (16%)
Query: 16 DIKSIIEYGWQQEWQRY--YRIDPQEFPGTPEQHSLVLGGEACIWGERVDESNVESRIWP 73
D+++ E W R+ +DP PE +W RVDE E + WP
Sbjct: 287 DLETSAERFWADTLARFENRGVDPMRPLLPPES----------LW-LRVDELFSELKNWP 335
Query: 74 RGAAIAERLWSWGYGNPNLLCKINITIPDLNTTQEYWGPID 114
R E L N NL + +PDL + P+D
Sbjct: 336 RVQLKTEHL-PTKAANTNLGYQ---KLPDLAVQAQQKAPLD 372
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 29.7 bits (66), Expect = 2.1
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 156 PNIRQFLADRGWDGQQLQSYYTRRALAIAKQLGFTSIVWQEV 197
P I+Q D + L++YYT+ + KQ GF W V
Sbjct: 155 PTIKQAQTDMTPKYEDLRAYYTKPSFEFEKQFGFLLKPWTTV 196
>gnl|CDD|200576 cd10952, CE4_MrCDA_like, Catalytic NodB homology domain of Mucor
rouxii chitin deacetylase and similar proteins. This
family is represented by the chitin deacetylase (MrCDA,
EC 3.5.1.41) encoded from the fungus Mucor rouxii (also
known as Amylomyces rouxii). MrCDA is an acidic
glycoprotein with a very stringent specificity for
beta1-4-linked N-acetylglucosamine homopolymers. It
requires at least four residues (chitotetraose) for
catalysis, and can achieve extensive deacetylation on
chitin polymers. MrCDA shows high sequence similarity to
Colletotrichum lindemuthianum chitin deacetylase
(endo-chitin de-N-acetylase, ClCDA), which consists of a
single catalytic domain similar to the deformed
(beta/alpha)8 barrel fold adopted by the carbohydrate
esterase 4 (CE4) superfamily, which encompasses a
mononuclear metalloenzyme employing a conserved
His-His-Asp zinc-binding triad closely associated with
the conserved catalytic base (aspartic acid) and acid
(histidine) to carry out acid/base catalysis. The family
also includes some uncharacterized eukaryotic and
bacterial homologs of MrCDA.
Length = 178
Score = 28.9 bits (65), Expect = 2.6
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 179 RALAIAKQLGFTSIVWQEVYENWRSESRRMDPDTVVQV 216
R AIAKQLG T+++W +W+ + TVV V
Sbjct: 105 RVRAIAKQLGLTTVLWNLDTNDWKLTTGPDATATVVDV 142
>gnl|CDD|234001 TIGR02764, spore_ybaN_pdaB, polysaccharide deacetylase family
sporulation protein PdaB. This model describes the YbaN
protein family, also called PdaB and SpoVIE, of
Gram-positive bacteria. Although ybaN null mutants have
only a mild sporulation defect, ybaN/ytrI double mutants
show drastically reducted sporulation efficiencies. This
synthetic defect suggests the role of this
sigmaE-controlled gene in sporulation had been masked by
functional redundancy. Members of this family are
homologous to a characterized polysaccharide
deacetylase; the exact function this protein family is
unknown [Cellular processes, Sporulation and
germination].
Length = 191
Score = 28.1 bits (63), Expect = 4.2
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 175 YYTRRALAIAKQLGFTSIVWQEVYENWRSESRRMDPDTVV 214
+ + L A+ LG+T + W +W++ D VV
Sbjct: 107 AFNKAVLKAAESLGYTVVHWSVDSRDWKNPGVESIVDRVV 146
>gnl|CDD|183333 PRK11835, PRK11835, hypothetical protein; Provisional.
Length = 114
Score = 27.2 bits (61), Expect = 4.5
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 53 GEACIWGERVDESNVESRIWPRGAAIAE 80
GE C++ R DES R+ G AIAE
Sbjct: 79 GEPCLFVNRQDESAATCRLKNFGVAIAE 106
Score = 27.2 bits (61), Expect = 4.5
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 282 GEACIWGERVDESNVESRIWPRGAAIAE 309
GE C++ R DES R+ G AIAE
Sbjct: 79 GEPCLFVNRQDESAATCRLKNFGVAIAE 106
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 27.9 bits (63), Expect = 5.1
Identities = 30/111 (27%), Positives = 45/111 (40%), Gaps = 27/111 (24%)
Query: 131 VRSVFHDEFLHTGGDEVDFYCWLNDPNIRQFLADRG------WD--GQQ----LQSYYTR 178
++ F +E++ T G VDFY + D WD GQ+ L+ Y R
Sbjct: 20 TQNKFPEEYIPTIG--VDFY-------TKTIEVDGKTVKLQIWDTAGQERFRALRPLYYR 70
Query: 179 RALAIAKQLGFTSIVWQEVYEN---WRSESRRMDPDTVVQVWYGNRNDLLN 226
A L + I ++ +EN W E R + V V GN+ DL +
Sbjct: 71 GAQGFL--LVY-DITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLED 118
>gnl|CDD|237369 PRK13376, pyrB, bifunctional aspartate carbamoyltransferase
catalytic subunit/aspartate carbamoyltransferase
regulatory subunit; Provisional.
Length = 525
Score = 28.6 bits (64), Expect = 5.4
Identities = 18/55 (32%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 134 VFHDEFLHTGGDEVDFYCWLN----DPNIRQFLAD---RGWDGQQLQSYYTRRAL 181
F EFL + V FY L P I FL GW+ Q + Y+ R L
Sbjct: 274 TFRKEFLDKLPEGVKFYHPLPRHKVYPTIPTFLDTLPLNGWETQAINGYWVRIVL 328
>gnl|CDD|206159 pfam13989, YejG, YejG-like protein. The YejG protein family is a
group of functionally uncharacterized proteins related
to E. coli yejG. This family of proteins is found in
bacteria. Proteins in this family are approximately 110
amino acids in length.
Length = 107
Score = 26.9 bits (60), Expect = 7.0
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 53 GEACIWGERVDESNVESRIWPRGAAIAE 80
GE C++ R DES R+ G AIAE
Sbjct: 76 GEPCLFVHREDESAAMCRLKNVGVAIAE 103
Score = 26.9 bits (60), Expect = 7.0
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 282 GEACIWGERVDESNVESRIWPRGAAIAE 309
GE C++ R DES R+ G AIAE
Sbjct: 76 GEPCLFVHREDESAAMCRLKNVGVAIAE 103
>gnl|CDD|236032 PRK07495, PRK07495, 4-aminobutyrate aminotransferase; Provisional.
Length = 425
Score = 28.2 bits (63), Expect = 7.3
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 178 RRALAIAKQLGFTSIVWQEVYEN---WRSESRR 207
RR AI++ +G T+ ++ + EN W E RR
Sbjct: 9 RRNAAISRGVGMTTQIYADRAENAEIWDKEGRR 41
>gnl|CDD|180374 PRK06060, PRK06060, acyl-CoA synthetase; Validated.
Length = 705
Score = 28.1 bits (62), Expect = 8.1
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 65 SNVESRIWPRGAAIAERLWSW 85
VE +W RG AIA+ W+
Sbjct: 336 PGVEGDLWVRGPAIAKGYWNR 356
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 28.2 bits (62), Expect = 8.4
Identities = 25/114 (21%), Positives = 43/114 (37%), Gaps = 16/114 (14%)
Query: 162 LADRGWDGQQLQSYYTRRALAIAKQLGFTS---IVWQEVYENWRSESRRMDPDTV-VQVW 217
LAD G+ +Q+ +L + ++ +V + NW+ E + PD V V+
Sbjct: 363 LADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASLLSNWKREFEKFAPDLRLVLVY 422
Query: 218 YGNRN----------DLLNRITRDGYTA-ITSAGWYLDVLDIRDGYGWQQEWQR 260
+G ++ DLL + IT+ L G + EW R
Sbjct: 423 HGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLK-KIEWDR 475
>gnl|CDD|224839 COG1928, PMT1, Dolichyl-phosphate-mannose--protein O-mannosyl
transferase [Posttranslational modification, protein
turnover, chaperones].
Length = 699
Score = 27.8 bits (62), Expect = 9.5
Identities = 16/102 (15%), Positives = 31/102 (30%), Gaps = 9/102 (8%)
Query: 80 ERLWSWGYGNPNLLCKINITIPDLNTTQEYWGPIDPTKS----SSYDFVRDLFTEVRSVF 135
+L WG+ +LC + +E P F + +++F
Sbjct: 450 LKLPEWGFSQREVLCAKDRDPSTTWNIEENVNDRLPNPEKKVYKKLSFWKKFIELNKAMF 509
Query: 136 H--DEFLHTGGDEVDFYCWLNDPNIRQFLADRGWDGQQLQSY 175
+ + + Y W P + + L GW + Y
Sbjct: 510 SSNNALVPDHDYSSEPYQW---PTLLRGLRFWGWGECIKKVY 548
>gnl|CDD|237846 PRK14876, PRK14876, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 928
Score = 27.9 bits (62), Expect = 9.9
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 10/42 (23%)
Query: 94 CKINITIPDLNTTQEYW--GPI--------DPTKSSSYDFVR 125
C ++++P L EY GPI D TK+ S DF R
Sbjct: 519 CGTDVSVPTLEKETEYQCGGPIRCMGDDCLDLTKTQSTDFAR 560
>gnl|CDD|183494 PRK12390, PRK12390, 1-aminocyclopropane-1-carboxylate deaminase;
Provisional.
Length = 337
Score = 27.3 bits (61), Expect = 9.9
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 173 QSYYTRRALAIAKQLGFTSIVWQEVYENW 201
QS +TR+ A+A LG ++ QE + N+
Sbjct: 77 QSNHTRQVAAVAAHLGMKCVLVQENWVNY 105
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 0.138 0.462
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,176,593
Number of extensions: 1660375
Number of successful extensions: 1620
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1586
Number of HSP's successfully gapped: 64
Length of query: 315
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 218
Effective length of database: 6,635,264
Effective search space: 1446487552
Effective search space used: 1446487552
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: 59 (26.6 bits)