RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy110
(358 letters)
>gnl|CDD|214829 smart00812, Alpha_L_fucos, Alpha-L-fucosidase. O-Glycosyl
hydrolases (EC 3.2.1.-) are a widespread group of
enzymes that hydrolyse the glycosidic bond between two
or more carbohydrates, or between a carbohydrate and a
non-carbohydrate moiety. A classification system for
glycosyl hydrolases, based on sequence similarity, has
led to the definition of 85 different families. This
classification is available on the CAZy
(CArbohydrate-Active EnZymes) web site. Because the fold
of proteins is better conserved than their sequences,
some of the families can be grouped in 'clans'. Family
29 encompasses alpha-L-fucosidases, which is a lysosomal
enzyme responsible for hydrolyzing the alpha-1,6-linked
fucose joined to the reducing-end N-acetylglucosamine of
the carbohydrate moieties of glycoproteins. Deficiency
of alpha-L-fucosidase results in the lysosomal storage
disease fucosidosis.
Length = 384
Score = 379 bits (975), Expect = e-131
Identities = 144/257 (56%), Positives = 181/257 (70%), Gaps = 14/257 (5%)
Query: 106 KYVPTWESLDARPLPAWYDEAKVGIFIHWGVFSVPSFRSEWFWKNWENPNSTVTKFMERN 165
Y PTWESLD RPLP W+ +AK GIFIHWGV+SVP F EW+W+ S K +N
Sbjct: 6 PYQPTWESLDKRPLPEWFRDAKFGIFIHWGVYSVPGFGGEWYWRQP---GSPEYKHHIKN 62
Query: 166 YKPGFTYQDFAKDFTAEFFDANHWADILASSGAKYVVLTSKHHEGYTLWPSKYAFSWNSM 225
Y P F Y+DFA FTAE FD WAD+ +GAKYVVLT+KHH+G+ LW SKY+ +WN++
Sbjct: 63 YGPEFGYKDFAPQFTAEKFDPEEWADLFKKAGAKYVVLTTKHHDGFCLWDSKYS-NWNAV 121
Query: 226 DIGPKRDLVGELATAIRRKYSDIHFGLYHSLYEWFNPLYVQ------DKANNFTTNQFVT 279
D GPKRDLVGELA A+R++ + FGLYHSL++WFNPLY D N +FV
Sbjct: 122 DTGPKRDLVGELADAVRKR--GLKFGLYHSLFDWFNPLYAGPTSSDEDSDNWPRFQEFV- 178
Query: 280 MKTLPELIEIVQKYQPEVIWSDGEWEAPAEYWKSREFLAWLYNESPVKNTVVVNDRWCNT 339
LP+L E+V +Y+P+++W DG WEAP +YW+S+EFLAWLYN SPVK+TVVVNDRW
Sbjct: 179 DDWLPQLRELVTRYKPDLLWFDGGWEAPDDYWRSKEFLAWLYNLSPVKDTVVVNDRWGG- 237
Query: 340 CLCKHGGYLTCEDKYNP 356
CKHGG+ T E++ P
Sbjct: 238 TGCKHGGFYTDEERGAP 254
>gnl|CDD|216307 pfam01120, Alpha_L_fucos, Alpha-L-fucosidase.
Length = 320
Score = 288 bits (739), Expect = 4e-96
Identities = 120/251 (47%), Positives = 156/251 (62%), Gaps = 20/251 (7%)
Query: 110 TWESLDARPLPAWYDEAKVGIFIHWGVFSVPSF-RSEWFWKNWENPNSTVTKFMERNYKP 168
TWESLD+RPLP W+ +AK GIFIHWG++SVP+F +EW+ + M + Y P
Sbjct: 1 TWESLDSRPLPEWFRDAKFGIFIHWGLYSVPAFGEAEWYARY--------MYSMFKAYIP 52
Query: 169 GFTYQDFAKDFTAEFFDANHWADILASSGAKYVVLTSKHHEGYTLWPSKYAFSWNSMDIG 228
TY DFAK F E FDA+ WA + +GAKYVVLT+KHH+G+T+W SKY+ WNS+D G
Sbjct: 53 VATYGDFAKQFNPEKFDADEWAKLAKEAGAKYVVLTTKHHDGFTMWDSKYS-DWNSVDTG 111
Query: 229 PKRDLVGELATAIRRKYSDIHFGLYHSLYEWFNPLYVQDKANNF---TTNQFVTMKTLPE 285
PKRD+VGELA A R+ I FG Y+SL +W +P Y DK NQ+V T +
Sbjct: 112 PKRDIVGELAKACRKN--GIKFGFYYSLLDWHHPDYKVDKEGQEDKGLWNQYVKEFTFNQ 169
Query: 286 LIEIVQKYQPEVIWSDGEWEAPAEYWKSREFLAWLYNESPVKNTVVVNDRWCNTCLCKHG 345
L E+V Y+P+++W DG+W+ P+EYW S EF A LY P VVVNDRW G
Sbjct: 170 LKELVTNYKPDILWFDGDWDNPSEYWDSAEFYALLYKLQP---GVVVNDRWGYG--PYGG 224
Query: 346 GYLTCEDKYNP 356
G ++ P
Sbjct: 225 GDYETPERGLP 235
>gnl|CDD|226195 COG3669, COG3669, Alpha-L-fucosidase [Carbohydrate transport and
metabolism].
Length = 430
Score = 126 bits (319), Expect = 5e-33
Identities = 73/216 (33%), Positives = 97/216 (44%), Gaps = 23/216 (10%)
Query: 133 HWGVFSVPSFRSEWFWKNWENPNSTVTKFMERNYKP--GFTYQDFAKDFTAEFFDANHWA 190
HWG+ SVP F SEW+ S F Y F Q+F FTAE +D WA
Sbjct: 1 HWGIKSVPPFPSEWYLAYLYQEGSPFYHFHPNTYGDQEWFGGQEFPPRFTAENWDPREWA 60
Query: 191 DILASSGAKYVVLTSKHHEGYTLWPSKYAFSWNSMDIGPKRDLVGELATAIRRKYSDIHF 250
+ +GAKYV+L +KHH+G+ LWP+ Y+ WNS+ GPKRDLVGELA A+R + + F
Sbjct: 61 RLFKEAGAKYVILVAKHHDGFALWPTDYS-VWNSVKRGPKRDLVGELAKAVREQ--GLRF 117
Query: 251 GLYHSLYE--WF--NPLYVQDKANNFTTNQFVTMKTLPELIEIVQKYQPEVI---WSDGE 303
G+Y S W + Y + + L EL+ W D
Sbjct: 118 GVYLSGAWHPWDFHSGYYADSDEK----DPNYYLAQLQELLSGANYGNAGPFDEVWLDNA 173
Query: 304 WEAPAE---YWKSREFLAWLYNESPVKNTVVVNDRW 336
W YW +R F + P +V D W
Sbjct: 174 WGNGPAKVNYWLARWF-ELIRRYQP---DLVYFDWW 205
>gnl|CDD|191631 pfam06882, DUF1263, Protein of unknown function (DUF1263). This
family represents a conserved region located towards
the C-terminus of a number proteins of unknown function
that seem to be specific to Oryza sativa.
Length = 108
Score = 31.4 bits (71), Expect = 0.18
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 3 PSSVTILFFILSCAQGIYSAVKPVPQPGAPNKVNSTNAKPRDDAFQILQSITANGE 58
PSS +++ GIY A VP PG T A RD+ + L T GE
Sbjct: 49 PSSYNDFLAMVAMKPGIYLAGTDVPTPGVN-----TPAPARDECLEALIIPTGRGE 99
>gnl|CDD|214564 smart00214, VWC, von Willebrand factor (vWF) type C domain.
Length = 59
Score = 28.6 bits (64), Expect = 0.71
Identities = 6/28 (21%), Positives = 9/28 (32%), Gaps = 4/28 (14%)
Query: 330 VVVNDRW----CNTCLCKHGGYLTCEDK 353
+ W C C C G + C+
Sbjct: 8 YNDGETWKPDPCQICTCLDGTTVLCDPV 35
>gnl|CDD|233914 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.
This model describes a protein of type IV pilus
biogenesis designated PilB in Pseudomonas aeruginosa but
PilF in Neisseria gonorrhoeae; the more common usage,
reflected here, is PilB. This protein is an ATPase
involved in protein export for pilin assembly and is
closely related to GspE (TIGR02533) of type II
secretion, also called the main terminal branch of the
general secretion pathway. Note that type IV pilus
systems are often divided into type IV-A and IV-B, with
the latter group including bundle-forming pilus,
mannose-sensitive hemagglutinin, etc. Members of this
family are found in type IV-A systems [Cell envelope,
Surface structures, Protein fate, Protein and peptide
secretion and trafficking].
Length = 564
Score = 29.6 bits (67), Expect = 2.7
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 237 LATAIRRKYSDIHFGLYHSLY 257
L AIR+ SDIHF Y Y
Sbjct: 189 LLDAIRKGASDIHFEPYEKSY 209
>gnl|CDD|219230 pfam06925, MGDG_synth, Monogalactosyldiacylglycerol (MGDG)
synthase. This family represents a conserved region of
approximately 180 residues within plant and bacterial
monogalactosyldiacylglycerol (MGDG) synthase
(EC:2.4.1.46). In Arabidopsis, there are two types of
MGDG synthase which differ in their N-terminal portion:
type A and type B.
Length = 169
Score = 28.9 bits (65), Expect = 2.9
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 5/50 (10%)
Query: 249 HFGLYHSLYEWFNPLYVQDKANNFTTNQFVTMKTLPELIEIVQKYQPEVI 298
H LY LY P K+ F + L +++++QP++I
Sbjct: 49 HSRLYRLLYYGTEPKI-PHKSILAKLATFFARE----LAALLKEFQPDII 93
>gnl|CDD|221154 pfam11640, TAN, Telomere-length maintenance and DNA damage
repair. ATM is a large protein kinase, in humans,
critical for responding to DNA double-strand breaks
(DSBs). Tel1, the orthologue from budding yeast, also
regulates responses to DSBs. Tel1 is important for
maintaining viability and for phosphorylation of the
DNA damage signal transducer kinase Rad53 (an
orthologue of mammalian CHK2). In addition to
functioning in the response to DSBs, numerous findings
indicate that Tel1/ATM regulates telomeres. The overall
domain structure of Tel1/ATM is shared by proteins of
the phosphatidylinositol 3-kinase (PI3K)-related kinase
(PIKK) family, but this family carries a unique and
functionally important TAN sequence motif, near its
N-terminal, LxxxKxxE/DRxxxL. which is conserved
specifically in the Tel1/ATM subclass of the PIKKs. The
TAN motif is essential for both telomere length
maintenance and Tel1 action in response to DNA damage.
It is classified as an EC:2.7.11.1.
Length = 154
Score = 28.1 bits (63), Expect = 4.8
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 33 NKVNSTNAKPRDDAFQILQSITANGEGHQSANVKFLETIKNIESANDILTKLILSEK 89
N ++S K R+DA +L++I + E + N K + + L +LI EK
Sbjct: 11 NLLSSDKIKDRNDALDLLENILKSNEEGKRLNDKQFHKL------FEALFRLIEKEK 61
>gnl|CDD|212103 cd10791, GH38N_AMII_like_1, N-terminal catalytic domain of mainly
uncharacterized eukaryotic proteins similar to
alpha-mannosidases; glycoside hydrolase family 38
(GH38). The subfamily of mainly uncharacterized
eukaryotic proteins shows sequence homology with class
II alpha-mannosidases (AlphaAMIIs). AlphaAMIIs possess
a-1,3, a-1,6, and a-1,2 hydrolytic activity, and
catalyze the degradation of N-linked oligosaccharides.
The N-terminal catalytic domain of alphaMII adopts a
structure consisting of parallel 7-stranded beta/alpha
barrel. This subfamily belongs to the GH38 family of
retaining glycosyl hydrolases, which employ a two-step
mechanism involving the formation of a covalent glycosyl
enzyme complex; two carboxylic acids positioned within
the active site act in concert: one as a catalytic
nucleophile and the other as a general acid/base
catalyst.
Length = 254
Score = 28.4 bits (64), Expect = 5.3
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 190 ADILASSGAKYVVLTSKHHEGYTLWPSKYAFSWNSMD 226
D+LA +G KY+ + H G F W S D
Sbjct: 135 VDVLADAGIKYLSIGVNGHSGPYPPRVPGPFYWESPD 171
>gnl|CDD|232833 TIGR00118, acolac_lg, acetolactate synthase, large subunit,
biosynthetic type. Two groups of proteins form
acetolactate from two molecules of pyruvate. The type of
acetolactate synthase described in this model also
catalyzes the formation of acetohydroxybutyrate from
pyruvate and 2-oxobutyrate, an early step in the
branched chain amino acid biosynthesis; it is therefore
also termed acetohydroxyacid synthase. In bacteria, this
catalytic chain is associated with a smaller regulatory
chain in an alpha2/beta2 heterotetramer. Acetolactate
synthase is a thiamine pyrophosphate enzyme. In this
type, FAD and Mg++ are also found. Several isozymes of
this enzyme are found in E. coli K12, one of which
contains a frameshift in the large subunit gene and is
not expressed [Amino acid biosynthesis, Pyruvate
family].
Length = 558
Score = 28.5 bits (64), Expect = 6.9
Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 3/56 (5%)
Query: 281 KTLPELIEIVQKYQPEVIWSDGEWEAPAEYWKSREFLAWLYNESPVKNTVVVNDRW 336
L EL++ + + + + W WK L Y E +K V+ +
Sbjct: 321 NVLEELLKKLFELKER---KESAWLEQINKWKKEYPLKMDYTEEGIKPQQVIEELS 373
>gnl|CDD|238538 cd01118, ArsB_permease, Anion permease ArsB. These permeases have
been shown to export arsenate and antimonite in
eubacteria and archaea. A typical ArsB permease
contains 8-13 transmembrane helices and can function
either independently as a chemiosmotic transporter or as
a channel-forming subunit of an ATP-driven anion pump
(ArsAB). The ArsAB complex is similar in many ways to
ATP-binding cassette transporters, which have two groups
of six transmembrane-spanning helical segments and two
nucleotide-binding domains. The ArsB proteins belong to
the ArsB/NhaD superfamily of permeases that translocate
sodium, arsenate, sulfate, and organic anions across
biological membranes in all three kingdoms of life.
Length = 416
Score = 28.0 bits (63), Expect = 7.6
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 226 DIGPKRDLVGELAT-----AIRRKYSDIHFGLY 253
D+GPK +G LAT +RRK + +G Y
Sbjct: 364 DLGPKLTPIGSLATLLWLHVLRRKGIRVSWGYY 396
>gnl|CDD|214575 smart00234, START, in StAR and phosphatidylcholine transfer
protein. putative lipid-binding domain in StAR and
phosphatidylcholine transfer protein.
Length = 205
Score = 27.4 bits (61), Expect = 9.0
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 8/53 (15%)
Query: 64 NVKFLETIKNIESANDILTKLILSEKGLDMPASAPLAVPRDFKYVPTWESLDA 116
NV ET++ I++ I + A PRDF +V W +
Sbjct: 76 NVAKAETLEVIDNGTVIYHYV------SKFAAG--PVSPRDFVFVRYWREDED 120
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.134 0.436
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,280,980
Number of extensions: 1699209
Number of successful extensions: 1554
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1539
Number of HSP's successfully gapped: 19
Length of query: 358
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 260
Effective length of database: 6,590,910
Effective search space: 1713636600
Effective search space used: 1713636600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.9 bits)