RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14258
(440 letters)
>gnl|CDD|214531 smart00135, LY, Low-density lipoprotein-receptor YWTD domain. Type
"B" repeats in low-density lipoprotein (LDL) receptor
that plays a central role in mammalian cholesterol
metabolism. Also present in a variety of molecules
similar to gp300/megalin.
Length = 43
Score = 51.1 bits (123), Expect = 7e-09
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 391 EVVIDTGIYNVEGMAVDWMANNLYWTDAGIGTINVAKIS 429
++ +G+ + G+AVDW+ LYWTD G+ I VA +
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLD 39
Score = 45.7 bits (109), Expect = 6e-07
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 212 VTHKIVYPYGVTVDFPTKHVYWVDTYLDFIDRINYDGTDR 251
++ + +P G+ VD+ +YW D LD I+ N DGT+R
Sbjct: 4 LSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 41.0 bits (97), Expect = 2e-05
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 98 IDLNLSKPRGIALDPTSGYMFFTKWGATRPMLERSLLDGTER 139
+ L P G+A+D G +++T WG ++E + LDGT R
Sbjct: 4 LSSGLGHPNGLAVDWIEGRLYWTDWG--LDVIEVANLDGTNR 43
Score = 41.0 bits (97), Expect = 2e-05
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 167 IDLNLSKPRGIALDPTSGYMFFTKWGATRPMLERSLLDGTER 208
+ L P G+A+D G +++T WG ++E + LDGT R
Sbjct: 4 LSSGLGHPNGLAVDWIEGRLYWTDWG--LDVIEVANLDGTNR 43
Score = 28.0 bits (63), Expect = 0.95
Identities = 8/37 (21%), Positives = 15/37 (40%)
Query: 353 TDLKRPSVIDYHEKEEYIYYAELTSYVIERRKMFGRG 389
+ L P+ + E +Y+ + VIE + G
Sbjct: 6 SGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTN 42
>gnl|CDD|215683 pfam00058, Ldl_recept_b, Low-density lipoprotein receptor repeat
class B. This domain is also known as the YWTD motif
after the most conserved region of the repeat. The YWTD
repeat is found in multiple tandem repeats and has been
predicted to form a beta-propeller structure.
Length = 42
Score = 31.0 bits (71), Expect = 0.081
Identities = 10/42 (23%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 184 GYMFFTKWGATRPMLERSLLDGTERFPMVTHKIVYPYGVTVD 225
G +++T R + + L+G++R + + + +P G+ VD
Sbjct: 1 GRLYWTDSS-LRASISVADLNGSDRRTLFSEDLQWPNGIAVD 41
Score = 30.2 bits (69), Expect = 0.16
Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 2/42 (4%)
Query: 271 NNLFVTSWRNQSIIRVNKFNSDDYETIA--NFSRPFAIHIYH 310
L+ T ++ I V N D T+ + P I +
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 29.1 bits (66), Expect = 0.44
Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 25/67 (37%)
Query: 115 GYMFFTKWGATRPMLERSLLDGTERFPMVTHKIVYPEAIYFCTHYMEHCMIAIDLNLSKP 174
G +++T R + + L+G++R + + +L P
Sbjct: 1 GRLYWTDSS-LRASISVADLNGSDRRTLFSE------------------------DLQWP 35
Query: 175 RGIALDP 181
GIA+DP
Sbjct: 36 NGIAVDP 42
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 30.3 bits (69), Expect = 0.12
Identities = 11/25 (44%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 13 DADECLIDGSCDQ--TCTNTHLSYT 35
D DEC C TC NT SY
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYR 25
>gnl|CDD|240466 cd12886, SPRY_like, SPRY domain-like in bacteria. This family
contains SPRY-like domains that are found only in
bacterial and are mostly uncharacterized. SPRY domains,
first identified in the SP1A kinase of Dictyostelium and
rabbit Ryanodine receptor (hence the name), are
homologous to B30.2. SPRY domains have been identified
in at least 11 eukaryotic protein families, covering a
wide range of functions, including regulation of
cytokine signaling (SOCS), RNA metabolism (DDX1 and
hnRNP), immunity to retroviruses (TRIM5alpha),
intracellular calcium release (ryanodine receptors or
RyR) and regulatory and developmental processes (HERC1
and Ash2L).
Length = 128
Score = 32.5 bits (74), Expect = 0.16
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 176 GIALDPTSGYMFFTK---WGATRPML--ERSLLDGTERFPMVTHKIVYPYGVTVDF 226
G+ALD +G ++F K W + GT+ +P VT T +F
Sbjct: 72 GVALDLDAGKIWFYKNGVWQGSGSPAPGTNPAFAGTQVYPAVTGGSSTGGSFTANF 127
>gnl|CDD|238011 cd00054, EGF_CA, Calcium-binding EGF-like domain, present in a
large number of membrane-bound and extracellular
(mostly animal) proteins. Many of these proteins
require calcium for their biological function and
calcium-binding sites have been found to be located at
the N-terminus of particular EGF-like domains;
calcium-binding may be crucial for numerous
protein-protein interactions. Six conserved core
cysteines form three disulfide bridges as in non
calcium-binding EGF domains, whose structures are very
similar. EGF_CA can be found in tandem repeat
arrangements.
Length = 38
Score = 29.5 bits (67), Expect = 0.27
Identities = 11/25 (44%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 13 DADECLIDGSC--DQTCTNTHLSYT 35
D DEC C TC NT SY
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYR 25
>gnl|CDD|225202 COG2320, GrpB, Uncharacterized conserved protein [Function
unknown].
Length = 185
Score = 30.5 bits (69), Expect = 1.1
Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 6/85 (7%)
Query: 257 GFPVQNLYDITVFENNLFVTSWRNQSIIRVNKFNSDDYETIANFSRPFAIHIYHRQKQPD 316
G P + + DI V +L ++ Y + N R ++ ++
Sbjct: 59 GLPAKPIIDILVVVESLDAADELA------EPLSAAGYPHVTNDGRTLRFRLWLKRVHAS 112
Query: 317 ALKPSTFLLYAKGKPAIIKGLTFKR 341
A +P+ + +G P I L F+
Sbjct: 113 AREPTHVHVVTRGSPEIEFALLFRD 137
>gnl|CDD|204232 pfam09406, DUF2004, Protein of unknown function (DUF2004). This is
a family of proteins with unknown function. The
structure of one of the proteins in this family has
revealed a novel alpha-beta fold.
Length = 106
Score = 29.6 bits (67), Expect = 1.1
Identities = 15/73 (20%), Positives = 22/73 (30%), Gaps = 1/73 (1%)
Query: 32 LSYTYTDEGFSFQGVKTHLYETIEAFWEECFGPMDIEEWDEGLSFLTFAQEAIYFCTHYM 91
Y D + + HL E + + E FG +E L L + I+
Sbjct: 11 AEYLKNDFDLVTEYIDFHLDELGKKYLEILFGSSKPTI-EEFLKKLVLVRVDIWPGEEDE 69
Query: 92 EHCMIAIDLNLSK 104
E D L
Sbjct: 70 EEVYATFDFTLDP 82
>gnl|CDD|184086 PRK13493, PRK13493, chemoreceptor glutamine deamidase CheD;
Provisional.
Length = 213
Score = 30.3 bits (68), Expect = 1.5
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 123 GATRPMLERSLLDGTERFPMVTHKIVYPEAIYFCTHYMEH---CMIAIDLNLSKPRGIAL 179
GA R L+ L G M +V + + F Y + ++A DL ++PR +
Sbjct: 113 GAERERLKFKLFGGAHL--MGYQSLVGEKNVEFVLEYAKREKLNVVAQDLGGAQPRKLLF 170
Query: 180 DPTSG 184
DP +G
Sbjct: 171 DPQTG 175
>gnl|CDD|224668 COG1754, COG1754, Uncharacterized C-terminal domain of
topoisomerase IA [General function prediction only].
Length = 298
Score = 29.3 bits (66), Expect = 3.5
Identities = 25/85 (29%), Positives = 34/85 (40%), Gaps = 12/85 (14%)
Query: 104 KPRGIALDPTSGYMFFTKWGATRPMLERSLLDGTE--RFPMVTHKIVYPEAIYFCTHYME 161
PR + +DP +G + K G P ++ L D + + K PE I T
Sbjct: 74 GPRVLGIDPETGEEIYLKNGRYGPYVQEQLGDPKPKPKRASLP-KGWKPETI---TL--- 126
Query: 162 HCMIAIDLNLSKPRGIALDPTSGYM 186
A+ L LS PR I P SG
Sbjct: 127 --EKALKL-LSLPRVIGKHPDSGEE 148
>gnl|CDD|173162 PRK14699, PRK14699, replication factor A; Provisional.
Length = 484
Score = 29.2 bits (65), Expect = 5.7
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 377 SYVIERRKMFGRGKEVVIDTGIYNVEGMAVDWMANNLYWTDAGIGTINVAKIS 429
S+VI + R +E V + G E MA +AN L ++DAG ++ + I+
Sbjct: 12 SHVISKEDFLQRIQEKVENMGGLCDEPMAAMLVANELGFSDAGRDSVKIENIT 64
>gnl|CDD|214992 smart01045, BURP, The BURP domain is found at the C-terminus of
several different plant proteins. It was named after
the proteins in which it was first identified: the BNM2
clone-derived protein from Brassica napus; USPs and
USP-like proteins; RD22 from Arabidopsis thaliana; and
PG1beta from Lycopersicon esculentum. This domain is
around 230 amino acid residues long. It possesses the
following conserved features: two phenylalanine residues
at its N-terminus; two cysteine residues; and four
repeated cysteine-histidine motifs, arranged as:
CH-X(10)-CH-X(25-27)-CH-X(25-26)-CH, where X can be any
amino acid. The function of this domain is unknown.
Length = 222
Score = 28.3 bits (63), Expect = 6.0
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 142 MVTHKIVYPEAIYFCTHYMEHCMIAIDLNLSK-PRGIALDPTSGYMFFTKWGA 193
+ H+ +YP A+Y+C + +DL K R I + P +M + W A
Sbjct: 139 VSCHQSLYPYAVYYCHSVPGVRVYEVDLLDPKGMRKINVGPAVCHMDTSAWDA 191
>gnl|CDD|215445 PLN02831, PLN02831, Bifunctional GTP cyclohydrolase II/
3,4-dihydroxy-2-butanone-4-phosphate synthase.
Length = 450
Score = 28.5 bits (64), Expect = 7.7
Identities = 11/24 (45%), Positives = 11/24 (45%)
Query: 120 TKWGATRPMLERSLLDGTERFPMV 143
TKWG RS LDG E V
Sbjct: 251 TKWGLFTAYCYRSKLDGIEHIAFV 274
Score = 28.5 bits (64), Expect = 7.7
Identities = 11/24 (45%), Positives = 11/24 (45%)
Query: 189 TKWGATRPMLERSLLDGTERFPMV 212
TKWG RS LDG E V
Sbjct: 251 TKWGLFTAYCYRSKLDGIEHIAFV 274
>gnl|CDD|133133 cd06602, GH31_MGAM_SI_GAA, This family includes the following three
closely related glycosyl hydrolase family 31 (GH31)
enzymes: maltase-glucoamylase (MGAM), sucrase-isomaltase
(SI), and lysosomal acid alpha-glucosidase (GAA), also
known as acid-maltase. MGAM is one of the two enzymes
responsible for catalyzing the last glucose-releasing
step in starch digestion. SI is implicated in the
digestion of dietary starch and major disaccharides such
as sucrose and isomaltose, while GAA degrades glycogen
in the lysosome, cleaving both alpha-1,4 and alpha-1,6
glucosidic linkages. MGAM and SI are anchored to
small-intestinal brush-border epithelial cells. The
absence of SI from the brush border membrane or its
malfunction is associated with malabsorption disorders
such as congenital sucrase-isomaltase deficiency (CSID).
The domain architectures of MGAM and SI include two
tandem GH31 catalytic domains, an N-terminal domain
found near the membrane-bound end, and a C-terminal
luminal domain. Both of the tandem GH31 domains of MGAM
and SI are included in this family. The domain
architecture of GAA includes an N-terminal TFF (trefoil
factor family) domain in addition to the GH31 catalytic
domain. Deficient GAA expression causes pompe disease,
an autosomal recessive genetic disorder also known as
glycogen storage disease type II (GSDII).
Length = 339
Score = 28.3 bits (64), Expect = 8.8
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 217 VYPYGVTV--DF--PTKHVYWVDTYLDFIDRINYDG 248
V+P G TV DF P +W D DF D++ +DG
Sbjct: 124 VWP-GYTVFPDFLNPNTQEWWTDEIKDFHDQVPFDG 158
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 0.139 0.441
Gapped
Lambda K H
0.267 0.0593 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,242,680
Number of extensions: 2314987
Number of successful extensions: 1567
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1563
Number of HSP's successfully gapped: 24
Length of query: 440
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 340
Effective length of database: 6,502,202
Effective search space: 2210748680
Effective search space used: 2210748680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 60 (27.2 bits)