RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11529
(244 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 66.2 bits (162), Expect = 8e-13
Identities = 39/190 (20%), Positives = 71/190 (37%), Gaps = 29/190 (15%)
Query: 47 QLDVLDGHDLKVTGIDWAPNTNRIVTCSADRNAYVWTQNNDDKKWKPTLVLLRINRAATC 106
L L GH V + ++P+ + + S D +W D + K L
Sbjct: 127 CLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLW----DLRTGKCVATLTGHTGEVNS 182
Query: 107 VKWSPLENKFAAGSGARLISVCYFESENDWWVAKHIKKPIKSTITCLDWHPNNHLLGCGS 166
V +SP K + S I + ++ + ++ + + + P+ +LL GS
Sbjct: 183 VAFSPDGEKLLSSSSDGTIKL--WDLSTGKCLGTLRGH--ENGVNSVAFSPDGYLLASGS 238
Query: 167 TDFKVRVFSAYIKDIESAPQSTNWGSKSTLGNCLVELNNSSSGGGWIHSVAFSKDGNKLC 226
D +RV+ + + + L NS + S+A+S DG +L
Sbjct: 239 EDGTIRVW--------------DLRTGECVQ-TLSGHTNS------VTSLAWSPDGKRLA 277
Query: 227 WTSHDGSINV 236
S DG+I +
Sbjct: 278 SGSADGTIRI 287
Score = 65.8 bits (161), Expect = 1e-12
Identities = 45/219 (20%), Positives = 76/219 (34%), Gaps = 51/219 (23%)
Query: 50 VLDGHDLKVTGIDWAPNTNRIVTCSADRNAYVWTQNNDDKKWKPTLVLLRINRAATCVKW 109
L GH VT + ++P+ + T S D VW + TL V
Sbjct: 4 TLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGEL--LRTLKGHTG--PVRDVAA 59
Query: 110 SPLENKFAAGSGARLISVCYFESENDWWVAKHIKKPI------KSTITCLDWHPNNHLLG 163
S A+GS + I + W + + + S ++ + + P+ +L
Sbjct: 60 SADGTYLASGSSDKTIRL--------WDLET--GECVRTLTGHTSYVSSVAFSPDGRILS 109
Query: 164 CGSTDFKVRVFSAYIKDIESAPQSTNWGSKSTLGNCLV--------------------EL 203
S D ++V+ D+E+ T + N + +L
Sbjct: 110 SSSRDKTIKVW-----DVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164
Query: 204 NNSSSGG------GWIHSVAFSKDGNKLCWTSHDGSINV 236
G ++SVAFS DG KL +S DG+I +
Sbjct: 165 RTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKL 203
Score = 55.8 bits (135), Expect = 3e-09
Identities = 29/130 (22%), Positives = 51/130 (39%), Gaps = 16/130 (12%)
Query: 50 VLDGHDLKVTGIDWAPNTNRIVTCSADRNAYVWTQNNDDKKWKPTLVLLRINRAATCVKW 109
L GH +V + ++P+ ++++ S+D +W D K L V +
Sbjct: 172 TLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLW----DLSTGKCLGTLRGHENGVNSVAF 227
Query: 110 SPLENKFAAGSGARLISVCYFESENDW-WVAKHIKKPIK---STITCLDWHPNNHLLGCG 165
SP A+GS I V W + + +++T L W P+ L G
Sbjct: 228 SPDGYLLASGSEDGTIRV--------WDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASG 279
Query: 166 STDFKVRVFS 175
S D +R++
Sbjct: 280 SADGTIRIWD 289
Score = 49.6 bits (119), Expect = 3e-07
Identities = 42/196 (21%), Positives = 71/196 (36%), Gaps = 43/196 (21%)
Query: 48 LDVLDGHDLKVTGIDWAPNTNRIVTCSADRNAYVWTQNNDDKKWKPTLVLLRINRAATCV 107
+ L GH V+ + ++P+ + + S D+ VW D + K L V
Sbjct: 86 VRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVW----DVETGKCLTTLRGHTDWVNSV 141
Query: 108 KWSPLENKFAAGSGA-RLISVCYFESENDWWVAKHIKKPIK------STITCLDWHPNNH 160
+SP + F A S I + + K + + + + P+
Sbjct: 142 AFSP-DGTFVASSSQDGTIKLWDLRTG----------KCVATLTGHTGEVNSVAFSPDGE 190
Query: 161 LLGCGSTDFKVRVFSAYIKDIESAPQSTNWGSKSTLGNCLVELNNSSSGGGWIHSVAFSK 220
L S+D ++++ D+ + G CL L ++SVAFS
Sbjct: 191 KLLSSSSDGTIKLW-----DLST-------------GKCLGTLRGHE---NGVNSVAFSP 229
Query: 221 DGNKLCWTSHDGSINV 236
DG L S DG+I V
Sbjct: 230 DGYLLASGSEDGTIRV 245
Score = 47.7 bits (114), Expect = 2e-06
Identities = 23/111 (20%), Positives = 47/111 (42%), Gaps = 8/111 (7%)
Query: 10 NPVTTHAWNNTRQQLAFTPNNQEVHLYQYEKAANDWSQLDVLDGHDLKVTGIDWAPNTNR 69
V + A++ ++L + ++ + L+ + L L GH+ V + ++P+
Sbjct: 178 GEVNSVAFSPDGEKLLSSSSDGTIKLWDL----STGKCLGTLRGHENGVNSVAFSPDGYL 233
Query: 70 IVTCSADRNAYVWTQNNDDKKWKPTLVLLRINRAATCVKWSPLENKFAAGS 120
+ + S D VW D + + L + T + WSP + A+GS
Sbjct: 234 LASGSEDGTIRVW----DLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGS 280
Score = 38.1 bits (89), Expect = 0.002
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 10 NPVTTHAWNNTRQQLAFTPNNQEVHLYQYEKAANDWSQLDVLDGHDLKVTGIDWAPNTNR 69
N V + A++ LA + + ++ + L GH VT + W+P+ R
Sbjct: 220 NGVNSVAFSPDGYLLASGSEDGTIRVWDLRT----GECVQTLSGHTNSVTSLAWSPDGKR 275
Query: 70 IVTCSADRNAYVW 82
+ + SAD +W
Sbjct: 276 LASGSADGTIRIW 288
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 55.9 bits (133), Expect = 4e-09
Identities = 41/196 (20%), Positives = 76/196 (38%), Gaps = 28/196 (14%)
Query: 43 NDWSQLDVLDGHDLKVTGIDWAPNTNRIVTCS-ADRNAYVWTQNNDDKKWKPTLVLLRIN 101
+ L+GH VT + ++P+ + + S D +W D + KP L
Sbjct: 143 TPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLW----DLRTGKPLSTLAGHT 198
Query: 102 RAATCVKWSPLENKFAAGSGARLISVCYFESENDWWVAKHIKKPIKSTITCLDWHPNNHL 161
+ + +SP A SG+ ++ ++ + + S ++ + P+ L
Sbjct: 199 DPVSSLAFSPDGGLLIA-SGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSS--FSPDGSL 255
Query: 162 LGCGSTDFKVRVFSAYIKDIESAPQSTNWGSKSTLGNCLVELNNSSSGGGWIHSVAFSKD 221
L GS+D +R++ + + L L+ SS + SVAFS D
Sbjct: 256 LASGSSDGTIRLWDL-----------------RSSSSLLRTLSGHSS---SVLSVAFSPD 295
Query: 222 GNKLCWTSHDGSINVR 237
G L S DG++ +
Sbjct: 296 GKLLASGSSDGTVRLW 311
Score = 55.9 bits (133), Expect = 5e-09
Identities = 38/222 (17%), Positives = 76/222 (34%), Gaps = 30/222 (13%)
Query: 15 HAWNNTRQQLAFTPNNQEVHLYQYEKAANDWSQLDVLDGHDLKVTGIDWAPNTNRIVTCS 74
+++ LA ++ + L+ + S L L GH V + ++P+ + + S
Sbjct: 247 SSFSPDGSLLASGSSDGTIRLW---DLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGS 303
Query: 75 ADRNAYVWTQNNDDKKWKPTLVLLRINRAATCVKWSPLENKFAAGSGARLISVCYFESEN 134
+D +W + + K +L L + + +SP + +G +
Sbjct: 304 SDGTVRLW--DLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTG 361
Query: 135 DWWVAKHIKKPIKSTITCLDWHPNNHLLGCGSTDFKVRVFSAYIKDIESAPQSTNWGSKS 194
S + + + P+ ++ GSTD VR++
Sbjct: 362 KPLK----TLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDL------------------ 399
Query: 195 TLGNCLVELNNSSSGGGWIHSVAFSKDGNKLCWTSHDGSINV 236
+ L N + S+ FS DG L S D +I +
Sbjct: 400 ---STGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRL 438
Score = 50.9 bits (120), Expect = 2e-07
Identities = 38/185 (20%), Positives = 70/185 (37%), Gaps = 13/185 (7%)
Query: 51 LDGHDLKVTGIDWAPNTNRIVTCSADRNAYVWTQNNDDKKWKPTLVLLRINRAATCVKWS 110
L GH+ +T I ++P+ +++ S+D +W +N +K K +L L + + S
Sbjct: 61 LRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIK-SLEGLHDSSVSKLALSS 119
Query: 111 PLENKFAAGSGARLISVCYFESENDWWVAKHIKKPIKSTITCLDWHPNN-HLLGCGSTDF 169
P N S + +V ++ + + ++ ++T L + P+ L S D
Sbjct: 120 PDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGH-SESVTSLAFSPDGKLLASGSSLDG 178
Query: 170 KVRVFSAYIKDIESAPQSTNWGSKSTLGNCLVELNNSSSGGGWIHSVAFSKDGNKLCWTS 229
++++ S S L S GG I S S DG W
Sbjct: 179 TIKLWDLRTGKPLSTLAGHTDPVSS--------LAFSPDGGLLIASG--SSDGTIRLWDL 228
Query: 230 HDGSI 234
G +
Sbjct: 229 STGKL 233
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 40.4 bits (95), Expect = 2e-05
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 45 WSQLDVLDGHDLKVTGIDWAPNTNRIVTCSADRNAYVW 82
L L GH VT + ++P+ N + + S D VW
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 34.3 bits (79), Expect = 0.003
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 147 KSTITCLDWHPNNHLLGCGSTDFKVRVFS 175
+T + + P+ +LL GS D VRV+
Sbjct: 11 TGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 29.6 bits (67), Expect = 0.15
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 211 GWIHSVAFSKDGNKLCWTSHDGSINV 236
G + SVAFS DGN L S DG++ V
Sbjct: 12 GPVTSVAFSPDGNLLASGSDDGTVRV 37
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 40.0 bits (94), Expect = 3e-05
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 44 DWSQLDVLDGHDLKVTGIDWAPNTNRIVTCSADRNAYVW 82
L L GH VT + ++P+ + + S D +W
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 33.1 bits (76), Expect = 0.008
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 147 KSTITCLDWHPNNHLLGCGSTDFKVRVFS 175
+T + + P+ L GS D ++++
Sbjct: 12 TGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 29.6 bits (67), Expect = 0.13
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 211 GWIHSVAFSKDGNKLCWTSHDGSINV 236
G + SVAFS DG L S DG+I +
Sbjct: 13 GPVTSVAFSPDGKYLASGSDDGTIKL 38
>gnl|CDD|204739 pfam11768, DUF3312, Protein of unknown function (DUF3312). This is
a eukaryotic family of uncharacterized proteins. This
family shows similarity to WD40 repeat proteins.
Length = 544
Score = 35.5 bits (82), Expect = 0.020
Identities = 29/127 (22%), Positives = 49/127 (38%), Gaps = 35/127 (27%)
Query: 24 LAFTPNNQEVHLYQYEKAANDWSQLDVLDGHDLKVTGIDWAPNTNRIV----TCSADRN- 78
L+F NQ + Q +K +L+ L D K++ + T R + ++ ++
Sbjct: 100 LSFLNENQ-LTFVQLQKPTARNRRLEKLSLMDPKISYVIIPGPTGRKLDRHLAVNSSQDL 158
Query: 79 AYVWTQ--NNDDKKWKPT--------LVLLRINRAATCVKWSPLENKFAAGSGARLISVC 128
VW N+ W+PT L +L+I SGA+L +C
Sbjct: 159 VVVWWPSSQNEVYPWRPTVGDQDRANLHVLKI-------------------SGAKLEVLC 199
Query: 129 YFESEND 135
Y +E D
Sbjct: 200 YCWTEGD 206
>gnl|CDD|203719 pfam07676, PD40, WD40-like Beta Propeller Repeat. This family
appears to be related to the pfam00400 repeat This This
repeat corresponds to the RIVW repeat identified in cell
surface proteins [Adindla et al. Comparative and
Functional Genomics 2004; 5:2-16].
Length = 37
Score = 26.3 bits (59), Expect = 1.9
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 208 SGGGWIHSVAFSKDGNKLCWTS-HDGSINV 236
+ G ++S DG +L +TS GS ++
Sbjct: 6 NTPGNEGEPSWSPDGKRLAFTSDRGGSPDI 35
>gnl|CDD|236902 PRK11372, PRK11372, lysozyme inhibitor; Provisional.
Length = 109
Score = 27.9 bits (62), Expect = 2.1
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 11 PVTTHAWNNTRQQLAFTPNNQEVHLYQ 37
P+T NN RQ+++F +NQ +HL Q
Sbjct: 41 PLTVKL-NNPRQEVSFVYDNQLLHLKQ 66
>gnl|CDD|197362 cd09804, Dcp1, mRNA decapping enzyme 1 (Dcp1). mRNA decapping
enzyme 1 (Dcp1), together with Dcp2, is part of the
decapping complex which catalyzes the removal of the 5'
cap structure of mRNA. This decapping reaction is an
essential step in mRNA degradation, by exposing the 5'
end for exonucleolytic digestion. Dcp1 binds to the
N-terminal helical domain of catalytic subunit Dcp2 and
enhances its function by promoting Dsp2's closed
conformation which is catalytically more active.
Length = 121
Score = 26.7 bits (60), Expect = 6.2
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 33 VHLYQYEKAANDWSQLDV 50
V +Y+++ N+W + DV
Sbjct: 28 VAVYEFDDDTNEWEKTDV 45
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 27.6 bits (61), Expect = 6.3
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 50 VLDGHDLKVTGIDWAPNTNRIVTCSADRNAYV--WTQNNDDKKWK 92
+L GH K++ IDW P N + CS+ +++V W N+ + ++
Sbjct: 120 ILKGHKKKISIIDWNP-MNYYIMCSSGFDSFVNIWDIENEKRAFQ 163
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
0.317 0.130 0.429
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,898,234
Number of extensions: 1035118
Number of successful extensions: 783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 749
Number of HSP's successfully gapped: 25
Length of query: 244
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 150
Effective length of database: 6,768,326
Effective search space: 1015248900
Effective search space used: 1015248900
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: 58 (26.1 bits)