RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16880
(84 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 = 55.0 bits (133), Expect = 1e-10
Identities = 25/90 (27%), Positives = 45/90 (50%), Gaps = 8/90 (8%)
Query: 2 GSIIHTFVHSNNSAVRSISFCSKQHTLISGGDDGSICMWNLNSKLC-------DSAVRSI 54
G + T + V S++F L+S DG+I +W+L++ C ++ V S+
Sbjct: 167 GKCVATL-TGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSV 225
Query: 55 SFCSKQRTLISGGDDGSICMWNLNSKLCDR 84
+F L SG +DG+I +W+L + C +
Sbjct: 226 AFSPDGYLLASGSEDGTIRVWDLRTGECVQ 255
Score = 47.3 bits (113), Expect = 8e-08
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 13 NSAVRSISFCSKQHTLISGGDDGSICMWNLNSKLCDS-------AVRSISFCSKQRTLIS 65
V ++F L +G DG+I +W+L + VR ++ + L S
Sbjct: 9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLAS 68
Query: 66 GGDDGSICMWNLNSKLCDR 84
G D +I +W+L + C R
Sbjct: 69 GSSDKTIRLWDLETGECVR 87
Score = 46.6 bits (111), Expect = 1e-07
Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 8/89 (8%)
Query: 1 DGSIIHTFVHSNNSAVRSISFCSKQHTLISGGDDGSICMWNLNSKLC-------DSAVRS 53
G + T + S V S++F L S D +I +W++ + C V S
Sbjct: 82 TGECVRTL-TGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNS 140
Query: 54 ISFCSKQRTLISGGDDGSICMWNLNSKLC 82
++F + S DG+I +W+L + C
Sbjct: 141 VAFSPDGTFVASSSQDGTIKLWDLRTGKC 169
Score = 46.2 bits (110), Expect = 2e-07
Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 1 DGSIIHTFVHSNNSAVRSISFCSKQHTLISGGDDGSICMWNLNSKLC-------DSAVRS 53
G + T + + V S++F + L SG +DG+I +W+L + C ++V S
Sbjct: 208 TGKCLGTL-RGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTS 266
Query: 54 ISFCSKQRTLISGGDDGSICMWN 76
+++ + L SG DG+I +W+
Sbjct: 267 LAWSPDGKRLASGSADGTIRIWD 289
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 31.6 bits (72), Expect = 0.005
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 2 GSIIHTFVHSNNSAVRSISFCSKQHTLISGGDDGSICMWN 41
G ++ T + V S++F + L SG DDG++ +W+
Sbjct: 1 GKLLRTL-KGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 30.8 bits (70), Expect = 0.010
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 48 DSAVRSISFCSKQRTLISGGDDGSICMWN 76
V S++F L SG DDG++ +W+
Sbjct: 11 TGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>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 = 31.5 bits (72), Expect = 0.006
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 1 DGSIIHTFVHSNNSAVRSISFCSKQHTLISGGDDGSICMWN 41
G ++ T + V S++F L SG DDG+I +W+
Sbjct: 1 SGELLKTL-KGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 29.6 bits (67), Expect = 0.024
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 48 DSAVRSISFCSKQRTLISGGDDGSICMWN 76
V S++F + L SG DDG+I +W+
Sbjct: 12 TGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 32.4 bits (72), Expect = 0.014
Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 11 SNNSAVRSISFCSKQHTLISGGDDGSICMWNLNSKLC--------DSAVRSISFCSKQRT 62
S +S SF L SG DG+I +W+L S S+V S++F +
Sbjct: 239 SGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKL 298
Query: 63 LISGGDDGSICMWNLNSKLC 82
L SG DG++ +W+L +
Sbjct: 299 LASGSSDGTVRLWDLETGKL 318
Score = 31.6 bits (70), Expect = 0.029
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 7/87 (8%)
Query: 3 SIIHTFVHSNNSAVRSISFCSKQHTLISGGDDGSICMWNLNSKLCD-------SAVRSIS 55
+ +S V S+SF + SG DG++ +W+L++ S V S+
Sbjct: 360 TGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLD 419
Query: 56 FCSKQRTLISGGDDGSICMWNLNSKLC 82
F ++L SG D +I +W+L + L
Sbjct: 420 FSPDGKSLASGSSDNTIRLWDLKTSLK 446
Score = 30.8 bits (68), Expect = 0.055
Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 10/94 (10%)
Query: 1 DGSIIHTFVHSNNSAVRSISFCSKQHTLISGGDDGSICMWNLNSKLC---------DSAV 51
S + + ++S+V S++F L SG DG++ +W+L + + V
Sbjct: 272 SSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPV 331
Query: 52 RSISFC-SKQRTLISGGDDGSICMWNLNSKLCDR 84
S+SF + G DDG+I +W+L + +
Sbjct: 332 SSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLK 365
Score = 28.5 bits (62), Expect = 0.33
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 11 SNNSAVRSISFCSKQHTLISGG-DDGSICMWNLNSKLCD------SAVRSISFCSKQRTL 63
+ V S+SF L+SGG DDG+I +W+L + S V S+SF R +
Sbjct: 326 GHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVV 385
Query: 64 ISGGDDGSICMWNLNSKLCDR 84
SG DG++ +W+L++ R
Sbjct: 386 SSGSTDGTVRLWDLSTGSLLR 406
Score = 27.0 bits (58), Expect = 1.1
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 10 HSNNSAVRSISFCSK-QHTLISGGDDGSICMWNLNSKLCDSAVRS-------ISFCSKQR 61
+ V S++F + SG DG+I +W+L++ + S SF
Sbjct: 195 AGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGS 254
Query: 62 TLISGGDDGSICMWNLNSK 80
L SG DG+I +W+L S
Sbjct: 255 LLASGSSDGTIRLWDLRSS 273
Score = 25.4 bits (54), Expect = 4.0
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 12/88 (13%)
Query: 4 IIHTFVHSNNSAVRSISFCSKQHTLI---SGGDDGSICMWNLNSKLC--------DSAVR 52
+I + ++S+V ++ S I S DG++ +W+L++ +V
Sbjct: 100 LIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVT 159
Query: 53 SISFCSKQRTLISGGD-DGSICMWNLNS 79
S++F + L SG DG+I +W+L +
Sbjct: 160 SLAFSPDGKLLASGSSLDGTIKLWDLRT 187
Score = 25.0 bits (53), Expect = 5.1
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 12 NNSAVRSISFCSKQHTLISGGD-DGSICMWNLNSKLC-------DSAVRSISFCSK-QRT 62
++ +V S++F L SG DG+I +W+L + V S++F
Sbjct: 154 HSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLL 213
Query: 63 LISGGDDGSICMWNLNSKLC 82
+ SG DG+I +W+L++
Sbjct: 214 IASGSSDGTIRLWDLSTGKL 233
Score = 24.7 bits (52), Expect = 8.8
Identities = 12/47 (25%), Positives = 22/47 (46%)
Query: 5 IHTFVHSNNSAVRSISFCSKQHTLISGGDDGSICMWNLNSKLCDSAV 51
+ + + S V S+ F +L SG D +I +W+L + L +
Sbjct: 404 LLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSF 450
Score = 24.3 bits (51), Expect = 9.6
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 12/85 (14%)
Query: 11 SNNSAVRSISFCSKQHTLISGGDDGSICMWNLNSK---------LCDSAVRSISFCSKQR 61
+ ++ SI+F L+SG DG+I +W+L++ L DS+V ++ S
Sbjct: 63 GHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDG 122
Query: 62 TLI---SGGDDGSICMWNLNSKLCD 83
I S DG++ +W+L++
Sbjct: 123 NSILLASSSLDGTVKLWDLSTPGKL 147
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 32.3 bits (74), Expect = 0.015
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 18/70 (25%)
Query: 13 NSAVRSISFCSKQHTLISGGDDGSICMWNLNS---------KLCDSAVRSISFCSKQ--- 60
N+ + + + + L++GG D + + +L KL D+ +IS +K
Sbjct: 311 NAKALAAALEKRGYDLVTGGTDNHLVLVDLRPFGITGSKMEKLLDAV--NIS-VNKNTIP 367
Query: 61 ---RTLISGG 67
L G
Sbjct: 368 GDKSALNPSG 377
Score = 24.6 bits (54), Expect = 8.8
Identities = 5/26 (19%), Positives = 12/26 (46%)
Query: 55 SFCSKQRTLISGGDDGSICMWNLNSK 80
+ + L++GG D + + +L
Sbjct: 318 ALEKRGYDLVTGGTDNHLVLVDLRPF 343
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 26.2 bits (57), Expect = 2.6
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 16 VRSISFCSKQHTLI-SGGDDGSICMWNLNSKLCDSAVRS-ISFCSKQ------RTLISGG 67
V SI + S TL+ SG DDGS+ +W++N + +++ + C Q R+L G
Sbjct: 578 VWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAFGS 637
Query: 68 DDGSICMWNL-NSKL 81
D + ++L N KL
Sbjct: 638 ADHKVYYYDLRNPKL 652
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 25.7 bits (57), Expect = 3.3
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 23 SKQHTLISGGDDGSICMWNLNS---------KLCDSA 50
SK + L++GG D + +W+L K+ D A
Sbjct: 332 SKGYKLVTGGTDNHLVLWDLRPLGLTGSRVEKVLDLA 368
>gnl|CDD|221494 pfam12257, DUF3608, Protein of unknown function (DUF3608). This
domain family is found in eukaryotes, and is
approximately 280 amino acids in length. The family is
found in association with pfam00610.
Length = 281
Score = 25.1 bits (55), Expect = 4.8
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 39 MWNLNSKLCDSAV---RSISFCSKQRTLISG 66
MWN +S L D+ V + ++F +R + G
Sbjct: 15 MWNFSSTLVDTCVFTDQRLTFLDSRRGTVKG 45
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 24.6 bits (53), Expect = 8.4
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 51 VRSISFCSKQRTLISGGDDGSICMWNLN 78
+ SISF S + TL+S DD I +WNL
Sbjct: 175 INSISFNSDKETLLS-ADDLRINLWNLE 201
Score = 24.6 bits (53), Expect = 9.1
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 16 VRSISFCSKQHTLISGGDDGSICMWNLN 43
+ SISF S + TL+S DD I +WNL
Sbjct: 175 INSISFNSDKETLLS-ADDLRINLWNLE 201
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
0.321 0.132 0.425
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: 3,704,890
Number of extensions: 257117
Number of successful extensions: 200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 184
Number of HSP's successfully gapped: 28
Length of query: 84
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 32
Effective length of database: 8,631,194
Effective search space: 276198208
Effective search space used: 276198208
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: 53 (24.2 bits)