RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11100
(110 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 = 46.6 bits (111), Expect = 3e-07
Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 14/81 (17%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMNQSLQGHSGKVRAI 76
VN +A+ + + DG +K+ L TGK +L+GH V ++
Sbjct: 180 VNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCL--------------GTLRGHENGVNSV 225
Query: 77 IWNEQYEKLTSSDETGLIIVW 97
++ L S E G I VW
Sbjct: 226 AFSPDGYLLASGSEDGTIRVW 246
Score = 45.4 bits (108), Expect = 7e-07
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 14/82 (17%)
Query: 16 KVNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMNQSLQGHSGKVRA 75
V C+A+ + +A G DG +KV L+TG+ +L+GH+G VR
Sbjct: 11 GVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLR--------------TLKGHTGPVRD 56
Query: 76 IIWNEQYEKLTSSDETGLIIVW 97
+ + L S I +W
Sbjct: 57 VAASADGTYLASGSSDKTIRLW 78
Score = 45.4 bits (108), Expect = 7e-07
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMNQSLQGHSGKVRAI 76
VN +A+ + +A G +DG ++V L TG+ Q+L GH+ V ++
Sbjct: 222 VNSVAFSPDGYLLASGSEDGTIRVWDLRTGECV--------------QTLSGHTNSVTSL 267
Query: 77 IWNEQYEKLTSSDETGLIIVW 97
W+ ++L S G I +W
Sbjct: 268 AWSPDGKRLASGSADGTIRIW 288
Score = 41.6 bits (98), Expect = 1e-05
Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 14/81 (17%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMNQSLQGHSGKVRAI 76
V+ +A+ + ++ D +KV ++TGK +L+GH+ V ++
Sbjct: 96 VSSVAFSPDGRILSSSSRDKTIKVWDVETGKCL--------------TTLRGHTDWVNSV 141
Query: 77 IWNEQYEKLTSSDETGLIIVW 97
++ + SS + G I +W
Sbjct: 142 AFSPDGTFVASSSQDGTIKLW 162
Score = 40.8 bits (96), Expect = 4e-05
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 14/81 (17%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMNQSLQGHSGKVRAI 76
VN +A+ + ++A DG +K+ L TGK +L GH+G+V ++
Sbjct: 138 VNSVAFSPDGTFVASSSQDGTIKLWDLRTGKC--------------VATLTGHTGEVNSV 183
Query: 77 IWNEQYEKLTSSDETGLIIVW 97
++ EKL SS G I +W
Sbjct: 184 AFSPDGEKLLSSSSDGTIKLW 204
Score = 35.8 bits (83), Expect = 0.002
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 14/81 (17%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMNQSLQGHSGKVRAI 76
V +A + ++A G D +++ L+TG+ ++L GH+ V ++
Sbjct: 54 VRDVAASADGTYLASGSSDKTIRLWDLETGECV--------------RTLTGHTSYVSSV 99
Query: 77 IWNEQYEKLTSSDETGLIIVW 97
++ L+SS I VW
Sbjct: 100 AFSPDGRILSSSSRDKTIKVW 120
Score = 31.2 bits (71), Expect = 0.077
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 64 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 97
++L+GH+G V + ++ + L + G I VW
Sbjct: 3 RTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVW 36
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 38.5 bits (88), Expect = 2e-04
Identities = 14/91 (15%), Positives = 35/91 (38%), Gaps = 13/91 (14%)
Query: 7 KKIAIPNNTKVNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMNQSL 66
+ + ++ ++ + +A G DG +++ L + ++L
Sbjct: 234 LRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLL-------------RTL 280
Query: 67 QGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 97
GHS V ++ ++ + L S G + +W
Sbjct: 281 SGHSSSVLSVAFSPDGKLLASGSSDGTVRLW 311
Score = 34.3 bits (77), Expect = 0.007
Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 13/91 (14%)
Query: 8 KIAIPNNTKVNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMNQSLQ 67
+ +++ V +A+ + +A G DG +++ L+TGK + +L+
Sbjct: 278 RTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLL------------SSLTLK 325
Query: 68 GHSGKVRAIIWNEQYEKLTSSDET-GLIIVW 97
GH G V ++ ++ L S G I +W
Sbjct: 326 GHEGPVSSLSFSPDGSLLVSGGSDDGTIRLW 356
Score = 31.6 bits (70), Expect = 0.062
Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 16/89 (17%)
Query: 11 IPNNTKVNCLAWHQNQGWIAVGGD-DGLLKVLKLDTGKESTGQVAAANVNLAMNQSLQGH 69
++ V LA+ + +A G DG +K+ L TGK +L GH
Sbjct: 152 EGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKP--------------LSTLAGH 197
Query: 70 SGKVRAIIWN-EQYEKLTSSDETGLIIVW 97
+ V ++ ++ + + S G I +W
Sbjct: 198 TDPVSSLAFSPDGGLLIASGSSDGTIRLW 226
Score = 29.7 bits (65), Expect = 0.31
Identities = 17/97 (17%), Positives = 33/97 (34%), Gaps = 15/97 (15%)
Query: 4 YLSKKIAIPNNTKVNCLAWHQNQGWIAVGGDDGLLKVLKLDTGKESTGQVAAANVNLAMN 63
LS + + + +A+ + + G DG +K+ LD G++ +
Sbjct: 55 DLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSL---------- 104
Query: 64 QSLQGHSGKVRAIIW---NEQYEKLTSSDETGLIIVW 97
H V + + L SS G + +W
Sbjct: 105 --EGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLW 139
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 34.3 bits (79), Expect = 8e-04
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKV 40
V +A+ + +A G DDG ++V
Sbjct: 14 VTSVAFSPDGNLLASGSDDGTVRV 37
Score = 29.2 bits (66), Expect = 0.072
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 64 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 97
++L+GH+G V ++ ++ L S + G + VW
Sbjct: 5 RTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
>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 = 32.7 bits (75), Expect = 0.003
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKV 40
V +A+ + ++A G DDG +K+
Sbjct: 15 VTSVAFSPDGKYLASGSDDGTIKL 38
Score = 30.4 bits (69), Expect = 0.021
Identities = 10/34 (29%), Positives = 21/34 (61%)
Query: 64 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 97
++L+GH+G V ++ ++ + L S + G I +W
Sbjct: 6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
>gnl|CDD|184420 PRK13960, PRK13960,
phosphoribosylaminoimidazole-succinocarboxamide
synthase; Provisional.
Length = 367
Score = 30.8 bits (70), Expect = 0.11
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 52 QVAAANVNLAMNQSLQGHSGKVRAIIWNEQYEKLTSSDETGLI 94
+V A N +L + HSGKVR++ W LT D LI
Sbjct: 6 KVLAVNDDLPIRTDKPVHSGKVRSVYW------LTEEDSRRLI 42
>gnl|CDD|180915 PRK07275, PRK07275, single-stranded DNA-binding protein;
Provisional.
Length = 162
Score = 28.7 bits (64), Expect = 0.38
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 52 QVAAANVNLAMNQSLQGHSGKVRA-----IIWNEQYEKLTSSDETGLII 95
VA A LA+N++ + +G+ A +IW +Q E L + + G +I
Sbjct: 23 NVAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALI 71
>gnl|CDD|131782 TIGR02735, purC_vibrio,
phosphoribosylaminoimidazole-succinocarboxamide
synthase, Vibrio type. Members of this protein family
appear to represent a novel form of
phosphoribosylaminoimidazole-succinocarboxamide
synthase (SAICAR synthetase), significantly different
in sequence and gap pattern from a form (see TIGR00081)
shared by a broad range of bacteria and eukaryotes.
Members of this family are found within the
gammaproteobacteria in the genera Vibrio, Shewanella,
and Colwellia, and also (reported as a fragment) in the
primitive eukarote Guillardia theta [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 365
Score = 27.2 bits (60), Expect = 2.0
Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 52 QVAAANVNLAMNQSLQGHSGKVRAIIWNEQYEKLTSSDETGLI 94
QV A N +L + HSGKVR++ W LT D LI
Sbjct: 5 QVLAVNDDLPIRTDEPVHSGKVRSVYW------LTEEDSRRLI 41
>gnl|CDD|149953 pfam09081, DUF1921, Domain of unknown function (DUF1921). This
domain, which is found in a set of prokaryotic
amylases, has no known function.
Length = 51
Score = 25.2 bits (55), Expect = 2.4
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 6/39 (15%)
Query: 40 VLKLDTGKESTGQVAAANVNLAMNQSLQGHSGKVRAIIW 78
V LD+ S GQVA+ + + A+N+ +G+VR IW
Sbjct: 18 VFALDSNLSSPGQVASGSFSQAVNED----NGQVR--IW 50
>gnl|CDD|180373 PRK06059, PRK06059, lipid-transfer protein; Provisional.
Length = 399
Score = 25.9 bits (57), Expect = 5.2
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 52 QVAAANVNLAMNQSLQGHSGKV 73
QV A V + NQ L GH V
Sbjct: 374 QVEGARVGITANQGLFGHGSSV 395
>gnl|CDD|213597 TIGR01259, comE, comEA protein. This model describes the ComEA
protein in bacteria. The com E locus is obligatory for
bacterial cell competence - the process of
internalizing the exogenous added DNA. Lesions in the
loci has been variously described for the appearance of
competence-related pheonotypes and impairment of
competence, suggesting their intimate functional role
in bacterial transformation [Cellular processes, DNA
transformation].
Length = 120
Score = 24.9 bits (54), Expect = 7.8
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 49 STGQVAAANVNLAMNQSLQGHSG----KVRAII-WNEQYEKLTSSDE 90
S G++AA N+N A + LQ G K +AII + E+ S D+
Sbjct: 53 SAGKLAAVNINAASLEELQALPGIGPAKAKAIIEYREENGAFKSVDD 99
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 25.1 bits (55), Expect = 8.1
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 62 MNQSLQGHSGKVR 74
MN L+G SGKV+
Sbjct: 1 MNDELKGKSGKVK 13
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
0.316 0.132 0.413
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: 5,358,994
Number of extensions: 419320
Number of successful extensions: 338
Number of sequences better than 10.0: 1
Number of HSP's gapped: 328
Number of HSP's successfully gapped: 30
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
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 (21.6 bits)
S2: 53 (24.2 bits)