RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17135
(106 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 = 58.9 bits (143), Expect = 1e-11
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +IR+W+L CVQ ++ H S+ +A+ P +AS ADG +++
Sbjct: 238 SEDGTIRVWDLRTGECVQTLSGH----TNSVTSLAWSPDGKRLASGSADGTIRIW 288
Score = 52.3 bits (126), Expect = 2e-09
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +I++W+++ C+ + H + VAF P F+AS+ DG K++
Sbjct: 112 SRDKTIKVWDVETGKCLTTLRGHTD----WVNSVAFSPDGTFVASSSQDGTIKLW 162
Score = 48.5 bits (116), Expect = 5e-08
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +I+LW+L CV +T H + VAF P + S+ +DG K++
Sbjct: 154 SQDGTIKLWDLRTGKCVATLTGH----TGEVNSVAFSPDGEKLLSSSSDGTIKLW 204
Score = 48.1 bits (115), Expect = 7e-08
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +I+LW+L C+ + H + + VAF P +AS DG +V+
Sbjct: 196 SSDGTIKLWDLSTGKCLGTLRGH----ENGVNSVAFSPDGYLLASGSEDGTIRVW 246
Score = 45.8 bits (109), Expect = 4e-07
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 53 DCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +IRLW+L+ CV+ +T H + VAF P ++S+ D KV+
Sbjct: 72 DKTIRLWDLETGECVRTLTGHTS----YVSSVAFSPDGRILSSSSRDKTIKVW 120
Score = 40.8 bits (96), Expect = 3e-05
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +I++W+L+ ++ + H + DVA ++AS +D +++
Sbjct: 28 SGDGTIKVWDLETGELLRTLKGHTG----PVRDVAASADGTYLASGSSDKTIRLW 78
Score = 36.2 bits (84), Expect = 0.001
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 66 CVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
+ + H + VAF P +A+ DG KV+
Sbjct: 1 LRRTLKGHTGG----VTCVAFSPDGKLLATGSGDGTIKVW 36
>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 = 37.3 bits (87), Expect = 4e-05
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 63 NKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
+ ++ + H + VAF P ++AS DG K++
Sbjct: 1 SGELLKTLKGHTG----PVTSVAFSPDGKYLASGSDDGTIKLW 39
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 37.3 bits (87), Expect = 5e-05
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 4/42 (9%)
Query: 64 KTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
++ + H + VAF P +AS DG +V+
Sbjct: 1 GKLLRTLKGHTG----PVTSVAFSPDGNLLASGSDDGTVRVW 38
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 37.4 bits (85), Expect = 6e-04
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 51 GHDCSIRLWNLDN-KTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +IRLW+L + + ++ ++ H S+L VAF P +AS +DG +++
Sbjct: 260 SSDGTIRLWDLRSSSSLLRTLSGH----SSSVLSVAFSPDGKLLASGSSDGTVRLW 311
Score = 36.6 bits (83), Expect = 0.001
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 40 SSNISLFDSRPGHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPF-IASAGA 98
S + L S D +I+LW+L + + H + +AF P IAS +
Sbjct: 164 SPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTD----PVSSLAFSPDGGLLIASGSS 219
Query: 99 DGLAKVF 105
DG +++
Sbjct: 220 DGTIRLW 226
Score = 32.8 bits (73), Expect = 0.021
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 44 SLFDSRPGHDCSIRLWNLDNKT-CVQEITAHRKKFDESILDVAFHPSKPFIASAG-ADGL 101
S+ + D +++LW+L ++ + H + S+ +AF P +AS DG
Sbjct: 124 SILLASSSLDGTVKLWDLSTPGKLIRTLEGHSE----SVTSLAFSPDGKLLASGSSLDGT 179
Query: 102 AKVF 105
K++
Sbjct: 180 IKLW 183
Score = 32.4 bits (72), Expect = 0.034
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +IRLW+L ++ + +F P +AS +DG +++
Sbjct: 218 SSDGTIRLWDLSTGKLLRST----LSGHSDSVVSSFSPDGSLLASGSSDGTIRLW 268
Score = 30.1 bits (66), Expect = 0.18
Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGA-DGLAKVF 105
D ++RLW+L+ + +T K + + ++F P + S G+ DG +++
Sbjct: 303 SSDGTVRLWDLETGKLLSSLT--LKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLW 356
Score = 28.9 bits (63), Expect = 0.41
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
D +IRLW+L ++ + H ++L V+F P ++S DG +++
Sbjct: 348 SDDGTIRLWDLRTGKPLKTLEGH-----SNVLSVSFSPDGRVVSSGSTDGTVRLW 397
Score = 27.7 bits (60), Expect = 1.3
Identities = 11/54 (20%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 51 GHDCSIRLWNLDNKTCVQEITAHRKKFDESILDVAFHPSKPFIASAGADGLAKV 104
D ++RLW+L + ++ + H + + + F P +AS +D ++
Sbjct: 389 STDGTVRLWDLSTGSLLRNLDGHTSR----VTSLDFSPDGKSLASGSSDNTIRL 438
Score = 27.0 bits (58), Expect = 2.1
Identities = 14/92 (15%), Positives = 37/92 (40%)
Query: 14 LLELQTYARNDCPELNSEPPACQTIPSSNISLFDSRPGHDCSIRLWNLDNKTCVQEITAH 73
L++ + + + +L + ++ S ++ S + L + + +
Sbjct: 1 LVDNSSTSSENKSKLLKKSELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLL 60
Query: 74 RKKFDESILDVAFHPSKPFIASAGADGLAKVF 105
+ ++SI +AF P + S +DG K++
Sbjct: 61 LRGHEDSITSIAFSPDGELLLSGSSDGTIKLW 92
>gnl|CDD|218539 pfam05287, PMG, PMG protein. This family consists of several
mouse anagen-specific protein mKAP13 (PMG1 and PMG2).
PMG1 and 2 contain characteristic repeats reminiscent
of the keratin-associated proteins (KAPs). Both genes
are expressed in growing hair follicles in skin as well
as in sebaceous and eccrine sweat glands.
Interestingly, expression is also detected in the
mammary epithelium where it is limited to the onset of
the pubertal growth phase and is independent of ovarian
hormones. Their broad, developmentally controlled
expression pattern, together with their unique amino
acid composition, demonstrate that pmg-1 and pmg-2
constitute a novel KAP gene family participating in the
differentiation of all epithelial cells forming the
epidermal appendages.
Length = 175
Score = 25.9 bits (57), Expect = 3.9
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 4 VPSSVIYIWTLLELQTYARNDCPELNSEPPACQTIPSSNISLFDSRP 50
V S+V+ + +L + + C E EP +CQT S S P
Sbjct: 35 VCSTVLCSPSSCQLGSSLLDGCQETCGEPTSCQT-TSCETSPCVPSP 80
>gnl|CDD|234416 TIGR03956, rSAM_HydE, [FeFe] hydrogenase H-cluster radical SAM
maturase HydE. This model describes the radical SAM
protein HydE, one of a pair of radical SAM proteins,
along with GTP-binding protein HydF, for maturation of
[Fe] hydrogenase in Chlamydomonas reinhardtii and
numerous bacteria [Protein fate, Protein modification
and repair].
Length = 340
Score = 25.2 bits (56), Expect = 6.8
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 9 IYIWTLLELQTYARNDC 25
+YI L+E Y +NDC
Sbjct: 47 VYIRGLIEFTNYCKNDC 63
>gnl|CDD|225387 COG2831, FhaC, Hemolysin activation/secretion protein
[Intracellular trafficking and secretion].
Length = 554
Score = 25.4 bits (56), Expect = 7.5
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 79 ESILDVAFHPSKPFIASAGAD 99
ES L + KP+ SA AD
Sbjct: 210 ESDLVIKVQQGKPWRVSASAD 230
>gnl|CDD|236112 PRK07845, PRK07845, flavoprotein disulfide reductase; Reviewed.
Length = 466
Score = 25.2 bits (56), Expect = 8.6
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 88 PSKPFIASAGA 98
PSK IA+A
Sbjct: 46 PSKTLIATAEV 56
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
0.320 0.134 0.418
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: 5,163,794
Number of extensions: 397244
Number of successful extensions: 279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 268
Number of HSP's successfully gapped: 24
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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 (21.8 bits)
S2: 53 (24.2 bits)