RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3599
(223 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 = 46.2 bits (110), Expect = 3e-06
Identities = 32/135 (23%), Positives = 56/135 (41%), Gaps = 21/135 (15%)
Query: 86 PITCLSWRSWISREARDPTLLVNIAANAVCILKVLDKEGAVQLKRKFNVNHKSSKYQVRS 145
+TC+++ + D LL + + +KV D E L+ H VR
Sbjct: 11 GVTCVAF-------SPDGKLLATGSGD--GTIKVWDLETGELLRT--LKGHTGP---VRD 56
Query: 146 TFCPIMSFREGACVVTGSEDSCVYFLDIQSKEHKNAVNKLQGHACPVLGVSFNYDESLLA 205
+ + +G + +GS D + D+++ E V L GH V V+F+ D +L+
Sbjct: 57 ----VAASADGTYLASGSSDKTIRLWDLETGE---CVRTLTGHTSYVSSVAFSPDGRILS 109
Query: 206 TSDYQGLIILWSREK 220
+S I +W E
Sbjct: 110 SSSRDKTIKVWDVET 124
Score = 38.1 bits (89), Expect = 0.002
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 159 VVTGSEDSCVYFLDIQSKEHKNAVNKLQGHACPVLGVSFNYDESLLATSDYQGLIILWS 217
+ + S D + D+++ + L+GH V V+F+ D + +A+S G I LW
Sbjct: 108 LSSSSRDKTIKVWDVETGKCLTT---LRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWD 163
Score = 36.9 bits (86), Expect = 0.005
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 156 GACVVTGSEDSCVYFLDIQSKEHKNAVNKLQGHACPVLGVSFNYDESLLATSDYQGLIIL 215
G +++ S D + D+ + + + L+GH V V+F+ D LLA+ G I +
Sbjct: 189 GEKLLSSSSDGTIKLWDLSTGKC---LGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRV 245
Query: 216 WSREKHEP 223
W E
Sbjct: 246 WDLRTGEC 253
Score = 36.5 bits (85), Expect = 0.006
Identities = 16/39 (41%), Positives = 20/39 (51%)
Query: 185 LQGHACPVLGVSFNYDESLLATSDYQGLIILWSREKHEP 223
L+GH V V+F+ D LLAT G I +W E E
Sbjct: 5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGEL 43
Score = 35.8 bits (83), Expect = 0.012
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 159 VVTGSEDSCVYFLDIQSKEHKNAVNKLQGHACPVLGVSFNYDESLLATSDYQGLIILWS 217
+ +GSED + D+++ E V L GH V ++++ D LA+ G I +W
Sbjct: 234 LASGSEDGTIRVWDLRTGEC---VQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 34.6 bits (80), Expect = 0.026
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 159 VVTGSEDSCVYFLDIQSKEHKNAVNKLQGHACPVLGVSFNYDESLLATSDYQGLIILWS 217
V + S+D + D+++ + V L GH V V+F+ D L +S G I LW
Sbjct: 150 VASSSQDGTIKLWDLRTGKC---VATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWD 205
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 43.2 bits (100), Expect = 6e-05
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 149 PIMSF-REGACVVTGSEDSCVYFLDIQSKEHKNAVNKLQGHACPVLGVSFNYDESLLATS 207
+ SF +G+ + +GS D + D++S + + L GH+ VL V+F+ D LLA+
Sbjct: 245 VVSSFSPDGSLLASGSSDGTIRLWDLRS--SSSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
Query: 208 DYQGLIILWSREKHE 222
G + LW E +
Sbjct: 303 SSDGTVRLWDLETGK 317
Score = 34.3 bits (77), Expect = 0.039
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 150 IMSFREGACVVTGSEDSCVYFLDIQSKEHKNAVNKLQGHACPVLGVSFNYDESLLATSDY 209
+ +G + +GS D V D+++ + + L+GH PV +SF+ D SLL +
Sbjct: 290 VAFSPDGKLLASGSSDGTVRLWDLETGKLLS-SLTLKGHEGPVSSLSFSPDGSLLVSGGS 348
Query: 210 Q-GLIILWSREKHEP 223
G I LW +P
Sbjct: 349 DDGTIRLWDLRTGKP 363
Score = 30.8 bits (68), Expect = 0.59
Identities = 27/159 (16%), Positives = 55/159 (34%), Gaps = 19/159 (11%)
Query: 64 SILCDDLGRLSKGKRLVLSQDCPITCLSWRSWISREARDPTLLVNIAANAVCILKVLDKE 123
+I DL S R + + +++ P + + ++ +++ D E
Sbjct: 264 TIRLWDLRSSSSLLRTLSGHSSSVLSVAF---------SPDGKLLASGSSDGTVRLWDLE 314
Query: 124 GAVQLKRKFNVNHKSSKYQVRSTFCPIMSFREGACVVTGSEDSCVYFLDIQSKEHKNAVN 183
L H+ + F P S V GS+D + D+++ + +
Sbjct: 315 TGKLLSSLTLKGHEGPVSSLS--FSPDGSL----LVSGGSDDGTIRLWDLRTGKPLKTLE 368
Query: 184 KLQGHACPVLGVSFNYDESLLATSDYQGLIILWSREKHE 222
VL VSF+ D ++++ G + LW
Sbjct: 369 GHS----NVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGS 403
Score = 28.5 bits (62), Expect = 3.5
Identities = 13/62 (20%), Positives = 21/62 (33%)
Query: 161 TGSEDSCVYFLDIQSKEHKNAVNKLQGHACPVLGVSFNYDESLLATSDYQGLIILWSREK 220
D + L+GH + ++F+ D LL + G I LW +
Sbjct: 37 ESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDN 96
Query: 221 HE 222
E
Sbjct: 97 GE 98
>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 = 35.8 bits (83), Expect = 9e-04
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 182 VNKLQGHACPVLGVSFNYDESLLATSDYQGLIILWS 217
+ L+GH PV V+F+ D LA+ G I LW
Sbjct: 5 LKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 35.0 bits (81), Expect = 0.001
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 182 VNKLQGHACPVLGVSFNYDESLLATSDYQGLIILWS 217
+ L+GH PV V+F+ D +LLA+ G + +W
Sbjct: 4 LRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|200517 cd11256, Sema_4A, The Sema domain, a protein interacting module, of
semaphorin 4A (Sema4A). Sema4A is expressed in immune
cells and is thus termed an "immune semaphorin". It
plays critical roles in T cell-DC interactions in the
immune response. It has been reported to enhance
activation and differentiation of T cells in vitro and
generation of antigen-specific T cells in vivo. The
function of Sema4A in the immune response implicates its
role in infectious and noninfectious diseases. Sema4A
exerts its function through three receptors, namely
Plexin B, Plexin D1, and Tim-2. Sema4A belongs to the
class 4 transmembrane semaphorin family of proteins.
Semaphorins are regulatory molecules in the development
of the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. TThe Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 447
Score = 33.7 bits (77), Expect = 0.069
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 111 ANAVCILKVLDKEGAVQLKRKFNVNHKSSKYQVRSTFCPIMSFREGACVVTGSEDSCVYF 170
++AVC K+ D E K K +N +SS++ P+ R G+C S D + F
Sbjct: 284 SSAVCAYKLNDIEKVFNGKYK-ELNKESSRWTRYMG--PVSDPRPGSCSGGKSSDKALNF 340
Query: 171 LDIQSKEH 178
+ K+H
Sbjct: 341 M----KDH 344
>gnl|CDD|227794 COG5507, COG5507, Uncharacterized conserved protein [Function
unknown].
Length = 117
Score = 28.7 bits (64), Expect = 1.0
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 62 IVSILCDDL--GRLSKGKRLVLSQDCPITCLSWRSWISREARD 102
V DD+ G+L+ R V ++D SW + S++ RD
Sbjct: 38 YVECWADDVPYGKLTDFPRAVKAKDDEEVVFSWIEYPSKQVRD 80
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 29.1 bits (65), Expect = 2.2
Identities = 38/155 (24%), Positives = 67/155 (43%), Gaps = 19/155 (12%)
Query: 55 QLRSTGVIVSILCDDLGRLSKGKRLVLSQDCPITCLSWRSWISREARDPTLLVNIAANAV 114
QL ST V+ D G+L+ ++L Q+ PI +++ + DP L + +
Sbjct: 49 QLGSTAVLKH---TDYGKLASNPPILLGQEGPIIDVAFNPF------DPQKLFTASEDGT 99
Query: 115 CILKVLDKEGAVQLKRKFNVNHKSSKYQVRSTFCPIMSFREGACVVTGSE--DSCVYFLD 172
+ + +EG Q N++ Q + I+SF A V S D V D
Sbjct: 100 IMGWGIPEEGLTQ-----NISDPIVHLQGHTKKVGIVSFHPSAMNVLASAGADMVVNVWD 154
Query: 173 IQSKEHKNAVNKLQGHACPVLGVSFNYDESLLATS 207
++ + AV ++ H+ + + +N D SLL T+
Sbjct: 155 VERGK---AVEVIKCHSDQITSLEWNLDGSLLCTT 186
>gnl|CDD|204301 pfam09735, Nckap1, Membrane-associated apoptosis protein.
Expression of this protein was found to be markedly
reduced in patients with Alzheimer's disease. It is
involved in the regulation of actin polymerisation in
the brain as part of a WAVE2 signalling complex.
Length = 1118
Score = 28.5 bits (64), Expect = 3.0
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 146 TFCPIMSFREGACVVTGSEDSCVYFLDI 173
TF +M F++ + + DSC LDI
Sbjct: 87 TFVDLMEFKDHVLELLTTIDSCQIHLDI 114
>gnl|CDD|188404 TIGR03889, nitrile_acc, nitrile hydratase accessory protein.
Members of this protein family are found in operons
with the alpha and beta subunits of nitrile hydratase,
an enzyme with Fe(III) or Co(III) at the active site,
and appear to be accessory proteins for maturation or
activation of the enzyme. This protein is homologous to
the beta subunit (see TIGR03888).
Length = 74
Score = 26.2 bits (58), Expect = 4.6
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 6 WQQQAFALDVRLNA 19
WQ QAFAL V L+
Sbjct: 5 WQAQAFALTVHLHE 18
>gnl|CDD|133012 cd02520, Glucosylceramide_synthase, Glucosylceramide synthase
catalyzes the first glycosylation step of
glycosphingolipid synthesis.
UDP-glucose:N-acylsphingosine D-glucosyltransferase
(glucosylceramide synthase or ceramide
glucosyltransferase) catalyzes the first glycosylation
step of glycosphingolipid synthesis. Its product,
glucosylceramide, serves as the core of more than 300
glycosphingolipids (GSL). GSLs are a group of membrane
components that have the lipid portion embedded in the
outer plasma membrane leaflet and the sugar chains
extended to the outer environment. Several lines of
evidence suggest the importance of GSLs in various
cellular processes such as differentiation, adhesion,
proliferation, and cell-cell recognition. In pathogenic
fungus Cryptococcus neoformans, glucosylceramide serves
as an antigen that elicits an antibody response in
patients and it is essential for fungal growth in host
extracellular environment.
Length = 196
Score = 27.6 bits (62), Expect = 4.9
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 65 ILCDD--LGRL--SKGKRLVLSQ---DCPITCLSWRSWISREAR 101
L +D LG+L G R+VLS P+ S S+ R+ R
Sbjct: 148 YLAEDYFLGKLIWRLGYRVVLSPYVVMQPLGSTSLASFWRRQLR 191
>gnl|CDD|240476 cd12896, SPRY_PRY_TRIM65, PRY/SPRY domain in tripartite
motif-containing domain 65 (TRIM65). This domain,
consisting of the distinct N-terminal PRY subdomain
followed by the SPRY subdomain, is found at the
C-terminus of TRIM65 proteins (composed of
RING/B-box/coiled-coil core and also known as RBCC
proteins). The SPRY/PRY combination is a possible
component of immune defense. This protein family has not
been characterized.
Length = 182
Score = 27.0 bits (60), Expect = 6.8
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 178 HKNAVNKLQGHACPVLGVSFNYDESLL 204
H +LQG + LGVS + + L
Sbjct: 117 HNGEEQQLQGPSYTKLGVSLDCEAGTL 143
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 0.133 0.400
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: 10,810,582
Number of extensions: 950146
Number of successful extensions: 637
Number of sequences better than 10.0: 1
Number of HSP's gapped: 633
Number of HSP's successfully gapped: 21
Length of query: 223
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 130
Effective length of database: 6,812,680
Effective search space: 885648400
Effective search space used: 885648400
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: 57 (25.7 bits)