RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10348
(291 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 = 86.2 bits (214), Expect = 1e-19
Identities = 65/290 (22%), Positives = 106/290 (36%), Gaps = 44/290 (15%)
Query: 18 WSMDLESGRPLLAVAGSRAVIRIFSPAFHACVRHFYGHGHAINELKFHPQDFNLLLSVSK 77
+ LLA I+++ +R GH + ++ D L S S
Sbjct: 13 TCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASA-DGTYLASGSS 71
Query: 78 DHTLRLWNIKTDICIAIFGGVEGHRDEVLSADFDLLGTKIMSCGMDHSLKLWDLTKPEIK 137
D T+RLW+++T C+ GH V S F G + S D ++K+WD+ +
Sbjct: 72 DKTIRLWDLETGECVRTL---TGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCL 128
Query: 138 DAC------AESYTFNPA----------RSTRPFDTQKEHFPQFSTRDIHRNYVDCVRWL 181
S F+P + + +D + +T H V+ V +
Sbjct: 129 TTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKC--VATLTGHTGEVNSVAFS 186
Query: 182 GD--FVLSKSCENCIICWKPGRLEDKELRTNETNVTIINRLNFKDCEIWFIRFSMDYWQK 239
D +LS S + I W +L T + T+ N + + FS D
Sbjct: 187 PDGEKLLSSSSDGTIKLW--------DLSTGKCLGTLRGHENG----VNSVAFSPD--GY 232
Query: 240 ILAVGNQSGRTYVWDLDVQDPSSIKFQILSHPRCMSAVRQTTLSKNGNVL 289
+LA G++ G VWDL + Q LS ++V S +G L
Sbjct: 233 LLASGSEDGTIRVWDLRTGECV----QTLSGHT--NSVTSLAWSPDGKRL 276
Score = 78.1 bits (193), Expect = 1e-16
Identities = 54/234 (23%), Positives = 89/234 (38%), Gaps = 46/234 (19%)
Query: 48 CVRHFYGHGHAINELKFHPQDFNLLLSVSKDHTLRLWNIKTDICIAIFGGVEGHRDEVLS 107
R GH + + F P D LL + S D T+++W+++T + +GH V
Sbjct: 1 LRRTLKGHTGGVTCVAFSP-DGKLLATGSGDGTIKVWDLETGELLRTL---KGHTGPVRD 56
Query: 108 ADFDLLGTKIMSCGMDHSLKLWDLTKPEIKDACAESYT----------FNPAR------- 150
GT + S D +++LWDL E C + T F+P
Sbjct: 57 VAASADGTYLASGSSDKTIRLWDLETGE----CVRTLTGHTSYVSSVAFSPDGRILSSSS 112
Query: 151 ---STRPFDTQKEHFPQFSTRDIHRNYVDCVRWLGD--FVLSKSCENCIICWKPGRLEDK 205
+ + +D + +T H ++V+ V + D FV S S + I W
Sbjct: 113 RDKTIKVWDVET--GKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLW-------- 162
Query: 206 ELRTNETNVTIINRLNFKDCEIWFIRFSMDYWQKILAVGNQSGRTYVWDLDVQD 259
+LRT + + L E+ + FS D + L + G +WDL
Sbjct: 163 DLRTGKC----VATLTGHTGEVNSVAFSPD--GEKLLSSSSDGTIKLWDLSTGK 210
Score = 74.7 bits (184), Expect = 2e-15
Identities = 32/121 (26%), Positives = 58/121 (47%), Gaps = 8/121 (6%)
Query: 10 EENFYTCAWSMDLESGRPLLAVAGSRAVIRIFSPAFHACVRHFYGHGHAINELKFHPQDF 69
+ A+S D E L + S I+++ + C+ GH + +N + F P
Sbjct: 177 TGEVNSVAFSPDGEK----LLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDG- 231
Query: 70 NLLLSVSKDHTLRLWNIKTDICIAIFGGVEGHRDEVLSADFDLLGTKIMSCGMDHSLKLW 129
LL S S+D T+R+W+++T C+ GH + V S + G ++ S D ++++W
Sbjct: 232 YLLASGSEDGTIRVWDLRTGECVQTL---SGHTNSVTSLAWSPDGKRLASGSADGTIRIW 288
Query: 130 D 130
D
Sbjct: 289 D 289
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 64.7 bits (156), Expect = 8e-12
Identities = 48/228 (21%), Positives = 85/228 (37%), Gaps = 26/228 (11%)
Query: 10 EENFYTCAWSMDLESGRPLLAVAGSRAVIRIFSPAFHACVRHFYGHGHAINELKFHPQDF 69
E+ + A+S G+ L + + I+++ + GH ++ L F P
Sbjct: 155 SESVTSLAFS---PDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGG 211
Query: 70 NLLLSVSKDHTLRLWNIKTDICIAIFGGVEGHRDEVLSADFDLLGTKIMSCGMDHSLKLW 129
L+ S S D T+RLW++ T + + GH D V+S+ F G+ + S D +++LW
Sbjct: 212 LLIASGSSDGTIRLWDLSTGKLLRST--LSGHSDSVVSS-FSPDGSLLASGSSDGTIRLW 268
Query: 130 D-------LTKPEIKDACAESYTFNP----------ARSTRPFDTQKEHFPQFSTRDIHR 172
D L + S F+P + R +D + T H
Sbjct: 269 DLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHE 328
Query: 173 NYVDCVRWLGD---FVLSKSCENCIICWKPGRLEDKELRTNETNVTII 217
V + + D V S + I W + + +NV +
Sbjct: 329 GPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSV 376
Score = 64.3 bits (155), Expect = 1e-11
Identities = 50/249 (20%), Positives = 94/249 (37%), Gaps = 35/249 (14%)
Query: 28 LLAVAGSRAVIRIFSPAFHA-CVRHFYGHGHAINELKFHPQDFNLLLSVSKDHTLRLWNI 86
LLA + ++++ + +R GH ++ L F P L S D T++LW++
Sbjct: 126 LLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDL 185
Query: 87 KTDICIAIFGGVEGHRDEVLSADFDLLGTK-IMSCGMDHSLKLWDLTKPEIKDACAESYT 145
+T ++ GH D V S F G I S D +++LWDL+ ++ + ++
Sbjct: 186 RTGKPLSTL---AGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHS 242
Query: 146 FNPARSTRP----------------FDTQKEHFPQFSTRDIHRNYVDCVRWLGD--FVLS 187
+ S P +D + T H + V V + D + S
Sbjct: 243 DSVVSSFSPDGSLLASGSSDGTIRLWDL-RSSSSLLRTLSGHSSSVLSVAFSPDGKLLAS 301
Query: 188 KSCENCIICWKPGRLEDKELRTNETNVTIINRLNFKDCEIWFIRFSMDYWQKILAVGNQS 247
S + + W + T + + + + + FS D +++ G+
Sbjct: 302 GSSDGTVRLWDLETGKLLSSLTLKGH----------EGPVSSLSFSPD-GSLLVSGGSDD 350
Query: 248 GRTYVWDLD 256
G +WDL
Sbjct: 351 GTIRLWDLR 359
Score = 46.2 bits (108), Expect = 1e-05
Identities = 57/263 (21%), Positives = 85/263 (32%), Gaps = 47/263 (17%)
Query: 52 FYGHGHAINELKFHPQDFNLLLSVSKDHTLRLWNIKTD-ICIAIFGGVEGHRDEVLSADF 110
GH +I + F P D LLLS S D T++LW++ I G+ H V
Sbjct: 61 LRGHEDSITSIAFSP-DGELLLSGSSDGTIKLWDLDNGEKLIKSLEGL--HDSSVSKLAL 117
Query: 111 DLL-GTKIMSCG--MDHSLKLWDLTKPEIKDACAE-------SYTFNPARSTRPFDTQKE 160
G I+ +D ++KLWDL+ P E S F+P + +
Sbjct: 118 SSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLD 177
Query: 161 HF---------PQFSTRDIHRNYVDCVRWLGD---FVLSKSCENCIICWKPGRLEDKELR 208
ST H + V + + D + S S + I W
Sbjct: 178 GTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWD---------- 227
Query: 209 TNETNVTIINRLNFKDCEIWFIR-FSMDYWQKILAVGNQSGRTYVWDLDVQDPSSIKFQI 267
+ + R + FS D +LA G+ G +WDL
Sbjct: 228 ---LSTGKLLRSTLSGHSDSVVSSFSPD--GSLLASGSSDGTIRLWDLRSSSSLLRTLSG 282
Query: 268 LSHPRCMSAVRQTTLSKNGNVLL 290
S V S +G +L
Sbjct: 283 HSSS-----VLSVAFSPDGKLLA 300
Score = 41.2 bits (95), Expect = 5e-04
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 12 NFYTCAWSMDLESGRPLLAVAGSRAVIRIFSPAFHACVRHFYGHGHAINELKFHPQDFNL 71
++ S+ +++ + +R++ + + +R+ GH + L F P D
Sbjct: 368 EGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSP-DGKS 426
Query: 72 LLSVSKDHTLRLWNIKTDICIAIFG 96
L S S D+T+RLW++KT + F
Sbjct: 427 LASGSSDNTIRLWDLKTSLKSVSFS 451
Score = 34.3 bits (77), Expect = 0.076
Identities = 39/217 (17%), Positives = 62/217 (28%), Gaps = 42/217 (19%)
Query: 98 VEGHRDEVLSADFDLLGTKIMSCGMDHSLKLWDLTKPEIKDACAESYTFNPARSTRPFDT 157
+ GH D + S F G ++S D ++KLWDL E E +
Sbjct: 61 LRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSP 120
Query: 158 QKEHFPQFSTR--------------------DIHRNYVDCVRWLGD---FVLSKSCENCI 194
S+ + H V + + D S + I
Sbjct: 121 DGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTI 180
Query: 195 ICWKPGRLEDKELRTNETNVTIINRLNFKDCEIWFIRFSMDYWQKILAVGNQSGRTYVWD 254
W K L T L + + FS D ++A G+ G +WD
Sbjct: 181 KLWDLR--TGKPLST----------LAGHTDPVSSLAFSPD-GGLLIASGSSDGTIRLWD 227
Query: 255 LDVQDPSSIKFQILSHPRCMSAVRQTTLSKNGNVLLC 291
L S ++ S +G++L
Sbjct: 228 LSTGKLLRSTL------SGHSDSVVSSFSPDGSLLAS 258
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 42.0 bits (99), Expect = 6e-06
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 48 CVRHFYGHGHAINELKFHPQDFNLLLSVSKDHTLRLWN 85
+R GH + + F P D NLL S S D T+R+W+
Sbjct: 3 LLRTLKGHTGPVTSVAFSP-DGNLLASGSDDGTVRVWD 39
Score = 37.3 bits (87), Expect = 3e-04
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 99 EGHRDEVLSADFDLLGTKIMSCGMDHSLKLWD 130
+GH V S F G + S D ++++WD
Sbjct: 8 KGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 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 = 40.8 bits (96), Expect = 2e-05
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 48 CVRHFYGHGHAINELKFHPQDFNLLLSVSKDHTLRLWN 85
++ GH + + F P D L S S D T++LW+
Sbjct: 4 LLKTLKGHTGPVTSVAFSP-DGKYLASGSDDGTIKLWD 40
Score = 36.9 bits (86), Expect = 4e-04
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 88 TDICIAIFGGVEGHRDEVLSADFDLLGTKIMSCGMDHSLKLWD 130
+ + +GH V S F G + S D ++KLWD
Sbjct: 1 SGELLKTL---KGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 40.7 bits (95), Expect = 7e-04
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 16/89 (17%)
Query: 54 GHGHAINELKFHPQDFNLLLSVSKDHTLRLWNI----------KTDICIAIFGGVEGHRD 103
GH +I +L+F+P +L S S+D T+R+W I K CI ++GH+
Sbjct: 72 GHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDESVKEIKDPQCI-----LKGHKK 126
Query: 104 EVLSADFDLLGTKIM-SCGMDHSLKLWDL 131
++ D++ + IM S G D + +WD+
Sbjct: 127 KISIIDWNPMNYYIMCSSGFDSFVNIWDI 155
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 39.1 bits (91), Expect = 0.002
Identities = 23/103 (22%), Positives = 46/103 (44%), Gaps = 6/103 (5%)
Query: 51 HFYGHGHAINELKFHPQDFNLLLSVSKDHTLRLWNIKTDICIAIFGGVEGHRDEVLSADF 110
H GH + + FHP N+L S D + +W+++ + + ++ H D++ S ++
Sbjct: 120 HLQGHTKKVGIVSFHPSAMNVLASAGADMVVNVWDVERGKAVEV---IKCHSDQITSLEW 176
Query: 111 DLLGTKIMSCGMDHSLKLWDLTKPEIKDACAESYTFNPARSTR 153
+L G+ + + D L + D P + A+S R
Sbjct: 177 NLDGSLLCTTSKDKKLNIID---PRDGTIVSSVEAHASAKSQR 216
Score = 29.9 bits (67), Expect = 1.7
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 5/80 (6%)
Query: 59 INELKFHPQDFNLLLSVSKDHTLRLWNIKTD----ICIAIFGGVEGHRDEVLSADFDLLG 114
I ++ F+P D L + S+D T+ W I + ++GH +V F
Sbjct: 78 IIDVAFNPFDPQKLFTASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGIVSFHPSA 137
Query: 115 TKIM-SCGMDHSLKLWDLTK 133
++ S G D + +WD+ +
Sbjct: 138 MNVLASAGADMVVNVWDVER 157
>gnl|CDD|221182 pfam11715, Nup160, Nucleoporin Nup120/160. Nup120 is conserved
from fungi to plants to humans, and is homologous with
the Nup160 of vertebrates. The nuclear core complex, or
NPC, mediates macromolecular transport across the
nuclear envelope. Deletion of the NUP120 gene causes
clustering of NPCs at one side of the nuclear envelope,
moderate nucleolar fragmentation and slower cell growth.
The vertebrate NPC is estimated to contain between 30
and 60 different proteins. most of which are not known.
Two important ones in creating the nucleoporin basket
are Nup98 and Nup153, and Nup120, in conjunction with
Nup 133, interacts with these two and itself plays a
role in mRNA export. Nup160, Nup133, Nup96, and Nup107
are all targets of phosphorylation. The phosphorylation
sites are clustered mainly at the N-terminal regions of
these proteins, which are predicted to be natively
disordered. The entire Nup107-160 subcomplex is stable
throughout the cell cycle, thus it seems unlikely that
phosphorylation affects interactions within the
Nup107-160 subcomplex, but rather that it regulates the
association of the subcomplex with the NPC and other
proteins.
Length = 511
Score = 32.1 bits (73), Expect = 0.38
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 70 NLLLSVSKDHTLRLWNIKTDIC 91
L ++S D TLR+WN+ T C
Sbjct: 233 TFLFTLSLDGTLRVWNLDTGQC 254
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 31.6 bits (71), Expect = 0.47
Identities = 34/143 (23%), Positives = 53/143 (37%), Gaps = 39/143 (27%)
Query: 29 LAVAGSRAVIRIFSPAFHACVRHFYGHGHAINELKFHPQDFNLLLSVSKDHTLRLWNI-- 86
+A + V++++ A V H + + + D LL S S D +++LW+I
Sbjct: 548 VASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQ 607
Query: 87 ---------KTDICIAIFGGVEGHRDEVLSAD-----FDLLGTKIMSCGM---------- 122
K +IC F G SAD +DL K+ C M
Sbjct: 608 GVSIGTIKTKANICCVQFPSESGRSLAFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYV 667
Query: 123 -------------DHSLKLWDLT 132
D++LKLWDL+
Sbjct: 668 RFVDSSTLVSSSTDNTLKLWDLS 690
Score = 27.7 bits (61), Expect = 8.6
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 54 GHGHAINELKFHPQDFNLLLSVSKDHTLRLWNIKTDI 90
GH ++ ++F D + L+S S D+TL+LW++ I
Sbjct: 659 GHSKTVSYVRF--VDSSTLVSSSTDNTLKLWDLSMSI 693
>gnl|CDD|185019 PRK15059, PRK15059, tartronate semialdehyde reductase; Provisional.
Length = 292
Score = 30.0 bits (67), Expect = 1.3
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 17/68 (25%)
Query: 28 LLAVAGSRAVIRIFSPAFHACVRHFYGHGHAINELKFHPQDFNLLLSVSKDHTLRLWNIK 87
+L V G R + R F+P F ++ H +D NL L +K L L N
Sbjct: 213 ILEVHGERMIKRTFNPGF---------------KIALHQKDLNLALQSAKALALNLPNTA 257
Query: 88 TDICIAIF 95
T C +F
Sbjct: 258 T--CQELF 263
>gnl|CDD|224247 COG1328, NrdD, Oxygen-sensitive ribonucleoside-triphosphate
reductase [Nucleotide transport and metabolism].
Length = 700
Score = 28.9 bits (65), Expect = 4.0
Identities = 11/44 (25%), Positives = 15/44 (34%)
Query: 175 VDCVRWLGDFVLSKSCENCIICWKPGRLEDKELRTNETNVTIIN 218
D V G F + C + + G E L T V +N
Sbjct: 368 YDWVVLTGTFKNAMGCRTFLSGNETGDGEGDTLGTGNLGVVTLN 411
>gnl|CDD|233289 TIGR01140, L_thr_O3P_dcar, L-threonine-O-3-phosphate decarboxylase.
This family contains pyridoxal phosphate-binding class
II aminotransferases (see pfam00222) closely related to,
yet distinct from, histidinol-phosphate aminotransferase
(HisC). It is found in cobalamin biosynthesis operons in
Salmonella typhimurium and Bacillus halodurans (each of
which also has HisC) and has been shown to have
L-threonine-O-3-phosphate decarboxylase activity in
Salmonella. Although the gene symbol cobD was assigned
in Salmonella, cobD in other contexts refers to a
different cobalamin biosynthesis enzyme, modeled by
pfam03186 and called cbiB in Salmonella [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 330
Score = 27.5 bits (62), Expect = 8.4
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 20/68 (29%)
Query: 28 LLAVAGSRAVIR------------IFSPAF--HACVRHFYGHGHAINELKFHPQDFNLLL 73
+L V G++ I + +P + +A R + GH + EL D + L
Sbjct: 67 VLPVNGAQEAIYLLPRLLAPGRVLVLAPTYSEYA--RAWRAAGHEVVEL----PDLDRLP 120
Query: 74 SVSKDHTL 81
+ ++ L
Sbjct: 121 AALEEADL 128
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
0.325 0.138 0.451
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: 14,601,806
Number of extensions: 1342370
Number of successful extensions: 1373
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1342
Number of HSP's successfully gapped: 31
Length of query: 291
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 195
Effective length of database: 6,679,618
Effective search space: 1302525510
Effective search space used: 1302525510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.5 bits)