RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13856
(271 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 = 48.5 bits (116), Expect = 1e-06
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 12/83 (14%)
Query: 137 LENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNTF---DDVVW 193
L H+DWV VA++P +AS SQD + +W D T + T V
Sbjct: 131 LRGHTDWVNSVAFSPD----GTFVASSSQDGTIKLW---DLRTGKC--VATLTGHTGEVN 181
Query: 194 NVSWSLTGDILTVSCGDNSVSLW 216
+V++S G+ L S D ++ LW
Sbjct: 182 SVAFSPDGEKLLSSSSDGTIKLW 204
Score = 46.9 bits (112), Expect = 3e-06
Identities = 25/101 (24%), Positives = 42/101 (41%), Gaps = 15/101 (14%)
Query: 125 ICGGDK----WIEETK-----LENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSN 175
DK W ET L H+ +V VA++P + ++S S+D+ + +W
Sbjct: 68 SGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRI----LSSSSRDKTIKVWDVE 123
Query: 176 DYVTWTPFIMNTFDDVVWNVSWSLTGDILTVSCGDNSVSLW 216
T D V +V++S G + S D ++ LW
Sbjct: 124 TGKCLTTL--RGHTDWVNSVAFSPDGTFVASSSQDGTIKLW 162
Score = 43.5 bits (103), Expect = 5e-05
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 134 ETKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIW-TSNDYVTWTPFIMNTFDDVV 192
L+ H+ VRDVA + +AS S D+ + +W T + V
Sbjct: 44 LRTLKGHTGPVRDVAASA----DGTYLASGSSDKTIRLWDLETGECVRT---LTGHTSYV 96
Query: 193 WNVSWSLTGDILTVSCGDNSVSLWKENT 220
+V++S G IL+ S D ++ +W T
Sbjct: 97 SSVAFSPDGRILSSSSRDKTIKVWDVET 124
Score = 42.3 bits (100), Expect = 1e-04
Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 15/97 (15%)
Query: 137 LENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNTF---DDVVW 193
L+ H+ V VA++P L +A+ S D + +W T ++ T V
Sbjct: 5 LKGHTGGVTCVAFSPDGKL----LATGSGDGTIKVWD-----LETGELLRTLKGHTGPVR 55
Query: 194 NVSWSLTGDILTVSCGDNSVSLWKENTDGAWQCITEM 230
+V+ S G L D ++ LW T +C+ +
Sbjct: 56 DVAASADGTYLASGSSDKTIRLWDLETG---ECVRTL 89
Score = 41.9 bits (99), Expect = 2e-04
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 12/84 (14%)
Query: 137 LENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNTF---DDVVW 193
L H + V VA++P L +AS S+D + +W D T + T + V
Sbjct: 215 LRGHENGVNSVAFSPDGYL----LASGSEDGTIRVW---DLRTGEC--VQTLSGHTNSVT 265
Query: 194 NVSWSLTGDILTVSCGDNSVSLWK 217
+++WS G L D ++ +W
Sbjct: 266 SLAWSPDGKRLASGSADGTIRIWD 289
Score = 40.0 bits (94), Expect = 7e-04
Identities = 21/108 (19%), Positives = 42/108 (38%), Gaps = 8/108 (7%)
Query: 123 VRICGGDKWIEETKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTP 182
+++ L H+ V VA++P + S S D + +W D T
Sbjct: 159 IKLWDLRTGKCVATLTGHTGEVNSVAFSPD----GEKLLSSSSDGTIKLW---DLSTGKC 211
Query: 183 F-IMNTFDDVVWNVSWSLTGDILTVSCGDNSVSLWKENTDGAWQCITE 229
+ ++ V +V++S G +L D ++ +W T Q ++
Sbjct: 212 LGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSG 259
Score = 32.7 bits (75), Expect = 0.15
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 136 KLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIW 172
L H++ V +AW+P +AS S D + IW
Sbjct: 256 TLSGHTNSVTSLAWSP----DGKRLASGSADGTIRIW 288
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 44.7 bits (104), Expect = 3e-05
Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 7/101 (6%)
Query: 123 VRICGGDKWIEETKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIW-TSNDYVTWT 181
+++ + L H+D V +A++P +IAS S D + +W S + +
Sbjct: 180 IKLWDLRTGKPLSTLAGHTDPVSSLAFSPD---GGLLIASGSSDGTIRLWDLSTGKLLRS 236
Query: 182 PFIMNTFDDVVWNVSWSLTGDILTVSCGDNSVSLWKENTDG 222
++ V S+S G +L D ++ LW +
Sbjct: 237 TLSGHSDSVV---SSFSPDGSLLASGSSDGTIRLWDLRSSS 274
Score = 43.2 bits (100), Expect = 1e-04
Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 5/93 (5%)
Query: 136 KLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNTFDDVVWNV 195
L HS V VA++P L +AS S D V +W + + + V ++
Sbjct: 279 TLSGHSSSVLSVAFSPDGKL----LASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSL 334
Query: 196 SWSLTGDILTVSCG-DNSVSLWKENTDGAWQCI 227
S+S G +L D ++ LW T + +
Sbjct: 335 SFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTL 367
Score = 40.1 bits (92), Expect = 8e-04
Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 6/93 (6%)
Query: 129 DKWIEETKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNTF 188
LE HS+ V +A++P K + + S D + +W +
Sbjct: 143 TPGKLIRTLEGHSESVTSLAFSPD---GKLLASGSSLDGTIKLWDLRT--GKPLSTLAGH 197
Query: 189 DDVVWNVSWSLTGDILTVSCG-DNSVSLWKENT 220
D V ++++S G +L S D ++ LW +T
Sbjct: 198 TDPVSSLAFSPDGGLLIASGSSDGTIRLWDLST 230
Score = 38.1 bits (87), Expect = 0.003
Identities = 21/94 (22%), Positives = 39/94 (41%), Gaps = 6/94 (6%)
Query: 128 GDKWIEETKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNT 187
K + L+ H V ++++P +++ S D + +W D T P
Sbjct: 315 TGKLLSSLTLKGHEGPVSSLSFSPD---GSLLVSGGSDDGTIRLW---DLRTGKPLKTLE 368
Query: 188 FDDVVWNVSWSLTGDILTVSCGDNSVSLWKENTD 221
V +VS+S G +++ D +V LW +T
Sbjct: 369 GHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTG 402
Score = 34.3 bits (77), Expect = 0.053
Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 6/106 (5%)
Query: 135 TKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNTFDDVVWN 194
+ L HSD V S+ ++AS S D + +W + ++ V +
Sbjct: 236 STLSGHSDSV-----VSSFSPDGSLLASGSSDGTIRLWDLRSSSSLL-RTLSGHSSSVLS 289
Query: 195 VSWSLTGDILTVSCGDNSVSLWKENTDGAWQCITEMGKTSEQRAIK 240
V++S G +L D +V LW T +T G ++
Sbjct: 290 VAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLS 335
Score = 31.2 bits (69), Expect = 0.63
Identities = 20/104 (19%), Positives = 38/104 (36%), Gaps = 6/104 (5%)
Query: 130 KWIEETKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNTFD 189
+ + K V V+++P +++S S D V +W + ++
Sbjct: 359 RTGKPLKTLEGHSNVLSVSFSPDGR----VVSSGSTDGTVRLW--DLSTGSLLRNLDGHT 412
Query: 190 DVVWNVSWSLTGDILTVSCGDNSVSLWKENTDGAWQCITEMGKT 233
V ++ +S G L DN++ LW T + GK
Sbjct: 413 SRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSFSPDGKV 456
Score = 30.1 bits (66), Expect = 1.5
Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 7/94 (7%)
Query: 132 IEETKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIWTSNDYVTWTPFIMNTFDDV 191
+ L H D + +A++P L + S S D + +W ++ + D
Sbjct: 56 LSSLLLRGHEDSITSIAFSPDGEL----LLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSS 111
Query: 192 VWNVSWSLTGD---ILTVSCGDNSVSLWKENTDG 222
V ++ S +L S D +V LW +T G
Sbjct: 112 VSKLALSSPDGNSILLASSSLDGTVKLWDLSTPG 145
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 36.9 bits (86), Expect = 4e-04
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 135 TKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIW 172
L+ H+ V VA++P ++AS S D V +W
Sbjct: 5 RTLKGHTGPVTSVAFSPD----GNLLASGSDDGTVRVW 38
Score = 26.5 bits (59), Expect = 2.2
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 189 DDVVWNVSWSLTGDILTVSCGDNSVSLWK 217
V +V++S G++L D +V +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 = 35.8 bits (83), Expect = 0.001
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 130 KWIEETKLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIW 172
L+ H+ V VA++P +AS S D + +W
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPD----GKYLASGSDDGTIKLW 39
Score = 26.1 bits (58), Expect = 3.0
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 189 DDVVWNVSWSLTGDILTVSCGDNSVSLWK 217
V +V++S G L D ++ LW
Sbjct: 12 TGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|173878 cd08513, PBP2_thermophilic_Hb8_like, The substrate-binding
component of ABC-type thermophilic oligopeptide-binding
protein Hb8-like import systems, contains the type 2
periplasmic binding fold. This family includes the
substrate-binding domain of an ABC-type
oligopeptide-binding protein Hb8 from Thermus
thermophilius and its closest homologs from other
bacteria. The structural topology of this
substrate-binding domain is similar to those of DppA
from Escherichia coli and OppA from Salmonella
typhimurium, and thus belongs to the type 2 periplasmic
binding fold protein (PBP2) superfamily. The DppA binds
dipeptides and some tripeptides and is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 amino acid
residues) and plays a role in recycling of cell wall
peptides, which precludes any involvement in chemotaxis.
The type 2 periplasmic binding proteins are soluble
ligand-binding components of ABC or tripartite
ATP-independent transporters and chemotaxis systems.
Members of the PBP2 superfamily function in uptake of a
variety of metabolites in bacteria such as amino acids,
carbohydrate, ions, and polyamines. Ligands are then
transported across the cytoplasmic membrane energized by
ATP hydrolysis or electrochemical ion gradient. Besides
transport proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 29.2 bits (66), Expect = 2.7
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 8/39 (20%)
Query: 164 SQDRKVIIWTSNDYVTW---TPFIMNTFDDVVWNVSWSL 199
S++ + +T V W TP T DDVV+ +W L
Sbjct: 54 SENGLSVTFTLRPGVKWSDGTPV---TADDVVF--TWEL 87
>gnl|CDD|177697 PLN00067, PLN00067, PsbP domain-containing protein 6; Provisional.
Length = 263
Score = 28.3 bits (63), Expect = 3.5
Identities = 15/73 (20%), Positives = 27/73 (36%)
Query: 28 TESPLRIGHTLISCDTQAHIGIRSTISLLQGSVYLRRESNKAGALSPKLNRSATSSFHEA 87
+ S T S + + + S++S V RRE AL+P + +
Sbjct: 10 SLSFSVSSSTSASSSASSPLAVASSVSPRAAVVIHRRELLLGLALAPLILIAPEPPAEAR 69
Query: 88 AKHLGTVQSSSPA 100
+G+ SP+
Sbjct: 70 EVEVGSYLPPSPS 82
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 28.8 bits (64), Expect = 3.9
Identities = 26/116 (22%), Positives = 50/116 (43%), Gaps = 11/116 (9%)
Query: 136 KLENHSDWVRDVAWAPSWGLSKCMIASCSQDRKVIIW------TSNDYVTWTPFIMNTFD 189
KL+ H+ + D+ + P + ++AS S+D + +W S + I+
Sbjct: 69 KLKGHTSSILDLQFNPCFSE---ILASGSEDLTIRVWEIPHNDESVKEIKDPQCILKGHK 125
Query: 190 DVVWNVSWS-LTGDILTVSCGDNSVSLWK-ENTDGAWQCITEMGKTSEQRAIKKEL 243
+ + W+ + I+ S D+ V++W EN A+Q +S + IK L
Sbjct: 126 KKISIIDWNPMNYYIMCSSGFDSFVNIWDIENEKRAFQINMPKKLSSLKWNIKGNL 181
>gnl|CDD|183507 PRK12407, flgH, flagellar basal body L-ring protein; Reviewed.
Length = 221
Score = 27.9 bits (62), Expect = 5.1
Identities = 12/41 (29%), Positives = 17/41 (41%)
Query: 194 NVSWSLTGDILTVSCGDNSVSLWKENTDGAWQCITEMGKTS 234
+WSL D GD + E+T + Q T GK +
Sbjct: 53 GYNWSLLQDRRAYRVGDILTVILDESTQSSKQAKTNFGKKN 93
>gnl|CDD|234978 PRK01747, mnmC, bifunctional tRNA
(mnm(5)s(2)U34)-methyltransferase/FAD-dependent
cmnm(5)s(2)U34 oxidoreductase; Reviewed.
Length = 662
Score = 28.3 bits (64), Expect = 5.6
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 67 NKAGALSPKLNR--SATSSFHEAA 88
N+ GAL P L++ +A S F AA
Sbjct: 302 NRQGALYPLLSKDDNALSRFFRAA 325
>gnl|CDD|221693 pfam12657, TFIIIC_delta, Transcription factor IIIC subunit delta
N-term. In humans there are six subunits of
transcription factor IIIC, and this one is the 90 kDa
subunit; whereas in fungi the complex resolves into nine
different subunits and this is No. 9 in yeasts. The
whole subunit is involved in RNA polymerase III-mediated
transcription. It is possible that this N-terminal
domain interacts with TFIIIC subunit 8.
Length = 167
Score = 27.4 bits (61), Expect = 6.0
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 5/42 (11%)
Query: 144 VRDVAWAPSWGLSK---CMIASCSQDRKVIIWT-SNDYVTWT 181
VR VAW+P GL+K C++A + + ++ ++ S++ WT
Sbjct: 89 VRAVAWSPP-GLAKNGRCLLAVLTSNLRLSLYEPSSNQGKWT 129
>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
Other tRNA synthetase sub-families are too dissimilar
to be included. This family includes only
phenylalanyl-tRNA synthetases. This is the core
catalytic domain.
Length = 245
Score = 27.5 bits (62), Expect = 7.1
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 5/32 (15%)
Query: 102 LQPKYFKLTVYSTKLTRILILVRICGGDKWIE 133
+P YF T S + + V C WIE
Sbjct: 162 FRPSYFPFTEPSAE-----VDVYCCKLGGWIE 188
>gnl|CDD|236370 PRK09064, PRK09064, 5-aminolevulinate synthase; Validated.
Length = 407
Score = 27.1 bits (61), Expect = 9.7
Identities = 7/12 (58%), Positives = 10/12 (83%)
Query: 166 DRKVIIWTSNDY 177
+R+V +W SNDY
Sbjct: 45 EREVTVWCSNDY 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
0.318 0.130 0.411
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: 13,044,104
Number of extensions: 1137351
Number of successful extensions: 775
Number of sequences better than 10.0: 1
Number of HSP's gapped: 754
Number of HSP's successfully gapped: 32
Length of query: 271
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 176
Effective length of database: 6,723,972
Effective search space: 1183419072
Effective search space used: 1183419072
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 (21.7 bits)
S2: 58 (26.1 bits)