RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11351
(224 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 = 55.0 bits (133), Expect = 4e-09
Identities = 33/168 (19%), Positives = 62/168 (36%), Gaps = 9/168 (5%)
Query: 32 FYLHERPVYGLSVDPSQDAIFASACDDGRVLLFDTRSREEATELAVNSGPFHAVMFNPVE 91
H V ++ P + A+ DG + ++D + E L ++GP V +
Sbjct: 5 LKGHTGGVTCVAFSPDGK-LLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADG 63
Query: 92 ARLVATANSKDGIALYDTRKPKEVLMQYGSCESCMSIRFNKAGTQLLGLRRRLPPVLYNT 151
L + ++ K I L+D + V G S+ F+ G L R +++
Sbjct: 64 TYLASGSSDKT-IRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV 122
Query: 152 RSSSPVAQF-DHEGYYNSCTMKSCCFAGTQDEYVVSGSDDFVLYMWRV 198
+ + H + N S F+ +V S S D + +W +
Sbjct: 123 ETGKCLTTLRGHTDWVN-----SVAFSPDGT-FVASSSQDGTIKLWDL 164
Score = 54.6 bits (132), Expect = 5e-09
Identities = 40/181 (22%), Positives = 76/181 (41%), Gaps = 10/181 (5%)
Query: 19 VISHDMASGDPI-DFYLHERPVYGLSVDPSQDAIFASACDDGRVLLFDTRSREEATELAV 77
+ D+ +G + H V ++ P + AS+ DG + L+D R+ + L
Sbjct: 117 IKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFV-ASSSQDGTIKLWDLRTGKCVATLTG 175
Query: 78 NSGPFHAVMFNPVEARLVATANSKDGIALYDTRKPKEVLMQYGSCESCMSIRFNKAGTQL 137
++G ++V F+P +L+++++ I L+D K + G S+ F+ G L
Sbjct: 176 HTGEVNSVAFSPDGEKLLSSSSDGT-IKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLL 234
Query: 138 LGLRRRLPPVLYNTRSSSPVAQFDHEGYYNSCTMKSCCFAGTQDE-YVVSGSDDFVLYMW 196
+++ R+ V G+ NS T A + D + SGS D + +W
Sbjct: 235 ASGSEDGTIRVWDLRTGECVQTL--SGHTNSVT----SLAWSPDGKRLASGSADGTIRIW 288
Query: 197 R 197
Sbjct: 289 D 289
Score = 54.6 bits (132), Expect = 5e-09
Identities = 29/144 (20%), Positives = 57/144 (39%), Gaps = 14/144 (9%)
Query: 5 DPIKVLRVIGNDDHVIS---------HDMASGDPI-DFYLHERPVYGLSVDPSQDAIFAS 54
D + + + V S D+ +G + H V ++ P + S
Sbjct: 136 DWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEK-LLS 194
Query: 55 ACDDGRVLLFDTRSREEATELAVNSGPFHAVMFNPVEARLVATANSKDG-IALYDTRKPK 113
+ DG + L+D + + L + ++V F+P + + S+DG I ++D R +
Sbjct: 195 SSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSP--DGYLLASGSEDGTIRVWDLRTGE 252
Query: 114 EVLMQYGSCESCMSIRFNKAGTQL 137
V G S S+ ++ G +L
Sbjct: 253 CVQTLSGHTNSVTSLAWSPDGKRL 276
Score = 50.0 bits (120), Expect = 2e-07
Identities = 43/190 (22%), Positives = 81/190 (42%), Gaps = 16/190 (8%)
Query: 14 GNDDHVISHDMASGDPID-FYLHERPVYGLSVDPSQDAIFASACDDGRVLLFDTRSREEA 72
+D + D+ +G+ + H V ++ P I +S+ D + ++D + +
Sbjct: 70 SSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGR-ILSSSSRDKTIKVWDVETGKCL 128
Query: 73 TELAVNSGPFHAVMFNPVEARLVATANSKDG-IALYDTRKPKEVLMQYGSCESCMSIRFN 131
T L ++ ++V F+P VA++ S+DG I L+D R K V G S+ F+
Sbjct: 129 TTLRGHTDWVNSVAFSPDG-TFVASS-SQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFS 186
Query: 132 KAGTQLL--GLRRRLPPVLYNTRSSSPVAQFD-HEGYYNSCTMKSCCFAGTQDEYVVSGS 188
G +LL + L++ + + HE NS F+ + SGS
Sbjct: 187 PDGEKLLSSSSDGTIK--LWDLSTGKCLGTLRGHENGVNSV-----AFSPDGY-LLASGS 238
Query: 189 DDFVLYMWRV 198
+D + +W +
Sbjct: 239 EDGTIRVWDL 248
Score = 46.2 bits (110), Expect = 4e-06
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 14 GNDDHVISHDMASGDPI-DFYLHERPVYGLSVDPSQDAIFASACDDGRVLLFDTRSREEA 72
+D + D+++G + HE V ++ P + AS +DG + ++D R+ E
Sbjct: 196 SSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGY-LLASGSEDGTIRVWDLRTGECV 254
Query: 73 TELAVNSGPFHAVMFNPVEARLVATANSKDGIA 105
L+ ++ ++ ++P RL + S DG
Sbjct: 255 QTLSGHTNSVTSLAWSPDGKRLASG--SADGTI 285
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 55.1 bits (131), Expect = 6e-09
Identities = 46/212 (21%), Positives = 83/212 (39%), Gaps = 11/212 (5%)
Query: 13 IGNDDHVISHDMASGDPIDFYLHERPVYGLSVDPSQDAIFASACDDGRVLLFDTRS-REE 71
+D + D+++G + L +S ++ AS DG + L+D RS
Sbjct: 217 GSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSL 276
Query: 72 ATELAVNSGPFHAVMFNPVEARLVATANSKDGIALYDTRKPKEV--LMQYGSCESCMSIR 129
L+ +S +V F+P L A+ +S + L+D K + L G S+
Sbjct: 277 LRTLSGHSSSVLSVAFSPDGKLL-ASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLS 335
Query: 130 FNKAGTQLL-GLRRRLPPVLYNTRSSSPVAQFDHEGYYNSCTMKSCCFAGTQDEYVVSGS 188
F+ G+ L+ G L++ R+ P+ + S + V SGS
Sbjct: 336 FSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGR------VVSSGS 389
Query: 189 DDFVLYMWRVPRDDIYVSSDIYVCRHGSLEVS 220
D + +W + + + D + R SL+ S
Sbjct: 390 TDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFS 421
Score = 52.8 bits (125), Expect = 4e-08
Identities = 38/179 (21%), Positives = 69/179 (38%), Gaps = 9/179 (5%)
Query: 32 FYLHERPVYGLSVDPSQDAIFASACDDGRVLLFDTRSREEATELAV--NSGPFHAVMFNP 89
H V ++ P + AS DG V L+D + + + L + + GP ++ F+P
Sbjct: 280 LSGHSSSVLSVAFSPD-GKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSP 338
Query: 90 VEARLVATANSKDGIALYDTRKPKEVLMQYGSCESCMSIRFNKAGTQLLGLRRRLPPVLY 149
+ LV+ + I L+D R K + G + +S+ F+ G + L+
Sbjct: 339 DGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGH-SNVLSVSFSPDGRVVSSGSTDGTVRLW 397
Query: 150 NTRSSSPVAQFDHEGYYNSCTMKSCCFAGTQDEYVVSGSDDFVLYMWRVPRDDIYVSSD 208
+ + S + D S F+ + SGS D + +W + VS
Sbjct: 398 DLSTGSLLRNLDGHTSRV----TSLDFSPDGK-SLASGSSDNTIRLWDLKTSLKSVSFS 451
Score = 47.4 bits (111), Expect = 2e-06
Identities = 38/180 (21%), Positives = 73/180 (40%), Gaps = 4/180 (2%)
Query: 31 DFYLHERPVYGLSVDPSQDAIFASACDDGRVLLFDTRSREEATELAVNSGPFHAVMFNPV 90
H V L+ P + + + DG + L+D R+ + + LA ++ P ++ F+P
Sbjct: 150 TLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPD 209
Query: 91 EARLVATANSKDGIALYDTRKPKEVLMQYGSCESCMSIRFNKAGTQLLGLRRRLPPVLYN 150
L+A+ +S I L+D K + + F+ G+ L L++
Sbjct: 210 GGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWD 269
Query: 151 TRSSSPVAQFDHEGYYNSCTMKSCCFAGTQDEYVVSGSDDFVLYMWRVPRDDIYVSSDIY 210
RSSS +S ++ S F+ + + SGS D + +W + + S +
Sbjct: 270 LRSSS---SLLRTLSGHSSSVLSVAFSP-DGKLLASGSSDGTVRLWDLETGKLLSSLTLK 325
Score = 40.5 bits (93), Expect = 4e-04
Identities = 36/163 (22%), Positives = 64/163 (39%), Gaps = 5/163 (3%)
Query: 8 KVLRVIGNDDHVISHDMASGDPI---DFYLHERPVYGLSVDPSQDAIFASACDDGRVLLF 64
K+L +D V D+ +G + HE PV LS P + + DDG + L+
Sbjct: 297 KLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLW 356
Query: 65 DTRSREEATELAVNSGPFHAVMFNPVEARLVATANSKDGIALYDTRKPKEVLMQYGSCES 124
D R+ + L +V F+P R+V++ ++ + L+D + G
Sbjct: 357 DLRTGKPLKTL-EGHSNVLSVSFSPDG-RVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSR 414
Query: 125 CMSIRFNKAGTQLLGLRRRLPPVLYNTRSSSPVAQFDHEGYYN 167
S+ F+ G L L++ ++S F +G
Sbjct: 415 VTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSFSPDGKVL 457
Score = 35.4 bits (80), Expect = 0.016
Identities = 35/197 (17%), Positives = 68/197 (34%), Gaps = 16/197 (8%)
Query: 14 GNDDHVISHDMASGDPIDFYL---HERPVYGLSVDPSQDAIFASAC--DDGRVLLFD-TR 67
+D + D+ +G+ + L H+ V L++ A DG V L+D +
Sbjct: 84 SSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLST 143
Query: 68 SREEATELAVNSGPFHAVMFNPVEARLVATANSKDGIALYDTRKPKEVLMQYGSCESCMS 127
+ L +S ++ F+P L + ++ I L+D R K + G + S
Sbjct: 144 PGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSS 203
Query: 128 IRFNKAGT-QLLGLRRRLPPVLYNTRSSSPVAQ--FDHEGYYNSCTMKSCCFAGTQDEYV 184
+ F+ G + L++ + + H S +
Sbjct: 204 LAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPD-------GSLL 256
Query: 185 VSGSDDFVLYMWRVPRD 201
SGS D + +W +
Sbjct: 257 ASGSSDGTIRLWDLRSS 273
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 31.9 bits (73), Expect = 0.019
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 32 FYLHERPVYGLSVDPSQDAIFASACDDGRVLLFD 65
H PV ++ P + + AS DDG V ++D
Sbjct: 7 LKGHTGPVTSVAFSPDGN-LLASGSDDGTVRVWD 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 = 31.9 bits (73), Expect = 0.020
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 32 FYLHERPVYGLSVDPSQDAIFASACDDGRVLLFD 65
H PV ++ P AS DDG + L+D
Sbjct: 8 LKGHTGPVTSVAFSPDGK-YLASGSDDGTIKLWD 40
>gnl|CDD|173856 cd08491, PBP2_NikA_DppA_OppA_like_12, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. 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. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. 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 = 473
Score = 33.1 bits (76), Expect = 0.11
Identities = 23/93 (24%), Positives = 29/93 (31%), Gaps = 6/93 (6%)
Query: 20 ISHDMASGDP---IDFYLHERPVYGLSVDPSQDAIFA---SACDDGRVLLFDTRSREEAT 73
HD SGD Y DP DA+ +A D R LF
Sbjct: 376 SQHDNNSGDASFTFPVYYLSEGSQSTFGDPELDALIKAAMAATGDERAKLFQEIFAYVHD 435
Query: 74 ELAVNSGPFHAVMFNPVEARLVATANSKDGIAL 106
E+ + FH V + V RL + L
Sbjct: 436 EIVADIPMFHMVGYTRVSKRLDYKPDIATNSEL 468
>gnl|CDD|181704 PRK09218, PRK09218, peptide deformylase; Validated.
Length = 136
Score = 29.5 bits (67), Expect = 0.76
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 21/53 (39%)
Query: 75 LAVNSGPFHAVMFNPVEARLVATANSKDGIALYDTRKPKEVLMQYGSCESCMS 127
+ + G VMFNPV +V+ + Y+T E C+S
Sbjct: 56 IIFSLGFVPVVMFNPV---IVSKSGP------YET------------EEGCLS 87
>gnl|CDD|225926 COG3391, COG3391, Uncharacterized conserved protein [Function
unknown].
Length = 381
Score = 29.5 bits (66), Expect = 1.2
Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 1/84 (1%)
Query: 2 ASGDPIKVLRVIGNDDHVISHDMASGDPIDFYLHERPVYGLSVDPSQDAIFASACDDGRV 61
G + V ND VI + P G++V+P+ + ++ + D V
Sbjct: 40 PDGTQVYVANSGSNDVSVIDATSNTVTQSLSVGGVYP-AGVAVNPAGNKVYVTTGDSNTV 98
Query: 62 LLFDTRSREEATELAVNSGPFHAV 85
+ DT + + V GP
Sbjct: 99 SVIDTATNTVLGSIPVGLGPVGLA 122
>gnl|CDD|237768 PRK14615, PRK14615, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 296
Score = 28.2 bits (63), Expect = 3.2
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 110 RKPKEVLMQYGSCESCMSIRFNKAGTQLLGLRRR 143
R+ KE L+++G+ + MS +G+ + GL RR
Sbjct: 244 RRLKETLLRHGAAAALMS----GSGSSVFGLFRR 273
>gnl|CDD|238793 cd01535, 4RHOD_Repeat_4, Member of the Rhodanese Homology Domain
superfamily, repeat 4. This CD includes putative
rhodanese-related sulfurtransferases which contain 4
copies of the Rhodanese Homology Domain. This CD aligns
the 4th repeat which, in general, contains the putative
catalytic Cys residue.
Length = 145
Score = 27.1 bits (60), Expect = 4.8
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 41 GLSVDPSQDAIFASACDDGRVLLFDTRSREEA 72
GL V+ + + + D R T + EA
Sbjct: 91 GLPVESGETRLASPRIDRYRRPYEGTDNPREA 122
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 27.7 bits (61), Expect = 6.8
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 1/79 (1%)
Query: 35 HERPVYGLSVDPSQDAIFASACDDGRVLLFDTRSREEATELAVNSGPFHAVMFNPVEARL 94
HE+ V+ + + + AS DDG V L+ + + V F R
Sbjct: 574 HEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKAN-ICCVQFPSESGRS 632
Query: 95 VATANSKDGIALYDTRKPK 113
+A ++ + YD R PK
Sbjct: 633 LAFGSADHKVYYYDLRNPK 651
>gnl|CDD|223408 COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid
metabolism].
Length = 310
Score = 26.9 bits (60), Expect = 9.3
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 61 VLLFDTRSREEATELAVNSGPFHAVMFNPVEARL 94
+ + A L V SGPFH+ + P L
Sbjct: 181 AEILKEAGAKRAIPLPV-SGPFHSPLMKPAADEL 213
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 0.136 0.414
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: 11,387,069
Number of extensions: 1036501
Number of successful extensions: 789
Number of sequences better than 10.0: 1
Number of HSP's gapped: 773
Number of HSP's successfully gapped: 26
Length of query: 224
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 131
Effective length of database: 6,812,680
Effective search space: 892461080
Effective search space used: 892461080
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)