RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6446
(134 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 = 71.2 bits (175), Expect = 7e-16
Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 5/105 (4%)
Query: 18 HPHIVKSSVHFATDSYRLATGSNDKNIRIYDLNKPDAEPTVYRGHSSGIKHVQFFKNNTR 77
H V + V F+ D LATGS D I+++DL +GH+ ++ V + T
Sbjct: 8 HTGGV-TCVAFSPDGKLLATGSGDGTIKVWDLE-TGELLRTLKGHTGPVRDVAASADGTY 65
Query: 78 LISCAEDKTVRLWDVSASAEVQKLE--FGAVPNSLEISRDGTTIT 120
L S + DKT+RLWD+ V+ L V +S+ S DG ++
Sbjct: 66 LASGSSDKTIRLWDLETGECVRTLTGHTSYV-SSVAFSPDGRILS 109
Score = 69.3 bits (170), Expect = 5e-15
Identities = 32/102 (31%), Positives = 52/102 (50%), Gaps = 7/102 (6%)
Query: 4 VWDAVSGEELHSFQ-HPHIVKSSVHFATDSYRLATGSNDKNIRIYDLN--KPDAEPTVYR 60
VWD +G+ L + + H V S V F+ D +A+ S D I+++DL K A
Sbjct: 119 VWDVETGKCLTTLRGHTDWVNS-VAFSPDGTFVASSSQDGTIKLWDLRTGKCVA---TLT 174
Query: 61 GHSSGIKHVQFFKNNTRLISCAEDKTVRLWDVSASAEVQKLE 102
GH+ + V F + +L+S + D T++LWD+S + L
Sbjct: 175 GHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLR 216
Score = 67.7 bits (166), Expect = 2e-14
Identities = 41/121 (33%), Positives = 60/121 (49%), Gaps = 6/121 (4%)
Query: 4 VWDAVSGEELHSFQ-HPHIVKSSVHFATDSYRLATGSNDKNIRIYDLNKPDAEPTVYRGH 62
VWD +GE L + + H V+ V + D LA+GS+DK IR++DL GH
Sbjct: 35 VWDLETGELLRTLKGHTGPVRD-VAASADGTYLASGSSDKTIRLWDLETG-ECVRTLTGH 92
Query: 63 SSGIKHVQFFKNNTRLISCAEDKTVRLWDVSASAEVQKLEF--GAVPNSLEISRDGTTIT 120
+S + V F + L S + DKT+++WDV + L V NS+ S DGT +
Sbjct: 93 TSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWV-NSVAFSPDGTFVA 151
Query: 121 V 121
Sbjct: 152 S 152
Score = 67.0 bits (164), Expect = 3e-14
Identities = 32/100 (32%), Positives = 53/100 (53%), Gaps = 3/100 (3%)
Query: 4 VWDAVSGEELHSFQ-HPHIVKSSVHFATDSYRLATGSNDKNIRIYDLNKPDAEPTVYRGH 62
+WD +G+ + + H V +SV F+ D +L + S+D I+++DL+ RGH
Sbjct: 161 LWDLRTGKCVATLTGHTGEV-NSVAFSPDGEKLLSSSSDGTIKLWDLST-GKCLGTLRGH 218
Query: 63 SSGIKHVQFFKNNTRLISCAEDKTVRLWDVSASAEVQKLE 102
+G+ V F + L S +ED T+R+WD+ VQ L
Sbjct: 219 ENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLS 258
Score = 65.0 bits (159), Expect = 1e-13
Identities = 30/89 (33%), Positives = 51/89 (57%), Gaps = 3/89 (3%)
Query: 4 VWDAVSGEELHSFQ-HPHIVKSSVHFATDSYRLATGSNDKNIRIYDLNKPDAEPTVYRGH 62
+WD +G+ L + + H + V +SV F+ D Y LA+GS D IR++DL + GH
Sbjct: 203 LWDLSTGKCLGTLRGHENGV-NSVAFSPDGYLLASGSEDGTIRVWDLRTGE-CVQTLSGH 260
Query: 63 SSGIKHVQFFKNNTRLISCAEDKTVRLWD 91
++ + + + + RL S + D T+R+WD
Sbjct: 261 TNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 39.6 bits (93), Expect = 2e-04
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 58 VYRGHSSGIKHVQFFKNNTRLISCAEDKTVRLWDVS 93
+GH+ G+ V F + L + + D T+++WD+
Sbjct: 4 TLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLE 39
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 58.9 bits (141), Expect = 3e-11
Identities = 38/125 (30%), Positives = 55/125 (44%), Gaps = 3/125 (2%)
Query: 4 VWDAVSGEELHSFQHPHIVKSSVHFATDSYRLATGSNDKNIRIYDLNKPDAEPTVYRGHS 63
+WD +G+ L S H F+ D LA+GS+D IR++DL + GHS
Sbjct: 225 LWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHS 284
Query: 64 SGIKHVQFFKNNTRLISCAEDKTVRLWDVSASAEVQKLEF---GAVPNSLEISRDGTTIT 120
S + V F + L S + D TVRLWD+ + L +SL S DG+ +
Sbjct: 285 SSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLV 344
Query: 121 VTHGS 125
Sbjct: 345 SGGSD 349
Score = 53.6 bits (127), Expect = 3e-09
Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 2/93 (2%)
Query: 4 VWDAVSGEELHSFQHPHIVKSSVHFATDS-YRLATGSNDKNIRIYDLNKPDAEPTVYRGH 62
+WD +G+ L + SS+ F+ D +A+GS+D IR++DL+ + GH
Sbjct: 182 LWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGH 241
Query: 63 SSGIKHVQFFKNNTRLISCAEDKTVRLWDVSAS 95
S + F + + L S + D T+RLWD+ +S
Sbjct: 242 SDSVVSS-FSPDGSLLASGSSDGTIRLWDLRSS 273
Score = 51.6 bits (122), Expect = 1e-08
Identities = 33/122 (27%), Positives = 55/122 (45%), Gaps = 3/122 (2%)
Query: 4 VWDAVSGEELHSFQHPHIVK-SSVHFATDSYRLATGSNDKNIRIYDLNKPD-AEPTVYRG 61
+WD S L H SV F+ D LA+GS+D +R++DL +G
Sbjct: 267 LWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKG 326
Query: 62 HSSGIKHVQFFKNNTRL-ISCAEDKTVRLWDVSASAEVQKLEFGAVPNSLEISRDGTTIT 120
H + + F + + L ++D T+RLWD+ ++ LE + S+ S DG ++
Sbjct: 327 HEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVS 386
Query: 121 VT 122
Sbjct: 387 SG 388
Score = 46.6 bits (109), Expect = 7e-07
Identities = 26/97 (26%), Positives = 44/97 (45%), Gaps = 2/97 (2%)
Query: 31 DSYRLATGSNDKNIRIYDLNKPDAEPTVYRGHSSGIKHVQFFKNNTRLISCAE-DKTVRL 89
+S LA+ S D ++++DL+ P GHS + + F + L S + D T++L
Sbjct: 123 NSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKL 182
Query: 90 WDVSASAEVQKLEF-GAVPNSLEISRDGTTITVTHGS 125
WD+ + L +SL S DG + + S
Sbjct: 183 WDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSS 219
Score = 44.3 bits (103), Expect = 4e-06
Identities = 27/90 (30%), Positives = 47/90 (52%), Gaps = 2/90 (2%)
Query: 4 VWDAVSGEELHSFQHPHIVKSSVHFATDSYRLATGSNDKNIRIYDLNKPDAEPTVYRGHS 63
+WD +G+ L + + H SV F+ D +++GS D +R++DL+ GH+
Sbjct: 355 LWDLRTGKPLKTLEG-HSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGS-LLRNLDGHT 412
Query: 64 SGIKHVQFFKNNTRLISCAEDKTVRLWDVS 93
S + + F + L S + D T+RLWD+
Sbjct: 413 SRVTSLDFSPDGKSLASGSSDNTIRLWDLK 442
Score = 40.8 bits (94), Expect = 8e-05
Identities = 35/120 (29%), Positives = 56/120 (46%), Gaps = 6/120 (5%)
Query: 4 VWDAVSGEELHSF---QHPHIVKSSVHFATDSYRLATGSNDKNIRIYDLNKPDAEPTVYR 60
+WD +G+ L S H V S S ++ GS+D IR++DL +P
Sbjct: 310 LWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRT--GKPLKTL 367
Query: 61 GHSSGIKHVQFFKNNTRLISCAEDKTVRLWDVSASAEVQKLEFGAVP-NSLEISRDGTTI 119
S + V F + + S + D TVRLWD+S + ++ L+ SL+ S DG ++
Sbjct: 368 EGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSL 427
Score = 37.4 bits (85), Expect = 0.001
Identities = 28/106 (26%), Positives = 46/106 (43%), Gaps = 6/106 (5%)
Query: 25 SVHFATDSYRLATGSNDKNIRIYDLNKPDAEPTVYRG-HSSGIKHVQFFKNNTRLISCA- 82
S+ F+ D L +GS+D I+++DL+ + G H S + + + I A
Sbjct: 70 SIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLAS 129
Query: 83 --EDKTVRLWDVSASAEVQKLEFG--AVPNSLEISRDGTTITVTHG 124
D TV+LWD+S ++ + G SL S DG +
Sbjct: 130 SSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSS 175
Score = 30.4 bits (67), Expect = 0.24
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 4 VWDAVSGEELHSFQHPHIVKSSVHFATDSYRLATGSNDKNIRIYDLNK 51
+WD +G L + +S+ F+ D LA+GS+D IR++DL
Sbjct: 396 LWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKT 443
Score = 28.5 bits (62), Expect = 1.3
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 50 NKPDAEPTVYRGHSSGIKHVQFFKNNTRLISCAEDKTVRLWDVS 93
+ PD + RGH I + F + L+S + D T++LWD+
Sbjct: 52 SLPDLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLD 95
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 50.5 bits (120), Expect = 3e-08
Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 26 VHFATDSYR-LATGSNDKNIRIYDLNKPDAEPTVYRGHSSGIKHVQFFKNNTRLISCAED 84
V F ++S R LA GS D + YDL P GHS + +V+F ++T L+S + D
Sbjct: 623 VQFPSESGRSLAFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFVDSST-LVSSSTD 681
Query: 85 KTVRLWDVSASA 96
T++LWD+S S
Sbjct: 682 NTLKLWDLSMSI 693
>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 = 43.1 bits (102), Expect = 6e-07
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 58 VYRGHSSGIKHVQFFKNNTRLISCAEDKTVRLWD 91
+GH+ + V F + L S ++D T++LWD
Sbjct: 7 TLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 33.8 bits (78), Expect = 0.002
Identities = 17/41 (41%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 9 SGEELHSFQ-HPHIVKSSVHFATDSYRLATGSNDKNIRIYD 48
SGE L + + H V +SV F+ D LA+GS+D I+++D
Sbjct: 1 SGELLKTLKGHTGPV-TSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 42.0 bits (99), Expect = 1e-06
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 57 TVYRGHSSGIKHVQFFKNNTRLISCAEDKTVRLWD 91
+GH+ + V F + L S ++D TVR+WD
Sbjct: 5 RTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 33.5 bits (77), Expect = 0.002
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 10 GEELHSFQHPHIVKSSVHFATDSYRLATGSNDKNIRIYD 48
G+ L + + +SV F+ D LA+GS+D +R++D
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 29.9 bits (67), Expect = 0.35
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 60 RGHSSGIKHVQFFKNNTR-LISCAEDKTVRLWDVSASAE 97
+GH+S I +QF + L S +ED T+R+W++ + E
Sbjct: 71 KGHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDE 109
>gnl|CDD|166487 PLN02846, PLN02846, digalactosyldiacylglycerol synthase.
Length = 462
Score = 26.7 bits (59), Expect = 4.8
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 44 IRIYDLNKPDAEPTVYRGHSSGIKHVQFFKNNTRLISCAEDKTVRLWDVSASAEVQKLEF 103
+R+ DL+ P + + + S +K+ F + L ED + L +V++ E + F
Sbjct: 386 LRVADLDLPSS----AKPNKSSLKN--FMSTSPNLKKNMEDASAYLHNVASGFETSRRAF 439
Query: 104 GAVPNSLE 111
GA+P SL+
Sbjct: 440 GAIPGSLQ 447
>gnl|CDD|178238 PLN02631, PLN02631, ferric-chelate reductase.
Length = 699
Score = 26.5 bits (58), Expect = 4.9
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 107 PNSLEISRDGTTITVTHGSCVT 128
PNS ++SR + I V+ GS +T
Sbjct: 404 PNSFDVSRHNSLILVSGGSGIT 425
>gnl|CDD|216115 pfam00780, CNH, CNH domain. Domain found in NIK1-like kinase,
mouse citron and yeast ROM1, ROM2. Unpublished
observations.
Length = 266
Score = 26.0 bits (58), Expect = 5.9
Identities = 18/99 (18%), Positives = 29/99 (29%), Gaps = 12/99 (12%)
Query: 41 DKNIRIYDL---NKPDAEPTVYRGHSSGIKHVQFFK----NNTRLISCAEDKTVRL--WD 91
DK + +Y L + + K FF R + A +T++L W
Sbjct: 54 DKQLYVYPLSALDSKELSSKSAPQKLPETKGCSFFARAGYCGGRFLVVAVKRTIKLYEWY 113
Query: 92 VSASAEVQKL-EFGAVPNSLEISRDGTTITVTHGSCVTF 129
+ EF I+ + V G F
Sbjct: 114 EPLKKFHKLFKEFYVPAEVFSIAFLKPKLCV--GCAKGF 150
>gnl|CDD|234567 PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed.
Length = 309
Score = 25.9 bits (58), Expect = 6.8
Identities = 5/37 (13%), Positives = 14/37 (37%), Gaps = 3/37 (8%)
Query: 83 EDKTVRLWDVSASAEVQKLEFGAVPNSLEISRDGTTI 119
+ + +++ + G + L I +DG +
Sbjct: 238 DGQRLKILEAELVEASGSGAPGTI---LAIDKDGIVV 271
>gnl|CDD|213866 TIGR03818, MotA1, flagellar motor stator protein MotA. The MotA
protein, along with its partner MotB, comprise the
stator complex of the bacterial flagellar motor. MotAB
span the cytoplasmic membrane and undergo conformational
changes powered by the translocation of protons. These
conformational changes in turn are communicated to the
rotor assembly, producing torque. This model represents
one family of MotA proteins which are often not
identified by the "transporter, MotA/TolQ/ExbB proton
channel family" model, pfam01618.
Length = 282
Score = 25.9 bits (58), Expect = 7.7
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 17 QHPHIVKSS--VHFATDSYRLATGSN 40
++P I+K V F D RL N
Sbjct: 112 KYPKILKDHHLVEFICDYLRLMVMGN 137
>gnl|CDD|221300 pfam11898, DUF3418, Domain of unknown function (DUF3418). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria. This domain is typically
between 582 to 594 amino acids in length. This domain is
found associated with pfam07717, pfam00271, pfam04408.
Length = 586
Score = 25.9 bits (58), Expect = 9.3
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 88 RLWDVSASAEVQKLE---FGAVPNSLEISRDGTTITV 121
+ E L FG +P +E+ R G T+T
Sbjct: 293 AFAAAADGIERSGLTTWDFGELPEEVELKRGGQTVTG 329
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
0.316 0.130 0.385
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,458,939
Number of extensions: 527139
Number of successful extensions: 517
Number of sequences better than 10.0: 1
Number of HSP's gapped: 497
Number of HSP's successfully gapped: 34
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
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 (21.6 bits)
S2: 54 (24.6 bits)