RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6859
(261 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 = 53.5 bits (129), Expect = 2e-08
Identities = 51/260 (19%), Positives = 96/260 (36%), Gaps = 28/260 (10%)
Query: 2 HRSPITHVV-VTKTDFVITASNDGHIKFWKKQEEGIEFVKHFRSHLGVIHSICTNYNGTL 60
H P+ V ++ + S+D I+ W + E V+ H + S+ + +G +
Sbjct: 50 HTGPVRDVAASADGTYLASGSSDKTIRLWDLETG--ECVRTLTGHTSYVSSVAFSPDGRI 107
Query: 61 LCTVASDKAMKVFDVINFDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSRVHIYD 120
L + + DK +KV+DV + L V + + D A S QD + + ++D
Sbjct: 108 LSSSSRDKTIKVWDVETGKCL--TTLRGHTDWVNSVAFSPDG-TFVASSSQDGT-IKLWD 163
Query: 121 CKGNDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSHVHIYDCKGNGTPLHVLDRL 180
+ L V + + D + S + ++D G L L R
Sbjct: 164 --LRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSS--SDGTIKLWDLST-GKCLGTL-RG 217
Query: 181 HTKPVVLIKFNPIYQVVVSVDKAGILEYWSGYKQEFKFPKCVHFESKLDTDLFEFAKNKT 240
H V + F+P ++ S + G + W E + + +
Sbjct: 218 HENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGEC---------------VQTLSGHTN 262
Query: 241 YPSGLSFSPDGNKFVTISMD 260
+ L++SPDG + + S D
Sbjct: 263 SVTSLAWSPDGKRLASGSAD 282
Score = 45.0 bits (107), Expect = 2e-05
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 2 HRSPITHVVV-TKTDFVITASNDGHIKFWKKQEEGIEFVKHFRSHLGVIHSICTNYNGTL 60
H + + V + + S DG I+ W + E V+ H + S+ + +G
Sbjct: 218 HENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTG--ECVQTLSGHTNSVTSLAWSPDGKR 275
Query: 61 LCTVASDKAMKVFD 74
L + ++D ++++D
Sbjct: 276 LASGSADGTIRIWD 289
Score = 42.3 bits (100), Expect = 1e-04
Identities = 46/223 (20%), Positives = 90/223 (40%), Gaps = 25/223 (11%)
Query: 39 VKHFRSHLGVIHSICTNYNGTLLCTVASDKAMKVFDVINFDMINMIKLDFTPLTVECIHY 98
+ + H G + + + +G LL T + D +KV+D+ +++ +K V +
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHT--GPVRDVAA 59
Query: 99 LGDAIPTAAVSDQDSSRVHIYDCKGNDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQD 158
D A+ S + R ++D + + + + + V + + D + S +D
Sbjct: 60 SADGTYLASGSSDKTIR--LWDLETGECVRTLTGHTSY--VSSVAFSPD-GRILSSSSRD 114
Query: 159 SSHVHIYDCKGNGTPLHVLDRLHTKPVVLIKFNPIYQVVVSVDKAGILEYWSGYKQEFKF 218
+ + ++D + G L L R HT V + F+P V S + G ++ W
Sbjct: 115 KT-IKVWDVE-TGKCLTTL-RGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTG---- 167
Query: 219 PKCVHFESKLDTDLFEFAKNKTYPSGLSFSPDGNKFVTISMDR 261
KCV + + ++FSPDG K ++ S D
Sbjct: 168 -KCVA----------TLTGHTGEVNSVAFSPDGEKLLSSSSDG 199
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 50.5 bits (119), Expect = 3e-07
Identities = 46/260 (17%), Positives = 95/260 (36%), Gaps = 23/260 (8%)
Query: 2 HRSPITHVVVTKTDFVITASNDGHIKFWKKQEEGIEFVKHFRSHLGVIHSICTNYNGTLL 61
+ + ++S DG +K W G + ++ H + S+ + +G LL
Sbjct: 112 VSKLALSSPDGNSILLASSSLDGTVKLWDLSTPG-KLIRTLEGHSESVTSLAFSPDGKLL 170
Query: 62 CTVAS-DKAMKVFDVINFDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSRVHIYD 120
+ +S D +K++D+ + L V + + D A D + + ++D
Sbjct: 171 ASGSSLDGTIKLWDLRTGK--PLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGT-IRLWD 227
Query: 121 CKGNDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSHVHIYDCKGNGTPLHVLDRL 180
++ + V G + A D + + ++D + + + L L
Sbjct: 228 LSTGKLLRSTLSGHSDSVVSSFSPDGSLL---ASGSSDGT-IRLWDLRSSSSLLRTLSG- 282
Query: 181 HTKPVVLIKFNPIYQVVVSVDKAGILEYWSGYKQEFKFPKCVHFESKLDTDLFEFAKNKT 240
H+ V+ + F+P +++ S G + W E+ ++
Sbjct: 283 HSSSVLSVAFSPDGKLLASGSSDGTVRLWD-------------LETGKLLSSLTLKGHEG 329
Query: 241 YPSGLSFSPDGNKFVTISMD 260
S LSFSPDG+ V+ D
Sbjct: 330 PVSSLSFSPDGSLLVSGGSD 349
Score = 47.8 bits (112), Expect = 2e-06
Identities = 43/262 (16%), Positives = 90/262 (34%), Gaps = 26/262 (9%)
Query: 2 HRSPITHVVVT--KTDFVITASNDGHIKFWKKQEEGIEFVKHFRSHLGVIHSICTNYNGT 59
H P++ + + + + S+DG I+ W G H + S +
Sbjct: 197 HTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLST-GKLLRSTLSGHSDSVVSSFSPDGSL 255
Query: 60 LLCTVASDKAMKVFDVINFDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSRVHIY 119
L + +SD ++++D + + L +V + + D A+ S + V ++
Sbjct: 256 LA-SGSSDGTIRLWD-LRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGT--VRLW 311
Query: 120 DCKGNDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSHVHIYDCKGNGTPLHVLDR 179
D + +++ + L V + + D D + ++D + T +
Sbjct: 312 DLETGKLLSSLTLKGHEGPVSSLSFSPD-GSLLVSGGSDDGTIRLWDLR---TGKPLKTL 367
Query: 180 LHTKPVVLIKFNPIYQVVVSVDKAGILEYWSGYKQEFKFPKCVHFESKLDTDLFEFAKNK 239
V+ + F+P +VV S G + W + + ++
Sbjct: 368 EGHSNVLSVSFSPDGRVVSSGSTDGTVRLWD-------------LSTGSLLRNLDGHTSR 414
Query: 240 TYPSGLSFSPDGNKFVTISMDR 261
L FSPDG + S D
Sbjct: 415 VTS--LDFSPDGKSLASGSSDN 434
Score = 46.6 bits (109), Expect = 6e-06
Identities = 32/216 (14%), Positives = 77/216 (35%), Gaps = 9/216 (4%)
Query: 2 HRSPITHVVVTKTDFVITASNDGHIKFWKKQEEGIEFVKHFRSHLGVIHSICTNYNGTLL 61
H + + + S+DG I+ W + ++ H + S+ + +G LL
Sbjct: 241 HSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSL-LRTLSGHSSSVLSVAFSPDGKLL 299
Query: 62 CTVASDKAMKVFDVINFDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSRVHIYDC 121
+ +SD ++++D+ +++ + L V + + D D + ++D
Sbjct: 300 ASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPD-GSLLVSGGSDDGTIRLWDL 358
Query: 122 KGNDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSHVHIYDCKGNGTPLHVLDRLH 181
+ + ++ V + + D ++ S + V ++D + L H
Sbjct: 359 RTGKPLKTLE---GHSNVLSVSFSPDGRVVSSGSTDGT--VRLWDL--STGSLLRNLDGH 411
Query: 182 TKPVVLIKFNPIYQVVVSVDKAGILEYWSGYKQEFK 217
T V + F+P + + S + W
Sbjct: 412 TSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKS 447
Score = 45.5 bits (106), Expect = 1e-05
Identities = 45/264 (17%), Positives = 90/264 (34%), Gaps = 25/264 (9%)
Query: 2 HRSPITHVVVTKT-DFVITASNDGHIKFWKKQEEGIEFVKHFRSHLGVIHSIC---TNYN 57
H IT + + + +++ S+DG IK W H + + + N
Sbjct: 64 HEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGN 123
Query: 58 GTLLCTVASDKAMKVFDVINFDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSRVH 117
LL + + D +K++D ++ + L+ +V + + D A +
Sbjct: 124 SILLASSSLDGTVKLWD-LSTPGKLIRTLEGHSESVTSLAFSPD-GKLLASGSSLDGTIK 181
Query: 118 IYDCKGNDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSSHVHIYDCKGNGTPLHVL 177
++D + + L V + + D A D + + ++D G L
Sbjct: 182 LWDLRTGK--PLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGT-IRLWDLS-TGKLLRST 237
Query: 178 DRLHTKPVVLIKFNPIYQVVVSVDKAGILEYWSGYKQEFKFPKCVHFESKLDTDLFEFAK 237
H+ VV F+P ++ S G + W + L +
Sbjct: 238 LSGHSDSVVSS-FSPDGSLLASGSSDGTIRLWD--------------LRSSSSLLRTLSG 282
Query: 238 NKTYPSGLSFSPDGNKFVTISMDR 261
+ + ++FSPDG + S D
Sbjct: 283 HSSSVLSVAFSPDGKLLASGSSDG 306
Score = 40.1 bits (92), Expect = 7e-04
Identities = 48/221 (21%), Positives = 82/221 (37%), Gaps = 21/221 (9%)
Query: 42 FRSHLGVIHSICTNYNGTLLCTVASDKAMKVFDVINFDMINMIKLDFTPLTVECIHYL-G 100
R H I SI + +G LL + +SD +K++D+ N + + +V +
Sbjct: 61 LRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSP 120
Query: 101 DAIPTAAVSDQDSSRVHIYDCKGNDMINMIKLDFTPLTVECIHYLGDAIPTAAVSDQDSS 160
D S V ++D + L+ +V + + D A+ S D +
Sbjct: 121 DGNSILLASSSLDGTVKLWD-LSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGT 179
Query: 161 HVHIYDCKGNGTPLHVLDRLHTKPVVLIKFNPI-YQVVVSVDKAGILEYWSGYKQEFKFP 219
+ ++D + G PL L HT PV + F+P ++ S G + W
Sbjct: 180 -IKLWDLR-TGKPLSTLA-GHTDPVSSLAFSPDGGLLIASGSSDGTIRLWD-----LSTG 231
Query: 220 KCVHFESKLDTDLFEFAKNKTYPSGLSFSPDGNKFVTISMD 260
K + +D SFSPDG+ + S D
Sbjct: 232 KLLRSTLSGHSD----------SVVSSFSPDGSLLASGSSD 262
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 30.4 bits (69), Expect = 0.069
Identities = 9/38 (23%), Positives = 22/38 (57%)
Query: 37 EFVKHFRSHLGVIHSICTNYNGTLLCTVASDKAMKVFD 74
+ ++ + H G + S+ + +G LL + + D ++V+D
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 28.9 bits (65), Expect = 0.25
Identities = 8/30 (26%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 2 HRSPITHVVVTKTD-FVITASNDGHIKFWK 30
H P+T V + + + S+DG ++ W
Sbjct: 10 HTGPVTSVAFSPDGNLLASGSDDGTVRVWD 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 = 30.4 bits (69), Expect = 0.087
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 37 EFVKHFRSHLGVIHSICTNYNGTLLCTVASDKAMKVFD 74
E +K + H G + S+ + +G L + + D +K++D
Sbjct: 3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 30.0 bits (68), Expect = 0.11
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 2 HRSPITHVVVTKTD-FVITASNDGHIKFWK 30
H P+T V + ++ + S+DG IK W
Sbjct: 11 HTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|237994 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1),
carboxy-terminal domain. The BRCT domain is found
within many DNA damage repair and cell cycle checkpoint
proteins. The unique diversity of this domain
superfamily allows BRCT modules to interact forming
homo/hetero BRCT multimers, BRCT-non-BRCT interactions,
and interactions within DNA strand breaks.
Length = 72
Score = 28.8 bits (65), Expect = 0.57
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 6 ITHVVVTKTDFVITASNDGHIKFWKKQEEGIEFVKH 41
+T V KT VI S+ G K K + GI V
Sbjct: 29 VTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTP 64
>gnl|CDD|215978 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain. The BRCT domain
is found predominantly in proteins involved in cell
cycle checkpoint functions responsive to DNA damage.
The BRCT domain of XRCC1 forms a homodimer in the
crystal structure. This suggests that pairs of BRCT
domains associate as homo- or heterodimers. BRCT
domains are often found as tandem-repeat pairs.
Structures of the BRCA1 BRCT domains revealed a basis
for a widely utilised head-to-tail BRCT-BRCT
oligomerisation mode. This conserved tandem BRCT
architecture facilitates formation of the canonical
BRCT phospho-peptide interaction cleft at a groove
between the BRCT domains. Disease associated missense
and nonsense mutations in the BRCA1 BRCT domains
disrupt peptide binding by directly occluding this
peptide binding groove, or by disrupting key conserved
BRCT core folding determinants.
Length = 77
Score = 28.9 bits (65), Expect = 0.66
Identities = 12/36 (33%), Positives = 15/36 (41%)
Query: 6 ITHVVVTKTDFVITASNDGHIKFWKKQEEGIEFVKH 41
+T + KT VI N G +K K GI V
Sbjct: 35 VTDSLSKKTTHVIVGENAGTLKLLKAIALGIPIVTE 70
>gnl|CDD|216410 pfam01283, Ribosomal_S26e, Ribosomal protein S26e.
Length = 113
Score = 29.2 bits (66), Expect = 0.99
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 10/40 (25%)
Query: 40 KHFRSHLGVIHSICTNYNGTLLC--TVASDKAMKVFDVIN 77
K R H+ + CTN C V DKA+K F V N
Sbjct: 12 KKNRGHVKPVR--CTN------CGRCVPKDKAIKRFVVRN 43
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 27.9 bits (62), Expect = 6.6
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 19 TASNDGHIKFWKKQEEGIEFVKHFRSHLGVIHSICTNYNGTLLCTVASDKAMKVFD 74
+A D + W E G V+ + H I S+ N +G+LLCT + DK + + D
Sbjct: 143 SAGADMVVNVWD-VERGKA-VEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIID 196
>gnl|CDD|129781 TIGR00698, TIGR00698, conserved hypothetical integral membrane
protein. Members of this family are found so far only
in one archaeal species, Archaeoglobus fulgidus, and in
two related bacterial species, Haemophilus influenzae
and Escherichia coli. It has 9 GES predicted
transmembrane regions at conserved locations in all
members. These proteins have a molecular weight of
approximately 35 to 38 kDa [Hypothetical proteins,
Conserved].
Length = 335
Score = 27.2 bits (60), Expect = 9.4
Identities = 8/48 (16%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 2 HRSPITHVVVTKTDFVITASNDGHIKFWKKQEEGIEFVKHFRSHLGVI 49
S + ++ + A N + + ++++ G+ F K F +G+
Sbjct: 30 ALSALFLAIL----LGMVAGNTIYPQRDEEKKRGVLFAKPFLLRIGIT 73
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
0.323 0.138 0.427
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: 13,027,528
Number of extensions: 1184531
Number of successful extensions: 934
Number of sequences better than 10.0: 1
Number of HSP's gapped: 907
Number of HSP's successfully gapped: 33
Length of query: 261
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 166
Effective length of database: 6,723,972
Effective search space: 1116179352
Effective search space used: 1116179352
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.1 bits)