RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4579
(368 letters)
>gnl|CDD|221499 pfam12265, CAF1C_H4-bd, Histone-binding protein RBBP4 or subunit
C of CAF1 complex. The CAF-1 complex is a conserved
heterotrimeric protein complex that promotes histone H3
and H4 deposition onto newly synthesized DNA during
replication or DNA repair; specifically it facilitates
replication-dependent nucleosome assembly with the
major histone H3 (H3.1). This domain is an alpha helix
which sits just upstream of the WD40 seven-bladed
beta-propeller in the human RbAp46 protein. RbAp46
folds into the beta-propeller and binds histone H4 in a
groove formed between this N-terminal helix and an
extended loop inserted into blade six.
Length = 73
Score = 93.8 bits (234), Expect = 4e-24
Identities = 41/82 (50%), Positives = 52/82 (63%), Gaps = 13/82 (15%)
Query: 17 NEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTSVQLPNEDAQFDASNYDTDK--- 73
NEEY++WKKN PFLYD++ THALEWPSL+ WLPD+ D T +
Sbjct: 1 NEEYELWKKNDPFLYDMLHTHALEWPSLSFDWLPDLLKG---------DNRYPHTQRLLL 51
Query: 74 GTHTSD-EQNHLLIASVQLPNE 94
GT TS EQN+LL+A V LP++
Sbjct: 52 GTQTSGQEQNYLLVAKVSLPSK 73
Score = 42.6 bits (101), Expect = 1e-05
Identities = 16/30 (53%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 237 YSIHRLILGTHTSD-EQNHLLIASVQLPNE 265
RL+LGT TS EQN+LL+A V LP++
Sbjct: 44 PHTQRLLLGTQTSGQEQNYLLVAKVSLPSK 73
>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 = 61.2 bits (149), Expect = 1e-10
Identities = 31/98 (31%), Positives = 42/98 (42%), Gaps = 18/98 (18%)
Query: 143 YLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGLSWNPSLNGYLLSASD 202
YL S S D TI LWD+ T + R TGHT+ V ++++P L S+S
Sbjct: 65 YLASGSSDKTIRLWDLE-TGECVR------TLTGHTSYV---SSVAFSPD-GRILSSSSR 113
Query: 203 DHTICLWDINATPKENRVIDAKTIFTGHTAVVEDYSIH 240
D TI +WD+ T GHT V +
Sbjct: 114 DKTIKVWDVETG-------KCLTTLRGHTDWVNSVAFS 144
Score = 55.8 bits (135), Expect = 9e-09
Identities = 31/121 (25%), Positives = 49/121 (40%), Gaps = 22/121 (18%)
Query: 129 KGGYGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGLS 188
G ++++P L + S D TI +WD+ + GHT V ++
Sbjct: 10 GGVTCVAFSPD-GKLLATGSGDGTIKVWDLETG-------ELLRTLKGHTGPV---RDVA 58
Query: 189 WNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEDYSIH---RLILG 245
+ YL S S D TI LWD+ T + R TGHT+ V + R++
Sbjct: 59 ASADGT-YLASGSSDKTIRLWDLE-TGECVR------TLTGHTSYVSSVAFSPDGRILSS 110
Query: 246 T 246
+
Sbjct: 111 S 111
Score = 55.4 bits (134), Expect = 1e-08
Identities = 32/113 (28%), Positives = 49/113 (43%), Gaps = 21/113 (18%)
Query: 134 LSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGLSWNPSL 193
++++P ++ S+S D TI LWD+ T K TGHT V ++++P
Sbjct: 141 VAFSPD-GTFVASSSQDGTIKLWDLR-TGKCVAT------LTGHTGEV---NSVAFSPDG 189
Query: 194 NGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVE--DYSIHRLIL 244
LLS+S D TI LWD++ GH V +S +L
Sbjct: 190 EK-LLSSSSDGTIKLWDLSTG-------KCLGTLRGHENGVNSVAFSPDGYLL 234
Score = 53.1 bits (128), Expect = 7e-08
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 19/103 (18%)
Query: 132 YGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGLSWNP 191
++++P LLS+S D TI LWD++ GH V ++++P
Sbjct: 181 NSVAFSPDGEK-LLSSSSDGTIKLWDLSTG-------KCLGTLRGHENGV---NSVAFSP 229
Query: 192 SLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVV 234
L S S+D TI +WD+ T + + + +GHT V
Sbjct: 230 D-GYLLASGSEDGTIRVWDLR-TGECVQTL------SGHTNSV 264
Score = 50.4 bits (121), Expect = 5e-07
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 12/83 (14%)
Query: 128 DKGGYGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGL 187
+ G ++++P L S S+D TI +WD+ T + + + +GHT V L
Sbjct: 219 ENGVNSVAFSPD-GYLLASGSEDGTIRVWDLR-TGECVQTL------SGHTNSV---TSL 267
Query: 188 SWNPSLNGYLLSASDDHTICLWD 210
+W+P L S S D TI +WD
Sbjct: 268 AWSPD-GKRLASGSADGTIRIWD 289
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 46.5 bits (110), Expect = 1e-05
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 6/95 (6%)
Query: 134 LSWNPSLNGYLLSASDDHTICLWDINATPKE-NRVIDAKTIFTGHTAVVEVRYGLSWNPS 192
L +NP + L S S+D TI +W+I + + D + I GH + + + WNP
Sbjct: 80 LQFNPCFSEILASGSEDLTIRVWEIPHNDESVKEIKDPQCILKGHKKKISI---IDWNP- 135
Query: 193 LNGYLLSASD-DHTICLWDINATPKENRVIDAKTI 226
+N Y++ +S D + +WDI + ++ K +
Sbjct: 136 MNYYIMCSSGFDSFVNIWDIENEKRAFQINMPKKL 170
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 41.2 bits (97), Expect = 2e-05
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 172 TIFTGHTAVVEVRYGLSWNPSLNGYLLSASDDHTICLWD 210
GHT V ++++P L S SDD T+ +WD
Sbjct: 5 RTLKGHTGPV---TSVAFSPD-GNLLASGSDDGTVRVWD 39
Score = 35.0 bits (81), Expect = 0.002
Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 132 YGLSWNPSLNGYLLSASDDHTICLWD 157
++++P L S SDD T+ +WD
Sbjct: 15 TSVAFSPD-GNLLASGSDDGTVRVWD 39
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 45.8 bits (107), Expect = 2e-05
Identities = 28/115 (24%), Positives = 47/115 (40%), Gaps = 17/115 (14%)
Query: 126 DTDKGGYGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRY 185
L+++P + S S D TI LWD++ ++ +GH+ V
Sbjct: 196 GHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLL------RSTLSGHSDSVV--- 246
Query: 186 GLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEDYSIH 240
S++P L S S D TI LWD+ ++ R +GH++ V +
Sbjct: 247 -SSFSPD-GSLLASGSSDGTIRLWDLRSSSSLLR------TLSGHSSSVLSVAFS 293
Score = 35.4 bits (80), Expect = 0.048
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 12/81 (14%)
Query: 132 YGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGLSWNP 191
LS++P + + SDD TI LWD+ GH+ V +S++P
Sbjct: 332 SSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLK-------TLEGHSNV----LSVSFSP 380
Query: 192 SLNGYLLSASDDHTICLWDIN 212
+ S S D T+ LWD++
Sbjct: 381 DGR-VVSSGSTDGTVRLWDLS 400
Score = 34.7 bits (78), Expect = 0.081
Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 12/104 (11%)
Query: 109 GNVQLPNEDAQFDASNYDTDKGGYGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVI 168
G ++L + + +S++P + S S D T+ LWD++
Sbjct: 351 GTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGR-VVSSGSTDGTVRLWDLSTGSL----- 404
Query: 169 DAKTIFTGHTAVVEVRYGLSWNPSLNGYLLSASDDHTICLWDIN 212
GHT+ V L ++P L S S D+TI LWD+
Sbjct: 405 --LRNLDGHTSRV---TSLDFSPD-GKSLASGSSDNTIRLWDLK 442
Score = 33.9 bits (76), Expect = 0.12
Identities = 34/236 (14%), Positives = 79/236 (33%), Gaps = 30/236 (12%)
Query: 112 QLPNEDAQFDASNYDTDKGGYGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAK 171
+ ++ + + + LL+ D + L D++
Sbjct: 10 ENKSKLLKKSELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLS-----------S 58
Query: 172 TIFTGHTAVVEVRYGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHT 231
+ GH + ++++P LLS S D TI LWD++ K + ++ +
Sbjct: 59 LLLRGHEDSI---TSIAFSPD-GELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSK 114
Query: 232 AVVEDYSIHRLILGTHTSD--------EQNHLLIASVQLPNEDAQFDASNYDTDKGDFGG 283
+ + ++L + + D LI +++ +E A + D G
Sbjct: 115 LALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGS 174
Query: 284 FGSVSGKI-------EIEIKINHEGEVNRARYMPQNPCVIATKTPSSDVLVFDYTK 332
+ K+ + H V+ + P +IA+ + + ++D +
Sbjct: 175 SLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLST 230
>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 = 40.4 bits (95), Expect = 3e-05
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 173 IFTGHTAVVEVRYGLSWNPSLNGYLLSASDDHTICLWD 210
GHT V ++++P YL S SDD TI LWD
Sbjct: 7 TLKGHTGPV---TSVAFSPDGK-YLASGSDDGTIKLWD 40
Score = 34.6 bits (80), Expect = 0.003
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 132 YGLSWNPSLNGYLLSASDDHTICLWD 157
++++P YL S SDD TI LWD
Sbjct: 16 TSVAFSPDGK-YLASGSDDGTIKLWD 40
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 43.0 bits (101), Expect = 2e-04
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 134 LSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGLSWNPSL 193
+++NP L +AS+D TI W I + D GHT V + +S++PS
Sbjct: 81 VAFNPFDPQKLFTASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGI---VSFHPSA 137
Query: 194 NGYLLSASDDHTICLWDIN 212
L SA D + +WD+
Sbjct: 138 MNVLASAGADMVVNVWDVE 156
Score = 34.1 bits (78), Expect = 0.13
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 13/78 (16%)
Query: 134 LSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGLSWNPSL 193
+S++PS L SA D + +WD+ A + H+ + L WN L
Sbjct: 131 VSFHPSAMNVLASAGADMVVNVWDVERGK-------AVEVIKCHS---DQITSLEWN--L 178
Query: 194 NGYLL-SASDDHTICLWD 210
+G LL + S D + + D
Sbjct: 179 DGSLLCTTSKDKKLNIID 196
>gnl|CDD|233594 TIGR01844, type_I_sec_TolC, type I secretion outer membrane
protein, TolC family. Members of This model are outer
membrane proteins from the TolC subfamily within the RND
(Resistance-Nodulation-cell Division) efflux systems.
These proteins, unlike the NodT subfamily, appear not to
be lipoproteins. All are believed to participate in type
I protein secretion, an ABC transporter system for
protein secretion without cleavage of a signal sequence,
although they may, like TolC, participate also in the
efflux of smaller molecules as well. This family
includes the well-documented examples TolC (E. coli),
PrtF (Erwinia), and AprF (Pseudomonas aeruginosa)
[Protein fate, Protein and peptide secretion and
trafficking, Transport and binding proteins, Porins].
Length = 415
Score = 30.0 bits (68), Expect = 2.2
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 77 TSDEQNHLLIASVQLPNEDAQFDASNYDTDKGGNVQLPNEDAQFDASNYDTDKGGYG 133
E ++ L+ + Q + A++ + + G+ LP N DT GG G
Sbjct: 218 EIAEASNPLLLAAQAAVDAARY---QVEQARAGH--LPTLSLTASTGNSDTSSGGSG 269
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 30.1 bits (67), Expect = 2.4
Identities = 32/104 (30%), Positives = 45/104 (43%), Gaps = 27/104 (25%)
Query: 138 PSLNGYLLS-ASDDHTICLWDINATPKENRVIDAKTIFTGHTAVVEVRYGLSWNPSLNGY 196
PS +G L+ S DH + +D+ PK + T+ V VR+ S
Sbjct: 626 PSESGRSLAFGSADHKVYYYDLR-NPK----LPLCTMIGHSKTVSYVRFVDS------ST 674
Query: 197 LLSASDDHTICLWD-------INATPKENRVIDAKTIFTGHTAV 233
L+S+S D+T+ LWD IN TP + F GHT V
Sbjct: 675 LVSSSTDNTLKLWDLSMSISGINETPLHS--------FMGHTNV 710
Score = 28.1 bits (62), Expect = 8.1
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 19/73 (26%)
Query: 144 LLSASDDHTICLWD-------INATPKENRVIDAKTIFTGHTAVVEVRYGLSWNPSLNGY 196
L+S+S D+T+ LWD IN TP + F GHT V GLS + +GY
Sbjct: 675 LVSSSTDNTLKLWDLSMSISGINETPLHS--------FMGHTNVKNF-VGLSVS---DGY 722
Query: 197 LLSASDDHTICLW 209
+ + S+ + + ++
Sbjct: 723 IATGSETNEVFVY 735
>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5
snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit D3
heterodimerizes with subunit B and three such
heterodimers form a hexameric ring structure with
alternating B and D3 subunits. The D3 - B heterodimer
also assembles into a heptameric ring containing D1, D2,
E, F, and G subunits.
Length = 70
Score = 27.1 bits (61), Expect = 3.5
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 176 GHTAVVEVRYGLSWNPSLNGYLLSASDDHTICLWDINATPKENRVIDAKTIF 227
GH VE++ G G L+ A D+ L D+ T ++ +V + ++
Sbjct: 10 GHIVTVELKTG----EVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQVY 57
>gnl|CDD|184877 PRK14877, PRK14877, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 1062
Score = 28.9 bits (64), Expect = 5.9
Identities = 22/71 (30%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 88 SVQLPNEDAQFDA-SNYDTDKGGNVQLPNEDAQFDASNYDTDKGGYGLSWNPSLNGYLLS 146
+VQ PN +FD + D G +LP Y+ DKG L+W +L GY
Sbjct: 470 AVQTPNTFCRFDRFKDMDV---GTKRLPESVLSMAKPLYEGDKGF--LTWKTNLEGYFCD 524
Query: 147 ASDDHTICLWD 157
IC +D
Sbjct: 525 PLAKDKICSYD 535
>gnl|CDD|215506 PLN02937, PLN02937, Putative isoaspartyl peptidase/L-asparaginase.
Length = 414
Score = 28.7 bits (64), Expect = 5.9
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 270 DASNYDTDKGDFGGFGSVSG 289
DAS D D G FG G+V G
Sbjct: 87 DASIMDGDSGAFGAVGAVPG 106
>gnl|CDD|216381 pfam01237, Oxysterol_BP, Oxysterol-binding protein.
Length = 335
Score = 27.9 bits (63), Expect = 9.6
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 182 EVRYGLS--WNPSLNGYLLSASDDHTICLWDINATPKENR 219
+V Y +S WN SL + +S LW N P +
Sbjct: 199 KVLYTISGKWNESLYIKKVKSSTGEKKLLWKANPLPPNSE 238
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
0.314 0.133 0.408
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: 18,702,851
Number of extensions: 1746034
Number of successful extensions: 927
Number of sequences better than 10.0: 1
Number of HSP's gapped: 897
Number of HSP's successfully gapped: 30
Length of query: 368
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 270
Effective length of database: 6,590,910
Effective search space: 1779545700
Effective search space used: 1779545700
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: 42 (22.0 bits)
S2: 60 (26.9 bits)