RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11524
(323 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 = 66.2 bits (162), Expect = 2e-12
Identities = 53/247 (21%), Positives = 97/247 (39%), Gaps = 24/247 (9%)
Query: 83 PVYSAAWSPDSNKVLLT-QAKSLVIKPLSPNNKATKWQAHDGLILKVAWCSSTDLILSGG 141
PV A S D + K++ + L H + VA+ ++ S
Sbjct: 53 PVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSS 112
Query: 142 EDCKYKASFVWDTD-GRQLYSSLTHDHPISSLAWAPGGDMFAVGSYN-TLRLCDKVGWS- 198
D K VWD + G+ L + H ++S+A++P G A S + T++L D
Sbjct: 113 RDKTIK---VWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKC 169
Query: 199 -HSLDKPDTGSVYDLVWSNDATQ-IAGACANVIHIFDISSSSSSNVTAPLSHSHEITQLA 256
+L TG V + +S D + ++ + I ++D+S+ H + + +A
Sbjct: 170 VATLTGH-TGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGT--LRGHENGVNSVA 226
Query: 257 VNQTGSLQERHVAFIDKNRDLYLSMWSHSLDKPD------TGSVYDLVWSSDATQIAGAC 310
+ G L + D + +W + T SV L WS D ++A
Sbjct: 227 FSPDGYL------LASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGS 280
Query: 311 ANGSLLL 317
A+G++ +
Sbjct: 281 ADGTIRI 287
Score = 62.7 bits (153), Expect = 3e-11
Identities = 56/258 (21%), Positives = 93/258 (36%), Gaps = 50/258 (19%)
Query: 83 PVYSAAWSPDSNKVLLTQAKSLVIK--PLSPNNKATKWQAHDGLILKVAWCSSTDLILSG 140
V A+SPD L T + IK L + H G + VA + + SG
Sbjct: 11 GVTCVAFSPDGKL-LATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASG 69
Query: 141 GEDCKYKASFVWDTDGRQLYSSLT-HDHPISSLAWAPGGDMFAVGSY-NTLRL------- 191
D K +WD + + +LT H +SS+A++P G + + S T+++
Sbjct: 70 SSD---KTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGK 126
Query: 192 CDKVGWSHSLDKPDTGSVYDLVWSNDATQIAGACAN-VIHIFDISSSSSSNVTAPLSHSH 250
C H T V + +S D T +A + + I ++D+ + V H+
Sbjct: 127 CLTTLRGH------TDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKC--VATLTGHTG 178
Query: 251 EITQLAVNQTGSLQERHVAFIDKNRDLYLS-------MWSHSLDKP------DTGSVYDL 297
E+ VAF L S +W S K V +
Sbjct: 179 EV-------------NSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSV 225
Query: 298 VWSSDATQIAGACANGSL 315
+S D +A +G++
Sbjct: 226 AFSPDGYLLASGSEDGTI 243
Score = 58.1 bits (141), Expect = 1e-09
Identities = 46/215 (21%), Positives = 86/215 (40%), Gaps = 31/215 (14%)
Query: 118 WQAHDGLILKVAWCSSTDLILSGGEDCKYKASFVWDTDGRQLYSSLT-HDHPISSLAWAP 176
+ H G + VA+ L+ +G D K VWD + +L +L H P+ +A +
Sbjct: 5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIK---VWDLETGELLRTLKGHTGPVRDVAASA 61
Query: 177 GGDMFAVGSY-NTLRLCDKVGWSHSLDKP------DTGSVYDLVWSNDATQIAGA-CANV 228
G A GS T+RL W + T V + +S D ++ +
Sbjct: 62 DGTYLASGSSDKTIRL-----WDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKT 116
Query: 229 IHIFDISSSSSSNVTAPLSHSHEITQLAVNQTGSLQERHVAFIDKNRDLYLSMWSHSLDK 288
I ++D+ + +T H+ + +A + G+ VA +D + +W K
Sbjct: 117 IKVWDV--ETGKCLTTLRGHTDWVNSVAFSPDGTF----VASSS--QDGTIKLWDLRTGK 168
Query: 289 PD------TGSVYDLVWSSDATQIAGACANGSLLL 317
TG V + +S D ++ + ++G++ L
Sbjct: 169 CVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKL 203
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 55.9 bits (133), Expect = 1e-08
Identities = 49/251 (19%), Positives = 90/251 (35%), Gaps = 24/251 (9%)
Query: 81 SPPVYSAAWSPDSNKVLLTQAKSLVIKPLSPNNKATKWQAHDGLILKV--AWCSSTDLIL 138
+ PV S A+SPD ++ + + I+ + G V ++ L+
Sbjct: 198 TDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLA 257
Query: 139 SGGEDCKYKASFVWD--TDGRQLYSSLTHDHPISSLAWAPGGDMFAVGSY-NTLRLCDKV 195
SG D + +WD + L + H + S+A++P G + A GS T+RL D
Sbjct: 258 SGSSDGTIR---LWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLE 314
Query: 196 GWSHSLDKPDTGS---VYDLVWSNDATQIAGACA--NVIHIFDISSSSSSNVTAPLSHSH 250
G V L +S D + + + I ++D+ + L
Sbjct: 315 TGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKT---LEGHS 371
Query: 251 EITQLAVNQTGSLQERHVAFIDKNRDLYLSMWSHSLDKP----DTGSVYDLVWSSDATQI 306
+ ++ S R V+ + + L S T V L +S D +
Sbjct: 372 NVLSVSF----SPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSL 427
Query: 307 AGACANGSLLL 317
A ++ ++ L
Sbjct: 428 ASGSSDNTIRL 438
Score = 43.5 bits (101), Expect = 9e-05
Identities = 50/250 (20%), Positives = 96/250 (38%), Gaps = 21/250 (8%)
Query: 83 PVYSAAWSPDSNKVLLTQAKSLVIKPLSPNNKATKWQ---AHDGLILKVAWCS--STDLI 137
+ S A+SPD +L + + N + HD + K+A S ++
Sbjct: 67 SITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSIL 126
Query: 138 LSGGEDCKYKASFVWDTDGRQLYSSLTHDHPISSLAWAPGGDMFAVGSY--NTLRLCDKV 195
L+ + T G+ + + H ++SLA++P G + A GS T++L D
Sbjct: 127 LASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLR 186
Query: 196 GWSH-SLDKPDTGSVYDLVWSNDATQIA--GACANVIHIFDISSSSSSNVTAPLSHSHEI 252
S T V L +S D + G+ I ++D+S+ T +
Sbjct: 187 TGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVV 246
Query: 253 TQLAVNQ----TGSLQERHVAF-IDKNRDLYLSMWSHSLDKPDTGSVYDLVWSSDATQIA 307
+ + + +GS + + + L ++ HS SV + +S D +A
Sbjct: 247 SSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHS------SSVLSVAFSPDGKLLA 300
Query: 308 GACANGSLLL 317
++G++ L
Sbjct: 301 SGSSDGTVRL 310
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 30.0 bits (68), Expect = 0.13
Identities = 14/39 (35%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 156 GRQLYSSLTHDHPISSLAWAPGGDMFAVGSY-NTLRLCD 193
G+ L + H P++S+A++P G++ A GS T+R+ D
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 28.5 bits (64), Expect = 0.42
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 116 TKWQAHDGLILKVAWCSSTDLILSGGEDCKYKASFVWD 153
+ H G + VA+ +L+ SG +D + VWD
Sbjct: 5 RTLKGHTGPVTSVAFSPDGNLLASGSDDGTVR---VWD 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 = 30.0 bits (68), Expect = 0.14
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 155 DGRQLYSSLTHDHPISSLAWAPGGDMFAVGSY-NTLRLCD 193
G L + H P++S+A++P G A GS T++L D
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 29.2 bits (66), Expect = 0.28
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 118 WQAHDGLILKVAWCSSTDLILSGGEDCKYKASFVWD 153
+ H G + VA+ + SG +D K +WD
Sbjct: 8 LKGHTGPVTSVAFSPDGKYLASGSDDGTIK---LWD 40
>gnl|CDD|218251 pfam04762, IKI3, IKI3 family. Members of this family are
components of the elongator multi-subunit component of a
novel RNA polymerase II holoenzyme for transcriptional
elongation. This region contains WD40 like repeats.
Length = 903
Score = 33.0 bits (76), Expect = 0.24
Identities = 23/113 (20%), Positives = 39/113 (34%), Gaps = 24/113 (21%)
Query: 182 AVGSYNTLRLCDKVGWSHSLDKPDTGSVYDLVWSNDATQIAGACANVIHIFDISSSSSSN 241
G + V S +L D G+V V I G+ ++ +N
Sbjct: 354 ESGQILIVDFAWTVARSPTLSPNDNGTV--AV-------IDGSTLL------LTPLRLAN 398
Query: 242 VTAPLSH-----SHEITQLAVNQTGSLQERHVAFIDKNRDLYLSMWSHSLDKP 289
V P+S I +A +++ S VA + + D+ + S KP
Sbjct: 399 VPPPMSARELELPSNINDVAFSKSNS----CVAVLTSDGDISIYELSLKKRKP 447
Score = 32.6 bits (75), Expect = 0.29
Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 27/96 (28%)
Query: 151 VWDTDGRQLYSS------LTHDHPISSLAWAPGGDMFAVGSYNTLRLCDKV--------G 196
V+ +G L S L +L+W P G++ A RL D++ G
Sbjct: 227 VYSREG-ALDSVSEPVDGLEG-----ALSWRPSGNLIAS----IQRLPDRLDVVFFERNG 276
Query: 197 WSH---SLDKPDTGSVYDLVWSNDATQIAGACANVI 229
H +L P+ V L W++D+ +A + + +
Sbjct: 277 LRHGEFTLRLPEEEKVISLEWNSDSEVLAVSLEDRV 312
>gnl|CDD|211578 TIGR00497, hsdM, type I restriction system adenine methylase
(hsdM). Function: methylation of specific adenine
residues; required for both restriction and modification
activities. The ECOR124/3 I enzyme recognizes
5'GAA(N7)RTCG. for E.coli see (J. Mol. Biol. 257:
960-969 (1996)) [DNA metabolism,
Restriction/modification].
Length = 501
Score = 32.2 bits (73), Expect = 0.40
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 80 VSPPVYSAAWSPDSNKVLLTQAKSLVIKPLSPNNKA 115
VS P YS +W+ D L++ + L+PN+KA
Sbjct: 298 VSNPPYSISWAGDKKSNLVSDVRFKDAGTLAPNSKA 333
>gnl|CDD|179892 PRK04922, tolB, translocation protein TolB; Provisional.
Length = 433
Score = 31.2 bits (71), Expect = 0.71
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 151 VWDTDGRQLYSSLTHDHPISSLAWAPGGDMFAVGSYNTLR 190
V D+DG + L PI S AW+P G A S+ R
Sbjct: 188 VADSDGYNPQTILRSAEPILSPAWSPDGKKLAYVSFERGR 227
>gnl|CDD|149648 pfam08662, eIF2A, Eukaryotic translation initiation factor eIF2A.
This is a family of eukaryotic translation initiation
factors.
Length = 194
Score = 29.9 bits (68), Expect = 1.2
Identities = 22/120 (18%), Positives = 37/120 (30%), Gaps = 41/120 (34%)
Query: 83 PVYSAAWSPDS-----------NKVLLTQAKSLVIKPLSPNNKATKWQAHDGLILKVAWC 131
P++ AWSP+ K+ K VI L + T + W
Sbjct: 61 PIHDFAWSPNGKEFAVIYGYMPAKITFFDLKGNVIHSLGEQPRNT-----------IFWS 109
Query: 132 SSTDLILSGGEDCKYKASF--------VWDTDGRQLYSSLTHDHPISSL-AWAPGGDMFA 182
L+L G F WD ++ ++ + ++ W+P G F
Sbjct: 110 PFGRLVLLAG--------FGNLAGQIEFWDVKNKKKIATA--EASNATDCEWSPDGRYFL 159
>gnl|CDD|166839 PRK00178, tolB, translocation protein TolB; Provisional.
Length = 430
Score = 28.9 bits (65), Expect = 4.0
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 141 GEDCKYKASFVWDTDGRQLYSSLTHDHPISSLAWAPGGDMFAVGSYNTLR 190
+ +Y D DG + + L PI S W+P G A S+ R
Sbjct: 174 SVNTRYTLQ-RSDYDGARAVTLLQSREPILSPRWSPDGKRIAYVSFEQKR 222
>gnl|CDD|211920 TIGR04197, T7SS_SACOL2603, type VII secretion effector, SACOL2603
family. Members of this protein family are similar in
length and sequence (although remotely) to the WXG100
family of type VII secretion system (T7SS) targets,
described by family TIGR03930. Phylogenetic profiling
shows that members of this family are similarly
restricted to species with T7SS, marking this family as
a related set of T7SS effectors. Members include
SACOL2603 from Staphylococcus aureus subsp. aureus COL.
Oddly, members of family pfam10824 (DUF2580), which
appears also to be related, seem not to be tied to T7SS.
Length = 85
Score = 26.5 bits (59), Expect = 5.7
Identities = 8/58 (13%), Positives = 19/58 (32%), Gaps = 1/58 (1%)
Query: 215 SNDATQIAGACANVIHIFDISSSSSSNVTAPLSHSHEITQLAVNQTGSLQERHVAFID 272
AT I A + + + ++ + +T +++HE +Q
Sbjct: 9 QQHATAIKSASSALSGVGSVTKDDQTTLTG-NTNAHEAIDQLQTLVSQIQSALEQDAT 65
>gnl|CDD|109180 pfam00113, Enolase_C, Enolase, C-terminal TIM barrel domain.
Length = 296
Score = 27.8 bits (62), Expect = 8.9
Identities = 20/53 (37%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 255 LAVNQTGSLQERHVAFIDKNRDLYLSMWSH-SLDKPDTGSVYDLVWSSDATQI 306
L VNQ GS+ E A + M SH S + DT + DLV +A QI
Sbjct: 206 LKVNQIGSVTESLAAVKMAKDAGWGVMVSHRSGETEDT-FIADLVVGLNAGQI 257
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
0.317 0.131 0.406
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: 16,052,874
Number of extensions: 1462576
Number of successful extensions: 1198
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1174
Number of HSP's successfully gapped: 33
Length of query: 323
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 226
Effective length of database: 6,635,264
Effective search space: 1499569664
Effective search space used: 1499569664
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: 59 (26.5 bits)