RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6444
(88 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 = 48.5 bits (116), Expect = 3e-08
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 10 TCSGHTRPVVHLAFSDITESGYFLISACKDGKPMLRQGDTGDWIGTFEGHKGCVWGVDIN 69
T GH V +AFS GY L S +DG + TG+ + T GH V + +
Sbjct: 214 TLRGHENGVNSVAFSP---DGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWS 270
Query: 70 KDASKAASGAADFQAK 85
D + ASG+AD +
Sbjct: 271 PDGKRLASGSADGTIR 286
Score = 45.8 bits (109), Expect = 3e-07
Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 10 TCSGHTRPVVHLAFSDITESGYFLISACKDGKPMLRQGDTGDWIGTFEGHKGCVWGVDIN 69
T GHT V +AFS G F+ S+ +DG L TG + T GH G V V +
Sbjct: 130 TLRGHTDWVNSVAFS---PDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFS 186
Query: 70 KDASKAASGAADFQAK 85
D K S ++D K
Sbjct: 187 PDGEKLLSSSSDGTIK 202
Score = 43.1 bits (102), Expect = 2e-06
Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 10 TCSGHTRPVVHLAFSDITESGYFLISACKDGKPMLRQGDTGDWIGTFEGHKGCVWGVDIN 69
T +GHT V +AFS G L+S+ DG L TG +GT GH+ V V +
Sbjct: 172 TLTGHTGEVNSVAFSP---DGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFS 228
Query: 70 KDASKAASGAAD 81
D ASG+ D
Sbjct: 229 PDGYLLASGSED 240
Score = 42.3 bits (100), Expect = 4e-06
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 10 TCSGHTRPVVHLAFSDITESGYFLISACKDGKPMLRQGDTGDWIGTFEGHKGCVWGVDIN 69
T GHT V +AFS + L + DG + +TG+ + T +GH G V V +
Sbjct: 4 TLKGHTGGVTCVAFSPDGK---LLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAAS 60
Query: 70 KDASKAASGAADFQAK 85
D + ASG++D +
Sbjct: 61 ADGTYLASGSSDKTIR 76
Score = 38.1 bits (89), Expect = 1e-04
Identities = 23/80 (28%), Positives = 33/80 (41%), Gaps = 3/80 (3%)
Query: 6 QIPLTCSGHTRPVVHLAFSDITESGYFLISACKDGKPMLRQGDTGDWIGTFEGHKGCVWG 65
++ T GHT PV +A S +L S D L +TG+ + T GH V
Sbjct: 42 ELLRTLKGHTGPVRDVAASADGT---YLASGSSDKTIRLWDLETGECVRTLTGHTSYVSS 98
Query: 66 VDINKDASKAASGAADFQAK 85
V + D +S + D K
Sbjct: 99 VAFSPDGRILSSSSRDKTIK 118
Score = 35.4 bits (82), Expect = 0.001
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 13 GHTRPVVHLAFSDITESGYFLISACKDGKPMLRQGDTGDWIGTFEGHKGCVWGVDINKDA 72
GHT V +AFS G L S+ +D + +TG + T GH V V + D
Sbjct: 91 GHTSYVSSVAFSP---DGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDG 147
Query: 73 SKAASGAADFQAK 85
+ AS + D K
Sbjct: 148 TFVASSSQDGTIK 160
Score = 26.1 bits (58), Expect = 2.4
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 53 IGTFEGHKGCVWGVDINKDASKAASGAAD 81
T +GH G V V + D A+G+ D
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGD 30
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 38.5 bits (88), Expect = 1e-04
Identities = 26/79 (32%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 5 RQIPLTCSGHTRPVVHLAFSDITESGYFLISACKDGKPMLRQGDTGDWIG--TFEGHKGC 62
+ T SGH+ V+ +AFS G L S DG L +TG + T +GH+G
Sbjct: 274 SSLLRTLSGHSSSVLSVAFSP---DGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGP 330
Query: 63 VWGVDINKDASKAASGAAD 81
V + + D S SG +D
Sbjct: 331 VSSLSFSPDGSLLVSGGSD 349
Score = 36.2 bits (82), Expect = 9e-04
Identities = 23/80 (28%), Positives = 31/80 (38%), Gaps = 5/80 (6%)
Query: 7 IPLTCSGHTRPVVHLAFSDITESGYFLISACKDGKPML-RQGDTGDWIGTFEGHKGCVWG 65
+ T SGH+ VV D G L S DG L + + T GH V
Sbjct: 234 LRSTLSGHSDSVVSSFSPD----GSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLS 289
Query: 66 VDINKDASKAASGAADFQAK 85
V + D ASG++D +
Sbjct: 290 VAFSPDGKLLASGSSDGTVR 309
Score = 35.4 bits (80), Expect = 0.001
Identities = 20/71 (28%), Positives = 26/71 (36%), Gaps = 4/71 (5%)
Query: 12 SGHTRPVVHLAFSDITESGYFLISA-CKDGKPMLRQGDTGDWIGTFEGHKGCVWGVDINK 70
GH+ V LAFS G L S DG L TG + T GH V + +
Sbjct: 152 EGHSESVTSLAFS---PDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSP 208
Query: 71 DASKAASGAAD 81
D + +
Sbjct: 209 DGGLLIASGSS 219
>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 = 0.016
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 10 TCSGHTRPVVHLAFSDITESGYFLISACKDGK 41
T GHT PV +AFS G +L S DG
Sbjct: 7 TLKGHTGPVTSVAFSP---DGKYLASGSDDGT 35
Score = 30.4 bits (69), Expect = 0.016
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 49 TGDWIGTFEGHKGCVWGVDINKDASKAASGAADFQAK 85
+G+ + T +GH G V V + D ASG+ D K
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIK 37
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 30.0 bits (68), Expect = 0.019
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 53 IGTFEGHKGCVWGVDINKDASKAASGAADFQAK 85
+ T +GH G V V + D + ASG+ D +
Sbjct: 4 LRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVR 36
Score = 29.6 bits (67), Expect = 0.031
Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 10 TCSGHTRPVVHLAFSDITESGYFLISACKDGK 41
T GHT PV +AFS G L S DG
Sbjct: 6 TLKGHTGPVTSVAFSP---DGNLLASGSDDGT 34
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 26.5 bits (59), Expect = 1.8
Identities = 8/33 (24%), Positives = 11/33 (33%), Gaps = 3/33 (9%)
Query: 47 GDTGDWIGTF---EGHKGCVWGVDINKDASKAA 76
G G + G + G D + KAA
Sbjct: 12 GLMGGSLARALKEAGLVVRIIGRDRSAATLKAA 44
>gnl|CDD|132624 TIGR03585, PseH, pseudaminic acid biosynthesis N-acetyl
transferase. Sequences in this family are members of
the pfam00583 (GNAT) superfamily of acetyltransferases
and are proposed to perform a N-acetylation step in the
process of pseudaminic acid biosynthesis in
Campylobacter species. This gene is commonly observed in
apparent operons with other genes responsible for the
biosynthesis of pseudaminic acid and as a component of
flagellar and exopolysaccharide biosynthesis loci.
Significantly, many genomes containing other components
of this pathway lack this gene, indicating that some
other N-acetyl transferases may be incolved and/or the
step is optional, resulting in a non-acetylated
pseudaminic acid variant sugar.
Length = 156
Score = 25.8 bits (57), Expect = 3.1
Identities = 12/72 (16%), Positives = 22/72 (30%), Gaps = 10/72 (13%)
Query: 20 HLAF----SDITESGYFLISACKDGKPMLRQGDTGDWIGTFEGHKGCVWGVDINKDASKA 75
HL F Y+++ C++ +P+ + HK WG+ N
Sbjct: 38 HLHFIEALKQDPNRRYWIV--CQESRPI----GVISFTDINLVHKSAFWGIYANPFCKPG 91
Query: 76 ASGAADFQAKAL 87
+ A
Sbjct: 92 VGSVLEEAALEY 103
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 25.5 bits (57), Expect = 4.2
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 3/25 (12%)
Query: 49 TGDWIGTFE---GHKGCVWGVDINK 70
TGD G G V G+D ++
Sbjct: 62 TGDLAIALAKAVGKTGEVVGLDFSE 86
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 25.4 bits (56), Expect = 4.7
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 9/44 (20%)
Query: 10 TCSGH------TRPVVHLAFSDITESGYFLISAC-KDGKPMLRQ 46
C GH RPVVH+ F+ L + C K G+ L +
Sbjct: 65 ECPGHFGHIELARPVVHVGFAKEIYK--ILRATCRKCGRITLTE 106
>gnl|CDD|165416 PHA03145, PHA03145, helicase-primase primase subunit; Provisional.
Length = 1058
Score = 25.3 bits (55), Expect = 5.3
Identities = 17/65 (26%), Positives = 21/65 (32%), Gaps = 10/65 (15%)
Query: 31 YFLISACKDGKPMLRQG--------DTGDWIGTFEGHKGCVWGVDINKDASKAASGAADF 82
YF SAC+ + G G W G D + DA A G D
Sbjct: 669 YFFKSACRPRAAAVDPGLGPDGEYDGDGPWFPAGGGPGDEED--DEDPDAEALAHGGVDE 726
Query: 83 QAKAL 87
+A L
Sbjct: 727 EAAYL 731
>gnl|CDD|233565 TIGR01770, NDH_I_N, proton-translocating NADH-quinone
oxidoreductase, chain N. This model describes the 14th
(based on E. coli) structural gene, N, of bacterial and
chloroplast energy-transducing NADH (or NADPH)
dehydrogenases. This model does not describe any subunit
of the mitochondrial complex I (for which the subunit
composition is very different), nor NADH dehydrogenases
that are not coupled to ion transport. The Enzyme
Commission designation 1.6.5.3, for NADH dehydrogenase
(ubiquinone), is applied broadly, perhaps unfortunately,
even if the quinone is menaquinone (Thermus,
Mycobacterium) or plastoquinone (chloroplast). For
chloroplast members, the name NADH-plastoquinone
oxidoreductase is used for the complex and this protein
is designated as subunit 2 or B. This model also
includes a subunit of a related complex in the archaeal
methanogen, Methanosarcina mazei, in which F420H2
replaces NADH and 2-hydroxyphenazine replaces the
quinone [Energy metabolism, Electron transport].
Length = 468
Score = 24.9 bits (55), Expect = 6.8
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 21 LAFSDITESGYFLISAC 37
LA+S I+ GY LI
Sbjct: 297 LAYSSISHVGYILIGLL 313
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
0.320 0.135 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: 4,336,198
Number of extensions: 328583
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 244
Number of HSP's successfully gapped: 20
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
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 (21.8 bits)
S2: 53 (24.2 bits)