RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy701
(158 letters)
>gnl|CDD|199917 cd11295, Mago_nashi, Mago nashi proteins, integral members of the
exon junction complex. Members of this family, which
was originally identified in Drosophila and called mago
nashi, are integral members of the exon junction complex
(EJC). The EJC is a multiprotein complex that is
deposited on spliced mRNAs after intron removal at a
conserved position upstream of the exon-exon junction,
and transported to the cytoplasm where it has been shown
to influence translation, surveillance, and localization
of the spliced mRNA. It consists of four core proteins
(eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP
and is supposed to be a binding platform for more
peripherally and transiently associated factors along
mRNA travel. Mago and Y14 form a stable heterodimer that
stabilizes the complex by inhibiting eIF4AIII's ATPase
activity. In humans, but not Drosophila, EJC is involved
in nonsense-mediated mRNA decay (NMD) via binding to
Upf3b, a central NMD effector. EJC is stripped off the
mRNA during the first round of translation and then the
complex components are transported back into the nucleus
and recycled. The Mago-Y14 heterodimer has been shown to
interact with the cytoplasmic protein PYM, an EJC
disassembly factor, and specifically binds to the
karyopherin nuclear receptor importin 13.
Length = 143
Score = 306 bits (786), Expect = e-109
Identities = 121/143 (84%), Positives = 133/143 (93%)
Query: 16 DFYIRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAYVHKCVMDELKRI 75
DFY+RYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAYV V++ELKRI
Sbjct: 1 DFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAYVSPAVLEELKRI 60
Query: 76 INESEVMHEDDSLWPQPDRIGRQELEIVIGDEHISFTTSKTGSLVDVNHSKDPDGLRCFY 135
I +SE++ EDD+ WP+PDR+GRQELEIV+GDEHISFTTSK GSLVDV SKDP+GLR FY
Sbjct: 61 IEDSEILKEDDAKWPEPDRVGRQELEIVMGDEHISFTTSKIGSLVDVQQSKDPEGLRVFY 120
Query: 136 YLVQDLKCLVFSLIGLHYKIKPI 158
YLVQDLKCLVFSLIGLH+KIKPI
Sbjct: 121 YLVQDLKCLVFSLIGLHFKIKPI 143
>gnl|CDD|111665 pfam02792, Mago_nashi, Mago nashi protein. This family was
originally identified in Drosophila and called mago
nashi, it is a strict maternal effect,
grandchildless-like, gene. The human homologue has been
shown to interact with an RNA binding protein. An RNAi
knockout of the C. elegans homologue causes
masculinization of the germ line (Mog phenotype)
hermaphrodites, suggesting it is involved in
hermaphrodite germ-line sex determination. Mago nashi
has been found to be part of the exon-exon junction
complex that binds 20 nucleotides upstream of exon-exon
junctions.
Length = 143
Score = 254 bits (651), Expect = 1e-88
Identities = 104/143 (72%), Positives = 123/143 (86%)
Query: 16 DFYIRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAYVHKCVMDELKRI 75
DFY+RYYVGHKGKFGHEFLEFEFR DG LRYANNSNYKNDT+IRKE +V + V+ E+KRI
Sbjct: 1 DFYVRYYVGHKGKFGHEFLEFEFRSDGLLRYANNSNYKNDTLIRKEMFVSELVLKEVKRI 60
Query: 76 INESEVMHEDDSLWPQPDRIGRQELEIVIGDEHISFTTSKTGSLVDVNHSKDPDGLRCFY 135
+++SE++ EDD WP+PD+ G+QELEI + +EHISF T K GSL DV +S DP+GLR FY
Sbjct: 61 VDDSEIIKEDDENWPEPDKDGKQELEIRMNNEHISFETCKIGSLADVQNSDDPEGLRVFY 120
Query: 136 YLVQDLKCLVFSLIGLHYKIKPI 158
YLVQDLKCLVFSLI LH+KIKPI
Sbjct: 121 YLVQDLKCLVFSLISLHFKIKPI 143
>gnl|CDD|236335 PRK08724, fliD, flagellar capping protein; Validated.
Length = 673
Score = 29.1 bits (65), Expect = 1.2
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 11/58 (18%)
Query: 79 SEVMHEDDSLWPQPDRIGRQELEIVIGDEHISFTTSKTGSLVDV----NHSKDPDGLR 132
S+V+ ED + G +L+I +GD+ + LVD+ N +K G+R
Sbjct: 111 SDVLDEDA-------KFGPGKLQISLGDKSFTLDVVGNSKLVDIVRGINGAKSNPGVR 161
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 28.3 bits (64), Expect = 2.2
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 24 GHKGKFGHEFLEFEFRPDGK 43
G +G++G ++EFE +GK
Sbjct: 499 GGRGQYGDVWIEFEPNEEGK 518
>gnl|CDD|238552 cd01132, F1_ATPase_alpha, F1 ATP synthase alpha, central domain.
The F-ATPase is found in bacterial plasma membranes,
mitochondrial inner membranes and in chloroplast
thylakoid membranes. It has also been found in the
archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain, F1, is composed of alpha, beta, gamma, delta and
epsilon subunits with a stoichiometry of 3:3:1:1:1. The
alpha subunit of the F1 ATP synthase can bind
nucleotides, but is non-catalytic.
Length = 274
Score = 27.6 bits (62), Expect = 2.5
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 86 DSLWPQPDRIGRQELEIVIGDEHISFTTSKTGSLVDVNHSKDPDGLRCFY 135
D++ P IGR + E++IGD T KT +D ++ + C Y
Sbjct: 61 DAMIP----IGRGQRELIIGDRQ----TGKTAIAIDTIINQKGKKVYCIY 102
>gnl|CDD|197316 cd09082, Deadenylase, C-terminal deadenylase domain of CCR4,
nocturnin, and related domains. This family contains
the C-terminal catalytic domains of the deadenylases,
CCR4 and nocturnin, and related domains. Nocturnin is a
poly(A)-specific 3' exonuclease that specifically
degrades the 3' poly(A) tail of RNA in a process known
as deadenylation. This nuclease activity is manganese
dependent. Nocturnin is expressed in the cytoplasm of
the Xenopus laevis retinal photoreceptor cells in a
rhythmic fashion, and it has been proposed that it
participates in posttranscriptional regulation of the
circadian clock or its outputs, and that the mRNA
target(s) of this deadenylase are circadian
clock-related. Saccharomyces cerevisiae CCR4p is a 3'-5'
poly(A) RNA and ssDNA exonuclease. It is the catalytic
subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not
complex). This complex participates in various ways in
mRNA metabolism, including transcription initiation and
elongation, and mRNA degradation. The deadenylase
activities of Ccr4p and nocturnin differ: nocturnin
degrades poly(A), Ccr4p degrades both poly(A) and
single-stranded DNA, and in contrast to Ccr4p, nocturnin
appears to function in a highly processive manner. This
family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 348
Score = 27.3 bits (59), Expect = 3.6
Identities = 14/92 (15%), Positives = 24/92 (26%), Gaps = 15/92 (16%)
Query: 67 CVMDELKRIINESEVMHEDDSLWPQPDRIGRQELEIVIGDEHISFTTSKTG--------- 117
C L + ++ + D I QE+E + G
Sbjct: 20 CPSWALN--WEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKS 77
Query: 118 --SLVDVNHSKDPDGLRCFYYLVQDLKCLVFS 147
++ K DG C + + LV
Sbjct: 78 RAKIMSEQERKHVDG--CAIFFKTEKFTLVQK 107
>gnl|CDD|183987 PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
Length = 502
Score = 27.6 bits (62), Expect = 3.6
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 10/54 (18%)
Query: 86 DSLWPQPDRIGRQELEIVIGDEHISFTTSKTGSLVD-VNHSKDPDGLRCFYYLV 138
D+L P IGR + E++IGD T KT +D + + KD D + C Y +
Sbjct: 154 DALIP----IGRGQRELIIGDR----QTGKTAIAIDAIINQKDSD-VICVYVAI 198
>gnl|CDD|200482 cd11344, AmyAc_GlgE_like, Alpha amylase catalytic domain found in
GlgE-like proteins. GlgE is a
(1,4)-a-D-glucan:phosphate a-D-maltosyltransferase,
involved in a-glucan biosynthesis in bacteria. It is
also an anti-tuberculosis drug target. GlgE isoform I
from Streptomyces coelicolor has the same catalytic and
very similar kinetic properties to GlgE from
Mycobacterium tuberculosis. GlgE from Streptomyces
coelicolor forms a homodimer with each subunit
comprising five domains (A, B, C, N, and S) and 2
inserts. Domain A is a catalytic alpha-amylase-type
domain that along with domain N, which has a
beta-sandwich fold and forms the core of the dimer
interface, binds cyclodextrins. Domain A, B, and the 2
inserts define a well conserved donor pocket that binds
maltose. Cyclodextrins competitively inhibit the binding
of maltooligosaccharides to the S. coelicolor enzyme,
indicating that the hydrophobic patch overlaps with the
acceptor binding site. This is not the case in M.
tuberculosis GlgE because cyclodextrins do not inhibit
this enzyme, despite acceptor length specificity being
conserved. Domain C is hypothesized to help stabilize
domain A and could be involved in substrate binding.
Domain S is a helix bundle that is inserted within the N
domain and it plays a role in the dimer interface and
interacts directly with domain B. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 355
Score = 27.2 bits (61), Expect = 3.8
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 36 FEFRPDGKLRYANN 49
F RPDG ++YA N
Sbjct: 129 FRHRPDGSIQYAEN 142
>gnl|CDD|233211 TIGR00962, atpA, proton translocating ATP synthase, F1 alpha
subunit. The sequences of ATP synthase F1 alpha and
beta subunits are related and both contain a
nucleotide-binding site for ATP and ADP. They have a
common amino terminal domain but vary at the C-terminus.
The beta chain has catalytic activity, while the alpha
chain is a regulatory subunit. The alpha-subunit
contains a highly conserved adenine-specific
noncatalytic nucleotide-binding domain. The conserved
amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton
translocating ATP synthase F1, alpha subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), B subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 501
Score = 27.4 bits (61), Expect = 4.0
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 86 DSLWPQPDRIGRQELEIVIGDEHISFTTSKTGSLVDVNHSKDPDGLRCFY 135
D++ P IGR + E++IGD T KT +D ++ + C Y
Sbjct: 153 DAMIP----IGRGQRELIIGDRQ----TGKTAVAIDTIINQKDSDVYCIY 194
>gnl|CDD|189049 cd09879, PIN_AF0591, PIN domain of Archaeoglobus fulgidus AF0591
protein and other similar archaeal homologs. PIN (PilT
N terminus) domain of Archaeoglobus fulgidus AF0591
protein and other similar uncharacterized archaeal
homologs are included in this family. These PIN domains
are structural homologs of flap endonuclease-1
(FEN1)-like PIN domains, but lack the extensive
arch/clamp region and the H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region,
seen in FEN1-like PIN domains. PIN domains within this
subgroup contain four highly conserved acidic residues
(putative metal-binding, active site residues) which
cluster at the C-terminal end of the beta-sheet and
form a negatively charged pocket near the center of the
molecule.
Length = 117
Score = 26.4 bits (59), Expect = 4.4
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 57 MIRKEAYVHKCVMDELKRIINES 79
+ E V V++EL+++ +
Sbjct: 25 LGYPEFVVPSAVLEELEKLSRKG 47
>gnl|CDD|241304 cd01274, PTB_Anks, Ankyrin repeat and sterile alpha motif (SAM)
domain-containing (Anks) protein family
Phosphotyrosine-binding (PTB) domain. Both AIDA-1b
(AbetaPP intracellular domain-associated protein 1b) and
Odin (also known as ankyrin repeat and sterile alpha
motif domain-containing 1A; ANKS1A) belong to the Anks
protein family. Both of these family members interacts
with the EphA8 receptor. Ank members consists of
ankyrin repeats, a SAM domain and a C-terminal PTB
domain which is crucial for interaction with the
juxtamembrane (JM) region of EphA8. PTB domains are
classified into three groups, namely,
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains of
which the Anks PTB is a member. PTB domains have a
common PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred by
residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 146
Score = 26.4 bits (59), Expect = 5.5
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 5/26 (19%)
Query: 127 DPDGLRCFYYLVQDLK-----CLVFS 147
DP+ L F Y+ +DLK C VF
Sbjct: 90 DPEDLNTFAYITKDLKTDHHYCHVFC 115
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
0.322 0.141 0.431
Gapped
Lambda K H
0.267 0.0653 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,222,525
Number of extensions: 744147
Number of successful extensions: 503
Number of sequences better than 10.0: 1
Number of HSP's gapped: 503
Number of HSP's successfully gapped: 20
Length of query: 158
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 69
Effective length of database: 6,990,096
Effective search space: 482316624
Effective search space used: 482316624
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 (21.9 bits)
S2: 55 (25.1 bits)