RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy488
(86 letters)
>gnl|CDD|212488 cd11677, Gemin7, Gemin 7. Gemins 7, together with the survival
motor neuron (SMN) protein, other Gemins, and
Unr-interacting protein (UNRIP) form the SMN complex,
which plays an important role in the Sm core assembly
reaction, by binding directly to the Sm proteins, as
well as UsnRNAs. Gemin 7 forms a heterodimer with Gemin
6, which serve as a surrogate for the SmB-SmD3 dimer
during the formation of the heptameric Sm ring.
Length = 77
Score = 87.3 bits (217), Expect = 1e-24
Identities = 32/77 (41%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 10 SDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGT 69
++E A +RE+FL+++ +L+G+P M E T VTA F+ + D+ F V NLKTP+G
Sbjct: 1 LEQEARAFLRERFLRSLLALAGKPVEFTMHENTTVTATFKACDIDVENFQVSNLKTPLGI 60
Query: 70 FHEHALLRVDDIVDIEI 86
ALLR DI+ I
Sbjct: 61 Q-PEALLRTSDIISITF 76
>gnl|CDD|151540 pfam11095, Gemin7, Gem-associated protein 7 (Gemin7). Gemin7 is
a novel component of the survival of motor neuron
complex which functions in the assembly of spliceosomal
small nuclear ribonucleoproteins. Gemin7 interacts with
several Sm proteins of spliceosomal small nuclear
ribonucleoproteins, especially SmE.
Length = 80
Score = 69.0 bits (169), Expect = 2e-17
Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 12 EEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFH 71
+ A +RE++L+++ ++ G+P + ER VTA F T+ D+ FYV L+TPIG
Sbjct: 5 QRARAVLRERYLRSLLAMVGKPVEFTLHERVSVTAVFGATDIDVENFYVSQLQTPIGVQK 64
Query: 72 EHALLRVDDIVDI 84
E ALLR D++
Sbjct: 65 E-ALLRCSDVISF 76
>gnl|CDD|119385 cd06525, GH25_Lyc-like, Lyc muramidase is an autolytic lysozyme
(autolysin) from Clostridium acetobutylicum encoded by
the lyc gene. Lyc has a glycosyl hydrolase family 25
(GH25) catalytic domain. Endo-N-acetylmuramidases are
lysozymes (also referred to as peptidoglycan hydrolases)
that degrade bacterial cell walls by catalyzing the
hydrolysis of 1,4-beta-linkages between N-acetylmuramic
acid and N-acetyl-D-glucosamine residues.
Length = 184
Score = 27.6 bits (62), Expect = 0.63
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 1 MDVDRTSSRSDEEIAAEMREKFLKAMSSLSGQPCTI 36
+DV+ S +E+ + F++ LSG I
Sbjct: 88 LDVEVNFGLSKDELNDYVLR-FIEEFEKLSGLKVGI 122
>gnl|CDD|226271 COG3748, COG3748, Predicted membrane protein [Function unknown].
Length = 407
Score = 27.5 bits (61), Expect = 0.82
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 10 SDEEIAAEMREKFLKAMSSLSGQPCTINMF---ERTVVTAEFQGTNS 53
+DE+IAA RE +L+A S + P + ER ++ A F+ S
Sbjct: 359 TDEQIAAHAREIYLQAGRSHAMPPGNVTQMTDEERALLAAWFESGAS 405
>gnl|CDD|212674 cd10232, ScSsz1p_like_NBD, Nucleotide-binding domain of
Saccharmomyces cerevisiae Ssz1pp and similar proteins.
Saccharomyces cerevisiae Ssz1p (also known as
/Pdr13p/YHR064C) belongs to the heat shock protein 70
(HSP70) family of chaperones that assist in protein
folding and assembly and can direct incompetent "client"
proteins towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). Some
family members are not chaperones but rather, function
as NEFs for their Hsp70 partners, while other family
members function as both chaperones and NEFs. Ssz1 does
not function as a chaperone; it facilitates the
interaction between the HSP70 Ssb protein and its
partner J-domain protein Zuo1 (also known as zuotin) on
the ribosome. Ssz1 is found in a stable heterodimer
(called RAC, ribosome associated complex) with Zuo1.
Zuo1 can only stimulate the ATPase activity of Ssb, when
it is in complex with Ssz1. Ssz1 binds ATP but neither
nucleotide-binding, hydrolysis, or its SBD, is needed
for its in vivo function.
Length = 386
Score = 27.4 bits (61), Expect = 0.90
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 40 ERTVVTAEFQGTNSDLTEFYVRN-LKTPIGTFHEHAL 75
+R VV A+F GT +D++ VR L T + T H+ L
Sbjct: 193 DRNVVVADFGGTRTDVSVIAVRGGLYTILATAHDPGL 229
>gnl|CDD|214838 smart00827, PKS_AT, Acyl transferase domain in polyketide synthase
(PKS) enzymes.
Length = 298
Score = 27.0 bits (61), Expect = 0.93
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 18 MREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL 63
+ ++F A++ L+ +P I TV G D +++VRNL
Sbjct: 200 ILDEFRAALAGLTPRPPRIPFV-STVTGTLIDGAELDDADYWVRNL 244
>gnl|CDD|241240 cd01204, PTB_IRS, Insulin receptor substrate
phosphotyrosine-binding domain (PTBi). Insulin receptor
substrate (IRS) molecules are mediators in insulin
signaling and play a role in maintaining basic cellular
functions such as growth and metabolism. They act as
docking proteins between the insulin receptor and a
complex network of intracellular signaling molecules
containing Src homology 2 (SH2) domains. Four members
(IRS-1, IRS-2, IRS-3, IRS-4) of this family have been
identified that differ as to tissue distribution,
subcellular localization, developmental expression,
binding to the insulin receptor, and interaction with
SH2 domain-containing proteins. IRS molecules have an
N-terminal PH domain, followed by an IRS-like PTB domain
which has a PH-like fold. 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 IRS-like subgroup.
Length = 106
Score = 26.1 bits (58), Expect = 1.6
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 6/30 (20%)
Query: 1 MDVDRTSSRSDEEIAAEMREKFLKAMSSLS 30
M VD D +A M E L+AM +LS
Sbjct: 81 MQVD------DSVVAQNMHETILEAMKALS 104
>gnl|CDD|220628 pfam10198, Ada3, Histone acetyltransferases subunit 3. Ada3 is a
family of proteins conserved from yeasts to humans. It
is an essential component of the Ada transcriptional
coactivator (alteration/deficiency in activation)
complex. Ada3 plays a key role in linking histone
acetyltransferase-containing complexes to p53 (tumour
suppressor protein) thereby regulating p53 acetylation,
stability and transcriptional activation following DNA
damage.
Length = 127
Score = 26.1 bits (58), Expect = 2.1
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 2 DVDRTSSRSDEEIAAEMRE 20
D D ++R D+EI AE+R
Sbjct: 25 DDDWATNREDDEILAELRR 43
>gnl|CDD|212689 cd11739, HSPH1_NBD, Nucleotide-binding domain of HSPH1. Human
HSPH1 (also known as heat shock 105kDa/110kDa protein 1,
HSP105; HSP105A; HSP105B; NY-CO-25; the human HSPH1 gene
maps to 13q12.3) suppresses the aggregation of denatured
proteins caused by heat shock in vitro, and may
substitute for HSP70 family proteins to suppress the
aggregation of denatured proteins in cells under severe
stress. It reduces the protein aggregation and
cytotoxicity associated with Polyglutamine (PolyQ)
diseases, including Huntington's disease, which are a
group of inherited neurodegenerative disorders sharing
the characteristic feature of having insoluble protein
aggregates in neurons. The expression of HSPH1 is
elevated in various malignant tumors, including
malignant melanoma, and there is a direct correlation
between HSPH1 expression and B-cell non-Hodgkin
lymphomas (B-NHLs) aggressiveness and proliferation.
HSPH1 belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as nucleotide
exchange factors (NEFs), to remove ADP from their HSP70
chaperone partners during the ATP hydrolysis cycle.
HSP70 chaperones assist in protein folding and assembly,
and can direct incompetent "client" proteins towards
degradation. Like HSP70 chaperones, HSP105/110s have an
N-terminal nucleotide-binding domain (NBD) and a
C-terminal substrate-binding domain (SBD). For HSP70
chaperones, the nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. Hsp70 chaperone
activity is also regulated by J-domain proteins.
Length = 383
Score = 26.5 bits (58), Expect = 2.1
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 11/74 (14%)
Query: 20 EKFLKAMSSLSGQ-PCTINMF--ERTVV----TAEFQGTNSDLTEFYVRNLKTPIGTFHE 72
EK K MSS S P I F ++ V ++F+ +DL + ++ P+ + E
Sbjct: 270 EKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCADLLQ----RIEVPLYSLLE 325
Query: 73 HALLRVDDIVDIEI 86
L+V+D+ +EI
Sbjct: 326 QTHLKVEDVSAVEI 339
>gnl|CDD|143423 cd07105, ALDH_SaliADH, Salicylaldehyde dehydrogenase, DoxF-like.
Salicylaldehyde dehydrogenase (DoxF, SaliADH,
EC=1.2.1.65) involved in the upper naphthalene catabolic
pathway of Pseudomonas strain C18 and other similar
sequences are present in this CD.
Length = 432
Score = 26.0 bits (58), Expect = 2.8
Identities = 9/26 (34%), Positives = 10/26 (38%)
Query: 11 DEEIAAEMREKFLKAMSSLSGQPCTI 36
E IA E EK A L P +
Sbjct: 253 HESIADEFVEKLKAAAEKLFAGPVVL 278
>gnl|CDD|241362 cd13208, PH-GRAM_MTMR5_MTMR13, Myotubularian (MTM) related 5 and 13
proteins (MTMR5 and MTMR13) Pleckstrin
Homology-Glucosyltransferases, Rab-like GTPase
activators and Myotubularins (PH-GRAM) domain. MTMR5 is
a catalytically inactive phosphatase that plays a role
as an adapter for the phosphatase myotubularin to
regulate myotubularintracellular location. It lacks
several amino acids in the dsPTPase catalytic pocket
which renders it catalytically inactive as a
phosphatase. MTMR5 is the most well-studied inactive
member of this family and has been implicated in
cellular growth control and oncogenic transformation.
MTMR13 is a catalytically inactive phosphatase that
plays a role as an adapter for the phosphatase
myotubularin to regulate myotubularintracellular
location. It contains a Leu residue instead of a
conserved Cys residue in the dsPTPase catalytic loop
which renders it catalytically inactive as a
phosphatase. MTMR13 has high sequence similarity to
MTMR5 and has recently been shown to be a second gene
mutated in type 4B Charcot-Marie-Tooth syndrome. Both
MTMR5 and MTMR13 contain an N-terminal DENN domain, a
PH-GRAM domain, an inactive PTP domain, a SET
interaction domain, a coiled-coil domain, and a
C-terminal PH domain. Myotubularin-related proteins are
a subfamily of protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids.
Mutations in this family cause the human neuromuscular
disorders myotubular myopathy and type 4B
Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs
5, 9-13) contain naturally occurring substitutions of
residues required for catalysis by PTP family enzymes.
Although these proteins are predicted to be
enzymatically inactive, they are thought to function as
antagonists of endogenous phosphatase activity or
interaction modules. Most MTMRs contain a N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, a PTP domain (which may be active or inactive),
a SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date. Although the majority of the sequences
are MTMR 5 and 13, this cd also contains MTM5 nematode
sequences.
Length = 146
Score = 25.3 bits (56), Expect = 4.3
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 11 DEEIAAEMREKFLKAMSSLS 30
DEE+++E EKF K + L
Sbjct: 118 DEEVSSEAIEKFRKVIHKLR 137
>gnl|CDD|216746 pfam01862, PvlArgDC, Pyruvoyl-dependent arginine decarboxylase
(PvlArgDC). Methanococcus jannaschii contains
homologues of most genes required for spermidine
polyamine biosynthesis. Yet genomes from neither this
organism nor any other euryarchaeon have orthologues of
the pyridoxal 5'-phosphate- dependent ornithine or
arginine decarboxylase genes, required to produce
putrescine. Instead,these organisms have a new class of
arginine decarboxylase (PvlArgDC) formed by the
self-cleavage of a proenzyme into a 5-kDa subunit and a
12-kDa subunit that contains a reactive pyruvoyl group.
Although this extremely thermostable enzyme has no
significant sequence similarity to previously
characterized proteins, conserved active site residues
are similar to those of the pyruvoyl-dependent histidine
decarboxylase enzyme, and its subunits form a similar
(alpha-beta)(3) complex. Homologues of PvlArgDC are
found in several bacterial genomes, including those of
Chlamydia spp., which have no agmatine ureohydrolase
enzyme to convert agmatine (decarboxylated arginine)
into putrescine. In these intracellular pathogens,
PvlArgDC may function analogously to pyruvoyl-dependent
histidine decarboxylase; the cells are proposed to
import arginine and export agmatine, increasing the pH
and affecting the host cell's metabolism. Phylogenetic
analysis of Pvl- ArgDC proteins suggests that this gene
has been recruited from the euryarchaeal polyamine
biosynthetic pathway to function as a degradative enzyme
in bacteria.
Length = 159
Score = 25.3 bits (56), Expect = 4.5
Identities = 15/45 (33%), Positives = 18/45 (40%), Gaps = 3/45 (6%)
Query: 10 SDEEIAAEMREKFLKAM--SSLSGQPC-TINMFERTVVTAEFQGT 51
S EE A E EK K M + L G+ T N+ V T
Sbjct: 106 SKEEQAGEYAEKLAKEMLETRLGGKIVETRNITAEAEVDDGKWTT 150
>gnl|CDD|152648 pfam12213, Dpoe2NT, DNA polymerases epsilon N terminal. This
domain is found in eukaryotes, and is approximately 70
amino acids in length. The family is found in
association with pfam04042. There is a single
completely conserved residue F that may be functionally
important. This domain is the N terminal domain of DNA
polymerase epsilon subunit B. It forms a primarily
alpha helical structure in which four helices are
arranged in two hairpins with connecting loops
containing beta strands which form a short parallel
sheet. DNA polymerase epsilon is required in DNA
replication for synthesis of the leading strand. This
domain has close structural relation to AAA+ protein C
terminal domains.
Length = 72
Score = 24.2 bits (53), Expect = 5.0
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 12 EEIAAEMREKFL-KAMSSLSGQPCTINMFERTVVTAEFQ 49
+ RE +L K + ++ QP + +M ER+V+ A Q
Sbjct: 33 LSLGEPEREDWLEKIIEAVEKQPLSSSMIERSVIEAAVQ 71
>gnl|CDD|211368 cd09257, AP_muniscins_like_MHD, Mu-homology domain (MHD) of
muniscins adaptor proteins (AP) and similar proteins.
This family corresponds to the MHD found in muniscins, a
novel family of endocytic adaptor proteins. The term,
muniscins, has been assigned to name the MHD of proteins
with both EFC/F-BAR domain and MHD. These two domains
are responsible for the membrane-tubulation activity
associated with transmembrane cargo proteins. Members in
this family include an endocytic adaptor Syp1, the
mammalian FCH domain only proteins (FCHo1/2),
SH3-containing GRB2-like protein 3-interacting protein 1
(SGIP1), and related uncharacterized proteins. Syp1 is a
poorly characterized yeast protein with multiple
biological functions. Syp1 contains an N-terminal
EFC/F-BAR domain that induces membrane tabulation, a
proline-rich domain (PRD) in the middle region, and a
C-terminal MHD that can directly binds to the endocytic
adaptor/scaffold protein Ede1 or a transmembrane stress
sensor cargo protein Mid2. Thus, Syp1 represents a novel
type of endocytic adaptor protein that participates in
endocytosis, promotes vesicle tabulation, and
contributes to cell polarity and stress response. Syp1
shares the same domain architecture with its two
ubiquitously expressed mammalian counterparts, the
membrane-sculpting F-BAR domain-containing Fer/Cip4
homology domain-only proteins 1 and 2 (FCHo1/2). FCHo1/2
represent key initial proteins ultimately controlling
cellular nutrient uptake, receptor regulation, and
synaptic vesicle retrieval. They are required for plasma
membrane clathrin-coated vesicle (CCV) budding and
marked sites of CCV formation. They bind specifically to
the plasma membrane and recruit the scaffold proteins
eps15 and intersectin, which subsequently engage the
adaptor complex AP2 and clathrin, leading to coated
vesicle formation. Another mammalian neuronal-specific
protein, neuronal-specific transcript Scr homology 3
(SH3)-domain growth factor receptor-bound 2 (GRB2)-like
(endophilin) interacting protein 1 [SGIP1] does not
contain EFC/F-BAR domain, but does have a PRD and a
C-terminal MHD and has been classified into this family
as well. SGIP1 is an endophilin-interacting protein that
plays an obligatory role in the regulation of energy
homeostasis. It is also involved in clathrin-mediated
endocytosis by interacting with phospholipids and eps15.
Length = 246
Score = 25.1 bits (55), Expect = 5.5
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 1 MDVDRTSSRSDEEIAAEMREKFLKAMSSLSG 31
+ D S + E++ + + L + S+LSG
Sbjct: 191 FEADAGPSLAAEKLQFPVLVRCLSSGSTLSG 221
>gnl|CDD|183473 PRK12361, PRK12361, hypothetical protein; Provisional.
Length = 547
Score = 25.0 bits (55), Expect = 6.6
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 44 VTAEFQGTNSDLTEFYVRNLKTPI 67
VTAEF G + LTE + L PI
Sbjct: 127 VTAEFDGLDWSLTEEDIDYLNIPI 150
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 24.9 bits (55), Expect = 6.7
Identities = 9/24 (37%), Positives = 15/24 (62%), Gaps = 6/24 (25%)
Query: 10 SDEEIA---AEMRE---KFLKAMS 27
SDEEIA E+RE +++ ++
Sbjct: 490 SDEEIAKLMQELREALDDYMRQLA 513
>gnl|CDD|214597 smart00281, LamB, Laminin B domain.
Length = 127
Score = 24.1 bits (53), Expect = 9.6
Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 7/43 (16%)
Query: 40 ERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEH-ALLRVDDI 81
R V + ++LT +R T+ + A R+ D+
Sbjct: 84 GRPVTREDLMMVLANLTAILIR------ATYSQQMAGSRLSDV 120
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
0.318 0.132 0.362
Gapped
Lambda K H
0.267 0.0893 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,265,544
Number of extensions: 327641
Number of successful extensions: 446
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 23
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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: 53 (23.9 bits)