RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3267
(105 letters)
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898). This
domain is predominantly found in Maelstrom homolog
proteins. It has no known function.
Length = 69
Score = 46.3 bits (110), Expect = 3e-08
Identities = 19/37 (51%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AY FFVQ R E K++ P+ AEFSK C+E+WK+
Sbjct: 10 AYFFFVQTMRPELKREGPQVP-GVAEFSKLCSEKWKA 45
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA
in a non-sequence specific fashion and contain two or
more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 43.0 bits (102), Expect = 6e-07
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AY F Q R + KK++P+ +V E +K E+WK
Sbjct: 7 AYFLFSQEQRPKLKKENPDASV--TEVTKILGEKWKE 41
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding
preferences. Two phylogenically distinct groups of
Class I proteins bind DNA in a sequence specific
fashion and contain a single HMG box. One group
(SOX-TCF) includes transcription factors, TCF-1, -3,
-4; and also SRY and LEF-1, which bind four-way DNA
junctions and duplex DNA targets. The second group
(MATA) includes fungal mating type gene products MC,
MATA1 and Ste11. Class II and III proteins (HMGB-UBF)
bind DNA in a non-sequence specific fashion and contain
two or more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 39.1 bits (92), Expect = 2e-05
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AY F Q R E K ++P + E SK E WKS
Sbjct: 7 AYFLFSQEHRAEVKAENPGLS--VGEISKILGEMWKS 41
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 36.5 bits (85), Expect = 2e-04
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWK 46
A+ F Q R + K ++P ++ AE SKK ERWK
Sbjct: 8 AFMLFSQENRAKIKAENP--DLSNAEISKKLGERWK 41
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 31.0 bits (71), Expect = 0.021
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
A+ F Q R + K ++P AE SK E+WK+
Sbjct: 7 AFFLFSQEQRAKLKAENPGLKN--AEISKILGEKWKN 41
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 28.3 bits (63), Expect = 0.61
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AY + R+E +K++P+ + F E K +E+WK
Sbjct: 77 AYFLYSAENRDEIRKENPK--LTFGEVGKLLSEKWKE 111
>gnl|CDD|238175 cd00283, GIY-YIG_Cterm, GIYX(10-11)YIG family of class I homing
endonucleases C-terminus (GIY-YIG_Cterm). Homing
endonucleases promote the mobility of intron or intein
by recognizing and cleaving a homologous allele that
lacks the sequence. They catalyze a double-strand break
in the DNA near the insertion site of that element to
facilitate homing at that site. Class I homing
endonucleases are sorted into four families based on
the presence of these motifs in their respective
N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG.
This CD contains several but not all members of the
GIY-YIG family. The C-terminus of GIY-YIG is a
DNA-binding domain which is separated from the
N-terminus by a long, flexible linker. The DNA-binding
domain consists of a minor-groove binding alpha-helix,
and a helix-turn-helix. Some also contain a zinc
finger (i.e. I-TevI) which is not required for DNA
binding or catalysis, but is a component of the linker
and directs the catalytic domain to cleave the homing
site at a fixed distance from the intron insertion
site.
Length = 113
Score = 25.9 bits (57), Expect = 2.9
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 6/40 (15%)
Query: 35 AEFSKKCAE--RWKSSRI----VNPFVGRKFAPVFLTFLS 68
F K +E + K S+ NP G+K + +S
Sbjct: 16 PMFGKTHSEETKAKISKNRSGENNPMFGKKHSDETKAKIS 55
>gnl|CDD|132851 cd07212, Pat_PNPLA9, Patatin-like phospholipase domain containing
protein 9. PNPLA9 is a Ca-independent phospholipase
that catalyzes the hydrolysis of glycerophospholipids at
the sn-2 position. PNPLA9 is also known as PLA2G6
(phospholipase A2 group VI) or iPLA2beta. PLA2G6 is
stimulated by ATP and inhibited by bromoenol lactone
(BEL). In humans, PNPLA9 in expressed ubiquitously and
is involved in signal transduction, cell proliferation,
and apoptotic cell death. Mutations in human PLA2G6
leads to infantile neuroaxonal dystrophy (INAD) and
idiopathic neurodegeneration with brain iron
accumulation (NBIA). This family includes PLA2G6 from
Homo sapiens and Rattus norvegicus.
Length = 312
Score = 26.1 bits (58), Expect = 4.1
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 60 APVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFG 100
AP + + R D L NP L + I ++++ L G
Sbjct: 159 APTYFRPMGRFLDGGLIANNPTLDAMTEI-HEYNKTLKSKG 198
>gnl|CDD|198240 cd10377, SH2_STAT6, Src homology 2 (SH2) domain found in signal
transducer and activator of transcription (STAT) 6
proteins. STAT6 mediate signals from the IL-4
receptor. Unlike the other STAT proteins which bind an
IFNgamma Activating Sequence (GAS), STAT6 stands out
as having a unique binding site preference. This site
consists of a palindromic sequence separated by a 3 bp
spacer (TTCNNNG-AA)(N3 site). STAT6 is able to bind the
GAS site but only at a low affinity. STAT6 may be an
important regulator of mitogenesis when cells respond
normally to IL-4. There is speculation that the
inappropriate activation of STAT6 is involved in
uncontrolled cell growth in an oncogenic state.
IFNgamma is a negative regulator of STAT6 dependent
transcription of target genes. Bcl-6 is another
negative regulator of STAT6 activity. Bcl-6 is a
transcriptional repressor normally expressed in
germinal center B cells and some T cells. IL-4
signaling via STAT6 initially occurs unopposed, but is
then dampened by a negative feedback mechanism through
the IL-4/Stat6 dependent induction of SOCS1 expression.
The IL-4 dependent aspect of Th2 differentiation
requires the activation of STAT6. IL-4 signaling and
STAT6 appear to play an important role in the immune
response. Recently, it was shown that large scale
chromatin remodeling of the IL-4 gene occurs as cells
differentiate into Th2 effectors is STAT6 dependent.
STAT proteins mediate the signaling of cytokines and a
number of growth factors from the receptors of these
extracellular signaling molecules to the cell nucleus.
STATs are specifically phosphorylated by
receptor-associated Janus kinases, receptor tyrosine
kinases, or cytoplasmic tyrosine kinases. The
phosphorylated STAT molecules dimerize by reciprocal
binding of their SH2 domains to the phosphotyrosine
residues. These dimeric STATs translocate into the
nucleus, bind to specific DNA sequences, and regulate
the transcription of their target genes. However there
are a number of unphosphorylated STATs that travel
between the cytoplasm and nucleus and some STATs that
exist as dimers in unstimulated cells that can exert
biological functions independent of being activated.
There are seven mammalian STAT family members which
have been identified: STAT1, STAT2, STAT3, STAT4, STAT5
(STAT5A and STAT5B), and STAT6. There are 6 conserved
domains in STAT: N-terminal domain (NTD), coiled-coil
domain (CCD), DNA-binding domain (DBD), alpha-helical
linker domain (LD), SH2 domain, and transactivation
domain (TAD). NTD is involved in dimerization of
unphosphorylated STATs monomers and for the
tetramerization between STAT1, STAT3, STAT4 and STAT5
on promoters with two or more tandem STAT binding
sites. It also plays a role in promoting interactions
with transcriptional co-activators such as CREB binding
protein (CBP)/p300, as well as being important for
nuclear import and deactivation of STATs involving
tyrosine de-phosphorylation. CCD interacts with other
proteins, such as IFN regulatory protein 9 (IRF-9/p48)
with STAT1 and c-JUN with STAT3 and is also thought to
participate in the negative regulation of these
proteins. Distinct genes are bound to STATs via their
DBD domain. This domain is also involved in nuclear
translocation of activated STAT1 and STAT3
phosphorylated dimers upon cytokine stimulation. LD
links the DNA-binding and SH2 domains and is important
for the transcriptional activation of STAT1 in response
to IFN-gamma. It also plays a role in protein-protein
interactions and has also been implicated in the
constitutive nucleocytoplasmic shuttling of
unphosphorylated STATs in resting cells. The SH2
domain is necessary for receptor association and
tyrosine phosphodimer formation. Residues within this
domain may be particularly important for some cellular
functions mediated by the STATs as well as residues
adjacent to this domain. The TAD interacts with
several proteins, namely minichromosome maintenance
complex component 5 (MCM5), breast cancer 1 (BRCA1) and
CBP/p300. TAD also contains a modulatory
phosphorylation site that regulates STAT activity and
is necessary for maximal transcription of a number of
target genes. The conserved tyrosine residue present in
the C-terminus is crucial for dimerization via
interaction with the SH2 domain upon the interaction of
the ligand with the receptor. STAT activation by
tyrosine phosphorylation also determines nuclear import
and retention, DNA binding to specific DNA elements in
the promoters of responsive genes, and transcriptional
activation of STAT dimers. In addition to the SH2
domain there is a coiled-coil domain, a DNA binding
domain, and a transactivation domain in the STAT
proteins. In general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 129
Score = 25.5 bits (56), Expect = 4.1
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 36 EFSKKCAERWKSSRIVNPFVGRKFAPVFL------TFLSRMKDS 73
+ +K+C + S R++ F+ +++ L TFL R DS
Sbjct: 7 DLTKRCLRSYWSDRLIIGFISKQYVTSLLLNEPDGTFLLRFSDS 50
>gnl|CDD|185308 PRK15410, PRK15410, DgsA anti-repressor MtfA; Provisional.
Length = 260
Score = 25.9 bits (57), Expect = 4.2
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 64 LTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDY 98
L L + ++LFC+ PVL +G L+ F E L Y
Sbjct: 60 LDSLMSARIALLFCL-PVLELGIEWLDGFHEVLIY 93
>gnl|CDD|132916 cd07033, TPP_PYR_DXS_TK_like, Pyrimidine (PYR) binding domain of
1-deoxy-D-xylulose-5-phosphate synthase (DXS),
transketolase (TK), and related proteins. Thiamine
pyrophosphate (TPP) family, pyrimidine (PYR) binding
domain of 1-deoxy-D-xylulose-5-phosphate synthase
(DXS), transketolase (TK), and the beta subunits of the
E1 component of the human pyruvate dehydrogenase
complex (E1- PDHc), subfamily. The PYR domain is found
in many key metabolic enzymes which use TPP (also known
as thiamine diphosphate) as a cofactor. TPP binds in
the cleft formed by a PYR domain and a PP domain. The
PYR domain, binds the aminopyrimidine ring of TPP, the
PP domain binds the diphosphate residue. A polar
interaction between the conserved glutamate of the PYR
domain and the N1' of the TPP aminopyrimidine ring is
shared by most TPP-dependent enzymes, and participates
in the activation of TPP. The PYR and PP domains have a
common fold, but do not share strong sequence
conservation. The PP domain is not included in this
sub-family. Like many TPP-dependent enzymes DXS and TK
are homodimers having a PYR and a PP domain on the same
subunit. TK has two active sites per dimer which lie
between PYR and PP domains of different subunits. For
DXS each active site is located at the interface of a
PYR and a PP domain from the same subunit. E1-PDHc is
an alpha2beta2 dimer-of-heterodimers having two active
sites but having the PYR and PP domains arranged on
separate subunits, the PYR domains on the beta
subunits, the PP domains on the alpha subunits. DXS is
a regulatory enzyme of the mevalonate-independent
pathway involved in terpenoid biosynthesis, it
catalyzes a transketolase-type condensation of pyruvate
with D-glyceraldehyde-3-phosphate to form
1-deoxy-D-xylulose-5-phosphate (DXP) and carbon
dioxide. TK catalyzes the transfer of a two-carbon unit
from ketose phosphates to aldose phosphates. In
heterotrophic organisms, TK provides a link between
glycolysis and the pentose phosphate pathway and
provides precursors for nucleotide, aromatic amino acid
and vitamin biosynthesis. TK also plays a central role
in the Calvin cycle in plants. PDHc catalyzes the
irreversible oxidative decarboxylation of pyruvate to
produce acetyl-CoA in the bridging step between
glycolysis and the citric acid cycle. This subfamily
includes the beta subunits of the E1 component of the
acetoin dehydrogenase complex (ADC) and the branched
chain alpha-keto acid dehydrogenase/2-oxoisovalerate
dehydrogenase complex (BCADC). ADC participates in the
breakdown of acetoin. BCADC catalyzes the oxidative
decarboxylation of 4-methyl-2-oxopentanoate,
3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate
during the breakdown of branched chain amino acids.
Length = 156
Score = 25.5 bits (57), Expect = 5.3
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 9/39 (23%)
Query: 53 PFVGRKFAPVFLTFLSRMKDSI--LFCVN--PVLAVGSR 87
PFV F FL R D I + PV VG+
Sbjct: 65 PFVS-----TFSFFLQRAYDQIRHDVALQNLPVKFVGTH 98
>gnl|CDD|204067 pfam08793, 2C_adapt, 2-cysteine adaptor domain. The
virus-specific 2-cysteine adaptor domain is found fused
to OTU/A20-like peptidases and S/T protein kinases. The
domain associations of these proteins indicate that
they might function as viral adaptors connecting the
kinases and OTU/A20 peptidases to specific targets.
Length = 37
Score = 23.7 bits (52), Expect = 6.0
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 40 KCAERWKSSRIVNPFVGRKFAP 61
KC E + + VNP GRK P
Sbjct: 2 KCEE-FLRNPTVNPITGRKIKP 22
>gnl|CDD|219457 pfam07534, TLD, TLD. This domain is predicted to be an enzyme
and is often found associated with pfam01476.
Length = 136
Score = 24.5 bits (54), Expect = 9.8
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 11/64 (17%)
Query: 29 EENVVFAEFSKKCAERWKSSRIVNPFVGRK------FAPVFLTFLSRMKDSILFCVNPVL 82
++ VF F ++ WK+S F G +P F + K++ F L
Sbjct: 32 DDGYVFGAF---LSQPWKNSG--KKFYGDGESFLFSLSPKFKVYKWTGKNNAYFNATSGL 86
Query: 83 AVGS 86
G
Sbjct: 87 GFGG 90
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
0.328 0.140 0.431
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,454,379
Number of extensions: 454390
Number of successful extensions: 475
Number of sequences better than 10.0: 1
Number of HSP's gapped: 469
Number of HSP's successfully gapped: 20
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)