RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16764
(113 letters)
>gnl|CDD|132748 cd06950, NR_LBD_Tlx_PNR_like, The ligand binding domain of
Tailless-like proteins, orphan nuclear receptors. The
ligand binding domain of the photoreceptor cell-specific
nuclear receptor (PNR) like family: This family
includes photoreceptor cell-specific nuclear receptor
(PNR), Tailless (TLX), and related receptors. TLX is an
orphan receptor that is expressed by neural
stem/progenitor cells in the adult brain of the
subventricular zone (SVZ) and the dentate gyrus (DG). It
plays a key role in neural development by promoting cell
cycle progression and preventing apoptosis in the
developing brain. PNR is expressed only in the outer
layer of retinal photoreceptor cells. It may be involved
in the signaling pathway regulating photoreceptor
differentiation and/or maintenance. Like other members
of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX and PNR
have a central well conserved DNA binding domain (DBD),
a variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 206
Score = 69.6 bits (171), Expect = 5e-16
Identities = 31/70 (44%), Positives = 42/70 (60%), Gaps = 6/70 (8%)
Query: 33 VRFKTGSKFT------AAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVL 86
V FK ++ A+Q Q+ LNK+I T YP+QP RF K+ L+LP L+ I S +
Sbjct: 136 VLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTI 195
Query: 87 EELFFRNIIG 96
EELFF+ IG
Sbjct: 196 EELFFKKTIG 205
>gnl|CDD|132746 cd06948, NR_LBD_COUP-TF, Ligand binding domain of chicken ovalbumin
upstream promoter transcription factors, a member of the
nuclear receptor family. The ligand binding domain of
chicken ovalbumin upstream promoter transcription
factors (COUP-TFs): COUP-TFs are orphan members of the
steroid/thyroid hormone receptor superfamily. They are
expressed in many tissues and are involved in the
regulation of several important biological processes,
such as neurogenesis, organogenesis, cell fate
determination, and metabolic homeostasis. In mammals two
isoforms named COUP-TFI and COUP-TFII have been
identified. Both genes show an exceptional homology and
overlapping expression patterns, suggesting that they
may serve redundant functions. Although COUP-TF was
originally characterized as a transcriptional activator
of the chicken ovalbumin gene, COUP-TFs are generally
considered to be repressors of transcription for other
nuclear hormone receptors, such as retinoic acid
receptor (RAR), thyroid hormone receptor (TR), vitamin D
receptor (VDR), peroxisome proliferator activated
receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4).
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
COUP-TFs have a central well cons erved DNA binding
domain (DBD), a variable N-terminal domain, a flexible
hinge and a C-terminal ligand binding domain (LBD).
Length = 236
Score = 57.5 bits (139), Expect = 3e-11
Identities = 28/65 (43%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 44 AIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKK 103
++Q +Q L +Y+ T YP+QPTRF K+ L LP L+++ S V+E+LFF ++G T I+
Sbjct: 159 SLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVG-KTPIET 217
Query: 104 TIWHM 108
I M
Sbjct: 218 LIRDM 222
>gnl|CDD|132749 cd06951, NR_LBD_Dax1_like, The ligand binding domain of DAX1
protein, a nuclear receptor lacking DNA binding domain.
The ligand binding domain of DAX1-like proteins: This
orphan nuclear receptor family includes DAX1
(dosage-sensitive sex reversal adrenal hypoplasia
congenita critical region on chromosome X gene 1) and
the Small Heterodimer Partner (SHP). Both receptors have
a typical ligand binding domain, but lack the DNA
binding domain, typical to almost all of the nuclear
receptors. They function as a transcriptional
coregulator by directly interacting with other nuclear
receptors. DAX1 and SHP can form heterodimers with each
other, as well as with many other nuclear receptors. In
addition, DAX1 can also form homodimers. DAX1 plays an
important role in the normal development of several
hormone-producing tissues. SHP has shown to regulate a
variety of target genes.
Length = 222
Score = 53.7 bits (129), Expect = 6e-10
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
+ A+Q Q LN++ P + R ++ L+L L+ I + + ELFFR IIG
Sbjct: 156 HYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIG 212
>gnl|CDD|132763 cd07349, NR_LBD_SHP, The ligand binding domain of DAX1 protein, a
nuclear receptor lacking DNA binding domain. The ligand
binding domain of the Small Heterodimer Partner (SHP):
SHP is a member of the nuclear receptor superfamily. SHP
has a ligand binding domain, but lacks the DNA binding
domain, typical to almost all of the nuclear receptors.
It functions as a transcriptional coregulator by
directly interacting with other nuclear receptors
through its AF-2 motif. The closest relative of SHP is
DAX1 and they can form heterodimer. SHP is an orphan
receptor, lacking an identified ligand.
Length = 222
Score = 47.1 bits (112), Expect = 2e-07
Identities = 22/60 (36%), Positives = 31/60 (51%)
Query: 37 TGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
T S +Q Q L + + ++P RF +I L LKSIP ++ +LFFR IIG
Sbjct: 151 TASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIG 210
>gnl|CDD|132750 cd06952, NR_LBD_TR2_like, The ligand binding domain of the orphan
nuclear receptors TR4 and TR2. The ligand binding
domain of the TR4 and TR2 (human testicular receptor 4
and 2): TR4 and TR2 are orphan nuclear receptors.
Several isoforms of TR4 and TR2 have been isolated in
various tissues. TR2 is abundantly expressed in the
androgen-sensitive prostate. TR4 transcripts are
expressed in many tissues, including central nervous
system, adrenal gland, spleen, thyroid gland, and
prostate. The expression of TR2 is negatively regulated
by androgen, retinoids, and radiation. The expression of
both mouse TR2 and TR4 is up-regulated by neurocytokine
ciliary neurotrophic factor (CNTF) in mouse. It has
shown that human TR2 binds to a wide spectrum of natural
hormone response elements (HREs) with distinct
affinities suggesting that TR2 may cross-talk with other
gene expression regulation systems. The genes responding
to TR2 or TR4 include genes that are regulated by
retinoic acid receptor, vitamin D receptor, peroxisome
proliferator-activated receptor. TR4/2 binds to HREs as
a dimer. Like other members of the nuclea r receptor
(NR) superfamily of ligand-activated transcription
factors, TR2-like receptors have a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 222
Score = 44.2 bits (105), Expect = 2e-06
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
L Y+ YP R K+ L LP L+S+ + EELFF +IG
Sbjct: 165 LRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLIG 208
>gnl|CDD|132764 cd07350, NR_LBD_Dax1, The ligand binding domain of DAX1 protein, a
nuclear receptor lacking DNA binding domain. The ligand
binding domain of the DAX1 protein: DAX1
(dosage-sensitive sex reversal adrenal hypoplasia
congenita critical region on chromosome X gene 1) is a
nuclear receptor with a typical ligand binding domain,
but lacks the DNA binding domain. DAX1 plays an
important role in the normal development of several
hormone-producing tissues. Duplications of the region of
the X chromosome containing DAX1 cause dosage sensitive
sex reversal. DAX1 acts as a global repressor of many
nuclear receptors, including SF-1, LRH-1, ERR, ER, AR
and PR. DAX1 can form homodimer and heterodimerizes with
its alternatively spliced isoform DAX1A and other
nuclear receptors such as SHP, ERalpha and SF-1.
Length = 232
Score = 43.3 bits (102), Expect = 5e-06
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
++ +Q Q LN+++ ++ RF K+ + L L++I + V+ ELFFR IIG
Sbjct: 166 QYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIG 222
>gnl|CDD|132741 cd06943, NR_LBD_RXR_like, The ligand binding domain of the retinoid
X receptor and Ultraspiracle, members of nuclear
receptor superfamily. The ligand binding domain of the
retinoid X receptor (RXR) and Ultraspiracle (USP): This
family includes two evolutionary related nuclear
receptors: retinoid X receptor (RXR) and Ultraspiracle
(USP). RXR is a nuclear receptor in mammalian and USP is
its counterpart in invertebrates. The native ligand of
retinoid X receptor is 9-cis retinoic acid (RA). RXR
functions as a DNA binding partner by forming
heterodimers with other nuclear receptors including CAR,
FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play
different roles in these heterodimers. It acts either
as a structural component of the heterodimer complex,
required for DNA binding but not acting as a receptor or
as both a structural and a functional component of the
heterodimer, allowing 9-cis RA to signal through the
corresponding heterodimer. In addition, RXR can also
form homodimers, functioning as a receptor for 9-cis RA,
independently of other nuclear receptors. Ultraspiracle
(USP) plays similar roles as DNA binding partner of
other nuclear rec eptors in invertebrates. USP has no
known high-affinity ligand and is thought to be a silent
component in the heterodimeric complex with partner
receptors. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, RXR and USP have a central well conserved DNA
binding domain (DBD), a variable N-terminal domain, a
flexible hinge and a C-terminal ligand binding domain
(LBD).
Length = 207
Score = 41.5 bits (98), Expect = 2e-05
Identities = 19/39 (48%), Positives = 23/39 (58%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFF 91
L +Y +P QP RF K+ L LP L+SI LE LFF
Sbjct: 167 LEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 205
>gnl|CDD|132729 cd06931, NR_LBD_HNF4_like, The ligand binding domain of heptocyte
nuclear factor 4, which is explosively expanded in
nematodes. The ligand binding domain of hepatocyte
nuclear factor 4 (HNF4) like proteins: HNF4 is a member
of the nuclear receptor superfamily. HNF4 plays a key
role in establishing and maintenance of hepatocyte
differentiation in the liver. It is also expressed in
gut, kidney, and pancreatic beta cells. HNF4 was
originally classified as an orphan receptor, but later
it is found that HNF4 binds with very high affinity to a
variety of fatty acids. However, unlike other nuclear
receptors, the ligands do not act as a molecular switch
for HNF4. They seem to constantly bind to the receptor,
which is constitutively active as a transcription
activator. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, HNF4 has a central well conserved DNA binding
domain (DBD), a variable N-terminal domain, a flexible
hinge and a C-terminal ligand binding domain (LBD). The
LBD domain is also responsible for recruiting
co-activator proteins. More than 280 nuclear receptors
are found in C. ele gans, most of which are originated
from an explosive burst of duplications of HNF4.
Length = 222
Score = 39.7 bits (93), Expect = 7e-05
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 50 QIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
Q+ L YI+ RF ++ L+LP L+SI ++E++ F + G
Sbjct: 165 QVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFG 211
>gnl|CDD|132728 cd06930, NR_LBD_F2, Ligand-binding domain of nuclear receptor
family 2. Ligand-binding domain (LBD) of nuclear
receptor (NR) family 2: This is one of the major
subfamily of nuclear receptors, including some well
known nuclear receptors such as glucocorticoid receptor
(GR), mineralocorticoid receptor (MR), estrogen receptor
(ER), progesterone receptor (PR), and androgen receptor
(AR), other related receptors. Nuclear receptors form a
superfamily of ligand-activated transcription
regulators, which regulate various physiological
functions, from development, reproduction, to
homeostasis and metabolism in animals (metazoans). The
family contains not only receptors for known ligands but
also orphan receptors for which ligands do not exist or
have not been identified. NRs share a common structural
organization with a central well conserved DNA binding
domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 165
Score = 39.1 bits (92), Expect = 1e-04
Identities = 16/29 (55%), Positives = 19/29 (65%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSI 81
L +YI YP QP RF K+ L LP L+SI
Sbjct: 137 LQEYIRKRYPQQPARFAKLLLRLPELRSI 165
>gnl|CDD|132743 cd06945, NR_LBD_Nurr1_like, The ligand binding domain of Nurr1 and
related nuclear receptor proteins, members of nuclear
receptor superfamily. The ligand binding domain of
nuclear receptor Nurr1_like: This family of nuclear
receptors, including Nurr1, Nerve growth
factor-induced-B (NGFI-B) and DHR38 are involved in the
embryo development. Nurr1 is a transcription factor that
is expressed in the embryonic ventral midbrain and is
critical for the development of dopamine (DA) neurons.
Structural studies have shown that the ligand binding
pocket of Nurr1 is filled by bulky hydrophobic residues,
making it unable to bind to ligands. Therefore, it
belongs to the class of orphan receptors. However, Nurr1
forms heterodimers with RXR and can promote signaling
via its partner, RXR. NGFI-B is an early immediate gene
product of embryo development that is rapidly produced
in response to a variety of cellular signals including
nerve growth factor. It is involved in T-cell-mediated
apoptosis, as well as neuronal differentiation and
function. NGFI-B regulates transcription by binding to a
specific DNA target upstream of its target genes and
regulating the rate of tr anscriptional initiation.
Another group of receptor in this family is DHR38.
DHR38 is the Drosophila homolog to the vertebrate
NGFI-B-type orphan receptor. It interacts with the USP
component of the ecdysone receptor complex, suggesting
that DHR38 might modulate ecdysone-triggered signals in
the fly, in addition to the ECR/USP pathway. Nurr1_like
proteins exhibit a modular structure that is
characteristic for nuclear receptors; they have a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a non-conserved hinge and a
C-terminal ligand binding domain (LBD).
Length = 239
Score = 28.9 bits (65), Expect = 0.47
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 53 LNKYIHTVYPSQ--PTRFCKIQLILPRLKSIPSLVLEELFF 91
L ++ + YP Q P R K+ L LP L+++ L+ +FF
Sbjct: 176 LRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFF 216
>gnl|CDD|132727 cd06929, NR_LBD_F1, Ligand-binding domain of nuclear receptor
family 1. Ligand-binding domain (LBD) of nuclear
receptor (NR) family 1: This is one of the major
subfamily of nuclear receptors, including thyroid
receptor, retinoid acid receptor, ecdysone receptor,
farnesoid X receptor, vitamin D receptor, and other
related receptors. Nuclear receptors form a superfamily
of ligand-activated transcription regulators, which
regulate various physiological functions, from
development, reproduction, to homeostasis and metabolism
in animals (metazoans). The family contains not only
receptors for known ligands but also orphan receptors
for which ligands do not exist or have not been
identified. NRs share a common structural organization
with a central well conserved DNA binding domain (DBD),
a variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 174
Score = 28.7 bits (65), Expect = 0.53
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSI 81
L +Y+ +P P F K+ L L+++
Sbjct: 138 LQRYLKVNHPDAPQMFAKLLKKLTELRTL 166
>gnl|CDD|132754 cd07069, NR_LBD_Lrh-1, The ligand binding domain of the liver
receptor homolog-1, a member of nuclear receptor
superfamily,. The ligand binding domain (LBD) of the
liver receptor homolog-1 (LRH-1): LRH-1 belongs to
nuclear hormone receptor superfamily, and is expressed
mainly in the liver, intestine, exocrine pancreas, and
ovary. Most nuclear receptors function as homodimer or
heterodimers. However, LRH-1 binds DNA as a monomer, and
is a regulator of bile-acid homeostasis,
steroidogenesis, reverse cholesterol transport and the
initial stages of embryonic development. Recently,
phospholipids have been identified as potential ligand
for LRH-1 and steroidogenic factor-1 (SF-1). Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, LRH-1 has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 241
Score = 28.1 bits (62), Expect = 0.90
Identities = 14/53 (26%), Positives = 26/53 (49%)
Query: 44 AIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
+Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 172 GVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 224
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 27.7 bits (62), Expect = 0.94
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 53 LNKYIHTVYPSQ-PTRFCKIQLILPRLKSI 81
L+ Y YP P RF K+ LILP L+ I
Sbjct: 134 LHDYYLKNYPMNYPGRFAKLLLILPELRKI 163
>gnl|CDD|132742 cd06944, NR_LBD_Ftz-F1_like, The ligand binding domain of FTZ-F1
like nuclear receptors. The ligand binding domain of
FTZ-F1 like nuclear receptors: This nuclear receptor
family includes at least three subgroups of receptors
that function in embryo development and differentiation,
and other processes. FTZ-F1 interacts with the
cis-acting DNA motif of ftz gene, which required at
several stages of development. Particularly, FTZ-F1
genes are strongly linked to steroid biosynthesis and
sex-determination; LRH-1 is a regulator of bile-acid
homeostasis, steroidogenesis, reverse cholesterol
transport and the initial stages of embryonic
development. SF-1 is an essential regulator of endocrine
development and function and is considered a master
regulator of reproduction; SF-1 functions cooperatively
with other transcription factors to modulate gene
expression. Phospholipids have been identified as
potential ligand for LRH-1 and steroidogenic factor-1
(SF-1). However, the ligand for FTZ-F1 has not yet been
identified. Most nuclear receptors function as homodimer
or heterodimers. However, LRH-1 and SF-1 bind to DNA as
a monomer. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, receptors in this family have a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 237
Score = 27.6 bits (62), Expect = 1.1
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 56 YIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 182 YTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 222
>gnl|CDD|132751 cd06953, NR_LBD_DHR4_like, The ligand binding domain of orphan
nuclear receptor Ecdysone-induced receptor DHR4. The
ligand binding domain of Ecdysone-induced receptor DHR4:
Ecdysone-induced orphan receptor DHR4 is a member of the
nuclear receptor family. DHR4 is expressed during the
early Drosophila larval development and is induced by
ecdysone. DHR4 coordinates growth and maturation in
Drosophila by mediating endocrine response to the
attainment of proper body size during larval
development. Mutations in DHR4 result in shorter larval
development which translates into smaller and lighter
flies. Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
DHR4 has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain (LBD). .
Length = 213
Score = 27.3 bits (61), Expect = 1.4
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFF 91
L + YP+QP RF + LP +++ +L F
Sbjct: 167 LQDFTELNYPNQPNRFSDLLSCLPEIRAAAGKLLHSKLF 205
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain forms one of the two distinctive lobes of the
Rpb2 structure. This domain is also known as the lobe
domain. DNA has been demonstrated to bind to the concave
surface of the lobe domain, and plays a role in
maintaining the transcription bubble. Many of the
bacterial members contain large insertions within this
domain, as region known as dispensable region 1 (DRI).
Length = 185
Score = 26.9 bits (60), Expect = 2.3
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 3/75 (4%)
Query: 1 MFQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTV 60
+ I T+E + I + RRG R + + + + LNK++ +
Sbjct: 86 LKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREILYSRDP--KYNLNKHL-GL 142
Query: 61 YPSQPTRFCKIQLIL 75
K Q IL
Sbjct: 143 NEPFENERLKAQDIL 157
>gnl|CDD|132738 cd06940, NR_LBD_REV_ERB, The ligand binding domain of REV-ERB
receptors, members of the nuclear receptor superfamily.
The ligand binding domain (LBD) of REV-ERB receptors:
REV-ERBs are transcriptional regulators belonging to the
nuclear receptor superfamily. They regulate a number of
physiological functions including the circadian rhythm,
lipid metabolism, and cellular differentiation. The LBD
domain of REV-ERB is unusual in the nuclear receptor
family by lacking the AF-2 region that is responsible
for coactivator interaction. REV-ERBs act as
constitutive repressors because of their inability to
bind coactivators. REV-ERB receptors can bind to two
classes of DNA response elements as either a monomer or
heterodimer, indicating functional diversity. When bound
to the DNA, they recruit corepressors (NcoR/histone
deacetylase 3) to the promoter, resulting in repression
of the target gene. The porphyrin heme has been
demonstrated to function as a ligand for REV-ERB. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, REV-ERB
receptors have a central well conserved DNA binding
domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 189
Score = 25.5 bits (56), Expect = 5.8
Identities = 11/29 (37%), Positives = 21/29 (72%)
Query: 61 YPSQPTRFCKIQLILPRLKSIPSLVLEEL 89
+P++P+ F K+ L LP L+++ +L E+L
Sbjct: 156 HPNEPSIFTKLLLKLPDLRTLNNLHSEKL 184
>gnl|CDD|215719 pfam00104, Hormone_recep, Ligand-binding domain of nuclear hormone
receptor. This all helical domain is involved in
binding the hormone in these receptors.
Length = 186
Score = 25.4 bits (56), Expect = 7.3
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 53 LNKYIHTVY--PSQPTRFCKIQLILPRLKSIPSLVLEELFFRNII 95
L+ Y P+ R K+ +LP L+ I + E+L +
Sbjct: 142 LHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLELAKLF 186
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
0.324 0.136 0.400
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,534,005
Number of extensions: 460165
Number of successful extensions: 463
Number of sequences better than 10.0: 1
Number of HSP's gapped: 462
Number of HSP's successfully gapped: 23
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)