RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11507
(113 letters)
>gnl|CDD|143544 cd07170, NR_DBD_ERR, DNA-binding domain of estrogen related
receptors (ERR) is composed of two C4-type zinc
fingers. DNA-binding domain of estrogen related
receptors (ERRs) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which coordinates a single zinc atom. ERR
interacts with the palindromic inverted repeat,
5'GGTCAnnnTGACC-3', upstream of the target gene and
modulates the rate of transcriptional initiation. The
estrogen receptor-related receptors (ERRs) are
transcriptional regulators, which are closely related
to the estrogen receptor (ER) family. Although ERRs
lack the ability to bind to estrogen and are so-called
orphan receptors, they share target genes,
co-regulators and promoters with the estrogen receptor
(ER) family. By targeting the same set of genes, ERRs
seem to interfere with the classic ER-mediated estrogen
response in various ways. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, ERR has 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 = 97
Score = 77.6 bits (191), Expect = 4e-20
Identities = 31/34 (91%), Positives = 34/34 (100%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQ 36
>gnl|CDD|143530 cd07155, NR_DBD_ER_like, DNA-binding domain of estrogen receptor
(ER) and estrogen related receptors (ERR) is composed
of two C4-type zinc fingers. DNA-binding domains of
estrogen receptor (ER) and estrogen related receptors
(ERR) are composed of two C4-type zinc fingers. Each
zinc finger contains a group of four Cys residues which
co-ordinates a single zinc atom. ER and ERR interact
with the palindromic inverted repeat,
5'GGTCAnnnTGACC-3', upstream of the target gene and
modulate the rate of transcriptional initiation. ERR
and ER are closely related and share sequence
similarity, target genes, co-regulators and promoters.
While ER is activated by endogenous estrogen, ERR lacks
the ability to bind to estrogen. Estrogen receptor
mediates the biological effects of hormone estrogen by
the binding of the receptor dimer to estrogen response
element of target genes. However, ERRs seem to
interfere with the classic ER-mediated estrogen
responsive signaling by targeting the same set of
genes. ERRs and ERs exhibit the common modular
structure with other nuclear receptors. They have a
central highly conserved DNA binding domain (DBD), a
non-conserved N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 75
Score = 72.5 bits (178), Expect = 2e-18
Identities = 28/30 (93%), Positives = 30/30 (100%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
CLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQ 30
>gnl|CDD|201004 pfam00105, zf-C4, Zinc finger, C4 type (two domains). In nearly
all cases, this is the DNA binding domain of a nuclear
hormone receptor. The alignment contains two Zinc
finger domains that are too dissimilar to be aligned
with each other.
Length = 70
Score = 70.7 bits (174), Expect = 1e-17
Identities = 22/32 (68%), Positives = 26/32 (81%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
LC VCGD ASG+HYGV +CE CK FF+R+IQ
Sbjct: 1 ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQ 32
>gnl|CDD|143512 cd06916, NR_DBD_like, DNA-binding domain of nuclear receptors is
composed of two C4-type zinc fingers. DNA-binding
domain of nuclear receptors is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. It
interacts with a specific DNA site upstream of the
target gene and modulates the rate of transcriptional
initiation. 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).
Most nuclear receptors bind as homodimers or
heterodimers to their target sites, which consist of
two hexameric half-sites. Specificity is determined by
the half-site sequence, the relative orientation of the
half-sites and the number of spacer nucleotides between
the half-sites. However, a growing number of nuclear
receptors have been reported to bind to DNA as
monomers.
Length = 72
Score = 70.7 bits (174), Expect = 1e-17
Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV 77
C VCGD ASG+HYGV +CE CK FF+R+++
Sbjct: 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYT 36
>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors.
Length = 70
Score = 65.2 bits (160), Expect = 1e-15
Identities = 24/33 (72%), Positives = 27/33 (81%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
LC VCGD ASGFH+GV SC ACKAFF+RT+ R
Sbjct: 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLR 33
>gnl|CDD|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER)
is composed of two C4-type zinc fingers. DNA-binding
domain of estrogen receptors (ER) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which coordinates a single zinc
atom. ER interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. Estrogen receptor is a
transcription regulator that mediates the biological
effects of hormone estrogen. The binding of estrogen to
the receptor triggers the dimerization and the binding
of the receptor dimer to estrogen response element,
which is a palindromic inverted repeat:
5'GGTCAnnnTGACC-3', of target genes. Through ER,
estrogen regulates development, reproduction and
homeostasis. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, ER has 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 = 82
Score = 64.5 bits (157), Expect = 4e-15
Identities = 23/34 (67%), Positives = 25/34 (73%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 2 DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQ 35
>gnl|CDD|143518 cd06960, NR_DBD_HNF4A, DNA-binding domain of heptocyte nuclear
factor 4 (HNF4) is composed of two C4-type zinc
fingers. DNA-binding domain of hepatocyte nuclear
factor 4 (HNF4) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which co-ordinates a single zinc atom. HNF4
interacts with a DNA site, composed of two direct
repeats of AGTTCA with 1 bp spacer, which is upstream
of target genes and modulates the rate of
transcriptional initiation. 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).
Length = 76
Score = 61.1 bits (149), Expect = 7e-14
Identities = 18/29 (62%), Positives = 22/29 (75%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTI 70
C VCGD A+G HYGV SC CK FF+R++
Sbjct: 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSV 29
>gnl|CDD|143540 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV-ERB
receptor-like is composed of two C4-type zinc fingers.
DNA-binding domain of REV-ERB receptor- like is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which coordinates
a single zinc atom. This domain interacts with specific
DNA sites upstream of the target gene and modulates the
rate of transcriptional initiation. REV-ERB receptors
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. REV-ERB
receptors bind as a monomer to a (A/G)GGTCA half-site
with a 5' AT-rich extension or as a homodimer to a
direct repeat 2 element (AGGTCA sequence with a 2-bp
spacer), indicating functional diversity. When bound to
the DNA, they recruit corepressors (NcoR/histone
deacetylase 3) to the promoter, resulting in repression
of the target genes. The porphyrin heme has been
demonstrated to function as a ligand for REV-ERB
receptor. 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 = 89
Score = 61.4 bits (149), Expect = 8e-14
Identities = 23/31 (74%), Positives = 26/31 (83%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
LC VCGD ASGFHYGV +CE CK FF+R+IQ
Sbjct: 5 LCKVCGDKASGFHYGVHACEGCKGFFRRSIQ 35
>gnl|CDD|143533 cd07158, NR_DBD_Ppar_like, The DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) like nuclear
receptor family. The DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) like nuclear
receptor family is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which co-ordinates a single zinc atom. These
domains interact with specific DNA sites upstream of
the target gene and modulate the rate of
transcriptional initiation. This family includes three
known types of nuclear receptors: peroxisome
proliferator-activated receptors (PPAR), REV-ERB
receptors and Drosophila ecdysone-induced protein 78
(E78). Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
PPAR-like 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 = 73
Score = 60.7 bits (147), Expect = 9e-14
Identities = 24/30 (80%), Positives = 25/30 (83%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C VCGD ASGFHYGV SCE CK FF+RTIQ
Sbjct: 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQ 30
>gnl|CDD|143519 cd06961, NR_DBD_TR, DNA-binding domain of thyroid hormone
receptors (TRs) is composed of two C4-type zinc
fingers. DNA-binding domain of thyroid hormone
receptors (TRs) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which co-ordinates a single zinc atom. TR
interacts with the thyroid response element, which is a
DNA site with direct repeats of the consensus sequence
5'-AGGTCA-3' separated by one to five base pairs,
upstream of target genes and modulates the rate of
transcriptional initiation. Thyroid hormone receptor
(TR) mediates the actions of thyroid hormones, which
play critical roles in growth, development, and
homeostasis in mammals. They regulate overall metabolic
rate, cholesterol and triglyceride levels, and heart
rate, and affect mood. TRs are expressed from two
separate genes (alpha and beta) in human and each gene
generates two isoforms of the receptor through
differential promoter usage or splicing. TRalpha
functions in the heart to regulate heart rate and
rhythm and TRbeta is active in the liver and other
tissues. The unliganded TRs function as transcription
repressors, by binding to thyroid hormone response
elements (TRE) predominantly as homodimers, or as
heterodimers with retinoid X-receptors (RXR), and being
associated with a complex of proteins containing
corepressor proteins. Ligand binding promotes
corepressor dissociation and binding of a coactivator
to activate transcription. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, TR 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 = 85
Score = 59.7 bits (145), Expect = 3e-13
Identities = 18/31 (58%), Positives = 24/31 (77%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C+VCGD A+G+HY +CE CK FF+RT+Q
Sbjct: 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQ 31
>gnl|CDD|143517 cd06959, NR_DBD_EcR_like, The DNA-binding domain of Ecdysone
receptor (EcR) like nuclear receptor family is composed
of two C4-type zinc fingers. The DNA-binding domain of
Ecdysone receptor (EcR) like nuclear receptor family is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which
co-ordinates a single zinc atom. EcR interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation. This
family includes three types of nuclear receptors:
Ecdysone receptor (EcR), Liver X receptor (LXR) and
Farnesoid X receptor (FXR). The DNA binding activity is
regulated by their corresponding ligands. The ligands
for EcR are ecdysteroids; LXR is regulated by oxidized
cholesterol derivatives or oxysterols; and bile acids
control FXR's activities. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, EcR-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 = 73
Score = 58.6 bits (142), Expect = 6e-13
Identities = 21/31 (67%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C+VCGD ASGFHYGV SCE CK FF+R++
Sbjct: 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVT 31
>gnl|CDD|143523 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) is composed of
two C4-type zinc fingers. DNA-binding domain of
peroxisome proliferator-activated receptors (PPAR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which
co-ordinates a single zinc atom. PPAR interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation.
Peroxisome proliferator-activated receptors (PPARs) are
members of the nuclear receptor superfamily of
ligand-activated transcription factors. PPARs play
important roles in regulating cellular differentiation,
development and lipid metabolism. Activated PPAR forms
a heterodimer with the retinoid X receptor (RXR) that
binds to the hormone response elements, which are
composed of two direct repeats of the consensus
sequence 5'-AGGTCA-3' separated by one to five base
pair located upstream of the peroxisome proliferator
responsive genes, and interacts with co-activators.
Several essential fatty acids, oxidized lipids and
prostaglandin J derivatives can bind and activate PPAR.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
PPAR has a central well conserved DNA binding domain
(DBD), a variable N-terminal regulatory domain, a
flexible hinge and a C-terminal ligand binding domain
(LBD).
Length = 84
Score = 58.6 bits (142), Expect = 9e-13
Identities = 22/31 (70%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C VCGD ASGFHYGV +CE CK FF+RTI+
Sbjct: 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIR 31
>gnl|CDD|143539 cd07165, NR_DBD_DmE78_like, DNA-binding domain of Drosophila
ecdysone-induced protein 78 (E78) like is composed of
two C4-type zinc fingers. DNA-binding domain of
proteins similar to Drosophila ecdysone-induced protein
78 (E78) is composed of two C4-type zinc fingers. Each
zinc finger contains a group of four Cys residues which
coordinates a single zinc atom. E78 interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation.
Drosophila ecdysone-induced protein 78 (E78) is a
transcription factor belonging to the nuclear receptor
superfamily. E78 is a product of the
ecdysone-inducible gene found in an early late puff
locus at position 78C during the onset of Drosophila
metamorphosis. An E78 orthologue from the Platyhelminth
Schistosoma mansoni (SmE78) has also been identified.
It is the first E78 orthologue known outside of the
molting animals--the Ecdysozoa. The SmE78 may be
involved in transduction of an ecdysone signal in S.
mansoni, consistent with its function in Drosophila.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
E78-like 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 = 81
Score = 58.3 bits (141), Expect = 1e-12
Identities = 24/40 (60%), Positives = 28/40 (70%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRG 81
C VCGD ASG+HYGV SCE CK FF+R+IQ + LR
Sbjct: 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRD 40
>gnl|CDD|143542 cd07168, NR_DBD_DHR4_like, DNA-binding domain of ecdysone-induced
DHR4 orphan nuclear receptor is composed of two C4-type
zinc fingers. DNA-binding domain of ecdysone-induced
DHR4 orphan nuclear receptor is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which coordinates a single zinc atom. This
domain interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. 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 = 90
Score = 58.3 bits (141), Expect = 1e-12
Identities = 20/40 (50%), Positives = 29/40 (72%)
Query: 34 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
+E+ +LC +C D A+G HYG+ +CE CK FFKRT+Q +
Sbjct: 1 DEDESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNK 40
>gnl|CDD|143541 cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain of Lrh-1 like
nuclear receptor family like is composed of two C4-type
zinc fingers. The DNA-binding domain of Lrh-1 like
nuclear receptor family like is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom.
This domain interacts with specific DNA sites upstream
of the target gene and modulates the rate of
transcriptional initiation. 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 is
required at several stages of development.
Particularly, FTZ-F1 regulated 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
monomers. 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 = 93
Score = 58.2 bits (141), Expect = 2e-12
Identities = 20/30 (66%), Positives = 25/30 (83%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C VCGD SG+HYG+ +CE+CK FFKRT+Q
Sbjct: 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQ 30
>gnl|CDD|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear
receptor, nerve growth factor-induced-B. DNA-binding
domain (DBD) of the orphan nuclear receptor, nerve
growth factor-induced-B (NGFI-B) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. NGFI-B interacts with specific DNA sites upstream
of the target gene and modulates the rate of
transcriptional initiation. NGFI-B is a member of the
nuclear-steroid receptor superfamily. NGFI-B is
classified as an orphan receptor because no ligand has
yet been identified. 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 transcriptional initiation.
NGFI-B binds to the NGFI-B response element (NBRE)
5'-(A/T)AAAGGTCA as a monomer. Like other members of
the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, NGFI-B 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 = 75
Score = 57.5 bits (139), Expect = 2e-12
Identities = 24/39 (61%), Positives = 27/39 (69%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSL 79
LC VCGD A+ HYGV +CE CK FFKRT+Q A V L
Sbjct: 2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCL 40
>gnl|CDD|143522 cd06964, NR_DBD_RAR, DNA-binding domain of retinoic acid receptor
(RAR) is composed of two C4-type zinc fingers.
DNA-binding domain of retinoic acid receptor (RAR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which
co-ordinates a single zinc atom. RAR interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation. RARs
mediate the biological effect of retinoids, including
both natural dietary vitamin A (retinol) metabolites
and active synthetic analogs. Retinoids play key roles
in a wide variety of essential biological processes,
such as vertebrate embryonic morphogenesis and
organogenesis, differentiation and apoptosis, and
homeostasis. RAR function as a heterodimer with
retinoic X receptor by binding to specific RAR response
elements (RAREs), which are composed of two direct
repeats of the consensus sequence 5'-AGGTCA-3'
separated by one to five base pair and found in the
promoter regions of retinoid target genes. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, retinoic acid
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 = 85
Score = 57.6 bits (139), Expect = 2e-12
Identities = 19/32 (59%), Positives = 26/32 (81%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+ C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 5 KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 36
>gnl|CDD|143525 cd06967, NR_DBD_TR2_like, DNA-binding domain of the TR2 and TR4
(human testicular receptor 2 and 4) is composed of two
C4-type zinc fingers. DNA-binding domain of the TR2
and TR4 (human testicular receptor 2 and 4) is composed
of two C4-type zinc fingers. Each zinc finger contains
a group of four Cys residues which coordinates a single
zinc atom. TR2 and TR4 interact with specific DNA sites
upstream of the target gene and modulate the rate of
transcriptional initiation. TR4 and TR2 are orphan
nuclear receptors; the physiological ligand is as yet
unidentified. 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. It has been 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, and peroxisome
proliferator-activated receptor. TR4/2 binds to HREs as
dimers. Like other members of the nuclear 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 = 87
Score = 57.5 bits (139), Expect = 2e-12
Identities = 23/37 (62%), Positives = 26/37 (70%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P LC+VCGD ASG HYG SCE CK FFKR+I+
Sbjct: 1 QPVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKN 37
>gnl|CDD|143543 cd07169, NR_DBD_GCNF_like, DNA-binding domain of Germ cell
nuclear factor (GCNF) F1 is composed of two C4-type
zinc fingers. DNA-binding domain of Germ cell nuclear
factor (GCNF) F1 is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which coordinates a single zinc atom. This
domain interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. GCNF is a transcription
factor expressed in post-meiotic stages of developing
male germ cells. In vitro, GCNF has the ability to bind
to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as
well as to an extended half-site sequence
5'-TCA.AGGTCA-3'. Like other members of the nuclear
receptor (NR) superfamily of ligand-activated
transcription factors, GCNF 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 = 90
Score = 56.0 bits (135), Expect = 1e-11
Identities = 21/31 (67%), Positives = 25/31 (80%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTI 70
R CL+CGD A+G HYG+ SCE CK FFKR+I
Sbjct: 7 RTCLICGDRATGLHYGIISCEGCKGFFKRSI 37
>gnl|CDD|143534 cd07160, NR_DBD_LXR, DNA-binding domain of Liver X receptors
(LXRs) family is composed of two C4-type zinc fingers.
DNA-binding domain of Liver X receptors (LXRs) family
is composed of two C4-type zinc fingers. Each zinc
finger contains a group of four Cys residues which
co-ordinates a single zinc atom. LXR interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation. LXR
operates as cholesterol sensor which protects cells
from cholesterol overload by stimulating reverse
cholesterol transport from peripheral tissues to the
liver and its excretion in the bile. Oxidized
cholesterol derivatives or oxysterols were identified
as specific ligands for LXRs. LXR functions as a
heterodimer with the retinoid X receptor (RXR) which
may be activated by either LXR agonist or 9-cis
retinoic acid, a specific RXR ligand. The LXR/RXR
complex binds to a liver X receptor response element
(LXRE) in the promoter region of target genes. The
ideal LXRE sequence is a direct repeat-4 (DR-4) DNA
fragment consisting of two AGGTCA hexameric half-sites
separated by a 4-nucleotide spacer. LXR has typical NR
modular structure with a central well conserved DNA
binding domain (DBD), a variable N-terminal domain, a
flexible hinge and the ligand binding domain (LBD) at
the C-terminal.
Length = 101
Score = 56.0 bits (135), Expect = 1e-11
Identities = 20/30 (66%), Positives = 24/30 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTI 70
+C VCGD ASGFHY V SCE CK FF+R++
Sbjct: 20 VCSVCGDKASGFHYNVLSCEGCKGFFRRSV 49
>gnl|CDD|143546 cd07172, NR_DBD_GR_PR, DNA-binding domain of glucocorticoid
receptor (GR) is composed of two C4-type zinc fingers.
DNA-binding domains of glucocorticoid receptor (GR) and
progesterone receptor (PR) are composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinate a single zinc atom. The
DBD from both receptors interact with the same hormone
response element (HRE), which is an imperfect
palindrome GGTACAnnnTGTTCT, upstream of target genes
and modulates the rate of transcriptional initiation.
GR is a transcriptional regulator that mediates the
biological effects of glucocorticoids and PR regulates
genes controlled by progesterone. GR is expressed in
almost every cell in the body and regulates genes
controlling a wide variety of processes including the
development, metabolism, and immune response of the
organism. PR functions in a variety of biological
processes including development of the mammary gland,
regulating cell cycle progression, protein processing,
and metabolism. Like other members of the nuclear
receptor (NR) superfamily of ligand-activated
transcription factors, GR and PR 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 = 78
Score = 55.6 bits (134), Expect = 1e-11
Identities = 20/34 (58%), Positives = 27/34 (79%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
P+++CLVC D ASG HYGV +C +CK FFKR ++
Sbjct: 1 PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVE 34
>gnl|CDD|143514 cd06956, NR_DBD_RXR, DNA-binding domain of retinoid X receptor
(RXR) is composed of two C4-type zinc fingers.
DNA-binding domain of retinoid X receptor (RXR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which
co-ordinates a single zinc atom. RXR functions as a DNA
binding partner by forming heterodimers with other
nuclear receptors including CAR, FXR, LXR, PPAR, PXR,
RAR, TR, and VDR. All RXR heterodimers preferentially
bind response elements composed of direct repeats of
two AGGTCA sites with a 1-5 bp spacer. RXRs can play
different roles in these heterodimers. RXR 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.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
RXR 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 = 77
Score = 53.7 bits (129), Expect = 5e-11
Identities = 21/31 (67%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+C +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVR 32
>gnl|CDD|143531 cd07156, NR_DBD_VDR_like, The DNA-binding domain of vitamin D
receptors (VDR) like nuclear receptor family is
composed of two C4-type zinc fingers. The DNA-binding
domain of vitamin D receptors (VDR) like nuclear
receptor family is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which co-ordinates a single zinc atom. This
domain interacts with specific DNA site upstream of the
target gene and modulates the rate of transcriptional
initiation. This family includes three types of nuclear
receptors: vitamin D receptors (VDR), constitutive
androstane receptor (CAR) and pregnane X receptor
(PXR). VDR regulates calcium metabolism, cellular
proliferation and differentiation. PXR and CAR
function as sensors of toxic byproducts of cell
metabolism and of exogenous chemicals, to facilitate
their elimination. The DNA binding activity is
regulated by their corresponding ligands. VDR is
activated by Vitamin D; CAR and PXR respond to a
diverse array of chemically distinct ligands, including
many endogenous compounds and clinical drugs. Like
other nuclear receptors, xenobiotic 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 = 72
Score = 53.2 bits (128), Expect = 8e-11
Identities = 16/35 (45%), Positives = 25/35 (71%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASL 76
C VCGD A+G+H+ +CE CK FF+R+++ +A
Sbjct: 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARF 35
>gnl|CDD|143538 cd07164, NR_DBD_PNR_like_1, DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR) like
proteins is composed of two C4-type zinc fingers.
DNA-binding domain of the photoreceptor cell-specific
nuclear receptor (PNR) like proteins is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. PNR interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. PNR is a member of nuclear
receptor superfamily of the ligand-activated
transcription factors. 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. It
most likely binds to DNA as a homodimer. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, PNR 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 = 78
Score = 52.5 bits (126), Expect = 2e-10
Identities = 20/30 (66%), Positives = 24/30 (80%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C VCGD ASG HYGV SC+ C+ FFKR+I+
Sbjct: 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIR 30
>gnl|CDD|143520 cd06962, NR_DBD_FXR, DNA-binding domain of Farnesoid X receptor
(FXR) family is composed of two C4-type zinc fingers.
DNA-binding domain of Farnesoid X receptor (FXR) family
is composed of two C4-type zinc fingers. Each zinc
finger contains a group of four Cys residues which
co-ordinates a single zinc atom. FXR interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation. FXR
is a member of the nuclear receptor family of ligand
activated transcription factors. Bile acids are
endogenous ligands for FXRs. Upon binding of a ligand,
FXR binds to FXR response element (FXRE), which is an
inverted repeat of TGACCT spaced by one nucleotide,
either as a monomer or as a heterodimer with retinoid X
receptor (RXR), to regulate the expression of various
genes involved in bile acid, lipid, and glucose
metabolism. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, FXR 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 = 84
Score = 52.3 bits (125), Expect = 3e-10
Identities = 20/34 (58%), Positives = 25/34 (73%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
LC+VCGD ASG+HY +CE CK FF+R+I A
Sbjct: 3 LCVVCGDKASGYHYNALTCEGCKGFFRRSITKNA 36
>gnl|CDD|143548 cd07179, 2DBD_NR_DBD2, The second DNA-binding domain (DBD) of the
2DBD nuclear receptor is composed of two C4-type zinc
fingers. The second DNA-binding domain (DBD) of the
2DBD nuclear receptor (NR) is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. NRs
interact with specific DNA sites upstream of the target
gene and modulate the rate of transcriptional
initiation. The proteins contain two DBDs in tandem,
probably resulting from an ancient recombination event.
The 2DBD-NRs are found only in flatworm species,
mollusks and arthropods. Their biological function is
unknown.
Length = 74
Score = 51.7 bits (124), Expect = 3e-10
Identities = 19/36 (52%), Positives = 24/36 (66%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV 77
C VCG +SGFH+G +CE CK FF+RT + S V
Sbjct: 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYV 36
>gnl|CDD|143535 cd07161, NR_DBD_EcR, DNA-binding domain of Ecdysone receptor
(ECR) family is composed of two C4-type zinc fingers.
DNA-binding domain of Ecdysone receptor (EcR) family is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which
co-ordinates a single zinc atom. EcR interacts with
highly degenerate pseudo-palindromic response elements,
resembling inverted repeats of 5'-AGGTCA-3' separated
by 1 bp, upstream of the target gene and modulates the
rate of transcriptional initiation. EcR is present only
in invertebrates and regulates the expression of a
large number of genes during development and
reproduction. EcR functions as a heterodimer by
partnering with ultraspiracle protein (USP), the
ortholog of the vertebrate retinoid X receptor (RXR).
The natural ligands of EcR are ecdysteroids, the
endogenous steroidal hormones found in invertebrates.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
EcRs 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 = 91
Score = 52.2 bits (125), Expect = 3e-10
Identities = 20/34 (58%), Positives = 25/34 (73%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
LCLVCGD ASG+HY +CE CK FF+R++ A
Sbjct: 3 LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSA 36
>gnl|CDD|143547 cd07173, NR_DBD_AR, DNA-binding domain of androgen receptor (AR)
is composed of two C4-type zinc fingers. DNA-binding
domain of androgen receptor (AR) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. To regulate gene expression, AR interacts with a
palindrome of the core sequence 5'-TGTTCT-3' with a
3-bp spacer. It also binds to the direct repeat
5'-TGTTCT-3' hexamer in some androgen controlled genes.
AR is activated by the androgenic hormones,
testosterone or dihydrotestosterone, which are
responsible for primary and for secondary male
characteristics, respectively. The primary mechanism of
action of ARs is by direct regulation of gene
transcription. The binding of androgen results in a
conformational change in the androgen receptor which
causes its transport from the cytosol into the cell
nucleus, and dimerization. The receptor dimer binds to
a hormone response element of AR regulated genes and
modulates their expression. Another mode of action of
androgen receptor is independent of their interactions
with DNA. The receptor interacts directly with signal
transduction proteins in the cytoplasm, causing rapid
changes in cell function, such as ion transport. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, AR 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 = 82
Score = 51.5 bits (123), Expect = 4e-10
Identities = 19/36 (52%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P++ CL+CGD ASG HYG +C +CK FFKR + +
Sbjct: 2 PQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGK 37
>gnl|CDD|143516 cd06958, NR_DBD_COUP_TF, DNA-binding domain of chicken ovalbumin
upstream promoter transcription factors (COUP-TFs) is
composed of two C4-type zinc fingers. DNA-binding
domain of chicken ovalbumin upstream promoter
transcription factors (COUP-TFs) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. 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. COUP-TFs
homodimerize or heterodimerize with retinoid X receptor
(RXR) and a few other nuclear receptors and bind to a
variety of response elements that are composed of
imperfect AGGTCA direct or inverted repeats with
various spacings. 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 conserved DNA binding domain (DBD),
a variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 73
Score = 51.0 bits (122), Expect = 7e-10
Identities = 18/30 (60%), Positives = 25/30 (83%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C+VCGD +SG HYG +CE CK+FFKR+++
Sbjct: 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVR 30
>gnl|CDD|143513 cd06955, NR_DBD_VDR, DNA-binding domain of vitamin D receptors
(VDR) is composed of two C4-type zinc fingers.
DNA-binding domain of vitamin D receptors (VDR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which coordinates
a single zinc atom. VDR interacts with a VDR response
element, a direct repeat of GGTTCA DNA site with 3 bp
spacer upstream of the target gene, and modulates the
rate of transcriptional initiation. VDR is a member of
the nuclear receptor (NR) superfamily that functions as
classical endocrine receptors. VDR controls a wide
range of biological activities including calcium
metabolism, cell proliferation and differentiation, and
immunomodulation. VDR is a high-affinity receptor for
the biologically most active Vitamin D metabolite,
1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The
binding of the ligand to the receptor induces a
conformational change of the ligand binding domain
(LBD) with consequent dissociation of corepressors.
Upon ligand binding, VDR forms a heterodimer with the
retinoid X receptor (RXR) that binds to vitamin D
response elements (VDREs), recruits coactivators. This
leads to the expression of a large number of genes.
Approximately 200 human genes are considered to be
primary targets of VDR and even more genes are
regulated indirectly. Like other members of the nuclear
receptor (NR) superfamily of ligand-activated
transcription factors, VDR 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 = 107
Score = 50.7 bits (121), Expect = 2e-09
Identities = 18/37 (48%), Positives = 27/37 (72%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL 76
R+C VCGD A+GFH+ +CE CK FF+R+++ +A
Sbjct: 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALF 43
>gnl|CDD|143526 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoid-related
orphan receptors (RORs) is composed of two C4-type zinc
fingers. DNA-binding domain of Retinoid-related orphan
receptors (RORs) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which coordinates a single zinc atom. ROR
interacts with specific DNA sites upstream of the
target gene and modulates the rate of transcriptional
initiation. RORS are key regulators of many
physiological processes during embryonic development.
RORs bind as monomers to specific ROR response elements
(ROREs) consisting of the consensus core motif AGGTCA
preceded by a 5-bp A/T-rich sequence. There are three
subtypes of retinoid-related orphan receptors (RORs),
alpha, beta, and gamma, which differ only in N-terminal
sequence and are distributed in distinct tissues.
RORalpha plays a key role in the development of the
cerebellum particularly in the regulation of the
maturation and survival of Purkinje cells. RORbeta
expression is largely restricted to several regions of
the brain, the retina, and pineal gland. RORgamma is
essential for lymph node organogenesis. Recently, it
has been suggested that cholesterol or a cholesterol
derivative are the natural ligands of RORalpha. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors,
retinoid-related orphan 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 = 95
Score = 50.2 bits (120), Expect = 2e-09
Identities = 19/34 (55%), Positives = 24/34 (70%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARAS 75
C +CGD +SG HYGV +CE CK FF+R+ Q S
Sbjct: 8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVS 41
>gnl|CDD|143521 cd06963, NR_DBD_GR_like, The DNA binding domain of GR_like
nuclear receptors is composed of two C4-type zinc
fingers. The DNA binding domain of GR_like nuclear
receptors is composed of two C4-type zinc fingers. Each
zinc finger contains a group of four Cys residues which
co-ordinates a single zinc atom. It interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation. This
family of NRs includes four types of nuclear hormone
receptors: glucocorticoid receptor (GR),
mineralocorticoid receptor (MR), progesterone receptor
(PR), and androgen receptor (AR). The receptors bind to
common DNA elements containing a partial palindrome of
the core sequence 5'-TGTTCT-3' with a 3bp spacer. These
four receptors regulate some of the most fundamental
physiological functions such as the stress response,
metabolism, electrolyte homeostasis, immune function,
growth, development, and reproduction. The NRs in this
family have high sequence homology and share similar
functional mechanisms. The dominant mechanism of
function is by direct DNA binding and transcriptional
regulation of target genes . The GR, MR, PR, and AR
exhibit same modular structure. They have a central
highly conserved DNA binding domain (DBD), a
non-conserved N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 73
Score = 49.2 bits (117), Expect = 3e-09
Identities = 19/32 (59%), Positives = 24/32 (75%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
CL+CGD ASG HYGV +C +CK FFKR + +
Sbjct: 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQ 32
>gnl|CDD|143528 cd06970, NR_DBD_PNR, DNA-binding domain of the photoreceptor
cell-specific nuclear receptor (PNR) is composed of two
C4-type zinc fingers. DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which
co-ordinates a single zinc atom. PNR interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation. PNR
is a member of the nuclear receptor superfamily of the
ligand-activated transcription factors. 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. It most likely
binds to DNA as a homodimer. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, PNR 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 = 92
Score = 49.6 bits (118), Expect = 4e-09
Identities = 18/36 (50%), Positives = 25/36 (69%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P LC VCGD +SG HYG+ +C C FFKR+++ +
Sbjct: 5 PGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRK 40
>gnl|CDD|143532 cd07157, 2DBD_NR_DBD1, The first DNA-binding domain (DBD) of the
2DBD nuclear receptors is composed of two C4-type zinc
fingers. The first DNA-binding domain (DBD) of the
2DBD nuclear receptors(NRs) is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. NRs
interact with specific DNA sites upstream of the target
gene and modulate the rate of transcriptional
initiation. Theses proteins contain two DBDs in tandem,
probably resulted from an ancient recombination event.
The 2DBD-NRs are found only in flatworm species,
mollusks and arthropods. Their biological function is
unknown.
Length = 86
Score = 49.0 bits (117), Expect = 5e-09
Identities = 18/32 (56%), Positives = 22/32 (68%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
C VCG+ A+GFH+G CEACK FF R+ A
Sbjct: 3 CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAI 34
>gnl|CDD|143529 cd07154, NR_DBD_PNR_like, The DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR)
nuclear receptor-like family. The DNA-binding domain
of the photoreceptor cell-specific nuclear receptor
(PNR) nuclear receptor-like family is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which coordinates a single zinc
atom. PNR interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. This family includes
nuclear receptor Tailless (TLX), photoreceptor
cell-specific nuclear receptor (PNR) and related
receptors. TLX is an orphan receptor that plays a key
role in neural development by regulating cell cycle
progression and exit of neural stem cells 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, PNR-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 = 73
Score = 47.9 bits (114), Expect = 1e-08
Identities = 18/30 (60%), Positives = 23/30 (76%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C VCGD +SG HYGV +C+ C FFKR+I+
Sbjct: 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIR 30
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
composed of two C4-type zinc fingers. DNA-binding
domain of Tailless (TLX) is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. TLX
interacts with specific DNA sites upstream of the
target gene and modulates the rate of transcriptional
initiation. 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. Like other members
of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX 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 = 92
Score = 47.9 bits (114), Expect = 2e-08
Identities = 17/30 (56%), Positives = 23/30 (76%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C VCGD +SG HYG+ +C+ C FFKR+I+
Sbjct: 9 CKVCGDRSSGKHYGIYACDGCSGFFKRSIR 38
>gnl|CDD|143515 cd06957, NR_DBD_PNR_like_2, DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR) like
is composed of two C4-type zinc fingers. The
DNA-binding domain of the photoreceptor cell-specific
nuclear receptor (PNR) nuclear receptor-like family is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which coordinates
a single zinc atom. PNR interacts with specific DNA
sites upstream of the target gene and modulates the
rate of transcriptional initiation. This family
includes nuclear receptor Tailless (TLX), photoreceptor
cell-specific nuclear receptor (PNR) and related
receptors. TLX is an orphan receptor that plays a key
role in neural development by regulating cell cycle
progression and exit of neural stem cells 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, PNR-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 = 82
Score = 47.5 bits (113), Expect = 2e-08
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRG 81
C VCGD + G HYGV C+ C FFKR+++ + G
Sbjct: 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAG 40
>gnl|CDD|143524 cd06966, NR_DBD_CAR, DNA-binding domain of constitutive
androstane receptor (CAR) is composed of two C4-type
zinc fingers. DNA-binding domain (DBD) of constitutive
androstane receptor (CAR) is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. CAR
DBD interacts with CAR response element, a perfect
repeat of two AGTTCA motifs with a 4 bp spacer upstream
of the target gene, and modulates the rate of
transcriptional initiation. The constitutive androstane
receptor (CAR) is a ligand-regulated transcription
factor that responds to a diverse array of chemically
distinct ligands, including many endogenous compounds
and clinical drugs. It functions as a heterodimer with
RXR. The CAR/RXR heterodimer binds many common response
elements in the promoter regions of a diverse set of
target genes involved in the metabolism, transport, and
ultimately, elimination of these molecules from the
body. CAR is a closest mammalian relative of PXR and is
activated by some of the same ligands as PXR and
regulates a subset of common genes. The sequence
homology and functional similarity suggests that the
CAR gene arose from a duplication of an ancestral PXR
gene. Like other nuclear receptors, CAR has a central
well conserved DNA binding domain, a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain.
Length = 94
Score = 46.3 bits (110), Expect = 6e-08
Identities = 15/29 (51%), Positives = 23/29 (79%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKR 68
++C VCGD A G+++ +CE+CKAFF+R
Sbjct: 1 KICGVCGDKALGYNFNAITCESCKAFFRR 29
>gnl|CDD|143536 cd07162, NR_DBD_PXR, DNA-binding domain of pregnane X receptor
(PXRs) is composed of two C4-type zinc fingers.
DNA-binding domain (DBD)of pregnane X receptor (PXR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which
co-ordinates a single zinc atom. PXR DBD interacts with
the PXR response element, a perfect repeat of two
AGTTCA motifs with a 4 bp spacer upstream of the target
gene, and modulates the rate of transcriptional
initiation. The pregnane X receptor (PXR) is a
ligand-regulated transcription factor that responds to
a diverse array of chemically distinct ligands,
including many endogenous compounds and clinical drugs.
PXR functions as a heterodimer with retinoic X
receptor-alpha (RXRa) and binds to a variety of
promoter regions of a diverse set of target genes
involved in the metabolism, transport, and ultimately,
elimination of these molecules from the body. Like
other nuclear receptors, PXR has a central well
conserved DNA-binding domain, a variable N-terminal
domain, a flexible hinge and a C-terminal ligand
binding domain.
Length = 87
Score = 44.9 bits (106), Expect = 2e-07
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL 76
+C VCGD A+G+H+ +CE CK FF+R ++ A L
Sbjct: 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARL 36
>gnl|CDD|188625 cd09905, H3TH_GEN1, H3TH domain of Gap Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. Gap Endonuclease 1 (GEN1): Holliday junction
resolvase reported to symmetrically cleave Holliday
junctions and allow religation without additional
processing. GEN1 is a member of the structure-specific,
5' nuclease family that catalyzes hydrolysis of DNA
duplex-containing nucleic acid structures during DNA
replication, repair, and recombination. Members of this
subgroup include the H3TH (helix-3-turn-helix) domains
of GEN1 and other similar eukaryotic 5' nucleases.
These nucleases contain a PIN (PilT N terminus) domain
with a helical arch/clamp region/I domain (not included
here) and inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. These nucleases have a
carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (Mg2+ or
Mn2+) required for nuclease activity. The first metal
binding site is composed entirely of Asp/Glu residues
from the PIN domain, whereas, the second metal binding
site is composed generally of two Asp residues from the
PIN domain and one Asp residue from the H3TH domain.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 108
Score = 25.8 bits (57), Expect = 3.9
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 22 EQKFRGSTDGIKEEELPRR---LCLVCGDVASGFHYGVASCEACK 63
+ +R ++D +EL ++ C CG + + + CE C
Sbjct: 44 LRNWRATSDPSSPQELKKKDKNHCSNCGHLGKKQEHIKSGCEDCD 88
>gnl|CDD|234951 PRK01392, citX,
2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate
lyase; Reviewed.
Length = 180
Score = 25.4 bits (56), Expect = 6.2
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 37 LPRRLCLVCGDVA 49
LP R CL+CG A
Sbjct: 137 LPPRRCLLCGQDA 149
>gnl|CDD|179648 PRK03776, PRK03776, phosphoglycerol transferase I; Provisional.
Length = 762
Score = 25.8 bits (57), Expect = 6.8
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 83 EPQKKSSQIPKEKYNLAYLMSDSLDTT 109
EP K IP K NL Y+ +SL+ T
Sbjct: 152 EPAKT---IPNPKLNLVYIYGESLERT 175
>gnl|CDD|99920 cd05537, POLBc_Pol_II, DNA polymerase type-II subfamily catalytic
domain. Bacteria contain five DNA polymerases (I, II,
III, IV and V). DNA polymerase II (Pol II) is a
prototype for the B-family of polymerases. The role of
Pol II in a variety of cellular activities, such as
repair of DNA damaged by UV irradiation or oxidation has
been proven by genetic studies. DNA polymerase III is
the main enzyme responsible for replication of the
bacterial chromosome; however, In vivo studies have also
shown that Pol II is able to participate in chromosomal
DNA replication with larger role in lagging-strand
replication.
Length = 371
Score = 25.3 bits (56), Expect = 8.4
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 54 YGVASCEACKAFFKRTIQAR-ASLVSLRGHEPQKKSSQ-IPKEKYNLAYLMSDSL 106
YGV C+ FF R AS ++LRGHE K++ I ++ Y + Y +DS
Sbjct: 104 YGVLGSTGCR-FF----DPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDST 153
>gnl|CDD|217739 pfam03802, CitX, Apo-citrate lyase phosphoribosyl-dephospho-CoA
transferase.
Length = 171
Score = 24.9 bits (55), Expect = 9.6
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 37 LPRRLCLVCGDVA 49
LP R CL+CG A
Sbjct: 130 LPPRRCLLCGRPA 142
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 0.132 0.388
Gapped
Lambda K H
0.267 0.0820 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,423,886
Number of extensions: 429994
Number of successful extensions: 366
Number of sequences better than 10.0: 1
Number of HSP's gapped: 366
Number of HSP's successfully gapped: 46
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: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.0 bits)