RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7884
(240 letters)
>gnl|CDD|132739 cd06941, NR_LBD_DmE78_like, The ligand binding domain of Drosophila
ecdysone-induced protein 78, a member of the nuclear
receptor superfamily. The ligand binding domain (LBD)
of Drosophila ecdysone-induced protein 78 (E78) like:
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. Two
isoforms of E78, E78A and E78B, are expressed from two
nested transcription units. 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. 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 = 195
Score = 132 bits (334), Expect = 1e-38
Identities = 52/81 (64%), Positives = 68/81 (83%), Gaps = 2/81 (2%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTD 219
+WLWQQ + +TPSVQRVVEFAKR+PGFCDLSQDDQL+LIK GFFE+W+ +SRL +
Sbjct: 1 IWLWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKS 60
Query: 220 SSLTFSDGMYVTRQQLEVMYD 240
S+TF DG+ ++RQQL+++YD
Sbjct: 61 GSITFDDGISISRQQLDIIYD 81
>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 = 123 bits (310), Expect = 2e-36
Identities = 52/60 (86%), Positives = 56/60 (93%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
+GFFRRSIQKQIEYRCLRDGKC +IRLNRNRCQYCRFKKCLA GMS+DSVRYGR+P R R
Sbjct: 22 KGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNRQR 81
>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 = 109 bits (274), Expect = 5e-31
Identities = 43/63 (68%), Positives = 56/63 (88%), Gaps = 1/63 (1%)
Query: 3 QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
+GFFRRSIQ++I+YR C ++ C ++R+NRNRCQYCRFKKCLAVGMSRD+VR+GR+PKR
Sbjct: 27 KGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKRE 86
Query: 62 RER 64
+ R
Sbjct: 87 KAR 89
>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 = 98.4 bits (245), Expect = 8e-27
Identities = 36/52 (69%), Positives = 44/52 (84%), Gaps = 1/52 (1%)
Query: 3 QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
+GFFRR+IQ + Y RCL GKC++ R NRNRCQYCRFKKCL+VGMSR++VR
Sbjct: 22 KGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73
>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 = 94.2 bits (235), Expect = 3e-25
Identities = 29/50 (58%), Positives = 39/50 (78%)
Query: 4 GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
GFFRRS+++ +EY C G C++ + NRNRCQ CR KKCLAVGM +++VR
Sbjct: 23 GFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72
>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 = 92.7 bits (231), Expect = 1e-24
Identities = 30/46 (65%), Positives = 35/46 (76%)
Query: 4 GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR 49
GFFRRSIQK I Y C + C++ + NRNRCQYCR KKCL VGMS+
Sbjct: 25 GFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRLKKCLEVGMSK 70
>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 = 90.7 bits (225), Expect = 1e-23
Identities = 36/67 (53%), Positives = 49/67 (73%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
+GFFRRS Q + Y C R CL+ R NRNRCQ+CR +KCLA+GMSRD+V++GR+ K+ R
Sbjct: 29 KGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQR 88
Query: 63 ERSDSET 69
+ +E
Sbjct: 89 DSLYAEV 95
>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 = 87.1 bits (216), Expect = 2e-22
Identities = 30/63 (47%), Positives = 48/63 (76%), Gaps = 3/63 (4%)
Query: 3 QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
+GFFRR+I+ ++ Y C D C + + +RN+CQYCRF+KCL VGMS +++R+GR+P+
Sbjct: 23 KGFFRRTIRLKLVYKPC--DLSCKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRVE 80
Query: 62 RER 64
+E+
Sbjct: 81 KEK 83
>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 = 84.8 bits (210), Expect = 2e-21
Identities = 30/60 (50%), Positives = 43/60 (71%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
+GFFRR++QK++ Y C +GKC + ++ RN+CQ CRFKKC+AVGM++D V R R
Sbjct: 23 KGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKR 82
>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 = 84.2 bits (208), Expect = 3e-21
Identities = 33/58 (56%), Positives = 43/58 (74%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60
+GFFRRSIQK + Y C RD C++ ++ RNRCQYCR +KC VGMS++SVR R K+
Sbjct: 28 KGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKK 85
>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 = 83.0 bits (206), Expect = 9e-20
Identities = 32/81 (39%), Positives = 46/81 (56%), Gaps = 2/81 (2%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS- 220
+ F +T +++RVVEFAKR+PGF +LSQ+DQ+ L+K G FE+ + + L
Sbjct: 1 QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEK 60
Query: 221 -SLTFSDGMYVTRQQLEVMYD 240
SLTF DG +R L
Sbjct: 61 NSLTFGDGKGNSRDVLLNGGF 81
>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 = 76.5 bits (189), Expect = 2e-18
Identities = 27/50 (54%), Positives = 35/50 (70%)
Query: 4 GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
GFFRRS++K Y C G C+V + RN C+YCRFKKCL VGM ++V+
Sbjct: 23 GFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQ 72
>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors.
Length = 70
Score = 76.0 bits (188), Expect = 2e-18
Identities = 21/47 (44%), Positives = 29/47 (61%)
Query: 4 GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50
FFRR++ + +YRC R C + + R RC+ CR KKCL VGM +
Sbjct: 24 AFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70
>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 = 75.6 bits (186), Expect = 6e-18
Identities = 29/56 (51%), Positives = 40/56 (71%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
+GFF+RSI+K + Y C C++ + +RNRCQYCR +KCLA+GM DSV+ R P
Sbjct: 27 KGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKP 82
>gnl|CDD|132737 cd06939, NR_LBD_ROR_like, The ligand binding domain of
Retinoid-related orphan receptors, of the nuclear
receptor superfamily. The ligand binding domain (LBD)
of Retinoid-related orphan receptors (RORs):
Retinoid-related orphan receptors (RORs) are
transcription factors belonging to the nuclear receptor
superfamily. 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. Transcription
regulation by RORs is mediated through certain
corepressors, as well as coactivators. There are three
subtypes of retinoid-related orphan receptors (RORs),
alpha, beta, and gamma that 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 su ggested that cholesterol or a cholesterol
derivative is the natural ligand 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 = 241
Score = 78.9 bits (195), Expect = 1e-17
Identities = 37/118 (31%), Positives = 63/118 (53%), Gaps = 14/118 (11%)
Query: 114 VSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLW-LWQQFAAHV 172
+ +AH C+Y E ++L K S E+ + ++++ +WQ A +
Sbjct: 10 ICKAHLETCQYLREELQQLRWKTFS--QEEILA----------YQNKSREEMWQLCAEKI 57
Query: 173 TPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMY 229
T ++Q VVEFAKR+PGF +L Q+DQ++L+K G E+ + +SR ++ DG Y
Sbjct: 58 TEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFDGKY 115
>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 = 73.0 bits (179), Expect = 6e-17
Identities = 29/56 (51%), Positives = 39/56 (69%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
+GFF+RSI + YRC RD C++ R RNRCQYCR KCL +GM+R ++R +P
Sbjct: 30 KGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP 85
>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 = 73.0 bits (179), Expect = 7e-17
Identities = 27/56 (48%), Positives = 40/56 (71%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
+GFF+R++Q + Y C+ DG+C + + RNRCQYCRF+KC+ GM +VR R+P
Sbjct: 30 KGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMP 85
>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 = 72.5 bits (178), Expect = 7e-17
Identities = 28/51 (54%), Positives = 38/51 (74%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
+GFF+R++QK +Y CL + C V + RNRCQYCRF+KCL VGM ++ VR
Sbjct: 24 KGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74
>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 = 72.5 bits (178), Expect = 8e-17
Identities = 29/57 (50%), Positives = 42/57 (73%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK 59
+GFF+RSI++ + Y C +G C+V RN+CQ CRFKKCL V M+RD+V++ R P+
Sbjct: 22 RGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAPR 78
>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 = 70.6 bits (173), Expect = 3e-16
Identities = 23/53 (43%), Positives = 30/53 (56%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYG 55
+GFFRR+ Y C C + RN C+ CRF++CLAVGMS+ R G
Sbjct: 22 KGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRIG 74
>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 = 70.2 bits (172), Expect = 7e-16
Identities = 24/55 (43%), Positives = 38/55 (69%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57
+GFF+R++Q + Y C+ + C + + R RC YCRF+KCL+VGM ++VR R+
Sbjct: 22 KGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRM 76
>gnl|CDD|132733 cd06935, NR_LBD_TR, The ligand binding domain of thyroid hormone
receptor, a members of a superfamily of nuclear
receptors. The ligand binding domain (LBD) of thyroid
hormone receptors: Thyroid hormone receptors are members
of a superfamily of nuclear receptors. Thyroid hormone
receptors (TR) mediate 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 = 243
Score = 73.7 bits (181), Expect = 8e-16
Identities = 40/130 (30%), Positives = 67/130 (51%), Gaps = 9/130 (6%)
Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
++I V++AH + T +K LP +P V++ + L + F
Sbjct: 5 ELIRTVTEAHVA----TNAQGSHWKQKRKFLPEDIGQAPIVSAPDGD---KVDLEAFSHF 57
Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SLTFSD 226
+TP++ RVV+FAK++P F +L +DQ+IL+K E+ + R +S +LT S
Sbjct: 58 TKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSG 117
Query: 227 GMYVTRQQLE 236
M VTR+QL+
Sbjct: 118 EMAVTREQLK 127
>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 = 69.1 bits (169), Expect = 1e-15
Identities = 26/54 (48%), Positives = 41/54 (75%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
+GFF+R+++K + Y C + CL+ + RNRCQYCR++KCLA+GM R++V+ R
Sbjct: 24 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77
>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 = 66.6 bits (163), Expect = 8e-15
Identities = 21/50 (42%), Positives = 34/50 (68%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
+GFFRRS++++ + C +G C + + NR CQ CR KKCL +GM ++ +
Sbjct: 22 KGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71
>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 = 64.5 bits (157), Expect = 7e-14
Identities = 25/51 (49%), Positives = 37/51 (72%), Gaps = 1/51 (1%)
Query: 4 GFFRRSIQKQIEYRCLR-DGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
GFF+RSI++ + Y C +G C+V + RN+CQ CR KKCL V M++D+V+
Sbjct: 23 GFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73
>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 = 64.6 bits (157), Expect = 9e-14
Identities = 27/57 (47%), Positives = 41/57 (71%), Gaps = 1/57 (1%)
Query: 4 GFFRRSIQKQIEYRC-LRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK 59
GFF+RS+++++ YRC G C V + +RN+CQ CR KKCL GM++D+V+ R P+
Sbjct: 31 GFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR 87
>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 = 64.1 bits (156), Expect = 1e-13
Identities = 26/55 (47%), Positives = 34/55 (61%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57
+ FF+R+IQ IEY C +C + + R CQ CRF KCL VGM ++ VR RV
Sbjct: 28 KAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRV 82
>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 = 66.0 bits (161), Expect = 2e-13
Identities = 34/77 (44%), Positives = 48/77 (62%), Gaps = 2/77 (2%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRL-TTDSS 221
+W++F+ TP+V+ VVEFAKR+PGF DLSQ DQ+ L+K G FE L + + S + S
Sbjct: 13 IWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERS 72
Query: 222 LTFSDGMYVTRQQLEVM 238
+TF G + L M
Sbjct: 73 VTFLSGQKYSVDDLHSM 89
>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 = 62.9 bits (153), Expect = 3e-13
Identities = 27/59 (45%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 5 FFRRSIQKQIEYRCLR-DGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
FF+RS++K I Y C+ +G C+V + RN C +CR +KC AVGM+R +V+ R P++ R
Sbjct: 24 FFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRKLR 82
>gnl|CDD|132740 cd06942, NR_LBD_Sex_1_like, The ligand binding domain of
Caenorhabditis elegans nuclear hormone receptor Sex-1
protein. The ligand binding domain (LBD) of
Caenorhabditis elegans nuclear hormone receptor Sex-1
protein like: Sex-1 protein of C. elegans is a
transcription factor belonging to the nuclear receptor
superfamily. Sex-1 plays pivotal role in sex fate of C.
elegans by regulating the transcription of the
sex-determination gene xol-1, which specifies male (XO)
fate when active and hermaphrodite (XX) fate when
inactive. The Sex-1 protein directly represses xol-1
transcription by binding to its promoter. However, the
active ligand for Sex-1 protein has not yet been
identified. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, Sex-1 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 = 191
Score = 64.3 bits (157), Expect = 1e-12
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
W FA +Q +V+F K +PGF LS +D+ L+K F L++ +SR
Sbjct: 4 WGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSR 54
>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 = 60.6 bits (147), Expect = 3e-12
Identities = 27/60 (45%), Positives = 41/60 (68%), Gaps = 2/60 (3%)
Query: 4 GFFRRSIQKQIEYRC--LRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
GFF+RSI++ +Y C G C V + +RN+C+ CR KKC VGM++D+V++ R P+ S
Sbjct: 31 GFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPRNS 90
>gnl|CDD|132735 cd06937, NR_LBD_RAR, The ligand binding domain (LBD) of retinoic
acid receptor (RAR), a members of the nuclear receptor
superfamily. The ligand binding domain (LBD) of
retinoic acid receptor (RAR): Retinoic acid receptors
are members of the nuclear receptor (NR) superfamily of
ligand-regulated transcription factors. RARs mediate the
biological effect of retinoids, including both naturally
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. RARs
function as heterodimers with retinoic X receptors by
binding to specific RAR response elements (RAREs) found
in the promoter regions of retinoid target genes. In the
absence of ligand, the RAR-RXR heterodimer recruits the
corepressor proteins NCoR or AMRT, and associated
factors such as histone deacetylases or
DNA-methyltransferases, leading to an inactive condensed
chromatin structure, preventing transcription. Upon
ligand binding, the corepressors are released, and
coactivator complexes such as histone acetyltransferase
or histone arginine methyltransferases are recruited to
activate transcription. There are three RAR subtypes
(alpha, beta, gamma), originating from three distinct
genes. For each subtype, several isoforms exist that
differ in their N-terminal region, allowing retinoids to
exert their pleiotropic effects. 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 = 231
Score = 62.9 bits (153), Expect = 6e-12
Identities = 31/90 (34%), Positives = 52/90 (57%), Gaps = 2/90 (2%)
Query: 150 ASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW 209
+S+A+ L LW +F+ T + ++VEFAKR+PGF L+ DQ+ L+K ++
Sbjct: 25 TNSSADQRVRLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDIL 84
Query: 210 IGYV-SRLT-TDSSLTFSDGMYVTRQQLEV 237
I + +R T ++TFSDG+ + R Q+
Sbjct: 85 ILRICTRYTPEQDTMTFSDGLTLNRTQMHN 114
>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 = 58.4 bits (141), Expect = 2e-11
Identities = 21/54 (38%), Positives = 30/54 (55%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
+ FF+RSIQ +Y C +C + + R CQ CR +KC VGM + +R R
Sbjct: 27 KAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER 80
>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 = 56.8 bits (137), Expect = 4e-11
Identities = 23/49 (46%), Positives = 36/49 (73%)
Query: 5 FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
FF+RS+++ + Y C + C + + +RN+CQYCR KKCL VGM R++V+
Sbjct: 24 FFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72
>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 = 56.7 bits (137), Expect = 4e-11
Identities = 23/52 (44%), Positives = 31/52 (59%)
Query: 5 FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
FF+R+IQ + Y C +C V + R CQ CR +KCL VGM ++ VR R
Sbjct: 24 FFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75
>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 = 58.2 bits (141), Expect = 2e-10
Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE---LWIGYVSRLTTDSS 221
+ + VVE+AKR PGF +LS DDQL L+K +FE L + S
Sbjct: 2 LNELFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDD 61
Query: 222 LTFSDGMYVTRQQLE 236
L FS+G+Y+ R +L+
Sbjct: 62 LLFSNGLYLDRDELK 76
>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 = 55.3 bits (133), Expect = 2e-10
Identities = 18/48 (37%), Positives = 32/48 (66%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50
+GFFRR++++ C C++ + NR +CQ CR +KCL++GM ++
Sbjct: 23 KGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKE 70
>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 = 55.0 bits (132), Expect = 2e-10
Identities = 21/45 (46%), Positives = 27/45 (60%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGM 47
+GFFRRSI K Y+C G C + R +CQ CR +KC +GM
Sbjct: 25 KGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGM 69
>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 = 55.7 bits (134), Expect = 3e-10
Identities = 22/61 (36%), Positives = 38/61 (62%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
+GFFRRS++++ + C +G C + + NR CQ CR K+C+ +GM ++ + +R R
Sbjct: 30 KGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKR 89
Query: 63 E 63
E
Sbjct: 90 E 90
>gnl|CDD|132726 cd06157, NR_LBD, The ligand binding domain of nuclear receptors, a
family of ligand-activated transcription regulators.
Ligand-binding domain (LBD) of nuclear receptor (NR):
Nuclear receptors form a superfamily of ligand-activated
transcription regulators, which regulate various
physiological functions in metazoans, from development,
reproduction, to homeostasis and metabolism. The
superfamily contains not only receptors for known
ligands but also orphan receptors for which ligands do
not exist or have not been identified. The members of
the family include receptors of steroids, thyroid
hormone, retinoids, cholesterol by-products, lipids and
heme. With few exceptions, 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 = 168
Score = 56.2 bits (136), Expect = 7e-10
Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
+ T + +VE+AK +PGF +L +DQ++L+K + EL +
Sbjct: 1 ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLV 45
>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 = 53.6 bits (129), Expect = 8e-10
Identities = 22/50 (44%), Positives = 28/50 (56%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
+GFFRRS+ K Y C KC + R +CQ CR +KC A GM D +
Sbjct: 23 KGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL 72
>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 = 53.3 bits (128), Expect = 2e-09
Identities = 23/51 (45%), Positives = 29/51 (56%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
+GFFRRS+ K Y C C + R +CQ CR KKCL+VGM + V
Sbjct: 25 KGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVV 75
>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 = 51.7 bits (124), Expect = 5e-09
Identities = 25/55 (45%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 5 FFRRSIQKQI--EYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57
FF RS C GKC++ + NR +CQ CR++KCL VGMS RYGR
Sbjct: 26 FFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRR 80
>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 = 54.3 bits (131), Expect = 6e-09
Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
QQF +T SV + ++A+++PGF DL ++DQ +L++ F EL++ Y S D L
Sbjct: 44 QQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNP-VDGKL 102
Query: 223 TFSDGMYVTRQQLEVMY 239
F +G+ + R Q +
Sbjct: 103 VFCNGLVLHRLQCVRGF 119
>gnl|CDD|132730 cd06932, NR_LBD_PPAR, The ligand binding domain of peroxisome
proliferator-activated receptors. The ligand binding
domain (LBD) of peroxisome proliferator-activated
receptors (PPAR): 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
element located upstream of the peroxisome proliferator
responsive genes and interacts with co-activators. There
are three subtypes of peroxisome proliferator activated
receptors, alpha, beta (or delta), and gamma, each with
a distinct tissue distribution. 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 a nd a C-terminal
ligand binding domain (LBD).
Length = 259
Score = 54.0 bits (130), Expect = 1e-08
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRLTTDSSL 222
L+Q+ +++ + EFAK +PGF +L +DQ+ L+K G E ++ S D L
Sbjct: 64 LFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYNKDGLL 123
Query: 223 TFSDGMYVTRQQLE 236
YVTR+ LE
Sbjct: 124 FPEGNGYVTREFLE 137
>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 = 51.0 bits (122), Expect = 1e-08
Identities = 22/50 (44%), Positives = 28/50 (56%)
Query: 3 QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
+GFFRRS+ K +Y C GKC + R +CQ CR +KC GM V
Sbjct: 42 KGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCV 91
>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 = 49.8 bits (119), Expect = 3e-08
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 5 FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50
FFRR+ K E++C + C + + R CQ CR KC A+GM ++
Sbjct: 26 FFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKE 71
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 50.8 bits (122), Expect = 5e-08
Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSLTFSDGMYV 230
+ VE+AK PGF +LS +DQ++L+K +FEL + Y S L DG Y+
Sbjct: 4 QLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYI 62
>gnl|CDD|132752 cd06954, NR_LBD_LXR, The ligand binding domain of Liver X
receptors, a family of nuclear receptors of
ligand-activated transcription factors. The ligand
binding domain of Liver X receptors: Liver X receptors
(LXRs) belong to a family of nuclear receptors of
ligand-activated transcription factors. LXRs operate as
cholesterol sensors which protect 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.
Upon ligand binding a conformational change leads to
recruitment of co-factors, which stimulates expression
of target genes. Among the LXR target genes are several
genes involved in cholesterol efflux from peripheral
tissues such as the ATP-binding-cassette transporters
ABCA1, ABCG1 and ApoE. There are two LXR isoforms in
mammals, LXRalpha and LXRbeta. LXRalpha is expressed
mainly in the liver, intestine, kidney, spleen, and
adipose tissue, whereas LXRbeta is ubiquitously
expressed at lower level. Both LXRalpha and LXRbeta
function as heterodimers with the retinoid X receptor
(RX R) which may be activated by either LXR ligands 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. 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 = 236
Score = 50.5 bits (121), Expect = 1e-07
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS- 220
QQ AH T SVQ +V+FAK++PGF L+++DQ+ L+K E+ + +R
Sbjct: 42 QQRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPES 101
Query: 221 -SLTFSDGMYVTRQQL 235
++TF +R
Sbjct: 102 EAITFLKDFPYSRDDF 117
>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 = 48.8 bits (117), Expect = 4e-07
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSS--LTFSDGMYVTRQQL 235
++VE+AKR+P F +L DDQ+IL++ G+ EL I + + + + G+++ R
Sbjct: 45 QLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSA 104
Query: 236 E 236
Sbjct: 105 H 105
>gnl|CDD|132757 cd07072, NR_LBD_DHR38_like, Ligand binding domain of DHR38_like
proteins, members of the nuclear receptor superfamily.
The ligand binding domain of nuclear receptor DHR38_like
proteins: DHR38 is a member of the steroid receptor
superfamily in Drosophila. DHR38 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. At least
four differentially expressed mRNA isoforms have been
detected during development. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, DHR38 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 = 239
Score = 47.1 bits (112), Expect = 2e-06
Identities = 25/74 (33%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
QQF + +T S+ + FA+++PGF DL ++DQ +L + EL++ Y + D+ L
Sbjct: 45 QQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAP-EDTKL 103
Query: 223 TFSDGMYVTRQQLE 236
TF +G+ + +QQ +
Sbjct: 104 TFCNGVVLHKQQCQ 117
>gnl|CDD|132736 cd06938, NR_LBD_EcR, The ligand binding domain (LBD) of the
Ecdysone receptor, a member of the nuclear receptors
super family. The ligand binding domain (LBD) of the
ecdysone receptor: The ecdysone receptor (EcR) belongs
to the superfamily of nuclear receptors (NRs) of
ligand-dependent transcription factors. Ecdysone
receptor 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 ecdysone receptor
are ecdysteroids#the endogenous steroidal hormones found
in invertebrates. In addition, insecticide
bisacylhydrazine used against pests has shown to act on
EcR. EcR must be dimerised with a USP for high-affinity
ligand binding to occur. The ligand binding triggers a
conformational change in the C-terminal part of the EcR
ligand-binding domain that leads to transcriptional
activation of genes controlled by EcR. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, ec dysone
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 = 231
Score = 47.0 bits (112), Expect = 2e-06
Identities = 17/28 (60%), Positives = 24/28 (85%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIK 202
+VQ +VEFAKR+PGF LS++DQ+ L+K
Sbjct: 51 TVQLIVEFAKRLPGFDKLSREDQITLLK 78
>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 = 43.7 bits (103), Expect = 3e-06
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 5 FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGM 47
FF+R+++ Q Y C C++ ++ R C CR +KCL GM
Sbjct: 28 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGM 70
>gnl|CDD|132762 cd07348, NR_LBD_NGFI-B, The ligand binding domain of Nurr1, a
member of conserved family of nuclear receptors. The
ligand binding domain of Nerve growth factor-induced-B
(NGFI-B): 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 the 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. 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 = 238
Score = 46.0 bits (109), Expect = 4e-06
Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
QQF ++ S++ + ++A+++PGF D ++DQ +L++ F EL+I Y S L
Sbjct: 44 QQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEG-KL 102
Query: 223 TFSDGMYVTRQQ 234
F +G+ + R Q
Sbjct: 103 IFCNGVVLHRTQ 114
>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 = 43.0 bits (101), Expect = 5e-06
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 5 FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMS 48
FF+R+ + Q Y C C++ ++ R C CR +KC GM+
Sbjct: 24 FFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMT 67
>gnl|CDD|132756 cd07071, NR_LBD_Nurr1, The ligand binding domain of Nurr1, a
member of conserved family of nuclear receptors. The
ligand binding domain of nuclear receptor Nurr1: Nurr1
belongs to the conserved family of nuclear receptors. It
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.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
Nurr1 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 = 238
Score = 44.3 bits (104), Expect = 2e-05
Identities = 33/114 (28%), Positives = 55/114 (48%), Gaps = 18/114 (15%)
Query: 132 LVRKPVSLPPSEVS--------SPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFA 183
LVR V P+ S +P+ S ++Q + QQF +T S++ + +A
Sbjct: 8 LVRAHVDSNPAMTSLDYSRFQANPDYQMSG---DDTQHI---QQFYDLLTGSMEIIRGWA 61
Query: 184 KRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSLTFSDGMYVTRQQ 234
+++PGF DL + DQ +L + F EL++ Y S L F +G+ + R Q
Sbjct: 62 EKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEG-KLIFCNGVVLHRLQ 114
>gnl|CDD|132731 cd06933, NR_LBD_VDR, The ligand binding domain of vitamin D
receptors, a member of the nuclear receptor superfamily.
The ligand binding domain of vitamin D receptors (VDR):
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 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 = 238
Score = 43.8 bits (103), Expect = 2e-05
Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS 220
RL + A V+ S+Q+V+ FAK +PGF DL+ +DQ+ L+K E V L ++
Sbjct: 35 RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIE-----VIMLRSNQ 89
Query: 221 SLTFSD 226
S + D
Sbjct: 90 SFSLDD 95
>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 = 41.4 bits (97), Expect = 2e-05
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 5 FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMS 48
FF+R+ + + +Y C C + + R C CR +KC GM+
Sbjct: 29 FFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMT 72
>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 = 41.1 bits (97), Expect = 1e-04
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILI 201
+ V++AK +P F +L DDQL L+
Sbjct: 14 KTVDWAKNLPAFRNLPLDDQLTLL 37
>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 = 39.3 bits (92), Expect = 8e-04
Identities = 12/24 (50%), Positives = 19/24 (79%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIK 202
+VE+AK +P FC+L DDQ+ L++
Sbjct: 48 LVEWAKYIPAFCELPLDDQVALLR 71
>gnl|CDD|132747 cd06949, NR_LBD_ER, Ligand binding domain of Estrogen receptor,
which are activated by the hormone 17beta-estradiol
(estrogen). The ligand binding domain (LBD) of Estrogen
receptor (ER): Estrogen receptor, a member of nuclear
receptor superfamily, is activated by the hormone
estrogen. Estrogen regulates many physiological
processes including reproduction, bone integrity,
cardiovascular health, and behavior. The main mechanism
of action of the estrogen receptor is as a transcription
factor by binding to the estrogen response element of
target genes upon activation by estrogen and then
recruiting coactivator proteins which are responsible
for the transcription of target genes. Additionally some
ERs may associate with other membrane proteins and can
be rapidly activated by exposure of cells to estrogen.
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 flexible hinge
and a C-terminal ligand binding domain (LBD). The
C-terminal LBD also contains AF-2 activation motif, the
dimerization motif, and part of the nuclear localization
region. Estrogen receptor has been linked to aging,
cancer, obesity and other diseases.
Length = 235
Score = 35.9 bits (83), Expect = 0.012
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
++ +AK++PGF DLS DQ+ L++ + E L +G V R + L F+ + + R Q
Sbjct: 48 MINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQ 105
>gnl|CDD|132761 cd07076, NR_LBD_GR, Ligand binding domain of the glucocorticoid
receptor, a member of the nuclear receptor superfamily.
The ligand binding domain of the glucocorticoid receptor
(GR): GR is a ligand-activated transcription factor
belonging to the nuclear receptor superfamily. It binds
with high affinity to cortisol and other
glucocorticoids. 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. In the absence of
hormone, the glucocorticoid receptor (GR) is complexes
with a variety of heat shock proteins in the cytosol.
The binding of the glucocorticoids results in release of
the heat shock proteins and transforms it to its active
state. One mechanism of action of GR is by direct
activation of gene transcription. The activated form of
GR forms dimers, translocates into the nucleus, and
binds to specific hormone responsive elements,
activating gene transcription. GR can also function as a
repressor of other gene transcription activators, such
as NF-kappaB and AF-1 by directly binding to them, and
bloc king the expression of their activated genes. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, GR 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 also
functions for dimerization and chaperone protein
association.
Length = 247
Score = 35.3 bits (81), Expect = 0.019
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 10/73 (13%)
Query: 176 VQRVVEFAKRVPGFCDLSQDDQLILIK------MGFFELWIGYVSRLTTDSSLTFSDGMY 229
V V++AK +PGF +L DDQ+ L++ M F W Y R + + L F+ +
Sbjct: 41 VVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSY--RQSNGNLLCFAPDLI 98
Query: 230 VT--RQQLEVMYD 240
+ R L MYD
Sbjct: 99 INEQRMTLPCMYD 111
>gnl|CDD|132753 cd07068, NR_LBD_ER_like, The ligand binding domain of estrogen
receptor and estrogen receptor-related receptors. The
ligand binding domain of estrogen receptor (ER) and
estrogen receptor-related receptors (ERRs): Estrogen
receptors are a group of receptors which are activated
by the hormone estrogen. Estrogen regulates many
physiological processes including reproduction, bone
integrity, cardiovascular health, and behavior. The main
mechanism of action of the estrogen receptor is as a
transcription factor by binding to the estrogen response
element of target genes upon activation by estrogen and
then recruiting coactivator proteins which are
responsible for the transcription of target genes.
Additionally some ERs may associate with other membrane
proteins and can be rapidly activated by exposure of
cells to estrogen. ERRs are closely related to the
estrogen receptor (ER) family. But, it lacks the ability
to bind estrogen. ERRs can interfere with the classic
ER-mediated estrogen signaling pathway, positively or
negatively. ERRs share target genes, co-regulators and
promoters with the estrogen receptor (ER) family. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, ER and ERRs
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 = 221
Score = 34.5 bits (80), Expect = 0.028
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 183 AKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQLEVM 238
AK +PGF DLS +DQ+ L++ + E L +G V R L L F+ + + R+Q V
Sbjct: 47 AKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARVE 104
>gnl|CDD|132734 cd06936, NR_LBD_Fxr, The ligand binding domain of Farnesoid X
receptor:a member of the nuclear receptor superfamily of
ligand-activated transcription factors. The ligand
binding domain (LBD) of Farnesoid X receptor: Farnesoid
X receptor (FXR) is a member of the nuclear receptor
superfamily of ligand-activated transcription factors.
FXR is highly expressed in the liver, the intestine, the
kidney, and the adrenals. FXR plays key roles in the
regulation of bile acid, cholesterol, triglyceride, and
glucose metabolism. Evidences show that it also
regulates liver regeneration. Upon binding of ligands,
such as bile acid, an endogenous ligand, FXRs bind to
FXR response elements (FXREs) either as a monomer or as
a heterodimer with retinoid X receptor (RXR), and
regulate the expression of various genes involved in
bile acid, lipid, and glucose metabolism. There are two
FXR genes (FXRalpha and FXRbeta) in mammals. A single
FXRalpha gene encodes four isoforms resulting from
differential use of promoters and alternative splicing.
FXRbeta is a functional receptor in mice, rats, rabbits
and dogs, but is a pseudogene in humans and primates.
Like other members of the nuclear receptor (NR)
superfamily, farnesoid X 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 = 221
Score = 33.6 bits (77), Expect = 0.058
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 173 TPSVQRVVEFAKRVPGFCDLSQDDQLILIK 202
T VQ +VEF K +PGF L +DQ+ L+K
Sbjct: 46 TSHVQVLVEFTKGLPGFETLDHEDQIALLK 75
>gnl|CDD|132732 cd06934, NR_LBD_PXR_like, The ligand binding domain of xenobiotic
receptors:pregnane X receptor and constitutive
androstane receptor. The ligand binding domain of
xenobiotic receptors: This xenobiotic receptor family
includes pregnane X receptor (PXR), constitutive
androstane receptor (CAR) and other related nuclear
receptors. They function as sensors of toxic byproducts
of cell metabolism and of exogenous chemicals, to
facilitate their elimination. The nuclear receptor
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. The ligand binding domain
of PXR shows remarkable flexibility to accommodate both
large and small molecules. PXR functions as a
heterodimer with retinoic X receptor-alpha (RXRa) and
binds to a variety of response elements in the promoter
regions of a diverse set of target genes involved in the
metabolism, transport, and elimination of these
molecules from the cell. Constitutive androstane
receptor (CAR) is a closest mammalian relative of PXR,
which has also been proposed to function as a
xenosensor. CAR 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,
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 = 226
Score = 33.5 bits (77), Expect = 0.065
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 168 FAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFEL 208
FA T ++++++FAK +P F L +DQ+ L+K FE+
Sbjct: 40 FADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEI 80
>gnl|CDD|132745 cd06947, NR_LBD_GR_Like, Ligand binding domain of nuclear hormone
receptors:glucocorticoid receptor, mineralocorticoid
receptor , progesterone receptor, and androgen receptor.
The ligand binding domain of GR_like nuclear receptors:
This family of NRs includes four distinct, but closely
related nuclear hormone receptors: glucocorticoid
receptor (GR), mineralocorticoid receptor (MR),
progesterone receptor (PR), and androgen receptor (AR).
These four receptors play key roles in 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 use multiple signaling pathways and share
similar functional mechanisms. The dominant signaling
pathway is via direct DNA binding and transcriptional
regulation of target genes. Another mechanism is via
protein-protein interactions, mainly with other
transcription factors such as nuclear factor-kappaB and
activator protein-1, to regulate gene expression
patterns. Both pathways can up-regulate or down-regulate
gene expression and require ligand activation of the
receptor and recruitment of other cofactors such as
chaperone proteins and coregulator proteins. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, GR, MR, PR, and
AR share the same modular structure 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 = 246
Score = 32.3 bits (74), Expect = 0.15
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIK---MGFFELWIGYVSRLTTDSS-LTFSDGMYVT-- 231
VV++AK +PGF +L DDQ+ LI+ M +G+ S +S L F+ +
Sbjct: 43 SVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQ 102
Query: 232 RQQLEVMYD 240
R MY
Sbjct: 103 RMHQSAMYS 111
>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 = 32.4 bits (74), Expect = 0.16
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 180 VEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
VE+A+ +P F DL DQ+ L+++ + EL++
Sbjct: 47 VEWARNIPFFPDLQVTDQVALLRLSWSELFV 77
>gnl|CDD|215174 PLN02305, PLN02305, lipoxygenase.
Length = 918
Score = 31.8 bits (72), Expect = 0.32
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 124 YTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHV 172
Y++ G R + +SLPP+ SSP H++ W+W+ AHV
Sbjct: 516 YSKAGALRPIAIELSLPPTP-SSPGNKFVYTHGHDATTHWIWKLAKAHV 563
>gnl|CDD|132758 cd07073, NR_LBD_AR, Ligand binding domain of the nuclear receptor
androgen receptor, ligand activated transcription
regulator. The ligand binding domain of the androgen
receptor (AR): AR is a member of the nuclear receptor
family. It is activated by binding either of the
androgenic hormones, testosterone or
dihydrotestosterone, which are responsible for male
primary sexual characteristics and for secondary male
characteristics, respectively. The primary mechanism of
action of ARs is by direct regulation of gene
transcription. The binding of an 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 is
independent of their interactions with DNA. The
receptors interact 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). The LBD is not
only involved in binding to androgen, but also involved
in binding of coactivator proteins and dimerization. A
ligand dependent nuclear export signal is also present
at the ligand binding domain.
Length = 246
Score = 30.7 bits (69), Expect = 0.62
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 3/50 (6%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIK---MGFFELWIGYVSRLTTDSSLTF 224
VV++AK +PGF +L DDQ+ +I+ MG +G+ S +S + +
Sbjct: 43 HVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLY 92
>gnl|CDD|234747 PRK00398, rpoP, DNA-directed RNA polymerase subunit P;
Provisional.
Length = 46
Score = 27.6 bits (62), Expect = 0.83
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 15 EYRCLRDGKCLVIRL--NRNRCQYCRFK 40
EY+C R G+ + + RC YC ++
Sbjct: 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30
>gnl|CDD|140237 PTZ00210, PTZ00210, UDP-GlcNAc-dependent glycosyltransferase;
Provisional.
Length = 382
Score = 30.2 bits (68), Expect = 0.84
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 8/82 (9%)
Query: 154 AECHESQRLWLWQQFAAHVTPSVQRVV----EFAKRVPGFCDLSQDDQLILIKMGFFELW 209
AE S++ +LW +FA H+ P+V +V + RVP + D ++ + G +
Sbjct: 178 AEVAMSRKTYLWLRFALHMFPNVSYIVKGDDDIFIRVPKYL----ADLRVMPRHGLYMGR 233
Query: 210 IGYVSRLTTDSSLTFSDGMYVT 231
Y +R+ + LT+ +G +T
Sbjct: 234 YNYYNRIWRRNQLTYVNGYCIT 255
>gnl|CDD|132759 cd07074, NR_LBD_PR, Ligand binding domain of the progesterone
receptor, a member of the nuclear hormone receptor. The
ligand binding domain of the progesterone receptor (PR):
PR is a member of the nuclear receptor superfamily of
ligand dependent transcription factors, mediating the
biological actions of progesterone. PR functions in a
variety of biological processes including development of
the mammary gland, regulating cell cycle progression,
protein processing, and metabolism. When no binding
hormone is present the carboxyl terminal inhibits
transcription. Binding to a hormone induces a structural
change that removes the inhibitory action. After
progesterone binds to the receptor, PR forms a dimer and
the complex enters the nucleus where it interacts with
the hormone response element (HRE) in the promoters of
progesterone responsive genes and alters their
transcription. In addition, rapid actions of PR that
occur independent of transcription, have also been
observed in several tissues like brain, liver, mammary
gland and spermatozoa. There are two natural PR isoforms
called PR-A and PR-B. PR-B has an additional stretc h of
164 amino acids at the N terminus. The extra domain in
PR-B performs activation functions by recruiting
coactivators that could not be recruited by PR-A. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, PR 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 is not
only involved in binding to progesterone, but also
involved in coactivator binding and dimerization.
Length = 248
Score = 29.9 bits (67), Expect = 0.96
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIK---MGFFELWIGYVS-RLTTDSSLTFSDGMYVTRQQ 234
VV+++K +PGF +L DDQ+ LI+ M +G+ S + + L F+ + + Q+
Sbjct: 44 VVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQR 103
Query: 235 LE 236
++
Sbjct: 104 MK 105
>gnl|CDD|132760 cd07075, NR_LBD_MR, Ligand binding domain of the mineralocorticoid
receptor, a member of the nuclear receptor superfamily.
The ligand binding domain of the mineralocorticoid
receptor (MR): MR, also called aldosterone receptor, is
a member of nuclear receptor superfamily involved in the
regulation of electrolyte and fluid balance. The
receptor is activated by mineralocorticoids such as
aldosterone and deoxycorticosterone as well as
glucocorticoids, like cortisol and cortisone. Binding of
its ligand results in its translocation to the cell
nucleus, homodimerization and binding to hormone
response elements (HREs) present in the promoter of MR
controlled genes. This results in the recruitment of the
coactivators and the transcription of the activated
genes. MR is expressed in many tissues and its
activation results in the expression of proteins
regulating electrolyte and fluid balance. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, MR 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, in
addition to binding ligand, contains a ligand-dependent
activation function-2 (AF-2).
Length = 248
Score = 29.5 bits (66), Expect = 1.4
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 10/71 (14%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFEL------WIGYVSRLTTDSSLTFSDGMYVT 231
+VV++AK +PGF +L +DQ+ LI+ + L W Y + T L F+ +
Sbjct: 43 QVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSY--KHTNSQFLYFAPDLVFN 100
Query: 232 --RQQLEVMYD 240
R MY+
Sbjct: 101 EERMHQSAMYE 111
>gnl|CDD|224907 COG1996, RPC10, DNA-directed RNA polymerase, subunit RPC10
(contains C4-type Zn-finger) [Transcription].
Length = 49
Score = 26.9 bits (60), Expect = 1.5
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 13 QIEYRCLRDGK--CLVIRLNRNRCQYCRFK 40
+EY+C R G+ L RC YC +
Sbjct: 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33
>gnl|CDD|132744 cd06946, NR_LBD_ERR, The ligand binding domain of estrogen
receptor-related nuclear receptors. The ligand binding
domain of estrogen receptor-related receptors (ERRs):
The family of estrogen receptor-related receptors
(ERRs), a subfamily of nuclear receptors, is closely
related to the estrogen receptor (ER) family, but it
lacks the ability to bind estrogen. ERRs can interfere
with the classic ER-mediated estrogen signaling pathway,
positively or negatively. ERRs share target genes,
co-regulators and promoters with the estrogen receptor
(ER) family. There are three subtypes of ERRs: alpha,
beta and gamma. ERRs bind at least two types of DNA
sequence, the estrogen response element and another
site, originally characterized as SF-1 (steroidogenic
factor 1) response element. 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 flexible hinge and a C-terminal ligand binding domain
(LBD).
Length = 221
Score = 28.9 bits (65), Expect = 1.8
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 6/49 (12%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRLTTDSSLTFSD 226
++ +AK +PGF LS +DQ+ L++ + E L +G V R SL F+
Sbjct: 43 IIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFR-----SLPFNG 86
>gnl|CDD|213251 cd03284, ABC_MutS1, ATP-binding cassette domain of MutS1 homolog.
The MutS protein initiates DNA mismatch repair by
recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 216
Score = 29.2 bits (66), Expect = 1.8
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 174 PSVQRVVEFAKRVPGFCDLSQDDQLILI 201
P V++V++ VP +L + Q++LI
Sbjct: 8 PVVEQVLDNEPFVPNDTELDPERQILLI 35
>gnl|CDD|233313 TIGR01210, TIGR01210, TIGR01210 family protein. This family of
exclusively archaeal proteins has no characterized
close homologs. Several rounds of PSI-BLAST with a
stringent cutoff of 1e-8 shows apparent similarity of
the central region of this family to the central
regions of the oxygen-independent coproporphyrinogen
III dehydrogenase HemN and to other enzymes
[Hypothetical proteins, Conserved].
Length = 313
Score = 29.0 bits (65), Expect = 2.0
Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 8/66 (12%)
Query: 22 GKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR-------YGRVPKR-SRERSDSETGSTR 73
GK L I L C + R C G DS + + + + + +
Sbjct: 13 GKSLTIILRTRGCYWAREGGCYMCGYLADSSPEVTEENLINQFDEAIEKYKEKIKDFVIK 72
Query: 74 VSTTGA 79
+ T+G+
Sbjct: 73 IFTSGS 78
>gnl|CDD|117723 pfam09169, BRCA-2_helical, BRCA2, helical. Members of this family
adopt a helical structure, consisting of a four-helix
cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and
two successive beta-hairpins (beta 1 to beta 4). An
approx. 50-amino acid segment that contains four short
helices (alpha 2 to alpha 4), meanders around the
surface of the core structure. In BRCA2, the alpha 9 and
alpha 10 helices pack with BRCA-2_OB1 (pfam09103)
through van der Waals contacts involving hydrophobic and
aromatic residues, and also through side-chain and
backbone hydrogen bonds. The domain binds the 70-amino
acid DSS1 (deleted in split-hand/split foot syndrome)
protein, which was originally identified as one of three
genes that map to a 1.5-Mb locus deleted in an inherited
developmental malformation syndrome.
Length = 195
Score = 28.3 bits (63), Expect = 2.6
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 45 VGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQ 104
G++RD ++ R+ K+ R++ + GS ++ + P SL+ A + + +E KQ
Sbjct: 9 DGVARD-IQEMRIKKKQRQQIYPQPGSLYLTKSSTLPRISLKAAVGGSTPSACSENRNKQ 67
Query: 105 LLTYDVILAVSQAHHSNCEY 124
L TY V + N E
Sbjct: 68 LYTYGVPKHCIDVNSKNAES 87
>gnl|CDD|132589 TIGR03550, F420_cofG, 7,8-didemethyl-8-hydroxy-5-deazariboflavin
synthase, CofG subunit. This model represents either a
subunit or a domain, depending on whether or not the
genes are fused, of a bifunctional protein that
completes the synthesis of
7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO
is the chromophore of coenzyme F(420), involved in
methanogenesis in methanogenic archaea but found in
certain other lineages as well. The chromophore also
occurs as a cofactor in DNA photolyases in
Cyanobacteria [Biosynthesis of cofactors, prosthetic
groups, and carriers, Other].
Length = 322
Score = 28.0 bits (63), Expect = 4.3
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 26 VIRLNRNRCQYCRFK----KCLAVGMSRDSVR 53
+ RL RNRC YC F+ + A +S + V
Sbjct: 10 LTRLCRNRCGYCTFRRPPGELEAALLSPEEVL 41
>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 = 27.6 bits (62), Expect = 4.3
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 180 VEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
V++AK +P F L DQLIL++ + EL++
Sbjct: 43 VKWAKSIPAFSTLPFRDQLILLEESWSELFL 73
>gnl|CDD|218974 pfam06284, Cytomega_UL84, Cytomegalovirus UL84 protein. This
family consists of several Cytomegalovirus UL84
proteins. The open reading frame UL84 of human
cytomegalovirus encodes a multifunctional regulatory
protein which is required for viral DNA replication and
binds with high affinity to the immediate-early
transactivator IE2-p86.
Length = 464
Score = 27.9 bits (62), Expect = 5.2
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 105 LLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSP 147
L + + IL ++ HH T GT RL++ V P ++ P
Sbjct: 23 LGSDETILTLTDQHHIKQPLTRRGTYRLIQLHVDFQPEDLQHP 65
>gnl|CDD|152960 pfam12526, DUF3729, Protein of unknown function (DUF3729). This
family of proteins is found in viruses. Proteins in this
family are typically between 145 and 1707 amino acids in
length. The family is found in association with
pfam01443, pfam01661, pfam05417, pfam01660, pfam00978.
There is a single completely conserved residue L that
may be functionally important.
Length = 115
Score = 26.6 bits (59), Expect = 7.3
Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 5/53 (9%)
Query: 57 VPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLL-TY 108
+ + D E A PPS L P + P ++LL TY
Sbjct: 66 PSEPAAPPPDPEPPVPG----PAGPPSPLAPPAPARKPPLPPPRPQRRLLHTY 114
>gnl|CDD|185355 PRK15458, PRK15458, tagatose 6-phosphate aldolase subunit KbaZ;
Provisional.
Length = 426
Score = 27.4 bits (61), Expect = 7.8
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 143 EVSSPEVASSTAECH----ESQRLW-LWQQFAAHVTPSVQRVVEF 182
V++P+ A +T E H E Q L +W + V VQ VEF
Sbjct: 190 AVTTPDAARATLEAHRHAFEKQGLNAIWPRIIGLV---VQPGVEF 231
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 27.4 bits (61), Expect = 8.2
Identities = 18/113 (15%), Positives = 32/113 (28%), Gaps = 3/113 (2%)
Query: 58 PKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQA 117
P +S + + G P S++ V P ST Q + +
Sbjct: 402 PSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPST---APQAVRPAQFKEEKKI 458
Query: 118 HHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAA 170
S T R +++ + + E + WQ+FA
Sbjct: 459 PVSKVSSLGPSTLRPIQEKAEQATGNIKEAPTGTQKEIFTEEDLQYYWQEFAG 511
>gnl|CDD|227746 COG5459, COG5459, Predicted rRNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 484
Score = 27.3 bits (60), Expect = 8.2
Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 4/65 (6%)
Query: 18 CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTT 77
C KC + N +C F + V S+ S+ + R D G+
Sbjct: 262 CPHQRKCPLQVPNGKDLDWCHFSQ--RVARSKFSIEL--KKRLHRTSKDGSQGNASRLKR 317
Query: 78 GAEPP 82
A P
Sbjct: 318 RAGRP 322
>gnl|CDD|220661 pfam10263, SprT-like, SprT-like family. This family represents a
domain found in eukaryotes and prokaryotes. The domain
contains a characteristic motif of the zinc
metallopeptidases. This family includes the bacterial
SprT protein.
Length = 153
Score = 26.6 bits (59), Expect = 8.6
Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 15 EYRCLRDGKC----LVIRLNRNRCQYCRFK 40
YRC G+ IR ++ RC C K
Sbjct: 119 IYRCGSCGQLYPRKRRIRRHKYRCGRCGGK 148
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 0.395
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: 11,567,404
Number of extensions: 1015190
Number of successful extensions: 950
Number of sequences better than 10.0: 1
Number of HSP's gapped: 934
Number of HSP's successfully gapped: 93
Length of query: 240
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 146
Effective length of database: 6,768,326
Effective search space: 988175596
Effective search space used: 988175596
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: 57 (25.8 bits)