RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11505
(312 letters)
>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 = 216 bits (551), Expect = 7e-70
Identities = 94/265 (35%), Positives = 126/265 (47%), Gaps = 76/265 (28%)
Query: 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
+L LL+ EP+ L + D ++ + +LSDL DRELV IIGWAK IPGF+ LSLND
Sbjct: 1 ILSHLLVAEPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLND 60
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY----QQVKH 192
QM LLQS W EILTL + +RSLP G++ FA D +LDE ARE G E+Y Q V+
Sbjct: 61 QMSLLQSAWMEILTLGVVFRSLP-FNGELVFAEDFILDEELAREAGLLELYSACLQLVRR 119
Query: 193 SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTL 252
L KEE Y + KA L
Sbjct: 120 LQRLRLEKEE------------------YVL-----LKA--------------------L 136
Query: 253 VLANSDVKL-DEFSSLKKFRNSILSSLGDCIY---------------------------V 284
LANSD ++ ++++ R+++L +L D
Sbjct: 137 ALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKA 196
Query: 285 LRFWSTVHKDGKVLMNKLFVEMLEA 309
RF+ V ++GKV M+KLF+EMLEA
Sbjct: 197 RRFFYGVKREGKVPMHKLFLEMLEA 221
>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 = 201 bits (513), Expect = 4e-64
Identities = 95/264 (35%), Positives = 129/264 (48%), Gaps = 74/264 (28%)
Query: 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
+L ALL+ EP+ L ++ D + + +LSDL DRELV II WAK IPGF+DLSLND
Sbjct: 1 LLSALLVAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLND 60
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGS- 195
QM LLQS W EIL L + +RSLPH GK+ FA DL+LD QAR G EI+ +
Sbjct: 61 QMHLLQSAWLEILMLGLVWRSLPH-PGKLVFAPDLLLDREQARVEGLLEIFDMLLQLVRR 119
Query: 196 --LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV 253
G++ EE +CL KA ++
Sbjct: 120 FRELGLQREEY---VCL-------------------KA--------------------II 137
Query: 254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIY---------------------------VL 285
LANSDV+ L++ ++++ R++IL +L D +
Sbjct: 138 LANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGV 197
Query: 286 RFWSTVHKDGKVLMNKLFVEMLEA 309
R +V +GKV M KLF+EMLEA
Sbjct: 198 RHLYSVKCEGKVPMYKLFLEMLEA 221
>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 = 120 bits (302), Expect = 3e-34
Identities = 46/58 (79%), Positives = 52/58 (89%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R D
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDA 95
Score = 77.6 bits (191), Expect = 4e-18
Identities = 31/34 (91%), Positives = 34/34 (100%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQ 36
>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 = 95.6 bits (238), Expect = 2e-23
Identities = 51/118 (43%), Positives = 73/118 (61%), Gaps = 8/118 (6%)
Query: 77 MLEALLLCEPEMLTVR--SETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
++ ALL EP + P ++ +L + L++L DRELV +I WAK+IPGF DLSL
Sbjct: 6 LISALLEAEPPHIYSEYDPTRPFTEASL--MMLLTNLADRELVHMINWAKKIPGFVDLSL 63
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQV 190
+DQ+ LL+S W E+L L + +RS+ H GK+ FA DL+LD Q C G EI+ +
Sbjct: 64 HDQVHLLESAWLELLMLGLVWRSMEH-PGKLLFAPDLLLDRNQGS-CVEGMVEIFDML 119
>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 = 83.1 bits (205), Expect = 1e-18
Identities = 31/108 (28%), Positives = 67/108 (62%), Gaps = 1/108 (0%)
Query: 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
++ L+ EP+++ + + + + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 2 LINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDD 61
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGF 183
Q+ L+Q +W ++ + +RS H +G+ + FA DL+L+E++ +E F
Sbjct: 62 QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSF 109
>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 = 78.3 bits (193), Expect = 1e-18
Identities = 30/44 (68%), Positives = 41/44 (93%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
N+ Y+CP++++CE++K+RRK+CQACR QKCL+ GMLKEGVRLDR
Sbjct: 32 NLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75
Score = 73.7 bits (181), Expect = 6e-17
Identities = 30/41 (73%), Positives = 32/41 (78%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGAC 249
CLVCGD+ASG+HYGVASCEACKAFFKRTIQ GY
Sbjct: 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTS 41
>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 = 78.3 bits (193), Expect = 2e-18
Identities = 28/51 (54%), Positives = 35/51 (68%)
Query: 3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
YTC + +C+I+K +RK C CRFQKCL GM E VR DR+RGGR K+
Sbjct: 34 RYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFG 84
Score = 58.2 bits (141), Expect = 5e-11
Identities = 20/30 (66%), Positives = 25/30 (83%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C VCGD SG+HYG+ +CE+CK FFKRT+Q
Sbjct: 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQ 30
>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 = 80.9 bits (200), Expect = 7e-18
Identities = 39/117 (33%), Positives = 67/117 (57%), Gaps = 4/117 (3%)
Query: 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
+L L EPE++ + Q D T + ++SL+ L +R+LV ++ WAK +PGF +L L+D
Sbjct: 2 LLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDD 61
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKI-RFASDLVLDERQARECGFSEIYQQVKH 192
QM L+Q +W ++ + +RS H ++ FA DLV +E++ + S +Y
Sbjct: 62 QMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQ---SAMYSLCLG 115
>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 = 76.1 bits (188), Expect = 8e-18
Identities = 26/41 (63%), Positives = 30/41 (73%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
N+EYTCPA +C I+KR R CQACR +KCL GM KE VR
Sbjct: 32 NLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72
Score = 68.4 bits (168), Expect = 5e-15
Identities = 19/30 (63%), Positives = 25/30 (83%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C VCGD ASG+HYGV +CE CK FF+R+++
Sbjct: 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVR 30
>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 = 75.5 bits (186), Expect = 2e-16
Identities = 31/89 (34%), Positives = 56/89 (62%)
Query: 104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAG 163
+N L ++++R+L+ ++ WAK+ PGF +LSL+DQ+ LL+S+W E L L +A RS
Sbjct: 1 GLNELFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKD 60
Query: 164 KIRFASDLVLDERQARECGFSEIYQQVKH 192
+ F++ L LD + + + I +Q++
Sbjct: 61 DLLFSNGLYLDRDELKSIEVNYINEQIRQ 89
>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 = 75.7 bits (186), Expect = 6e-16
Identities = 39/117 (33%), Positives = 67/117 (57%), Gaps = 4/117 (3%)
Query: 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
++ L + EPE+L ++ D T + +++L+ L R++V + WAK IPGF +L L+D
Sbjct: 2 LVSLLEVIEPEVLYSGYDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDD 61
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDERQARECGFSEIYQQVKH 192
QM LLQ +W ++ + +RS G + FA DL+++E++ +Y Q KH
Sbjct: 62 QMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMT---LPCMYDQCKH 115
>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 = 69.5 bits (171), Expect = 2e-15
Identities = 22/32 (68%), Positives = 26/32 (81%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
LC VCGD ASG+HYGV +CE CK FF+R+IQ
Sbjct: 1 ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQ 32
Score = 68.0 bits (167), Expect = 6e-15
Identities = 22/37 (59%), Positives = 25/37 (67%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 37
NI YTCP + DC I+KR R CQ CR +KCL GM K
Sbjct: 34 NIVYTCPFNKDCVIDKRNRNRCQYCRLKKCLEVGMSK 70
>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 = 68.4 bits (167), Expect = 7e-15
Identities = 26/48 (54%), Positives = 31/48 (64%)
Query: 4 YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
YTC CEI K +R CQ CRF+KC+RKGM+ VR DR+ GGR
Sbjct: 43 YTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGGRNS 90
Score = 56.8 bits (137), Expect = 1e-10
Identities = 20/38 (52%), Positives = 28/38 (73%)
Query: 201 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
+E+ +LC +C D A+G HYG+ +CE CK FFKRT+Q
Sbjct: 1 DEDESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQ 38
>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 = 70.3 bits (173), Expect = 1e-14
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDL 171
DR L + WAK +P F +L L+DQ+ LLQ++WAE+L L +A RS+ + + + L
Sbjct: 9 DRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLL 68
Query: 172 VLDERQARECGFSEI 186
V+ + G +E+
Sbjct: 69 VILTEREALLGLAEL 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 = 67.4 bits (165), Expect = 1e-14
Identities = 23/51 (45%), Positives = 31/51 (60%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
+ Y+C CEI+K R CQ CRF+KC+ GM K+ V DR RG ++K
Sbjct: 33 KLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKRK 83
Score = 59.0 bits (143), Expect = 2e-11
Identities = 18/31 (58%), Positives = 24/31 (77%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C+VCGD A+G+HY +CE CK FF+RT+Q
Sbjct: 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQ 31
>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 = 71.1 bits (174), Expect = 2e-14
Identities = 31/109 (28%), Positives = 62/109 (56%), Gaps = 1/109 (0%)
Query: 81 LLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRL 140
L EPE++ ++ + D +++L+ L ++++ ++ WAK +PGF +L L DQ+ L
Sbjct: 6 LENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITL 65
Query: 141 LQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQ 188
+Q +W + + +++RS H + + FA DLV +E + + E+ Q
Sbjct: 66 IQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMHQSAMYELCQ 114
>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 = 70.4 bits (172), Expect = 4e-14
Identities = 36/114 (31%), Positives = 67/114 (58%), Gaps = 7/114 (6%)
Query: 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
+LEA+ EP ++ + Q D ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 5 VLEAI---EPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 61
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
QM ++Q +W ++ + +RS + + + FA DLV +E + + S +Y Q
Sbjct: 62 QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 112
>gnl|CDD|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER)
is composed of two C4-type zinc fingers. DNA-binding
domain of estrogen receptors (ER) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which coordinates a single zinc
atom. ER interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. Estrogen receptor is a
transcription regulator that mediates the biological
effects of hormone estrogen. The binding of estrogen to
the receptor triggers the dimerization and the binding
of the receptor dimer to estrogen response element,
which is a palindromic inverted repeat:
5'GGTCAnnnTGACC-3', of target genes. Through ER,
estrogen regulates development, reproduction and
homeostasis. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, ER has a central well-conserved DNA binding
domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 82
Score = 64.9 bits (158), Expect = 1e-13
Identities = 24/44 (54%), Positives = 32/44 (72%)
Query: 3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
+Y CPA+N C I+K RRK+CQACR +KC GM+K G+R +R
Sbjct: 39 DYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERRG 82
Score = 64.5 bits (157), Expect = 2e-13
Identities = 24/39 (61%), Positives = 28/39 (71%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
C VC D ASG+HYGV SCE CKAFFKR+IQ ++ Y
Sbjct: 2 DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDY 40
>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors.
Length = 70
Score = 63.7 bits (156), Expect = 3e-13
Identities = 23/31 (74%), Positives = 26/31 (83%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
LC VCGD ASGFH+GV SC ACKAFF+RT+
Sbjct: 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVN 31
Score = 60.6 bits (148), Expect = 3e-12
Identities = 19/38 (50%), Positives = 23/38 (60%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
+Y C N+C INKR R C+ACR +KCL GM E
Sbjct: 33 RYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70
>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 = 66.7 bits (163), Expect = 6e-13
Identities = 33/91 (36%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 87 EMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWA 146
E + P S + DL + I WA++IPGF DL DQ LL+S +
Sbjct: 29 ENVDPVPPKPDSQQ----VQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFL 84
Query: 147 EILTLTIAYRSLPHCAGKIRFASDLVLDERQ 177
E+ L +AYRS P GK+ F + LVL Q
Sbjct: 85 ELFVLRLAYRSNP-VDGKLVFCNGLVLHRLQ 114
>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 = 62.6 bits (152), Expect = 9e-13
Identities = 25/38 (65%), Positives = 29/38 (76%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
LC VCGD ASGFHYGV +CE CK FF+R+IQ YR+
Sbjct: 5 LCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRK 42
Score = 44.5 bits (105), Expect = 3e-06
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 1 NIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
I+Y C + C I + R CQ CRF+KCL GM ++ VR R+ R+K R
Sbjct: 37 KIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIP-KREKAR 89
>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 = 60.9 bits (148), Expect = 3e-12
Identities = 24/41 (58%), Positives = 31/41 (75%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
N +Y C A+ +C ++KRRR CQ CRFQKCL+ GM+KE VR
Sbjct: 34 NAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74
Score = 56.7 bits (137), Expect = 1e-10
Identities = 29/65 (44%), Positives = 37/65 (56%), Gaps = 13/65 (20%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSL 267
LC VCGD A+ HYGV +CE CK FFKRT+Q + Y + LAN + +D
Sbjct: 2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKY--------VCLANKNCPVD----- 48
Query: 268 KKFRN 272
K+ RN
Sbjct: 49 KRRRN 53
>gnl|CDD|143533 cd07158, NR_DBD_Ppar_like, The DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) like nuclear
receptor family. The DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) like nuclear
receptor family is composed of two C4-type zinc fingers.
Each zinc finger contains a group of four Cys residues
which co-ordinates a single zinc atom. These domains
interact with specific DNA sites upstream of the target
gene and modulate the rate of transcriptional
initiation. This family includes three known types of
nuclear receptors: peroxisome proliferator-activated
receptors (PPAR), REV-ERB receptors and Drosophila
ecdysone-induced protein 78 (E78). Like other members of
the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, PPAR-like
receptors have a central well conserved DNA binding
domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 73
Score = 60.3 bits (146), Expect = 4e-12
Identities = 26/37 (70%), Positives = 28/37 (75%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
C VCGD ASGFHYGV SCE CK FF+RTIQ YR+
Sbjct: 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRR 37
Score = 45.6 bits (108), Expect = 8e-07
Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 1 NIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
N+ Y C C I ++ R CQ CRF+KCL GM + VR
Sbjct: 32 NLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73
>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 = 60.3 bits (147), Expect = 5e-12
Identities = 18/29 (62%), Positives = 22/29 (75%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTI 237
C VCGD A+G HYGV SC CK FF+R++
Sbjct: 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSV 29
Score = 58.7 bits (143), Expect = 2e-11
Identities = 20/45 (44%), Positives = 28/45 (62%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
N YTC +C ++K +R AC+ CRF+KCL GM E V+ +R
Sbjct: 32 NRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76
>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 = 64.1 bits (156), Expect = 5e-12
Identities = 40/139 (28%), Positives = 67/139 (48%), Gaps = 7/139 (5%)
Query: 82 LLCEPEMLTVRSETPQSDPT-LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRL 140
LC+ T S Q L + S+L + ++ I+ +AK++PGFT L++ DQ+ L
Sbjct: 16 SLCQLGKYTTNSSADQRVRLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITL 75
Query: 141 LQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV-KHSGSLDGI 199
L++ +IL L I R P + F+ L L+ Q GF + V + L +
Sbjct: 76 LKAACLDILILRICTRYTPEQD-TMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPL 134
Query: 200 KEEE----LPRRLCLVCGD 214
+ ++ L +CL+CGD
Sbjct: 135 EMDDTEIGLLSAICLICGD 153
>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 = 62.7 bits (153), Expect = 6e-12
Identities = 27/60 (45%), Positives = 38/60 (63%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
L +L R+L+ I+ WAK IPGF +L L DQ+ LL+S W E+L L +AYRS + +
Sbjct: 1 ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLL 60
>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 = 63.1 bits (154), Expect = 8e-12
Identities = 36/117 (30%), Positives = 62/117 (52%), Gaps = 8/117 (6%)
Query: 76 KMLEALLLCEPEMLTVRSETPQSDP--TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLS 133
++LEA L EP +SE P ++++ D++L ++ WAK+IP F++L
Sbjct: 6 RILEAELAVEP-----KSEAVAMVPPEYRDPVSNICQAADKQLFQLVEWAKRIPHFSELP 60
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
L+DQ+ LL++ W E+L A+RS+ I A+ L L A + G I+ ++
Sbjct: 61 LDDQVILLRAGWNELLIAAFAHRSI-AVKDGILLATGLHLHRNSAHQAGVGAIFDRI 116
>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 = 58.6 bits (142), Expect = 3e-11
Identities = 27/48 (56%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
P LC+VCGD ASG HYG SCE CK FFKR+I+ GY R + C
Sbjct: 1 QPVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDC 48
Score = 54.0 bits (130), Expect = 1e-09
Identities = 22/44 (50%), Positives = 27/44 (61%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
N+ Y+C S DC INK R CQ CR QKCL GM + V+ +R
Sbjct: 37 NLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCER 80
>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 = 58.7 bits (142), Expect = 3e-11
Identities = 19/48 (39%), Positives = 30/48 (62%)
Query: 4 YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
Y C +C +++++R CQ CR KCL+ GM ++ +R D + GGR K
Sbjct: 43 YRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGRNK 90
Score = 54.9 bits (132), Expect = 7e-10
Identities = 21/31 (67%), Positives = 25/31 (80%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTI 237
R CL+CGD A+G HYG+ SCE CK FFKR+I
Sbjct: 7 RTCLICGDRATGLHYGIISCEGCKGFFKRSI 37
>gnl|CDD|143523 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) is composed of
two C4-type zinc fingers. DNA-binding domain of
peroxisome proliferator-activated receptors (PPAR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which co-ordinates
a single zinc atom. PPAR interacts with specific DNA
sites upstream of the target gene and modulates the rate
of transcriptional initiation. Peroxisome
proliferator-activated receptors (PPARs) are members of
the nuclear receptor superfamily of ligand-activated
transcription factors. PPARs play important roles in
regulating cellular differentiation, development and
lipid metabolism. Activated PPAR forms a heterodimer
with the retinoid X receptor (RXR) that binds to the
hormone response elements, which are composed of two
direct repeats of the consensus sequence 5'-AGGTCA-3'
separated by one to five base pair located upstream of
the peroxisome proliferator responsive genes, and
interacts with co-activators. Several essential fatty
acids, oxidized lipids and prostaglandin J derivatives
can bind and activate PPAR. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, PPAR has a central well conserved
DNA binding domain (DBD), a variable N-terminal
regulatory domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 84
Score = 58.3 bits (141), Expect = 3e-11
Identities = 22/31 (70%), Positives = 25/31 (80%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C VCGD ASGFHYGV +CE CK FF+RTI+
Sbjct: 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIR 31
Score = 45.9 bits (109), Expect = 7e-07
Identities = 20/45 (44%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
+ Y C S C+I+K+ R CQ CRFQKCL GM +R R+
Sbjct: 34 LVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRM 76
>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 = 57.8 bits (140), Expect = 4e-11
Identities = 21/31 (67%), Positives = 25/31 (80%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C+VCGD ASGFHYGV SCE CK FF+R++
Sbjct: 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVT 31
Score = 35.9 bits (83), Expect = 0.002
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
Y C N CE++ R+ CQ CR +KC GM +
Sbjct: 33 GAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPD 70
>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 = 58.0 bits (140), Expect = 4e-11
Identities = 19/32 (59%), Positives = 26/32 (81%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
+ C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 5 KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 36
Score = 55.7 bits (134), Expect = 3e-10
Identities = 24/44 (54%), Positives = 26/44 (59%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
N+ YTC +C INK R CQ CR QKC GM KE VR DR
Sbjct: 38 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDR 81
>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 = 57.0 bits (138), Expect = 6e-11
Identities = 21/38 (55%), Positives = 25/38 (65%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
+TCP + DCEI K R+ CQACR +KCL GM KE
Sbjct: 32 KARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKE 69
Score = 51.6 bits (124), Expect = 6e-09
Identities = 15/30 (50%), Positives = 23/30 (76%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C VCGD A+G+H+ +CE CK FF+R+++
Sbjct: 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMK 30
>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 = 56.4 bits (136), Expect = 1e-10
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
+ Y CP +C I R AC++CRF++CL GM K G R+
Sbjct: 32 SNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73
Score = 49.8 bits (119), Expect = 3e-08
Identities = 18/36 (50%), Positives = 23/36 (63%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
C VCG +SGFH+G +CE CK FF+RT + Y
Sbjct: 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYV 36
>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 = 56.4 bits (136), Expect = 1e-10
Identities = 24/36 (66%), Positives = 27/36 (75%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
C VCGD ASG+HYGV SCE CK FF+R+IQ YR
Sbjct: 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYR 36
Score = 49.9 bits (119), Expect = 3e-08
Identities = 22/45 (48%), Positives = 26/45 (57%)
Query: 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
IEY C CEI + R CQ CRF+KCL GM K+ VR R+
Sbjct: 33 IEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIP 77
>gnl|CDD|143534 cd07160, NR_DBD_LXR, DNA-binding domain of Liver X receptors (LXRs)
family is composed of two C4-type zinc fingers.
DNA-binding domain of Liver X receptors (LXRs) family is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which co-ordinates
a single zinc atom. LXR interacts with specific DNA
sites upstream of the target gene and modulates the rate
of transcriptional initiation. LXR operates as
cholesterol sensor which protects cells from cholesterol
overload by stimulating reverse cholesterol transport
from peripheral tissues to the liver and its excretion
in the bile. Oxidized cholesterol derivatives or
oxysterols were identified as specific ligands for LXRs.
LXR functions as a heterodimer with the retinoid X
receptor (RXR) which may be activated by either LXR
agonist or 9-cis retinoic acid, a specific RXR ligand.
The LXR/RXR complex binds to a liver X receptor response
element (LXRE) in the promoter region of target genes.
The ideal LXRE sequence is a direct repeat-4 (DR-4) DNA
fragment consisting of two AGGTCA hexameric half-sites
separated by a 4-nucleotide spacer. LXR has typical NR
modular structure with a central well conserved DNA
binding domain (DBD), a variable N-terminal domain, a
flexible hinge and the ligand binding domain (LBD) at
the C-terminal.
Length = 101
Score = 56.0 bits (135), Expect = 4e-10
Identities = 20/30 (66%), Positives = 24/30 (80%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTI 237
+C VCGD ASGFHY V SCE CK FF+R++
Sbjct: 20 VCSVCGDKASGFHYNVLSCEGCKGFFRRSV 49
Score = 36.8 bits (85), Expect = 0.002
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGV 40
+Y C C+++ R+ CQ CR +KC GM ++ V
Sbjct: 54 QYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCV 91
>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 = 54.5 bits (131), Expect = 6e-10
Identities = 24/44 (54%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
+C +CGD ASG HYGV SCE CK FFKRT++ Y R C
Sbjct: 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDC 45
Score = 54.1 bits (130), Expect = 9e-10
Identities = 22/41 (53%), Positives = 29/41 (70%)
Query: 4 YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
YTC + DC I+KR+R CQ CR+QKCL GM +E V+ +R
Sbjct: 37 YTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77
>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 = 54.5 bits (131), Expect = 6e-10
Identities = 21/39 (53%), Positives = 28/39 (71%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
P+++CLVC D ASG HYGV +C +CK FFKR ++ Y
Sbjct: 1 PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY 39
Score = 48.3 bits (115), Expect = 1e-07
Identities = 19/39 (48%), Positives = 23/39 (58%)
Query: 4 YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
Y C NDC I+K RRK C ACR +KCL+ GM +
Sbjct: 39 YLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKT 77
>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 = 54.0 bits (130), Expect = 1e-09
Identities = 19/43 (44%), Positives = 23/43 (53%)
Query: 3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
CP C I+K+ R CQACR++KCL GM G R R
Sbjct: 38 ISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRR 80
Score = 47.1 bits (112), Expect = 3e-07
Identities = 17/27 (62%), Positives = 20/27 (74%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKR 235
C VCG+ A+GFH+G CEACK FF R
Sbjct: 3 CQVCGEPAAGFHHGAYVCEACKKFFMR 29
>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 = 57.0 bits (137), Expect = 1e-09
Identities = 40/118 (33%), Positives = 58/118 (49%), Gaps = 9/118 (7%)
Query: 75 NKMLEALLLCEPEMLTVRSETPQSDPTLQT-------INSLSDLYDRELVCIIGWAKQIP 127
+ ++ A + P M ++ Q++P Q I DL + I GWA++IP
Sbjct: 6 SALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIP 65
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSE 185
GFTDL DQ L +S + E+ L +AYRS P GK+ F + +VL Q GF E
Sbjct: 66 GFTDLPKADQDLLFESAFLELFVLRLAYRSNP-VEGKLIFCNGVVLHRLQCVR-GFGE 121
>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 = 56.2 bits (136), Expect = 2e-09
Identities = 28/84 (33%), Positives = 49/84 (58%), Gaps = 7/84 (8%)
Query: 83 LCEPEMLTVRSETP----QSDPTLQTINSLSDLYD---RELVCIIGWAKQIPGFTDLSLN 135
L + E L+ + +P D + I S++D+ + ++L+ ++ WAK IP F +L L+
Sbjct: 5 LLQAEALSRQQSSPIPTCSGDIRPKKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLD 64
Query: 136 DQMRLLQSTWAEILTLTIAYRSLP 159
DQ+ LL++ E L L +A RS+P
Sbjct: 65 DQVALLRAHAGEHLLLGVARRSMP 88
>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 = 56.4 bits (136), Expect = 2e-09
Identities = 30/73 (41%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK 164
I DL L I WA++IPGF+D DQ LL+S + E+ L +AYRS P GK
Sbjct: 43 IQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPE-EGK 101
Query: 165 IRFASDLVLDERQ 177
+ F + +VL Q
Sbjct: 102 LIFCNGVVLHRTQ 114
>gnl|CDD|143538 cd07164, NR_DBD_PNR_like_1, DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR) like
proteins is composed of two C4-type zinc fingers.
DNA-binding domain of the photoreceptor cell-specific
nuclear receptor (PNR) like proteins is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. PNR interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. PNR is a member of nuclear
receptor superfamily of the ligand-activated
transcription factors. PNR is expressed only in the
outer layer of retinal photoreceptor cells. It may be
involved in the signaling pathway regulating
photoreceptor differentiation and/or maintenance. It
most likely binds to DNA as a homodimer. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, PNR has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 78
Score = 52.9 bits (127), Expect = 3e-09
Identities = 18/44 (40%), Positives = 28/44 (63%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
N+ Y C + C ++ RR CQACRF+KCL+ M ++ V+ +R
Sbjct: 32 NLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHER 75
Score = 52.1 bits (125), Expect = 5e-09
Identities = 20/30 (66%), Positives = 24/30 (80%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C VCGD ASG HYGV SC+ C+ FFKR+I+
Sbjct: 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIR 30
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 54.7 bits (132), Expect = 3e-09
Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLV 172
+R+L+ + WAK PGF +LSL DQ+ LL+S W E+L L +AYRS+ + A D
Sbjct: 2 ERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELL-LAPDGT 60
Query: 173 LDERQAR 179
A
Sbjct: 61 YIRPDAV 67
>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 = 51.5 bits (123), Expect = 8e-09
Identities = 20/37 (54%), Positives = 27/37 (72%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
LC+VCGD ASG+HY +CE CK FF+R+I + Y+
Sbjct: 3 LCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYK 39
Score = 38.0 bits (88), Expect = 6e-04
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
N Y C +CE++ R+ CQ CR +KC GML E
Sbjct: 35 NAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAE 72
>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 = 51.7 bits (124), Expect = 1e-08
Identities = 18/36 (50%), Positives = 21/36 (58%)
Query: 3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
E+ CP + CEIN R+ CQ CR KC GM KE
Sbjct: 36 EFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKE 71
Score = 46.3 bits (110), Expect = 9e-07
Identities = 15/29 (51%), Positives = 23/29 (79%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKR 235
++C VCGD A G+++ +CE+CKAFF+R
Sbjct: 1 KICGVCGDKALGYNFNAITCESCKAFFRR 29
>gnl|CDD|143516 cd06958, NR_DBD_COUP_TF, DNA-binding domain of chicken ovalbumin
upstream promoter transcription factors (COUP-TFs) is
composed of two C4-type zinc fingers. DNA-binding
domain of chicken ovalbumin upstream promoter
transcription factors (COUP-TFs) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. COUP-TFs are orphan members of the steroid/thyroid
hormone receptor superfamily. They are expressed in many
tissues and are involved in the regulation of several
important biological processes, such as neurogenesis,
organogenesis, cell fate determination, and metabolic
homeostasis. COUP-TFs homodimerize or heterodimerize
with retinoid X receptor (RXR) and a few other nuclear
receptors and bind to a variety of response elements
that are composed of imperfect AGGTCA direct or inverted
repeats with various spacings. COUP-TFs are generally
considered to be repressors of transcription for other
nuclear hormone receptors such as retinoic acid receptor
(RAR), thyroid hormone receptor (TR), vitamin D receptor
(VDR), peroxisome proliferator activated receptor
(PPAR), and hepatocyte nuclear factor 4 (HNF4). Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, COUP-TFs have
a central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 73
Score = 51.0 bits (122), Expect = 1e-08
Identities = 18/30 (60%), Positives = 25/30 (83%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C+VCGD +SG HYG +CE CK+FFKR+++
Sbjct: 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVR 30
Score = 47.9 bits (114), Expect = 1e-07
Identities = 18/41 (43%), Positives = 27/41 (65%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
N+ YTC + +C I++ R CQ CR +KCL+ GM +E V+
Sbjct: 32 NLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72
>gnl|CDD|143547 cd07173, NR_DBD_AR, DNA-binding domain of androgen receptor (AR) is
composed of two C4-type zinc fingers. DNA-binding
domain of androgen receptor (AR) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. To regulate gene expression, AR interacts with a
palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp
spacer. It also binds to the direct repeat 5'-TGTTCT-3'
hexamer in some androgen controlled genes. AR is
activated by the androgenic hormones, testosterone or
dihydrotestosterone, which are responsible for primary
and for secondary male characteristics, respectively.
The primary mechanism of action of ARs is by direct
regulation of gene transcription. The binding of
androgen results in a conformational change in the
androgen receptor which causes its transport from the
cytosol into the cell nucleus, and dimerization. The
receptor dimer binds to a hormone response element of AR
regulated genes and modulates their expression. Another
mode of action of androgen receptor is independent of
their interactions with DNA. The receptor interacts
directly with signal transduction proteins in the
cytoplasm, causing rapid changes in cell function, such
as ion transport. Like other members of the nuclear
receptor (NR) superfamily of ligand-activated
transcription factors, AR has a central well conserved
DNA binding domain (DBD), a variable N-terminal domain,
a flexible hinge and a C-terminal ligand binding domain
(LBD).
Length = 82
Score = 51.1 bits (122), Expect = 1e-08
Identities = 19/31 (61%), Positives = 24/31 (77%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKR 235
P++ CL+CGD ASG HYG +C +CK FFKR
Sbjct: 2 PQKTCLICGDEASGCHYGALTCGSCKVFFKR 32
Score = 43.4 bits (102), Expect = 6e-06
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
+Y C + NDC I+K RRK C +CR +KC GM +L ++
Sbjct: 39 KYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKKLG 82
>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 = 51.0 bits (122), Expect = 1e-08
Identities = 19/30 (63%), Positives = 24/30 (80%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTI 237
LCLVCGD ASG+HY +CE CK FF+R++
Sbjct: 3 LCLVCGDRASGYHYNALTCEGCKGFFRRSV 32
Score = 40.6 bits (95), Expect = 7e-05
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 4 YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
Y C CE++ R+ CQ CR +KCL GM E V +
Sbjct: 38 YHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPE 77
>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 = 50.3 bits (120), Expect = 3e-08
Identities = 19/38 (50%), Positives = 21/38 (55%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
N CP C I K R+ CQACR +KCL GM KE
Sbjct: 33 NARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKE 70
Score = 43.4 bits (102), Expect = 6e-06
Identities = 15/31 (48%), Positives = 23/31 (74%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
+C VCGD A+G+H+ +CE CK FF+R ++
Sbjct: 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMK 31
>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 = 49.8 bits (119), Expect = 4e-08
Identities = 22/40 (55%), Positives = 27/40 (67%), Gaps = 3/40 (7%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYRQ 245
C +CGD +SG HYGV +CE CK FF+R+ Q YS RQ
Sbjct: 8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQ 47
Score = 49.1 bits (117), Expect = 7e-08
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
N+ Y+CP +C I++ R CQ CR QKCL GM ++ V+ R+
Sbjct: 39 NVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSK 85
>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 = 49.1 bits (117), Expect = 5e-08
Identities = 21/44 (47%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYRQTGAC 249
C VCGD +SG HYGV +C+ C FFKR+I+ +Y+ G+C
Sbjct: 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSC 44
Score = 47.2 bits (112), Expect = 2e-07
Identities = 21/42 (50%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 1 NIEYTCPASN-DCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
N+ YTC A N C ++K RR CQACR +KCL M K+ V+
Sbjct: 32 NLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 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 = 49.6 bits (118), Expect = 5e-08
Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYRQTGAC 249
P LC VCGD +SG HYG+ +C C FFKR+++ +Y TG C
Sbjct: 5 PGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMC 52
Score = 42.6 bits (100), Expect = 1e-05
Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 4 YTCPA-SNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
Y C A + C ++K R CQACR +KCL+ GM K+ V+ +R
Sbjct: 43 YRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNER 84
>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 = 47.6 bits (113), Expect = 1e-07
Identities = 20/35 (57%), Positives = 24/35 (68%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
CL+CGD ASG HYGV +C +CK FFKR + Y
Sbjct: 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNY 35
Score = 46.1 bits (109), Expect = 5e-07
Identities = 19/39 (48%), Positives = 23/39 (58%)
Query: 4 YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
Y C NDC I+K RRK C ACR +KC + GM +L
Sbjct: 35 YLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARKL 73
>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 = 48.0 bits (114), Expect = 2e-07
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 4 YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
+TCP + DC I K R+ CQACR ++C+ GM+KE + D
Sbjct: 43 FTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82
Score = 47.6 bits (113), Expect = 4e-07
Identities = 17/32 (53%), Positives = 25/32 (78%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
R+C VCGD A+GFH+ +CE CK FF+R+++
Sbjct: 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMK 38
>gnl|CDD|132754 cd07069, NR_LBD_Lrh-1, The ligand binding domain of the liver
receptor homolog-1, a member of nuclear receptor
superfamily,. The ligand binding domain (LBD) of the
liver receptor homolog-1 (LRH-1): LRH-1 belongs to
nuclear hormone receptor superfamily, and is expressed
mainly in the liver, intestine, exocrine pancreas, and
ovary. Most nuclear receptors function as homodimer or
heterodimers. However, LRH-1 binds DNA as a monomer, and
is a regulator of bile-acid homeostasis,
steroidogenesis, reverse cholesterol transport and the
initial stages of embryonic development. Recently,
phospholipids have been identified as potential ligand
for LRH-1 and steroidogenic factor-1 (SF-1). Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, LRH-1 has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 241
Score = 50.4 bits (120), Expect = 3e-07
Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 10/90 (11%)
Query: 81 LLLCEPEMLTVRS------ETPQSDPT----LQTINSLSDLYDRELVCIIGWAKQIPGFT 130
LL CEP+ V++ + Q++ + L T + + D+ L I+ WA+ F
Sbjct: 8 LLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFR 67
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
+L ++DQM+LLQ+ W+E+L L YR + H
Sbjct: 68 ELKVDDQMKLLQNCWSELLILDHIYRQVVH 97
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
composed of two C4-type zinc fingers. DNA-binding
domain of Tailless (TLX) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which co-ordinates a single zinc atom. TLX
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. TLX is an orphan receptor that is expressed
by neural stem/progenitor cells in the adult brain of
the subventricular zone (SVZ) and the dentate gyrus
(DG). It plays a key role in neural development by
promoting cell cycle progression and preventing
apoptosis in the developing brain. Like other members of
the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX has a
central well conserved DNA-binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 92
Score = 47.5 bits (113), Expect = 3e-07
Identities = 17/30 (56%), Positives = 23/30 (76%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C VCGD +SG HYG+ +C+ C FFKR+I+
Sbjct: 9 CKVCGDRSSGKHYGIYACDGCSGFFKRSIR 38
Score = 43.6 bits (103), Expect = 6e-06
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 1 NIEYTCPASN--DCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
N +Y C + C ++K R C+ACR +KC GM K+ V+ +R
Sbjct: 40 NRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHER 85
>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 = 49.8 bits (119), Expect = 5e-07
Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLP 159
I+++ +L R L + WA+ IP F DL + DQ+ LL+ +W+E+ L A +P
Sbjct: 32 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMP 86
>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 = 48.4 bits (116), Expect = 9e-07
Identities = 18/40 (45%), Positives = 25/40 (62%)
Query: 120 IGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLP 159
+ WAK IP F+ L DQ+ LL+ +W+E+ L A SLP
Sbjct: 43 VKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLP 82
>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 = 45.1 bits (107), Expect = 1e-06
Identities = 16/30 (53%), Positives = 21/30 (70%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
C VCGD + G HYGV C+ C FFKR+++
Sbjct: 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVR 30
Score = 43.2 bits (102), Expect = 6e-06
Identities = 20/45 (44%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 1 NIEYTCPASN-DCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
I YTC A N +C ++K RR C CR QKC GM + V+ +R
Sbjct: 32 GIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEER 76
>gnl|CDD|132742 cd06944, NR_LBD_Ftz-F1_like, The ligand binding domain of FTZ-F1
like nuclear receptors. The ligand binding domain of
FTZ-F1 like nuclear receptors: This nuclear receptor
family includes at least three subgroups of receptors
that function in embryo development and differentiation,
and other processes. FTZ-F1 interacts with the
cis-acting DNA motif of ftz gene, which required at
several stages of development. Particularly, FTZ-F1
genes are strongly linked to steroid biosynthesis and
sex-determination; LRH-1 is a regulator of bile-acid
homeostasis, steroidogenesis, reverse cholesterol
transport and the initial stages of embryonic
development. SF-1 is an essential regulator of endocrine
development and function and is considered a master
regulator of reproduction; SF-1 functions cooperatively
with other transcription factors to modulate gene
expression. Phospholipids have been identified as
potential ligand for LRH-1 and steroidogenic factor-1
(SF-1). However, the ligand for FTZ-F1 has not yet been
identified. Most nuclear receptors function as homodimer
or heterodimers. However, LRH-1 and SF-1 bind to DNA as
a monomer. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, receptors in this family have a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 237
Score = 47.7 bits (114), Expect = 2e-06
Identities = 20/48 (41%), Positives = 31/48 (64%)
Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
D+ L I+ WA+ F +L ++DQM+LLQ+ W+E+L L YR + H
Sbjct: 48 DQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHH 95
>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 = 47.5 bits (113), Expect = 2e-06
Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 8/90 (8%)
Query: 93 SETPQSDPTLQTINSLSDLYDRELVC-----IIGWAKQIPGFTDLSLNDQMRLLQSTWAE 147
E +P + + Y L+ I +A++IPGF DL DQ L QS E
Sbjct: 29 REPSPLEPPMSEAEKVQQFYS--LLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLE 86
Query: 148 ILTLTIAYRSLPHCAGKIRFASDLVLDERQ 177
+ L +AYR+ P K+ F + +VL ++Q
Sbjct: 87 LFVLRLAYRTAPE-DTKLTFCNGVVLHKQQ 115
>gnl|CDD|132755 cd07070, NR_LBD_SF-1, The ligand binding domain of nuclear receptor
steroidogenic factor 1, a member of nuclear receptor
superfamily. The ligand binding domain of nuclear
receptor steroidogenic factor 1 (SF-1): SF-1, a member
of the nuclear hormone receptor superfamily, is an
essential regulator of endocrine development and
function and is considered a master regulator of
reproduction. Most nuclear receptors function as
homodimer or heterodimers, however SF-1 binds to its
target genes as a monomer, recognizing the variations of
the DNA sequence motif, T/CCA AGGTCA. SF-1 functions
cooperatively with other transcription factors to
modulate gene expression. Phospholipids have been
determined as potential ligands of SF-1. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, SF-1 has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 237
Score = 46.5 bits (110), Expect = 5e-06
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 81 LLLCEPEMLTVRS--------ETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDL 132
LL EP+ VR+ L + D+ + I+ WA++ F +L
Sbjct: 8 LLQLEPDEDQVRARILGCLQEPQKSRPDQPAPFGLLCRMADQTFISIVDWARRCMVFKEL 67
Query: 133 SLNDQMRLLQSTWAEILTLTIAYRSLPH 160
+ DQM LLQ+ W+E+L YR + H
Sbjct: 68 EVADQMTLLQNCWSELLVFDHIYRQVQH 95
>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 = 45.3 bits (108), Expect = 7e-06
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
++ +AK+IPGF +LS DQ+ LL+ EIL L A + F
Sbjct: 18 VVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATL-YDPEKNSLTFGDGKGNSRDVL 76
Query: 179 RECGFSEIYQQVKH 192
GF E + +
Sbjct: 77 LNGGFGEFIEPLFE 90
>gnl|CDD|132751 cd06953, NR_LBD_DHR4_like, The ligand binding domain of orphan
nuclear receptor Ecdysone-induced receptor DHR4. The
ligand binding domain of Ecdysone-induced receptor DHR4:
Ecdysone-induced orphan receptor DHR4 is a member of the
nuclear receptor family. DHR4 is expressed during the
early Drosophila larval development and is induced by
ecdysone. DHR4 coordinates growth and maturation in
Drosophila by mediating endocrine response to the
attainment of proper body size during larval
development. Mutations in DHR4 result in shorter larval
development which translates into smaller and lighter
flies. Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
DHR4 has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain (LBD). .
Length = 213
Score = 43.5 bits (103), Expect = 4e-05
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 80 ALLLCEPEMLTVRSETPQSDPTLQTINSLSDLY----DRELVCIIGWAKQIPGFTDLSLN 135
LL+ E + + D L L D L I W K++P FT+LS+
Sbjct: 1 QLLVAEDLEPLI-TPMLIEDGATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIK 59
Query: 136 DQMRLLQSTWAEILTLTIAYR 156
D LL + WAE++ L+
Sbjct: 60 DHTHLLTTKWAELILLSTITV 80
>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 = 4e-05
Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
L + L+DL + +IG+AK IPGF DL+ DQ+ LL+S+ E++ L
Sbjct: 36 LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIML 85
>gnl|CDD|132749 cd06951, NR_LBD_Dax1_like, The ligand binding domain of DAX1
protein, a nuclear receptor lacking DNA binding domain.
The ligand binding domain of DAX1-like proteins: This
orphan nuclear receptor family includes DAX1
(dosage-sensitive sex reversal adrenal hypoplasia
congenita critical region on chromosome X gene 1) and
the Small Heterodimer Partner (SHP). Both receptors have
a typical ligand binding domain, but lack the DNA
binding domain, typical to almost all of the nuclear
receptors. They function as a transcriptional
coregulator by directly interacting with other nuclear
receptors. DAX1 and SHP can form heterodimers with each
other, as well as with many other nuclear receptors. In
addition, DAX1 can also form homodimers. DAX1 plays an
important role in the normal development of several
hormone-producing tissues. SHP has shown to regulate a
variety of target genes.
Length = 222
Score = 42.9 bits (101), Expect = 8e-05
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 116 LVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLP 159
L+ I + + +P FT L +DQ+RLL+ +WA +L L +A +P
Sbjct: 32 LLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVP 75
>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 = 39.7 bits (93), Expect = 9e-04
Identities = 16/38 (42%), Positives = 26/38 (68%)
Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR 156
I+ +AKQ+PGF L+ DQ+ LL+++ E++ L A R
Sbjct: 59 IVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARR 96
>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 = 39.3 bits (92), Expect = 0.001
Identities = 16/48 (33%), Positives = 31/48 (64%)
Query: 107 SLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
LS+ + ++ +AK+IPGF DLS +DQ+ L+++ + E+ + I+
Sbjct: 6 QLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRIS 53
>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 = 37.8 bits (88), Expect = 0.005
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 123 AKQIPGFTDLSLNDQMRLLQ 142
AK +PGF +L LNDQ+ LL+
Sbjct: 83 AKSLPGFRNLDLNDQVTLLK 102
>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 = 37.1 bits (86), Expect = 0.006
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLP 159
++ +AK++P FT+L DQ+ LL+ EI++L A R P
Sbjct: 68 VVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDP 108
>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 = 37.0 bits (86), Expect = 0.007
Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 93 SETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLT 152
++ QSD + I ++ L + I+ +AK++PGF LS DQ+ LL++ +E++ L
Sbjct: 32 NDEDQSDMRFRHITEMTIL---TVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLR 88
Query: 153 IAYR 156
+A R
Sbjct: 89 VARR 92
>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 = 35.5 bits (82), Expect = 0.018
Identities = 16/36 (44%), Positives = 26/36 (72%)
Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
++ +AK+IPGF DLS +DQ+ LL++ E+L + A
Sbjct: 28 VVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFA 63
>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 = 34.6 bits (80), Expect = 0.031
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
+ + I+ + K IPGF LS D+ +LL+ + L ++
Sbjct: 12 EMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLS 53
>gnl|CDD|132750 cd06952, NR_LBD_TR2_like, The ligand binding domain of the orphan
nuclear receptors TR4 and TR2. The ligand binding
domain of the TR4 and TR2 (human testicular receptor 4
and 2): TR4 and TR2 are orphan nuclear receptors.
Several isoforms of TR4 and TR2 have been isolated in
various tissues. TR2 is abundantly expressed in the
androgen-sensitive prostate. TR4 transcripts are
expressed in many tissues, including central nervous
system, adrenal gland, spleen, thyroid gland, and
prostate. The expression of TR2 is negatively regulated
by androgen, retinoids, and radiation. The expression of
both mouse TR2 and TR4 is up-regulated by neurocytokine
ciliary neurotrophic factor (CNTF) in mouse. It has
shown that human TR2 binds to a wide spectrum of natural
hormone response elements (HREs) with distinct
affinities suggesting that TR2 may cross-talk with other
gene expression regulation systems. The genes responding
to TR2 or TR4 include genes that are regulated by
retinoic acid receptor, vitamin D receptor, peroxisome
proliferator-activated receptor. TR4/2 binds to HREs as
a dimer. Like other members of the nuclea r receptor
(NR) superfamily of ligand-activated transcription
factors, TR2-like receptors have a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 222
Score = 33.8 bits (78), Expect = 0.070
Identities = 16/41 (39%), Positives = 22/41 (53%)
Query: 114 RELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
R L I WA+ IP F L Q L+++ W E+ TL +A
Sbjct: 32 RLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLA 72
>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 = 33.1 bits (76), Expect = 0.13
Identities = 12/25 (48%), Positives = 20/25 (80%)
Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQS 143
++ +AK+IPGF +L NDQ+ LL++
Sbjct: 64 VVEFAKRIPGFMELCQNDQIVLLKA 88
>gnl|CDD|114220 pfam05484, LRV_FeS, LRV protein FeS4 cluster. This Iron sulphur
cluster is found at the N-terminus of some proteins
containing pfam01816 repeats.
Length = 57
Score = 29.8 bits (67), Expect = 0.21
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 22 CQACRFQKCLRKGMLKEGVRLDRVRGGRQK---YRRNPDL 58
C+ CRF+ L G G R R+ +R NP+L
Sbjct: 14 CRDCRFRDLLESGRCTPGDSCVADRSARRIDRFFRLNPEL 53
>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 = 32.0 bits (73), Expect = 0.28
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEI 148
P + +DL + II +AK +P F L + DQ+ LL+ EI
Sbjct: 32 PPFSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEI 80
>gnl|CDD|132763 cd07349, NR_LBD_SHP, The ligand binding domain of DAX1 protein, a
nuclear receptor lacking DNA binding domain. The ligand
binding domain of the Small Heterodimer Partner (SHP):
SHP is a member of the nuclear receptor superfamily. SHP
has a ligand binding domain, but lacks the DNA binding
domain, typical to almost all of the nuclear receptors.
It functions as a transcriptional coregulator by
directly interacting with other nuclear receptors
through its AF-2 motif. The closest relative of SHP is
DAX1 and they can form heterodimer. SHP is an orphan
receptor, lacking an identified ligand.
Length = 222
Score = 31.7 bits (72), Expect = 0.31
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 116 LVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
LV + + + +P F L DQ+ LLQ+ W + L +A
Sbjct: 32 LVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLA 70
>gnl|CDD|132764 cd07350, NR_LBD_Dax1, The ligand binding domain of DAX1 protein, a
nuclear receptor lacking DNA binding domain. The ligand
binding domain of the DAX1 protein: DAX1
(dosage-sensitive sex reversal adrenal hypoplasia
congenita critical region on chromosome X gene 1) is a
nuclear receptor with a typical ligand binding domain,
but lacks the DNA binding domain. DAX1 plays an
important role in the normal development of several
hormone-producing tissues. Duplications of the region of
the X chromosome containing DAX1 cause dosage sensitive
sex reversal. DAX1 acts as a global repressor of many
nuclear receptors, including SF-1, LRH-1, ERR, ER, AR
and PR. DAX1 can form homodimer and heterodimerizes with
its alternatively spliced isoform DAX1A and other
nuclear receptors such as SHP, ERalpha and SF-1.
Length = 232
Score = 31.7 bits (72), Expect = 0.39
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 124 KQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
K +P F +L L+DQ+ L++S WA +L L +A
Sbjct: 40 KGVPCFQELPLDDQLVLVRSCWAPLLVLGLA 70
>gnl|CDD|176456 cd01702, PolY_Pol_eta, DNA Polymerase eta. Pol eta, also called
Rad30A, is a translesion synthesis (TLS) polymerase.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Unlike other
Y-family members, Pol eta can efficiently and accurately
replicate DNA past UV-induced lesions. Its activity is
initiated by two simultaneous interactions: the PIP box
in pol eta interacting with PCNA, and the UBZ
(ubiquitin-binding zinc finger) in pol eta interacting
with monoubiquitin attached to PCNA. Pol eta is more
efficient in copying damaged DNA than undamaged DNA and
seems to recognize when a lesion has been passed,
facilitating a lesion-dependent dissociation from the
DNA.
Length = 359
Score = 31.9 bits (73), Expect = 0.40
Identities = 23/96 (23%), Positives = 30/96 (31%), Gaps = 12/96 (12%)
Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLV 172
R L +G +K PG T LS D W +L + R R LV
Sbjct: 246 PRPLPKSMGSSKNFPGKTALSTEDVQH-----WLLVLASELNSRLEDDRYENNRRPKTLV 300
Query: 173 L-------DERQARECGFSEIYQQVKHSGSLDGIKE 201
L R++R C Q + IK
Sbjct: 301 LSLRQRGDGVRRSRSCALPRYDAQKIVKDAFKLIKA 336
>gnl|CDD|220597 pfam10139, Virul_Fac, Putative bacterial virulence factor. Members
of this family of prokaryotic proteins include various
putative virulence factor effector proteins. Their exact
function is, as yet, unknown.
Length = 852
Score = 29.7 bits (67), Expect = 2.4
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 132 LSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDL 171
LS++D+ RL W EI LT AYR L H ++ A +L
Sbjct: 206 LSIDDRARLFSLLWGEIPELTDAYRHLAHALQRLGHAEEL 245
>gnl|CDD|183499 PRK12396, PRK12396, 5-methylribose kinase; Reviewed.
Length = 409
Score = 28.6 bits (64), Expect = 4.5
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 12/72 (16%)
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY-QQVKHSGSL 196
M LQST E++ L K A D+ + E A+E GF+EIY Q V +
Sbjct: 291 MDWLQSTMVEVIDLFKK---------KFLDAWDIHVTEIMAKEEGFNEIYLQSVLEDTA- 340
Query: 197 DGIKEEELPRRL 208
+ EL RR+
Sbjct: 341 -AVTGLELIRRI 351
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
0.322 0.137 0.417
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: 15,776,473
Number of extensions: 1490175
Number of successful extensions: 1225
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1214
Number of HSP's successfully gapped: 127
Length of query: 312
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 215
Effective length of database: 6,635,264
Effective search space: 1426581760
Effective search space used: 1426581760
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 (21.9 bits)
S2: 59 (26.6 bits)