RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16825
(183 letters)
>gnl|CDD|143544 cd07170, NR_DBD_ERR, DNA-binding domain of estrogen related
receptors (ERR) is composed of two C4-type zinc fingers.
DNA-binding domain of estrogen related receptors (ERRs)
is composed of two C4-type zinc fingers. Each zinc
finger contains a group of four Cys residues which
coordinates a single zinc atom. ERR interacts with the
palindromic inverted repeat, 5'GGTCAnnnTGACC-3',
upstream of the target gene and modulates the rate of
transcriptional initiation. The estrogen
receptor-related receptors (ERRs) are transcriptional
regulators, which are closely related to the estrogen
receptor (ER) family. Although ERRs lack the ability to
bind to estrogen and are so-called orphan receptors,
they share target genes, co-regulators and promoters
with the estrogen receptor (ER) family. By targeting the
same set of genes, ERRs seem to interfere with the
classic ER-mediated estrogen response in various ways.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
ERR has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a non-conserved
hinge and a C-terminal ligand binding domain (LBD).
Length = 97
Score = 185 bits (470), Expect = 2e-61
Identities = 78/93 (83%), Positives = 87/93 (93%)
Query: 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQAC
Sbjct: 3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQAC 62
Query: 69 RFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
RF KCL+ GMLKEGVRLDRVRGGRQKY+R D
Sbjct: 63 RFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDA 95
>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 = 139 bits (353), Expect = 7e-44
Identities = 59/75 (78%), Positives = 72/75 (96%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
CLVCGD+ASG+HYGVASCEACKAFFKRTIQGN+ Y+CP++++CE++K+RRK+CQACR QK
Sbjct: 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQK 60
Query: 73 CLRKGMLKEGVRLDR 87
CL+ GMLKEGVRLDR
Sbjct: 61 CLKVGMLKEGVRLDR 75
>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 = 132 bits (335), Expect = 5e-41
Identities = 45/72 (62%), Positives = 55/72 (76%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C VCGD ASG+HYGV +CE CK FF+R+++ N+EYTCPA +C I+KR R CQACR +K
Sbjct: 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKK 60
Query: 73 CLRKGMLKEGVR 84
CL GM KE VR
Sbjct: 61 CLAVGMRKEAVR 72
>gnl|CDD|201004 pfam00105, zf-C4, Zinc finger, C4 type (two domains). In nearly
all cases, this is the DNA binding domain of a nuclear
hormone receptor. The alignment contains two Zinc
finger domains that are too dissimilar to be aligned
with each other.
Length = 70
Score = 126 bits (319), Expect = 1e-38
Identities = 44/70 (62%), Positives = 51/70 (72%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
LC VCGD ASG+HYGV +CE CK FF+R+IQ NI YTCP + DC I+KR R CQ CR
Sbjct: 1 ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRL 60
Query: 71 QKCLRKGMLK 80
+KCL GM K
Sbjct: 61 KKCLEVGMSK 70
>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 = 124 bits (313), Expect = 1e-37
Identities = 48/84 (57%), Positives = 60/84 (71%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C VCGD SG+HYG+ +CE+CK FFKRT+Q YTC + +C+I+K +RK C CRFQK
Sbjct: 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQK 60
Query: 73 CLRKGMLKEGVRLDRVRGGRQKYR 96
CL GM E VR DR+RGGR K+
Sbjct: 61 CLSVGMKLEAVRADRMRGGRNKFG 84
>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 = 119 bits (299), Expect = 1e-35
Identities = 48/81 (59%), Positives = 59/81 (72%)
Query: 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
C VC D ASG+HYGV SCE CKAFFKR+IQG+ +Y CPA+N C I+K RRK+CQAC
Sbjct: 2 DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQAC 61
Query: 69 RFQKCLRKGMLKEGVRLDRVR 89
R +KC GM+K G+R +R
Sbjct: 62 RLRKCYEVGMMKGGIRRERRG 82
>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 = 114 bits (288), Expect = 8e-34
Identities = 41/83 (49%), Positives = 55/83 (66%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
C+VCGD A+G+HY +CE CK FF+RT+Q + Y+C CEI+K R CQ CRF+
Sbjct: 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFK 60
Query: 72 KCLRKGMLKEGVRLDRVRGGRQK 94
KC+ GM K+ V DR RG ++K
Sbjct: 61 KCIAVGMAKDLVLDDRKRGAKRK 83
>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors.
Length = 70
Score = 111 bits (280), Expect = 1e-32
Identities = 42/70 (60%), Positives = 49/70 (70%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
LC VCGD ASGFH+GV SC ACKAFF+RT+ +Y C N+C INKR R C+ACR +
Sbjct: 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLK 60
Query: 72 KCLRKGMLKE 81
KCL GM E
Sbjct: 61 KCLGVGMDPE 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 = 111 bits (280), Expect = 1e-32
Identities = 46/90 (51%), Positives = 59/90 (65%)
Query: 5 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKA 64
+E+ +LC +C D A+G HYG+ +CE CK FFKRT+Q YTC CEI K +R
Sbjct: 1 DEDESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNR 60
Query: 65 CQACRFQKCLRKGMLKEGVRLDRVRGGRQK 94
CQ CRF+KC+RKGM+ VR DR+ GGR
Sbjct: 61 CQYCRFRKCIRKGMMLAAVREDRMPGGRNS 90
>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 = 106 bits (266), Expect = 1e-30
Identities = 38/76 (50%), Positives = 51/76 (67%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C VCGD A+G HYGV SC CK FF+R+++ N YTC +C ++K +R AC+ CRF+K
Sbjct: 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKK 60
Query: 73 CLRKGMLKEGVRLDRV 88
CL GM E V+ +R
Sbjct: 61 CLEVGMDPEAVQNERD 76
>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 = 104 bits (261), Expect = 7e-30
Identities = 45/73 (61%), Positives = 55/73 (75%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
LC VCGD A+ HYGV +CE CK FFKRT+Q N +Y C A+ +C ++KRRR CQ CRFQ
Sbjct: 2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQ 61
Query: 72 KCLRKGMLKEGVR 84
KCL+ GM+KE VR
Sbjct: 62 KCLQVGMVKEVVR 74
>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 = 101 bits (253), Expect = 1e-28
Identities = 43/77 (55%), Positives = 52/77 (67%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
+ C VC D +SG+HYGV++CE CK FF+R+IQ N+ YTC +C INK R CQ CR
Sbjct: 5 KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRL 64
Query: 71 QKCLRKGMLKEGVRLDR 87
QKC GM KE VR DR
Sbjct: 65 QKCFEVGMSKESVRNDR 81
>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 = 100 bits (250), Expect = 4e-28
Identities = 45/80 (56%), Positives = 53/80 (66%)
Query: 8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
P LC+VCGD ASG HYG SCE CK FFKR+I+ N+ Y+C S DC INK R CQ
Sbjct: 1 QPVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQY 60
Query: 68 CRFQKCLRKGMLKEGVRLDR 87
CR QKCL GM + V+ +R
Sbjct: 61 CRLQKCLAMGMKSDSVQCER 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 = 99.2 bits (247), Expect = 1e-27
Identities = 40/84 (47%), Positives = 55/84 (65%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
R CL+CGD A+G HYG+ SCE CK FFKR+I Y C +C +++++R CQ CR
Sbjct: 7 RTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRL 66
Query: 71 QKCLRKGMLKEGVRLDRVRGGRQK 94
KCL+ GM ++ +R D + GGR K
Sbjct: 67 LKCLQMGMNRKAIREDGMPGGRNK 90
>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 = 98.2 bits (245), Expect = 1e-27
Identities = 36/69 (52%), Positives = 48/69 (69%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C VCGD A+G+H+ +CE CK FF+R+++ +TCP + DCEI K R+ CQACR +K
Sbjct: 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKK 60
Query: 73 CLRKGMLKE 81
CL GM KE
Sbjct: 61 CLDIGMKKE 69
>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 = 96.1 bits (239), Expect = 1e-26
Identities = 43/76 (56%), Positives = 56/76 (73%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
+C +CGD ASG HYGV SCE CK FFKRT++ ++ YTC + DC I+KR+R CQ CR+Q
Sbjct: 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 61
Query: 72 KCLRKGMLKEGVRLDR 87
KCL GM +E V+ +R
Sbjct: 62 KCLAMGMKREAVQEER 77
>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 = 95.3 bits (237), Expect = 3e-26
Identities = 35/73 (47%), Positives = 46/73 (63%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C VCG +SGFH+G +CE CK FF+RT + Y CP +C I R AC++CRF++
Sbjct: 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRR 60
Query: 73 CLRKGMLKEGVRL 85
CL GM K G R+
Sbjct: 61 CLAVGMSKTGSRI 73
>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 = 93.8 bits (233), Expect = 1e-25
Identities = 42/73 (57%), Positives = 48/73 (65%), Gaps = 1/73 (1%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQACRFQ 71
C VCGD ASGFHYGV SCE CK FF+RTIQ N+ Y C C I ++ R CQ CRF+
Sbjct: 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFK 60
Query: 72 KCLRKGMLKEGVR 84
KCL GM + VR
Sbjct: 61 KCLSVGMSRNAVR 73
>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 = 94.2 bits (234), Expect = 1e-25
Identities = 42/78 (53%), Positives = 52/78 (66%), Gaps = 1/78 (1%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRF 70
LC VCGD ASGFHYGV +CE CK FF+R+IQ I+Y C + C I + R CQ CRF
Sbjct: 5 LCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRF 64
Query: 71 QKCLRKGMLKEGVRLDRV 88
+KCL GM ++ VR R+
Sbjct: 65 KKCLAVGMSRDAVRFGRI 82
>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 = 93.4 bits (232), Expect = 2e-25
Identities = 40/77 (51%), Positives = 51/77 (66%)
Query: 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
P+++CLVC D ASG HYGV +C +CK FFKR ++G Y C NDC I+K RRK C AC
Sbjct: 1 PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 60
Query: 69 RFQKCLRKGMLKEGVRL 85
R +KCL+ GM +
Sbjct: 61 RLRKCLQAGMNLGARKT 77
>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 = 93.0 bits (231), Expect = 2e-25
Identities = 44/77 (57%), Positives = 51/77 (66%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C VCGD ASG+HYGV SCE CK FF+R+IQ IEY C CEI + R CQ CRF+K
Sbjct: 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKK 60
Query: 73 CLRKGMLKEGVRLDRVR 89
CL GM K+ VR R+
Sbjct: 61 CLAAGMSKDSVRYGRIP 77
>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 = 92.9 bits (231), Expect = 3e-25
Identities = 38/75 (50%), Positives = 52/75 (69%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C VCGD ASG HYGV SC+ C+ FFKR+I+ N+ Y C + C ++ RR CQACRF+K
Sbjct: 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKK 60
Query: 73 CLRKGMLKEGVRLDR 87
CL+ M ++ V+ +R
Sbjct: 61 CLQVNMNRDAVQHER 75
>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 = 92.5 bits (230), Expect = 3e-25
Identities = 42/78 (53%), Positives = 51/78 (65%), Gaps = 3/78 (3%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRF 70
C VCGD ASGFHYGV +CE CK FF+RTI+ + Y C S C+I+K+ R CQ CRF
Sbjct: 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRF 58
Query: 71 QKCLRKGMLKEGVRLDRV 88
QKCL GM +R R+
Sbjct: 59 QKCLNVGMSHNAIRFGRM 76
>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 = 89.1 bits (221), Expect = 1e-23
Identities = 37/78 (47%), Positives = 51/78 (65%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C +CGD +SG HYGV +CE CK FF+R+ Q N+ Y+CP +C I++ R CQ CR QK
Sbjct: 8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQK 67
Query: 73 CLRKGMLKEGVRLDRVRG 90
CL GM ++ V+ R+
Sbjct: 68 CLALGMSRDAVKFGRMSK 85
>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 = 88.0 bits (218), Expect = 2e-23
Identities = 36/72 (50%), Positives = 52/72 (72%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
C+VCGD +SG HYG +CE CK+FFKR+++ N+ YTC + +C I++ R CQ CR +K
Sbjct: 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKK 60
Query: 73 CLRKGMLKEGVR 84
CL+ GM +E V+
Sbjct: 61 CLKVGMRREAVQ 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 = 86.9 bits (215), Expect = 7e-23
Identities = 38/81 (46%), Positives = 52/81 (64%)
Query: 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
P++ CL+CGD ASG HYG +C +CK FFKR +G +Y C + NDC I+K RRK C +C
Sbjct: 2 PQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSC 61
Query: 69 RFQKCLRKGMLKEGVRLDRVR 89
R +KC GM +L ++
Sbjct: 62 RLRKCFEAGMTLGARKLKKLG 82
>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 = 86.0 bits (213), Expect = 1e-22
Identities = 36/78 (46%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNI--EYTCPASNDCEINKRRRKACQACRF 70
C VCG+ A+GFH+G CEACK FF R+ CP C I+K+ R CQACR+
Sbjct: 3 CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRY 62
Query: 71 QKCLRKGMLKEGVRLDRV 88
+KCL GM G R R
Sbjct: 63 RKCLNVGMSLGGPRYGRR 80
>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 = 85.4 bits (211), Expect = 2e-22
Identities = 39/73 (53%), Positives = 47/73 (64%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
CL+CGD ASG HYGV +C +CK FFKR +G Y C NDC I+K RRK C ACR +K
Sbjct: 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRK 60
Query: 73 CLRKGMLKEGVRL 85
C + GM +L
Sbjct: 61 CYQAGMTLGARKL 73
>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 = 84.4 bits (209), Expect = 6e-22
Identities = 34/71 (47%), Positives = 45/71 (63%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
++C VCGD A G+++ +CE+CKAFF+R N E+ CP + CEIN R+ CQ CR
Sbjct: 1 KICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRL 60
Query: 71 QKCLRKGMLKE 81
KC GM KE
Sbjct: 61 DKCFAIGMKKE 71
>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 = 83.6 bits (207), Expect = 8e-22
Identities = 35/70 (50%), Positives = 44/70 (62%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
C+VCGD ASGFHYGV SCE CK FF+R++ Y C N CE++ R+ CQ CR +
Sbjct: 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLR 60
Query: 72 KCLRKGMLKE 81
KC GM +
Sbjct: 61 KCKAAGMRPD 70
>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 = 84.6 bits (209), Expect = 1e-21
Identities = 36/76 (47%), Positives = 52/76 (68%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
R+C VCGD A+GFH+ +CE CK FF+R+++ +TCP + DC I K R+ CQACR
Sbjct: 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 66
Query: 71 QKCLRKGMLKEGVRLD 86
++C+ GM+KE + D
Sbjct: 67 KRCVDIGMMKEFILTD 82
>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 = 83.4 bits (206), Expect = 1e-21
Identities = 39/73 (53%), Positives = 50/73 (68%), Gaps = 1/73 (1%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASN-DCEINKRRRKACQACRFQ 71
C VCGD +SG HYGV +C+ C FFKR+I+ N+ YTC A N C ++K RR CQACR +
Sbjct: 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLK 60
Query: 72 KCLRKGMLKEGVR 84
KCL M K+ V+
Sbjct: 61 KCLEVSMNKDAVQ 73
>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 = 83.4 bits (206), Expect = 1e-21
Identities = 34/70 (48%), Positives = 44/70 (62%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
+C VCGD A+G+H+ +CE CK FF+R ++ N CP C I K R+ CQACR +
Sbjct: 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLR 60
Query: 72 KCLRKGMLKE 81
KCL GM KE
Sbjct: 61 KCLSIGMKKE 70
>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 = 81.5 bits (201), Expect = 1e-20
Identities = 33/72 (45%), Positives = 45/72 (62%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
+C VCGD ASGFHY V SCE CK FF+R++ +Y C C+++ R+ CQ CR +
Sbjct: 20 VCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLR 79
Query: 72 KCLRKGMLKEGV 83
KC GM ++ V
Sbjct: 80 KCREAGMREQCV 91
>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 = 80.7 bits (199), Expect = 2e-20
Identities = 35/75 (46%), Positives = 46/75 (61%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
LCLVCGD ASG+HY +CE CK FF+R++ + Y C CE++ R+ CQ CR +
Sbjct: 3 LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLK 62
Query: 72 KCLRKGMLKEGVRLD 86
KCL GM E V +
Sbjct: 63 KCLSVGMRPECVVPE 77
>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 = 80.6 bits (199), Expect = 2e-20
Identities = 34/77 (44%), Positives = 49/77 (63%), Gaps = 2/77 (2%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASN--DCEINKRRRKACQACRF 70
C VCGD +SG HYG+ +C+ C FFKR+I+ N +Y C + C ++K R C+ACR
Sbjct: 9 CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRL 68
Query: 71 QKCLRKGMLKEGVRLDR 87
+KC GM K+ V+ +R
Sbjct: 69 KKCFEVGMNKDAVQHER 85
>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 = 80.0 bits (197), Expect = 4e-20
Identities = 37/80 (46%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA-SNDCEINKRRRKACQA 67
P LC VCGD +SG HYG+ +C C FFKR+++ + Y C A + C ++K R CQA
Sbjct: 5 PGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQA 64
Query: 68 CRFQKCLRKGMLKEGVRLDR 87
CR +KCL+ GM K+ V+ +R
Sbjct: 65 CRLKKCLQAGMNKDAVQNER 84
>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 = 78.9 bits (194), Expect = 7e-20
Identities = 35/70 (50%), Positives = 45/70 (64%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
LC+VCGD ASG+HY +CE CK FF+R+I N Y C +CE++ R+ CQ CR +
Sbjct: 3 LCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLR 62
Query: 72 KCLRKGMLKE 81
KC GML E
Sbjct: 63 KCKEMGMLAE 72
>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 = 78.7 bits (194), Expect = 1e-19
Identities = 36/76 (47%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASN-DCEINKRRRKACQACRFQ 71
C VCGD + G HYGV C+ C FFKR+++ I YTC A N +C ++K RR C CR Q
Sbjct: 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQ 60
Query: 72 KCLRKGMLKEGVRLDR 87
KC GM + V+ +R
Sbjct: 61 KCFAVGMNRAAVQEER 76
>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 = 70.1 bits (172), Expect = 4e-15
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVKL-DEFSSLKKFRNSILSSLGDCIYVLR 183
C Q++ RL+ + + KEEY LKAL LANSD ++ ++++ R+++L +L D
Sbjct: 113 CLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRH 171
>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 = 61.9 bits (151), Expect = 4e-12
Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR 183
Q++ R + + +EEY LKA++LANSDV+ L++ ++++ R++IL +L D
Sbjct: 113 LLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRH 171
>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 = 40.7 bits (96), Expect = 8e-05
Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGD 177
+++ +L + + +EY LKA+VL N D+ L +++ + +L +
Sbjct: 89 ELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQE 139
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 33.9 bits (78), Expect = 0.020
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSS-----LKKFRNSILSSL 175
+++ L + + EEY LKA+VL N V S ++K + ++L
Sbjct: 84 ELVKPLRELKLDDEEYALLKAIVLFNPAVP--GLSEEGKEIVEKLQEKYANAL 134
>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 = 32.7 bits (75), Expect = 0.049
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 138 VSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCI 179
+ EEY LKA+VL + D K L++ +++ + +L +L D +
Sbjct: 100 LDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYL 143
>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 = 32.4 bits (74), Expect = 0.067
Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSS-----LKKFRNSILSSLGDCI 179
+++ L+ + ++ EE LKAL+L N K S ++K + I ++L +
Sbjct: 90 LFELVQPLKELKLTDEELAALKALLLFNPAGK--RLSGEILEVVEKLQEVIANALHNYY 146
>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 = 28.6 bits (64), Expect = 0.38
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 65 CQACRFQKCLRKGMLKEGVRLDRVRGGRQK---YRRNPDL 101
C+ CRF+ L G G R R+ +R NP+L
Sbjct: 14 CRDCRFRDLLESGRCTPGDSCVADRSARRIDRFFRLNPEL 53
>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 = 28.5 bits (64), Expect = 2.0
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 133 LEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
L + + EY LKA+V + D K L + +K+ R + SL D I
Sbjct: 125 LRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYI 172
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 28.4 bits (63), Expect = 2.2
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 20/91 (21%)
Query: 59 KRRRKACQACRFQKCLRKGMLKEGVR--LDRVRGGRQKY--------RRNPDLLSQQWPP 108
+R R A A + L +G E ++ D++R Q Y R NP L++ P
Sbjct: 503 RRLRAAQDALK--DALERGASDEEIKQLTDKLRAAMQTYMRQLAQQLRNNPQQLARPLDP 560
Query: 109 NKSIPSLEDLERNTEISCTQVIDRLEHVAVS 139
N + +DL+ ++D++E++A S
Sbjct: 561 NTKVLRQQDLQN--------MMDQIENLARS 583
>gnl|CDD|185145 PRK15223, PRK15223, pilin outer membrane usher protein SafC;
Provisional.
Length = 836
Score = 28.4 bits (63), Expect = 2.4
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 80 KEGVRLDRVRGGRQKYRRNPDLLSQQWPPN 109
+G RL R Q R +LSQ W +
Sbjct: 474 HDGNRLWSWRENLQPSSRTTLMLSQSWGRH 503
>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 = 28.1 bits (63), Expect = 2.6
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 130 IDRLEHVAVSKEEYYFLKALVLANSD-VKLDEFSSLKKFRNSILSSLGD 177
++ ++ + V EY +LKA+VL + D + ++K + L L D
Sbjct: 119 VNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRD 167
>gnl|CDD|218165 pfam04597, Ribophorin_I, Ribophorin I. Ribophorin I is an
essential subunit of oligosaccharyltransferase (OST),
which is also known as
Dolichyl-diphosphooligosaccharide--protein
glycosyltransferase, (EC:2.4.1.119). OST catalyzes the
transfer of an oligosaccharide from dolichol
pyrophosphate to selected asparagine residues of nascent
polypeptides as they are translocated into the lumen of
the rough endoplasmic reticulum. Ribophorin I and OST48
are though to be responsible for OST catalytic activity.
Both yeast and mammalian proteins are glycosylated but
the sites are not conserved. Glycosylation may
contribute towards general solubility but is unlikely to
be involved in a specific biochemical function Most
family members are predicted to have a transmembrane
helix at the C terminus of this region.
Length = 429
Score = 28.0 bits (63), Expect = 3.3
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 16/56 (28%)
Query: 109 NKSIPSLEDLERNTEISCTQVIDRLEHVA-VSKEEYYFLKALVLANSDVKLD-EFS 162
NK + ++ +LER+ E+S H ++ EEYY L N+ KL FS
Sbjct: 189 NKPLITVTNLERDIEVS---------HWGNIAVEEYYELT-----NNGAKLKGGFS 230
>gnl|CDD|132742 cd06944, NR_LBD_Ftz-F1_like, The ligand binding domain of FTZ-F1
like nuclear receptors. The ligand binding domain of
FTZ-F1 like nuclear receptors: This nuclear receptor
family includes at least three subgroups of receptors
that function in embryo development and differentiation,
and other processes. FTZ-F1 interacts with the
cis-acting DNA motif of ftz gene, which required at
several stages of development. Particularly, FTZ-F1
genes are strongly linked to steroid biosynthesis and
sex-determination; LRH-1 is a regulator of bile-acid
homeostasis, steroidogenesis, reverse cholesterol
transport and the initial stages of embryonic
development. SF-1 is an essential regulator of endocrine
development and function and is considered a master
regulator of reproduction; SF-1 functions cooperatively
with other transcription factors to modulate gene
expression. Phospholipids have been identified as
potential ligand for LRH-1 and steroidogenic factor-1
(SF-1). However, the ligand for FTZ-F1 has not yet been
identified. Most nuclear receptors function as homodimer
or heterodimers. However, LRH-1 and SF-1 bind to DNA as
a monomer. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, receptors in this family have a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 237
Score = 27.6 bits (62), Expect = 3.7
Identities = 16/69 (23%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 111 SIPSLEDLERNTEISCTQ-VIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFR 168
++ S L ++ + Q ++++L + ++E+ LK L+L N DVK L+ ++ +
Sbjct: 113 TLASQAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQ 172
Query: 169 NSILSSLGD 177
+ ++L D
Sbjct: 173 EQVNAALLD 181
>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 = 27.4 bits (61), Expect = 3.7
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 138 VSKEEYYFLKALVLANSDVK------LDEFSSLKKFRNSILSSLGDCI 179
+ +EEY LKA++L NS V L+ +++ + I +L
Sbjct: 131 LQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHAC 178
>gnl|CDD|132751 cd06953, NR_LBD_DHR4_like, The ligand binding domain of orphan
nuclear receptor Ecdysone-induced receptor DHR4. The
ligand binding domain of Ecdysone-induced receptor DHR4:
Ecdysone-induced orphan receptor DHR4 is a member of the
nuclear receptor family. DHR4 is expressed during the
early Drosophila larval development and is induced by
ecdysone. DHR4 coordinates growth and maturation in
Drosophila by mediating endocrine response to the
attainment of proper body size during larval
development. Mutations in DHR4 result in shorter larval
development which translates into smaller and lighter
flies. Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
DHR4 has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain (LBD). .
Length = 213
Score = 27.3 bits (61), Expect = 4.3
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 109 NKSIPSLEDLERNTEISCTQVIDRL-------EHVAVSKEEYYFLKALVLANSDVKLDEF 161
+K +PS ++LER + +V++RL + VS EEY LK + N D+
Sbjct: 94 SKYLPSEDELERFGD-EGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTN 152
Query: 162 SS 163
+S
Sbjct: 153 AS 154
>gnl|CDD|177918 PLN02279, PLN02279, ent-kaur-16-ene synthase.
Length = 784
Score = 27.5 bits (61), Expect = 4.6
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 101 LLSQQWPPNKSIPSLEDLERNTEIS 125
L QW NKS P+L++ N +S
Sbjct: 607 LTEAQWSSNKSTPTLDEYMTNAYVS 631
>gnl|CDD|184100 PRK13509, PRK13509, transcriptional repressor UlaR; Provisional.
Length = 251
Score = 27.3 bits (61), Expect = 4.9
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 13/56 (23%)
Query: 115 LEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDV-KLDEFSSLKKFRN 169
LE L + ++ +VI+RL +S A D+ KLDE LKK RN
Sbjct: 11 LELLAQLGFVTVEKVIERLG---IS---------PATARRDINKLDESGKLKKVRN 54
>gnl|CDD|205059 pfam12760, Zn_Tnp_IS1595, Transposase zinc-ribbon domain. This
zinc binding domain is found in a range of transposase
proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is
likely a zinc-binding beta ribbon domain that could
bind the DNA.
Length = 46
Score = 24.9 bits (55), Expect = 5.5
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 31 EACKAFFKRTIQGNIEYTCPASND---CEINKRRRKACQACRFQ 71
EAC+A+ ++ N + CP I +R C+ACR Q
Sbjct: 4 EACRAYLEQLRWPN-GFVCPHCGSEEAYRITRRGLYQCKACRHQ 46
>gnl|CDD|238553 cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit,
nucleotide-binding domain. The F-ATPase is found in
bacterial plasma membranes, mitochondrial inner
membranes and in chloroplast thylakoid membranes. It has
also been found in the archaea Methanosarcina barkeri.
It uses a proton gradient to drive ATP synthesis and
hydrolyzes ATP to build the proton gradient. The
extrinisic membrane domain, F1, is composed of alpha,
beta, gamma, delta and epsilon subunits with a
stoichiometry of 3:3:1:1:1. The beta subunit of ATP
synthase is catalytic.
Length = 274
Score = 26.8 bits (60), Expect = 7.2
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 96 RRNPDLLSQQWPPNKSIPSLEDLERNTEISCT--QVIDRL 133
R P + WP ++ P + TEI T +VID L
Sbjct: 24 ERGPIKTKKTWPIHREAPEFVEQSTKTEILETGIKVIDLL 63
>gnl|CDD|223133 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy
production and conversion].
Length = 468
Score = 26.8 bits (60), Expect = 8.0
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 105 QWPPNKSIPSLEDLERNTEISCT--QVIDRL 133
+WP ++ PS E+L TEI T +VID L
Sbjct: 111 KWPIHRKAPSFEELSTKTEILETGIKVIDLL 141
>gnl|CDD|222107 pfam13406, SLT_2, Transglycosylase SLT domain. This family is
related to the SLT domain pfam01464.
Length = 292
Score = 26.3 bits (59), Expect = 8.5
Identities = 5/19 (26%), Positives = 10/19 (52%)
Query: 86 DRVRGGRQKYRRNPDLLSQ 104
R+ GR + + LL++
Sbjct: 61 ARIARGRAFLQEHAALLAR 79
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 0.138 0.419
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: 9,219,276
Number of extensions: 826774
Number of successful extensions: 756
Number of sequences better than 10.0: 1
Number of HSP's gapped: 746
Number of HSP's successfully gapped: 76
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
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: 56 (25.4 bits)