RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1615
(295 letters)
>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 = 247 bits (633), Expect = 2e-82
Identities = 110/117 (94%), Positives = 115/117 (98%)
Query: 1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRL WSELFVLNA+QC MPLHV
Sbjct: 30 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHV 89
Query: 61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAE+SCLKAIVLFT+
Sbjct: 90 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTS 146
Score = 127 bits (321), Expect = 1e-35
Identities = 55/60 (91%), Positives = 56/60 (93%)
Query: 228 YLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
YLSSYISLLLRAEPYPT+RY QPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ
Sbjct: 1 YLSSYISLLLRAEPYPTSRYGSQCQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 60
>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 = 138 bits (349), Expect = 5e-40
Identities = 56/117 (47%), Positives = 75/117 (64%), Gaps = 2/117 (1%)
Query: 4 DNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPL 63
+++CE AARLLF AV+WA++IP F L DQ+ LL WSELF+L A+Q S+PL PL
Sbjct: 29 ESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPL 88
Query: 64 LAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
LA GL A+R F+ +R QE + + + L VD+ E++CLKAIVLF R
Sbjct: 89 LAVPGLSPDNTEAER--TFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETR 143
Score = 48.1 bits (115), Expect = 1e-06
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 238 RAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHR 289
PY T + +++CE AARLLF AV+WA++IP F L R
Sbjct: 14 PPFPYGTISSYEV-------SPESVCESAARLLFMAVKWAKSIPAFSTLPFR 58
>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 = 130 bits (330), Expect = 1e-37
Identities = 43/119 (36%), Positives = 70/119 (58%), Gaps = 2/119 (1%)
Query: 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
+++CELA R+LF V+WA+N+P F +L + DQ+ LL+ W+EL +L +Q S+ ++
Sbjct: 1 PESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSE 60
Query: 63 LLAAA-GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
LL + L + + ++ QE + KL++L +D EY+CLKAIVLF
Sbjct: 61 LLLPSPLLVILTEREALLG-LAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLP 118
Score = 45.7 bits (109), Expect = 4e-06
Identities = 14/29 (48%), Positives = 22/29 (75%)
Query: 259 IDNICELAARLLFSAVEWARNIPFFPDLQ 287
+++CELA R+LF V+WA+N+P F +L
Sbjct: 1 PESLCELADRVLFKTVDWAKNLPAFRNLP 29
>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 = 112 bits (281), Expect = 2e-30
Identities = 47/116 (40%), Positives = 67/116 (57%), Gaps = 2/116 (1%)
Query: 5 NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
+CELA R L VEWA++IP F +L + DQ+ LL+ W EL VL+ + S ++ LL
Sbjct: 2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLL 61
Query: 65 AAAGLHASPMAAD--RVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
A G H D +++ + IR+ E V L+AL +D EY+ LKAIVLF+
Sbjct: 62 APNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPD 117
Score = 39.6 bits (93), Expect = 5e-04
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 261 NICELAARLLFSAVEWARNIPFFPDLQH 288
+CELA R L VEWA++IP F +L
Sbjct: 2 LLCELATRDLLLIVEWAKSIPGFRELPL 29
>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 = 106 bits (266), Expect = 1e-27
Identities = 53/118 (44%), Positives = 70/118 (59%), Gaps = 6/118 (5%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
ICE A+RLLF ++ WAR+IP F L Q +L+R W ELF L +QCS L + +LA
Sbjct: 26 ICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILA 85
Query: 66 A--AGLHAS----PMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
A L S ++AD+V M+HI QE V ++ L VD EY+ LKAIVLF+
Sbjct: 86 AIINHLQTSIQQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSP 143
Score = 38.9 bits (91), Expect = 0.001
Identities = 15/27 (55%), Positives = 19/27 (70%)
Query: 262 ICELAARLLFSAVEWARNIPFFPDLQH 288
ICE A+RLLF ++ WAR+IP F L
Sbjct: 26 ICESASRLLFLSIHWARSIPAFQALGA 52
>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 = 102 bits (256), Expect = 2e-26
Identities = 43/143 (30%), Positives = 64/143 (44%), Gaps = 13/143 (9%)
Query: 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
G++ + E+ R L VEWA+ P F +L + DQ+ALL+ W E L + S
Sbjct: 1 GLNELFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKD 60
Query: 62 PLLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
LL + GL+ V + IR E V+ LK L + E + LKA++LF
Sbjct: 61 DLLFSNGLYLDRDELKSIEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLLFNPAG 120
Query: 120 RIFTG-----------VLLKALH 131
+ +G V+ ALH
Sbjct: 121 KRLSGEILEVVEKLQEVIANALH 143
Score = 36.2 bits (84), Expect = 0.009
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 258 GIDNICELAARLLFSAVEWARNIPFFPDLQH 288
G++ + E+ R L VEWA+ P F +L
Sbjct: 1 GLNELFEIWERDLLLVVEWAKRFPGFRELSL 31
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 92.0 bits (229), Expect = 6e-23
Identities = 40/123 (32%), Positives = 60/123 (48%), Gaps = 2/123 (1%)
Query: 10 AARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAG- 68
A R L VEWA++ P F +L + DQ+ LL+ W EL +L + S+ L LLA G
Sbjct: 1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGT 60
Query: 69 -LHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLL 127
+ + R + R+ E V+ L+ L +D EY+ LKAIVLF +
Sbjct: 61 YIRPDAVLELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGK 120
Query: 128 KAL 130
+ +
Sbjct: 121 EIV 123
Score = 30.0 bits (68), Expect = 0.77
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 266 AARLLFSAVEWARNIPFFPDLQHR 289
A R L VEWA++ P F +L
Sbjct: 1 AERQLLLTVEWAKSFPGFRELSLE 24
>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 = 92.0 bits (229), Expect = 2e-22
Identities = 46/115 (40%), Positives = 64/115 (55%), Gaps = 9/115 (7%)
Query: 5 NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP-- 62
NIC+ A + LF VEWA+ IP F +L + DQV LLR W+EL + + S+
Sbjct: 34 NICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSI---AVKDG 90
Query: 63 LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
+L A GLH +A + V A D R+ E V K++ L +D E CL+AI+LF
Sbjct: 91 ILLATGLHLHRNSAHQAGVGAIFD--RILTELVVKMRDLKMDRTELGCLRAIILF 143
Score = 36.5 bits (85), Expect = 0.009
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 261 NICELAARLLFSAVEWARNIPFFPDL 286
NIC+ A + LF VEWA+ IP F +L
Sbjct: 34 NICQAADKQLFQLVEWAKRIPHFSEL 59
>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 = 85.1 bits (211), Expect = 9e-20
Identities = 44/117 (37%), Positives = 60/117 (51%), Gaps = 8/117 (6%)
Query: 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
I+++CE + L VEWA+ IP F +L + DQVALLR E +L ++ SMP
Sbjct: 33 SINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDI 92
Query: 62 PLLAAAGL---HASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
LL + H RV R+ E V L+ L++D EY+CLKAIV F
Sbjct: 93 LLLGNDLIIPRHCPEPEISRVAN-----RILDELVLPLRDLNIDDNEYACLKAIVFF 144
Score = 34.7 bits (80), Expect = 0.035
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 233 ISLLLRAEPY------PTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
IS+LL+AE P S ++P I I+++CE + L VEWA+ IP F +L
Sbjct: 2 ISVLLQAEALSRQQSSPIPTCSGDIRPKKIASINDVCESMKQQLLVLVEWAKYIPAFCEL 61
Query: 287 Q 287
Sbjct: 62 P 62
>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 = 85.0 bits (211), Expect = 2e-19
Identities = 46/126 (36%), Positives = 66/126 (52%), Gaps = 25/126 (19%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVL--------NASQCSMP 57
+C++A + LFS VEWARN FF +L+V DQ+ LL+ WSEL VL + + S+
Sbjct: 43 MCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSIL 102
Query: 58 LH------VAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKA 111
L ++ L + AGL S + +D QE V KL+ L D E+ CLK
Sbjct: 103 LVTGQEVDLSTLASQAGLGLS--------SLVDR---AQELVNKLRELQFDRQEFVCLKF 151
Query: 112 IVLFTT 117
++LF
Sbjct: 152 LILFNP 157
Score = 40.3 bits (95), Expect = 4e-04
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 7/44 (15%)
Query: 246 RYSQCMQPN--NIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
Y++ + + +M C++A + LFS VEWARN FF +L+
Sbjct: 30 TYNRGEELDTFGLM-----CKMADQTLFSIVEWARNSVFFKELK 68
>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 = 73.5 bits (180), Expect = 3e-15
Identities = 41/115 (35%), Positives = 64/115 (55%), Gaps = 5/115 (4%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV--APL 63
+C++A + LFS VEWAR+ FF +L+V DQ+ LL+ WSEL +L+ + +H +
Sbjct: 45 MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV-VHGKEGSI 103
Query: 64 LAAAGLHA--SPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
G S +A+ + + QE V KL++L D E+ CLK +VLF+
Sbjct: 104 FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 158
Score = 33.8 bits (77), Expect = 0.061
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 262 ICELAARLLFSAVEWARNIPFFPDLQ 287
+C++A + LFS VEWAR+ FF +L+
Sbjct: 45 MCKMADQTLFSIVEWARSSIFFRELK 70
>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 = 69.2 bits (170), Expect = 6e-14
Identities = 36/119 (30%), Positives = 57/119 (47%), Gaps = 6/119 (5%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
+ +LA R L + WA++IP F DL + DQ+ LL+ W E+ +L S+P H L+
Sbjct: 32 LSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLP-HPGKLVF 90
Query: 66 AAGLH--ASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
A L + ++ D + V + + L + EY CLKAI+L + R
Sbjct: 91 APDLLLDREQARVEGLLEIFDMLLQL---VRRFRELGLQREEYVCLKAIILANSDVRHL 146
Score = 28.0 bits (63), Expect = 5.9
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 13/61 (21%)
Query: 233 ISLLLRAEPYPTARYSQCMQPN-------NIMGIDNICELAARLLFSAVEWARNIPFFPD 285
+S LL AEP M +++ + +LA R L + WA++IP F D
Sbjct: 2 LSALLVAEPDK----LYAMNDPTGPDTEVSLLAT--LSDLADRELVHIISWAKHIPGFSD 55
Query: 286 L 286
L
Sbjct: 56 L 56
>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 = 66.9 bits (163), Expect = 4e-13
Identities = 36/114 (31%), Positives = 56/114 (49%), Gaps = 3/114 (2%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPL---HVAP 62
+C +A + S V+WAR F +L+V DQ+ LL+ WSEL V + +
Sbjct: 43 LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSIL 102
Query: 63 LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
L+ + S +AA + QE V +L AL +D E+ CLK ++LF+
Sbjct: 103 LVTGQEVELSTVAAQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFS 156
Score = 33.8 bits (77), Expect = 0.078
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 6/54 (11%)
Query: 240 EPYPTARYSQCMQPNNIMGIDN------ICELAARLLFSAVEWARNIPFFPDLQ 287
E AR C+Q D +C +A + S V+WAR F +L+
Sbjct: 15 EDQVRARILGCLQEPQKSRPDQPAPFGLLCRMADQTFISIVDWARRCMVFKELE 68
>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 = 58.9 bits (143), Expect = 2e-10
Identities = 30/110 (27%), Positives = 51/110 (46%), Gaps = 4/110 (3%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
+ +LA R L + WA++IP F L + DQ++LL+ W E+ L S+P + + A
Sbjct: 32 LSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFA 91
Query: 66 A-AGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
L ++ + V +L+ L ++ EY LKA+ L
Sbjct: 92 EDFILDEELAREAGLLELYSACL---QLVRRLQRLRLEKEEYVLLKALAL 138
Score = 28.5 bits (64), Expect = 3.9
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 262 ICELAARLLFSAVEWARNIPFFPDL 286
+ +LA R L + WA++IP F L
Sbjct: 32 LSDLADRELVVIIGWAKHIPGFSSL 56
>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 = 56.7 bits (137), Expect = 2e-09
Identities = 42/129 (32%), Positives = 53/129 (41%), Gaps = 21/129 (16%)
Query: 9 LAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAG 68
LA R L + WA+ IP F DL + DQV LL W EL +L SM H LL A
Sbjct: 40 LADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSME-HPGKLLFAPD 98
Query: 69 LHASPMAADRVVAFMDHIRVFQEQVE----------KLKALHVDSAEYSCLKAIVLFTTG 118
L DR + + VE + + L + EY CLKAI+L +
Sbjct: 99 L-----LLDR-----NQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSS 148
Query: 119 KRIFTGVLL 127
F L
Sbjct: 149 VYTFLLESL 157
>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 = 55.6 bits (134), Expect = 4e-09
Identities = 33/124 (26%), Positives = 55/124 (44%), Gaps = 13/124 (10%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
+C A+++L + + RN+P F L DQ+ LLR W+ L +L +Q +P + A
Sbjct: 24 VCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPA 83
Query: 66 AAGLH-------------ASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAI 112
+ L P + ++ Q+ + K +L +D EY+ LK
Sbjct: 84 PSILCEILTGAEMHWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGA 143
Query: 113 VLFT 116
VLFT
Sbjct: 144 VLFT 147
>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 = 52.4 bits (126), Expect = 4e-08
Identities = 29/115 (25%), Positives = 46/115 (40%), Gaps = 10/115 (8%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
+C L LLF ++W + +PFF +L + D LL W+EL +L ++ + L
Sbjct: 32 LCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILL----STITVASLQNLG 87
Query: 66 AAG-----LHASPMAADRVVAFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVL 114
S +R + + K + L V + EY CLK I
Sbjct: 88 LLQDCLSKYLPSEDELERFGDEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINF 142
Score = 30.8 bits (70), Expect = 0.57
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 262 ICELAARLLFSAVEWARNIPFFPDL 286
+C L LLF ++W + +PFF +L
Sbjct: 32 LCRLGDELLFRQIQWTKKLPFFTEL 56
>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 = 46.7 bits (111), Expect = 4e-06
Identities = 33/131 (25%), Positives = 53/131 (40%), Gaps = 22/131 (16%)
Query: 7 CELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVL------------NASQC 54
C+ A+ +L + + + +P F +L + DQ+ L+R W+ L VL S+
Sbjct: 25 CKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEP 84
Query: 55 SM----------PLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSA 104
SM P A L P A + IR + + K +L + +
Sbjct: 85 SMLQRILTTRPPPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTK 144
Query: 105 EYSCLKAIVLF 115
EY+ LK VLF
Sbjct: 145 EYAYLKGTVLF 155
>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 = 45.6 bits (108), Expect = 1e-05
Identities = 33/119 (27%), Positives = 50/119 (42%), Gaps = 10/119 (8%)
Query: 7 CELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV----AP 62
C A+ +L V + RN+P F L DQ+ LL+ W LF+L +Q + V P
Sbjct: 25 CREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVP 84
Query: 63 ------LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
LL DR + ++ Q + K +L + EY+ LK +LF
Sbjct: 85 SMLKKILLEGQSSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILF 143
>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 = 44.1 bits (105), Expect = 2e-05
Identities = 33/121 (27%), Positives = 51/121 (42%), Gaps = 18/121 (14%)
Query: 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLR--------LVWSELFVLNASQC 54
D+ E+ + VE+A+ IP F +L DQ+ALL+ L + L+ + +
Sbjct: 4 FDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLY--DPEKN 61
Query: 55 SMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
S+ + L F + I E EK+ L +D EY+ L AIVL
Sbjct: 62 SLTFGDGKGNSRDVLLNGG--------FGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVL 113
Query: 115 F 115
F
Sbjct: 114 F 114
>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 = 44.2 bits (104), Expect = 3e-05
Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 26/122 (21%)
Query: 9 LAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVL-----NASQCSMP-LHVAP 62
L R + +AV+WA+ IP F +L + DQ+ LL+ W L + Q + L AP
Sbjct: 36 LGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAP 95
Query: 63 LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEK-------LKALHVDSAEYSCLKAIVLF 115
L + R+ + +Q + L L V EY C+K ++L
Sbjct: 96 DLI--------INEQRM-----TLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLL 142
Query: 116 TT 117
+T
Sbjct: 143 ST 144
>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 = 43.3 bits (102), Expect = 5e-05
Identities = 31/98 (31%), Positives = 45/98 (45%), Gaps = 3/98 (3%)
Query: 19 EWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADR 78
+WA IP F D DQ LL + ELF+L + S P L+ G+ R
Sbjct: 59 KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNP-EEGKLIFCNGVVLHRTQCVR 117
Query: 79 VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
F D I E + L +++D + +SCL A+V+ T
Sbjct: 118 --GFGDWIDSILEFSQSLHRMNLDVSAFSCLAALVIIT 153
>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 = 42.6 bits (100), Expect = 9e-05
Identities = 31/120 (25%), Positives = 58/120 (48%), Gaps = 13/120 (10%)
Query: 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
++ +CE R L S V+W++++P F +L + DQ+ L++ W L V S HV+
Sbjct: 33 LNQLCE---RQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYK-HVSG 88
Query: 63 LLAAAGLHASP---MAADRV--VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
+ L+ +P + R+ +F + ++ L V E+ C+KA++L T
Sbjct: 89 QM----LYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNT 144
>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 = 42.0 bits (99), Expect = 1e-04
Identities = 35/118 (29%), Positives = 52/118 (44%), Gaps = 16/118 (13%)
Query: 8 ELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP------LHVA 61
L R L S V+WA+ +P F +L + DQ+ L++ W L V S L+ A
Sbjct: 35 RLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFA 94
Query: 62 P--LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
P + +H S M + M I QE V L V E+ C+K ++L +T
Sbjct: 95 PDLVFNEQRMHQSAM-YSLCLG-MRQIS--QEFVR----LQVTYEEFLCMKVLLLLST 144
Score = 29.3 bits (66), Expect = 2.4
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 231 SYISLLLRAEP---YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
S +S+L EP Y SQ ++ N L R L S V+WA+ +P F +L
Sbjct: 1 SLLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLN--RLGERQLVSVVKWAKALPGFRNL 57
>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 = 42.2 bits (99), Expect = 1e-04
Identities = 35/118 (29%), Positives = 55/118 (46%), Gaps = 16/118 (13%)
Query: 8 ELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP------LHVA 61
EL R L V+WA+ +P F +L V DQ+A+++ W L V S L+ A
Sbjct: 35 ELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFA 94
Query: 62 PLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
P L +H S M + V M H+ ++ L + E+ C+KA++LF+
Sbjct: 95 PDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLLFSI 144
>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 = 42.0 bits (99), Expect = 2e-04
Identities = 34/110 (30%), Positives = 46/110 (41%), Gaps = 8/110 (7%)
Query: 12 RLLFSAVE----WARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAA 67
LL +V+ WA IP F DL DQ LL + ELFVL + S P L+
Sbjct: 48 DLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNP-VDGKLVFCN 106
Query: 68 GLHASPMAADRVVA-FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
GL + R ++D I F L D + + CL ++L T
Sbjct: 107 GLVLHRLQCVRGFGEWLDSILAFSSS--LQSLLLDDISAFCCLALLLLIT 154
>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 = 37.8 bits (88), Expect = 0.003
Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 6/101 (5%)
Query: 18 VEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAAD 77
VE+A+ +P F L DQ+ LL+ SE+ +L ++ + + A + P D
Sbjct: 56 VEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFA----NNQPYTRD 111
Query: 78 --RVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
R D + ++ VD+AEY+ L AIV+F+
Sbjct: 112 SYRKAGMGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS 152
>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 = 37.1 bits (86), Expect = 0.006
Identities = 29/117 (24%), Positives = 46/117 (39%), Gaps = 14/117 (11%)
Query: 4 DNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVL------NASQCSMP 57
D EL+ + + VE+A+ +P F L + DQ+ LL+ ++ +L Q +M
Sbjct: 41 DKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 100
Query: 58 LHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
L +H + D + F Q L L +D E L AI L
Sbjct: 101 FSDGLTLNRTQMHNAGFG-----PLTDLVFTFANQ---LLPLEMDDTEIGLLSAICL 149
>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 = 36.9 bits (85), Expect = 0.008
Identities = 29/97 (29%), Positives = 45/97 (46%), Gaps = 3/97 (3%)
Query: 20 WARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRV 79
WA IP F DL DQ L + ELFVL + S P+ L+ G+ + R
Sbjct: 60 WAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVE-GKLIFCNGVVLHRLQCVR- 117
Query: 80 VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
F + I E L+ +++D + +SC+ A+ + T
Sbjct: 118 -GFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVT 153
>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 = 34.4 bits (79), Expect = 0.041
Identities = 32/109 (29%), Positives = 48/109 (44%), Gaps = 9/109 (8%)
Query: 13 LLFSAVE----WARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA-AA 67
LL S+++ +A IP FPDL DQ L + ELFVL + + P
Sbjct: 50 LLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGV 109
Query: 68 GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
LH +F D + E + L A+ +D + ++CL A+ L T
Sbjct: 110 VLHKQQC----QRSFGDWLHAILEFSKSLHAMDIDISAFACLCALTLIT 154
>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 = 33.6 bits (77), Expect = 0.072
Identities = 28/105 (26%), Positives = 44/105 (41%), Gaps = 14/105 (13%)
Query: 18 VEWARNIPFFPDLQVTDQVALLRL-VWSELFV-----LNASQCSMPLHVAPLLAAAGLHA 71
VE+A+ IP F DL DQV LL+ + L V +A + S+ + LH+
Sbjct: 29 VEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLHS 88
Query: 72 SPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
++ + F EKL +L + E A+VL +
Sbjct: 89 MGAG-----DLLNSMFDFS---EKLNSLQLSDEEMGLFTAVVLVS 125
>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 = 33.6 bits (77), Expect = 0.092
Identities = 34/122 (27%), Positives = 54/122 (44%), Gaps = 23/122 (18%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNAS-------QCSMPL 58
ELA + V++A+ +P F L DQ+ALL+ E+ +L + + L
Sbjct: 48 FTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFL 107
Query: 59 HVAPL----LAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
P A AGL V F++ I F + ++ L +D AEY+ L AI +
Sbjct: 108 KDFPYSRDDFARAGL---------QVEFINPIFEFS---KSMRELQLDDAEYALLIAINI 155
Query: 115 FT 116
F+
Sbjct: 156 FS 157
>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 = 32.6 bits (74), Expect = 0.17
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 8 ELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVW 43
LA + + V+WA+ +P F +L + DQ+ L++ W
Sbjct: 35 RLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSW 70
>gnl|CDD|132734 cd06936, NR_LBD_Fxr, The ligand binding domain of Farnesoid X
receptor:a member of the nuclear receptor superfamily of
ligand-activated transcription factors. The ligand
binding domain (LBD) of Farnesoid X receptor: Farnesoid
X receptor (FXR) is a member of the nuclear receptor
superfamily of ligand-activated transcription factors.
FXR is highly expressed in the liver, the intestine, the
kidney, and the adrenals. FXR plays key roles in the
regulation of bile acid, cholesterol, triglyceride, and
glucose metabolism. Evidences show that it also
regulates liver regeneration. Upon binding of ligands,
such as bile acid, an endogenous ligand, FXRs bind to
FXR response elements (FXREs) either as a monomer or as
a heterodimer with retinoid X receptor (RXR), and
regulate the expression of various genes involved in
bile acid, lipid, and glucose metabolism. There are two
FXR genes (FXRalpha and FXRbeta) in mammals. A single
FXRalpha gene encodes four isoforms resulting from
differential use of promoters and alternative splicing.
FXRbeta is a functional receptor in mice, rats, rabbits
and dogs, but is a pseudogene in humans and primates.
Like other members of the nuclear receptor (NR)
superfamily, farnesoid X receptors have a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a non-conserved hinge and a
C-terminal ligand binding domain (LBD).
Length = 221
Score = 32.1 bits (73), Expect = 0.21
Identities = 25/102 (24%), Positives = 44/102 (43%), Gaps = 11/102 (10%)
Query: 18 VEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQC---SMPLHVAPLLAAAGLHASPM 74
VE+ + +P F L DQ+ALL+ E L ++Q +P A LL + +S +
Sbjct: 53 VEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKKLPAGHADLLEER-IRSSGI 111
Query: 75 AADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
+ + + + + E L + EY+ L AI +
Sbjct: 112 SDEFITPMFNFYKSMGE-------LKMTQEEYALLTAITILF 146
>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 = 30.6 bits (69), Expect = 0.91
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 18 VEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQ 53
V++A+ +P F +L DQ+ LL+ E+ L A+
Sbjct: 69 VDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAV 104
>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 = 30.1 bits (68), Expect = 1.1
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 9/49 (18%)
Query: 6 ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRL-VWSELFVLNASQ 53
I EL E+A+++P F +L + DQV LL+ V +F + AS
Sbjct: 76 IRELT--------EFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASL 116
>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 = 29.3 bits (66), Expect = 1.7
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 18 VEWARNIPFFPDLQVTDQVALLRLVWSELFVLNAS 52
VE+A+ IP F DL DQ+ L++ + E++++ S
Sbjct: 19 VEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRIS 53
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 29.6 bits (67), Expect = 1.8
Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 177 STAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGL 222
ST + G+V S L G L N SASA+ I A L
Sbjct: 266 STRGRNGKVNVYFSASGEALYDGPLVVLVNEGSASASE--IFAGAL 309
>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 = 28.9 bits (65), Expect = 2.2
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 17 AVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQ 53
V++ ++IP F L D+ LL+ L++L S+
Sbjct: 18 IVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSR 54
>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 = 28.8 bits (64), Expect = 2.6
Identities = 15/49 (30%), Positives = 29/49 (59%)
Query: 5 NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQ 53
++ +L + + + +A+ IP F DL DQ+ALL+ E+ +L ++Q
Sbjct: 41 HLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQ 89
>gnl|CDD|179855 PRK04460, PRK04460, nickel responsive regulator; Provisional.
Length = 137
Score = 28.0 bits (63), Expect = 2.9
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 98 ALHVDSAEYSCLKAIVLFTTGKRI 121
+LHV ++CL+ +VL K I
Sbjct: 86 SLHVHLDHHNCLEVLVLKGKAKEI 109
>gnl|CDD|226918 COG4544, COG4544, Uncharacterized conserved protein [Function
unknown].
Length = 260
Score = 28.2 bits (63), Expect = 4.6
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 185 VPPNQSCLPGGLGP-GQFAALTNGDSASAASAAIAAA 220
VPP + LPGG G+ L G + +A AA A A
Sbjct: 39 VPPIDAALPGGGLALGEIHELEGGGAGAADGAAAALA 75
>gnl|CDD|237691 PRK14366, PRK14366, Maf-like protein; Provisional.
Length = 195
Score = 27.8 bits (62), Expect = 4.7
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 12/66 (18%)
Query: 86 IRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL 145
IR+ +E+ EK+++L D L A + G+RI LLKA + AE L+ +
Sbjct: 50 IRMAKEKAEKVQSLRPD---KFVLGADTVVCCGRRI----LLKAETEEQAE-EYLELL-- 99
Query: 146 FTTGKR 151
+G+R
Sbjct: 100 --SGRR 103
>gnl|CDD|234289 TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype
II/NMENI. The CRISPR-associated protein Cas1 is
virtually universal to CRISPR systems. CRISPR, an
acronym for Clustered Regularly Interspaced Short
Palindromic Repeats, is a prokaryotic immunity system
for foreign DNA, mostly from phage. CRISPR systems
belong to different subtypes, distinguished by both
nature of the repeats, the makeup of the cohort of
associated Cas proteins, and by molecular phylogeny
within the more universal Cas proteins such as this one.
This model is of type EXCEPTION and provides more
specific information than the EQUIVALOG model TIGR00287.
It describes the Cas1 variant of the NMENI subtype of
CRISPR/Cas system.
Length = 278
Score = 28.4 bits (64), Expect = 5.0
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 111 AIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKRM-FGKPLPLNQHY 163
++L + + LL AL AE + ++F K + G+ LP H+
Sbjct: 36 DVILIENPQITISSALLSAL----AENNI---ALIFCDEKHLPVGQLLPFYGHH 82
>gnl|CDD|132005 TIGR02960, SigX5, RNA polymerase sigma-70 factor, TIGR02960 family.
This group of sigma factors are members of the sigma-70
family (TIGR02937). They and appear by homology, tree
building, bidirectional best hits and one-to-a-genome
distribution, to represent a conserved family.
Length = 324
Score = 28.3 bits (63), Expect = 5.1
Identities = 15/63 (23%), Positives = 23/63 (36%)
Query: 60 VAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
V P AAG+ P A+ A ++R + LHV + + F G
Sbjct: 257 VCPGEGAAGMRLLPTIANGQPAAAMYMRRPDAERHTAFQLHVLEIRGGRITHVTAFLDGP 316
Query: 120 RIF 122
+F
Sbjct: 317 SLF 319
>gnl|CDD|238923 cd01948, EAL, EAL domain. This domain is found in diverse bacterial
signaling proteins. It is called EAL after its conserved
residues and is also known as domain of unknown function
2 (DUF2). The EAL domain has been shown to stimulate
degradation of a second messenger, cyclic di-GMP, and is
a good candidate for a diguanylate phosphodiesterase
function. Together with the GGDEF domain, EAL might be
involved in regulating cell surface adhesiveness in
bacteria.
Length = 240
Score = 27.9 bits (63), Expect = 5.3
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 35 QVALLRLVWSELFV---LNASQCSMPLHVAPLLAAAGLHASPMAADRVV------AFMDH 85
Q+A + +L + L+A Q P + LL L + + R+V A +D
Sbjct: 73 QLARWQAGGPDLRLSVNLSARQLRDPDFLDRLLEL--LAETGLPPRRLVLEITESALIDD 130
Query: 86 IRVFQEQVEKLKAL 99
+ + +L+AL
Sbjct: 131 LEEALATLRRLRAL 144
>gnl|CDD|236599 PRK09632, PRK09632, ATP-dependent DNA ligase; Reviewed.
Length = 764
Score = 28.4 bits (64), Expect = 5.7
Identities = 19/61 (31%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 29 DLQVTDQVALLRLVWSE----LFVLNASQCSMPLHVAPLLAAAGLHASPMAADR----VV 80
DL D +LLR + + L L S L V PLL G A + + VV
Sbjct: 563 DLLYLDGRSLLRKPYRDRRKLLEALAPSGG--SLTVPPLLPGDGAEALAYSRELGWEGVV 620
Query: 81 A 81
A
Sbjct: 621 A 621
>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 = 27.7 bits (62), Expect = 6.7
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 18 VEWARNIPFFPDLQVTDQVALLR 40
VE+A+ IP F +L DQ+ LL+
Sbjct: 65 VEFAKRIPGFMELCQNDQIVLLK 87
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
0.323 0.134 0.403
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: 15,153,871
Number of extensions: 1434668
Number of successful extensions: 1553
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1526
Number of HSP's successfully gapped: 92
Length of query: 295
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 199
Effective length of database: 6,679,618
Effective search space: 1329243982
Effective search space used: 1329243982
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 (22.0 bits)
S2: 59 (26.6 bits)