RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6602
(367 letters)
>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 = 254 bits (650), Expect = 3e-84
Identities = 97/194 (50%), Positives = 126/194 (64%), Gaps = 1/194 (0%)
Query: 74 QPPPHPGLLQI-LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELF 132
+PP G + +S E E+ ARLLFMAV+W + + F TL RDQL+LL+ESW ELF
Sbjct: 13 RPPFPYGTISSYEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELF 72
Query: 133 LLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCM 192
LL AQWS+P D L+ + +E++ +QE L+RFRQL D +E C+
Sbjct: 73 LLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLSEVRALQETLSRFRQLRVDATEFACL 132
Query: 193 KAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
KA++LF PET GL D VE LQDQAQ +L ++R RY QP RFG+LLL+LPSLR +
Sbjct: 133 KAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISS 192
Query: 253 STIERLFFKETIGD 266
STIE LFFK+TIG+
Sbjct: 193 STIEELFFKKTIGN 206
Score = 108 bits (273), Expect = 3e-28
Identities = 41/66 (62%), Positives = 49/66 (74%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
ET GL D VE LQDQAQ +L ++R RY QP RFG+LLL+LPSLR + STIE LFF
Sbjct: 141 ETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTIEELFF 200
Query: 344 KETIGD 349
K+TIG+
Sbjct: 201 KKTIGN 206
>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 = 175 bits (446), Expect = 3e-53
Identities = 84/206 (40%), Positives = 117/206 (56%), Gaps = 2/206 (0%)
Query: 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
+M + E ARLLF AV W R + F L DQ+ LL+ SW ELF+L+ AQ +P
Sbjct: 29 IMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLH 88
Query: 145 LS--LLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET 202
++ L A V + I++ QE + + + L D +E C+KA++LFT +
Sbjct: 89 VAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDA 148
Query: 203 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
GL D +E LQ+++QC L +YVR +Y QPTRFG+LLL LPSLR V S IE+LFF
Sbjct: 149 CGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVR 208
Query: 263 TIGDIPIQRLLGDMYTMEKSYETPGL 288
+G PI+ L+ DM S+ P L
Sbjct: 209 LVGKTPIETLIRDMLLSGSSFVWPYL 234
Score = 96.8 bits (241), Expect = 2e-23
Identities = 40/76 (52%), Positives = 52/76 (68%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
+ GL D +E LQ+++QC L +YVR +Y QPTRFG+LLL LPSLR V S IE+LFF
Sbjct: 147 DACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 206
Query: 344 KETIGDIPIQRLLGDM 359
+G PI+ L+ DM
Sbjct: 207 VRLVGKTPIETLIRDM 222
>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 = 147 bits (374), Expect = 2e-43
Identities = 70/166 (42%), Positives = 97/166 (58%), Gaps = 14/166 (8%)
Query: 93 ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS------ 146
E R+LF V W + L F+ L DQL LLQ SW EL LL LAQ S+ ++LS
Sbjct: 6 ELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPS 65
Query: 147 --LLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG 204
L+I E+ + V+ +QE+L++ R L D E C+KA++LF P+ PG
Sbjct: 66 PLLVILTEREALLGLAELVQR------LQELLSKLRSLQLDPKEYACLKAIVLFNPDLPG 119
Query: 205 LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 250
L + Q VE LQ++AQ L +Y+R RY +QP RF +LLL LP LR++
Sbjct: 120 LKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI 165
Score = 61.9 bits (151), Expect = 2e-11
Identities = 26/49 (53%), Positives = 35/49 (71%)
Query: 285 TPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 333
PGL + Q VE LQ++AQ L +Y+R RY +QP RF +LLL LP LR++
Sbjct: 117 LPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI 165
>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 = 119 bits (300), Expect = 6e-32
Identities = 67/185 (36%), Positives = 101/185 (54%), Gaps = 8/185 (4%)
Query: 93 ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQ----WSIPWDLSLL 148
E+ +RLLF+++ W R + FQ L Q L++ W ELF L LAQ S+P L+ +
Sbjct: 28 ESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAI 87
Query: 149 INCEK---ARERLPPDDVR-VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG 204
IN + +++L D V+ V I +QE + ++L D E +KA++LF+P+ PG
Sbjct: 88 INHLQTSIQQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPG 147
Query: 205 LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
Q +E LQ++A L DYV Y R +LLL LP LR++ + E LFF I
Sbjct: 148 QELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLI 207
Query: 265 GDIPI 269
G++ I
Sbjct: 208 GNVQI 212
Score = 55.0 bits (133), Expect = 8e-09
Identities = 27/67 (40%), Positives = 36/67 (53%)
Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 345
PG Q +E LQ++A L DYV Y R +LLL LP LR++ + E LFF
Sbjct: 146 PGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAG 205
Query: 346 TIGDIPI 352
IG++ I
Sbjct: 206 LIGNVQI 212
>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 = 110 bits (276), Expect = 5e-29
Identities = 55/170 (32%), Positives = 80/170 (47%), Gaps = 10/170 (5%)
Query: 89 EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
E E R L + V W + + F+ L DQ++LL+ W EL +L LA S L
Sbjct: 1 ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYK--NGLS 58
Query: 149 INCEKARERLPPDDVRVNNE------IKLIQEILARFRQLSPDGSECGCMKAVILFTPET 202
+ D I+L+ E + R L D E +KA++LF+P+
Sbjct: 59 LLLAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDR 118
Query: 203 P-GLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLRAV 250
L D + VE LQ++ L DY+R Y P+RF +LLL+LPSLR +
Sbjct: 119 KESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 168
Score = 43.4 bits (103), Expect = 3e-05
Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 285 TPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLRAV 333
L D + VE LQ++ L DY+R Y P+RF +LLL+LPSLR +
Sbjct: 119 KESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 168
>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 = 104 bits (262), Expect = 2e-26
Identities = 63/180 (35%), Positives = 95/180 (52%), Gaps = 4/180 (2%)
Query: 99 LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW-DLSLLIN-CEKARE 156
L + V W + + F L DQ+ LL+ E LL +A+ S+P+ D+ LL N R
Sbjct: 45 LLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRH 104
Query: 157 RLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD 216
P+ RV N I + E++ R L+ D +E C+KA++ F P+ GL D Q ++ L+
Sbjct: 105 CPEPEISRVANRI--LDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRF 162
Query: 217 QAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
Q Q L DY+ R RFG LLL+LP+L+++ IE++ F G I LL +M
Sbjct: 163 QVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222
Score = 60.5 bits (147), Expect = 1e-10
Identities = 28/76 (36%), Positives = 41/76 (53%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
+ GL D Q ++ L+ Q Q L DY+ R RFG LLL+LP+L+++ IE++ F
Sbjct: 147 DAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQF 206
Query: 344 KETIGDIPIQRLLGDM 359
G I LL +M
Sbjct: 207 ARLFGVAKIDNLLQEM 222
>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 = 103 bits (260), Expect = 3e-26
Identities = 57/171 (33%), Positives = 88/171 (51%), Gaps = 2/171 (1%)
Query: 91 CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
CQ + LF V W + + F L DQ++LL+ W EL + A SI +L+
Sbjct: 36 CQAAD-KQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLA 94
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
R V +++ E++ + R L D +E GC++A+ILF P+ GL Q
Sbjct: 95 TGLHLHRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQ 154
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
VE L+++ L +Y R ++ QP RF +LLL LP+LR++ +E LFF
Sbjct: 155 EVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 205
Score = 55.8 bits (135), Expect = 4e-09
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 287 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
GL Q VE L+++ L +Y R ++ QP RF +LLL LP+LR++ +E LFF
Sbjct: 149 GLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 205
>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 = 104 bits (260), Expect = 3e-26
Identities = 66/216 (30%), Positives = 95/216 (43%), Gaps = 17/216 (7%)
Query: 75 PPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL 134
+Q+ C+ + LL +R+VR L F L DQL LL+ SW L LL
Sbjct: 9 SCHQHRPVQLCAPQMVCRAASQVLL-KTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLL 67
Query: 135 HLAQWSIPWDL------SLLINC----EKARERLPPDDVRVNNEIKL-----IQEILARF 179
LAQ +P+D S+L E PP + + I L IQ+ L +
Sbjct: 68 GLAQDKVPFDTVEVPAPSILCEILTGAEMHWGGTPPPTLTMPPCIPLADVQDIQQFLMKC 127
Query: 180 RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR 239
L D E +K +LFTP P L +E LQ +AQ L ++ + R R
Sbjct: 128 WSLDLDCKEYAYLKGAVLFTPVPPLLC-PHYIEALQKEAQQALNEHTMMTRPLEQLRSAR 186
Query: 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 275
LLLML LR ++ + LFF+ IG++ + +L
Sbjct: 187 LLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLLQ 222
Score = 54.4 bits (131), Expect = 1e-08
Identities = 23/73 (31%), Positives = 37/73 (50%)
Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 345
P L+ +E LQ +AQ L ++ + R RLLLML LR ++ + LFF+
Sbjct: 150 PPLLCPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRP 209
Query: 346 TIGDIPIQRLLGD 358
IG++ + +L
Sbjct: 210 IIGNVSMDDVLLQ 222
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 100 bits (252), Expect = 1e-25
Identities = 53/163 (32%), Positives = 79/163 (48%), Gaps = 7/163 (4%)
Query: 95 TARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN---- 150
R L + V W + F+ LS DQ++LL+ W EL LL LA S+ LL+
Sbjct: 1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGT 60
Query: 151 CEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA-- 208
+ L + +++ E++ R+L D E +KA++LF P PGL +
Sbjct: 61 YIRPDAVLELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGK 120
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQ-PTRFGRLLLMLPSLRAV 250
+ VE LQ++ L DY Y P RF +LLL+LP LR +
Sbjct: 121 EIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPELRKI 163
Score = 38.1 bits (89), Expect = 0.002
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 282 SYETPGLVDA--QPVEMLQDQAQCILGDYVRGRYSRQ-PTRFGRLLLMLPSLRAV 333
+ PGL + + VE LQ++ L DY Y P RF +LLL+LP LR +
Sbjct: 109 NPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPELRKI 163
>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 = 98.6 bits (245), Expect = 6e-24
Identities = 62/188 (32%), Positives = 92/188 (48%), Gaps = 15/188 (7%)
Query: 99 LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
LF V W R F+ L DQ+ LLQ W EL +L H + SI L+
Sbjct: 53 LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-----FLVT 107
Query: 151 CEKARERL--PPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
++ + +NN + QE++A+ R L D E C+K ++LF+ + L +
Sbjct: 108 GQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENF 167
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
Q VE +Q+Q L DY Y +Q +FG+LLL LP +RA+ E L++K GD+P
Sbjct: 168 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVP 227
Query: 269 IQRLLGDM 276
LL +M
Sbjct: 228 YNNLLIEM 235
Score = 57.7 bits (139), Expect = 1e-09
Identities = 30/78 (38%), Positives = 43/78 (55%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
S + L + Q VE +Q+Q L DY Y +Q +FG+LLL LP +RA+ E L
Sbjct: 158 SLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 217
Query: 342 FFKETIGDIPIQRLLGDM 359
++K GD+P LL +M
Sbjct: 218 YYKHLNGDVPYNNLLIEM 235
>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 = 94.5 bits (235), Expect = 1e-22
Identities = 65/200 (32%), Positives = 97/200 (48%), Gaps = 13/200 (6%)
Query: 89 EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS-- 146
C+ + +L V ++R L F L +DQLLLLQ W LFLL LAQ + ++++
Sbjct: 23 RTCR-EASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEA 81
Query: 147 ---------LLINCEKARERLPPDDVRVN-NEIKLIQEILARFRQLSPDGSECGCMKAVI 196
LL + PD + + ++ +Q L +F L E +K I
Sbjct: 82 PVPSMLKKILLEGQSSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTI 141
Query: 197 LFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIE 256
LF P+ PGL + V LQ +AQ L + + + + RF R+LL +L+++ S I
Sbjct: 142 LFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLIT 201
Query: 257 RLFFKETIGDIPIQRLLGDM 276
LFF+ IGD I LLGDM
Sbjct: 202 DLFFRPIIGDADIAELLGDM 221
Score = 51.4 bits (123), Expect = 1e-07
Identities = 29/76 (38%), Positives = 42/76 (55%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
+ PGL + V LQ +AQ L + + + + RF R+LL +L+++ S I LFF
Sbjct: 146 DVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFF 205
Query: 344 KETIGDIPIQRLLGDM 359
+ IGD I LLGDM
Sbjct: 206 RPIIGDADIAELLGDM 221
>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 = 94.3 bits (235), Expect = 2e-22
Identities = 62/188 (32%), Positives = 95/188 (50%), Gaps = 15/188 (7%)
Query: 99 LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL-HLAQW-------SIPWDLSLLIN 150
LF V W R F+ L DQ+ LLQ W EL +L H+ + SI LL+
Sbjct: 51 LFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSI-----LLVT 105
Query: 151 CEKARERLPPDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
++ + +++ + QE++ + R+L D E C+K +ILF P+ GL +
Sbjct: 106 GQEVDLSTLASQAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENR 165
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
Q VE +Q+Q L DY Y +Q +FG+LLL LP +RA+ E L++K G++P
Sbjct: 166 QLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVP 225
Query: 269 IQRLLGDM 276
LL +M
Sbjct: 226 CNNLLIEM 233
Score = 54.6 bits (132), Expect = 1e-08
Identities = 29/76 (38%), Positives = 43/76 (56%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
+ GL + Q VE +Q+Q L DY Y +Q +FG+LLL LP +RA+ E L++
Sbjct: 158 DVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYY 217
Query: 344 KETIGDIPIQRLLGDM 359
K G++P LL +M
Sbjct: 218 KHLNGEVPCNNLLIEM 233
>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 = 90.1 bits (224), Expect = 2e-21
Identities = 50/182 (27%), Positives = 78/182 (42%), Gaps = 8/182 (4%)
Query: 91 CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS-LLI 149
E R L + V W + F+ LS DQL LL+ SW E L LA S + LL
Sbjct: 5 LFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDDLLF 64
Query: 150 NCEKARERLPPDDVRVN---NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV 206
+ +R + VN +I+ + E++ ++L E +KA++LF P L
Sbjct: 65 SNGLYLDRDELKSIEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLLFNPAGKRLS 124
Query: 207 DAQP--VEMLQDQAQCILGDYVRG--RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
VE LQ+ L +Y + R +LL +LP+LR + + E+L +
Sbjct: 125 GEILEVVEKLQEVIANALHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLELAK 184
Query: 263 TI 264
Sbjct: 185 LF 186
Score = 36.6 bits (85), Expect = 0.009
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 294 VEMLQDQAQCILGDYVRG--RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 347
VE LQ+ L +Y + R +LL +LP+LR + + E+L +
Sbjct: 131 VEKLQEVIANALHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLELAKLF 186
>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 = 75.9 bits (187), Expect = 6e-16
Identities = 59/194 (30%), Positives = 89/194 (45%), Gaps = 9/194 (4%)
Query: 97 RLLFMAVRWVRCLAP----FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
LL +V +R A F+ L + DQ LLL+ ++ ELF+L LA S P D L+
Sbjct: 48 DLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNG 107
Query: 153 KARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
RL VR E + I + + L D C A++L E GL + + V
Sbjct: 108 LVLHRL--QCVRGFGEWLDSILAFSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKV 165
Query: 212 EMLQDQAQCILGDYVRGRYSRQ--PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
E LQ++ L D+V Y Q P R +LLL LP LR + + ++R+FF + +P
Sbjct: 166 EELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPP 225
Query: 270 QRLLGDMYTMEKSY 283
L+ + +
Sbjct: 226 PPLIDKRFLDTLPF 239
Score = 52.4 bits (126), Expect = 7e-08
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ--PTRFGRLLLMLPSLRAVRQSTIERL 341
E GL + + VE LQ++ L D+V Y Q P R +LLL LP LR + + ++R+
Sbjct: 155 ERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRI 214
Query: 342 FFKETIGDIPIQRLLGDMYTMEKSY 366
FF + +P L+ + +
Sbjct: 215 FFLKLEDLLPPPPLIDKRFLDTLPF 239
>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 = 73.6 bits (181), Expect = 3e-15
Identities = 52/161 (32%), Positives = 74/161 (45%), Gaps = 10/161 (6%)
Query: 97 RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC----- 151
LLF ++W + L F LS +D LL W EL LL + +L LL +C
Sbjct: 38 ELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYL 97
Query: 152 --EKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
E ER + V ++ + +LA+FRQL E C+K + + GL +A
Sbjct: 98 PSEDELERFGDEGGEV---VERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNAS 154
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 250
+E LQ + +L D+ Y QP RF LL LP +RA
Sbjct: 155 QLESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAA 195
Score = 37.4 bits (87), Expect = 0.006
Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 333
+ GL +A +E LQ + +L D+ Y QP RF LL LP +RA
Sbjct: 146 DIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAA 195
>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 = 70.9 bits (174), Expect = 3e-14
Identities = 53/187 (28%), Positives = 88/187 (47%), Gaps = 13/187 (6%)
Query: 97 RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
R L + + W + + F +LS DQ+ LLQ +W E+ L + S+P++ L
Sbjct: 38 RELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGEL---VFAEDF 94
Query: 157 RLPPDDVRVNNEIKL---IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEM 213
L + R ++L +++ R ++L + E +KA+ L ++ + D + V
Sbjct: 95 ILDEELAREAGLLELYSACLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQ 154
Query: 214 LQDQAQCILGDYVRGRYSRQ-PTRFGRLLLMLPSLRAVRQSTIERLFF---KETIGDIPI 269
L+D L DY GR+ + P R G+LLL LP LR R FF K G +P+
Sbjct: 155 LRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQT--DGKARRFFYGVKRE-GKVPM 211
Query: 270 QRLLGDM 276
+L +M
Sbjct: 212 HKLFLEM 218
Score = 41.6 bits (98), Expect = 2e-04
Identities = 27/74 (36%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQ-PTRFGRLLLMLPSLRAVRQSTIERLFF---KE 345
D + V L+D L DY GR+ + P R G+LLL LP LR R FF K
Sbjct: 148 DVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQT--DGKARRFFYGVKR 205
Query: 346 TIGDIPIQRLLGDM 359
G +P+ +L +M
Sbjct: 206 E-GKVPMHKLFLEM 218
>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 = 69.9 bits (171), Expect = 8e-14
Identities = 55/213 (25%), Positives = 94/213 (44%), Gaps = 24/213 (11%)
Query: 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
L S + + + +L +R+V+ + FQ L DQL+L++ W L +L LAQ + ++
Sbjct: 18 LKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFE 77
Query: 145 L----------SLLINCEKARERLPPDDVRVNN--------------EIKLIQEILARFR 180
+L P + + +I+ I+ LA+
Sbjct: 78 TVETSEPSMLQRILTTRPPPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCW 137
Query: 181 QLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRL 240
L E +K +LF P+ PGL Q ++ LQ +AQ L ++VR + RF +L
Sbjct: 138 SLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKL 197
Query: 241 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLL 273
+ L LRA+ + I LFF+ IG + + +L
Sbjct: 198 NIALSLLRAINANVIAELFFRPIIGTVNMDDML 230
>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 = 67.6 bits (166), Expect = 4e-13
Identities = 48/141 (34%), Positives = 70/141 (49%), Gaps = 7/141 (4%)
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
F LS DQ+ LLQ +W E+ +L L S+P L+ L + RV +++
Sbjct: 53 FSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVF---APDLLLDREQARVEGLLEI 109
Query: 172 IQEILA---RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRG 228
+L RFR+L E C+KA+IL + L D + V+ L+D L D
Sbjct: 110 FDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAK 169
Query: 229 RY-SRQPTRFGRLLLMLPSLR 248
R+ S+QP R +LLL+LP LR
Sbjct: 170 RHGSQQPRRLAQLLLLLPHLR 190
Score = 32.2 bits (74), Expect = 0.29
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRY-SRQPTRFGRLLLMLPSLR 331
D + V+ L+D L D R+ S+QP R +LLL+LP LR
Sbjct: 148 DREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLR 190
>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 = 56.1 bits (135), Expect = 4e-09
Identities = 50/188 (26%), Positives = 80/188 (42%), Gaps = 15/188 (7%)
Query: 99 LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
V W R F+ L DQ+ LLQ W EL + H + SI LL+
Sbjct: 51 FISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSI-----LLVT 105
Query: 151 CEKARERLPPDDV--RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
++ +++ + QE++ + L D E C+K +ILF+ + L +
Sbjct: 106 GQEVELSTVAAQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNH 165
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
V+ Q++A L DY Y +F +LLL L +RA+ E L+ K ++P
Sbjct: 166 SLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMP 225
Query: 269 IQRLLGDM 276
LL +M
Sbjct: 226 RNNLLIEM 233
Score = 32.6 bits (74), Expect = 0.24
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 298 QDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLG 357
Q++A L DY Y +F +LLL L +RA+ E L+ K ++P LL
Sbjct: 172 QEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLI 231
Query: 358 DM 359
+M
Sbjct: 232 EM 233
>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 = 54.9 bits (133), Expect = 5e-09
Identities = 42/143 (29%), Positives = 67/143 (46%), Gaps = 8/143 (5%)
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
F+ LS+ DQ+ LL+ E+ LL A P SL K R D + +
Sbjct: 28 FRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSR---DVLLNGGFGEF 84
Query: 172 IQEILA---RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ-AQCILGDYVR 227
I+ + + +L D +E + A++LF+P+ PGL D VE LQ++ + L Y++
Sbjct: 85 IEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEA-LQRYLK 143
Query: 228 GRYSRQPTRFGRLLLMLPSLRAV 250
+ P F +LL L LR +
Sbjct: 144 VNHPDAPQMFAKLLKKLTELRTL 166
Score = 38.0 bits (89), Expect = 0.003
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 286 PGLVDAQPVEMLQDQ-AQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 333
PGL D VE LQ++ + L Y++ + P F +LL L LR +
Sbjct: 119 PGLQDVDTVEKLQERLLEA-LQRYLKVNHPDAPQMFAKLLKKLTELRTL 166
>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 = 55.1 bits (133), Expect = 6e-09
Identities = 36/139 (25%), Positives = 67/139 (48%)
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
F LS+ DQLLL++ + E++L+ +++ S+ + + R D + ++ +K
Sbjct: 28 FCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDSDFVKA 87
Query: 172 IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS 231
+ E F L +E AV+L +P+ GL + + V +LQD+ L V
Sbjct: 88 LFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRP 147
Query: 232 RQPTRFGRLLLMLPSLRAV 250
+ F LL+ +P LR++
Sbjct: 148 AEAQLFASLLMKIPELRSI 166
Score = 31.2 bits (71), Expect = 0.50
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 333
GL + + V +LQD+ L V + F LL+ +P LR++
Sbjct: 119 IGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPELRSI 166
>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 = 52.9 bits (127), Expect = 5e-08
Identities = 64/228 (28%), Positives = 99/228 (43%), Gaps = 18/228 (7%)
Query: 57 SPPPPSHHHPSMFLATHQPPPHPGLLQILMS-AEKCQETTARLLFMAVRWVRCLAP---- 111
SP + + +P P L+ MS AEK Q+ + LL ++ ++ A
Sbjct: 17 SPDFANLDYSQY----REPSP----LEPPMSEAEKVQQFYS-LLTSSIDVIKTFAEKIPG 67
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
F L K DQ LL Q + ELF+L LA + P D + L C + +
Sbjct: 68 FPDLCKEDQELLFQSASLELFVLRLAYRTAPED-TKLTFCNGVVLHKQQCQRSFGDWLHA 126
Query: 172 IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYV--RGR 229
I E + D S C+ A+ L T E GL + VE LQ + L D+V
Sbjct: 127 ILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAE 185
Query: 230 YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
++P F RLL LP LR++ ++R+F+ + +P L+ +M+
Sbjct: 186 AQKKPHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMF 233
Score = 32.9 bits (75), Expect = 0.21
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYV--RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
E GL + VE LQ + L D+V ++P F RLL LP LR++ ++R+
Sbjct: 155 ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELRSLSVQGLQRI 214
Query: 342 FFKETIGDIPIQRLLGDMY 360
F+ + +P L+ +M+
Sbjct: 215 FYLKLEDLVPAPPLIENMF 233
>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 = 52.5 bits (126), Expect = 8e-08
Identities = 48/160 (30%), Positives = 78/160 (48%), Gaps = 6/160 (3%)
Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
+W + F K DQ LLL+ ++ ELF+L LA S P + L+ R V
Sbjct: 59 KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRT--QCV 116
Query: 164 RVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCIL 222
R + I I E +++ D S C+ A+++ T + GL + + VE LQ++ L
Sbjct: 117 RGFGDWIDSILEFSQSLHRMNLDVSAFSCLAALVIIT-DRHGLKEPKRVEELQNRLISCL 175
Query: 223 GDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
++V G S ++P RLL LP LR + ++R+F+
Sbjct: 176 KEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRIFY 215
Score = 30.6 bits (69), Expect = 1.1
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 287 GLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
GL + + VE LQ++ L ++V G S ++P RLL LP LR + ++R+F+
Sbjct: 157 GLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRIFY 215
>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 = 50.0 bits (119), Expect = 4e-07
Identities = 49/159 (30%), Positives = 75/159 (47%), Gaps = 6/159 (3%)
Query: 105 WVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR 164
W + F L K DQ LL + ++ ELF+L LA S P + L+ RL VR
Sbjct: 60 WAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRL--QCVR 117
Query: 165 VNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
E I I E + + ++ D S C+ A+ + T E GL + + VE LQ++ L
Sbjct: 118 GFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLK 176
Query: 224 DYV--RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
D+V +P +LL LP LR + ++R+F+
Sbjct: 177 DHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFY 215
Score = 28.5 bits (63), Expect = 4.8
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYV--RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
E GL + + VE LQ++ L D+V +P +LL LP LR + ++R+
Sbjct: 154 ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRI 213
Query: 342 FF 343
F+
Sbjct: 214 FY 215
>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 = 48.7 bits (116), Expect = 1e-06
Identities = 39/174 (22%), Positives = 72/174 (41%), Gaps = 6/174 (3%)
Query: 89 EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
+K E + + + V + + L F TL+ DQ+ LL+ + ++ +L + P ++
Sbjct: 41 DKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 100
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSP---DGSECGCMKAVILFTPETPGL 205
+ R + L + QL P D +E G + A+ L + L
Sbjct: 101 FSDGLTLNR---TQMHNAGFGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDL 157
Query: 206 VDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
+ VE LQ+ L Y R R +P F ++L+ + LR++ ER+
Sbjct: 158 EEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVI 211
Score = 34.4 bits (79), Expect = 0.063
Identities = 16/56 (28%), Positives = 26/56 (46%)
Query: 287 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 342
L + VE LQ+ L Y R R +P F ++L+ + LR++ ER+
Sbjct: 156 DLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVI 211
>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 = 47.8 bits (114), Expect = 3e-06
Identities = 41/151 (27%), Positives = 70/151 (46%), Gaps = 5/151 (3%)
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
F TL++ DQ+ LL+ S E+ LL A+ P ++ + R D R +++
Sbjct: 69 FLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSR--DDFARAGLQVEF 126
Query: 172 IQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRG 228
I I R+L D +E + A+ +F+ + P + D VE LQ+ L Y++
Sbjct: 127 INPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKI 186
Query: 229 RYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
+ F R+L+ L SLR + E++F
Sbjct: 187 KRPSDRLMFPRMLMKLVSLRTLSSVHSEQVF 217
Score = 30.5 bits (69), Expect = 1.1
Identities = 18/61 (29%), Positives = 29/61 (47%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
S + P + D VE LQ+ L Y++ + F R+L+ L SLR + E++
Sbjct: 157 SADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQV 216
Query: 342 F 342
F
Sbjct: 217 F 217
>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 = 47.4 bits (113), Expect = 3e-06
Identities = 58/240 (24%), Positives = 95/240 (39%), Gaps = 41/240 (17%)
Query: 59 PPP--SHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLS 116
PP S + P+ +P L+ +L + R L + W + + F LS
Sbjct: 15 PPHIYSEYDPT------RPFTEASLMMLLTN------LADRELVHMINWAKKIPGFVDLS 62
Query: 117 KRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEIL 176
DQ+ LL+ +W EL +L L S+ LL PD + N+ ++ ++
Sbjct: 63 LHDQVHLLESAWLELLMLGLVWRSMEHPGKLL---------FAPDLLLDRNQGSCVEGMV 113
Query: 177 ----------ARFRQLSPDGSECGCMKAVILFT-----PETPGLVDAQPVEMLQDQAQCI 221
+RFR+L E C+KA+IL L + V+ L D+
Sbjct: 114 EIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDA 173
Query: 222 LGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278
L R +Q R +LLL+L +R V +E L+ + +P+ LL +M
Sbjct: 174 LVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLD 233
>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 = 43.9 bits (104), Expect = 5e-05
Identities = 44/209 (21%), Positives = 77/209 (36%), Gaps = 23/209 (11%)
Query: 52 PSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAP 111
+G + P + L ++ + ++CQ + + + + L
Sbjct: 29 LTGKTTDHAPFVIYDIESLKLNKDGQPQEKTIRIRLFQRCQVRSVETIRELTEFAKSLPG 88
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE--- 168
F+ L DQ+ LL+ E+ LA L N K P + V E
Sbjct: 89 FRNLDLNDQVTLLKYGVHEVIFTMLAS---------LYN--KDGLLFPEGNGYVTREFLE 137
Query: 169 ---------IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQ 219
++ E +F L SE AVI+ +P+ PGL++ +PVE +Q+
Sbjct: 138 SLRKPFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVL 197
Query: 220 CILGDYVRGRYSRQPTRFGRLLLMLPSLR 248
L ++ + P F +LL + LR
Sbjct: 198 QALELQLKKNHPDSPQLFAKLLQKMVDLR 226
Score = 30.5 bits (69), Expect = 1.1
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLR 331
PGL++ +PVE +Q+ L ++ + P F +LL + LR
Sbjct: 181 PGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLR 226
>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 = 42.5 bits (100), Expect = 2e-04
Identities = 37/156 (23%), Positives = 65/156 (41%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
V + + L F L DQ++LL+ E+ L A P +L ++ E A R +
Sbjct: 69 VDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKN 128
Query: 163 VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCIL 222
+ I ++ + D +E ++AV+L + + PGL + +E LQD
Sbjct: 129 GGLGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAF 188
Query: 223 GDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
Y+ R P + +LL+ + LR + R
Sbjct: 189 EHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRF 224
Score = 28.6 bits (64), Expect = 4.9
Identities = 15/56 (26%), Positives = 23/56 (41%)
Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
PGL + +E LQD Y+ R P + +LL+ + LR + R
Sbjct: 169 PGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRF 224
>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 = 41.0 bits (96), Expect = 4e-04
Identities = 39/156 (25%), Positives = 62/156 (39%), Gaps = 3/156 (1%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
V + + L F+TL DQ+ LL+ S E L AQ I + + ER+
Sbjct: 53 VEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQ--IYNKKLPAGHADLLEERIRSSG 110
Query: 163 VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCIL 222
+ + I + +L E + A+ + P+ P L D + VE LQ+ +L
Sbjct: 111 I-SDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLL 169
Query: 223 GDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
+ + + P F LL L LR + E L
Sbjct: 170 QKFCKLYHPEDPQHFACLLGRLTELRTLNHHHAEML 205
>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 = 40.3 bits (94), Expect = 6e-04
Identities = 35/147 (23%), Positives = 73/147 (49%), Gaps = 8/147 (5%)
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
F+ L+ DQ+ LL+ S E+ +L Q D+S + ++ D + + ++L
Sbjct: 63 FRDLTAEDQIALLKSSAIEVIMLRSNQSFSLDDMSWTCGSPDFKYKVS-DVTKAGHSLEL 121
Query: 172 IQEILARF----RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVR 227
+ E L +F ++L+ E + A+ + +P+ PG+ D +E +QD+ L Y+R
Sbjct: 122 L-EPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIR 180
Query: 228 GRYSRQPTR--FGRLLLMLPSLRAVRQ 252
R+ +R + +++ L LR++ +
Sbjct: 181 CRHPPPGSRLLYAKMIQKLADLRSLNE 207
Score = 27.6 bits (61), Expect = 9.1
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 335
S + PG+ D +E +QD+ L Y+R R+ +R + +++ L LR++ +
Sbjct: 152 SPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYAKMIQKLADLRSLNE 207
>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 = 39.8 bits (93), Expect = 7e-04
Identities = 37/150 (24%), Positives = 63/150 (42%), Gaps = 6/150 (4%)
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
F+ LS+ DQ+ LL+ E+ ++ A + S+ + DD+ L
Sbjct: 38 FRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSV---DDLHSMGAGDL 94
Query: 172 IQ---EILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRG 228
+ + + L E G AV+L + + GL + VE LQ+ L +
Sbjct: 95 LNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAK 154
Query: 229 RYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
+ +P+ F +LLL LP LR + E+L
Sbjct: 155 NHPNEPSIFTKLLLKLPDLRTLNNLHSEKL 184
Score = 29.8 bits (67), Expect = 1.7
Identities = 19/60 (31%), Positives = 29/60 (48%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
S + GL + VE LQ+ L + + +P+ F +LLL LP LR + E+L
Sbjct: 125 SADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLPDLRTLNNLHSEKL 184
>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 = 38.2 bits (89), Expect = 0.004
Identities = 41/145 (28%), Positives = 65/145 (44%), Gaps = 10/145 (6%)
Query: 109 LAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE 168
L F LS+ DQ+ LL+ E+ +L +A+ S++ + R D R
Sbjct: 62 LPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTR---DSYRKAGM 118
Query: 169 IKLIQEILARF-RQLSP---DGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGD 224
E L RF R + D +E + A+++F+ + PGL+ + VE +Q+ L
Sbjct: 119 GDSA-EDLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRA 176
Query: 225 YVRGRYS-RQPTRFGRLLLMLPSLR 248
YV R Q F +LL +L LR
Sbjct: 177 YVDNRRPPSQRVIFAKLLSILTELR 201
Score = 30.9 bits (70), Expect = 0.79
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLR 331
+ PGL+ + VE +Q+ L YV R Q F +LL +L LR
Sbjct: 153 DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSILTELR 201
>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 = 35.7 bits (82), Expect = 0.028
Identities = 37/146 (25%), Positives = 57/146 (39%), Gaps = 27/146 (18%)
Query: 97 RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
R L V+W + L F+ L DQ+ L+Q SW L + L S +
Sbjct: 39 RQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYK-------HVSGQML 91
Query: 157 RLPPDDVRVNNEIK---------LIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVD 207
PD + +K + +I F +L E CMKA++ L++
Sbjct: 92 YFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALL--------LLN 143
Query: 208 AQPVEMLQDQAQCILGDYVRGRYSRQ 233
P+E L+ Q Q D +R Y R+
Sbjct: 144 TIPLEGLRSQTQF---DEMRSSYIRE 166
>gnl|CDD|132732 cd06934, NR_LBD_PXR_like, The ligand binding domain of xenobiotic
receptors:pregnane X receptor and constitutive
androstane receptor. The ligand binding domain of
xenobiotic receptors: This xenobiotic receptor family
includes pregnane X receptor (PXR), constitutive
androstane receptor (CAR) and other related nuclear
receptors. They function as sensors of toxic byproducts
of cell metabolism and of exogenous chemicals, to
facilitate their elimination. The nuclear receptor
pregnane X receptor (PXR) is a ligand-regulated
transcription factor that responds to a diverse array of
chemically distinct ligands, including many endogenous
compounds and clinical drugs. The ligand binding domain
of PXR shows remarkable flexibility to accommodate both
large and small molecules. PXR functions as a
heterodimer with retinoic X receptor-alpha (RXRa) and
binds to a variety of response elements in the promoter
regions of a diverse set of target genes involved in the
metabolism, transport, and elimination of these
molecules from the cell. Constitutive androstane
receptor (CAR) is a closest mammalian relative of PXR,
which has also been proposed to function as a
xenosensor. CAR is activated by some of the same ligands
as PXR and regulates a subset of common genes. The
sequence homology and functional similarity suggests
that the CAR gene arose from a duplication of an
ancestral PXR gene. Like other nuclear receptors,
xenobiotic receptors have a central well conserved DNA
binding domain (DBD), a variable N-terminal domain, a
flexible hinge and a C-terminal ligand binding domain
(LBD).
Length = 226
Score = 35.1 bits (81), Expect = 0.033
Identities = 27/98 (27%), Positives = 45/98 (45%), Gaps = 7/98 (7%)
Query: 161 DDVRVNNEIKLIQEILARF----RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD 216
D R + L+ E L RF R+L E M+A+ LF+P+ PG+ ++ LQ+
Sbjct: 107 DAARAGFQQLLL-EPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQE 165
Query: 217 QAQCILGDYVRGRYSRQPTRF--GRLLLMLPSLRAVRQ 252
+ L Y+ + RF ++L L LR + +
Sbjct: 166 KMALTLKSYIDSKRPGPEKRFLYPKILACLTELRTINE 203
>gnl|CDD|132761 cd07076, NR_LBD_GR, Ligand binding domain of the glucocorticoid
receptor, a member of the nuclear receptor superfamily.
The ligand binding domain of the glucocorticoid receptor
(GR): GR is a ligand-activated transcription factor
belonging to the nuclear receptor superfamily. It binds
with high affinity to cortisol and other
glucocorticoids. GR is expressed in almost every cell in
the body and regulates genes controlling a wide variety
of processes including the development, metabolism, and
immune response of the organism. In the absence of
hormone, the glucocorticoid receptor (GR) is complexes
with a variety of heat shock proteins in the cytosol.
The binding of the glucocorticoids results in release of
the heat shock proteins and transforms it to its active
state. One mechanism of action of GR is by direct
activation of gene transcription. The activated form of
GR forms dimers, translocates into the nucleus, and
binds to specific hormone responsive elements,
activating gene transcription. GR can also function as a
repressor of other gene transcription activators, such
as NF-kappaB and AF-1 by directly binding to them, and
bloc king the expression of their activated genes. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, GR has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD). The LBD also
functions for dimerization and chaperone protein
association.
Length = 247
Score = 35.3 bits (81), Expect = 0.034
Identities = 29/111 (26%), Positives = 49/111 (44%), Gaps = 14/111 (12%)
Query: 97 RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWS--------IPWDLSLL 148
R + AV+W + + F+ L DQ+ LLQ SW L L S + + L+
Sbjct: 39 RQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLI 98
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFT 199
IN + R LP + ++ K + + + +L E CMK ++L +
Sbjct: 99 INEQ--RMTLP----CMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLS 143
>gnl|CDD|219053 pfam06482, Endostatin, Collagenase NC10 and Endostatin. NC10
stands for Non-helical region 10 and is taken from human
COL15A1. A mutation in this region in human COL18A1 is
associated with an increased risk of prostrate cancer.
This domain is cleaved from the precursor and forms
endostatin. Endostatin is a key tumour suppressor and
has been used highly successfully to treat cancer. It is
a potent angiogenesis inhibitor. Endostatin also binds a
zinc ion near the N-terminus; this is likely to be of
structural rather than functional importance according
to.
Length = 291
Score = 33.2 bits (76), Expect = 0.17
Identities = 19/52 (36%), Positives = 25/52 (48%)
Query: 32 DLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQ 83
+L+P G ++ + PP VL P S + P PP P AT PHP L
Sbjct: 51 ELVPLPGTTATQPPPVVLTPWSDPRLPDPPHLPDPQTHSATAHRNPHPPLNS 102
>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 = 33.0 bits (75), Expect = 0.19
Identities = 44/166 (26%), Positives = 63/166 (37%), Gaps = 37/166 (22%)
Query: 66 PSMFLATH---QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLL 122
P + A H QP LL L E R L V+W + L F+ L DQ+
Sbjct: 11 PGVVCAGHDNNQPDSFAALLSSL------NELGERQLVHVVKWAKALPGFRNLHVDDQMA 64
Query: 123 LLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL----IQEILAR 178
++Q SW L + + S N PD V NE ++ + R
Sbjct: 65 VIQYSWMGLMVFAMGWRSFT-------NVNSRMLYFAPD--LVFNEYRMHKSRMYSQCVR 115
Query: 179 FRQLSPD-------GSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
R LS + E CMKA++LF+ PV+ L++Q
Sbjct: 116 MRHLSQEFGWLQITPQEFLCMKALLLFS--------IIPVDGLKNQ 153
>gnl|CDD|218163 pfam04592, SelP_N, Selenoprotein P, N terminal region. SelP is the
only known eukaryotic selenoprotein that contains
multiple selenocysteine (Sec) residues, and accounts for
more than 50% of the selenium content of rat and human
plasma. It is thought to be glycosylated. SelP may have
antioxidant properties. It can attach to epithelial
cells, and may protect vascular endothelial cells
against peroxynitrite toxicity. The high selenium
content of SelP suggests that it may be involved in
selenium intercellular transport or storage. The
promoter structure of bovine SelP suggest that it may be
involved in countering heavy metal intoxication, and may
also have a developmental function. The N-terminal
region of SelP can exist independently of the C terminal
region. Zebrafish selenoprotein Pb lacks the C terminal
Sec-rich region, and a protein encoded by the rat SelP
gene and lacking this region has also been reported.
N-terminal region contains a conserved SecxxCys motif,
which is similar to the CysxxCys found in thioredoxins.
It is speculated that the N terminal region may adopt a
thioredoxin fold and catalyze redox reactions. The
N-terminal region also contains a His-rich region, which
is thought to mediate heparin binding. Binding to
heparan proteoglycans could account for the membrane
binding properties of SelP. The function of the
bacterial members of this family is uncharcterised.
Length = 238
Score = 32.9 bits (75), Expect = 0.21
Identities = 18/66 (27%), Positives = 21/66 (31%), Gaps = 9/66 (13%)
Query: 1 VQHERGPRKPKIHNAHHQDSKLEPHN-PHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPP 59
V+ E P H+ H H HH P N S + P P PP
Sbjct: 177 VEAEPRQDHPHHHSHHEHQGHAHHHPHGHHHP---GSNSHSESQQP-----DPDKPTEPP 228
Query: 60 PPSHHH 65
HHH
Sbjct: 229 SGLHHH 234
>gnl|CDD|132745 cd06947, NR_LBD_GR_Like, Ligand binding domain of nuclear hormone
receptors:glucocorticoid receptor, mineralocorticoid
receptor , progesterone receptor, and androgen receptor.
The ligand binding domain of GR_like nuclear receptors:
This family of NRs includes four distinct, but closely
related nuclear hormone receptors: glucocorticoid
receptor (GR), mineralocorticoid receptor (MR),
progesterone receptor (PR), and androgen receptor (AR).
These four receptors play key roles in some of the most
fundamental physiological functions such as the stress
response, metabolism, electrolyte homeostasis, immune
function, growth, development, and reproduction. The NRs
in this family use multiple signaling pathways and share
similar functional mechanisms. The dominant signaling
pathway is via direct DNA binding and transcriptional
regulation of target genes. Another mechanism is via
protein-protein interactions, mainly with other
transcription factors such as nuclear factor-kappaB and
activator protein-1, to regulate gene expression
patterns. Both pathways can up-regulate or down-regulate
gene expression and require ligand activation of the
receptor and recruitment of other cofactors such as
chaperone proteins and coregulator proteins. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, GR, MR, PR, and
AR share the same modular structure with a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 246
Score = 32.7 bits (75), Expect = 0.22
Identities = 31/133 (23%), Positives = 54/133 (40%), Gaps = 26/133 (19%)
Query: 97 RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS--------LL 148
R L V+W + L F+ L DQ+ L+Q SW L + L S S L+
Sbjct: 39 RQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLV 98
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFR--QLSPDGSECGCMKAVILFTPETPGLV 206
N ++ + + + +++I F Q++ + E CMK ++L +
Sbjct: 99 FNEQRMHQS------AMYSLCLGMRQISQEFVRLQVTYE--EFLCMKVLLLLS------- 143
Query: 207 DAQPVEMLQDQAQ 219
P + L+ QA
Sbjct: 144 -TIPKDGLKSQAA 155
>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 = 30.2 bits (68), Expect = 0.39
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 1 VQHERGPRKPKI 12
VQHERGPR +
Sbjct: 81 VQHERGPRNSTL 92
>gnl|CDD|218147 pfam04556, DpnII, DpnII restriction endonuclease. Members of this
family are type II restriction enzymes (EC:3.1.21.4).
They recognise the double-stranded unmethylated sequence
GATC and cleave before G-1.
http://rebase.neb.com/rebase/enz/DpnII.html.
Length = 284
Score = 31.1 bits (71), Expect = 0.91
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 22/91 (24%)
Query: 230 YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI-------PIQRLLGDMYT--ME 280
+ + P +L +LP L A+R ++L + + + Y +E
Sbjct: 57 FKKYPE----VLKVLPILLAIRDKKKDKLLANGNLDFLNLDFKKKNYDDENIEDYYEFLE 112
Query: 281 KSYETPGLVDAQPVEMLQDQAQCILGDYVRG 311
K+ GL+D + Q++ L DYV G
Sbjct: 113 KT----GLLD-----LFQNKLIKSLVDYVFG 134
>gnl|CDD|223009 PHA03211, PHA03211, serine/threonine kinase US3; Provisional.
Length = 461
Score = 31.0 bits (70), Expect = 0.95
Identities = 14/49 (28%), Positives = 18/49 (36%), Gaps = 6/49 (12%)
Query: 30 SPDLLPPNGISSVKIPPTVLY-PPSGLKSPPPPSHHHPSMFLATHQPPP 77
+ + P + PP Y PP G+ PPPP H PS
Sbjct: 19 REEAVEPETTTRCVFPPETFYNPPRGVCFPPPPEHDPPS-----PHGAR 62
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 30.8 bits (70), Expect = 1.2
Identities = 15/71 (21%), Positives = 18/71 (25%), Gaps = 1/71 (1%)
Query: 10 PKIHNAHHQDSKLEPHNPHHSPDL-LPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSM 68
P + P +P D LPP S P SPPP P
Sbjct: 187 PPSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPP 246
Query: 69 FLATHQPPPHP 79
+ P
Sbjct: 247 PVQQVPPLSTA 257
>gnl|CDD|215379 PLN02708, PLN02708, Probable pectinesterase/pectinesterase
inhibitor.
Length = 553
Score = 30.6 bits (69), Expect = 1.4
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 24 PHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQ 83
H+ HH+P PP SS PP +L + + P S + PP P +Q
Sbjct: 24 RHHHHHTPSPSPPPP-SSPSTPPQILLACNATRFPD----TCVSSLSNAGRVPPDPKPIQ 78
Query: 84 ILMSA 88
I+ SA
Sbjct: 79 IIQSA 83
>gnl|CDD|220708 pfam10349, WWbp, WW-domain ligand protein. The WWbp domain is
characterized by several short PY and PT-like motifs of
the PPPPY form. These appear to bind directly to the WW
domains of WWP1 and WWP2 and other such diverse proteins
as dystrophin and YAP (Yes-associated protein). This is
the WW-domain binding protein WWbp via PY and PY_like
motifs. The presence of a phosphotyrosine residue in the
pWBP-1 peptide abolishes WW domain binding which
suggests a potential regulatory role for tyrosine
phosphorylation in modulating WW domain-ligand
interactions. Given the likelihood that WWP1 and WWP2
function as E3 ubiquitin-protein ligases, it is possible
that initial substrate-specific recognition occurs via
WW domain-substrate protein interaction followed by
ubiquitin transfer and subsequent proteolysis. This
domain lies just downstream of the GRAM (pfam02893) in
many members.
Length = 111
Score = 28.9 bits (65), Expect = 1.4
Identities = 25/83 (30%), Positives = 28/83 (33%), Gaps = 11/83 (13%)
Query: 1 VQHERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPP 60
V E G P H LEP + PP G PP YP P P
Sbjct: 40 VSRESGYYPPPGAYVH-----LEPLPAYGQYAAPPPYG------PPPPYYPAPPGVYPTP 88
Query: 61 PSHHHPSMFLATHQPPPHPGLLQ 83
P + M PPP+PG Q
Sbjct: 89 PPPNSGYMADPQEPPPPYPGPPQ 111
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 30.2 bits (68), Expect = 1.8
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 9/66 (13%)
Query: 23 EPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFL-----ATHQPPP 77
P P P P G P +PP G + PPP+ +P + T+Q P
Sbjct: 135 VPQMPASPPG---PEGEPQPGNTPVS-FPPQGSVAVPPPTAFYPGNGVTPPPQVTYQSVP 190
Query: 78 HPGLLQ 83
P +Q
Sbjct: 191 VPNRIQ 196
>gnl|CDD|218878 pfam06061, Baculo_ME53, Baculoviridae ME53. ME53 is one of the
major early-transcribed genes. The ME53 protein is
reported to contain a putative zinc finger motif.
Length = 326
Score = 30.0 bits (68), Expect = 2.0
Identities = 10/62 (16%), Positives = 19/62 (30%), Gaps = 9/62 (14%)
Query: 253 STIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQP-----VEMLQDQAQCILGD 307
T + F+ET + + R + + V P + L+D +
Sbjct: 180 RTYGGVVFRETFYNCRVDR-YRNDF---GDPTFADDVSVVPGPSRLLSFLKDNFFFTILT 235
Query: 308 YV 309
Y
Sbjct: 236 YF 237
>gnl|CDD|218397 pfam05044, Prox1, Homeobox prospero-like protein (PROX1). The
homeobox gene Prox1 is expressed in a subpopulation of
endothelial cells that, after budding from veins, gives
rise to the mammalian lymphatic system. Prox1 has been
found to be an early specific marker for the developing
liver and pancreas in the mammalian foregut endoderm.
This family contains an atypical homeobox domain.
Length = 908
Score = 30.0 bits (67), Expect = 2.5
Identities = 22/90 (24%), Positives = 31/90 (34%), Gaps = 13/90 (14%)
Query: 7 PRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPP---PPSH 63
P I N S++ P SP L P+G P SP P +
Sbjct: 642 PLTVAIPNPSLHQSEVFMGYPFQSPHLGAPSG----------SPPGKDRDSPDLPRPTTS 691
Query: 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQE 93
HP + A H P P L + + +C +
Sbjct: 692 LHPKLLSAHHHPGSSPDGLSLSLIKSECGD 721
>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 = 28.8 bits (64), Expect = 4.4
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143
V+W + L F+ L DQ+ L+Q SW + L+ +++ W
Sbjct: 45 VKWAKVLPGFRNLPLEDQITLIQYSW-----MCLSSFALSW 80
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 28.6 bits (64), Expect = 6.4
Identities = 24/87 (27%), Positives = 32/87 (36%), Gaps = 9/87 (10%)
Query: 2 QHERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGI-----SSVKIPPTVLYPPSGLK 56
Q +P+ + +P P P PP S ++PP PP +
Sbjct: 208 QGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQ 267
Query: 57 SPPPPSHHHPSMFLATHQPPPHPGLLQ 83
PP P P +QP PHPGL Q
Sbjct: 268 QPPQPQAQPPPQ----NQPTPHPGLPQ 290
>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 = 28.1 bits (63), Expect = 6.5
Identities = 39/168 (23%), Positives = 73/168 (43%), Gaps = 23/168 (13%)
Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK-----ARERLPPDDVRVN 166
F L + DQ++LL+ E+ L+ +++ N + P D +
Sbjct: 74 FMELCQNDQIVLLKAGSLEVVLVRMSR---------AFNPSNNTVLFDGKYAPIDLFKSL 124
Query: 167 NEIKLIQEILARFR-----QLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCI 221
LI + + +L+ D E A++L + + PGL + + VE LQ + +
Sbjct: 125 GCDDLISAVFDFAKSLCELKLTED--EIALFSALVLISADRPGLQEKRKVEKLQQKIELA 182
Query: 222 LGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKETIGDIP 268
L ++ + T +LL +P+LRA+ +E+L FK++ DI
Sbjct: 183 LRHVLQ-KNHGDDTILTKLLAKMPTLRALCSLHMEKLQKFKQSYPDIV 229
>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 = 27.7 bits (62), Expect = 7.1
Identities = 25/106 (23%), Positives = 43/106 (40%), Gaps = 7/106 (6%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
V++V+ + F LS D+ LL+ + L+LL L++ L L
Sbjct: 18 IVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNEGTVLCDFRPVEFASLLSQ 77
Query: 162 DVRVNNEIKLIQEILA---RFRQLSPDGSECGCMKAVILFTPETPG 204
+ KLI E+L + L+ +E + A L P++ G
Sbjct: 78 LL----HGKLIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLG 119
>gnl|CDD|214385 CHL00175, minD, septum-site determining protein; Validated.
Length = 281
Score = 28.2 bits (63), Expect = 7.5
Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 23/101 (22%)
Query: 119 DQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILAR 178
DQ L+ + WK L LL ++ K R+R +N + ++
Sbjct: 84 DQALIRDKRWKNLSLLAIS---------------KNRQRYNVTRKNMNMLVDSLKNRGYD 128
Query: 179 FRQL-SPDGSECG-------CMKAVILFTPETPGLVDAQPV 211
+ + P G + G +A+++ TPE + DA V
Sbjct: 129 YILIDCPAGIDVGFINAIAPAQEAIVVTTPEITAIRDADRV 169
>gnl|CDD|148133 pfam06335, DUF1054, Protein of unknown function (DUF1054). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 194
Score = 27.6 bits (62), Expect = 7.7
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 158 LPPDDVRVNNEIKLIQEILARFRQLSP 184
+P +D + + + + I F+QL P
Sbjct: 166 IPKEDPLLMSPDEFLATIEDTFKQLLP 192
>gnl|CDD|177328 PHA01929, PHA01929, putative scaffolding protein.
Length = 306
Score = 28.1 bits (62), Expect = 8.6
Identities = 14/67 (20%), Positives = 20/67 (29%), Gaps = 2/67 (2%)
Query: 6 GPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHH 65
P++ I Q PH P + P P L+ PPPP+
Sbjct: 46 APQQLAIPTQQPQPVPTSAMTPHVVQQ--APAQPAPAAPPAAGAALPEALEVPPPPAFTP 103
Query: 66 PSMFLAT 72
+ T
Sbjct: 104 NGEIVGT 110
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 0.139 0.430
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,582,854
Number of extensions: 1940791
Number of successful extensions: 2004
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1888
Number of HSP's successfully gapped: 134
Length of query: 367
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 269
Effective length of database: 6,590,910
Effective search space: 1772954790
Effective search space used: 1772954790
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: 60 (27.1 bits)