RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16761
(261 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 = 132 bits (335), Expect = 2e-38
Identities = 60/167 (35%), Positives = 82/167 (49%), Gaps = 29/167 (17%)
Query: 85 HLLLAESWRELFILGLAQYLPSLDLGELVESCKS------RHVDIEEEVIRFQSVLNEFK 138
+LL ESW ELF+LG AQ+ LD L+ EV Q L+ F+
Sbjct: 61 LILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLSEVRALQETLSRFR 120
Query: 139 VLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESC-LRDVIAIAAIQGHT 197
L +D E+ ++AI LFK PE+ L+D + A+Q
Sbjct: 121 QLRVDATEFACLKAIVLFK----------------------PETRGLKDPAQVEALQDQA 158
Query: 198 QIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 244
Q+ LNK+I T YP+QP RF K+ L+LP L+ I S +EELFF+ IG
Sbjct: 159 QLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTIEELFFKKTIG 205
Score = 78.1 bits (193), Expect = 1e-17
Identities = 29/89 (32%), Positives = 41/89 (46%), Gaps = 6/89 (6%)
Query: 1 HLLLAESWRELFILGLAQYLPSLDLGELVESCKS------RHVDIEEEVIRFQSVLNEFK 54
+LL ESW ELF+LG AQ+ LD L+ EV Q L+ F+
Sbjct: 61 LILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLSEVRALQETLSRFR 120
Query: 55 VLNIDPYEYDYIRAITLFKTAFTSRRELA 83
L +D E+ ++AI LFK ++ A
Sbjct: 121 QLRVDATEFACLKAIVLFKPETRGLKDPA 149
>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 = 88.8 bits (221), Expect = 6e-22
Identities = 45/152 (29%), Positives = 68/152 (44%), Gaps = 29/152 (19%)
Query: 86 LLLAESWRELFILGLAQYLPSLDL--------GELVESCKSRHVDIEEEVIRFQSVLNEF 137
LL SW EL +LGLAQ +L ++ + + + + E V R Q +L++
Sbjct: 35 TLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAELVQRLQELLSKL 94
Query: 138 KVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLRDVIAIAAIQGHT 197
+ L +DP EY ++AI LF + L++ + +Q
Sbjct: 95 RSLQLDPKEYACLKAIVLFNPDLP---------------------GLKNQQQVEELQEKA 133
Query: 198 QIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 229
Q L +YI YP QP RF K+ L LP L+SI
Sbjct: 134 QQALQEYIRKRYPQQPARFAKLLLRLPELRSI 165
Score = 62.6 bits (153), Expect = 4e-12
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 2 LLLAESWRELFILGLAQYLPSLDL--------GELVESCKSRHVDIEEEVIRFQSVLNEF 53
LL SW EL +LGLAQ +L ++ + + + + E V R Q +L++
Sbjct: 35 TLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAELVQRLQELLSKL 94
Query: 54 KVLNIDPYEYDYIRAITLFK 73
+ L +DP EY ++AI LF
Sbjct: 95 RSLQLDPKEYACLKAIVLFN 114
>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 = 85.6 bits (212), Expect = 4e-20
Identities = 56/179 (31%), Positives = 85/179 (47%), Gaps = 32/179 (17%)
Query: 87 LLAESWRELFILGLAQYLPSLDLGELV--------ESCKSRHVDIEEEVIRFQSVLNEFK 138
LL SW ELF+L AQ L + L+ R V + + FQ + + K
Sbjct: 67 LLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLK 126
Query: 139 VLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESC-LRDVIAIAAIQGHT 197
L++D E+ ++AI LF ++C L D I ++Q +
Sbjct: 127 ALHVDSAEFSCLKAIVLFT----------------------SDACGLSDPAHIESLQEKS 164
Query: 198 QIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHM 256
Q L +Y+ T YP+QPTRF K+ L LP L+++ S V+E+LFF ++G T I+ I M
Sbjct: 165 QCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVG-KTPIETLIRDM 222
Score = 39.4 bits (92), Expect = 0.001
Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 3 LLAESWRELFILGLAQYLPSLDLGELV--------ESCKSRHVDIEEEVIRFQSVLNEFK 54
LL SW ELF+L AQ L + L+ R V + + FQ + + K
Sbjct: 67 LLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLK 126
Query: 55 VLNIDPYEYDYIRAITLFKT 74
L++D E+ ++AI LF +
Sbjct: 127 ALHVDSAEFSCLKAIVLFTS 146
>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 = 71.8 bits (176), Expect = 5e-15
Identities = 44/180 (24%), Positives = 63/180 (35%), Gaps = 43/180 (23%)
Query: 86 LLLAESWRELFILGLAQYLPSLDLGELVESCKSRHVDIEEE------------------- 126
LL SW L +LGLAQ D E+ + E
Sbjct: 55 RLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMHWGGTPPPTLTMPPCIPL 114
Query: 127 --VIRFQSVLNEFKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCL 184
V Q L + L++D EY Y++ LF + P
Sbjct: 115 ADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLF---------------TPVPPLLCPHY-- 157
Query: 185 RDVIAIAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 244
I A+Q Q LN++ P + R ++ L+L L+ I + + ELFFR IIG
Sbjct: 158 -----IEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIG 212
>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 = 71.2 bits (175), Expect = 6e-15
Identities = 49/172 (28%), Positives = 73/172 (42%), Gaps = 35/172 (20%)
Query: 87 LLAESWRELFILGLAQ--YLPSLD--LGELVESCK----------SRHVDIEEEVIRFQS 132
L+ W ELF LGLAQ SL L ++ + + + E + + Q
Sbjct: 58 LVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQDKLSADKVKQVMEHINKLQE 117
Query: 133 VLNEFKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLRDVIAIAA 192
+N + L++D +EY Y++AI LF +HP LR I
Sbjct: 118 FVNSMQKLDVDDHEYAYLKAIVLFSP-------------------DHPGQELRQ--QIEK 156
Query: 193 IQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 244
+Q + L Y+ YP R K+ L LP L+S+ + EELFF +IG
Sbjct: 157 LQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLIG 208
Score = 46.6 bits (111), Expect = 3e-06
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 14/84 (16%)
Query: 3 LLAESWRELFILGLAQ--YLPSLD--LGELVESCK----------SRHVDIEEEVIRFQS 48
L+ W ELF LGLAQ SL L ++ + + + E + + Q
Sbjct: 58 LVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQDKLSADKVKQVMEHINKLQE 117
Query: 49 VLNEFKVLNIDPYEYDYIRAITLF 72
+N + L++D +EY Y++AI LF
Sbjct: 118 FVNSMQKLDVDDHEYAYLKAIVLF 141
>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 = 64.5 bits (157), Expect = 2e-12
Identities = 48/177 (27%), Positives = 71/177 (40%), Gaps = 39/177 (22%)
Query: 86 LLLAESWRELFILGLAQYLPSLDLGE----------LVESCKSRHVDIEEE--------V 127
LLL W LF+LGLAQ + ++ E L+E S + + V
Sbjct: 55 LLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQSSSGGSGQPDRPQPSLAAV 114
Query: 128 IRFQSVLNEFKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLRDV 187
Q LN+F L++ P EY Y++ LF + L
Sbjct: 115 QWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPG---------------------LTAS 153
Query: 188 IAIAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 244
+ +Q Q L + + ++P RF +I L LKSIP ++ +LFFR IIG
Sbjct: 154 SHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIG 210
Score = 38.6 bits (90), Expect = 0.001
Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 18/89 (20%)
Query: 2 LLLAESWRELFILGLAQYLPSLDLGE----------LVESCKSRHVDIEEE--------V 43
LLL W LF+LGLAQ + ++ E L+E S + + V
Sbjct: 55 LLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQSSSGGSGQPDRPQPSLAAV 114
Query: 44 IRFQSVLNEFKVLNIDPYEYDYIRAITLF 72
Q LN+F L++ P EY Y++ LF
Sbjct: 115 QWLQCCLNKFWSLDLSPKEYAYLKGTILF 143
>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 = 50.2 bits (120), Expect = 2e-07
Identities = 42/194 (21%), Positives = 70/194 (36%), Gaps = 52/194 (26%)
Query: 82 LAGHLLLAES-WRELFILGLAQ------------------------------YLPSLDLG 110
L L+L S W L +LGLAQ
Sbjct: 50 LDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPPPTSGAEPGEPQAL 109
Query: 111 ELVESCKSRHVDIEEEVIRFQSVLNEFKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSS 170
+ ++ H+ ++ ++ L + L+I EY Y++ LF +
Sbjct: 110 PQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPG-------- 161
Query: 171 SSSDDGSEHPESCLRDVIAIAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIP 230
L+ V I +Q Q LN+++ ++ RF K+ + L L++I
Sbjct: 162 -------------LQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAIN 208
Query: 231 SLVLEELFFRNIIG 244
+ V+ ELFFR IIG
Sbjct: 209 ANVIAELFFRPIIG 222
>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 = 47.8 bits (114), Expect = 1e-06
Identities = 44/166 (26%), Positives = 71/166 (42%), Gaps = 31/166 (18%)
Query: 87 LLAESWRELFILGLA-QYLPSLDLGELVESCK-SRHVDIEEEVIRFQS-VLNE----FKV 139
LL E +LG+A + +P D+ L RH E E+ R + +L+E +
Sbjct: 69 LLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHC-PEPEISRVANRILDELVLPLRD 127
Query: 140 LNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPES-CLRDVIAIAAIQGHTQ 198
LNID EY ++AI F P++ L D I ++ Q
Sbjct: 128 LNIDDNEYACLKAIVFF----------------------DPDAKGLSDPQKIKRLRFQVQ 165
Query: 199 IFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 244
+ L YI+ RF ++ L+LP L+SI ++E++ F + G
Sbjct: 166 VSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFG 211
Score = 27.7 bits (62), Expect = 5.1
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 3 LLAESWRELFILGLA-QYLPSLDLGELVESCK-SRHVDIEEEVIRFQS-VLNE----FKV 55
LL E +LG+A + +P D+ L RH E E+ R + +L+E +
Sbjct: 69 LLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHC-PEPEISRVANRILDELVLPLRD 127
Query: 56 LNIDPYEYDYIRAITLF 72
LNID EY ++AI F
Sbjct: 128 LNIDDNEYACLKAIVFF 144
>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 = 47.0 bits (112), Expect = 2e-06
Identities = 41/169 (24%), Positives = 63/169 (37%), Gaps = 31/169 (18%)
Query: 87 LLAESWRELFILGLA---------QYLPSLDLGELVESCKSRHVD-IEEEVIRFQSVLNE 136
LL SW E L LA L S L + KS V+ I E++ + ++
Sbjct: 37 LLKSSWFEWLRLELASRSAECEKDDLLFSNGLYLDRDELKSIEVNYINEQIRQLFELVQP 96
Query: 137 FKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLRDVIAIAAIQGH 196
K L + E ++A+ LF S + E E L++VIA A
Sbjct: 97 LKELKLTDEELAALKALLLFNPA---------GKRLSGEILEVVEK-LQEVIANA----- 141
Query: 197 TQIFLNKYIHTVY--PSQPTRFCKIQLILPRLKSIPSLVLEELFFRNII 243
L+ Y P+ R K+ +LP L+ I + E+L +
Sbjct: 142 ----LHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLELAKLF 186
Score = 35.8 bits (83), Expect = 0.011
Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 10/84 (11%)
Query: 3 LLAESWRELFILGLA---------QYLPSLDLGELVESCKSRHVD-IEEEVIRFQSVLNE 52
LL SW E L LA L S L + KS V+ I E++ + ++
Sbjct: 37 LLKSSWFEWLRLELASRSAECEKDDLLFSNGLYLDRDELKSIEVNYINEQIRQLFELVQP 96
Query: 53 FKVLNIDPYEYDYIRAITLFKTAF 76
K L + E ++A+ LF A
Sbjct: 97 LKELKLTDEELAALKALLLFNPAG 120
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 45.4 bits (108), Expect = 5e-06
Identities = 39/154 (25%), Positives = 56/154 (36%), Gaps = 30/154 (19%)
Query: 87 LLAESWRELFILGLAQY----------LPSLDLGELVESCKSRHVDIEEEVIRFQSVLNE 136
LL W EL +L LA P + R + ++
Sbjct: 29 LLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLFSPFLDRILSELVKP 88
Query: 137 FKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLRDVIAIAAIQGH 196
+ L +D EY ++AI LF + S++G E E L++ A A
Sbjct: 89 LRELKLDDEEYALLKAIVLFNPAVPG---------LSEEGKEIVEK-LQEKYANA----- 133
Query: 197 TQIFLNKYIHTVYPSQ-PTRFCKIQLILPRLKSI 229
L+ Y YP P RF K+ LILP L+ I
Sbjct: 134 ----LHDYYLKNYPMNYPGRFAKLLLILPELRKI 163
Score = 34.6 bits (80), Expect = 0.023
Identities = 24/113 (21%), Positives = 37/113 (32%), Gaps = 14/113 (12%)
Query: 3 LLAESWRELFILGLAQY----------LPSLDLGELVESCKSRHVDIEEEVIRFQSVLNE 52
LL W EL +L LA P + R + ++
Sbjct: 29 LLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLFSPFLDRILSELVKP 88
Query: 53 FKVLNIDPYEYDYIRAITLFKTAFTSRRELAGHLL-LAESWRELFILGLAQYL 104
+ L +D EY ++AI LF A L+ + E +E + L Y
Sbjct: 89 LRELKLDDEEYALLKAIVLFNPA---VPGLSEEGKEIVEKLQEKYANALHDYY 138
>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 = 44.6 bits (106), Expect = 1e-05
Identities = 34/114 (29%), Positives = 46/114 (40%), Gaps = 25/114 (21%)
Query: 130 FQSVLNE----FKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLR 185
F +L E + L +D E +RAI LF +VK +S + E + L
Sbjct: 113 FDRILTELVVKMRDLKMDRTELGCLRAIILFNP----DVKGLKSRQEVESLREKVYASLE 168
Query: 186 DVIAIAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFF 239
+ Y +P QP RF K+ L LP L+SI LE LFF
Sbjct: 169 E-----------------YCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 205
>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 = 41.1 bits (97), Expect = 1e-04
Identities = 39/155 (25%), Positives = 63/155 (40%), Gaps = 31/155 (20%)
Query: 86 LLLAESWRELFILGLAQY--------LPSLDLGELVESCKSR-HVDIEEEVIRF-QSVLN 135
+LL W EL +L LA L + + G + + + ++ E+IR +N
Sbjct: 34 VLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVN 93
Query: 136 EFKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLRDVIAIAAIQG 195
+ L +D EY ++AI LF + ES L D + +Q
Sbjct: 94 PLRALKLDDEEYALLKAIVLFS-------------------PDRKES-LEDRKIVEELQE 133
Query: 196 HTQIFLNKYIHTVYP-SQPTRFCKIQLILPRLKSI 229
L Y+ YP P+RF K+ L+LP L+ +
Sbjct: 134 RLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 168
Score = 33.0 bits (76), Expect = 0.083
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 10/82 (12%)
Query: 2 LLLAESWRELFILGLAQY--------LPSLDLGELVESCKSR-HVDIEEEVIRF-QSVLN 51
+LL W EL +L LA L + + G + + + ++ E+IR +N
Sbjct: 34 VLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVN 93
Query: 52 EFKVLNIDPYEYDYIRAITLFK 73
+ L +D EY ++AI LF
Sbjct: 94 PLRALKLDDEEYALLKAIVLFS 115
>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 = 41.2 bits (97), Expect = 2e-04
Identities = 34/164 (20%), Positives = 61/164 (37%), Gaps = 33/164 (20%)
Query: 87 LLAESWRELFILGLAQYLPSLDLGELVESCKSRHVDIEEE-----------VIRFQSVLN 135
LL W EL +L +LG L + C S+++ E+E V R +L
Sbjct: 64 LLTTKWAELILLSTITVASLQNLGLLQD-CLSKYLPSEDELERFGDEGGEVVERLTYLLA 122
Query: 136 EFKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLRDVIAIAAIQG 195
+F+ L + EY ++ I +D +++ + ++Q
Sbjct: 123 KFRQLKVSNEEYVCLKVINFLN-------QDIDGLTNASQ--------------LESLQK 161
Query: 196 HTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFF 239
L + YP+QP RF + LP +++ +L F
Sbjct: 162 RYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAAAGKLLHSKLF 205
Score = 30.8 bits (70), Expect = 0.49
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 12/80 (15%)
Query: 3 LLAESWRELFILGLAQYLPSLDLGELVESCKSRHVDIEEE-----------VIRFQSVLN 51
LL W EL +L +LG L + C S+++ E+E V R +L
Sbjct: 64 LLTTKWAELILLSTITVASLQNLGLLQD-CLSKYLPSEDELERFGDEGGEVVERLTYLLA 122
Query: 52 EFKVLNIDPYEYDYIRAITL 71
+F+ L + EY ++ I
Sbjct: 123 KFRQLKVSNEEYVCLKVINF 142
>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 = 33.0 bits (76), Expect = 0.069
Identities = 24/109 (22%), Positives = 39/109 (35%), Gaps = 24/109 (22%)
Query: 121 VDIEEEVIRFQSVLNEFKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHP 180
+ E + F + L +D EY + AI LF S D
Sbjct: 82 GEFIEPLFEF---AEKMNKLQLDDNEYALLTAIVLF----------------SPDRPG-- 120
Query: 181 ESCLRDVIAIAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 229
L+DV + +Q L +Y+ +P P F K+ L L+++
Sbjct: 121 ---LQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLTELRTL 166
>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 = 29.6 bits (67), Expect = 1.5
Identities = 26/118 (22%), Positives = 50/118 (42%), Gaps = 21/118 (17%)
Query: 127 VIRFQSVLNEFKVLNIDPYEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESCLRD 186
V R Q ++N+ + L D E+ ++ + LF +VK L +
Sbjct: 126 VDRAQELVNKLRELQFDRQEFVCLKFLILFNP----DVKG-----------------LEN 164
Query: 187 VIAIAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 244
+ ++Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 165 RQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 222
>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 = 29.3 bits (66), Expect = 1.9
Identities = 34/159 (21%), Positives = 64/159 (40%), Gaps = 24/159 (15%)
Query: 86 LLLAESWRELFILGLAQYLPSLDLGELVESCKSRHVDIEEEVIRF-QSVLNEFKVLNIDP 144
LLL ++ ELF+L LA R ++ +++ VL+ + +
Sbjct: 77 LLLESAFLELFVLRLAY----------------RSNPVDGKLVFCNGLVLHRLQCVRGFG 120
Query: 145 YEYDYIRAITLFKTVIEDEVKDNRSSSSSDDGSEHPESC--LRDVIAIAAIQGHTQIFLN 202
D I A F + ++ + D+ S+ L++ + +Q L
Sbjct: 121 EWLDSILA---FSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLR 177
Query: 203 KYIHTVYPSQ--PTRFCKIQLILPRLKSIPSLVLEELFF 239
++ + YP Q P R K+ L LP L+++ L+ +FF
Sbjct: 178 DHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFF 216
>gnl|CDD|216738 pfam01850, PIN, PIN domain.
Length = 120
Score = 27.4 bits (61), Expect = 4.3
Identities = 16/66 (24%), Positives = 30/66 (45%)
Query: 4 LAESWRELFILGLAQYLPSLDLGELVESCKSRHVDIEEEVIRFQSVLNEFKVLNIDPYEY 63
LAE+ REL + +L L EL+ + + D ++ +L+ F+VL +D
Sbjct: 17 LAEAARELLESDGELVISALVLAELLYGLRRKRRDKAAALVELLLLLSAFEVLPLDEEVA 76
Query: 64 DYIRAI 69
+ +
Sbjct: 77 EEAAEL 82
Score = 27.4 bits (61), Expect = 4.3
Identities = 16/66 (24%), Positives = 30/66 (45%)
Query: 88 LAESWRELFILGLAQYLPSLDLGELVESCKSRHVDIEEEVIRFQSVLNEFKVLNIDPYEY 147
LAE+ REL + +L L EL+ + + D ++ +L+ F+VL +D
Sbjct: 17 LAEAARELLESDGELVISALVLAELLYGLRRKRRDKAAALVELLLLLSAFEVLPLDEEVA 76
Query: 148 DYIRAI 153
+ +
Sbjct: 77 EEAAEL 82
>gnl|CDD|238500 cd01018, ZntC, Metal binding protein ZntC. These proteins are
predicted to function as initial receptors in ABC
transport of metal ions. They belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
They are comprised of two globular subdomains connected
by a long alpha helix and bind their specific ligands in
the cleft between these domains. In addition, many of
these proteins possess a metal-binding histidine-rich
motif (repetitive HDH sequence).
Length = 266
Score = 27.7 bits (62), Expect = 5.3
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 24 DLGELVESCKSRHVD---IEEEVIRFQS--VLNEF--KVLNIDPYEYDYIRAITLFKTAF 76
DL L++ K + V ++ + + + E KV+ IDP D+ + AF
Sbjct: 205 DLKRLIDLAKEKGVRVVFVQPQFSTKSAEAIAREIGAKVVTIDPLAADWEENLLKVADAF 264
Query: 77 TS 78
Sbjct: 265 AH 266
>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 = 27.7 bits (61), Expect = 5.4
Identities = 14/55 (25%), Positives = 27/55 (49%)
Query: 190 IAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 244
+ +Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 170 VEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 224
>gnl|CDD|107164 PHA02277, PHA02277, hypothetical protein.
Length = 150
Score = 27.0 bits (59), Expect = 7.6
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 118 SRHVDIEEEVIRFQSVLNEFKVLNIDPYEYDYIRAITLFKTVIEDEV 164
SR V +EE R VLN + D AI L ++EDE+
Sbjct: 47 SRSVSLEE-ATRIAKVLNAVTAQEVTGDFNDAFNAIDLMMIIMEDEL 92
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 0.407
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,889,073
Number of extensions: 1359665
Number of successful extensions: 1172
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1139
Number of HSP's successfully gapped: 49
Length of query: 261
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 166
Effective length of database: 6,723,972
Effective search space: 1116179352
Effective search space used: 1116179352
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: 58 (26.2 bits)