RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17882
(181 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 = 239 bits (613), Expect = 2e-81
Identities = 97/168 (57%), Positives = 118/168 (70%), Gaps = 2/168 (1%)
Query: 1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
MAVKWAK++P+F+ LPFRDQ+ILLEESWSELFLL A QWSLPL +S PL
Sbjct: 41 MAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPL-DSCPLLAVPGLSPDNT 99
Query: 61 NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
++VR L L RFR + VD EFACLKA+VLFK ETRGLKD QVE LQDQA
Sbjct: 100 -EAERTFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQA 158
Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVAN 168
Q+ML +H+RT +P QPARFG+LLL+ R I S+ ++ +FF KT+ N
Sbjct: 159 QLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTIEELFFKKTIGN 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 = 158 bits (401), Expect = 4e-49
Identities = 74/178 (41%), Positives = 110/178 (61%), Gaps = 2/178 (1%)
Query: 2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN 61
AV+WA+N+P F L DQV LL SWSELF+LNA Q +PL +PL A+ A+ +
Sbjct: 46 AVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPL-HVAPLLAAAGLHASPMS 104
Query: 62 GKASQTAAD-VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
D +R+ +++ + + VD AEF+CLKA+VLF S+ GL D +E+LQ+++
Sbjct: 105 ADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKS 164
Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
Q L ++VRT +P QP RFG+LLL R + S+ ++ +FF + V T +E L+ DM
Sbjct: 165 QCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDM 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 = 152 bits (387), Expect = 9e-48
Identities = 64/152 (42%), Positives = 88/152 (57%)
Query: 1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
V WAKNLP+F LP DQ+ LL+ SW+EL LL Q S+ S L + V
Sbjct: 14 KTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTE 73
Query: 61 NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
A V+ L +L + R + +DP E+ACLKA+VLF + GLK+ QVE LQ++A
Sbjct: 74 REALLGLAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKA 133
Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNI 152
Q L +++R +P QPARF +LLL + R+I
Sbjct: 134 QQALQEYIRKRYPQQPARFAKLLLRLPELRSI 165
>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 = 116 bits (292), Expect = 6e-33
Identities = 57/167 (34%), Positives = 89/167 (53%), Gaps = 11/167 (6%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
V+WAK +P F+ LP DQVILL W+EL L+ A ++ L H+
Sbjct: 47 VEWAKRIPHFSELPLDDQVILLRAGWNEL-LIAAFAHRSIAVKDGILLATGLHL-----H 100
Query: 63 KASQTAADV-----RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
+ S A V R+L ++ + R + +D E CL+A++LF + +GLK +VE+L+
Sbjct: 101 RNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLR 160
Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
++ L ++ R HP QP RF +LLL R+I ++H+FF K
Sbjct: 161 EKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 207
>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 = 110 bits (278), Expect = 1e-30
Identities = 52/176 (29%), Positives = 87/176 (49%), Gaps = 2/176 (1%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
V+WAK +P+F LP DQV LL E LL + S+P L ++ +
Sbjct: 49 VEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPY--KDILLLGNDLIIPRHCP 106
Query: 63 KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
+ + R+L+ ++ R + +D E+ACLKA+V F + +GL D +++ L+ Q QV
Sbjct: 107 EPEISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQV 166
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
L ++ RFG LLL+ ++I ++ I FA+ ++ LL +M
Sbjct: 167 SLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222
>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 = 107 bits (269), Expect = 7e-30
Identities = 48/156 (30%), Positives = 78/156 (50%), Gaps = 4/156 (2%)
Query: 1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
+ V+WAK++P F LP DQ++LL+ W EL +L+ S S L H
Sbjct: 13 LIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDK 72
Query: 61 NGKASQTAAD--VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSE-TRGLKDSLQVENLQ 117
+ +R+L + R + +D E+A LKA+VLF + L+D VE LQ
Sbjct: 73 EDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQ 132
Query: 118 DQAQVMLAQHVRTHHPAQ-PARFGRLLLMTSQCRNI 152
++ L ++R ++P + P+RF +LLL+ R +
Sbjct: 133 ERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 168
>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 = 98.4 bits (245), Expect = 7e-26
Identities = 58/186 (31%), Positives = 88/186 (47%), Gaps = 10/186 (5%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQ---------WSLPLLESSPLFNAS 53
V + +NLPSF LP +DQ++LL+ W LFLL Q +P + L
Sbjct: 36 VAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQ 95
Query: 54 EHVAAVPNGKASQ-TAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQ 112
Q + A V+ L L +F + + P E+A LK +LF + GL S
Sbjct: 96 SSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSH 155
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
V +LQ +AQ L + + HP RF R+LL S ++IP + + +FF + + +
Sbjct: 156 VGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIA 215
Query: 173 KLLCDM 178
+LL DM
Sbjct: 216 ELLGDM 221
>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 = 94.9 bits (236), Expect = 2e-24
Identities = 58/188 (30%), Positives = 82/188 (43%), Gaps = 14/188 (7%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL---------LESSPLFNAS 53
+++ +NLP F LP DQ+ LL SW+ L LL Q +P + L A
Sbjct: 36 IRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAE 95
Query: 54 EHVAAVPNGKASQ----TAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKD 109
H P + ADV+ + L + + +D E+A LK VLF L
Sbjct: 96 MHWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLLCP 155
Query: 110 SLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANT 169
+E LQ +AQ L +H P + R RLLLM S R I + V +FF + N
Sbjct: 156 H-YIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGNV 214
Query: 170 SMEKLLCD 177
SM+ +L
Sbjct: 215 SMDDVLLQ 222
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 88.6 bits (220), Expect = 9e-23
Identities = 45/153 (29%), Positives = 73/153 (47%), Gaps = 11/153 (7%)
Query: 1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
+ V+WAK+ P F L DQ++LL+ W EL LL S+ L + L +
Sbjct: 7 LTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAP---DGTYIR 63
Query: 61 NGKASQTAAD-----VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQ--V 113
+ R+L+ +++ R + +D E+A LKA+VLF GL + + V
Sbjct: 64 PDAVLELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIV 123
Query: 114 ENLQDQAQVMLAQHVRTHHPAQ-PARFGRLLLM 145
E LQ++ L + ++P P RF +LLL+
Sbjct: 124 EKLQEKYANALHDYYLKNYPMNYPGRFAKLLLI 156
>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 = 86.3 bits (214), Expect = 1e-21
Identities = 42/171 (24%), Positives = 68/171 (39%), Gaps = 6/171 (3%)
Query: 1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLF--NASEHVAA 58
+ V+WAK P F L DQ+ LL+ SW E L S + LF
Sbjct: 15 LVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDDLLFSNGLYLDRDE 74
Query: 59 VPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQ--VENL 116
+ + + + +R L ++Q + + + E A LKA++LF + L + VE L
Sbjct: 75 LKSIEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLLFNPAGKRLSGEILEVVEKL 134
Query: 117 QDQAQVMLAQHVRT--HHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT 165
Q+ L + + P R +LL + R I + + AK
Sbjct: 135 QEVIANALHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLELAKL 185
>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 = 85.0 bits (211), Expect = 8e-21
Identities = 55/181 (30%), Positives = 86/181 (47%), Gaps = 15/181 (8%)
Query: 5 WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL---LESSPLFNASEHVAAVPN 61
WAK++P F+ L DQ+ LL+ +W E+ +L + SLP L +P A V
Sbjct: 46 WAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARV-- 103
Query: 62 GKASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
+ + + +LQ RFR +G+ E+ CLKA++L S+ R L+D V+ L+D
Sbjct: 104 ------EGLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRD 157
Query: 119 QAQVMLAQHV-RTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
L + H QP R +LLL+ R + V+H++ K M KL +
Sbjct: 158 AILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLE 217
Query: 178 M 178
M
Sbjct: 218 M 218
>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 = 81.9 bits (203), Expect = 1e-19
Identities = 46/153 (30%), Positives = 78/153 (50%), Gaps = 3/153 (1%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAI--QWSLPLLESSPLFNASE-HVAAV 59
V+WA+N F L DQ+ LL+ WSEL +L+ I Q +S L E ++ +
Sbjct: 55 VEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTL 114
Query: 60 PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
+ ++ V ++ + R + D EF CLK ++LF + +GL++ VE++Q+Q
Sbjct: 115 ASQAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQ 174
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNI 152
L + ++P Q +FG+LLL + R I
Sbjct: 175 VNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAI 207
>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 = 77.4 bits (191), Expect = 7e-18
Identities = 51/181 (28%), Positives = 87/181 (48%), Gaps = 6/181 (3%)
Query: 1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL-LES--SPLFN---ASE 54
+++ WA+++P+F AL Q L+ W ELF L Q S L L + + + N S
Sbjct: 36 LSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSI 95
Query: 55 HVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
+ K Q + L + + + VD E+A LKA+VLF + G + Q+E
Sbjct: 96 QQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIE 155
Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKL 174
LQ++A + L +V +P R +LLL R++ A + +FFA + N ++ +
Sbjct: 156 KLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSV 215
Query: 175 L 175
+
Sbjct: 216 I 216
>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 = 76.4 bits (188), Expect = 2e-17
Identities = 51/194 (26%), Positives = 86/194 (44%), Gaps = 22/194 (11%)
Query: 4 KWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSL--------------------PL 43
++ K +P F LP DQ++L+ W+ L +L Q + P
Sbjct: 37 RFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPP 96
Query: 44 LESSPLFNASEHVAAVPNGKASQ--TAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFK 101
S + + +P +AS +AAD+R + L + + + E+A LK VLF
Sbjct: 97 PTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFN 156
Query: 102 SETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF 161
+ GL+ ++ LQ +AQ L +HVR H ARF +L + S R I + + +F
Sbjct: 157 PDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELF 216
Query: 162 FAKTVANTSMEKLL 175
F + +M+ +L
Sbjct: 217 FRPIIGTVNMDDML 230
>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 = 71.6 bits (175), Expect = 1e-15
Identities = 52/181 (28%), Positives = 86/181 (47%), Gaps = 7/181 (3%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAI-QWSLPLLESSPLFNASEHVAAVPN 61
V+WA++ F L DQ+ LL+ WSEL +L+ I + + E S + V +
Sbjct: 57 VEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDY--S 114
Query: 62 GKASQTAADVRVLNGVLQ----RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
ASQ A + L Q + R + D EF CLK +VLF + + L++ VE +Q
Sbjct: 115 IIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQ 174
Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
+Q L + ++P Q +FG+LLL + R I +++++ + LL +
Sbjct: 175 EQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIE 234
Query: 178 M 178
M
Sbjct: 235 M 235
>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 = 70.9 bits (174), Expect = 1e-15
Identities = 44/158 (27%), Positives = 68/158 (43%), Gaps = 10/158 (6%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAI-----QWSLPLLESSPLFNASEHVA 57
++W K LP F L +D LL W+EL LL+ I Q L + + SE
Sbjct: 44 IQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSED-- 101
Query: 58 AVPNGKASQTAAD-VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENL 116
+ + V L +L +FR + V E+ CLK + + GL ++ Q+E+L
Sbjct: 102 --ELERFGDEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESL 159
Query: 117 QDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPS 154
Q + +L ++P QP RF LL + R
Sbjct: 160 QKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAAAG 197
>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 = 68.2 bits (167), Expect = 2e-14
Identities = 48/178 (26%), Positives = 81/178 (45%), Gaps = 9/178 (5%)
Query: 5 WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL---LESSPLFNASEHVAAVPN 61
WAK++P F++L DQ+ LL+ +W E+ L + SLP L + F E +A
Sbjct: 46 WAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEELARE-A 104
Query: 62 GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
G +A +++R + + ++ E+ LKA+ L S++ ++D V L+D
Sbjct: 105 GLLELYSA----CLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALL 160
Query: 122 VMLAQHVRTHHPAQ-PARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
L+ + HP + P R G+LLL R + + K M KL +M
Sbjct: 161 EALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEM 218
>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 = 65.5 bits (160), Expect = 2e-13
Identities = 49/190 (25%), Positives = 81/190 (42%), Gaps = 21/190 (11%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLP-----LLESSPLFNASEHVA 57
+ WAK +P F L DQV LLE +W EL +L + S+ L L + ++
Sbjct: 49 INWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQ--- 105
Query: 58 AVPNGKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-----ETRGLKDSL 111
G + ++ +L RFR + + E+ CLKA++L S L+
Sbjct: 106 ----GSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRR 161
Query: 112 QVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVAN 168
QV+ L D+ L Q R +LLL+ S R++ + ++H++ K
Sbjct: 162 QVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNV 221
Query: 169 TSMEKLLCDM 178
+ LL +M
Sbjct: 222 VPLYDLLLEM 231
>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 = 64.1 bits (156), Expect = 7e-13
Identities = 50/170 (29%), Positives = 79/170 (46%), Gaps = 20/170 (11%)
Query: 4 KWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK 63
KWA+ +P F+ DQ +LLE ++ ELF+L S P E L NG
Sbjct: 59 KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNP--EEGKLIFC--------NGV 108
Query: 64 ASQTAADVRV----LNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENL 116
VR ++ +L Q + +D + F+CL A+V+ ++ GLK+ +VE L
Sbjct: 109 VLHRTQCVRGFGDWIDSILEFSQSLHRMNLDVSAFSCLAALVII-TDRHGLKEPKRVEEL 167
Query: 117 QDQAQVMLAQHVRT--HHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
Q++ L +HV P +P RLL + R + + +Q IF+ K
Sbjct: 168 QNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRIFYLK 217
>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 = 62.0 bits (151), Expect = 4e-12
Identities = 52/180 (28%), Positives = 80/180 (44%), Gaps = 7/180 (3%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASE-HVAAVPN 61
+WA+ +P F L DQ +LLE ++ ELF+L S P+ N H
Sbjct: 58 RQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQCVR 117
Query: 62 GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
G + + LQ L+ D + F CL ++L +E GLK+ +VE LQ++
Sbjct: 118 GFGEWLD-SILAFSSSLQS--LLLDDISAFCCLALLLLI-TERHGLKEPKKVEELQNKII 173
Query: 122 VMLAQHVRTHHPAQ--PARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
L HV +++P Q P R +LLL + R + +Q IFF K L+ +
Sbjct: 174 SCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRF 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 = 59.5 bits (145), Expect = 1e-11
Identities = 39/150 (26%), Positives = 69/150 (46%), Gaps = 18/150 (12%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
V++AK +P F L DQ+ LL+ E+ LL S+ L++ ++ +G
Sbjct: 19 VEFAKRIPGFRELSQEDQIALLKGGCFEILLL----------RSATLYDPEKNSLTFGDG 68
Query: 63 KA-----SQTAADVRVLNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
K + + ++ + +D E+A L A+VLF + GL+D VE
Sbjct: 69 KGNSRDVLLNGGFGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVE 128
Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLL 144
LQ++ L ++++ +HP P F +LL
Sbjct: 129 KLQERLLEALQRYLKVNHPDAPQMFAKLLK 158
>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 = 56.0 bits (135), Expect = 6e-10
Identities = 46/162 (28%), Positives = 69/162 (42%), Gaps = 7/162 (4%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNA-SEHVAAVPN 61
V +AK LP F LP DQ+ILL+ E+ L A P E+ L + + N
Sbjct: 69 VDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKN 128
Query: 62 GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
G + + L L F L D E A L+AV+L S+ GL ++E LQD
Sbjct: 129 GGLGVVSDAIFDLGVSLSSFNL---DDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFL 185
Query: 122 VMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSA---RVQHI 160
+ ++ P + +LL+ + R I + R H+
Sbjct: 186 LAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFLHM 227
>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 = 55.6 bits (134), Expect = 8e-10
Identities = 33/141 (23%), Positives = 57/141 (40%), Gaps = 5/141 (3%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
V++ K LP F L DQ+ LL+ S E L + Q + + L +
Sbjct: 53 VEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQ-----IYNKKLPAGHADLLEERIR 107
Query: 63 KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
+ + + + + + + E+A L A+ + + LKD VE LQ+
Sbjct: 108 SSGISDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLD 167
Query: 123 MLAQHVRTHHPAQPARFGRLL 143
+L + + +HP P F LL
Sbjct: 168 LLQKFCKLYHPEDPQHFACLL 188
>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 = 55.3 bits (133), Expect = 1e-09
Identities = 44/179 (24%), Positives = 78/179 (43%), Gaps = 3/179 (1%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL-LESSPLFNASEHV--AAV 59
V WA+ F L DQ+ LL+ WSEL + + I + E S L + V + V
Sbjct: 55 VDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTV 114
Query: 60 PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
S + V ++ + + +D EF CLK ++LF + + L + V++ Q++
Sbjct: 115 AAQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEK 174
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
A L + H+P +F +LLL + R + ++++ LL +M
Sbjct: 175 ANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEM 233
>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 = 55.1 bits (133), Expect = 1e-09
Identities = 41/164 (25%), Positives = 72/164 (43%), Gaps = 11/164 (6%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
V +AK LP F L DQ+ LL+ S E+ LL + P E+ P
Sbjct: 60 VDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKD------FPYS 113
Query: 63 KAS--QTAADVRVLNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
+ + V +N + + R + +D AE+A L A+ +F ++ ++D +VE LQ
Sbjct: 114 RDDFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQ 173
Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF 161
+ L +++ P+ F R+L+ R + S + +F
Sbjct: 174 ETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQVF 217
>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 = 50.1 bits (120), Expect = 5e-08
Identities = 39/159 (24%), Positives = 70/159 (44%), Gaps = 9/159 (5%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
V++AK +P F L DQ++L++ + E++L+ S + S + ++ +
Sbjct: 19 VEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRI---SRLINSKSGSITFDDGIS--ISR 73
Query: 63 KASQTAADVRVLNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
+ D + + F +G+ E A AVVL + GL + +V LQD+
Sbjct: 74 QQLDIIYDSDFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDR 133
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ 158
L V + PA+ F LL+ + R+I A+ Q
Sbjct: 134 VLEALKVQVSRNRPAEAQLFASLLMKIPELRSI-GAKHQ 171
>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 = 49.0 bits (117), Expect = 2e-07
Identities = 43/187 (22%), Positives = 77/187 (41%), Gaps = 14/187 (7%)
Query: 1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLL------NAIQWSLPLLESSPLFNASE 54
V++AK LP F L DQ+ LL+ + ++ +L Q ++ + L
Sbjct: 53 KIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQM 112
Query: 55 HVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
H A G T N +L + +D E L A+ L + + L++ +VE
Sbjct: 113 HNA----GFGPLTDLVFTFANQLLP----LEMDDTEIGLLSAICLICGDRQDLEEPDRVE 164
Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKL 174
LQ+ L + R P +P F ++L+ + R+I + + + K M L
Sbjct: 165 KLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPL 224
Query: 175 LCDMYKN 181
+ +M +N
Sbjct: 225 ISEMLEN 231
>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 = 47.3 bits (112), Expect = 7e-07
Identities = 43/169 (25%), Positives = 80/169 (47%), Gaps = 20/169 (11%)
Query: 5 WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKA 64
WA+ +P F LP DQ +L E ++ ELF+L + + +E +F NG
Sbjct: 60 WAEKIPGFTDLPKADQDLLFESAFLELFVLR-LAYRSNPVEGKLIFC---------NGVV 109
Query: 65 SQTAADVR----VLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
VR ++ +++ + + +D + F+C+ A+ + +E GLK+ +VE LQ
Sbjct: 110 LHRLQCVRGFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQ 168
Query: 118 DQAQVMLAQHVRTHHPA--QPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
++ L HV ++ +P +LL + R + + +Q IF+ K
Sbjct: 169 NKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLK 217
>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 = 47.0 bits (112), Expect = 1e-06
Identities = 47/192 (24%), Positives = 77/192 (40%), Gaps = 30/192 (15%)
Query: 4 KWAKNLPSFAALPFRDQVILLEESWSE-LFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
++AK+LP F L DQV LL+ E +F + + L+N P G
Sbjct: 81 EFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTM-----------LASLYNKD--GLLFPEG 127
Query: 63 KASQTAADVRVLNGVL-----------QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSL 111
T + L ++F + + +E A AV++ + GL +
Sbjct: 128 NGYVTREFLESLRKPFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGLINRK 187
Query: 112 QVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPS---ARVQHIFFAKTVAN 168
VE +Q+ L ++ +HP P F +LL R + + VQ I KT +
Sbjct: 188 PVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQMVQQI--KKTETD 245
Query: 169 TSMEKLLCDMYK 180
S+ LL ++YK
Sbjct: 246 ASLPPLLQEIYK 257
>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 = 46.1 bits (109), Expect = 2e-06
Identities = 35/109 (32%), Positives = 54/109 (49%), Gaps = 3/109 (2%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQW-SLPLLESSPLFNASEHVAAVPN 61
VKWAK LP F L DQ+ +++ SW L + A+ W S + S L+ A + V
Sbjct: 45 VKWAKALPGFRNLHVDDQMAVIQYSWMGLMVF-AMGWRSFTNVNSRMLYFAPDLVFNEYR 103
Query: 62 GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-ETRGLKD 109
S+ + + + Q F + + P EF C+KA++LF GLK+
Sbjct: 104 MHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKN 152
>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 = 45.5 bits (108), Expect = 3e-06
Identities = 44/153 (28%), Positives = 69/153 (45%), Gaps = 12/153 (7%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
V++AK LP F L DQ+ LL+ SE+ +L + S +F ++ P
Sbjct: 56 VEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVAR-RYDAKTDSIVFANNQ-----PYT 109
Query: 63 KASQTAADVRVLNGVLQRF----RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
+ S A + L RF + VD AE+A L A+V+F S+ GL +VE +Q+
Sbjct: 110 RDSYRKAGMGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIF-SDRPGLLQPKKVEKIQE 168
Query: 119 QAQVMLAQHVRTHHPAQPA-RFGRLLLMTSQCR 150
L +V P F +LL + ++ R
Sbjct: 169 IYLEALRAYVDNRRPPSQRVIFAKLLSILTELR 201
>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 = 43.7 bits (103), Expect = 1e-05
Identities = 47/169 (27%), Positives = 73/169 (43%), Gaps = 20/169 (11%)
Query: 5 WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKA 64
+A+ +P F L DQ +L + + ELF+L + P + NG
Sbjct: 61 FAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAP----------EDTKLTFCNGVV 110
Query: 65 SQTAADVRV----LNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
R L+ +L + + +D + FACL A+ L +E GLK+ +VE LQ
Sbjct: 111 LHKQQCQRSFGDWLHAILEFSKSLHAMDIDISAFACLCALTLI-TERHGLKEPHKVEQLQ 169
Query: 118 DQAQVMLAQHVRTHHPAQ--PARFGRLLLMTSQCRNIPSARVQHIFFAK 164
+ L HV + AQ P F RLL + R++ +Q IF+ K
Sbjct: 170 MKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELRSLSVQGLQRIFYLK 218
>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 = 43.5 bits (103), Expect = 2e-05
Identities = 34/117 (29%), Positives = 52/117 (44%), Gaps = 3/117 (2%)
Query: 2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQW-SLPLLESSPLFNASEHVAAVP 60
VKWAK LP F L DQ+ L++ SW L + A+ W S + S L+ A + V
Sbjct: 44 VVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVF-ALGWRSYKHVNSQMLYFAPDLVFNEQ 102
Query: 61 NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENL 116
S + + + Q F + V EF C+K ++L + GLK + +
Sbjct: 103 RMHQSAMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEM 159
>gnl|CDD|132759 cd07074, NR_LBD_PR, Ligand binding domain of the progesterone
receptor, a member of the nuclear hormone receptor. The
ligand binding domain of the progesterone receptor (PR):
PR is a member of the nuclear receptor superfamily of
ligand dependent transcription factors, mediating the
biological actions of progesterone. PR functions in a
variety of biological processes including development of
the mammary gland, regulating cell cycle progression,
protein processing, and metabolism. When no binding
hormone is present the carboxyl terminal inhibits
transcription. Binding to a hormone induces a structural
change that removes the inhibitory action. After
progesterone binds to the receptor, PR forms a dimer and
the complex enters the nucleus where it interacts with
the hormone response element (HRE) in the promoters of
progesterone responsive genes and alters their
transcription. In addition, rapid actions of PR that
occur independent of transcription, have also been
observed in several tissues like brain, liver, mammary
gland and spermatozoa. There are two natural PR isoforms
called PR-A and PR-B. PR-B has an additional stretc h of
164 amino acids at the N terminus. The extra domain in
PR-B performs activation functions by recruiting
coactivators that could not be recruited by PR-A. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, PR has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD). The LBD is not
only involved in binding to progesterone, but also
involved in coactivator binding and dimerization.
Length = 248
Score = 42.2 bits (99), Expect = 4e-05
Identities = 32/117 (27%), Positives = 55/117 (47%), Gaps = 3/117 (2%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQW-SLPLLESSPLFNASEHVAAVPN 61
VKW+K+LP F L DQ+ L++ SW L + + W S + L+ A + +
Sbjct: 45 VKWSKSLPGFRNLHIDDQITLIQYSWMSLMVF-GLGWRSYKHVSGQMLYFAPDLILNEQR 103
Query: 62 GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQ 117
K S + + + Q F + V EF C+KA++L + GL+ Q + ++
Sbjct: 104 MKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMR 160
>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 = 40.2 bits (94), Expect = 1e-04
Identities = 45/181 (24%), Positives = 73/181 (40%), Gaps = 32/181 (17%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
V++AK +P F L DQV LL+ E+ ++ LF+A E +G
Sbjct: 29 VEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFAS----------LFDAKERSVTFLSG 78
Query: 63 KA----SQTAADVRVLNGVL----QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
+ + L + ++ + + E AVVL ++ GL++ VE
Sbjct: 79 QKYSVDDLHSMGAGDLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVE 138
Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKL 174
LQ+ L + +HP +P+ F +LLL +P R T+ N EKL
Sbjct: 139 ALQETLIRALRTLIAKNHPNEPSIFTKLLL------KLPDLR--------TLNNLHSEKL 184
Query: 175 L 175
L
Sbjct: 185 L 185
>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 = 38.8 bits (90), Expect = 6e-04
Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 3/39 (7%)
Query: 2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLN-AIQW 39
AVKWAK +P F L DQ+ LL+ SW +FL+ A+ W
Sbjct: 44 AVKWAKAIPGFRNLHLDDQMTLLQYSW--MFLMAFALGW 80
>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 = 38.8 bits (90), Expect = 6e-04
Identities = 15/26 (57%), Positives = 18/26 (69%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESW 28
VKWAK LP F LP DQ+ L++ SW
Sbjct: 45 VKWAKVLPGFRNLPLEDQITLIQYSW 70
>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 = 36.5 bits (84), Expect = 0.004
Identities = 33/138 (23%), Positives = 61/138 (44%), Gaps = 2/138 (1%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN- 61
+ +AK +P F L DQ+ LL+ S E+ +L + Q S L + S + + V +
Sbjct: 54 IGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQ-SFSLDDMSWTCGSPDFKYKVSDV 112
Query: 62 GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
KA + + L + + + E L A+ + + G++D +E +QD+
Sbjct: 113 TKAGHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLS 172
Query: 122 VMLAQHVRTHHPAQPARF 139
L ++R HP +R
Sbjct: 173 DTLQTYIRCRHPPPGSRL 190
>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 = 0.009
Identities = 37/167 (22%), Positives = 77/167 (46%), Gaps = 15/167 (8%)
Query: 3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
+K+AK+LP F +LP DQ+ LL+ + E+ I+++ E + + + +
Sbjct: 52 IKFAKDLPYFRSLPIEDQISLLKGATFEICQ---IRFNTVFNEETGTWECGPLTYCIEDA 108
Query: 63 KASQTAADVRVLNGVLQRF----RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
A ++L L RF R + + E+ ++A+ LF + G+ ++ LQ+
Sbjct: 109 AR---AGFQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQE 165
Query: 119 QAQVMLAQHVRTHHPAQPARF--GRLLLMTSQCRNIP---SARVQHI 160
+ + L ++ + P RF ++L ++ R I + ++ HI
Sbjct: 166 KMALTLKSYIDSKRPGPEKRFLYPKILACLTELRTINEEYTKQILHI 212
>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 = 31.2 bits (71), Expect = 0.17
Identities = 25/128 (19%), Positives = 47/128 (36%), Gaps = 5/128 (3%)
Query: 2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN 61
V++ K++P F L D+ LL+ + L+LL + F E A++ +
Sbjct: 18 IVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNEGTVLCDFRPVEF-ASLLS 76
Query: 62 GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
D + + + + AE A L A L + L L+ +
Sbjct: 77 QLLHGKLID--EMLQFANKILTLNLTNAELALLCAAELL--QPDSLGIQLEETAKSNLQL 132
Query: 122 VMLAQHVR 129
+L Q ++
Sbjct: 133 SVLFQFLK 140
>gnl|CDD|153335 cd07651, F-BAR_PombeCdc15_like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Schizosaccharomyces pombe
Cdc15, and similar proteins. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. This subfamily is composed of
Schizosaccharomyces pombe Cdc15 and Imp2, and similar
proteins. These proteins contain an N-terminal F-BAR
domain and a C-terminal SH3 domain. S. pombe Cdc15 and
Imp2 play both distinct and overlapping roles in the
maintenance and strengthening of the contractile ring at
the division site, which is required in cell division.
Cdc15 is a component of the actomyosin ring and is
required in normal cytokinesis. Imp2 colocalizes with
the medial ring during septation and is required for
normal septation. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
Length = 236
Score = 28.8 bits (65), Expect = 1.5
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 7/84 (8%)
Query: 94 LKAVVLFKSETRGLKDSLQ---VEN-LQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQC 149
L L SE GLK+SL +E ++ + A+ +R + A F +Q
Sbjct: 45 LSRKSLGGSEEGGLKNSLDTLRLETESMAKSHLKFAKQIRQDLEEKLAAFAS---SYTQK 101
Query: 150 RNIPSARVQHIFFAKTVANTSMEK 173
R + ++ + K +EK
Sbjct: 102 RKKIQSHMEKLLKKKQDQEKYLEK 125
>gnl|CDD|223152 COG0074, SucD, Succinyl-CoA synthetase, alpha subunit [Energy
production and conversion].
Length = 293
Score = 28.3 bits (64), Expect = 2.1
Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 6/43 (13%)
Query: 56 VAAVPNGKASQTAADVRVLNGVLQRFRLVGVD------PAEFA 92
V V GK QT + V N V + + G + P FA
Sbjct: 36 VGGVTPGKGGQTILGLPVFNTVEEAVKETGANASVIFVPPPFA 78
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 27.8 bits (63), Expect = 3.9
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 9/33 (27%)
Query: 66 QTAADVRVLNG---------VLQRFRLVGVDPA 89
Q A + VL G L RF L G+ PA
Sbjct: 426 QPAVTIHVLQGEREMAADNKSLGRFNLTGIPPA 458
>gnl|CDD|132737 cd06939, NR_LBD_ROR_like, The ligand binding domain of
Retinoid-related orphan receptors, of the nuclear
receptor superfamily. The ligand binding domain (LBD)
of Retinoid-related orphan receptors (RORs):
Retinoid-related orphan receptors (RORs) are
transcription factors belonging to the nuclear receptor
superfamily. RORs are key regulators of many
physiological processes during embryonic development.
RORs bind as monomers to specific ROR response elements
(ROREs) consisting of the consensus core motif AGGTCA
preceded by a 5-bp A/T-rich sequence. Transcription
regulation by RORs is mediated through certain
corepressors, as well as coactivators. There are three
subtypes of retinoid-related orphan receptors (RORs),
alpha, beta, and gamma that differ only in N-terminal
sequence and are distributed in distinct tissues.
RORalpha plays a key role in the development of the
cerebellum, particularly in the regulation of the
maturation and survival of Purkinje cells. RORbeta
expression is largely restricted to several regions of
the brain, the retina, and pineal gland. RORgamma is
essential for lymph node organogenesis. Recently, it has
been su ggested that cholesterol or a cholesterol
derivative is the natural ligand of RORalpha. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, retinoid-related
orphan receptors have a central well conserved DNA
binding domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 241
Score = 27.3 bits (61), Expect = 4.8
Identities = 13/43 (30%), Positives = 25/43 (58%)
Query: 90 EFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHH 132
E A A+VL ++ GL++ +VE LQ + ++ L ++ +H
Sbjct: 149 EIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNH 191
>gnl|CDD|165315 PHA03016, PHA03016, hypothetical protein; Provisional.
Length = 441
Score = 27.2 bits (60), Expect = 5.3
Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 133 PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
+P +F +++L + +N S +++ IF N EK++ D+ +
Sbjct: 85 NIEPEKFKKIILDNIKNKNKESYKIEDIF-----ENIIDEKIINDISQ 127
>gnl|CDD|149159 pfam07925, RdRP_5, Reovirus RNA-dependent RNA polymerase lambda 3.
The sequences in this family are similar to the reoviral
minor core protein lambda 3, which functions as a
RNA-dependent RNA polymerase within the protein capsid.
It is organised into 3 domains. N- and C-terminal domains
create a 'cage' that encloses a conserved central
catalytic domain within a hollow centre; this catalytic
domain is arranged to form 'fingers', 'palm' and 'thumb'
subdomains. Unlike other RNA polymerases, like HIV
reverse transcriptase and T7 RNA polymerase, lambda 3
protein binds template and substrate with only localised
rearrangements, and catalytic activity can occur with
little structural change. However, the structure of the
catalytic complex is similar to that of other polymerase
catalytic complexes with known structure.
Length = 1271
Score = 27.2 bits (60), Expect = 5.5
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 14/97 (14%)
Query: 42 PLLESS-PLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEF-ACLKAVVL 99
P+L+S+ F + V +G DV ++ L R R++G DP A L + +
Sbjct: 1105 PILQSTRKYFAQTLFVGKTVSG------LDVEAVDATLLRLRILGADPEALTAQLLGIGM 1158
Query: 100 FKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQP 136
SE + + + + Q Q R + A P
Sbjct: 1159 SDSEAHAIAGKISLADAQ------TVQLARVVNLAVP 1189
>gnl|CDD|214615 smart00318, SNc, Staphylococcal nuclease homologues.
Length = 137
Score = 26.1 bits (58), Expect = 6.7
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 70 DVRVLNGVLQRFRLVGVDPAEFA 92
VR+ G L RL G+D E A
Sbjct: 17 RVRLPKGPLITIRLSGIDAPETA 39
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 26.9 bits (60), Expect = 7.4
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 9/33 (27%)
Query: 66 QTAADVRVLNG---------VLQRFRLVGVDPA 89
Q A D+ VL G L RF L G+ PA
Sbjct: 424 QPAVDIHVLQGERPMAADNKSLGRFELTGIPPA 456
>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2. Histone
deacetylase 6 is a class IIb Zn-dependent enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDACs usually act via association with DNA
binding proteins to target specific chromatin regions.
HDAC6 is the only histone deacetylase with internal
duplication of two catalytic domains which appear to
function independently of each other, and also has a
C-terminal ubiquitin-binding domain. It is located in
the cytoplasm and associates with microtubule motor
complex, functioning as the tubulin deacetylase and
regulating microtubule-dependent cell motility. Known
interaction partners of HDAC6 are alpha tubulin and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 350
Score = 26.9 bits (60), Expect = 7.5
Identities = 8/31 (25%), Positives = 11/31 (35%), Gaps = 6/31 (19%)
Query: 130 THHPAQPARFGRLLLM------TSQCRNIPS 154
HP P R R+ +C +PS
Sbjct: 14 PGHPECPQRISRIYERHNDLGLLERCLRLPS 44
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 0.132 0.390
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,000,574
Number of extensions: 796340
Number of successful extensions: 704
Number of sequences better than 10.0: 1
Number of HSP's gapped: 665
Number of HSP's successfully gapped: 69
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.4 bits)