RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12692
(187 letters)
>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 = 166 bits (422), Expect = 4e-52
Identities = 61/172 (35%), Positives = 89/172 (51%), Gaps = 50/172 (29%)
Query: 64 QIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGL---LGVPTL 120
+++VDDQMKLLQ+ WS++LVLDH+++++H+ D L GQ+ DL +L LG+ +L
Sbjct: 66 ELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLASQAGLGLSSL 125
Query: 121 RDRFTQVTHKLSELKF-------------------------------------------- 136
DR ++ +KL EL+F
Sbjct: 126 VDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLC 185
Query: 137 --PNC-DKFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185
P DKFG+L+ LPE+ I+ + EE+LY+KH NG P LL+EMLHAK
Sbjct: 186 NYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHAK 237
Score = 84.6 bits (210), Expect = 2e-20
Identities = 29/54 (53%), Positives = 38/54 (70%)
Query: 13 ELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQ 66
EL+FD +++C+KFL+L NPDV+G+ NR VE EQV ALLDY + YPQ
Sbjct: 138 ELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQT 191
>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 = 77.0 bits (189), Expect = 2e-17
Identities = 55/175 (31%), Positives = 82/175 (46%), Gaps = 50/175 (28%)
Query: 62 YPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFD------------- 108
+ +++VDDQMKLLQ+ WS++L+LDH+++++ + L GQ+ D
Sbjct: 66 FRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLN 125
Query: 109 -LLSLGLLGVPTLRD-----------RF---------------------TQVTHKLSELK 135
L+S V LR +F QV L +
Sbjct: 126 NLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYT 185
Query: 136 FPN----CDKFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAKR 186
N +KFG+L+ LPE+ I+ + EE+LY+KH NG P LL+EMLHAKR
Sbjct: 186 MCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKR 240
Score = 52.0 bits (124), Expect = 2e-08
Identities = 27/61 (44%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 14 LKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKL 73
L+FD +++C+KFL+L + DV+ + N VE EQV ALLDY + YPQ Q + +L
Sbjct: 141 LQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQ-QTEKFGQL 199
Query: 74 L 74
L
Sbjct: 200 L 200
>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 = 69.6 bits (170), Expect = 9e-15
Identities = 47/174 (27%), Positives = 76/174 (43%), Gaps = 50/174 (28%)
Query: 62 YPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLG-----LLG 116
+ +++V DQM LLQ+ WS++LV DH+++++ + L GQ+ +L ++ LL
Sbjct: 64 FKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAAQAGSLLH 123
Query: 117 VPTLR-DRFTQVTHKLS-----------------ELKF---------------------- 136
LR H L ++KF
Sbjct: 124 SLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYT 183
Query: 137 ----PNC-DKFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185
P+C DKF +L+ L E+ ++ + +E+LYHKH P LL+EML AK
Sbjct: 184 LCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAK 237
Score = 41.5 bits (97), Expect = 7e-05
Identities = 22/61 (36%), Positives = 36/61 (59%)
Query: 14 LKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKL 73
L+ D +++C+KFL+L + DV+ + N + V++ E+ ALLDY + YP Q L
Sbjct: 139 LQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLL 198
Query: 74 L 74
L
Sbjct: 199 L 199
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 21/82 (25%), Positives = 39/82 (47%)
Query: 59 ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVP 118
+ A+ + +DDQ+ LLQ+SW+++L+L + +H L + LLG+
Sbjct: 22 LPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLA 81
Query: 119 TLRDRFTQVTHKLSELKFPNCD 140
L R ++ KL L+ +
Sbjct: 82 ELVQRLQELLSKLRSLQLDPKE 103
Score = 57.6 bits (140), Expect = 6e-11
Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 14 LKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64
L+ D +Y C+K ++L NPD+ G+ N+ VEE E+ Q+AL +Y YPQ
Sbjct: 97 LQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQ 147
>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 = 48.1 bits (115), Expect = 4e-07
Identities = 19/52 (36%), Positives = 34/52 (65%)
Query: 13 ELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64
+LK D ++ C++ ++L NPDV+G+ +R VE E+V +L +YC +P+
Sbjct: 126 DLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPE 177
Score = 32.3 bits (74), Expect = 0.086
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 64 QIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVPTLRDR 123
++ +DDQ+ LL+ W+++L+ H+ + A+ D L G S GV + DR
Sbjct: 58 ELPLDDQVILLRAGWNELLIAAFAHRSI--AVKDGILLATGLHLHRNSAHQAGVGAIFDR 115
Query: 124 -FTQVTHKLSELK 135
T++ K+ +LK
Sbjct: 116 ILTELVVKMRDLK 128
>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 = 47.5 bits (113), Expect = 7e-07
Identities = 17/50 (34%), Positives = 28/50 (56%)
Query: 14 LKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYP 63
L D +++ C+K ++L D G+ + H+E E+ Q AL +Y T YP
Sbjct: 128 LHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYP 177
Score = 31.7 bits (72), Expect = 0.15
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 141 KFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEML 182
+FGKL+ LP L ++S E L+ G P +TL+ +ML
Sbjct: 182 RFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 223
Score = 30.9 bits (70), Expect = 0.30
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 59 ITAYPQIQVDDQMKLLQHSWSDMLVLD 85
I +P +QV DQ+ LL+ SWS++ VL+
Sbjct: 53 IPFFPDLQVTDQVALLRLSWSELFVLN 79
>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 = 46.5 bits (111), Expect = 9e-07
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 13 ELKFDISDYICVKFLLLLNPDV-RGILNRTHVEEGHEQVQKALLDYCITAYPQ 64
LK D +Y +K ++L +PD + +R VEE E++ +AL DY YP+
Sbjct: 97 ALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLRKNYPE 149
Score = 35.4 bits (82), Expect = 0.007
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 2/80 (2%)
Query: 58 CITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQ--KFDLLSLGLL 115
I + ++ ++DQ+ LL+ W ++LVLD ++ N L + G + LL
Sbjct: 20 SIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLL 79
Query: 116 GVPTLRDRFTQVTHKLSELK 135
L + + L LK
Sbjct: 80 LKGELIRLLFEFVNPLRALK 99
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 46.2 bits (110), Expect = 9e-07
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 13 ELKFDISDYICVKFLLLLNPDVRGILN--RTHVEEGHEQVQKALLDYCITAYPQ 64
ELK D +Y +K ++L NP V G+ + VE+ E+ AL DY + YP
Sbjct: 91 ELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPM 144
Score = 37.0 bits (86), Expect = 0.002
Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 58 CITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFD----LLSLG 113
+ ++ ++DQ+ LL+ W ++L+L+ ++ + E L + +L L
Sbjct: 14 SFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKL--KKELLLAPDGTYIRPDAVLELR 71
Query: 114 LLGVPTLRDRFTQVTHKLSELKF 136
L P L +++ L ELK
Sbjct: 72 KLFSPFLDRILSELVKPLRELKL 94
>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 = 36.6 bits (85), Expect = 0.004
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 13 ELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYP 63
+L D ++Y C+K ++ +PD +G+ + ++ QVQ +L DY
Sbjct: 127 DLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQY 177
Score = 28.1 bits (63), Expect = 2.4
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 141 KFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEM 181
+FG+L+ +LP L I + E + G A LL EM
Sbjct: 182 RFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222
Score = 27.0 bits (60), Expect = 6.2
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 59 ITAYPQIQVDDQMKLLQHSWSDMLVL 84
I A+ ++ +DDQ+ LL+ + L+L
Sbjct: 55 IPAFCELPLDDQVALLRAHAGEHLLL 80
>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 = 34.5 bits (80), Expect = 0.015
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 143 GKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHA 184
+L+ +LP L + +++G HLY C G P L +EML A
Sbjct: 180 AQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLEA 221
Score = 33.0 bits (76), Expect = 0.060
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 13 ELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYC 58
EL +Y+C+K ++L N DVR + +R V++ + + AL+D
Sbjct: 122 ELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVE 167
Score = 31.0 bits (71), Expect = 0.26
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 59 ITAYPQIQVDDQMKLLQHSWSDMLVLD 85
I + + ++DQM LLQ +W ++L+L
Sbjct: 50 IPGFSDLSLNDQMHLLQSAWLEILMLG 76
>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 = 34.2 bits (79), Expect = 0.021
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 14 LKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYP 63
L+ D +++ C+K ++L P+ RG+ + VE +Q Q L + T YP
Sbjct: 122 LRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYP 171
Score = 29.2 bits (66), Expect = 1.1
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 58 CITAYPQIQVDDQMKLLQHSWSDMLVL 84
I A+ + DQ+ LL+ SWS++ +L
Sbjct: 48 SIPAFSTLPFRDQLILLEESWSELFLL 74
>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 = 33.3 bits (76), Expect = 0.050
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 17 DIS--DYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQ 66
D+S +Y +K +L NPDV G+ +HV ++ Q AL + +PQ Q
Sbjct: 128 DLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQ 179
>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 = 32.8 bits (75), Expect = 0.072
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 144 KLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHA 184
+L+ IL + ++++G EHLY C P LL+EML A
Sbjct: 194 QLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDA 234
>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 = 32.7 bits (75), Expect = 0.077
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 14 LKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYP 63
L D +Y +K ++L +PD G R +E+ E+ L DY YP
Sbjct: 125 LDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYP 174
>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 = 31.6 bits (72), Expect = 0.15
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 69 DQMKLLQHSWSDMLVL 84
DQM LLQ +W ++L L
Sbjct: 60 DQMSLLQSAWMEILTL 75
>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 = 31.2 bits (71), Expect = 0.25
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 14 LKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDY 57
LK +Y+C+K + LN D+ G+ N + +E ++ L D+
Sbjct: 127 LKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDF 170
Score = 30.4 bits (69), Expect = 0.39
Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 62 YPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHN---ALPDETTLHNGQKFDLLSLGLLGVP 118
+ ++ + D LL W+++++L + L D + + + +L G G
Sbjct: 53 FTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELERFGDEGGE 112
Query: 119 TLRDRFTQVTHKLSELKFPN 138
+ +R T + K +LK N
Sbjct: 113 VV-ERLTYLLAKFRQLKVSN 131
Score = 28.9 bits (65), Expect = 1.5
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 117 VPTLRDRFTQVTHKLSELKFPN-CDKFGKLMSILPELHEIAS 157
+ +L+ R+ V +EL +PN ++F L+S LPE+ A
Sbjct: 156 LESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAAAG 197
>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 = 30.8 bits (70), Expect = 0.28
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 13 ELKFDISDYICVKFLLLLNPDVRGIL--NRTHVEEGHEQVQKALLDYCIT 60
ELK + +K LLL NP + + VE+ E + AL +Y
Sbjct: 99 ELKLTDEELAALKALLLFNPAGKRLSGEILEVVEKLQEVIANALHNYYKD 148
Score = 30.4 bits (69), Expect = 0.32
Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 1/78 (1%)
Query: 65 IQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVPTLRDRF 124
+ +DDQ+ LL+ SW + L L+ + D+ NG D L + V + ++
Sbjct: 29 LSLDDQLALLKSSWFEWLRLELASRSAEC-EKDDLLFSNGLYLDRDELKSIEVNYINEQI 87
Query: 125 TQVTHKLSELKFPNCDKF 142
Q+ + LK
Sbjct: 88 RQLFELVQPLKELKLTDE 105
>gnl|CDD|226515 COG4028, COG4028, Predicted P-loop ATPase/GTPase [General function
prediction only].
Length = 271
Score = 29.4 bits (66), Expect = 0.84
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 111 SLGLLGVPTLRDRFTQVTHKLSELKFPNCDKFGKLMSILPELHEIASRGEEHLYHKH 167
+L L VP + FT + L P KL IL E IA +++ K
Sbjct: 125 NLADLYVPLRMEVFT----RNLALN-PEPLSVDKLEEILSESRRIADECLSYVFGKE 176
>gnl|CDD|182152 PRK09932, PRK09932, glycerate kinase II; Provisional.
Length = 381
Score = 29.5 bits (66), Expect = 1.1
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 145 LMSILPELH---EIASRGEEHLYHKHCN 169
+ SILP L E+ + GE +L++ N
Sbjct: 341 VFSILPRLAPLAEVLASGETNLFNSARN 368
>gnl|CDD|223822 COG0751, GlyS, Glycyl-tRNA synthetase, beta subunit [Translation,
ribosomal structure and biogenesis].
Length = 691
Score = 29.5 bits (67), Expect = 1.1
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 151 ELHEIASRGEEHLYHKHCNGGAPTQTLLMEML 182
E + +GEE++Y G PT+ LL E++
Sbjct: 106 ERRKDDKKGEEYVYRVKKEEGQPTEELLPEIV 137
>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 = 28.8 bits (64), Expect = 1.5
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 65 IQVDDQMKLLQHSWSDMLVL 84
+ VDDQM ++Q+SW ++V
Sbjct: 57 LHVDDQMAVIQYSWMGLMVF 76
>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 = 28.6 bits (64), Expect = 1.6
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 11/92 (11%)
Query: 1 MGNYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCIT 60
M N+Y ELK +Y + + +L PD + ++ VE+ E + L +C
Sbjct: 119 MFNFYKSMG---ELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKL 175
Query: 61 AYPQ--------IQVDDQMKLLQHSWSDMLVL 84
+P+ + +++ L H ++ML+
Sbjct: 176 YHPEDPQHFACLLGRLTELRTLNHHHAEMLMS 207
>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 = 28.5 bits (64), Expect = 1.8
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 67 VDDQMKLLQHSW 78
+DDQM L+Q+SW
Sbjct: 59 LDDQMTLIQYSW 70
>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 = 28.0 bits (63), Expect = 2.1
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 27 LLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQM--KLLQ 75
++L +PD G+ + VE+ E++ +AL Y +P QM KLL+
Sbjct: 111 IVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPD---APQMFAKLLK 158
Score = 27.6 bits (62), Expect = 2.6
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 120 LRDRFTQVTHKLSELKFPN-CDKFGKLMSILPELHEIASRGEEHL 163
L++R + + ++ P+ F KL+ L EL + E L
Sbjct: 130 LQERLLEALQRYLKVNHPDAPQMFAKLLKKLTELRTLNELHAELL 174
>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 = 27.9 bits (62), Expect = 2.9
Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 14 LKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQ 66
L D +Y +K +L P +L ++E ++ Q+AL ++ + P Q
Sbjct: 130 LDLDCKEYAYLKGAVLFTPVP-PLLCPHYIEALQKEAQQALNEHTMMTRPLEQ 181
Score = 27.1 bits (60), Expect = 5.6
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 61 AYPQIQVDDQMKLLQHSWSDMLVL----DHMH 88
+ + DDQ++LL+ SW+ +L+L D +
Sbjct: 44 CFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVP 75
>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 = 27.6 bits (61), Expect = 3.3
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 59 ITAYPQIQVDDQMKLLQHSWSDMLVL 84
I + + +DDQM LLQ+SW ++
Sbjct: 51 IPGFRNLHLDDQMTLLQYSWMFLMAF 76
>gnl|CDD|232875 TIGR00211, glyS, glycyl-tRNA synthetase, tetrameric type, beta
subunit. The glycyl-tRNA synthetases differ even among
the eubacteria in oligomeric structure. In Escherichia
coli and most others, it is a heterodimer of two alpha
chains and two beta chains, encoded by tandem genes. The
genes are similar, but fused, in Chlamydia trachomatis.
By contrast, the glycyl-tRNA synthetases of Thermus
thermophilus and of archaea and eukaryotes differ
considerably; they are homodimeric, mutually similar,
and not detected by this model [Protein synthesis, tRNA
aminoacylation].
Length = 691
Score = 27.5 bits (61), Expect = 4.7
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 137 PNCDKFGKLMSILPELHEI-ASRGEEHLYHKHCNGGAPTQTLLMEM 181
F K I E EI + E L+ + + G PT+ LL +
Sbjct: 89 KAALGFAKGQGINVEDAEIFQTDKGEWLFVRKIHEGQPTKDLLPPL 134
>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 = 26.8 bits (59), Expect = 6.7
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 65 IQVDDQMKLLQHSWSDMLVL 84
+ +DDQ+ L+Q+SW ++V
Sbjct: 57 LHIDDQITLIQYSWMSLMVF 76
>gnl|CDD|182749 PRK10809, PRK10809, ribosomal-protein-S5-alanine
N-acetyltransferase; Provisional.
Length = 194
Score = 26.2 bits (58), Expect = 9.7
Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 26 FLLLLNPD---VRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDML 82
+ LL+PD + G+ N ++V G L Y + Q Q + LQ + M
Sbjct: 77 YFALLDPDEKEIIGVANFSNVVRG--SFHACYLGYSLGQKWQGQ-GLMFEALQAAIRYMQ 133
Query: 83 VLDHMHQRMHNALPDETTLHNGQKFDLLS 111
HMH+ M N +P HN + DLL+
Sbjct: 134 RQQHMHRIMANYMP-----HNKRSGDLLA 157
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 0.422
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,510,871
Number of extensions: 862228
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 712
Number of HSP's successfully gapped: 68
Length of query: 187
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 96
Effective length of database: 6,901,388
Effective search space: 662533248
Effective search space used: 662533248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.6 bits)