RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3123
(585 letters)
>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 = 276 bits (708), Expect = 2e-90
Identities = 94/192 (48%), Positives = 132/192 (68%), Gaps = 3/192 (1%)
Query: 105 CPLNPNSHPLQGQQELLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEV 164
P P + E+ ++FS F+P +R+VVEFAKRIPGF L DQVTLLKAG FEV
Sbjct: 1 SPYVD---PPKSGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEV 57
Query: 165 LLVRLACMFDSQTNSMICLNGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGL 224
L+VR A +FD++ S+ L+G+ D +HS A L++SMFDF+E+LN L LSD E+GL
Sbjct: 58 LMVRFASLFDAKERSVTFLSGQKYSVDDLHSMGAGDLLNSMFDFSEKLNSLQLSDEEMGL 117
Query: 225 FSSIVVISPSRSGLRNKELVERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLN 284
F+++V++S RSGL N LVE ++ L L ++ +NHP + ++ +L+ LPDLRTLN
Sbjct: 118 FTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLPDLRTLN 177
Query: 285 QLHSEKLVAFQM 296
LHSEKL+AF++
Sbjct: 178 NLHSEKLLAFKV 189
>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 = 181 bits (462), Expect = 3e-54
Identities = 73/174 (41%), Positives = 110/174 (63%)
Query: 118 QELLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQT 177
QE F+E + IR VVEFAKRIPGF L +DQ+ LLK G FE+LL+R A ++D +
Sbjct: 1 QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEK 60
Query: 178 NSMICLNGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSG 237
NS+ +G+ RD + + ++ +F+FAE++N L L D E L ++IV+ SP R G
Sbjct: 61 NSLTFGDGKGNSRDVLLNGGFGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPG 120
Query: 238 LRNKELVERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKL 291
L++ + VE+++ +L L L NHP+ + A+L+ L +LRTLN+LH+E L
Sbjct: 121 LQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLTELRTLNELHAELL 174
>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 = 166 bits (421), Expect = 2e-47
Identities = 83/238 (34%), Positives = 136/238 (57%), Gaps = 15/238 (6%)
Query: 59 DDEQRMLSTVVRAHLDTCAFTADKIEPMLRRAREHPTYTACPSTLACPLNPNSHPLQGQQ 118
D+ + + + +AHL+TC + ++++ + + + N + ++
Sbjct: 1 DELEHLAQNICKAHLETCQYLREELQQLRWKTFS-------QEEILAYQN------KSRE 47
Query: 119 ELLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTN 178
E+ Q +E+ + I+ VVEFAKRIPGF LC +DQ+ LLKAG EV+LVR++ F+ N
Sbjct: 48 EMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNN 107
Query: 179 SMICLNGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGL 238
+ + +G+ D S L+ ++FDFA+ L L L++ EI LFS++V+IS R GL
Sbjct: 108 T-VLFDGKYAPIDLFKSLGCDDLISAVFDFAKSLCELKLTEDEIALFSALVLISADRPGL 166
Query: 239 RNKELVERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKLVAFQM 296
+ K VE+++ K+E L HVL +NH + L +L++ +P LR L LH EKL F+
Sbjct: 167 QEKRKVEKLQQKIELALRHVLQKNHGDDTIL-TKLLAKMPTLRALCSLHMEKLQKFKQ 223
>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 = 127 bits (322), Expect = 4e-34
Identities = 64/186 (34%), Positives = 109/186 (58%)
Query: 120 LLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNS 179
L Q SE +P+++ VVEFAKRIPGF L DDQ+ L+KAG FEV LVR++ + +S++ S
Sbjct: 3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGS 62
Query: 180 MICLNGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLR 239
+ +G + R + + ++F+F++ N L LSDTE+ LF ++V++SP R GL
Sbjct: 63 ITFDDGISISRQQLDIIYDSDFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLS 122
Query: 240 NKELVERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKLVAFQMTEQ 299
+ V ++ ++ L +++N P + L A L+ +P+LR++ H L +++
Sbjct: 123 EPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPELRSIGAKHQMHLDWYRVNWP 182
Query: 300 QQQLAA 305
+L
Sbjct: 183 LLRLPP 188
>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 = 120 bits (302), Expect = 1e-31
Identities = 51/168 (30%), Positives = 83/168 (49%), Gaps = 6/168 (3%)
Query: 122 QDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMI 181
+ E + + +VE+AK IPGF L +DQ+ LLK+ E+L++ LA S++
Sbjct: 1 ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLL 60
Query: 182 CLNGEVLV----RDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSR-S 236
D + L+ +F+F L L L D E L +IV+ SP R
Sbjct: 61 LAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE 120
Query: 237 GLRNKELVERMRGKLENMLMHVLNQNHP-EQMNLCAELISMLPDLRTL 283
L ++++VE ++ +L L L +N+P E + A+L+ +LP LR L
Sbjct: 121 SLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 168
>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 = 121 bits (306), Expect = 2e-31
Identities = 50/210 (23%), Positives = 104/210 (49%), Gaps = 1/210 (0%)
Query: 92 EHPTYTACPSTLACPLNPNSHPLQGQQELLQDFSERFSPTIRDVVEFAKRIPGFSLLCHD 151
++ P P + + +Q+ F+E +++++V+FAK++PGF L +
Sbjct: 16 NKRSFEDVPKVTPWPEGQDPQSREARQQRFAHFTELAILSVQEIVDFAKQLPGFLTLTRE 75
Query: 152 DQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEVLVRDSIHSSNARF-LMDSMFDFAE 210
DQ+ LLKA EV+L+ A ++ ++ ++ L RD + + ++ +F+F++
Sbjct: 76 DQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFARAGLQVEFINPIFEFSK 135
Query: 211 RLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRGKLENMLMHVLNQNHPEQMNLC 270
+ L L D E L +I + S R +++ VER++ L + P +
Sbjct: 136 SMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMF 195
Query: 271 AELISMLPDLRTLNQLHSEKLVAFQMTEQQ 300
++ L LRTL+ +HSE++ A ++ +++
Sbjct: 196 PRMLMKLVSLRTLSSVHSEQVFALRLQDKK 225
>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 = 121 bits (305), Expect = 5e-31
Identities = 69/186 (37%), Positives = 103/186 (55%), Gaps = 9/186 (4%)
Query: 118 QELLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQT 177
L Q R TIR++ EFAK +PGF L +DQVTLLK GV EV+ M S
Sbjct: 62 IRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIF----TMLASLY 117
Query: 178 NS--MICLNGEVLV-RDSIHSSNARF--LMDSMFDFAERLNGLHLSDTEIGLFSSIVVIS 232
N ++ G V R+ + S F +M+ F+FAE+ N L L+D+E+ LF +++++S
Sbjct: 118 NKDGLLFPEGNGYVTREFLESLRKPFCDIMEPKFEFAEKFNALELTDSELALFCAVIILS 177
Query: 233 PSRSGLRNKELVERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKLV 292
P R GL N++ VER++ + L L +NHP+ L A+L+ + DLR L H + +
Sbjct: 178 PDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQMVQ 237
Query: 293 AFQMTE 298
+ TE
Sbjct: 238 QIKKTE 243
>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 = 117 bits (296), Expect = 5e-30
Identities = 44/179 (24%), Positives = 91/179 (50%)
Query: 118 QELLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQT 177
E F++ +P I VV+FAK++P F+ L +DQ+ LLK E++ +R A +D ++
Sbjct: 51 LEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPES 110
Query: 178 NSMICLNGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSG 237
++ + R+ + + + D++FD L+ +L DTE+ L +++++S R G
Sbjct: 111 ETLTLSGEMAVTREQLKNGGLGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPG 170
Query: 238 LRNKELVERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKLVAFQM 296
L E +E+++ H +N + +L+ + DLR + H+ + + ++
Sbjct: 171 LACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFLHMKV 229
>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 = 117 bits (294), Expect = 6e-30
Identities = 63/233 (27%), Positives = 116/233 (49%), Gaps = 19/233 (8%)
Query: 64 MLSTVVRAHLDTCAFTADKIEPMLRRAREHPTYTACPSTLACPLNPNSHPLQGQQELLQD 123
+++ V +AH +T + YT + ++ L
Sbjct: 2 LITKVRKAHQET-----------FPSLCQLGKYTT--------NSSADQRVRLDLGLWDK 42
Query: 124 FSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICL 183
FSE + I +VEFAKR+PGF+ L DQ+TLLKA ++L++R+ + + ++M
Sbjct: 43 FSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFS 102
Query: 184 NGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKEL 243
+G L R +H++ L D +F FA +L L + DTEIGL S+I +I R L +
Sbjct: 103 DGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDR 162
Query: 244 VERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKLVAFQM 296
VE+++ L L + P++ ++ +++ + DLR+++ +E+++ +M
Sbjct: 163 VEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVITLKM 215
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 111 bits (280), Expect = 9e-29
Identities = 46/163 (28%), Positives = 75/163 (46%), Gaps = 7/163 (4%)
Query: 128 FSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEV 187
+ VE+AK PGF L +DQ+ LLK+ FE+LL+ LA ++
Sbjct: 1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGT 60
Query: 188 LVRDSIHSSNARFLM----DSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRN--K 241
+R + + + + L L L D E L +IV+ +P+ GL K
Sbjct: 61 YIRPDAVLELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGK 120
Query: 242 ELVERMRGKLENMLMHVLNQNHPEQMNLC-AELISMLPDLRTL 283
E+VE+++ K N L +N+P A+L+ +LP+LR +
Sbjct: 121 EIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPELRKI 163
>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 = 105 bits (264), Expect = 8e-26
Identities = 57/168 (33%), Positives = 100/168 (59%), Gaps = 2/168 (1%)
Query: 131 TIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEVLVR 190
T++ +VEFAKR+PGF L +DQ+TLLKA EV+++R+A +D++T+S++ N + R
Sbjct: 51 TVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTR 110
Query: 191 DSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRG- 249
DS + + +F F + + + + E L ++IV+ S R GL + VE+++
Sbjct: 111 DSYRKAGMGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEI 169
Query: 250 KLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKLVAFQMT 297
LE + +V N+ P Q + A+L+S+L +LRTL +SE + ++
Sbjct: 170 YLEALRAYVDNRRPPSQRVIFAKLLSILTELRTLGNQNSEMCFSLKLK 217
>gnl|CDD|215719 pfam00104, Hormone_recep, Ligand-binding domain of nuclear hormone
receptor. This all helical domain is involved in
binding the hormone in these receptors.
Length = 186
Score = 102 bits (257), Expect = 2e-25
Identities = 51/184 (27%), Positives = 92/184 (50%), Gaps = 8/184 (4%)
Query: 121 LQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSM 180
L + E + + VVE+AKR PGF L DDQ+ LLK+ FE L + LA
Sbjct: 2 LNELFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDD 61
Query: 181 ICL-NGEVLVRDSIHSSNARFLMDS---MFDFAERLNGLHLSDTEIGLFSSIVVISPSRS 236
+ NG L RD + S ++ + +F+ + L L L+D E+ ++++ +P+
Sbjct: 62 LLFSNGLYLDRDELKSIEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLLFNPAGK 121
Query: 237 GL--RNKELVERMRGKL-ENMLMHVLNQNHPEQMNL-CAELISMLPDLRTLNQLHSEKLV 292
L E+VE+++ + + + ++N P + A+L+ +LP LR +++ EKL
Sbjct: 122 RLSGEILEVVEKLQEVIANALHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLE 181
Query: 293 AFQM 296
++
Sbjct: 182 LAKL 185
>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 = 101 bits (252), Expect = 3e-24
Identities = 57/194 (29%), Positives = 101/194 (52%), Gaps = 15/194 (7%)
Query: 113 PLQGQQELLQD----------FSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVF 162
P + ++LLQ+ +E + ++ +VEF K +PGF L H+DQ+ LLK
Sbjct: 20 PQEITKKLLQEEFSPEENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAV 79
Query: 163 EVLLVRLACMFDSQTNSMICLNGEVLVRDSIHSSN-ARFLMDSMFDFAERLNGLHLSDTE 221
E + +R A ++ N + L+ + I SS + + MF+F + + L ++ E
Sbjct: 80 EAMFLRSAQIY----NKKLPAGHADLLEERIRSSGISDEFITPMFNFYKSMGELKMTQEE 135
Query: 222 IGLFSSIVVISPSRSGLRNKELVERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLR 281
L ++I ++ P R L++KE VE+++ L ++L HPE A L+ L +LR
Sbjct: 136 YALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLLGRLTELR 195
Query: 282 TLNQLHSEKLVAFQ 295
TLN H+E L++++
Sbjct: 196 TLNHHHAEMLMSWK 209
>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 = 85.4 bits (212), Expect = 2e-19
Identities = 41/151 (27%), Positives = 77/151 (50%), Gaps = 2/151 (1%)
Query: 135 VVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLA-CMFDSQTNSMICL-NGEVLVRDS 192
V++AK +P F L DDQ+TLL+ E+LL+ LA + + ++ V++ +
Sbjct: 15 TVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTER 74
Query: 193 IHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRGKLE 252
L+ + + +L L L E +IV+ +P GL+N++ VE ++ K +
Sbjct: 75 EALLGLAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQ 134
Query: 253 NMLMHVLNQNHPEQMNLCAELISMLPDLRTL 283
L + + +P+Q A+L+ LP+LR++
Sbjct: 135 QALQEYIRKRYPQQPARFAKLLLRLPELRSI 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 = 84.3 bits (209), Expect = 1e-18
Identities = 51/153 (33%), Positives = 84/153 (54%), Gaps = 1/153 (0%)
Query: 132 IRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEVLVRD 191
+ +VE+AKRIP FS L DDQV LL+AG E+L+ A + + ++ G L R+
Sbjct: 43 LFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRN 102
Query: 192 SIHSSNARFLMDSMF-DFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRGK 250
S H + + D + + ++ L + TE+G +I++ +P GL++++ VE +R K
Sbjct: 103 SAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREK 162
Query: 251 LENMLMHVLNQNHPEQMNLCAELISMLPDLRTL 283
+ L Q HPEQ A+L+ LP LR++
Sbjct: 163 VYASLEEYCRQKHPEQPGRFAKLLLRLPALRSI 195
>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 = 83.6 bits (207), Expect = 3e-18
Identities = 41/166 (24%), Positives = 91/166 (54%), Gaps = 2/166 (1%)
Query: 132 IRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEVLVRD 191
I+ +++FAK +P F L +DQ++LLK FE+ +R +F+ +T + C + D
Sbjct: 48 IKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWECGPLTYCIED 107
Query: 192 SIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRGKL 251
+ + + L++ + F L L L + E L ++ + SP R G+ +++++++ K+
Sbjct: 108 AARAGFQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKM 167
Query: 252 ENMLMHVL--NQNHPEQMNLCAELISMLPDLRTLNQLHSEKLVAFQ 295
L + + PE+ L ++++ L +LRT+N+ ++++++ Q
Sbjct: 168 ALTLKSYIDSKRPGPEKRFLYPKILACLTELRTINEEYTKQILHIQ 213
>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 = 83.5 bits (206), Expect = 5e-18
Identities = 54/175 (30%), Positives = 95/175 (54%), Gaps = 4/175 (2%)
Query: 120 LLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNS 179
+L ++ S +I+ V+ FAK IPGF L +DQ+ LLK+ EV+++R F S
Sbjct: 38 MLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQSFSLDDMS 97
Query: 180 MICLNGEV--LVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSG 237
C + + V D + ++ L++ + F L L+L + E L +I ++SP R G
Sbjct: 98 WTCGSPDFKYKVSDVTKAGHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPG 157
Query: 238 LRNKELVERMRGKLENMLMHVLNQNHPEQMN--LCAELISMLPDLRTLNQLHSEK 290
+++ L+E ++ +L + L + HP + L A++I L DLR+LN+ HS++
Sbjct: 158 VQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYAKMIQKLADLRSLNEEHSKQ 212
>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 = 75.2 bits (185), Expect = 3e-15
Identities = 58/224 (25%), Positives = 118/224 (52%), Gaps = 26/224 (11%)
Query: 64 MLSTVVRAHLDTCAFTADKIEPMLRRAREHPTYTACPSTLACPLNPNSHPLQGQQEL--L 121
+++++VRAH+D+ +A L ++ + + PL +++ +
Sbjct: 4 LIASLVRAHIDSNPSSAK-----LDYSKFQESVS---------------PLFEKEDASDI 43
Query: 122 QDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMI 181
Q F + S ++ + ++A++IPGFS C +DQ LL++ E+ ++RLA + + +I
Sbjct: 44 QQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLI 103
Query: 182 CLNGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNK 241
NG VL R ++ DS+ +F++ L+ ++L + +++V+I+ R GL+
Sbjct: 104 FCNGVVLHRTQCVRGFGDWI-DSILEFSQSLHRMNLDVSAFSCLAALVIIT-DRHGLKEP 161
Query: 242 ELVERMRGKLENMLM-HVLN-QNHPEQMNLCAELISMLPDLRTL 283
+ VE ++ +L + L HV + P++ N + L+ LP+LRTL
Sbjct: 162 KRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTL 205
>gnl|CDD|132743 cd06945, NR_LBD_Nurr1_like, The ligand binding domain of Nurr1 and
related nuclear receptor proteins, members of nuclear
receptor superfamily. The ligand binding domain of
nuclear receptor Nurr1_like: This family of nuclear
receptors, including Nurr1, Nerve growth
factor-induced-B (NGFI-B) and DHR38 are involved in the
embryo development. Nurr1 is a transcription factor that
is expressed in the embryonic ventral midbrain and is
critical for the development of dopamine (DA) neurons.
Structural studies have shown that the ligand binding
pocket of Nurr1 is filled by bulky hydrophobic residues,
making it unable to bind to ligands. Therefore, it
belongs to the class of orphan receptors. However, Nurr1
forms heterodimers with RXR and can promote signaling
via its partner, RXR. NGFI-B is an early immediate gene
product of embryo development that is rapidly produced
in response to a variety of cellular signals including
nerve growth factor. It is involved in T-cell-mediated
apoptosis, as well as neuronal differentiation and
function. NGFI-B regulates transcription by binding to a
specific DNA target upstream of its target genes and
regulating the rate of tr anscriptional initiation.
Another group of receptor in this family is DHR38.
DHR38 is the Drosophila homolog to the vertebrate
NGFI-B-type orphan receptor. It interacts with the USP
component of the ecdysone receptor complex, suggesting
that DHR38 might modulate ecdysone-triggered signals in
the fly, in addition to the ECR/USP pathway. Nurr1_like
proteins exhibit a modular structure that is
characteristic for nuclear receptors; they have a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a non-conserved hinge and a
C-terminal ligand binding domain (LBD).
Length = 239
Score = 75.1 bits (185), Expect = 3e-15
Identities = 56/228 (24%), Positives = 103/228 (45%), Gaps = 33/228 (14%)
Query: 64 MLSTVVRAHLDTCAFTAD----KIEPMLRRAREHPTYTACPSTLACPLNPNSHPLQGQQE 119
+++ +VRAH+D+ D KI+ P +
Sbjct: 4 LITALVRAHVDSTPRKTDLDYSKIQE--------------NVDPVPPKPDSQQ------- 42
Query: 120 LLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNS 179
+Q F + + ++ + ++A++IPGF L +DQ LL++ E+ ++RLA +
Sbjct: 43 -VQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGK 101
Query: 180 MICLNGEVLVRDSIHSSNARFL--MDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSG 237
++ NG VL R F +DS+ F+ L L L D +++++ R G
Sbjct: 102 LVFCNGLVLHRL--QCVRG-FGEWLDSILAFSSSLQSLLLDDISAFCCLALLLLITERHG 158
Query: 238 LRNKELVERMRGKLENMLMHVLNQNHPEQM--NLCAELISMLPDLRTL 283
L+ + VE ++ K+ + L + N+P Q N ++L+ LP+LRTL
Sbjct: 159 LKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTL 206
>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 = 72.8 bits (179), Expect = 9e-15
Identities = 41/177 (23%), Positives = 82/177 (46%), Gaps = 11/177 (6%)
Query: 128 FSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEV 187
F I+++V+F K IPGF+ L +D+ LLK +F + L+RL+ ++++ + +
Sbjct: 11 FEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNEGTVLC--DFRP 68
Query: 188 LVRDSIHSSNARF-LMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVER 246
+ S+ S L+D M FA ++ L+L++ E+ L + ++ P G +L E
Sbjct: 69 VEFASLLSQLLHGKLIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLG---IQLEET 125
Query: 247 MRGKLE--NMLMHVLNQNHPEQMNLCA---ELISMLPDLRTLNQLHSEKLVAFQMTE 298
+ L+ + + + + + +L +L LR +N+ H L
Sbjct: 126 AKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFDILNRLRNMNKEHQNILADRDKRS 182
>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 = 65.9 bits (161), Expect = 3e-12
Identities = 45/167 (26%), Positives = 77/167 (46%), Gaps = 9/167 (5%)
Query: 135 VVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEVLVRDSIH 194
+VE+AK IP F L DDQV LL+A E LL+ +A + ++ N ++ R
Sbjct: 48 LVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHCPE 107
Query: 195 SSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRGKLENM 254
+R + + L L++ D E +IV P GL + + ++R+R +++
Sbjct: 108 PEISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVS 167
Query: 255 LMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKLVAFQMTEQQQ 301
L +N + EL+ +LP L++ + +QM EQ Q
Sbjct: 168 LEDYINDRQYDSRGRFGELLLLLPTLQS---------ITWQMIEQIQ 205
>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 = 61.8 bits (150), Expect = 9e-11
Identities = 55/230 (23%), Positives = 99/230 (43%), Gaps = 36/230 (15%)
Query: 64 MLSTVVRAHLDTCAFTADKIEPMLRRAREHPTYTACPSTLACPLNPNSHPLQGQQELLQD 123
+++ +VRAH+DT + D + RE P + E +Q
Sbjct: 5 LITALVRAHVDT---SPDFANLDYSQYREPSPL---------------EPPMSEAEKVQQ 46
Query: 124 FSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICL 183
F + +I + FA++IPGF LC +DQ L ++ E+ ++RLA + +
Sbjct: 47 FYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFC 106
Query: 184 NGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSI--VVISPSRSGLRNK 241
NG VL + S +L ++ +F+ LH D +I F+ + + + R GL+
Sbjct: 107 NGVVLHKQQCQRSFGDWL-HAILEFS---KSLHAMDIDISAFACLCALTLITERHGLKEP 162
Query: 242 ELVERMRGKLENML-------MHVLNQNHPEQMNLCAELISMLPDLRTLN 284
VE+++ K+ + L + H L+ LP+LR+L+
Sbjct: 163 HKVEQLQMKIISSLRDHVTYNAEAQKKPHYFS-----RLLGKLPELRSLS 207
>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 = 62.0 bits (150), Expect = 1e-10
Identities = 58/224 (25%), Positives = 107/224 (47%), Gaps = 26/224 (11%)
Query: 64 MLSTVVRAHLDTCAFTADKIEPMLRRAREHPTYTACPSTLACPLNPNSHPLQGQQELLQD 123
++S +VRAH+D+ P + ++ + A NP+ + +Q
Sbjct: 4 LISALVRAHVDS--------NPAMTSL-DYSRFQA---------NPDYQMSGDDTQHIQQ 45
Query: 124 FSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICL 183
F + + ++ + +A++IPGF+ L DQ L ++ E+ ++RLA + +I
Sbjct: 46 FYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFC 105
Query: 184 NGEVLVRDSIHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVIS--PSRSGLRNK 241
NG VL R ++ DS+ +F+ L +++ +I FS I ++ R GL+
Sbjct: 106 NGVVLHRLQCVRGFGEWI-DSIVEFSSNLQNMNI---DISAFSCIAALAMVTERHGLKEP 161
Query: 242 ELVERMRGKLENMLM-HV-LNQNHPEQMNLCAELISMLPDLRTL 283
+ VE ++ K+ N L HV N + N ++L+ LP+LRTL
Sbjct: 162 KRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTL 205
>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 = 53.6 bits (129), Expect = 5e-08
Identities = 43/162 (26%), Positives = 71/162 (43%), Gaps = 10/162 (6%)
Query: 136 VEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLA-CMFDSQTNSMICLNGEVLVRDSIH 194
VE+A+ IP F L DQV LL+ E+ ++ A C ++ G +
Sbjct: 47 VEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGL----HASP 102
Query: 195 SSNARFL--MDSMFDF---AERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRG 249
S R + MD + F E+L LH+ E +IV+ + GL + +E ++
Sbjct: 103 MSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQE 162
Query: 250 KLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKL 291
K + L + +P Q +L+ LP LRT++ E+L
Sbjct: 163 KSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQL 204
>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 = 52.3 bits (126), Expect = 1e-07
Identities = 39/167 (23%), Positives = 80/167 (47%), Gaps = 14/167 (8%)
Query: 136 VEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLA-CMFDSQTNSMICLNGEV------- 187
+ +A+ IP F L + Q +L++A E+ + LA C SQ S+ + +
Sbjct: 38 IHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQC---SQQLSLPTILAAIINHLQTS 94
Query: 188 LVRDSIHSSNARFLMDSMF---DFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELV 244
+ +D + + + +M+ + +F + L + D E +IV+ SP G ++ +
Sbjct: 95 IQQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQI 154
Query: 245 ERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKL 291
E+++ K L + + +PE ++L+ LP LR+L+ +E+L
Sbjct: 155 EKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEEL 201
>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 = 48.8 bits (117), Expect = 2e-06
Identities = 38/146 (26%), Positives = 70/146 (47%), Gaps = 5/146 (3%)
Query: 139 AKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDS-QTNSMICLNGEVLV-RDSIHSS 196
AK IPGFS L +DQ+ LL++ E+L+ L ++ S + ++L+ R+
Sbjct: 47 AKHIPGFSDLSLNDQMHLLQSAWLEILM--LGLVWRSLPHPGKLVFAPDLLLDREQARVE 104
Query: 197 NARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRGKLENMLM 256
+ D + R L L E +I++ + L ++E V+++R + + L+
Sbjct: 105 GLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALV 164
Query: 257 HVLNQNHP-EQMNLCAELISMLPDLR 281
V + H +Q A+L+ +LP LR
Sbjct: 165 DVEAKRHGSQQPRRLAQLLLLLPHLR 190
>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 = 44.3 bits (105), Expect = 6e-05
Identities = 38/173 (21%), Positives = 75/173 (43%), Gaps = 9/173 (5%)
Query: 135 VVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEVLVRDSIH 194
++ +AK+IPGF L DQV LL++ E+L++ L ++ +L R+
Sbjct: 48 MINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQGS 107
Query: 195 SSNARFLM-DSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKEL-----VERMR 248
+ D + A R L L E +I++++ S + L V+R+
Sbjct: 108 CVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLL 167
Query: 249 GKLENMLMHVLNQNH---PEQMNLCAELISMLPDLRTLNQLHSEKLVAFQMTE 298
K+ + L+H ++ +Q A+L+ +L +R ++ E L + +
Sbjct: 168 DKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKN 220
>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 = 40.0 bits (93), Expect = 0.002
Identities = 41/167 (24%), Positives = 78/167 (46%), Gaps = 7/167 (4%)
Query: 131 TIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVR--LACMFDSQTNSMICLNGEVL 188
T+ +VE+A+ F L DDQ+ LL+ E+L++ + + S+ + G+
Sbjct: 52 TLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQ-Q 110
Query: 189 VRDSIHSSNARFLMDSMFDFAE----RLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELV 244
V SI +S A ++++ A+ +L L E +V+ S L N +LV
Sbjct: 111 VDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLV 170
Query: 245 ERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQLHSEKL 291
E ++ ++ L+ N+P+Q +L+ LP++R ++ E L
Sbjct: 171 EGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 217
>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 = 37.4 bits (87), Expect = 0.011
Identities = 41/206 (19%), Positives = 85/206 (41%), Gaps = 15/206 (7%)
Query: 103 LACPLNPNSHPLQGQQELLQDFSERFSPTIR-------DVVEFAKRIPGFSLLCHDDQVT 155
+A L P P+ + D +E F+ R +++ K++P F+ L D
Sbjct: 4 VAEDLEPLITPMLIEDGATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTH 63
Query: 156 LLKAGVFEVLLVRLACMFDSQTNSMI--CLNGEVLVRDSIH--SSNARFLMDSMFDFAER 211
LL E++L+ + Q ++ CL+ + D + +++ + +
Sbjct: 64 LLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELERFGDEGGEVVERLTYLLAK 123
Query: 212 LNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRGKLENMLMHVLNQNHPEQMNLCA 271
L +S+ E I ++ GL N +E ++ + +L N+P Q N +
Sbjct: 124 FRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFS 183
Query: 272 ELISMLPDLRTLNQLHSEKLVAFQMT 297
+L+S LP++R + KL+ ++
Sbjct: 184 DLLSCLPEIRAA----AGKLLHSKLF 205
>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 = 37.2 bits (86), Expect = 0.014
Identities = 29/116 (25%), Positives = 58/116 (50%), Gaps = 3/116 (2%)
Query: 136 VEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTN-SMICLNGEVLV-RDSI 193
V++AK IPGF L DDQ+TLL+ ++ L Q+N +++C ++++ +
Sbjct: 45 VKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRM 104
Query: 194 HSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISP-SRSGLRNKELVERMR 248
M + L+ L +S E +++++S + GL+++EL + +R
Sbjct: 105 TLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIR 160
>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 = 36.6 bits (85), Expect = 0.020
Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 20/184 (10%)
Query: 106 PLNPNSHPLQGQQELLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVL 165
P P+S + L S+ + ++ +AK IPGFS L +DQ++LL++ E+L
Sbjct: 19 PALPDSD-----IKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEIL 73
Query: 166 LVRLACMFDSQTNSMICLNGEVLVRD--SIHSSNARF-----LMDSMFDFAERLNGLHLS 218
+ + F S NGE++ + + AR L + RL L L
Sbjct: 74 TLGVV--FRSLPF-----NGELVFAEDFILDEELAREAGLLELYSACLQLVRRLQRLRLE 126
Query: 219 DTEIGLFSSIVVISPSRSGLRNKELVERMRGKLENMLMHVLNQNHPEQMNL-CAELISML 277
E L ++ + + + + E V ++R L L HP + +L+ L
Sbjct: 127 KEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTL 186
Query: 278 PDLR 281
P LR
Sbjct: 187 PLLR 190
>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 = 35.3 bits (82), Expect = 0.044
Identities = 40/156 (25%), Positives = 68/156 (43%), Gaps = 14/156 (8%)
Query: 136 VEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEVLVR-DSIH 194
V++AK IP FS L DQ+ LL+ E+ L+ A + L+ L+ +
Sbjct: 43 VKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAA-------QWSLPLDSCPLLAVPGLS 95
Query: 195 SSN---ARFLMDSMFDFAE---RLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMR 248
N R + + E R L + TE +IV+ P GL++ VE ++
Sbjct: 96 PDNTEAERTFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQ 155
Query: 249 GKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLN 284
+ + ML + +P Q +L+ +LP LR ++
Sbjct: 156 DQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFIS 191
>gnl|CDD|143540 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV-ERB
receptor-like is composed of two C4-type zinc fingers.
DNA-binding domain of REV-ERB receptor- like is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which coordinates
a single zinc atom. This domain interacts with specific
DNA sites upstream of the target gene and modulates the
rate of transcriptional initiation. REV-ERB receptors
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. REV-ERB
receptors bind as a monomer to a (A/G)GGTCA half-site
with a 5' AT-rich extension or as a homodimer to a
direct repeat 2 element (AGGTCA sequence with a 2-bp
spacer), indicating functional diversity. When bound to
the DNA, they recruit corepressors (NcoR/histone
deacetylase 3) to the promoter, resulting in repression
of the target genes. The porphyrin heme has been
demonstrated to function as a ligand for REV-ERB
receptor. 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 = 89
Score = 33.3 bits (76), Expect = 0.058
Identities = 12/13 (92%), Positives = 13/13 (100%)
Query: 24 VRFGRVPKREKAR 36
VRFGR+PKREKAR
Sbjct: 77 VRFGRIPKREKAR 89
>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 = 34.6 bits (80), Expect = 0.086
Identities = 35/153 (22%), Positives = 74/153 (48%), Gaps = 5/153 (3%)
Query: 136 VEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLAC--MFDSQTNSMICLNGEVLVRDSI 193
VE+A+ F L DDQ+ LL+ E+L++ + + +S++ + G+ + ++
Sbjct: 55 VEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTL 114
Query: 194 HSSNARF---LMDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKELVERMRGK 250
S L+D + +L L E +++ +P GL N++LVE ++ +
Sbjct: 115 ASQAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQ 174
Query: 251 LENMLMHVLNQNHPEQMNLCAELISMLPDLRTL 283
+ L+ N+P+Q + +L+ LP++R +
Sbjct: 175 VNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAI 207
>gnl|CDD|143523 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) is composed of
two C4-type zinc fingers. DNA-binding domain of
peroxisome proliferator-activated receptors (PPAR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which
co-ordinates a single zinc atom. PPAR interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation.
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 elements, which are
composed of two direct repeats of the consensus
sequence 5'-AGGTCA-3' separated by one to five base
pair located upstream of the peroxisome proliferator
responsive genes, and interacts with co-activators.
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 and a C-terminal ligand binding domain
(LBD).
Length = 84
Score = 30.5 bits (69), Expect = 0.46
Identities = 10/18 (55%), Positives = 15/18 (83%), Gaps = 1/18 (5%)
Query: 20 HNAPVRFGRVPKREKARI 37
HNA +RFGR+P+ EK ++
Sbjct: 68 HNA-IRFGRMPRVEKEKL 84
>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 = 31.6 bits (72), Expect = 0.86
Identities = 31/122 (25%), Positives = 53/122 (43%), Gaps = 13/122 (10%)
Query: 135 VVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNS-MICLNGE-VLVRDS 192
VV++AK +PGF L DDQ+TL++ +++ L NS M+ + V
Sbjct: 44 VVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQR 103
Query: 193 IHSSNARFLMDSMFDFAERLNGLHLSDTE------IGLFSSIVVISPSRSGLRNKELVER 246
+H S L M ++ L ++ E + L S+I GL+++ +
Sbjct: 104 MHQSAMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPK-----DGLKSQAAFDE 158
Query: 247 MR 248
MR
Sbjct: 159 MR 160
>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 = 31.1 bits (70), Expect = 1.4
Identities = 31/117 (26%), Positives = 54/117 (46%), Gaps = 3/117 (2%)
Query: 135 VVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNSMICLNGEVLV--RDS 192
VV++AK +PGF L +DQ+TL++ + L+ TNS LV +
Sbjct: 44 VVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEER 103
Query: 193 IHSSNARFLMDSMFDFAERLNGLHLSDTEIGLFSSIVVISP-SRSGLRNKELVERMR 248
+H S L M + + L L+ E + ++++S + GL+++ E MR
Sbjct: 104 MHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMR 160
>gnl|CDD|239317 cd03019, DsbA_DsbA, DsbA family, DsbA subfamily; DsbA is a
monomeric thiol disulfide oxidoreductase protein
containing a redox active CXXC motif imbedded in a TRX
fold. It is involved in the oxidative protein folding
pathway in prokaryotes, and is the strongest thiol
oxidant known, due to the unusual stability of the
thiolate anion form of the first cysteine in the CXXC
motif. The highly unstable oxidized form of DsbA
directly donates disulfide bonds to reduced proteins
secreted into the bacterial periplasm. This rapid and
unidirectional process helps to catalyze the folding of
newly-synthesized polypeptides. To regain catalytic
activity, reduced DsbA is then reoxidized by the
membrane protein DsbB, which generates its disulfides
from oxidized quinones, which in turn are reoxidized by
the electron transport chain.
Length = 178
Score = 29.9 bits (68), Expect = 2.5
Identities = 10/42 (23%), Positives = 14/42 (33%)
Query: 2 MEDELPILKSILKGNARYHNAPVRFGRVPKREKARILAAMQQ 43
E L L + ++ PV FG AR A +
Sbjct: 33 FEPILEAWVKKLPKDVKFEKVPVVFGGGEGEPLARAFYAAEA 74
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 30.1 bits (68), Expect = 3.0
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 258 VLNQNHPEQM---NLCAELISMLPDLRTLNQLHSEKLVAFQMTEQQQQLAAQQQQWHGED 314
+L Q PE + L E I LP + TL +L E L+A +T+ + L Q Q D
Sbjct: 287 LLRQVEPEDLVKFGLIPEFIGRLPVIATLEKLDEEALIAI-LTKPKNALVKQYQALFKMD 345
Query: 315 N 315
N
Sbjct: 346 N 346
>gnl|CDD|220594 pfam10136, SpecificRecomb, Site-specific recombinase. Members of
this family of bacterial proteins are found in various
putative site-specific recombinase transmembrane
proteins.
Length = 647
Score = 30.2 bits (69), Expect = 3.5
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 243 LVERMRGKLENM--LMHVLNQNHPEQMNLCAELISML----PDLRTLNQLHSE--KLVAF 294
L+ER+R +L+ + L+ +L P + EL++ L R++ L + L+A
Sbjct: 248 LLERLRQRLDRIELLLDLLLAPAPNRARAAVELLADLVRAAQRRRSVRALWRQNSSLLAR 307
Query: 295 QMTEQ 299
++TE+
Sbjct: 308 KVTER 312
>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 = 29.5 bits (66), Expect = 3.7
Identities = 43/192 (22%), Positives = 78/192 (40%), Gaps = 20/192 (10%)
Query: 120 LLQDFSERFSPTIRDVVEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLACMFDSQTNS 179
LL +E + VV++AK +PGF L DDQ+ +++ +++ + + NS
Sbjct: 29 LLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNS 88
Query: 180 MICLNGEVLVRDS--IHSSNARFLMDSMFDFAERLNGLHLSDTE------IGLFSSIVVI 231
+ LV + +H S M ++ L ++ E + LFS I V
Sbjct: 89 RMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPV- 147
Query: 232 SPSRSGLRNKELVERMRGKLENMLMHVLN--QNHPEQ-----MNLCAELISMLPDLRTLN 284
GL+N++ + +R L ++ + +P L L S+ P R L+
Sbjct: 148 ----DGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELH 203
Query: 285 QLHSEKLVAFQM 296
Q + L+ M
Sbjct: 204 QFTFDLLIKSHM 215
>gnl|CDD|227911 COG5624, TAF61, Transcription initiation factor TFIID, subunit
TAF12 (also component of histone acetyltransferase SAGA)
[Transcription].
Length = 505
Score = 29.3 bits (65), Expect = 7.4
Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 13/81 (16%)
Query: 295 QMTEQQQQLAAQQQQWHGE---DNSKSPTGSSWSD--------VTMEEVKSPLGSVSSTE 343
Q+Q L+ QQ+ HG + S P + W+ EEV + S E
Sbjct: 237 FQQGQKQVLSPQQRFLHGMERYEASGMPPPAEWAGSNGLHVLPGRREEVPRGIFRCPSPE 296
Query: 344 SVCSNEVATLNEYTSTHAQNA 364
S S T +Y + A NA
Sbjct: 297 S--SRGEPTHLDYRNGMANNA 315
>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 = 28.6 bits (64), Expect = 8.2
Identities = 34/165 (20%), Positives = 59/165 (35%), Gaps = 16/165 (9%)
Query: 136 VEFAKRIPGFSLLCHDDQVTLLKAGVFEVLLVRLA---CMFDSQTNSMICLNGEVLVRDS 192
+ F + +P F+ L DDQ+ LL+ +LL+ LA FD+ + E+L
Sbjct: 36 IRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAE 95
Query: 193 IHSSNARFL------------MDSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRN 240
+H + + F + L L E V+ +P L
Sbjct: 96 MHWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-C 154
Query: 241 KELVERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLNQ 285
+E ++ + + L P + A L+ ML LR +
Sbjct: 155 PHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKT 199
>gnl|CDD|217451 pfam03249, TSA, Type specific antigen. There are several antigenic
variants in Rickettsia tsutsugamushi, and a
type-specific antigen (TSA) of 56-kilodaltons located on
the rickettsial surface is responsible for the
variation. TSA proteins are probably integral membrane
proteins.
Length = 502
Score = 29.1 bits (65), Expect = 8.5
Identities = 25/105 (23%), Positives = 41/105 (39%), Gaps = 31/105 (29%)
Query: 217 LSD------TEIGLFSSIVVISPSRSGLRNKELVERMRGKLENMLMHVLNQNHPEQMNLC 270
LSD ++I F+ I I + L N VE+++ K++
Sbjct: 234 LSDKITQIYSDIKPFADIAGIDVPDTPLPNSASVEQIQNKMQ------------------ 275
Query: 271 AELISMLPDLR------TLNQLHSEKLVAFQMTEQQQQLAAQQQQ 309
EL +L +LR N ++ + F + +Q QQ QQQ
Sbjct: 276 -ELNDVLEELRESFDGYIGNAFANQIQLNFVIPQQAQQQGQGQQQ 319
>gnl|CDD|233000 TIGR00508, bioA, adenosylmethionine-8-amino-7-oxononanoate
transaminase. All members of the seed alignment have
been demonstrated experimentally to act as EC 2.6.1.62,
an enzyme in the biotin biosynthetic pathway. Alternate
names include 7,8-diaminopelargonic acid
aminotransferase, DAPA aminotransferase, and
adenosylmethionine-8-amino-7-oxononanoate
aminotransferase. The gene symbol is bioA in E. coli and
BIO3 in S. cerevisiae [Biosynthesis of cofactors,
prosthetic groups, and carriers, Biotin].
Length = 417
Score = 28.6 bits (65), Expect = 9.2
Identities = 9/45 (20%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 237 GLRNKELVERMRGKLENMLMHV--LNQNHPEQMNLCAELISMLPD 279
G + E+ ++ +L+ + HV H + L L+ + P+
Sbjct: 46 GHNHPEINAAIKEQLDKL-EHVMFGGLTHEPAIELAERLVEITPE 89
>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 = 28.2 bits (63), Expect = 9.5
Identities = 31/161 (19%), Positives = 58/161 (36%), Gaps = 12/161 (7%)
Query: 136 VEFAKRIPGFSLLCHDDQVTLLK---AGVFEVLLVRLACMFDSQTNSM------ICLNGE 186
V F + +P F L DQ+ LL+ +F + L + F+ + I L G+
Sbjct: 36 VAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQ 95
Query: 187 VLVRDSIHSSNARFLM---DSMFDFAERLNGLHLSDTEIGLFSSIVVISPSRSGLRNKEL 243
S + + + + L LS E ++ +P GL
Sbjct: 96 SSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSH 155
Query: 244 VERMRGKLENMLMHVLNQNHPEQMNLCAELISMLPDLRTLN 284
V ++ + + L VL HP+ A ++ L+++
Sbjct: 156 VGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIP 196
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
0.315 0.128 0.365
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: 28,931,815
Number of extensions: 2754486
Number of successful extensions: 2611
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2571
Number of HSP's successfully gapped: 53
Length of query: 585
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 483
Effective length of database: 6,413,494
Effective search space: 3097717602
Effective search space used: 3097717602
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.7 bits)