RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2636
(335 letters)
>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 = 237 bits (605), Expect = 2e-77
Identities = 121/197 (61%), Positives = 135/197 (68%), Gaps = 44/197 (22%)
Query: 139 PPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQEL 198
PPVSLITAL +R D P F++L D
Sbjct: 1 PPVSLITAL------------------------------VRAHVDTSPDFANL---DYSQ 27
Query: 199 LFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE 258
YREP+PLEPP++E EK+QQFYSLLT+S+DVI+ FA+KIPGF DLCKEDQE
Sbjct: 28 ----------YREPSPLEPPMSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQE 77
Query: 259 LLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHL 318
LLFQSASLELFVLRLAYRT EDTKL FCNGVVL KQQCQRSFG DWL+AILEF +SLH
Sbjct: 78 LLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQRSFG-DWLHAILEFSKSLHA 136
Query: 319 MEIDISAFACLCALTLI 335
M+IDISAFACLCALTLI
Sbjct: 137 MDIDISAFACLCALTLI 153
>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 = 170 bits (433), Expect = 1e-51
Identities = 75/127 (59%), Positives = 96/127 (75%), Gaps = 1/127 (0%)
Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
++E + IQQFY LL+ S++VIR +A+KIPGFSD CKEDQELL +SA +EL
Sbjct: 27 FQESVSPLFEKEDASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVEL 86
Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFAC 328
F+LRLAYR+ E+ KLIFCNGVVL + QC R FG DW+++ILEF QSLH M +D+SAF+C
Sbjct: 87 FILRLAYRSNPEEGKLIFCNGVVLHRTQCVRGFG-DWIDSILEFSQSLHRMNLDVSAFSC 145
Query: 329 LCALTLI 335
L AL +I
Sbjct: 146 LAALVII 152
Score = 76.8 bits (189), Expect = 2e-16
Identities = 43/87 (49%), Positives = 54/87 (62%), Gaps = 18/87 (20%)
Query: 140 PVSLITALYR---EPNP------------LEPPIAEPEK---IQQFYSLLTTSVDVIRHF 181
PV+LI +L R + NP P+ E E IQQFY LL+ S++VIR +
Sbjct: 1 PVNLIASLVRAHIDSNPSSAKLDYSKFQESVSPLFEKEDASDIQQFYDLLSGSLEVIRKW 60
Query: 182 ADKIPGFSDLCKEDQELLFQSASLELF 208
A+KIPGFSD CKEDQELL +SA +ELF
Sbjct: 61 AEKIPGFSDFCKEDQELLLESAFVELF 87
>gnl|CDD|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear
receptor, nerve growth factor-induced-B. DNA-binding
domain (DBD) of the orphan nuclear receptor, nerve
growth factor-induced-B (NGFI-B) 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. NGFI-B interacts with specific DNA sites upstream
of the target gene and modulates the rate of
transcriptional initiation. 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 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.
NGFI-B binds to the NGFI-B response element (NBRE)
5'-(A/T)AAAGGTCA as a monomer. 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 = 75
Score = 164 bits (416), Expect = 3e-51
Identities = 68/75 (90%), Positives = 71/75 (94%)
Query: 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K CPVDKRRRNRCQ+CRF
Sbjct: 1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRF 60
Query: 101 QKCLQVGMVKEVVRT 115
QKCLQVGMVKEVVRT
Sbjct: 61 QKCLQVGMVKEVVRT 75
>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 = 167 bits (426), Expect = 1e-50
Identities = 74/128 (57%), Positives = 92/128 (71%), Gaps = 2/128 (1%)
Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
+E PP + +++QQFY LLT SVDVIR +A+KIPGF DL +EDQ+LL +SA LEL
Sbjct: 27 IQENVDPVPPKPDSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLEL 86
Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLH-LMEIDISAFA 327
FVLRLAYR+ D KL+FCNG+VL + QC R FG +WL++IL F SL L+ DISAF
Sbjct: 87 FVLRLAYRSNPVDGKLVFCNGLVLHRLQCVRGFG-EWLDSILAFSSSLQSLLLDDISAFC 145
Query: 328 CLCALTLI 335
CL L LI
Sbjct: 146 CLALLLLI 153
Score = 89.4 bits (222), Expect = 8e-21
Identities = 43/87 (49%), Positives = 53/87 (60%), Gaps = 18/87 (20%)
Query: 140 PVSLITAL------------------YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHF 181
PVSLITAL +E PP + +++QQFY LLT SVDVIR +
Sbjct: 1 PVSLITALVRAHVDSTPRKTDLDYSKIQENVDPVPPKPDSQQVQQFYDLLTGSVDVIRQW 60
Query: 182 ADKIPGFSDLCKEDQELLFQSASLELF 208
A+KIPGF DL +EDQ+LL +SA LELF
Sbjct: 61 AEKIPGFKDLHREDQDLLLESAFLELF 87
>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 = 145 bits (367), Expect = 6e-42
Identities = 68/115 (59%), Positives = 91/115 (79%), Gaps = 1/115 (0%)
Query: 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE 280
+ + IQQFY LLT S+++IR +A+KIPGF+DL K DQ+LLF+SA LELFVLRLAYR+
Sbjct: 39 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPV 98
Query: 281 DTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
+ KLIFCNGVVL + QC R FG +W+++I+EF +L M IDISAF+C+ AL ++
Sbjct: 99 EGKLIFCNGVVLHRLQCVRGFG-EWIDSIVEFSSNLQNMNIDISAFSCIAALAMV 152
Score = 71.6 bits (175), Expect = 2e-14
Identities = 45/100 (45%), Positives = 58/100 (58%), Gaps = 24/100 (24%)
Query: 140 PVSLITALYREPNPLEPPIA------------------EPEKIQQFYSLLTTSVDVIRHF 181
PVSLI+AL R P + + + IQQFY LLT S+++IR +
Sbjct: 1 PVSLISALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGW 60
Query: 182 ADKIPGFSDLCKEDQELLFQSASLELF-----YREPNPLE 216
A+KIPGF+DL K DQ+LLF+SA LELF YR NP+E
Sbjct: 61 AEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRS-NPVE 99
>gnl|CDD|143512 cd06916, NR_DBD_like, DNA-binding domain of nuclear receptors is
composed of two C4-type zinc fingers. DNA-binding
domain of nuclear receptors 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. It
interacts with a specific DNA site upstream of the
target gene and modulates the rate of transcriptional
initiation. 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). Most nuclear
receptors bind as homodimers or heterodimers to their
target sites, which consist of two hexameric half-sites.
Specificity is determined by the half-site sequence, the
relative orientation of the half-sites and the number of
spacer nucleotides between the half-sites. However, a
growing number of nuclear receptors have been reported
to bind to DNA as monomers.
Length = 72
Score = 138 bits (351), Expect = 2e-41
Identities = 46/72 (63%), Positives = 54/72 (75%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
CAVCGD A+ HYGV TCEGCKGFF+R+V++ +Y C A C +DKR RNRCQ CR +K
Sbjct: 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKK 60
Query: 103 CLQVGMVKEVVR 114
CL VGM KE VR
Sbjct: 61 CLAVGMRKEAVR 72
>gnl|CDD|201004 pfam00105, zf-C4, Zinc finger, C4 type (two domains). In nearly
all cases, this is the DNA binding domain of a nuclear
hormone receptor. The alignment contains two Zinc finger
domains that are too dissimilar to be aligned with each
other.
Length = 70
Score = 135 bits (341), Expect = 4e-40
Identities = 44/70 (62%), Positives = 54/70 (77%)
Query: 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
+LC VCGD A+ HYGV TCEGCKGFF+R++QK Y C +K C +DKR RNRCQ+CR
Sbjct: 1 ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRL 60
Query: 101 QKCLQVGMVK 110
+KCL+VGM K
Sbjct: 61 KKCLEVGMSK 70
>gnl|CDD|143519 cd06961, NR_DBD_TR, DNA-binding domain of thyroid hormone receptors
(TRs) is composed of two C4-type zinc fingers.
DNA-binding domain of thyroid hormone receptors (TRs) 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. TR interacts with the thyroid
response element, which is a DNA site with direct
repeats of the consensus sequence 5'-AGGTCA-3' separated
by one to five base pairs, upstream of target genes and
modulates the rate of transcriptional initiation.
Thyroid hormone receptor (TR) mediates 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 = 85
Score = 118 bits (297), Expect = 2e-33
Identities = 44/84 (52%), Positives = 55/84 (65%)
Query: 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
C VCGD A HY TCEGCKGFF+RTVQK Y C + C +DK RN+CQ CRF+
Sbjct: 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFK 60
Query: 102 KCLQVGMVKEVVRTDSLKGRRGRL 125
KC+ VGM K++V D +G + +L
Sbjct: 61 KCIAVGMAKDLVLDDRKRGAKRKL 84
>gnl|CDD|143541 cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain of Lrh-1 like
nuclear receptor family like is composed of two C4-type
zinc fingers. The DNA-binding domain of Lrh-1 like
nuclear receptor family like 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. This
domain interacts with specific DNA sites upstream of the
target gene and modulates the rate of transcriptional
initiation. 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 is required at several stages
of development. Particularly, FTZ-F1 regulated 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
monomers. 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 = 93
Score = 116 bits (291), Expect = 2e-32
Identities = 45/82 (54%), Positives = 57/82 (69%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C VCGD + HYG+ TCE CKGFFKRTVQ +Y C+ ++ C +DK +R RC +CRFQK
Sbjct: 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQK 60
Query: 103 CLQVGMVKEVVRTDSLKGRRGR 124
CL VGM E VR D ++G R +
Sbjct: 61 CLSVGMKLEAVRADRMRGGRNK 82
>gnl|CDD|143514 cd06956, NR_DBD_RXR, DNA-binding domain of retinoid X receptor
(RXR) is composed of two C4-type zinc fingers.
DNA-binding domain of retinoid X receptor (RXR) 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. RXR functions as a DNA binding
partner by forming heterodimers with other nuclear
receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR,
and VDR. All RXR heterodimers preferentially bind
response elements composed of direct repeats of two
AGGTCA sites with a 1-5 bp spacer. RXRs can play
different roles in these heterodimers. RXR 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. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, RXR 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 = 77
Score = 114 bits (288), Expect = 3e-32
Identities = 45/73 (61%), Positives = 59/73 (80%)
Query: 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
+CA+CGD A+ +HYGV +CEGCKGFFKRTV+K Y C +K C +DKR+RNRCQ+CR+Q
Sbjct: 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 61
Query: 102 KCLQVGMVKEVVR 114
KCL +GM +E V+
Sbjct: 62 KCLAMGMKREAVQ 74
>gnl|CDD|143542 cd07168, NR_DBD_DHR4_like, DNA-binding domain of ecdysone-induced
DHR4 orphan nuclear receptor is composed of two C4-type
zinc fingers. DNA-binding domain of ecdysone-induced
DHR4 orphan nuclear receptor 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. 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 = 90
Score = 115 bits (289), Expect = 3e-32
Identities = 44/83 (53%), Positives = 57/83 (68%)
Query: 40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCR 99
+LC++C D A HYG+ TCEGCKGFFKRTVQ Y C+ D C + K +RNRCQ+CR
Sbjct: 6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCR 65
Query: 100 FQKCLQVGMVKEVVRTDSLKGRR 122
F+KC++ GM+ VR D + G R
Sbjct: 66 FRKCIRKGMMLAAVREDRMPGGR 88
>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors.
Length = 70
Score = 113 bits (284), Expect = 1e-31
Identities = 36/70 (51%), Positives = 44/70 (62%)
Query: 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
LC VCGD A+ H+GV +C CK FF+RTV KY C C ++KR R RC+ CR +
Sbjct: 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLK 60
Query: 102 KCLQVGMVKE 111
KCL VGM E
Sbjct: 61 KCLGVGMDPE 70
>gnl|CDD|143544 cd07170, NR_DBD_ERR, DNA-binding domain of estrogen related
receptors (ERR) is composed of two C4-type zinc fingers.
DNA-binding domain of estrogen related receptors (ERRs)
is composed of two C4-type zinc fingers. Each zinc
finger contains a group of four Cys residues which
coordinates a single zinc atom. ERR interacts with the
palindromic inverted repeat, 5'GGTCAnnnTGACC-3',
upstream of the target gene and modulates the rate of
transcriptional initiation. The estrogen
receptor-related receptors (ERRs) are transcriptional
regulators, which are closely related to the estrogen
receptor (ER) family. Although ERRs lack the ability to
bind to estrogen and are so-called orphan receptors,
they share target genes, co-regulators and promoters
with the estrogen receptor (ER) family. By targeting the
same set of genes, ERRs seem to interfere with the
classic ER-mediated estrogen response in various ways.
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 non-conserved
hinge and a C-terminal ligand binding domain (LBD).
Length = 97
Score = 113 bits (284), Expect = 2e-31
Identities = 49/93 (52%), Positives = 62/93 (66%)
Query: 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
P +LC VCGDIA+ HYGV +CE CK FFKRT+Q +Y C A C + KRRR CQ C
Sbjct: 3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQAC 62
Query: 99 RFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKS 131
RF KCL+VGM+KE VR D ++G R + + +
Sbjct: 63 RFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDA 95
>gnl|CDD|143518 cd06960, NR_DBD_HNF4A, DNA-binding domain of heptocyte nuclear
factor 4 (HNF4) is composed of two C4-type zinc fingers.
DNA-binding domain of hepatocyte nuclear factor 4
(HNF4) 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. HNF4 interacts with a
DNA site, composed of two direct repeats of AGTTCA with
1 bp spacer, which is upstream of target genes and
modulates the rate of transcriptional initiation. 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).
Length = 76
Score = 110 bits (278), Expect = 1e-30
Identities = 41/74 (55%), Positives = 53/74 (71%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
CAVCGD A +HYGV +C GCKGFF+R+V+K Y C C VDK +RN C++CRF+K
Sbjct: 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKK 60
Query: 103 CLQVGMVKEVVRTD 116
CL+VGM E V+ +
Sbjct: 61 CLEVGMDPEAVQNE 74
>gnl|CDD|143525 cd06967, NR_DBD_TR2_like, DNA-binding domain of the TR2 and TR4
(human testicular receptor 2 and 4) is composed of two
C4-type zinc fingers. DNA-binding domain of the TR2 and
TR4 (human testicular receptor 2 and 4) is composed of
two C4-type zinc fingers. Each zinc finger contains a
group of four Cys residues which coordinates a single
zinc atom. TR2 and TR4 interact with specific DNA sites
upstream of the target gene and modulate the rate of
transcriptional initiation. TR4 and TR2 are orphan
nuclear receptors; the physiological ligand is as yet
unidentified. 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. It has been 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, and peroxisome
proliferator-activated receptor. TR4/2 binds to HREs as
dimers. Like other members of the nuclear 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 = 87
Score = 107 bits (270), Expect = 2e-29
Identities = 41/76 (53%), Positives = 54/76 (71%)
Query: 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
P +LC VCGD A+ +HYG +CEGCKGFFKR+++K Y C K C ++K RNRCQ+C
Sbjct: 2 PVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYC 61
Query: 99 RFQKCLQVGMVKEVVR 114
R QKCL +GM + V+
Sbjct: 62 RLQKCLAMGMKSDSVQ 77
>gnl|CDD|143522 cd06964, NR_DBD_RAR, DNA-binding domain of retinoic acid receptor
(RAR) is composed of two C4-type zinc fingers.
DNA-binding domain of retinoic acid receptor (RAR) 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. RAR interacts with specific DNA
sites upstream of the target gene and modulates the rate
of transcriptional initiation. RARs mediate the
biological effect of retinoids, including both natural
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. RAR
function as a heterodimer with retinoic X receptor by
binding to specific RAR response elements (RAREs), which
are composed of two direct repeats of the consensus
sequence 5'-AGGTCA-3' separated by one to five base pair
and found in the promoter regions of retinoid target
genes. 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 = 85
Score = 107 bits (268), Expect = 3e-29
Identities = 45/85 (52%), Positives = 56/85 (65%)
Query: 37 PSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQ 96
P + C VC D ++ HYGV CEGCKGFF+R++QK Y C DK C ++K RNRCQ
Sbjct: 1 PRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQ 60
Query: 97 FCRFQKCLQVGMVKEVVRTDSLKGR 121
+CR QKC +VGM KE VR D K +
Sbjct: 61 YCRLQKCFEVGMSKESVRNDRNKKK 85
>gnl|CDD|143543 cd07169, NR_DBD_GCNF_like, DNA-binding domain of Germ cell nuclear
factor (GCNF) F1 is composed of two C4-type zinc
fingers. DNA-binding domain of Germ cell nuclear factor
(GCNF) F1 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. GCNF
is a transcription factor expressed in post-meiotic
stages of developing male germ cells. In vitro, GCNF has
the ability to bind to direct repeat elements of
5'-AGGTCA.AGGTCA-3', as well as to an extended half-site
sequence 5'-TCA.AGGTCA-3'. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, GCNF 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 = 90
Score = 106 bits (267), Expect = 5e-29
Identities = 40/82 (48%), Positives = 56/82 (68%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C +CGD A HYG+ +CEGCKGFFKR++ Y C DK C + +++RNRCQ+CR K
Sbjct: 9 CLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLK 68
Query: 103 CLQVGMVKEVVRTDSLKGRRGR 124
CLQ+GM ++ +R D + G R +
Sbjct: 69 CLQMGMNRKAIREDGMPGGRNK 90
>gnl|CDD|143530 cd07155, NR_DBD_ER_like, DNA-binding domain of estrogen receptor
(ER) and estrogen related receptors (ERR) is composed of
two C4-type zinc fingers. DNA-binding domains of
estrogen receptor (ER) and estrogen related receptors
(ERR) are composed of two C4-type zinc fingers. Each
zinc finger contains a group of four Cys residues which
co-ordinates a single zinc atom. ER and ERR interact
with the palindromic inverted repeat,
5'GGTCAnnnTGACC-3', upstream of the target gene and
modulate the rate of transcriptional initiation. ERR and
ER are closely related and share sequence similarity,
target genes, co-regulators and promoters. While ER is
activated by endogenous estrogen, ERR lacks the ability
to bind to estrogen. Estrogen receptor mediates the
biological effects of hormone estrogen by the binding of
the receptor dimer to estrogen response element of
target genes. However, ERRs seem to interfere with the
classic ER-mediated estrogen responsive signaling by
targeting the same set of genes. ERRs and ERs exhibit
the common modular structure with other nuclear
receptors. They have a central highly conserved DNA
binding domain (DBD), a non-conserved N-terminal domain,
a flexible hinge and a C-terminal ligand binding domain
(LBD).
Length = 75
Score = 103 bits (259), Expect = 5e-28
Identities = 45/74 (60%), Positives = 52/74 (70%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C VCGDIA+ HYGV +CE CK FFKRT+Q Y C + C VDK+RR CQ CR QK
Sbjct: 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQK 60
Query: 103 CLQVGMVKEVVRTD 116
CL+VGM+KE VR D
Sbjct: 61 CLKVGMLKEGVRLD 74
>gnl|CDD|143539 cd07165, NR_DBD_DmE78_like, DNA-binding domain of Drosophila
ecdysone-induced protein 78 (E78) like is composed of
two C4-type zinc fingers. DNA-binding domain of
proteins similar to Drosophila ecdysone-induced protein
78 (E78) is composed of two C4-type zinc fingers. Each
zinc finger contains a group of four Cys residues which
coordinates a single zinc atom. E78 interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation.
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. 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. The 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 = 81
Score = 103 bits (259), Expect = 7e-28
Identities = 45/88 (51%), Positives = 60/88 (68%), Gaps = 7/88 (7%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C VCGD A+ HYGV +CEGCKGFF+R++QK +Y CL D C + + RNRCQ+CRF+K
Sbjct: 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKK 60
Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKPK 130
CL GM K+ V R GR+P++ +
Sbjct: 61 CLAAGMSKDSV-------RYGRIPNRQR 81
>gnl|CDD|143538 cd07164, NR_DBD_PNR_like_1, DNA-binding domain of the photoreceptor
cell-specific nuclear receptor (PNR) like proteins is
composed of two C4-type zinc fingers. DNA-binding
domain of the photoreceptor cell-specific nuclear
receptor (PNR) like proteins 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. PNR
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. PNR is a member of nuclear receptor
superfamily of the ligand-activated transcription
factors. 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. It most likely binds
to DNA as a homodimer. Like other members of the nuclear
receptor (NR) superfamily of ligand-activated
transcription factors, PNR 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 = 78
Score = 102 bits (257), Expect = 1e-27
Identities = 39/72 (54%), Positives = 55/72 (76%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C VCGD A+ +HYGV +C+GC+GFFKR++++ YVC + +C VD RRN+CQ CRF+K
Sbjct: 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKK 60
Query: 103 CLQVGMVKEVVR 114
CLQV M ++ V+
Sbjct: 61 CLQVNMNRDAVQ 72
>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 = 103 bits (257), Expect = 2e-27
Identities = 44/91 (48%), Positives = 61/91 (67%), Gaps = 8/91 (8%)
Query: 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRF 100
LC VCGD A+ HYGV CEGCKGFF+R++Q+ +Y C ++ C + + RNRCQ+CRF
Sbjct: 5 LCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRF 64
Query: 101 QKCLQVGMVKEVVRTDSLKGRRGRLPSKPKS 131
+KCL VGM ++ VR GR+P + K+
Sbjct: 65 KKCLAVGMSRDAVRF-------GRIPKREKA 88
>gnl|CDD|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER)
is composed of two C4-type zinc fingers. DNA-binding
domain of estrogen receptors (ER) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which coordinates a single zinc
atom. ER interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. Estrogen receptor is a
transcription regulator that mediates the biological
effects of hormone estrogen. The binding of estrogen to
the receptor triggers the dimerization and the binding
of the receptor dimer to estrogen response element,
which is a palindromic inverted repeat:
5'GGTCAnnnTGACC-3', of target genes. Through ER,
estrogen regulates development, reproduction and
homeostasis. 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
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 82
Score = 101 bits (254), Expect = 3e-27
Identities = 42/85 (49%), Positives = 55/85 (64%), Gaps = 4/85 (4%)
Query: 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
+ CAVC D A+ HYGV +CEGCK FFKR++Q + Y+C A C +DK RR CQ C
Sbjct: 2 DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQAC 61
Query: 99 RFQKCLQVGMVKEVVRTDSLKGRRG 123
R +KC +VGM+K +R + RRG
Sbjct: 62 RLRKCYEVGMMKGGIR----RERRG 82
>gnl|CDD|143516 cd06958, NR_DBD_COUP_TF, DNA-binding domain of chicken ovalbumin
upstream promoter transcription factors (COUP-TFs) is
composed of two C4-type zinc fingers. DNA-binding
domain of chicken ovalbumin upstream promoter
transcription factors (COUP-TFs) 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. 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. COUP-TFs homodimerize or heterodimerize
with retinoid X receptor (RXR) and a few other nuclear
receptors and bind to a variety of response elements
that are composed of imperfect AGGTCA direct or inverted
repeats with various spacings. 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 conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 73
Score = 100 bits (250), Expect = 8e-27
Identities = 38/72 (52%), Positives = 54/72 (75%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C VCGD ++ +HYG TCEGCK FFKR+V++ Y C ++ CP+D+ RN+CQ+CR +K
Sbjct: 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKK 60
Query: 103 CLQVGMVKEVVR 114
CL+VGM +E V+
Sbjct: 61 CLKVGMRREAVQ 72
>gnl|CDD|143529 cd07154, NR_DBD_PNR_like, The DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR)
nuclear receptor-like family. The DNA-binding domain of
the photoreceptor cell-specific nuclear receptor (PNR)
nuclear receptor-like family is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which coordinates a single zinc atom. PNR
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. This family includes nuclear receptor
Tailless (TLX), photoreceptor cell-specific nuclear
receptor (PNR) and related receptors. TLX is an orphan
receptor that plays a key role in neural development by
regulating cell cycle progression and exit of neural
stem cells 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, PNR-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 = 73
Score = 98.8 bits (246), Expect = 3e-26
Identities = 38/73 (52%), Positives = 53/73 (72%), Gaps = 1/73 (1%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLA-DKACPVDKRRRNRCQFCRFQ 101
C VCGD ++ +HYGV C+GC GFFKR++++ Y C A + +C VDK RRN+CQ CR +
Sbjct: 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLK 60
Query: 102 KCLQVGMVKEVVR 114
KCL+V M K+ V+
Sbjct: 61 KCLEVSMNKDAVQ 73
>gnl|CDD|143533 cd07158, NR_DBD_Ppar_like, The DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) like nuclear
receptor family. The DNA-binding domain of peroxisome
proliferator-activated receptors (PPAR) like nuclear
receptor family 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. These domains
interact with specific DNA sites upstream of the target
gene and modulate the rate of transcriptional
initiation. This family includes three known types of
nuclear receptors: peroxisome proliferator-activated
receptors (PPAR), REV-ERB receptors and Drosophila
ecdysone-induced protein 78 (E78). Like other members of
the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, PPAR-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 = 73
Score = 98.8 bits (246), Expect = 3e-26
Identities = 41/73 (56%), Positives = 51/73 (69%), Gaps = 1/73 (1%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADKACPVDKRRRNRCQFCRFQ 101
C VCGD A+ HYGV +CEGCKGFF+RT+Q Y CL C + ++ RNRCQ+CRF+
Sbjct: 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFK 60
Query: 102 KCLQVGMVKEVVR 114
KCL VGM + VR
Sbjct: 61 KCLSVGMSRNAVR 73
>gnl|CDD|143528 cd06970, NR_DBD_PNR, DNA-binding domain of the photoreceptor
cell-specific nuclear receptor (PNR) is composed of two
C4-type zinc fingers. DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR) 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. PNR interacts with specific DNA
sites upstream of the target gene and modulates the rate
of transcriptional initiation. PNR is a member of the
nuclear receptor superfamily of the ligand-activated
transcription factors. 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. It
most likely binds to DNA as a homodimer. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, PNR has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 92
Score = 95.4 bits (237), Expect = 1e-24
Identities = 41/83 (49%), Positives = 54/83 (65%), Gaps = 1/83 (1%)
Query: 35 TPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA-CPVDKRRRN 93
+P LC VCGD ++ +HYG+ C GC GFFKR+V++ Y C A CPVDK RN
Sbjct: 1 KGLNPGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRN 60
Query: 94 RCQFCRFQKCLQVGMVKEVVRTD 116
+CQ CR +KCLQ GM K+ V+ +
Sbjct: 61 QCQACRLKKCLQAGMNKDAVQNE 83
>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 = 94.8 bits (236), Expect = 2e-24
Identities = 43/86 (50%), Positives = 54/86 (62%), Gaps = 10/86 (11%)
Query: 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRF 100
C VCGD A+ HYGV CEGCKGFF+RT++ Y C D +C + K+ RN+CQ+CRF
Sbjct: 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPC--DLSCKIHKKSRNKCQYCRF 58
Query: 101 QKCLQVGMVKEVVRTDSLKGRRGRLP 126
QKCL VGM +R GR+P
Sbjct: 59 QKCLNVGMSHNAIRF-------GRMP 77
>gnl|CDD|143526 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoid-related orphan
receptors (RORs) is composed of two C4-type zinc
fingers. DNA-binding domain of Retinoid-related orphan
receptors (RORs) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which coordinates a single zinc atom. ROR
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. 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. There are three
subtypes of retinoid-related orphan receptors (RORs),
alpha, beta, and gamma, which 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 suggested that cholesterol or a cholesterol
derivative are the natural ligands 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 = 95
Score = 94.9 bits (236), Expect = 2e-24
Identities = 38/72 (52%), Positives = 49/72 (68%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C +CGD ++ HYGV TCEGCKGFF+R+ Q Y C K C +D+ RNRCQ CR QK
Sbjct: 8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQK 67
Query: 103 CLQVGMVKEVVR 114
CL +GM ++ V+
Sbjct: 68 CLALGMSRDAVK 79
>gnl|CDD|143515 cd06957, NR_DBD_PNR_like_2, DNA-binding domain of the photoreceptor
cell-specific nuclear receptor (PNR) like is composed of
two C4-type zinc fingers. The DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR)
nuclear receptor-like family is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which coordinates a single zinc atom. PNR
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. This family includes nuclear receptor
Tailless (TLX), photoreceptor cell-specific nuclear
receptor (PNR) and related receptors. TLX is an orphan
receptor that plays a key role in neural development by
regulating cell cycle progression and exit of neural
stem cells 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, PNR-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 = 82
Score = 94.1 bits (234), Expect = 3e-24
Identities = 40/75 (53%), Positives = 49/75 (65%), Gaps = 1/75 (1%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADK-ACPVDKRRRNRCQFCRFQ 101
C VCGD + +HYGV C+GC FFKR+V+KG Y C+A C VDK RRN C FCR Q
Sbjct: 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQ 60
Query: 102 KCLQVGMVKEVVRTD 116
KC VGM + V+ +
Sbjct: 61 KCFAVGMNRAAVQEE 75
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
composed of two C4-type zinc fingers. DNA-binding
domain of Tailless (TLX) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which co-ordinates a single zinc atom. TLX
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. TLX is an orphan receptor that is expressed
by neural stem/progenitor cells in the adult brain of
the subventricular zone (SVZ) and the dentate gyrus
(DG). It plays a key role in neural development by
promoting cell cycle progression and preventing
apoptosis in the developing brain. Like other members of
the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX has a
central well conserved DNA-binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 92
Score = 93.7 bits (233), Expect = 5e-24
Identities = 36/74 (48%), Positives = 53/74 (71%), Gaps = 2/74 (2%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADK--ACPVDKRRRNRCQFCRF 100
C VCGD ++ +HYG+ C+GC GFFKR++++ +YVC + CPVDK RN+C+ CR
Sbjct: 9 CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRL 68
Query: 101 QKCLQVGMVKEVVR 114
+KC +VGM K+ V+
Sbjct: 69 KKCFEVGMNKDAVQ 82
>gnl|CDD|143548 cd07179, 2DBD_NR_DBD2, The second DNA-binding domain (DBD) of the
2DBD nuclear receptor is composed of two C4-type zinc
fingers. The second DNA-binding domain (DBD) of the
2DBD nuclear receptor (NR) 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. NRs
interact with specific DNA sites upstream of the target
gene and modulate the rate of transcriptional
initiation. The proteins contain two DBDs in tandem,
probably resulting from an ancient recombination event.
The 2DBD-NRs are found only in flatworm species,
mollusks and arthropods. Their biological function is
unknown.
Length = 74
Score = 92.6 bits (230), Expect = 7e-24
Identities = 34/72 (47%), Positives = 44/72 (61%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C VCG ++ H+G TCEGCKGFF+RT + YVC + C + RN C+ CRF++
Sbjct: 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRR 60
Query: 103 CLQVGMVKEVVR 114
CL VGM K R
Sbjct: 61 CLAVGMSKTGSR 72
>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 = 94.7 bits (236), Expect = 2e-23
Identities = 32/113 (28%), Positives = 53/113 (46%), Gaps = 4/113 (3%)
Query: 226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI 285
+ L T + +I +A IPGF +L EDQ +L +S LEL VL LAYR+ L+
Sbjct: 1 ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLL 60
Query: 286 FCNGVVL----EKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
++ + + + + + EF L +++D +A L A+ L
Sbjct: 61 LAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVL 113
>gnl|CDD|143531 cd07156, NR_DBD_VDR_like, The DNA-binding domain of vitamin D
receptors (VDR) like nuclear receptor family is composed
of two C4-type zinc fingers. The DNA-binding domain of
vitamin D receptors (VDR) like nuclear receptor family
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. This domain interacts
with specific DNA site upstream of the target gene and
modulates the rate of transcriptional initiation. This
family includes three types of nuclear receptors:
vitamin D receptors (VDR), constitutive androstane
receptor (CAR) and pregnane X receptor (PXR). VDR
regulates calcium metabolism, cellular proliferation and
differentiation. PXR and CAR function as sensors of
toxic byproducts of cell metabolism and of exogenous
chemicals, to facilitate their elimination. The DNA
binding activity is regulated by their corresponding
ligands. VDR is activated by Vitamin D; CAR and PXR
respond to a diverse array of chemically distinct
ligands, including many endogenous compounds and
clinical drugs. 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 = 72
Score = 89.7 bits (223), Expect = 8e-23
Identities = 32/71 (45%), Positives = 47/71 (66%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C VCGD A H+ TCEGCKGFF+R++++ +++ C + C + K R CQ CR +K
Sbjct: 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKK 60
Query: 103 CLQVGMVKEVV 113
CL +GM KE++
Sbjct: 61 CLDIGMKKEMI 71
>gnl|CDD|143535 cd07161, NR_DBD_EcR, DNA-binding domain of Ecdysone receptor (ECR)
family is composed of two C4-type zinc fingers.
DNA-binding domain of Ecdysone receptor (EcR) family 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. EcR interacts with highly degenerate
pseudo-palindromic response elements, resembling
inverted repeats of 5'-AGGTCA-3' separated by 1 bp,
upstream of the target gene and modulates the rate of
transcriptional initiation. EcR 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 EcR are ecdysteroids, the endogenous
steroidal hormones found in invertebrates. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, EcRs 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 = 91
Score = 88.4 bits (219), Expect = 4e-22
Identities = 40/77 (51%), Positives = 50/77 (64%)
Query: 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
+LC VCGD A+ HY TCEGCKGFF+R+V K + Y C +AC +D R +CQ CR
Sbjct: 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRL 61
Query: 101 QKCLQVGMVKEVVRTDS 117
+KCL VGM E V +S
Sbjct: 62 KKCLSVGMRPECVVPES 78
>gnl|CDD|143534 cd07160, NR_DBD_LXR, DNA-binding domain of Liver X receptors (LXRs)
family is composed of two C4-type zinc fingers.
DNA-binding domain of Liver X receptors (LXRs) family 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. LXR interacts with specific DNA
sites upstream of the target gene and modulates the rate
of transcriptional initiation. LXR operates as
cholesterol sensor which protects cells 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.
LXR functions as a heterodimer with the retinoid X
receptor (RXR) which may be activated by either LXR
agonist 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.
The ideal LXRE sequence is a direct repeat-4 (DR-4) DNA
fragment consisting of two AGGTCA hexameric half-sites
separated by a 4-nucleotide spacer. 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 = 101
Score = 88.4 bits (219), Expect = 5e-22
Identities = 39/88 (44%), Positives = 58/88 (65%), Gaps = 4/88 (4%)
Query: 33 RPTPPSP----SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVD 88
R P+P +++C+VCGD A+ HY V +CEGCKGFF+R+V KG++YVC C +D
Sbjct: 7 RKKGPAPKMLGNEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMD 66
Query: 89 KRRRNRCQFCRFQKCLQVGMVKEVVRTD 116
R +CQ CR +KC + GM ++ V ++
Sbjct: 67 MYMRRKCQECRLRKCREAGMREQCVLSE 94
>gnl|CDD|143517 cd06959, NR_DBD_EcR_like, The DNA-binding domain of Ecdysone
receptor (EcR) like nuclear receptor family is composed
of two C4-type zinc fingers. The DNA-binding domain of
Ecdysone receptor (EcR) like nuclear receptor family 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. EcR interacts with specific DNA
sites upstream of the target gene and modulates the rate
of transcriptional initiation. This family includes
three types of nuclear receptors: Ecdysone receptor
(EcR), Liver X receptor (LXR) and Farnesoid X receptor
(FXR). The DNA binding activity is regulated by their
corresponding ligands. The ligands for EcR are
ecdysteroids; LXR is regulated by oxidized cholesterol
derivatives or oxysterols; and bile acids control FXR's
activities. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, EcR-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 = 73
Score = 87.5 bits (217), Expect = 7e-22
Identities = 35/72 (48%), Positives = 45/72 (62%)
Query: 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
C VCGD A+ HYGV +CEGCKGFF+R+V KG+ Y C C +D R +CQ CR +
Sbjct: 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLR 60
Query: 102 KCLQVGMVKEVV 113
KC GM + +
Sbjct: 61 KCKAAGMRPDCL 72
>gnl|CDD|143536 cd07162, NR_DBD_PXR, DNA-binding domain of pregnane X receptor
(PXRs) is composed of two C4-type zinc fingers.
DNA-binding domain (DBD)of pregnane X receptor (PXR) 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. PXR DBD interacts with the PXR
response element, a perfect repeat of two AGTTCA motifs
with a 4 bp spacer upstream of the target gene, and
modulates the rate of transcriptional initiation. The
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. PXR functions as a
heterodimer with retinoic X receptor-alpha (RXRa) and
binds to a variety of promoter regions of a diverse set
of target genes involved in the metabolism, transport,
and ultimately, elimination of these molecules from the
body. Like other nuclear receptors, PXR has a central
well conserved DNA-binding domain, a variable N-terminal
domain, a flexible hinge and a C-terminal ligand binding
domain.
Length = 87
Score = 83.8 bits (207), Expect = 2e-20
Identities = 35/81 (43%), Positives = 51/81 (62%)
Query: 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
+C VCGD A H+ TCEGCKGFF+R +++ ++ C K C + K R +CQ CR +
Sbjct: 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLR 60
Query: 102 KCLQVGMVKEVVRTDSLKGRR 122
KCL +GM KE++ +D +R
Sbjct: 61 KCLSIGMKKELIMSDEAVEKR 81
>gnl|CDD|143520 cd06962, NR_DBD_FXR, DNA-binding domain of Farnesoid X receptor
(FXR) family is composed of two C4-type zinc fingers.
DNA-binding domain of Farnesoid X receptor (FXR) family
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. FXR interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation. FXR
is a member of the nuclear receptor family of ligand
activated transcription factors. Bile acids are
endogenous ligands for FXRs. Upon binding of a ligand,
FXR binds to FXR response element (FXRE), which is an
inverted repeat of TGACCT spaced by one nucleotide,
either as a monomer or as a heterodimer with retinoid X
receptor (RXR), to regulate the expression of various
genes involved in bile acid, lipid, and glucose
metabolism. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, FXR 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 = 84
Score = 83.5 bits (206), Expect = 2e-20
Identities = 35/76 (46%), Positives = 49/76 (64%)
Query: 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
+LC VCGD A+ HY TCEGCKGFF+R++ K + Y C C +D R +CQ CR
Sbjct: 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRL 61
Query: 101 QKCLQVGMVKEVVRTD 116
+KC ++GM+ E + T+
Sbjct: 62 RKCKEMGMLAECLLTE 77
>gnl|CDD|143513 cd06955, NR_DBD_VDR, DNA-binding domain of vitamin D receptors
(VDR) is composed of two C4-type zinc fingers.
DNA-binding domain of vitamin D receptors (VDR) is
composed of two C4-type zinc fingers. Each zinc finger
contains a group of four Cys residues which coordinates
a single zinc atom. VDR interacts with a VDR response
element, a direct repeat of GGTTCA DNA site with 3 bp
spacer upstream of the target gene, and modulates the
rate of transcriptional initiation. 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 a 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 = 107
Score = 84.2 bits (208), Expect = 3e-20
Identities = 35/91 (38%), Positives = 55/91 (60%)
Query: 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
++C VCGD A H+ TCEGCKGFF+R++++ + + C + C + K R CQ CR
Sbjct: 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 66
Query: 101 QKCLQVGMVKEVVRTDSLKGRRGRLPSKPKS 131
++C+ +GM+KE + TD R+ + K K
Sbjct: 67 KRCVDIGMMKEFILTDEEVQRKREMILKRKE 97
>gnl|CDD|143546 cd07172, NR_DBD_GR_PR, DNA-binding domain of glucocorticoid
receptor (GR) is composed of two C4-type zinc fingers.
DNA-binding domains of glucocorticoid receptor (GR) and
progesterone receptor (PR) are composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinate a single zinc atom. The
DBD from both receptors interact with the same hormone
response element (HRE), which is an imperfect palindrome
GGTACAnnnTGTTCT, upstream of target genes and modulates
the rate of transcriptional initiation. GR is a
transcriptional regulator that mediates the biological
effects of glucocorticoids and PR regulates genes
controlled by progesterone. 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. PR
functions in a variety of biological processes including
development of the mammary gland, regulating cell cycle
progression, protein processing, and metabolism. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, GR and PR
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 = 78
Score = 83.0 bits (205), Expect = 4e-20
Identities = 35/71 (49%), Positives = 42/71 (59%)
Query: 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
P ++C VC D A+ HYGV TC CK FFKR V+ Y+C C +DK RR C C
Sbjct: 1 PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 60
Query: 99 RFQKCLQVGMV 109
R +KCLQ GM
Sbjct: 61 RLRKCLQAGMN 71
>gnl|CDD|143532 cd07157, 2DBD_NR_DBD1, The first DNA-binding domain (DBD) of the
2DBD nuclear receptors is composed of two C4-type zinc
fingers. The first DNA-binding domain (DBD) of the 2DBD
nuclear receptors(NRs) 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. NRs
interact with specific DNA sites upstream of the target
gene and modulate the rate of transcriptional
initiation. Theses proteins contain two DBDs in tandem,
probably resulted from an ancient recombination event.
The 2DBD-NRs are found only in flatworm species,
mollusks and arthropods. Their biological function is
unknown.
Length = 86
Score = 77.5 bits (191), Expect = 5e-18
Identities = 31/72 (43%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTV--QKGSKYVCLADKACPVDKRRRNRCQFC 98
Q C VCG+ AA H+G CE CK FF R+ + C C +DK+ R +CQ C
Sbjct: 1 QTCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQAC 60
Query: 99 RFQKCLQVGMVK 110
R++KCL VGM
Sbjct: 61 RYRKCLNVGMSL 72
>gnl|CDD|143521 cd06963, NR_DBD_GR_like, The DNA binding domain of GR_like nuclear
receptors is composed of two C4-type zinc fingers. The
DNA binding domain of GR_like nuclear receptors 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. It interacts with specific DNA sites
upstream of the target gene and modulates the rate of
transcriptional initiation. This family of NRs includes
four types of nuclear hormone receptors: glucocorticoid
receptor (GR), mineralocorticoid receptor (MR),
progesterone receptor (PR), and androgen receptor (AR).
The receptors bind to common DNA elements containing a
partial palindrome of the core sequence 5'-TGTTCT-3'
with a 3bp spacer. These four receptors regulate 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 have high sequence homology and
share similar functional mechanisms. The dominant
mechanism of function is by direct DNA binding and
transcriptional regulation of target genes . The GR, MR,
PR, and AR exhibit same modular structure. They have a
central highly conserved DNA binding domain (DBD), a
non-conserved N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 73
Score = 76.9 bits (189), Expect = 6e-18
Identities = 32/73 (43%), Positives = 39/73 (53%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C +CGD A+ HYGV TC CK FFKR + Y+C C +DK RR C CR +K
Sbjct: 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRK 60
Query: 103 CLQVGMVKEVVRT 115
C Q GM +
Sbjct: 61 CYQAGMTLGARKL 73
>gnl|CDD|143524 cd06966, NR_DBD_CAR, DNA-binding domain of constitutive androstane
receptor (CAR) is composed of two C4-type zinc fingers.
DNA-binding domain (DBD) of constitutive androstane
receptor (CAR) 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. CAR DBD interacts
with CAR response element, a perfect repeat of two
AGTTCA motifs with a 4 bp spacer upstream of the target
gene, and modulates the rate of transcriptional
initiation. The constitutive androstane receptor (CAR)
is a ligand-regulated transcription factor that responds
to a diverse array of chemically distinct ligands,
including many endogenous compounds and clinical drugs.
It functions as a heterodimer with RXR. The CAR/RXR
heterodimer binds many common response elements in the
promoter regions of a diverse set of target genes
involved in the metabolism, transport, and ultimately,
elimination of these molecules from the body. CAR is a
closest mammalian relative of PXR and 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, CAR has a central well conserved DNA binding
domain, a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain.
Length = 94
Score = 74.4 bits (183), Expect = 7e-17
Identities = 29/92 (31%), Positives = 49/92 (53%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
C VCGD A ++ TCE CK FF+R K ++ C +++C ++ R CQ CR K
Sbjct: 3 CGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDK 62
Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQE 134
C +GM KE + ++ K + + + ++ +
Sbjct: 63 CFAIGMKKEWIMSEEDKSEKRQKIEENRAKKR 94
>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors.
Length = 163
Score = 76.3 bits (188), Expect = 9e-17
Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 4/100 (4%)
Query: 239 IRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVL----EK 294
+A PGF +L EDQ +L +S EL +L LAYR+ +L+
Sbjct: 8 TVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAV 67
Query: 295 QQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
+ ++ F + E + L +++D +A L A+ L
Sbjct: 68 LELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVL 107
Score = 33.5 bits (77), Expect = 0.061
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 178 IRHFADKIPGFSDLCKEDQELLFQSASLELF 208
+A PGF +L EDQ +L +S EL
Sbjct: 8 TVEWAKSFPGFRELSLEDQIVLLKSFWFELL 38
>gnl|CDD|143547 cd07173, NR_DBD_AR, DNA-binding domain of androgen receptor (AR) is
composed of two C4-type zinc fingers. DNA-binding
domain of androgen receptor (AR) 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. To regulate gene expression, AR interacts with a
palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp
spacer. It also binds to the direct repeat 5'-TGTTCT-3'
hexamer in some androgen controlled genes. AR is
activated by the androgenic hormones, testosterone or
dihydrotestosterone, which are responsible for primary
and for secondary male characteristics, respectively.
The primary mechanism of action of ARs is by direct
regulation of gene transcription. The binding of
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 of androgen receptor is independent of
their interactions with DNA. The receptor interacts
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).
Length = 82
Score = 73.4 bits (180), Expect = 1e-16
Identities = 32/71 (45%), Positives = 41/71 (57%)
Query: 38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQF 97
P + C +CGD A+ HYG TC CK FFKR + KY+C + C +DK RR C
Sbjct: 1 PPQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPS 60
Query: 98 CRFQKCLQVGM 108
CR +KC + GM
Sbjct: 61 CRLRKCFEAGM 71
>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 = 68.8 bits (169), Expect = 5e-14
Identities = 30/114 (26%), Positives = 56/114 (49%)
Query: 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED 281
EK F ++T ++ + FA +IPGF +L +EDQ L + E+ +LR A E
Sbjct: 1 QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEK 60
Query: 282 TKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
L F +G + +++ + EF + ++ +++D + +A L A+ L
Sbjct: 61 NSLTFGDGKGNSRDVLLNGGFGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLF 114
Score = 41.1 bits (97), Expect = 2e-04
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 161 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
EK F ++T ++ + FA +IPGF +L +EDQ L + E+
Sbjct: 1 QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEI 47
>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 = 66.3 bits (162), Expect = 5e-13
Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 4/98 (4%)
Query: 241 HFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT-RAEDTKLIFCNGVVLEKQQCQR 299
+A + PGF +L +DQ L +S+ E L LA R+ E L+F NG+ L++ + +
Sbjct: 18 EWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDDLLFSNGLYLDRDELKS 77
Query: 300 SFGD---DWLNAILEFCQSLHLMEIDISAFACLCALTL 334
+ + + + E Q L +++ A L AL L
Sbjct: 78 IEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLL 115
Score = 32.0 bits (73), Expect = 0.25
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 180 HFADKIPGFSDLCKEDQELLFQSASLELF 208
+A + PGF +L +DQ L +S+ E
Sbjct: 18 EWAKRFPGFRELSLDDQLALLKSSWFEWL 46
>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 = 64.4 bits (157), Expect = 5e-12
Identities = 31/110 (28%), Positives = 53/110 (48%)
Query: 226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI 285
+F L T + I FA ++PGF+ L DQ L ++A L++ +LR+ R E +
Sbjct: 41 DKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 100
Query: 286 FCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
F +G+ L + Q + + + F L +E+D + L A+ LI
Sbjct: 101 FSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLI 150
Score = 32.9 bits (75), Expect = 0.16
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 165 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
+F L T + I FA ++PGF+ L DQ L ++A L++
Sbjct: 41 DKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDI 83
>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 = 63.4 bits (155), Expect = 8e-12
Identities = 36/130 (27%), Positives = 61/130 (46%), Gaps = 6/130 (4%)
Query: 211 EPNPL--EPPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKEDQELLFQSA 264
EP+ L P+ + L+ D I +A IPGFSDL DQ L QSA
Sbjct: 9 EPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSA 68
Query: 265 SLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDIS 324
LE+ +L L +R+ KL+F ++L+++Q + + + +L+ + + +
Sbjct: 69 WLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARVEGLLEIFDMLLQLVRRFRELGLQRE 128
Query: 325 AFACLCALTL 334
+ CL A+ L
Sbjct: 129 EYVCLKAIIL 138
Score = 36.8 bits (86), Expect = 0.007
Identities = 26/72 (36%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 143 LITALYR-EPNPL--EPPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKED 195
L++AL EP+ L P+ + L+ D I +A IPGFSDL D
Sbjct: 1 LLSALLVAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLND 60
Query: 196 QELLFQSASLEL 207
Q L QSA LE+
Sbjct: 61 QMHLLQSAWLEI 72
>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 = 61.3 bits (149), Expect = 3e-11
Identities = 33/109 (30%), Positives = 61/109 (55%)
Query: 226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI 285
QQ LT SV + FA +IPGF DL ++DQ LL ++ E++++R++ ++ +
Sbjct: 5 QQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSIT 64
Query: 286 FCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
F +G+ + +QQ + D++ A+ EF S + + + + A CA+ L
Sbjct: 65 FDDGISISRQQLDIIYDSDFVKALFEFSDSFNSLGLSDTEVALFCAVVL 113
Score = 40.8 bits (96), Expect = 3e-04
Identities = 19/43 (44%), Positives = 26/43 (60%)
Query: 165 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
QQ LT SV + FA +IPGF DL ++DQ LL ++ E+
Sbjct: 5 QQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEV 47
>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 = 61.7 bits (150), Expect = 4e-11
Identities = 31/108 (28%), Positives = 56/108 (51%), Gaps = 1/108 (0%)
Query: 228 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFC 287
F L SV I FA ++PGF L +EDQ L +++++E+ +L A R E + F
Sbjct: 48 FTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFL 107
Query: 288 NGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISAFACLCALTL 334
+ R+ +++N I EF +S+ +++D + +A L A+ +
Sbjct: 108 KDFPYSRDDFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINI 155
Score = 35.1 bits (81), Expect = 0.029
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 167 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
F L SV I FA ++PGF L +EDQ L +++++E+
Sbjct: 48 FTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEV 88
>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 = 60.6 bits (147), Expect = 5e-11
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 7/126 (5%)
Query: 214 PLEPPIAEPEKIQQFYSL-LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLR 272
P P +I + +S+ T +V + FA +IPGF DL + DQ L ++ + E+ ++R
Sbjct: 2 PYVDPPKSGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVR 61
Query: 273 LAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFC---QSLHLMEIDISAFACL 329
A A++ + F +G D LN++ +F SL L + ++ F
Sbjct: 62 FASLFDAKERSVTFLSGQKYSVDDLHSMGAGDLLNSMFDFSEKLNSLQLSDEEMGLF--- 118
Query: 330 CALTLI 335
A+ L+
Sbjct: 119 TAVVLV 124
Score = 36.7 bits (85), Expect = 0.008
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 153 PLEPPIAEPEKIQQFYSL-LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE-LFYR 210
P P +I + +S+ T +V + FA +IPGF DL + DQ L ++ + E L R
Sbjct: 2 PYVDPPKSGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVR 61
>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 = 56.9 bits (138), Expect = 6e-10
Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 2/96 (2%)
Query: 241 HFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT--KLIFCNGVVLEKQQCQ 298
+A +P F +L +DQ L Q++ EL +L LA R+ + L+ +V+ ++
Sbjct: 17 DWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREA 76
Query: 299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
+ + + E L +++D +ACL A+ L
Sbjct: 77 LLGLAELVQRLQELLSKLRSLQLDPKEYACLKAIVL 112
Score = 33.0 bits (76), Expect = 0.099
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 6/47 (12%)
Query: 180 HFADKIPGFSDLCKEDQELLFQSASLELF------YREPNPLEPPIA 220
+A +P F +L +DQ L Q++ EL L +
Sbjct: 17 DWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLL 63
>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 = 57.8 bits (140), Expect = 9e-10
Identities = 29/110 (26%), Positives = 58/110 (52%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
+ + + +V +I FA ++PGF L +EDQ L ++ S E+ +LR+A R A+
Sbjct: 39 MRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTD 98
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCAL 332
++F N + +++ D + FC+++ M++D + +A L A+
Sbjct: 99 SIVFANNQPYTRDSYRKAGMGDSAEDLFRFCRAMCSMKVDNAEYALLTAI 148
Score = 32.8 bits (75), Expect = 0.17
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 162 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206
+ + + +V +I FA ++PGF L +EDQ L ++ S E
Sbjct: 39 MRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSE 83
>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 = 56.7 bits (137), Expect = 2e-09
Identities = 35/132 (26%), Positives = 60/132 (45%), Gaps = 7/132 (5%)
Query: 211 EPNPL------EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSA 264
EP + P E + +L + + ++A KIPGF DL DQ L +SA
Sbjct: 14 EPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESA 73
Query: 265 SLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDI 323
LEL +L L +R+ KL+F ++L++ Q G + + +L +++
Sbjct: 74 WLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQR 133
Query: 324 SAFACLCALTLI 335
+ CL A+ L+
Sbjct: 134 EEYVCLKAIILL 145
Score = 39.3 bits (92), Expect = 0.001
Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 7/76 (9%)
Query: 139 PPVSLITALY-REPNPL------EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDL 191
LI+AL EP + P E + +L + + ++A KIPGF DL
Sbjct: 2 SAEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDL 61
Query: 192 CKEDQELLFQSASLEL 207
DQ L +SA LEL
Sbjct: 62 SLHDQVHLLESAWLEL 77
>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 = 55.6 bits (134), Expect = 6e-09
Identities = 30/113 (26%), Positives = 53/113 (46%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
E F ++T ++ + FA K+P F++L EDQ +L + +E+ LR A R E
Sbjct: 52 EAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 111
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
L + + ++Q + +AI + SL +D + A L A+ L+
Sbjct: 112 TLTLSGEMAVTREQLKNGGLGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLM 164
Score = 33.6 bits (77), Expect = 0.086
Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 9/84 (10%)
Query: 124 RLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFAD 183
K K E P+ + + + E F ++T ++ + FA
Sbjct: 23 HWKQKRKFLPEDIGQAPIV---------SAPDGDKVDLEAFSHFTKIITPAITRVVDFAK 73
Query: 184 KIPGFSDLCKEDQELLFQSASLEL 207
K+P F++L EDQ +L + +E+
Sbjct: 74 KLPMFTELPCEDQIILLKGCCMEI 97
>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 = 52.4 bits (126), Expect = 5e-08
Identities = 36/130 (27%), Positives = 64/130 (49%), Gaps = 6/130 (4%)
Query: 211 EPNPL--EPPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKEDQELLFQSA 264
EP+ L P A P+ + + L+ D VI +A IPGFS L DQ L QSA
Sbjct: 9 EPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSA 68
Query: 265 SLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDIS 324
+E+ L + +R+ + +L+F +L+++ + + + +A L+ + L + ++
Sbjct: 69 WMEILTLGVVFRSLPFNGELVFAEDFILDEELAREAGLLELYSACLQLVRRLQRLRLEKE 128
Query: 325 AFACLCALTL 334
+ L AL L
Sbjct: 129 EYVLLKALAL 138
Score = 32.0 bits (73), Expect = 0.28
Identities = 24/64 (37%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 150 EPNPL--EPPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKEDQELLFQSA 203
EP+ L P A P+ + + L+ D VI +A IPGFS L DQ L QSA
Sbjct: 9 EPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSA 68
Query: 204 SLEL 207
+E+
Sbjct: 69 WMEI 72
>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 = 51.2 bits (123), Expect = 1e-07
Identities = 38/113 (33%), Positives = 62/113 (54%), Gaps = 19/113 (16%)
Query: 232 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV 291
+T ++ + FA +IPGF +LC+ DQ +L ++ SLE+ ++R++ RA + N V
Sbjct: 57 ITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMS---RAFNPS----NNTV 109
Query: 292 L--EK---QQCQRSFG-DDWLNAILEFCQS---LHLMEIDISAFACLCALTLI 335
L K +S G DD ++A+ +F +S L L E +I+ F AL LI
Sbjct: 110 LFDGKYAPIDLFKSLGCDDLISAVFDFAKSLCELKLTEDEIALF---SALVLI 159
Score = 40.0 bits (94), Expect = 8e-04
Identities = 32/111 (28%), Positives = 46/111 (41%), Gaps = 24/111 (21%)
Query: 171 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFY----REPNPLEPPIAEPEK-- 224
+T ++ + FA +IPGF +LC+ DQ +L ++ SLE+ R NP + K
Sbjct: 57 ITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFDGKYA 116
Query: 225 -IQQFYSLLTTSVDVIRHFADKIPGFSDLCK--------EDQELLFQSASL 266
I F SL D I D K ED+ LF + L
Sbjct: 117 PIDLFKSLGC---------DDLISAVFDFAKSLCELKLTEDEIALFSALVL 158
>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 = 43.8 bits (104), Expect = 3e-05
Identities = 37/132 (28%), Positives = 58/132 (43%), Gaps = 14/132 (10%)
Query: 210 REPNPLEP---PIAEPEKIQQFYS-LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
R P P PE + + + LL +V +A IP FS L DQ +L + +
Sbjct: 13 RPPFPYGTISSYEVSPESVCESAARLLFMAV----KWAKSIPAFSTLPFRDQLILLEESW 68
Query: 266 LELFVLRLAYRTRAED-TKLIFCNGVVLEKQQCQRSFGDD--WLNAILEFCQSLHLMEID 322
ELF+L A + D L+ G+ + + +R+F + L L + L + D
Sbjct: 69 SELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLSEVRALQETLSRFRQLRV---D 125
Query: 323 ISAFACLCALTL 334
+ FACL A+ L
Sbjct: 126 ATEFACLKAIVL 137
Score = 32.7 bits (75), Expect = 0.19
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 149 REPNPLEP---PIAEPEKIQQFYS-LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 204
R P P PE + + + LL +V +A IP FS L DQ +L + +
Sbjct: 13 RPPFPYGTISSYEVSPESVCESAARLLFMAV----KWAKSIPAFSTLPFRDQLILLEESW 68
Query: 205 LELF 208
ELF
Sbjct: 69 SELF 72
>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 = 41.5 bits (97), Expect = 2e-04
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
Y + N PP+ + L++ S+ + FA IPGF DL EDQ L +S+++E+
Sbjct: 24 YSDFNKFRPPVRLS-MLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEV 82
Query: 269 FVLR 272
+LR
Sbjct: 83 IMLR 86
Score = 38.0 bits (88), Expect = 0.004
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 148 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
Y + N PP+ + L++ S+ + FA IPGF DL EDQ L +S+++E+
Sbjct: 24 YSDFNKFRPPVRLS-MLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEV 82
Query: 208 FYREPN 213
N
Sbjct: 83 IMLRSN 88
>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 = 39.9 bits (93), Expect = 0.001
Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 2/96 (2%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT--RAEDTKLIFCNGVVLEKQQCQR 299
+A IPGF +L +DQ L Q + + L L +R+ ++ L F +++ +Q+
Sbjct: 47 WAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMTL 106
Query: 300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
D +L LH +++ + C+ L L+
Sbjct: 107 PCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLL 142
>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 = 37.4 bits (87), Expect = 0.007
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 3/76 (3%)
Query: 137 PSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRH---FADKIPGFSDLCK 193
P + + N P + +I+ F SV+ IR FA +PGF +L
Sbjct: 35 DHAPFVIYDIESLKLNKDGQPQEKTIRIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDL 94
Query: 194 EDQELLFQSASLELFY 209
DQ L + E+ +
Sbjct: 95 NDQVTLLKYGVHEVIF 110
Score = 37.0 bits (86), Expect = 0.008
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 3/69 (4%)
Query: 211 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRH---FADKIPGFSDLCKEDQELLFQSASLE 267
+ N P + +I+ F SV+ IR FA +PGF +L DQ L + E
Sbjct: 48 KLNKDGQPQEKTIRIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHE 107
Query: 268 LFVLRLAYR 276
+ LA
Sbjct: 108 VIFTMLASL 116
>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 = 36.9 bits (86), Expect = 0.007
Identities = 27/95 (28%), Positives = 38/95 (40%), Gaps = 5/95 (5%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF 301
F IPGF+ L ED+ L + L++LRL+ E T L V Q
Sbjct: 21 FVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNEGTVLCDFRPVEFASLLSQLLH 80
Query: 302 GD--DWLNAILEFCQSLHLMEIDISAFACLCALTL 334
G D + +L+L ++ A LCA L
Sbjct: 81 GKLIDEMLQFANKILTLNLTNAEL---ALLCAAEL 112
>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 = 36.7 bits (85), Expect = 0.008
Identities = 27/103 (26%), Positives = 53/103 (51%), Gaps = 3/103 (2%)
Query: 233 TTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVL 292
T+ V V+ F +PGF L EDQ L + +++E LR A + + KL + +L
Sbjct: 46 TSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSA---QIYNKKLPAGHADLL 102
Query: 293 EKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
E++ D+++ + F +S+ +++ +A L A+T++
Sbjct: 103 EERIRSSGISDEFITPMFNFYKSMGELKMTQEEYALLTAITIL 145
Score = 28.6 bits (64), Expect = 3.9
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 172 TTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE-LFYR 210
T+ V V+ F +PGF L EDQ L + +++E +F R
Sbjct: 46 TSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLR 85
>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 = 35.0 bits (81), Expect = 0.027
Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 1/94 (1%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF 301
+A +IP FS+L +DQ +L ++ EL + A+R+ A ++ G+ L + ++
Sbjct: 49 WAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQAG 108
Query: 302 GDDWLNAIL-EFCQSLHLMEIDISAFACLCALTL 334
+ IL E + +++D + CL A+ L
Sbjct: 109 VGAIFDRILTELVVKMRDLKMDRTELGCLRAIIL 142
Score = 29.2 bits (66), Expect = 2.6
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 181 FADKIPGFSDLCKEDQELLFQSASLEL 207
+A +IP FS+L +DQ +L ++ EL
Sbjct: 49 WAKRIPHFSELPLDDQVILLRAGWNEL 75
>gnl|CDD|237479 PRK13719, PRK13719, conjugal transfer transcriptional regulator
TraJ; Provisional.
Length = 217
Score = 34.7 bits (80), Expect = 0.036
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 265 SLELFVLRLAYRT--RAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
SL F+ +Y R E K IF N + L++ Q + W + ++ L E+D
Sbjct: 20 SLTAFIDDYSYPACIRNESGKFIFYNTLFLKEFLGQLQSKEWWFSLPIDTATLLSRAELD 79
>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 = 34.1 bits (78), Expect = 0.068
Identities = 23/92 (25%), Positives = 43/92 (46%), Gaps = 2/92 (2%)
Query: 246 IPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK--LIFCNGVVLEKQQCQRSFGD 303
+PGF +L +DQ L Q + + L V L +R+ + L F ++L +Q+ + S
Sbjct: 51 LPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFY 110
Query: 304 DWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
+ + Q +++ F C+ AL L+
Sbjct: 111 SLCLTMWQIPQEFVKLQVSQEEFLCMKALLLL 142
>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 = 33.9 bits (78), Expect = 0.080
Identities = 28/129 (21%), Positives = 53/129 (41%), Gaps = 3/129 (2%)
Query: 209 YREPNPLEPPIAEPEKIQQFYSL---LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
P P P+KI + + + V+ +A IP F +L +DQ L ++ +
Sbjct: 15 QSSPIPTCSGDIRPKKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHA 74
Query: 266 LELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISA 325
E +L +A R+ L+ N +++ + + + E L + ID +
Sbjct: 75 GEHLLLGVARRSMPYKDILLLGNDLIIPRHCPEPEISRVANRILDELVLPLRDLNIDDNE 134
Query: 326 FACLCALTL 334
+ACL A+
Sbjct: 135 YACLKAIVF 143
>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 = 33.1 bits (76), Expect = 0.14
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 2/95 (2%)
Query: 243 ADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT--RAEDTKLIFCNGVVLEKQQCQRS 300
A +PGF +L +DQ L Q + + L V L +R+ L F +V +Q+ +S
Sbjct: 48 AKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQS 107
Query: 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
+ + Q +++ F C+ L L+
Sbjct: 108 AMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLL 142
>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 = 31.1 bits (71), Expect = 0.55
Identities = 26/102 (25%), Positives = 43/102 (42%), Gaps = 8/102 (7%)
Query: 241 HFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFC-------NGVVLE 293
H+A IP F L E Q L ++ ELF L LA ++ I + +
Sbjct: 39 HWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQD 98
Query: 294 KQQCQR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
K + + +N + EF S+ +++D +A L A+ L
Sbjct: 99 KLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVL 140
>gnl|CDD|177609 PHA03372, PHA03372, DNA packaging terminase subunit 1; Provisional.
Length = 668
Score = 31.3 bits (71), Expect = 0.88
Identities = 13/56 (23%), Positives = 25/56 (44%)
Query: 96 QFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREP 151
FC + +++ +D+LK L +P S ++ + +T LYR+P
Sbjct: 65 AFCGRYRDYNSEERRKLTISDALKSALDELKFRPCSEEQRQYQQKLEALTGLYRDP 120
>gnl|CDD|237658 PRK14284, PRK14284, chaperone protein DnaJ; Provisional.
Length = 391
Score = 30.6 bits (69), Expect = 1.2
Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 6/70 (8%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRR-RNRCQFCRFQ 101
C C A G++ C+ CKG + +G + C + R + C CR Q
Sbjct: 161 CDACSGSGANSSQGIKVCDRCKGSGQVVQSRGFFSMASTCPECGGEGRVITDPCSVCRGQ 220
Query: 102 KCLQVGMVKE 111
G +K+
Sbjct: 221 -----GRIKD 225
>gnl|CDD|177317 PHA01752, PHA01752, hypothetical protein.
Length = 488
Score = 30.4 bits (68), Expect = 1.4
Identities = 30/135 (22%), Positives = 58/135 (42%), Gaps = 31/135 (22%)
Query: 131 SPQESPPSPP----------VSLITALYREPNPLEPPIAEPE-KIQQFYSL-------LT 172
+P E+ P S+I++L N L + P Q F +L ++
Sbjct: 70 TPLENIQIPLGINTNYGIAYASIISSLLSALNNLAISVFNPNFNSQTFLNLGQSANFGIS 129
Query: 173 TSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEP------EKIQ 226
++++ ++ + +LC +L+Q A + Y + + +P +A KI+
Sbjct: 130 NGINLLNNYTSLYDNYVELCN----ILYQPAVFDETYFDLSVYQPALATEYQNQSCGKIE 185
Query: 227 QFYSLLTT---SVDV 238
Q++S LTT SVD+
Sbjct: 186 QYFSSLTTTNVSVDI 200
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 30.2 bits (68), Expect = 1.4
Identities = 11/55 (20%), Positives = 19/55 (34%)
Query: 112 VVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQ 166
V + + G+ + P S PSPP S + + P + E+
Sbjct: 74 VSKPKTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASAVEEKSPSEESAT 128
>gnl|CDD|178376 PLN02777, PLN02777, photosystem I P subunit (PSI-P).
Length = 167
Score = 29.2 bits (65), Expect = 1.8
Identities = 16/36 (44%), Positives = 20/36 (55%)
Query: 6 SSSSESPKLRHSAPLSSASSSPGCDTSRPTPPSPSQ 41
S SS S + AP SSA++SP C + PP P Q
Sbjct: 5 SISSSSTLIDSKAPRSSAAASPQCVSLPTLPPPPVQ 40
>gnl|CDD|214412 MTH00047, COX2, cytochrome c oxidase subunit II; Provisional.
Length = 194
Score = 29.5 bits (67), Expect = 1.9
Identities = 13/29 (44%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 167 FYSLLTTSVDVIRHFA--------DKIPG 187
Y LL TS DVI F+ D IPG
Sbjct: 125 PYHLLVTSSDVIHSFSVPDLNLKMDAIPG 153
Score = 29.5 bits (67), Expect = 1.9
Identities = 13/29 (44%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 228 FYSLLTTSVDVIRHFA--------DKIPG 248
Y LL TS DVI F+ D IPG
Sbjct: 125 PYHLLVTSSDVIHSFSVPDLNLKMDAIPG 153
>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 = 29.5 bits (66), Expect = 2.0
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT--RAEDTKLIFCNGVVLEKQQCQR 299
+A +PGF +L EDQ L Q + + L L++R+ L F +V +++ +
Sbjct: 47 WAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMHQ 106
Query: 300 SFGDDWLNAILEFCQSLH 317
S A+ E CQ +H
Sbjct: 107 S-------AMYELCQGMH 117
>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional.
Length = 584
Score = 30.0 bits (68), Expect = 2.2
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 121 RRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQ 166
R RLP+ P+ P+E PP PP + +PP E E+
Sbjct: 254 RATRLPAPPQPPEEEPPPPPPP-------PEDDDDPPEDEEEQDDA 292
>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria. Unlike subunit I (TIGR02030),
this subunit is not found in archaea [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 589
Score = 29.8 bits (67), Expect = 2.2
Identities = 14/46 (30%), Positives = 16/46 (34%), Gaps = 5/46 (10%)
Query: 118 LKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEK 163
L R RLP P PP P E P EP +P+
Sbjct: 259 LLPRATRLPEPEPQPPPPPPPPEPP-----EPEEEPDEPDQTDPDD 299
>gnl|CDD|234428 TIGR03979, His_Ser_Rich, His-Xaa-Ser repeat protein HxsA.
Members of this protein share two defining regions. One
is a histidine/serine-rich cluster, typically
H-R-S-H-S-S-H-R-S-H-S-S-H. Members are found always in
the context of a pair of radical SAM proteins, HxsB and
HxsC, and a fourth protein HxsD. The system is
predicted to perform peptide modifications, likely in
the His-Xaa-Ser region, to produce some uncharacterized
natural product.
Length = 186
Score = 28.7 bits (64), Expect = 2.8
Identities = 12/37 (32%), Positives = 15/37 (40%)
Query: 5 RSSSSESPKLRHSAPLSSASSSPGCDTSRPTPPSPSQ 41
S S S H + + S P DTS + P PS
Sbjct: 57 SSHRSHSSHSSHYSGAGGSYSVPSGDTSTYSYPVPSP 93
>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 = 28.9 bits (65), Expect = 3.0
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
+R P L P A+ L T + I FA +P F L EDQ L + A+ E+
Sbjct: 30 FRPPFSLLPHFAD---------LTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEI 80
Query: 269 FVLRL 273
+R
Sbjct: 81 CQIRF 85
>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 = 29.1 bits (65), Expect = 3.0
Identities = 25/102 (24%), Positives = 44/102 (43%), Gaps = 3/102 (2%)
Query: 236 VDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYR--TRAEDTKLIFCNGVVLE 293
V V++ +A +PGF +L +DQ + Q + + L V + +R T L F +V
Sbjct: 42 VHVVK-WAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFN 100
Query: 294 KQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
+ + +S + Q ++I F C+ AL L
Sbjct: 101 EYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLF 142
>gnl|CDD|224852 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit
[Energy production and conversion].
Length = 247
Score = 28.5 bits (64), Expect = 4.1
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADK 83
C C A+C + C GC+G R ++ G+ +V C K
Sbjct: 195 CGTCA--ASCPSRAI-PCRGCRGNIPRCIKCGACFVSCPRSK 233
>gnl|CDD|173589 PTZ00398, PTZ00398, phosphoenolpyruvate carboxylase; Provisional.
Length = 974
Score = 29.0 bits (65), Expect = 4.3
Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 13/86 (15%)
Query: 238 VIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQC 297
++ D I S + +EL + S L L Y + + I G +L+ +
Sbjct: 400 TRDYYKDLISNHSVDPEFRRELAYHSTDEILEPLIECYNSLEDVGNTILARGRLLDVIRQ 459
Query: 298 QRSFGDDWLNAILEFCQSLHLMEIDI 323
++FG LHLM++DI
Sbjct: 460 VKTFG-------------LHLMKLDI 472
>gnl|CDD|189650 pfam00645, zf-PARP, Poly(ADP-ribose) polymerase and DNA-Ligase
Zn-finger region. Poly(ADP-ribose) polymerase is an
important regulatory component of the cellular response
to DNA damage. The amino-terminal region of
Poly(ADP-ribose) polymerase consists of two PARP-type
zinc fingers. This region acts as a DNA nick sensor.
Length = 81
Score = 26.9 bits (60), Expect = 4.6
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 182 ADKIPGFSDLCKEDQELL 199
D + GF +L EDQE +
Sbjct: 59 VDDLDGFEELRPEDQEKI 76
Score = 26.9 bits (60), Expect = 4.6
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 243 ADKIPGFSDLCKEDQELL 260
D + GF +L EDQE +
Sbjct: 59 VDDLDGFEELRPEDQEKI 76
>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 = 5.3
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLA 274
F +P F L +DQ LL Q+ LF+L LA
Sbjct: 38 FMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLA 70
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.8 bits (64), Expect = 5.8
Identities = 14/48 (29%), Positives = 19/48 (39%)
Query: 114 RTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEP 161
R GR + S P+ P+ P V +T+L P P P P
Sbjct: 2665 RRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAP 2712
>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509). This
family consists of several uncharacterized viral
proteins from the Marek's disease-like viruses. Members
of this family are typically around 400 residues in
length. The function of this family is unknown.
Length = 377
Score = 28.1 bits (62), Expect = 6.4
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 1/58 (1%)
Query: 112 VVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYS 169
V + RG PS P++ P A+ R P P PE +++ +
Sbjct: 221 RVLDAPVATNRGEAPSPPRTDTLDPDPAIAGPSRAVNRTP-SPRPSSPPPEIDEEYNA 277
>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 = 27.8 bits (62), Expect = 7.5
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLA 274
+A IP F DL DQ L + + ELFVL A
Sbjct: 49 WARNIPFFPDLQVTDQVALLRLSWSELFVLNAA 81
>gnl|CDD|181066 PRK07649, PRK07649, para-aminobenzoate/anthranilate synthase
glutamine amidotransferase component II; Validated.
Length = 195
Score = 27.5 bits (61), Expect = 7.7
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 174 SVDVIRHFADKIPGF 188
S++VIR+FA KIP F
Sbjct: 62 SMEVIRYFAGKIPIF 76
Score = 27.5 bits (61), Expect = 7.7
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 235 SVDVIRHFADKIPGF 249
S++VIR+FA KIP F
Sbjct: 62 SMEVIRYFAGKIPIF 76
>gnl|CDD|235552 PRK05670, PRK05670, anthranilate synthase component II;
Provisional.
Length = 189
Score = 27.4 bits (62), Expect = 8.7
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 174 SVDVIRHFADKIP 186
S+++IR FA K+P
Sbjct: 62 SLELIREFAGKVP 74
Score = 27.4 bits (62), Expect = 8.7
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 235 SVDVIRHFADKIP 247
S+++IR FA K+P
Sbjct: 62 SLELIREFAGKVP 74
>gnl|CDD|216062 pfam00688, TGFb_propeptide, TGF-beta propeptide. This propeptide
is known as latency associated peptide (LAP) in
TGF-beta. LAP is a homodimer which is disulfide linked
to TGF-beta binding protein.
Length = 229
Score = 27.4 bits (61), Expect = 8.8
Identities = 23/109 (21%), Positives = 35/109 (32%), Gaps = 27/109 (24%)
Query: 124 RLPSKPKSPQESPPSPPVSLITALYR----EPNPLEPPIAEPEKIQQFYSLLTTSVDVIR 179
L +P Q P S P ++ LY + + + E E + + +R
Sbjct: 33 GLKRRPNPSQSLPKSVPQYML-DLYNSQSADDSGASADLEELETLAD-------RANTVR 84
Query: 180 HFADKIPGFSDLC--KEDQELLF-----------QSASLELFYREPNPL 215
FAD+ F + L F +A L L Y EP
Sbjct: 85 SFADE-EEFELEQVDGHRKRLFFNLSSIPEDELLTAAELRL-YLEPVEE 131
>gnl|CDD|219401 pfam07404, TEBP_beta, Telomere-binding protein beta subunit (TEBP
beta). This family consists of several telomere-binding
protein beta subunits which appear to be specific to the
family Oxytrichidae. Telomeres are specialised
protein-DNA complexes that compose the ends of
eukaryotic chromosomes. Telomeres protect chromosome
termini from degradation and recombination and act
together with telomerase to ensure complete genome
replication. TEBP beta forms a complex with TEBP alpha
and this complex is able to recognise and bind ssDNA to
form a sequence-specific, telomeric nucleoprotein
complex that caps the very 3' ends of chromosomes.
Length = 375
Score = 27.8 bits (61), Expect = 9.0
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 6 SSSSESPKLRHSAPLSSASSSPGCDTSRPTPPSPS 40
SS E+P+ + S+ ++ G + P PSPS
Sbjct: 290 SSRKETPQKSQAGKSSAKKTTTGSKKAVPANPSPS 324
>gnl|CDD|133061 cd06439, CESA_like_1, CESA_like_1 is a member of the cellulose
synthase (CESA) superfamily. This is a subfamily of
cellulose synthase (CESA) superfamily. CESA superfamily
includes a wide variety of glycosyltransferase family 2
enzymes that share the common characteristic of
catalyzing the elongation of polysaccharide chains. The
members of the superfamily include cellulose synthase
catalytic subunit, chitin synthase, glucan biosynthesis
protein and other families of CESA-like proteins.
Length = 251
Score = 27.5 bits (62), Expect = 9.6
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 6/48 (12%)
Query: 123 GRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSL 170
RL KP S + P V++I Y E E I K++ +L
Sbjct: 13 ARLRPKPPSLPDPAYLPTVTIIIPAYNE----EAVIE--AKLENLLAL 54
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 26.5 bits (59), Expect = 9.7
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 2/65 (3%)
Query: 253 CKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEF 312
C E++ LL A+L L Y + + L + ++ + ILE
Sbjct: 25 CSEEEALLL--AALALQAEFGDYNPEKHSSSYLKELEYFLPSRLIKKEKSKELEKRILEA 82
Query: 313 CQSLH 317
++L
Sbjct: 83 HKNLR 87
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
0.321 0.136 0.416
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: 16,494,808
Number of extensions: 1544921
Number of successful extensions: 1938
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1909
Number of HSP's successfully gapped: 145
Length of query: 335
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 238
Effective length of database: 6,635,264
Effective search space: 1579192832
Effective search space used: 1579192832
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: 59 (26.6 bits)