RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12688
(222 letters)
>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 = 161 bits (408), Expect = 2e-51
Identities = 60/69 (86%), Positives = 64/69 (92%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK YTC+ ++C IDKTQRKRCP+CRFQK
Sbjct: 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQK 60
Query: 190 CLEVGMKLE 198
CL VGMKLE
Sbjct: 61 CLSVGMKLE 69
>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 = 134 bits (339), Expect = 3e-41
Identities = 43/69 (62%), Positives = 50/69 (72%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGDK SGYHYG+LTCE CKGFF+R+V+ YTC A +C IDK R RC CR +K
Sbjct: 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKK 60
Query: 190 CLEVGMKLE 198
CL VGM+ E
Sbjct: 61 CLAVGMRKE 69
>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 = 131 bits (333), Expect = 3e-40
Identities = 45/70 (64%), Positives = 52/70 (74%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
ELC VCGDK SGYHYG+LTCE CKGFF+R++Q VYTC + C IDK R RC +CR
Sbjct: 1 ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRL 60
Query: 188 QKCLEVGMKL 197
+KCLEVGM
Sbjct: 61 KKCLEVGMSK 70
>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 = 120 bits (302), Expect = 2e-35
Identities = 44/72 (61%), Positives = 54/72 (75%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+LC +C DK +G HYG++TCE CKGFFKRTVQNK+VYTCV + C I K QR RC +CR
Sbjct: 6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCR 65
Query: 187 FQKCLEVGMKLE 198
F+KC+ GM L
Sbjct: 66 FRKCIRKGMMLA 77
>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 = 119 bits (299), Expect = 4e-35
Identities = 43/72 (59%), Positives = 52/72 (72%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
LC VCGD + HYG+ TCE CKGFFKRTVQ Y C+A ++C +DK +R RC +CRF
Sbjct: 1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRF 60
Query: 188 QKCLEVGMKLEV 199
QKCL+VGM EV
Sbjct: 61 QKCLQVGMVKEV 72
>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors.
Length = 70
Score = 116 bits (292), Expect = 6e-34
Identities = 35/70 (50%), Positives = 46/70 (65%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
LC VCGD SG+H+G+ +C +CK FF+RTV + Y C + +C I+K R RC CR +
Sbjct: 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLK 60
Query: 189 KCLEVGMKLE 198
KCL VGM E
Sbjct: 61 KCLGVGMDPE 70
>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 = 111 bits (278), Expect = 8e-32
Identities = 36/79 (45%), Positives = 55/79 (69%), Gaps = 2/79 (2%)
Query: 120 PDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQR 179
D E + C +CGD+ +G HYG+++CE CKGFFKR++ NK+VY C +++C + + QR
Sbjct: 1 DDRAE--QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQR 58
Query: 180 KRCPFCRFQKCLEVGMKLE 198
RC +CR KCL++GM +
Sbjct: 59 NRCQYCRLLKCLQMGMNRK 77
>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 = 110 bits (277), Expect = 9e-32
Identities = 40/70 (57%), Positives = 48/70 (68%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
C VCGDK +GYHY +TCE CKGFF+RTVQ K Y+C E C IDK R +C CRF+
Sbjct: 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFK 60
Query: 189 KCLEVGMKLE 198
KC+ VGM +
Sbjct: 61 KCIAVGMAKD 70
>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 = 109 bits (275), Expect = 2e-31
Identities = 37/69 (53%), Positives = 50/69 (72%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGD+ +G HYG+L+C CKGFF+R+V+ + YTC +C +DK +R C +CRF+K
Sbjct: 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKK 60
Query: 190 CLEVGMKLE 198
CLEVGM E
Sbjct: 61 CLEVGMDPE 69
>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 = 107 bits (270), Expect = 9e-31
Identities = 34/69 (49%), Positives = 47/69 (68%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGD+ +GYH+ +TCE CKGFF+R+++ K +TC C I K R+ C CR +K
Sbjct: 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKK 60
Query: 190 CLEVGMKLE 198
CL++GMK E
Sbjct: 61 CLDIGMKKE 69
>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 (268), Expect = 2e-30
Identities = 39/71 (54%), Positives = 50/71 (70%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
ELC VCGDK SG HYG ++CE CKGFFKR+++ Y+C + C I+K R RC +CR
Sbjct: 4 ELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRL 63
Query: 188 QKCLEVGMKLE 198
QKCL +GMK +
Sbjct: 64 QKCLAMGMKSD 74
>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 = 105 bits (263), Expect = 1e-29
Identities = 41/70 (58%), Positives = 51/70 (72%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
+C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +CR+Q
Sbjct: 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 61
Query: 189 KCLEVGMKLE 198
KCL +GMK E
Sbjct: 62 KCLAMGMKRE 71
>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 = 5e-29
Identities = 36/66 (54%), Positives = 47/66 (71%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGDK SGYHYG+ +CE CKGFF+R++Q + Y C+ + C I + R RC +CRF+K
Sbjct: 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKK 60
Query: 190 CLEVGM 195
CL GM
Sbjct: 61 CLAAGM 66
>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 = 102 bits (255), Expect = 2e-28
Identities = 41/72 (56%), Positives = 50/72 (69%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
EELC VCGD+ SGYHY LTCE CKGFF+R+V VY C R+C +D R++C CR
Sbjct: 1 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECR 60
Query: 187 FQKCLEVGMKLE 198
+KCL VGM+ E
Sbjct: 61 LKKCLSVGMRPE 72
>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 = 98.7 bits (246), Expect = 4e-27
Identities = 39/69 (56%), Positives = 48/69 (69%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGD SGYHYG+ +CE+CK FFKRT+Q Y+C + C +DK +RK C CR QK
Sbjct: 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQK 60
Query: 190 CLEVGMKLE 198
CL+VGM E
Sbjct: 61 CLKVGMLKE 69
>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 = 98.8 bits (246), Expect = 4e-27
Identities = 41/73 (56%), Positives = 51/73 (69%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
I + C VC DK SGYHYG+ CE CKGFF+R++Q VYTC +++C I+K R RC +C
Sbjct: 3 IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYC 62
Query: 186 RFQKCLEVGMKLE 198
R QKC EVGM E
Sbjct: 63 RLQKCFEVGMSKE 75
>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 = 98.8 bits (246), Expect = 6e-27
Identities = 40/67 (59%), Positives = 47/67 (70%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
LC VCGD SGYHYG+ +CE+CK FFKRT+Q Y+C A C I K +RK C CRF
Sbjct: 6 LCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFM 65
Query: 189 KCLEVGM 195
KCL+VGM
Sbjct: 66 KCLKVGM 72
>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 = 96.8 bits (241), Expect = 3e-26
Identities = 38/66 (57%), Positives = 49/66 (74%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C +CGDK SG HYG++TCE CKGFF+R+ QN Y+C +++C ID+T R RC CR QK
Sbjct: 8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQK 67
Query: 190 CLEVGM 195
CL +GM
Sbjct: 68 CLALGM 73
>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 = 95.6 bits (238), Expect = 6e-26
Identities = 34/70 (48%), Positives = 45/70 (64%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
C VCGDK SG+HYG+L+CE CKGFF+R+V VY C C +D R++C CR +
Sbjct: 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLR 60
Query: 189 KCLEVGMKLE 198
KC GM+ +
Sbjct: 61 KCKAAGMRPD 70
>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 = 95.3 bits (237), Expect = 1e-25
Identities = 39/72 (54%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCP 183
G+ LC VCGDK SG+HYG+ CE CKGFF+R++Q K Y C +C I + R RC
Sbjct: 1 GMVVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQ 60
Query: 184 FCRFQKCLEVGM 195
+CRF+KCL VGM
Sbjct: 61 YCRFKKCLAVGM 72
>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 = 93.7 bits (233), Expect = 3e-25
Identities = 38/72 (52%), Positives = 48/72 (66%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+++C VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR
Sbjct: 2 QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACR 61
Query: 187 FQKCLEVGMKLE 198
+KCL+ GM L
Sbjct: 62 LRKCLQAGMNLG 73
>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 = 93.8 bits (233), Expect = 3e-25
Identities = 37/67 (55%), Positives = 43/67 (64%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
C VC D SGYHYG+ +CE CK FFKR++Q Y C A C IDK +RK C CR +
Sbjct: 5 FCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLR 64
Query: 189 KCLEVGM 195
KC EVGM
Sbjct: 65 KCYEVGM 71
>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 = 93.3 bits (232), Expect = 5e-25
Identities = 40/68 (58%), Positives = 48/68 (70%), Gaps = 3/68 (4%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRF 187
C VCGDK SG+HYG+ CE CKGFF+RT++ K VY C + SC I K R +C +CRF
Sbjct: 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPC--DLSCKIHKKSRNKCQYCRF 58
Query: 188 QKCLEVGM 195
QKCL VGM
Sbjct: 59 QKCLNVGM 66
>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 = 92.2 bits (229), Expect = 1e-24
Identities = 37/67 (55%), Positives = 47/67 (70%), Gaps = 1/67 (1%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRKRCPFCRFQ 188
C VCGDK SG+HYG+ +CE CKGFF+RT+Q+ Y C+ C I + R RC +CRF+
Sbjct: 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFK 60
Query: 189 KCLEVGM 195
KCL VGM
Sbjct: 61 KCLSVGM 67
>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 = 91.4 bits (227), Expect = 3e-24
Identities = 32/67 (47%), Positives = 45/67 (67%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGD+ SG HYG+ +C+ C+GFFKR+++ Y C SC +D +R +C CRF+K
Sbjct: 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKK 60
Query: 190 CLEVGMK 196
CL+V M
Sbjct: 61 CLQVNMN 67
>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 = 91.0 bits (226), Expect = 3e-24
Identities = 34/66 (51%), Positives = 42/66 (63%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCG K SG+H+G LTCE CKGFF+RT + Y C ++C I R C CRF++
Sbjct: 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRR 60
Query: 190 CLEVGM 195
CL VGM
Sbjct: 61 CLAVGM 66
>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 = 91.1 bits (226), Expect = 3e-24
Identities = 39/71 (54%), Positives = 48/71 (67%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGDK SG HYG TCE CK FFKR+V+ YTC R+C ID+ R +C +CR +K
Sbjct: 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKK 60
Query: 190 CLEVGMKLEVS 200
CL+VGM+ E
Sbjct: 61 CLKVGMRREAV 71
>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 = 90.8 bits (225), Expect = 4e-24
Identities = 36/69 (52%), Positives = 44/69 (63%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C +CGD+ SG HYG+LTC SCK FFKR + + Y C C IDK +RK CP CR +K
Sbjct: 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRK 60
Query: 190 CLEVGMKLE 198
C + GM L
Sbjct: 61 CYQAGMTLG 69
>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 = 90.3 bits (224), Expect = 7e-24
Identities = 35/67 (52%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAER-SCHIDKTQRKRCPFCRFQ 188
C VCGD+ SG HYG+ C+ C GFFKR+++ +YTC A SC +DK +R +C CR +
Sbjct: 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLK 60
Query: 189 KCLEVGM 195
KCLEV M
Sbjct: 61 KCLEVSM 67
>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 = 89.6 bits (222), Expect = 2e-23
Identities = 39/72 (54%), Positives = 48/72 (66%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
EELC VCGDK SGYHY LTCE CKGFF+R++ VY C +C +D R++C CR
Sbjct: 1 EELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECR 60
Query: 187 FQKCLEVGMKLE 198
+KC E+GM E
Sbjct: 61 LRKCKEMGMLAE 72
>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 = 88.7 bits (220), Expect = 3e-23
Identities = 36/67 (53%), Positives = 45/67 (67%), Gaps = 1/67 (1%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAER-SCHIDKTQRKRCPFCRFQ 188
C VCGDK G HYG+ C+ C FFKR+V+ +YTC+A +C +DK +R CPFCR Q
Sbjct: 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQ 60
Query: 189 KCLEVGM 195
KC VGM
Sbjct: 61 KCFAVGM 67
>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 = 88.4 bits (219), Expect = 4e-23
Identities = 38/71 (53%), Positives = 47/71 (66%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
++ C +CGD+ SG HYG LTC SCK FFKR + K+ Y C + C IDK +RK CP CR
Sbjct: 3 QKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 62
Query: 187 FQKCLEVGMKL 197
+KC E GM L
Sbjct: 63 LRKCFEAGMTL 73
>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 = 88.5 bits (219), Expect = 8e-23
Identities = 30/74 (40%), Positives = 49/74 (66%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
+ +C VCGD+ +G+H+ +TCE CKGFF+R+++ K ++TC C I K R+ C
Sbjct: 4 NVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQA 63
Query: 185 CRFQKCLEVGMKLE 198
CR ++C+++GM E
Sbjct: 64 CRLKRCVDIGMMKE 77
>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 = 86.9 bits (215), Expect = 3e-22
Identities = 34/71 (47%), Positives = 46/71 (64%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
E+C VCGDK SG+HY +L+CE CKGFF+R+V Y C C +D R++C CR
Sbjct: 19 EVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRL 78
Query: 188 QKCLEVGMKLE 198
+KC E GM+ +
Sbjct: 79 RKCREAGMREQ 89
>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 = 86.1 bits (213), Expect = 4e-22
Identities = 32/71 (45%), Positives = 48/71 (67%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
+C VCGD+ +GYH+ +TCE CKGFF+R ++ C ++ C I K+ R++C CR +
Sbjct: 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLR 60
Query: 189 KCLEVGMKLEV 199
KCL +GMK E+
Sbjct: 61 KCLSIGMKKEL 71
>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 = 85.6 bits (212), Expect = 6e-22
Identities = 33/68 (48%), Positives = 45/68 (66%), Gaps = 2/68 (2%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVA--ERSCHIDKTQRKRCPFCRF 187
C VCGD+ SG HYG+ C+ C GFFKR+++ + Y C + + C +DKT R +C CR
Sbjct: 9 CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRL 68
Query: 188 QKCLEVGM 195
+KC EVGM
Sbjct: 69 KKCFEVGM 76
>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 = 85.2 bits (211), Expect = 1e-21
Identities = 32/69 (46%), Positives = 40/69 (57%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGDK GY++ +TCESCK FF+R K + C SC I+ R+ C CR K
Sbjct: 3 CGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDK 62
Query: 190 CLEVGMKLE 198
C +GMK E
Sbjct: 63 CFAIGMKKE 71
>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 = 79.2 bits (195), Expect = 2e-19
Identities = 35/68 (51%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERS-CHIDKTQRKRCPFCRF 187
LC VCGD SG HYG+ C C GFFKR+V+ K +Y C A C +DK R +C CR
Sbjct: 8 LCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRL 67
Query: 188 QKCLEVGM 195
+KCL+ GM
Sbjct: 68 KKCLQAGM 75
>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 = 76.4 bits (188), Expect = 2e-18
Identities = 30/70 (42%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTV--QNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
C VCG+ +G+H+G CE+CK FF R+ + + C C IDK R +C CR+
Sbjct: 3 CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRY 62
Query: 188 QKCLEVGMKL 197
+KCL VGM L
Sbjct: 63 RKCLNVGMSL 72
>gnl|CDD|221334 pfam11949, DUF3466, Protein of unknown function (DUF3466). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 564 to 612 amino acids in
length.
Length = 589
Score = 30.5 bits (69), Expect = 0.65
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 4/41 (9%)
Query: 47 HSNNDTQSSQLSPMLGNNTSASAGGAGYNFNNMVDNSYLFQ 87
S+++ + LG N + G GY+ N D Y
Sbjct: 303 ASDDEVFQAS---ALGVNVNGIVVGVGYSTYN-DDTDYRMN 339
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 30.7 bits (70), Expect = 0.68
Identities = 10/25 (40%), Positives = 11/25 (44%), Gaps = 3/25 (12%)
Query: 128 ELCPVCGDKVSGYHY--GLLTCESC 150
CP CG +S GL CE C
Sbjct: 8 NSCPNCGGDISDERLEKGLP-CEKC 31
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 29.0 bits (65), Expect = 1.4
Identities = 13/75 (17%), Positives = 22/75 (29%), Gaps = 2/75 (2%)
Query: 18 CKKRKKLKPKTPIQQLLSAATGAQTPQMQHSNNDTQSSQLSPMLGNNTSASAGGAGYN-F 76
C K +P+ P+ ++ T TP Q + G + G +
Sbjct: 101 CCLEKACRPQRPVMTRATSTTVQTTPLPQPPSTAPSYPGPQYQ-GYHPMPPQPGMPAPPY 159
Query: 77 NNMVDNSYLFQSPGG 91
+ L Q G
Sbjct: 160 SLQYPPPGLLQPQGP 174
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 29.1 bits (66), Expect = 1.6
Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 13/82 (15%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGF-FKRTVQNKKVYTCVAERSCH-------IDKTQ 178
C C + TC +C G RTVQ + +++C I K
Sbjct: 142 SVTCSTCHGSGAKPGTDPKTCPTCNGSGQVRTVQRTGFF--SFQQTCPTCNGTGKIIK-- 197
Query: 179 RKRCPFCRFQKCLEVGMKLEVS 200
C C+ + ++ + V+
Sbjct: 198 -DPCGKCKGKGRVKKKKSISVN 218
>gnl|CDD|205631 pfam13453, zf-TFIIB, Transcription factor zinc-finger.
Length = 41
Score = 26.1 bits (58), Expect = 2.2
Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 3/28 (10%)
Query: 130 CPVCGDKVSGYHYGLLT---CESCKGFF 154
CP CG ++ + C SC G +
Sbjct: 2 CPKCGSELEPVERDGVEIDYCPSCGGVW 29
>gnl|CDD|164789 PHA00327, PHA00327, minor capsid protein.
Length = 187
Score = 28.5 bits (63), Expect = 2.4
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 44 QMQHSNNDTQSSQLSPML--GNNTSASAGGAGYNFNNMVDN 82
Q + D + + L+P+L G ++S GAG++ NN V++
Sbjct: 62 AYQRAMEDMKKAGLNPLLAFGKGGASSPSGAGWSPNNPVES 102
>gnl|CDD|218049 pfam04373, DUF511, Protein of unknown function (DUF511).
Bacterial protein of unknown function.
Length = 310
Score = 28.5 bits (64), Expect = 2.5
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 5 SQIHENILDLVQRCKKRKKLKPKTPIQQLLSAATGAQTPQMQHS 48
+I E L+ K + K KTPI Q L A G+ ++
Sbjct: 15 REIAEWALEKGLDKKLNSREKGKTPIAQ-LGAEIGSDRKELAKK 57
>gnl|CDD|239922 cd04476, RPA1_DBD_C, RPA1_DBD_C: A subfamily of OB folds
corresponding to the C-terminal OB fold, the
ssDNA-binding domain (DBD)-C, of human RPA1 (also called
RPA70). RPA1 is the large subunit of Replication protein
A (RPA). RPA is a nuclear ssDNA-binding protein (SSB)
which appears to be involved in all aspects of DNA
metabolism including replication, recombination, and
repair. RPA also mediates specific interactions of
various nuclear proteins. In animals, plants, and fungi,
RPA is a heterotrimer with subunits of 70KDa (RPA1),
32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C,
RPA1 contains three other OB folds: DBD-A, DBD-B, and
RPA1N. The major DNA binding activity of RPA is
associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is
involved in DNA binding and trimerization. It contains
two structural insertions not found to date in other
OB-folds: a zinc ribbon and a three-helix bundle. RPA1
DBD-C also contains a Cys4-type zinc-binding motif,
which plays a role in the ssDNA binding function of this
domain. It appears that zinc itself may not be required
for ssDNA binding.
Length = 166
Score = 28.0 bits (63), Expect = 3.1
Identities = 9/25 (36%), Positives = 9/25 (36%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFF 154
CP C KV G CE C
Sbjct: 37 CPGCNKKVVEEGNGTYRCEKCNKSV 61
>gnl|CDD|215935 pfam00471, Ribosomal_L33, Ribosomal protein L33.
Length = 48
Score = 25.2 bits (56), Expect = 5.4
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 10/43 (23%)
Query: 145 LTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQ-RKRCPFCR 186
L C C G T +NK+ ++ + +K CP CR
Sbjct: 6 LECTECGGRNYTTTKNKRN---------TPERLELKKYCPKCR 39
>gnl|CDD|223345 COG0267, RpmG, Ribosomal protein L33 [Translation, ribosomal
structure and biogenesis].
Length = 50
Score = 25.3 bits (56), Expect = 5.8
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 10/43 (23%)
Query: 145 LTCESCKGFFKRTVQNKKVYTCVAERSCHIDK-TQRKRCPFCR 186
L C +C T +NK+ ++ +K CP CR
Sbjct: 8 LACTACTSRNYTTTKNKRN---------KPERLELKKYCPVCR 41
>gnl|CDD|219494 pfam07642, DUF1597, Outer membrane protein family (DUF1597). This
family of proteins are likely to be outer membrane beta
barrel proteins. Possibly acting as porins.
Length = 336
Score = 27.2 bits (61), Expect = 6.7
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 70 GGAGYNFNNMVDNSYLFQSPGGGSTNMDLSSA--GISY 105
G YNFN +N+ + + +L+ A +S
Sbjct: 10 GYYTYNFNKPANNTNPGVTFTDRANEFNLNQAQLKLSK 47
>gnl|CDD|235840 PRK06599, PRK06599, DNA topoisomerase I; Validated.
Length = 675
Score = 27.5 bits (62), Expect = 6.7
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 5/36 (13%)
Query: 105 YHPFHTSTIAATPEHPD----TKEGIEELCPVCGDK 136
+ PF S + E T+E +E CP CG
Sbjct: 560 WEPFI-SNLEKVEEDVRTEKVTQEETDETCPKCGGG 594
>gnl|CDD|218654 pfam05605, Di19, Drought induced 19 protein (Di19). This family
consists of several drought induced 19 (Di19) like
proteins. Di19 has been found to be strongly expressed
in both the roots and leaves of Arabidopsis thaliana
during progressive drought. The precise function of Di19
is unknown.
Length = 209
Score = 26.6 bits (59), Expect = 8.7
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 4/22 (18%)
Query: 118 EHP-DTKEGIEELCPVCGDKVS 138
EHP + K G+ CPVC D+V
Sbjct: 55 EHPFEAKNGV---CPVCADRVG 73
>gnl|CDD|184604 PRK14283, PRK14283, chaperone protein DnaJ; Provisional.
Length = 378
Score = 27.1 bits (60), Expect = 8.8
Identities = 28/93 (30%), Positives = 38/93 (40%), Gaps = 8/93 (8%)
Query: 71 GAGYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELC 130
G G+ N+ D +F GGGS + A I T AA+ D K + C
Sbjct: 94 GFGFGIGNIFD---MFGF-GGGSRHGPQRGADIYTEVEITLEEAASGVEKDIKVRHTKKC 149
Query: 131 PVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKV 163
PVC + + TC +C G T Q K+V
Sbjct: 150 PVCNGSRAEPGSEVKTCPTCGG----TGQVKQV 178
>gnl|CDD|219927 pfam08601, PAP1, Transcription factor PAP1. The transcription
factor Pap1 regulates antioxidant-gene transcription in
response to H2O2. This region is cysteine rich.
Alkylation of cysteine residues following treatment with
a cysteine alkylating agent can mask the accessibility
of the nuclear exporter Crm1, triggering nuclear
accumulation and Pap1 dependent transcriptional
expression.
Length = 344
Score = 26.8 bits (59), Expect = 9.4
Identities = 23/114 (20%), Positives = 35/114 (30%), Gaps = 19/114 (16%)
Query: 16 QRCKKRKKLKPKTPIQQLLSAATGAQTPQMQHSNNDTQSSQLSPMLGNN---------TS 66
K K +P+ LL++ T + ++ N S + M + +
Sbjct: 43 PIPKLAKNSSVSSPVPGLLNS-TESNVSSPNNNPNGYTSPSSAAMNNKSNNRAVDPSANA 101
Query: 67 ASAGGAGYNFNNMVDNSYL------FQSPGGGSTNMD---LSSAGISYHPFHTS 111
++A N Y SP GS LSS G S P S
Sbjct: 102 SAASTNSPNGLQSSATQYNSNDNSSSDSPSSGSDGFTNQLLSSLGTSPEPSTES 155
>gnl|CDD|180178 PRK05637, PRK05637, anthranilate synthase component II;
Provisional.
Length = 208
Score = 26.7 bits (59), Expect = 9.8
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 91 GGSTNMDLSSAGISYHPFHTSTIAATPEHPD 121
G + NM L+ AG+ F P+HP+
Sbjct: 102 GTTDNMILTDAGVQSPVFAGLATDVEPDHPE 132
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
0.316 0.129 0.392
Gapped
Lambda K H
0.267 0.0820 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,435,253
Number of extensions: 882918
Number of successful extensions: 947
Number of sequences better than 10.0: 1
Number of HSP's gapped: 937
Number of HSP's successfully gapped: 65
Length of query: 222
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 129
Effective length of database: 6,812,680
Effective search space: 878835720
Effective search space used: 878835720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.6 bits)