RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9231
(134 letters)
>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 = 143 bits (363), Expect = 4e-46
Identities = 61/70 (87%), Positives = 64/70 (91%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C+VCGD+ASGKHYGVPSCDGCRGFFKRSIRRNL YVCKE G C+VDV RRNQCQACRF K
Sbjct: 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKK 60
Query: 124 CLQVKMNRDA 133
CLQV MNRDA
Sbjct: 61 CLQVNMNRDA 70
>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 = 124 bits (313), Expect = 2e-38
Identities = 44/70 (62%), Positives = 55/70 (78%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C VCGDKASG HYGV +C+GC+GFF+RS+RRNLEY C G+C++D RN+CQACR K
Sbjct: 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKK 60
Query: 124 CLQVKMNRDA 133
CL V M ++A
Sbjct: 61 CLAVGMRKEA 70
>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 = 119 bits (299), Expect = 3e-36
Identities = 50/77 (64%), Positives = 62/77 (80%), Gaps = 2/77 (2%)
Query: 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKER--GHCIVDVTRRNQCQ 117
+D+ CKVCGD++SGKHYG+ +CDGC GFFKRSIRRN +YVCK + G C VD T RNQC+
Sbjct: 5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCR 64
Query: 118 ACRFSKCLQVKMNRDAM 134
ACR KC +V MN+DA+
Sbjct: 65 ACRLKKCFEVGMNKDAV 81
>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 = 117 bits (296), Expect = 6e-36
Identities = 40/70 (57%), Positives = 53/70 (75%)
Query: 62 VLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRF 121
LCKVCGDKASG HYGV +C+GC+GFF+RSI++N+ Y C C++D RN+CQ CR
Sbjct: 1 ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRL 60
Query: 122 SKCLQVKMNR 131
KCL+V M++
Sbjct: 61 KKCLEVGMSK 70
>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 = 116 bits (292), Expect = 2e-35
Identities = 52/72 (72%), Positives = 59/72 (81%), Gaps = 1/72 (1%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCK-ERGHCIVDVTRRNQCQACRFS 122
CKVCGD++SGKHYGV +CDGC GFFKRSIRRNL Y CK G C+VD RRNQCQACR
Sbjct: 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLK 60
Query: 123 KCLQVKMNRDAM 134
KCL+V MN+DA+
Sbjct: 61 KCLEVSMNKDAV 72
>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 = 108 bits (271), Expect = 4e-32
Identities = 41/70 (58%), Positives = 56/70 (80%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C VCGD+A+GKHYGV SC+GC+GFF+RS+R+N Y C+ G+C+VD +RN C+ CRF K
Sbjct: 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKK 60
Query: 124 CLQVKMNRDA 133
CL+V M+ +A
Sbjct: 61 CLEVGMDPEA 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 = 102 bits (256), Expect = 1e-29
Identities = 37/71 (52%), Positives = 49/71 (69%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
C VCGDKA+G HY +C+GC+GFF+R++++ L Y CK G C +D RNQCQ CRF
Sbjct: 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFK 60
Query: 123 KCLQVKMNRDA 133
KC+ V M +D
Sbjct: 61 KCIAVGMAKDL 71
>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 = 102 bits (255), Expect = 1e-29
Identities = 39/72 (54%), Positives = 58/72 (80%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
+C +CGD+ASGKHYGV SC+GC+GFFKR++R++L Y C++ C++D +RN+CQ CR+
Sbjct: 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 61
Query: 123 KCLQVKMNRDAM 134
KCL + M R+A+
Sbjct: 62 KCLAMGMKREAV 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 = 102 bits (255), Expect = 2e-29
Identities = 46/74 (62%), Positives = 56/74 (75%), Gaps = 1/74 (1%)
Query: 62 VLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKE-RGHCIVDVTRRNQCQACR 120
+LC+VCGD +SGKHYG+ +C+GC GFFKRS+RR L Y C+ G C VD RNQCQACR
Sbjct: 7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACR 66
Query: 121 FSKCLQVKMNRDAM 134
KCLQ MN+DA+
Sbjct: 67 LKKCLQAGMNKDAV 80
>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 = 99.2 bits (247), Expect = 2e-28
Identities = 41/71 (57%), Positives = 53/71 (74%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
CKVCGDKASG HYGV SC+GC+GFF+RSI++ +EY C G C + RN+CQ CRF K
Sbjct: 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKK 60
Query: 124 CLQVKMNRDAM 134
CL M++D++
Sbjct: 61 CLAAGMSKDSV 71
>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 = 99.5 bits (248), Expect = 2e-28
Identities = 41/71 (57%), Positives = 52/71 (73%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
LC VCGDKASG+HYG SC+GC+GFFKRSIR+NL Y C+ C+++ RN+CQ CR
Sbjct: 5 LCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQ 64
Query: 123 KCLQVKMNRDA 133
KCL + M D+
Sbjct: 65 KCLAMGMKSDS 75
>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 = 98.8 bits (246), Expect = 2e-28
Identities = 42/70 (60%), Positives = 52/70 (74%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C VCGDK+SGKHYG +C+GC+ FFKRS+RRNL Y C+ +C +D RNQCQ CR K
Sbjct: 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKK 60
Query: 124 CLQVKMNRDA 133
CL+V M R+A
Sbjct: 61 CLKVGMRREA 70
>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 = 98.3 bits (245), Expect = 5e-28
Identities = 42/72 (58%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVC-KERGHCIVDVTRRNQCQACRFS 122
CKVCGDK+ GKHYGV CDGC FFKRS+R+ + Y C G+C+VD RRN C CR
Sbjct: 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQ 60
Query: 123 KCLQVKMNRDAM 134
KC V MNR A+
Sbjct: 61 KCFAVGMNRAAV 72
>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors.
Length = 70
Score = 96.8 bits (242), Expect = 1e-27
Identities = 31/70 (44%), Positives = 45/70 (64%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
LC VCGD ASG H+GV SC C+ FF+R++ +Y C + +C ++ R +C+ACR
Sbjct: 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLK 60
Query: 123 KCLQVKMNRD 132
KCL V M+ +
Sbjct: 61 KCLGVGMDPE 70
>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 = 96.7 bits (241), Expect = 1e-27
Identities = 40/67 (59%), Positives = 52/67 (77%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
LC VCGD A+ +HYGV +C+GC+GFFKR++++N +YVC +C VD RRN+CQ CRF
Sbjct: 2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQ 61
Query: 123 KCLQVKM 129
KCLQV M
Sbjct: 62 KCLQVGM 68
>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 = 95.7 bits (238), Expect = 5e-27
Identities = 44/76 (57%), Positives = 57/76 (75%), Gaps = 1/76 (1%)
Query: 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEY-VCKERGHCIVDVTRRNQCQA 118
M VLCKVCGDKASG HYGV +C+GC+GFF+RSI++ ++Y C + C + RN+CQ
Sbjct: 2 MVVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQY 61
Query: 119 CRFSKCLQVKMNRDAM 134
CRF KCL V M+RDA+
Sbjct: 62 CRFKKCLAVGMSRDAV 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 = 95.7 bits (238), Expect = 6e-27
Identities = 39/70 (55%), Positives = 54/70 (77%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
CK+CGDK+SG HYGV +C+GC+GFF+RS + N+ Y C + +C++D T RN+CQ CR K
Sbjct: 8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQK 67
Query: 124 CLQVKMNRDA 133
CL + M+RDA
Sbjct: 68 CLALGMSRDA 77
>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 = 94.2 bits (234), Expect = 2e-26
Identities = 43/72 (59%), Positives = 54/72 (75%), Gaps = 1/72 (1%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYV-CKERGHCIVDVTRRNQCQACRFS 122
CKVCGDKASG HYGV SC+GC+GFF+R+I+ NL Y C G C++ RN+CQ CRF
Sbjct: 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFK 60
Query: 123 KCLQVKMNRDAM 134
KCL V M+R+A+
Sbjct: 61 KCLSVGMSRNAV 72
>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 = 93.8 bits (233), Expect = 2e-26
Identities = 35/71 (49%), Positives = 53/71 (74%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C VC DK+SG HYGV +C+GC+GFF+RSI++N+ Y C +CI++ RN+CQ CR K
Sbjct: 7 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQK 66
Query: 124 CLQVKMNRDAM 134
C +V M+++++
Sbjct: 67 CFEVGMSKESV 77
>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 = 94.1 bits (234), Expect = 3e-26
Identities = 35/70 (50%), Positives = 47/70 (67%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C VCGDK SG HYG+ +C+ C+GFFKR+++ Y C E +C +D T+R +C CRF K
Sbjct: 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQK 60
Query: 124 CLQVKMNRDA 133
CL V M +A
Sbjct: 61 CLSVGMKLEA 70
>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 = 91.4 bits (227), Expect = 2e-25
Identities = 38/72 (52%), Positives = 50/72 (69%), Gaps = 1/72 (1%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
C+VCGDKASG HYGV +C+GC+GFF+R+IR L Y + C + RN+CQ CRF
Sbjct: 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDL-SCKIHKKSRNKCQYCRFQ 59
Query: 123 KCLQVKMNRDAM 134
KCL V M+ +A+
Sbjct: 60 KCLNVGMSHNAI 71
>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 = 90.3 bits (224), Expect = 7e-25
Identities = 36/70 (51%), Positives = 45/70 (64%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
C VC D ASG HYGV SC+GC+ FFKRSI+ + +Y+C C +D RR CQACR
Sbjct: 5 FCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLR 64
Query: 123 KCLQVKMNRD 132
KC +V M +
Sbjct: 65 KCYEVGMMKG 74
>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 = 89.1 bits (221), Expect = 2e-24
Identities = 39/72 (54%), Positives = 49/72 (68%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
LC VCGD ASG HYGV SC+ C+ FFKR+I+ N+EY C C + RR CQACRF
Sbjct: 6 LCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFM 65
Query: 123 KCLQVKMNRDAM 134
KCL+V M ++ +
Sbjct: 66 KCLKVGMLKEGV 77
>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 = 88.8 bits (220), Expect = 3e-24
Identities = 37/71 (52%), Positives = 50/71 (70%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C +CGD+A+G HYG+ SC+GC+GFFKRSI Y C +C++ +RN+CQ CR K
Sbjct: 9 CLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLK 68
Query: 124 CLQVKMNRDAM 134
CLQ+ MNR A+
Sbjct: 69 CLQMGMNRKAI 79
>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 = 87.9 bits (218), Expect = 5e-24
Identities = 39/69 (56%), Positives = 46/69 (66%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C VCGD ASG HYGV SC+ C+ FFKR+I+ NL Y C C VD RR CQACR K
Sbjct: 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQK 60
Query: 124 CLQVKMNRD 132
CL+V M ++
Sbjct: 61 CLKVGMLKE 69
>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 = 88.0 bits (218), Expect = 7e-24
Identities = 36/67 (53%), Positives = 47/67 (70%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
+C VCGDKASG HY V SC+GC+GFF+RS+ + +YVCK G C +D+ R +CQ CR
Sbjct: 20 VCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLR 79
Query: 123 KCLQVKM 129
KC + M
Sbjct: 80 KCREAGM 86
>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 = 3e-22
Identities = 36/69 (52%), Positives = 48/69 (69%)
Query: 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACR 120
+ LC VCGDKASG HY +C+GC+GFF+RSI +N Y CK G+C +D+ R +CQ CR
Sbjct: 1 EELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECR 60
Query: 121 FSKCLQVKM 129
KC ++ M
Sbjct: 61 LRKCKEMGM 69
>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 = 82.5 bits (204), Expect = 5e-22
Identities = 36/72 (50%), Positives = 45/72 (62%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
C VCGDKASG HYGV SC+GC+GFF+RS+ + Y CK C +D+ R +CQ CR
Sbjct: 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLR 60
Query: 123 KCLQVKMNRDAM 134
KC M D +
Sbjct: 61 KCKAAGMRPDCL 72
>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 = 82.4 bits (204), Expect = 5e-22
Identities = 30/69 (43%), Positives = 44/69 (63%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C VCGD+A+G H+ +C+GC+GFF+RS++R + C G C + R CQACR K
Sbjct: 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKK 60
Query: 124 CLQVKMNRD 132
CL + M ++
Sbjct: 61 CLDIGMKKE 69
>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 = 82.6 bits (204), Expect = 7e-22
Identities = 32/67 (47%), Positives = 46/67 (68%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
LC +C DKA+G HYG+ +C+GC+GFFKR+++ Y C G C + +RN+CQ CRF
Sbjct: 8 LCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFR 67
Query: 123 KCLQVKM 129
KC++ M
Sbjct: 68 KCIRKGM 74
>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 = 82.6 bits (204), Expect = 7e-22
Identities = 34/67 (50%), Positives = 45/67 (67%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
LC VCGD+ASG HY +C+GC+GFF+RS+ ++ Y CK C +D+ R +CQ CR
Sbjct: 3 LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLK 62
Query: 123 KCLQVKM 129
KCL V M
Sbjct: 63 KCLSVGM 69
>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 = 80.4 bits (198), Expect = 6e-21
Identities = 30/70 (42%), Positives = 49/70 (70%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
+C+VCGD+A+G H+ +C+GC+GFF+R+++RN C + C++ + R QCQACR
Sbjct: 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLR 60
Query: 123 KCLQVKMNRD 132
KCL + M ++
Sbjct: 61 KCLSIGMKKE 70
>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 = 79.1 bits (195), Expect = 1e-20
Identities = 30/70 (42%), Positives = 46/70 (65%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C+VCG K+SG H+G +C+GC+GFF+R+ + YVC +C + RN C++CRF +
Sbjct: 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRR 60
Query: 124 CLQVKMNRDA 133
CL V M++
Sbjct: 61 CLAVGMSKTG 70
>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 = 79.1 bits (195), Expect = 1e-20
Identities = 36/71 (50%), Positives = 44/71 (61%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
+C VC D+ASG HYGV +C C+ FFKR++ Y+C R CI+D RR C ACR
Sbjct: 4 ICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLR 63
Query: 123 KCLQVKMNRDA 133
KCLQ MN A
Sbjct: 64 KCLQAGMNLGA 74
>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 = 75.0 bits (184), Expect = 5e-19
Identities = 34/70 (48%), Positives = 41/70 (58%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C +CGD+ASG HYGV +C C+ FFKR+ Y+C R CI+D RR C ACR K
Sbjct: 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRK 60
Query: 124 CLQVKMNRDA 133
C Q M A
Sbjct: 61 CYQAGMTLGA 70
>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 = 73.4 bits (180), Expect = 5e-18
Identities = 28/70 (40%), Positives = 45/70 (64%)
Query: 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFS 122
+C VCGD+A+G H+ +C+GC+GFF+RS++R + C G C + R CQACR
Sbjct: 8 ICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLK 67
Query: 123 KCLQVKMNRD 132
+C+ + M ++
Sbjct: 68 RCVDIGMMKE 77
>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 = 67.6 bits (165), Expect = 5e-16
Identities = 29/66 (43%), Positives = 39/66 (59%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C +CGD+ASG HYG +C C+ FFKR+ +Y+C R C +D RR C +CR K
Sbjct: 6 CLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRK 65
Query: 124 CLQVKM 129
C + M
Sbjct: 66 CFEAGM 71
>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 = 67.9 bits (166), Expect = 5e-16
Identities = 26/69 (37%), Positives = 40/69 (57%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSK 123
C VCGDKA G ++ +C+ C+ FF+R+ +N E+ C C ++V R CQ CR K
Sbjct: 3 CGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDK 62
Query: 124 CLQVKMNRD 132
C + M ++
Sbjct: 63 CFAIGMKKE 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 = 66.4 bits (162), Expect = 1e-15
Identities = 30/68 (44%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNL--EYVCKERGHCIVDVTRRNQCQACRF 121
C+VCG+ A+G H+G C+ C+ FF RS C G CI+D R +CQACR+
Sbjct: 3 CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRY 62
Query: 122 SKCLQVKM 129
KCL V M
Sbjct: 63 RKCLNVGM 70
>gnl|CDD|216212 pfam00955, HCO3_cotransp, HCO3- transporter family. This family
contains Band 3 anion exchange proteins that exchange
CL-/HCO3-. This family also includes cotransporters of
Na+/HCO3-.
Length = 501
Score = 31.1 bits (71), Expect = 0.14
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 3/37 (8%)
Query: 24 FILPGVSTMVKASLRTLLFISMSSFFPVFVWTGITSM 60
F+L G+S ++ L+ FI M F VF++ G+TS+
Sbjct: 429 FLLVGLSVLMAPILK---FIPMPVLFGVFLYMGVTSL 462
>gnl|CDD|218878 pfam06061, Baculo_ME53, Baculoviridae ME53. ME53 is one of the
major early-transcribed genes. The ME53 protein is
reported to contain a putative zinc finger motif.
Length = 326
Score = 30.4 bits (69), Expect = 0.21
Identities = 13/43 (30%), Positives = 17/43 (39%)
Query: 57 ITSMDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYV 99
I D+L C D K +CD C FK + R+ Y
Sbjct: 31 INVNDLLLMGCADLKKVKLVQTTTCDKCGKKFKDNTRKWYLYC 73
>gnl|CDD|177084 CHL00182, tatC, Sec-independent translocase component C;
Provisional.
Length = 249
Score = 28.8 bits (65), Expect = 0.87
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 20 QINFFILPGVSTMVKASLRTLLFISMSSFFPVFVWTGI 57
QI FILPG + K + +L + +SS V G+
Sbjct: 100 QIILFILPG---LTKKERKIILPLLISSL--VLFGLGL 132
>gnl|CDD|114907 pfam06215, ISAV_HA, Infectious salmon anaemia virus haemagglutinin.
This family consists of several infectious salmon
anaemia virus haemagglutinin proteins. Infectious salmon
anaemia virus (ISAV), an orthomyxovirus-like virus, is
an important fish pathogen in marine aquaculture.
Length = 391
Score = 28.8 bits (64), Expect = 0.92
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 36 SLRTLLFISMSSFFPVFVWTGITSMDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIR 93
S++ L F S P V G+ M + KVC SG GV +GC G+F +R
Sbjct: 147 SVKVLTFSS-----PTIVVVGLNGMSGIYKVCIAATSGNVGGVNLINGC-GYFNTPLR 198
>gnl|CDD|233143 TIGR00834, ae, anion exchange protein. The Anion Exchanger (AE)
Family (TC 2.A.31)Characterized protein members of the
AE family are found only in animals.They preferentially
catalyze anion exchange (antiport) reactions, typically
acting as HCO3-:Cl- antiporters, but also transporting a
range of other inorganic and organic anions.
Additionally, renal Na+:HCO3- cotransporters have been
found to be members of the AE family. They catalyze the
reabsorption of HCO3- in the renal proximal tubule
[Transport and binding proteins, Anions].
Length = 900
Score = 29.0 bits (65), Expect = 0.93
Identities = 10/37 (27%), Positives = 23/37 (62%), Gaps = 3/37 (8%)
Query: 24 FILPGVSTMVKASLRTLLFISMSSFFPVFVWTGITSM 60
+L G+S +++ L+ I ++ F +F++ G+TS+
Sbjct: 757 AVLVGLSILMEPILK---RIPLAVLFGIFLYMGVTSL 790
>gnl|CDD|172788 PRK14300, PRK14300, chaperone protein DnaJ; Provisional.
Length = 372
Score = 27.7 bits (61), Expect = 1.8
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 59 SMDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYV------CKERGHCIVDVTR 112
S +V C C S K V +CD C G +++ + C+ G I
Sbjct: 143 SSEVKCDTCHGSGSEKGETVTTCDACSGVGATRMQQGFFTIEQACHKCQGNGQII----- 197
Query: 113 RNQCQAC 119
+N C+ C
Sbjct: 198 KNPCKKC 204
>gnl|CDD|217128 pfam02592, DUF165, Uncharacterized ACR, YhhQ family COG1738.
Length = 143
Score = 26.8 bits (60), Expect = 2.5
Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 16 RKNTQINFFIL-PGVSTMVKASLRTLLFISMSSFFPVFVWTGITSM 60
++ T+ L ST+V + TL+F ++ +F+ +F + S+
Sbjct: 91 KRRTKGKHLWLRNNGSTLVSQLVDTLIFFTI-AFYGIFPAETLLSI 135
>gnl|CDD|237749 PRK14543, PRK14543, nucleoside diphosphate kinase; Provisional.
Length = 169
Score = 26.4 bits (58), Expect = 4.8
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 42 FISMSSFFPVFVWTGITSMDVLCKVCG 68
FIS S F VFV G+ S++V+ K CG
Sbjct: 73 FISSSPVF-VFVVEGVESVEVVRKFCG 98
>gnl|CDD|236724 PRK10604, PRK10604, sensor protein RstB; Provisional.
Length = 433
Score = 26.1 bits (58), Expect = 6.3
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 40 LLFISMSSFFPVFVW 54
L I +S FPVF+W
Sbjct: 142 LALIGLSLAFPVFLW 156
>gnl|CDD|237199 PRK12772, PRK12772, bifunctional flagellar biosynthesis protein
FliR/FlhB; Provisional.
Length = 609
Score = 26.2 bits (58), Expect = 6.8
Identities = 10/45 (22%), Positives = 17/45 (37%)
Query: 8 LAETIDHGRKNTQINFFILPGVSTMVKASLRTLLFISMSSFFPVF 52
L + + K T I F + SL +L I++ +F
Sbjct: 305 LGGYVANTLKETMIYFLNNYLNMNLNYNSLNSLAIITLLRVAKIF 349
>gnl|CDD|214418 MTH00071, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 322
Score = 25.7 bits (57), Expect = 8.5
Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 23 FFILPGVST---MVKASLRTLLFISMSSFFPVF 52
+ P +ST M+KAS+ ++LF+ + + +P F
Sbjct: 253 NHLQPELSTMNLMIKASILSMLFLWVRASYPRF 285
>gnl|CDD|237658 PRK14284, PRK14284, chaperone protein DnaJ; Provisional.
Length = 391
Score = 26.0 bits (57), Expect = 8.7
Identities = 18/69 (26%), Positives = 21/69 (30%), Gaps = 23/69 (33%)
Query: 64 CKVCGDKASGKHYGVPSCDGC---------RGFFKRSIRRNLEYVCKE---RGHCIVDVT 111
C C + G+ CD C RGFF + C E G I D
Sbjct: 161 CDACSGSGANSSQGIKVCDRCKGSGQVVQSRGFFSMAS------TCPECGGEGRVITD-- 212
Query: 112 RRNQCQACR 120
C CR
Sbjct: 213 ---PCSVCR 218
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 25.7 bits (57), Expect = 9.0
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 34 KASLRTLLFISMSSF 48
KASL T FIS +SF
Sbjct: 1171 KASLNTDSFISAASF 1185
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
0.329 0.140 0.455
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: 6,453,431
Number of extensions: 534528
Number of successful extensions: 727
Number of sequences better than 10.0: 1
Number of HSP's gapped: 719
Number of HSP's successfully gapped: 69
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (24.4 bits)