RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10221
(67 letters)
>gnl|CDD|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH). The
first LIM domain of Arrowhead (AWH): Arrowhead belongs
to the LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Members of LHX family are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 81.3 bits (201), Expect = 8e-23
Identities = 33/54 (61%), Positives = 41/54 (75%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CGE ITD++LL+VS +SWH CLRCC+CQ L+R PSCF +D +YCK DY
Sbjct: 1 CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9
family. The first LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Although Lhx2 and Lhx9 are highly homologous, they
seems to play regulatory roles in different organs. In
animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. Lhx9 is expressed in several
regions of the developing mouse brain , the spinal
cord, the pancreas, in limb mesenchyme, and in the
urogenital region. Lhx9 plays critical roles in gonad
development. Homozygous mice lacking functional Lhx9
alleles exhibit numerous urogenital defects, such as
gonadal agenesis, infertility, and undetectable levels
of testosterone and estradiol coupled with high FSH
levels. Lhx9 null mice are phenotypically female, even
those that are genotypically male. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 54
Score = 64.7 bits (158), Expect = 3e-16
Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CGE I D++ L D+ WHA CL+CC C+L LD SCF +D +YCK+DY
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8.
The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as
the pituitary gland and the pancreas. Studies using
mutant mice have revealed roles for Lhx7 and Lhx8 in
the development of cholinergic neurons in the
telencephalon and in basal forebrain development. Mice
lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8
display dramatically reduced number of forebrain
cholinergic neurons. In addition, Lhx7 mutation affects
male and female mice differently, with females
appearing more affected than males. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 56
Score = 59.6 bits (144), Expect = 4e-14
Identities = 29/54 (53%), Positives = 39/54 (72%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C +CG I DKYLL+V+D WH +CL C +C+ L RH SC+IKD+ ++CK DY
Sbjct: 2 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 55
>gnl|CDD|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2. The first LIM
domain of Lhx2: Lhx2 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. The Lhx2 protein has been shown
to bind to the mouse M71 olfactory receptor promoter.
Similar to other LIM domains, this domain family is
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 64
Score = 56.9 bits (137), Expect = 4e-13
Identities = 27/54 (50%), Positives = 37/54 (68%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG I+D+Y L DK WH +CL+CC C+L L+ +CF KD ++YCK+DY
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX
protein family. The first LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved
members of this family. Proteins in this group are
found in the nucleus and act as transcription factors
or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Isl-1 is one of
the LHX proteins isolated originally by virtue of its
ability to bind DNA sequences from the 5'-flanking
region of the rat insulin gene in pancreatic
insulin-producing cells. Mice deficient in Isl-1 fail
to form the dorsal exocrine pancreas and islet cells
fail to differentiate. On the other hand, Isl-1 takes
part in the pituitary development by activating the
gonadotropin-releasing hormone receptor gene together
with LHX3 and steroidogenic factor 1. Mouse Is l2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Same as Isl1, Isl2 may also be able
to bind to the insulin gene enhancer to promote gene
activation. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 56.6 bits (137), Expect = 5e-13
Identities = 27/55 (49%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 12 CVACGESITDKYLLQVS-DKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
CV CG I D+Y+L+V+ D WHA CL+C C LD +CF++D YCK+DY
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>gnl|CDD|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9. The first LIM
domain of Lhx9: Lhx9 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx9 is highly homologous to Lhx2. It is expressed in
several regions of the developing mouse brain, the
spinal cord, the pancreas, in limb mesenchyme, and in
the urogenital region. Lhx9 plays critical roles in
gonad development. Homozygous mice lacking functional
Lhx9 alleles exhibit numerous urogenital defects, such
as gonadal agenesis, infertility, and undetectable
levels of testosterone and estradiol coupled with high
FSH levels. Lhx9 null mice have reduced levels of the
Sf1 nuclear receptor that is required for
gonadogenesis, and recent studies have shown that Lhx9
is able to activate the Sf1/FtzF1 gene. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 54
Score = 54.7 bits (131), Expect = 3e-12
Identities = 27/54 (50%), Positives = 37/54 (68%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG I+D+Y L DK WH +CL+CC C+L L+ +CF KD ++YCK+DY
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b. The first
LIM domain of Lmx1b: Lmx1b belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In mouse, Lmx1b functions in the developing limbs and
eyes, the kidneys, the brain, and in cranial
mesenchyme. The disruption of Lmx1b gene results kidney
and limb defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 54.3 bits (131), Expect = 4e-12
Identities = 26/54 (48%), Positives = 38/54 (70%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C I+D+YLL+V+++SWH +CL+C +CQ L SC+ +D +YCKQDY
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPL--TTSCYFRDRKLYCKQDY 52
>gnl|CDD|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6. The first LIM
domain of Lhx6. Lhx6 is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Lhx6 functions in the brain and nervous system. It is
expressed at high levels in several regions of the
embryonic mouse CNS, including the telencephalon and
hypothalamus, and the first branchial arch. Lhx6 is
proposed to have a role in patterning of the mandible
and maxilla, and in signaling during odontogenesis. In
brain sections, knockdown of Lhx6 gene blocks the
normal migration of neurons to the cortex. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 54
Score = 54.3 bits (130), Expect = 5e-12
Identities = 25/54 (46%), Positives = 39/54 (72%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C +CG I D+YLL+V++ WH +CL C +C+ L +H SC+IK++ ++CK DY
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain,
containing two zinc fingers. LIM domains are
identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. LIM domains
are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. The consensus sequence of LIM
domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 53
Score = 50.0 bits (120), Expect = 2e-10
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG+ I + LL+ K WH +C +C +C L S + KD YC++ Y
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLG-GDSFYEKDGKPYCEKCY 53
>gnl|CDD|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a. The first
LIM domain of Lmx1a: Lmx1a belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. Human Lmx1a can be found in pancreas,
skeletal muscle, adipose tissue, developing brain,
mammary glands, and pituitary. The functions of Lmx1a
in the developing nervous system were revealed by
studies of mutant mouse. In mouse, mutations in Lmx1a
result in failure of the roof plate to develop. Lmx1a
may act upstream of other roof plate markers such as
MafB, Gdf7, Bmp 6, and Bmp7. Further characterization
of these mice reveals numerous defects including
disorganized cerebellum, hippocampus, and cortex;
altered pigmentation; female sterility; skeletal
defects; and behavioral abnormalities. Within
pancreatic cells, the Lmx1a protein interacts
synergistically with the bHLH transcription factor E47
to activate the insulin gene enhancer/promoter. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 52
Score = 50.2 bits (120), Expect = 2e-10
Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C I D++LL+V+D WH +CL+C C+ L +CF +D+ +YCK+DY
Sbjct: 1 CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPL--ETTCFYRDKKLYCKEDY 52
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
The LHX3 and LHX4 LIM-homeodomain transcription factors
play essential roles in pituitary gland and nervous
system development. Although LHX3 and LHX4 share marked
sequence homology, the genes have different expression
patterns. They play overlapping, but distinct functions
during the establishment of the specialized cells of
the mammalian pituitary gland and the nervous system.
Lhx3 proteins have been demonstrated the ability to
directly bind to the promoters/enhancers of several
pituitary hormone gene promoters to cause increased
transcription. Lhx3a and Lhx3b, whose mRNAs have
distinct temporal expression profiles during
development, are two isoforms of Lhx3. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 52
Score = 49.3 bits (118), Expect = 4e-10
Identities = 23/54 (42%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C E I D+++L+V D++WHA+CL+C C L CF ++ VYCK D+
Sbjct: 1 CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTD--KCFARNGHVYCKDDF 52
>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a. The first
LIM domain of Lhx3a: Lhx3a is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 56
Score = 48.6 bits (116), Expect = 7e-10
Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C I D+++L+V DK WH++CL+C CQ L CF + VYCK+D+
Sbjct: 4 CAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTD--KCFSRGGQVYCKEDF 55
>gnl|CDD|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only
protein 4). The first LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact
with Smad proteins, and associate with the promoter of
the PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential
role for LMO4 as a negative regulator of BRCA1 in
sporadic breast cancer. LMO4 also forms complex to
both ERa (oestrogen receptor alpha), MTA1 (metastasis
tumor antigen 1), and HDACs (histone deacetylases),
implying that LMO4 is also a component of the MTA1
corepressor complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 47.4 bits (113), Expect = 2e-09
Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDY 65
C CG I D++LL D+ WH CL+C CQ L + SC+ K + CK DY
Sbjct: 1 CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 47.3 bits (113), Expect = 3e-09
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 12 CVACGESITDKYLLQVS-DKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
C CG+ I D+ L++ + K WH +C RC +C L F KD +YCK DY K
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPG-DFFEKDGKLYCKHDYFK 56
>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4. The first LIM
domain of Lhx4. Lhx4 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows
significant sequence similarity to LHX3, particularly
to isoforms Lhx3a. In gene regulation experiments, the
LHX4 protein exhibits regulation roles towards
pituitary genes, acting on their promoters/enhancers.
As in other LIM domains, this domain family is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 52
Score = 46.1 bits (109), Expect = 6e-09
Identities = 23/54 (42%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C + I DK++L+V D+ WH+ CL+C CQ+ L CF + VYCK+D+
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAER--CFSRAGNVYCKEDF 52
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx1 is required
for regulating the vertebrate head organizer, the
nervous system, and female reproductive tract
development. During embryogenesis in the mouse, Lhx1 is
expressed early in mesodermal tissue, then later during
urogenital, kidney, liver, and nervous system
development. In the adult, expression is restricted to
the kidney and brain. A mouse embryos with Lhx1 gene
knockout cannot grow normal anterior head structures,
kidneys, and gonads, but with normally developed trunk
and tail morphology. In the developing nervous system,
Lhx1 is required to direct the trajectories of motor
axons in the limb. Lhx1 null female mice lack the
oviducts and uterus. Lhx5 protein may play
complementary or overlapping roles with Lhx1. The
expression of Lhx5 in the anterior portion of the mouse
neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 45.5 bits (108), Expect = 1e-08
Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C I DK+LL V D++WHA+C++CC C+ L CF ++ +YC+ D+
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTE--KCFSREGKLYCRNDF 52
>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b. The first
LIM domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 45.7 bits (108), Expect = 1e-08
Identities = 22/54 (40%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C + I D+++L+V D+ WH++CL+C CQ L CF + ++VYCK D+
Sbjct: 4 CAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAE--KCFSRGDSVYCKDDF 55
>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain
Kinase 1). The first LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture
of the actin cytoskeleton by regulating the activity of
the cofilin family proteins cofilin1, cofilin2, and
destrin. The mechanism of the activation is to
phosphorylates cofilin on serine 3 and inactivates its
actin-severing activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. LIMK1 is expressed in all tissues and is
localized to focal adhesions in the cell. LIMK1 can
form homodimers upon binding of HSP90 and is activated
by Rho effector Rho kinase and MAPKAPK2. LIMK1 is
important for normal central nervous system
development, and its deletion has been implicated in
the development of the human genetic disorder Williams
syndrome. Moreover, LIMK1 up-regulates the promoter
activity of urokinase type plasminogen activator and
induces its mRNA and protein expression in breast
cancer cells. The LIM domains have been shown to play
an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 74
Score = 43.3 bits (102), Expect = 1e-07
Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
L C +CG+SI D LQ + WHA C RCC C L + KD ++CK+DY
Sbjct: 17 NVLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHW--YYEKDGRLFCKKDY 73
>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1,
Mec-3. Zinc-binding domain family. Some LIM domains
bind protein partners via tyrosine-containing motifs.
LIM domains are found in many key regulators of
developmental pathways.
Length = 54
Score = 41.6 bits (98), Expect = 3e-07
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 12 CVACGESITD-KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64
C CG+ I + +L+ K WH +C +C C L + F KD +YCK
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPL-SGDTFFEKDGKLYCKDC 54
>gnl|CDD|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like
proteins. The second LIM domain of Ajuba-like
proteins: Ajuba like LIM protein family includes three
highly homologous proteins Ajuba, Limd1, and WTIP.
Members of the family contain three tandem C-terminal
LIM domains and a proline-rich N-terminal region. This
family of proteins functions as scaffolds,
participating in the assembly of numerous protein
complexes. In the cytoplasm, Ajuba binds Grb2 to
modulate serum-stimulated ERK activation. Ajuba also
recruits the TNF receptor-associated factor 6 (TRAF6)
to p62 and activates PKCKappa activity. Ajuba interacts
with alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 39.2 bits (92), Expect = 4e-06
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG I + +LQ KS+H C RCC+C LD P + +YC +DY
Sbjct: 1 CAVCGHLIMEM-ILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain
Kinase ). The first LIM domain of LIMK (LIM domain
Kinase ): LIMK protein family is comprised of two
members LIMK1 and LIMK2. LIMK contains two LIM domains,
a PDZ domain and a kinase domain. LIMK is involved in
the regulation of actin polymerization and microtubule
disassembly. LIMK influences architecture of the actin
cytoskeleton by regulating the activity of the cofilin
family proteins cofilin1, cofilin2, and destrin. The
mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerisation. LIMKs can function in both cytoplasm
and nucleus and are expressed in all tissues. Both
LIMK1 and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. However,
LIMK1 and LIMk2 have different cellular locations.
While LIMK1 localizes mainly at focal adhesions, LIMK2
is found in cytoplasmic punctae, suggesting that they
may have different cellular functions. The LIM domains
of LIMK have been shown to play an important role in
regulating kinase activity and likely also contribute
to LIMK function by acting as sites of
protein-to-protein interactions. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 38.2 bits (89), Expect = 9e-06
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C I D +Q ++ WH C RC +C L F KD +YC++DY
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL--SNWYFEKDGKLYCRKDY 52
>gnl|CDD|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The first LIM
domain of LMO1 and LMO3 (LIM domain only protein 1 and
3): LMO1 and LMO3 are highly homologous and belong to
the LMO protein family. LMO1 and LMO3 are nuclear
protein that plays important roles in transcriptional
regulation and development. As LIM domains lack
intrinsic DNA-binding activity, nuclear LMOs are
involved in transcriptional regulation by forming
complexes with other transcription factors or
cofactors. For example, LMO1 interacts with the the
bHLH domain of bHLH transcription factor, TAL1 (T-cell
acute leukemia1)/SCL (stem cell leukemia) . LMO1
inhibits the expression of TAL1/SCL target genes. LMO3
facilitates p53 binding to its response elements, which
suggests that LMO3 acts as a co-repressor of p53,
suppressing p53-dependent transcriptional regulation.
In addition, LMO3 interacts with neuronal transcription
factor, HEN2, and acts as an oncogene in neuroblastoma.
Another binding partner of LMO3 is calcium- and
integrin-binding protein CIB, which binds via the
second LIM domain (LIM2) of LMO3. One role of the
CIB/LMO3 complex is to inhibit cell proliferation.
Although LMO1 and LMO3 are highly homologous proteins,
they play different roles in the regulation of the
pituitary glycoprotein hormone alpha-subunit (alpha
GSU) gene. Alpha GSU promoter activity was markedly
repressed by LMO1 but activated by LMO3. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 37.9 bits (88), Expect = 1e-05
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSC-FIKDEAVYCKQDY 65
C C I D+YLL+ D+ WH CL+C C L S + K + C++DY
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain
Kinase 2). The first LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein
family, which comprises LIMK1 and LIMK2. LIMK contains
two LIM domains, a PDZ domain, and a kinase domain.
LIMK is involved in the regulation of actin
polymerization and microtubule disassembly. LIMK
influences architecture of the actin cytoskeleton by
regulating the activity of the cofilin family proteins
cofilin1, cofilin2, and destrin. The mechanism of the
activation is to phosphorylates cofilin on serine 3 and
inactivates its actin-severing activity, altering the
rate of actin depolymerization. LIMK activity is
activated by phosphorylation of a threonine residue
within the activation loop of the kinase by
p21-activated kinases 1 and 4 and by Rho kinase. LIMKs
can function in both cytoplasm and nucleus. Both LIMK1
and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is
expressed in all tissues. While LIMK1 localizes mainly
at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 34.8 bits (80), Expect = 2e-04
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG I D + +V ++WH C +C +CQ +L + KD +YC + Y
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNW--YYEKDGKLYCHKHY 52
>gnl|CDD|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only
protein 2). The first LIM domain of LMO2 (LIM domain
only protein 2): LMO2 is a nuclear protein that plays
important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex
that is capable of transcriptional activation. LMOs
have also been shown to be involved in oncogenesis.
LMO1 and LMO2 are activated in T-cell acute
lymphoblastic leukemia by distinct chromosomal
translocations. LMO2 was also shown to be involved in
erythropoiesis and is required for the hematopoiesis in
the adult animals. All LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 34.4 bits (79), Expect = 3e-04
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL---DRHPSCFIKDEAVYCKQDY 65
C C ++I D+Y L+ D+ WH CL C +C L R + K C++DY
Sbjct: 1 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRR--LYYKLGRKLCRRDY 55
>gnl|CDD|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM
(abLIM) proteins. The third LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to
function as a tumor suppressor. AbLIM-2 and -3, mainly
expressed in muscle and neuronal tissue, bind to
F-actin strongly. They may serve as a scaffold for
signaling modules of the actin cytoskeleton and thereby
modulate transcription. It has shown that LIM domains
of abLIMs interact with STARS (striated muscle
activator of Rho signaling), which directly binds actin
and stimulates serum-response factor (SRF)-dependent
transcription. All LIM domains are 50-60 amino acids in
size and share two characteristic highly conserved zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 33.1 bits (76), Expect = 0.001
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG+ I + L DK WH C +C C VL KD YC++DY
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVL--TGEYMGKDGKPYCERDY 52
>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin. The second
LIM domain of Zyxin: Zyxin exhibits three copies of the
LIM domain, an extensive proline-rich domain and a
nuclear export signal. Localized at sites of
cellsubstratum adhesion in fibroblasts, Zyxin interacts
with alpha-actinin, members of the cysteine-rich
protein (CRP) family, proteins that display Src
homology 3 (SH3) domains and Ena/VASP family members.
Zyxin and its partners have been implicated in the
spatial control of actin filament assembly as well as
in pathways important for cell differentiation. In
addition to its functions at focal adhesion plaques,
recent work has shown that zyxin moves from the sites
of cell contacts to the nucleus, where it directly
participates in the regulation of gene expression. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors o r scaffolds to support the
assembly of multimeric protein.
Length = 60
Score = 33.0 bits (75), Expect = 0.001
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEA--VYCKQDYAK 67
C C + ITD+ +L+ + KS+H QC C +C+ L+ FI D+A +C DY +
Sbjct: 1 CAVCDQKITDR-MLKATGKSYHPQCFTCVVCKCPLEGES--FIVDQANQPHCVNDYHR 55
>gnl|CDD|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred
partner (LPP). The second LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at
the N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of
cell adhesion, cell-cell contacts and transiently in
the nucleus. In nucleus, it acts as a coactivator for
the ETS domain transcription factor PEA3. In addition
to PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and
vasodilator- stimulated phosphoprotein (VASP), has a
weak targeting capacity. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 60
Score = 30.6 bits (69), Expect = 0.009
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
C C + I D+ +L+ + K +H QC C +C LD P ++C +D+ K
Sbjct: 1 CSVCSKPILDR-ILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHK 55
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a
Rho-type GTPase activating protein (RhoGap) domain. Rga
activates GTPases during polarized morphogenesis. In
yeast, a known regulating target of Rga is CDC42p, a
small GTPase. The LIM domain is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 55
Score = 30.4 bits (69), Expect = 0.012
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCIC 42
CV C ESIT+ + ++ WH C +C C
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKC 31
>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and
Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a
and Lmx1b belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. In mouse, mutations in Lmx1a result in
failure of the roof plate to develop. Lmx1a may act
upstream of other roof plate markers such as MafB,
Gdf7, Bmp6, and Bmp7. Further characterization of these
mice reveals numerous defects including disorganized
cerebellum, hippocampus, and cortex; altered
pigmentation; female sterility, skeletal defects, and
behavioral abnormalities. In the mouse, Lmx1b
functions in the developing limbs and eyes, the
kidneys, the brain, and in cranial mesenchyme. The
disruption of Lmx1b gene results kidney and limb
defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 29.7 bits (67), Expect = 0.017
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C E I + +++ + +H +C CC+C+ L + +K+ + CK DY
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin. The
first LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 29.1 bits (65), Expect = 0.032
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C +C + I + + + ++WH + CC C L P F ++ YC++DY
Sbjct: 3 CASCQKPIAGQVVTALG-QTWHPEHFVCCQCGKELGSRPF-FERNGQAYCEEDY 54
>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1. The Lim domain of DA1:
DA1 contains one copy of LIM domain and a domain of
unknown function. DA1 is predicted as an ubiquitin
receptor, which sets final seed and organ size by
restricting the period of cell proliferation. The LIM
domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 28.8 bits (65), Expect = 0.040
Identities = 10/31 (32%), Positives = 11/31 (35%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCIC 42
C C I L WH +C RC C
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHAC 31
>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP). The second LIM domain of
Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich
proteins (CRPs) are characterized by the presence of
two LIM domains linked to short glycine-rich repeats
(GRRs). The CRP family members include CRP1, CRP2,
CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved
nuclear targeting signal (K/R-K/R-Y-G-P-K), which
supports the fact that these proteins function not only
in the cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation,
and involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network.CRP3 also called
Muscle LIM Protein (MLP), which is a striated
muscle-specific factor that enhances myogenic
differentiation. The second LIM domain of CRP3/MLP
interacts with cytoskeletal protein beta-spectrin.
CRP3/MLP also interacts with the basic helix-loop-helix
myogenic transcription factors MyoD, myogenin, and MRF4
thereby increasing their affinity for specific DNA
regulatory elements. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 28.8 bits (64), Expect = 0.045
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
C CG+S+ + K WH C RC IC L+ + KD +YCK YA
Sbjct: 1 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLES-TTVTDKDGELYCKVCYA 54
>gnl|CDD|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich
Protein 2 (CRP2). The second LIM domain of Cysteine
Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs)
are characterized by the presence of two LIM domains
linked to short glycine-rich repeats (GRRs). The CRP
family members include CRP1, CRP2, CRP3/MLP and
TLPCRP1, CRP2 and CRP3 share a conserved nuclear
targeting signal (K/R-K/R-Y-G-P-K), which supports the
fact that these proteins function not only in the
cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation,
and involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network.CRP3 also called
Muscle LIM Protein (MLP), which is a striated
muscle-specific factor that enhances myogenic
differentiation. The second LIM domain of CRP3/MLP
interacts with cytoskeletal protein beta-spectrin.
CRP3/MLP also interacts with the basic helix-loop-helix
myogenic transcription factors MyoD, myogenin, and MRF4
thereby increasing their affinity for specific DNA
regulatory elements. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 28.9 bits (64), Expect = 0.050
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
C CG+S+ + + K WH C RC C L+ + K+ +YCK YA
Sbjct: 1 CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLES-TTLTEKEGEIYCKGCYA 54
>gnl|CDD|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein
(CRP). The second LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function
not only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the
arrangement of the myofibrillar/cytoskeletal network.
It is evident that CRP1, CRP2, and CRP3/MLP are
involved in promoting protein assembly along the
actin-based cytoskeleton. Although members of the CRP
family share common binding partners, they are also
capable of recognizing different and specific targets.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residu es, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 28.7 bits (64), Expect = 0.050
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
C CG+S+ + + K WH C RC C L+ + KD +YCK YA
Sbjct: 1 CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLES-TTLADKDGEIYCKGCYA 54
>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The third LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 56
Score = 28.1 bits (63), Expect = 0.073
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPS---CFIKDEAVYCKQ 63
C +CG+SI D+ ++ DK WH +C C C + S KD+ + C
Sbjct: 1 CASCGKSIEDE-CIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSN 54
>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX
protein family. The second LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved
members of this family. Proteins in this group are
found in the nucleus and act as transcription factors
or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Isl-1 is one of
the LHX proteins isolated originally by virtue of its
ability to bind DNA sequences from the 5'-flanking
region of the rat insulin gene in pancreatic
insulin-producing cells. Mice deficient in Isl-1 fail
to form the dorsal exocrine pancreas and islet cells
fail to differentiate. On the other hand, Isl-1 takes
part in the pituitary development by activating the
gonadotropin-releasing hormone receptor gene together
with LHX3 and steroidogenic factor 1. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Same as Isl1, Isl2 may also be able
to bind to the insulin gene enhancer to promote gene
activation. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 28.2 bits (63), Expect = 0.081
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C +S + + ++++ K +H +C RC C L ++D+ ++CK D+
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKADH 55
>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma. The
second LIM domain of Enigma: Enigma was initially
characterized in humans as a protein containing three
LIM domains at the C-terminus and a PDZ domain at
N-terminus. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes, such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. Enigma is expressed in multiple
tissues, such as skeletal muscle, heart, bone and
brain. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 28.0 bits (62), Expect = 0.087
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C + IT + ++ +WH C C C+ + R+ + ++++ A YC++DY
Sbjct: 1 CAKCKKKITGE-IMHALKMTWHVHCFTCAACKTPI-RNRAFYMEEGAPYCERDY 52
>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM
(abLIM) proteins. The first LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to
function as a tumor suppressor. AbLIM-2 and -3, mainly
expressed in muscle and neuronal tissue, bind to
F-actin strongly. They may serve as a scaffold for
signaling modules of the actin cytoskeleton and thereby
modulate transcription. It has shown that LIM domains
of abLIMs interact with STARS (striated muscle
activator of Rho signaling), which directly binds actin
and stimulates serum-response factor (SRF)-dependent
transcription. All LIM domains are 50-60 amino acids in
size and share two characteristic highly conserved zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 27.6 bits (62), Expect = 0.10
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 25 LQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
L+V DK +H +C C +C L F+K+ YC DY
Sbjct: 13 LRVQDKYFHIKCFTCKVCGCDL-AQGGFFVKEGEYYCTDDY 52
>gnl|CDD|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function.
The first Lim domain of a LIM domain containing
protein: The functions of the proteins are unknown. The
members of this family contain two copies of LIM
domain. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 58
Score = 27.6 bits (62), Expect = 0.12
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 12 CVACGESITDKYLLQVSDKS------WHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG I K +S K WH +C C C C++ D+ YC+Q Y
Sbjct: 1 CRKCGLEIEGK---SISSKDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The second LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved
in actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic
acid (LPA)-induced cell migration. TRIP6 can shuttle to
the nucleus to serve as a coactivator of AP-1 and
NF-kappaB transcriptional factors. Moreover, TRIP6 can
form a ternary complex with the NHERF2 PDZ protein and
LPA2 receptor to regulate LPA-induced activation of ERK
and AKT, rendering cells resistant to chemotherapy.
Recent evidence shows that TRIP6 antagonizes
Fas-Induced apoptosis by enhancing the antiapoptotic
effect of LPA in cells. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 53
Score = 27.5 bits (61), Expect = 0.12
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C + I ++ +L+ + K++H C C +C LD P ++C +D+
Sbjct: 1 CSVCSKPIMER-ILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53
>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein
2 (CRP2). The first LIM domain of Cysteine Rich
Protein 2 (CRP2): The CRP family members include CRP1,
CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a
conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function
not only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
circuits, and the organization as well as the
arrangement of the myofibrillar/cytoskeletal network.
CRP2 specifically binds to protein inhibitor of
activated STAT-1 (PIAS1) and a novel human protein
designed CRP2BP (for CRP2 binding partner). PIAS1
specifically inhibits the STAT-1 pathway and CRP2BP is
homologous to members of the histone acetyltransferase
family raising the possibility that CRP2 is a modulator
of cytokine-controlled pathways or is functionally
active in the transcriptional regulatory network. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 27.6 bits (61), Expect = 0.15
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
C ACG ++ +Q +S+H C C +C+ LD + I D+ +YCK Y
Sbjct: 2 CGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDS-TTVAIHDQEIYCKSCYG 55
>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4
family. The second LIM domain of Lhx3-Lhx4 family:
Lhx3 and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
The LHX3 and LHX4 LIM-homeodomain transcription factors
play essential roles in pituitary gland and nervous
system development. Although LHX3 and LHX4 share marked
sequence homology, the genes have different expression
patterns. They play overlapping, but distinct functions
during the establishment of the specialized cells of
the mammalian pituitary gland and the nervous system.
Lhx3 proteins have been demonstrated the ability to
directly bind to the promoters/enhancers of several
pituitary hormone gene promoters to cause increased
transcription.Lhx3a and Lhx3b, whose mRNAs have
distinct temporal expression profiles during
development, are two isoforms of Lhx3. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 56
Score = 27.3 bits (61), Expect = 0.18
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCF-IKDEAVYCKQDY 65
C C E I + + + D +H +C C +C+ L+ + ++D+ + CK+DY
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like
family. The first LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion
events. Prickles have been implicated in roles of
regulating tissue polarity or planar cell polarity
(PCP). Dyxin involves in lung and heart development by
interaction with GATA6 and blocking GATA6 activated
target genes. LIMPETin might be the recombinant product
of genes coding testin and four and half LIM proteins
and its function is not well understood. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 58
Score = 27.2 bits (61), Expect = 0.23
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 29 DKSWHAQCLRCCIC-QLVLDRHPSCFIKDEAVYCKQDY 65
D WH C C C +L++D F D +YC + Y
Sbjct: 23 DACWHPGCFVCETCNELLVDL--IYFYHDGKIYCGRHY 58
>gnl|CDD|188781 cd09395, LIM2_Rga, The second LIM domain of Rga
GTPase-Activating Proteins. The second LIM domain of
Rga GTPase-Activating Proteins: The members of this
family contain two tandem repeats of LIM domains and a
Rho-type GTPase activating protein (RhoGap) domain. Rga
activates GTPases during polarized morphogenesis. In
yeast, a known regulating target of Rga is CDC42p, a
small GTPase. The LIM domain is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 27.1 bits (60), Expect = 0.23
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQL 44
C CG+ I D +L SD+++ + C RC C
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSR 33
>gnl|CDD|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM
domains protein (FHL). The first LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in
tandem and an N-terminal single zinc finger domain
with a consensus sequence equivalent to the C-terminal
half of a LIM domain. LIMPETin is an exception,
containing six LIM domains. FHL1, 2 and 3 are
predominantly expressed in muscle tissues, and FHL5 is
highly expressed in male germ cells. FHL proteins
exert their roles as transcription co-activators or
co-repressors through a wide array of interaction
partners. For example, FHL1 binds to Myosin-binding
protein C, regulating myosin filament formation and
sarcomere assembly. FHL2 has shown to interact with
more than 50 different proteins, including receptors,
structural proteins, transcription factors and
cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
FHL3 int eracts with many transcription factors, such
as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 26.6 bits (59), Expect = 0.32
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 11 YCVACGESI-TDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C + I D L D+ WH C +C CQ L P KDE + C + Y
Sbjct: 4 TCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFA-AKDEDLLCTECY 58
>gnl|CDD|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase
domains protein (Ltd-1). The LIM domain of LIM and
transglutaminase domains protein (Ltd-1): This family
includes mouse Ky protein and Caenorhabditis elegans
Ltd-1 protein. The members of this family consists a
N-terminal Lim domain and a C-terminal
transglutaminase domain. The mouse Ky protein has
putative function in muscle development. The mouse with
ky mutant exhibits combined posterior and lateral
curvature of the spine. The Ltd-1 gene in C. elegans is
expressed in developing hypodermal cells from the
twofold stage embryo through adulthood. These data
define the ltd-1 gene as a novel marker for C. elegans
epithelial cell development. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 55
Score = 26.2 bits (58), Expect = 0.38
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIK-DEAVYCKQD 64
C CG++ + +H C +C C L F++ D VYC +
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54
>gnl|CDD|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function.
LIM domain in proteins of unknown function: LIM domains
are identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation, and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. The LIM
domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. The consensus sequence of LIM
domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 61
Score = 26.6 bits (59), Expect = 0.39
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCIC 42
C +CG + L + K +H C +C C
Sbjct: 5 CASCGLPVFLAERLLIEGKVYHRTCFKCARC 35
>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).
The LIM domain of LIM and SH3 Protein (LASP): LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their
LIM, nebulin-like, and SH3 domains ,but differ
significantly at their linker regions. Both proteins
are ubiquitously expressed and involved in cytoskeletal
architecture, especially in the organization of focal
adhesions. LASP-1 and LASP-2, are important during
early embryo- and fetogenesis and are highly expressed
in the central nervous system of the adult. However,
only LASP-1 seems to participate significantly in
neuronal differentiation and plays an important
functional role in migration and proliferation of
certain cancer cells while the role of LASP-2 is more
structural. The expression of LASP-1 in breast tumors
is increased significantly. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 53
Score = 26.2 bits (58), Expect = 0.40
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL 46
C CG+++ L DK WH C +C +C + L
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTL 35
>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also
known as Lim1) and Lhx5. The second LIM domain of Lhx1
(also known as Lim1) and Lhx5. Lhx1 and Lhx5 are
closely related members of LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx1 is required for regulating the vertebrate head
organizer, the nervous system, and female reproductive
tract development. During embryogenesis in the mouse,
Lhx1 is expressed early in mesodermal tissue, then
later during urogenital, kidney, liver, and nervous
system development. In the adult, expression is
restricted to the kidney and brain. A mouse embryos
with Lhx1 gene knockout cannot grow normal anterior
head structures, kidneys, and gonads, but with normally
developed trunk and tail morphology. In the developing
nervous system, Lhx1 is required to direct the
trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 56
Score = 26.2 bits (58), Expect = 0.47
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 12 CVACGESITDKYLL-QVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVY-CKQDY 65
C C + I+ L+ + DK +H C C +C+ L +I DE + CK+DY
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific
protein SF3. The second Lim domain of pollen specific
protein SF3: SF3 is a Lim protein that is found
exclusively in mature plant pollen grains. It contains
two LIM domains. The exact function of SF3 is unknown.
It may be a transcription factor required for the
expression of late pollen genes. It is possible that
SF3 protein is involved in controlling pollen-specific
processes such as male gamete maturation, pollen tube
formation, or even fertilization. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 61
Score = 26.3 bits (58), Expect = 0.51
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAV-YCKQDYAK 67
CVACG+++ + V S+H C +C + PS + E YCK +++
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTIS--PSNYAAHEGRLYCKHHHSQ 55
>gnl|CDD|221152 pfam11635, Med16, Mediator complex subunit 16. Mediator is a large
complex of up to 33 proteins that is conserved from
plants through fungi to humans - the number and
representation of individual subunits varying with
species. It is arranged into four different sections, a
core, a head, a tail and a kinase-activity part, and the
number of subunits within each of these is what varies
with species. Overall, Mediator regulates the
transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Med16 is one of the
subunits of the Tail portion of the Mediator complex and
is required for lipopolysaccharide gene-expression.
Several members including a human protein have one or
more WD40 domains on them, pfam00400.
Length = 744
Score = 27.0 bits (60), Expect = 0.53
Identities = 14/43 (32%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 1 MFKTIITELRYCVACGESITDKYLL-QVSDKSWHAQCLRCCIC 42
M +LR C CG Y ++ K W LR CIC
Sbjct: 696 MRPDSGGKLRRCTRCGSVSEAGYPPTSITTKRWTMMYLRTCIC 738
>gnl|CDD|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM
domains protein (FHL). The second LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in
tandem and an N-terminal single zinc finger domain with
a consensus sequence equivalent to the C-terminal half
of a LIM domain. LIMPETin is an exception, containing
six LIM domains. FHL1, 2 and 3 are predominantly
expressed in muscle tissues, and FHL5 is highly
expressed in male germ cells. FHL proteins exert their
roles as transcription co-activators or co-repressors
through a wide array of interaction partners. For
example, FHL1 binds to Myosin-binding protein C,
regulating myosin filament formation and sarcomere
assembly. FHL2 has shown to interact with more than 50
different proteins, including receptors, structural
proteins, transcription factors and cofactors, signal
transducers, splicing factors, DNA replication and
repair enzymes, and metabolic enzymes. FHL3 int eracts
with many transcription factors, such as CREB,
BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 25.7 bits (57), Expect = 0.65
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 12 CVACGESI--TDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFI-KDEAVYC 61
C ACG++I K ++ K WH +C C C+ + FI KD+ +YC
Sbjct: 1 CKACGKAIMPGSK-KMEYKGKFWHEKCFTCSECKKPIGTKS--FIPKDDKIYC 50
>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin. The
third LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 25.6 bits (56), Expect = 0.69
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCIC 42
C CG + + YL ++ WH +C C C
Sbjct: 1 CSGCGRPVKENYL-SAANGVWHPECFVCSDC 30
>gnl|CDD|188716 cd09330, LIM4_abLIM, The fourth LIM domain of actin binding LIM
(abLIM) proteins. The fourth LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to
function as a tumor suppressor. AbLIM-2 and -3, mainly
expressed in muscle and neuronal tissue, bind to
F-actin strongly. They may serve as a scaffold for
signaling modules of the actin cytoskeleton and thereby
modulate transcription. It has shown that LIM domains
of abLIMs interact with STARS (striated muscle
activator of Rho signaling), which directly binds actin
and stimulates serum-response factor (SRF)-dependent
transcription. All LIM domains are 50-60 amino acids in
size and share two characteristic highly conserved zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 25.8 bits (57), Expect = 0.74
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQ 43
C AC + IT K +L+ K +H C RC C
Sbjct: 1 CEACDKFITGK-VLEAGGKHYHPTCARCSRCG 31
>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH. The
second LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated
protein-protein interactions. PINCH comprises an array
of five LIM domains that interact with integrin-linked
kinase (ILK), Nck2 (also called Nckbeta or Grb4) and
other interaction partners. These interactions are
essential for triggering the FA assembly and for
relaying diverse mechanical and biochemical signals
between Cell-extracellular matrix and the actin
cytoskeleton. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 25.4 bits (56), Expect = 0.79
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL 46
C CGE + + +++ + +WH C RC IC L
Sbjct: 1 CGKCGEFVIGR-VIKAMNNNWHPDCFRCEICNKEL 34
>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL. The LIM domain of RIL:
RIL contains an N-terminal PDZ domain, a LIM domain,
and a short consensus C-terminal region. It is the
smallest molecule in the ALP LIM domain containing
protein family. RIL was identified in rat fibroblasts
and in human lymphocytes. The LIM domain interacts with
the AMPA glutamate receptor in dendritic spines. The
consensus C-terminus interacts with PTP-BL, a
submembranous protein tyrosine phosphatase and the PDZ
domain is responsible to interact with alpha-actinin
molecules. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 25.7 bits (56), Expect = 0.87
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK 62
C CG I +++ DK +H +C C C L L + FI DE +YC+
Sbjct: 1 CTRCGNGIVGT-IVKARDKLYHPECFMCDDCGLNLKQRGYFFI-DEQLYCE 49
>gnl|CDD|188797 cd09413, LIM1_Testin, The first LIM domain of Testin. The first
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction
domain at the N-terminal. Testin is a cytoskeleton
associated focal adhesion protein that localizes along
actin stress fibers, at cell-cell-contact areas, and at
focal adhesion plaques. Testin interacts with a variety
of cytoskeletal proteins, including zyxin, mena, VASP,
talin, and actin and it is involved in cell motility
and adhesion events. Knockout mice experiments reveal
that tumor repressor function of Testin. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 58
Score = 25.5 bits (56), Expect = 0.89
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 29 DKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
DK WH C C C +L F K+ +YC + Y
Sbjct: 23 DKLWHPACFVCSTCGELL-VDMIYFWKNGKLYCGRHY 58
>gnl|CDD|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein
(LASP)-like proteins. The LIM domain of LIM and SH3
Protein (LASP) like proteins: This family contains two
types of LIM containing proteins; LASP and N-RAP. LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their
LIM, nebulin-like, and SH3 domains, but differ
significantly at their linker regions. Both proteins
are ubiquitously expressed and involved in cytoskeletal
architecture, especially in the organization of focal
adhesions. LASP-1 and LASP-2, are important during
early embryo- and fetogenesis and are highly expressed
in the central nervous system of the adult. However,
only LASP-1 seems to participate significantly in
neuronal differentiation and plays an important
functional role in migration and proliferation of
certain cancer cells while the role of LASP-2 is more
structural. The expression of LASP-1 in breast tumors
is increased significantly. N-RAP is a muscle-specific
protein concentrated at myotendinous junctions in
skeletal muscle and intercalated disks in cardiac
muscle. LIM domain is found at the N-terminus of N-RAP
and the C-terminal of N-RAP contains a region with
multiple of nebulin repeats. N-RAP functions as a
scaffolding protein that organizes alpha-actinin and
actin into symmetrical I-Z-I structures in developing
myofibrils. Nebulin repeat is known as actin binding
domain. The N-RAP is hypothesized to form antiparallel
dimerization via its LIM domain. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 25.3 bits (55), Expect = 0.99
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLD 47
C CG+ + + DK+WH C C +C++ L+
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLN 36
>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like
proteins. The first LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate
serum-stimulated ERK activation. Ajuba also recruits
the TNF receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 54
Score = 25.1 bits (55), Expect = 1.1
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 12 CVACGESITD-KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
CV CG+ + Q +H C CC C L R + + + VYC++DY
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL-RGKAFYNVNGKVYCEEDY 54
>gnl|CDD|188821 cd09437, LIM3_LPP, The third LIM domain of lipoma preferred
partner (LPP). The third LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at
the N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of
cell adhesion, cell-cell contacts and transiently in
the nucleus. In nucleus, it acts as a coactivator for
the ETS domain transcription factor PEA3. In addition
to PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP), Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and
vasodilator- stimulated phosphoprotein (VASP), has a
weak targeting capacity. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 68
Score = 25.5 bits (56), Expect = 1.2
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 29 DKSWHAQCLRCCICQLVLDRHPS---CFIKDEAVYCKQDYAK 67
D+S+H QC +C C L+L C+ D+ V CK AK
Sbjct: 24 DRSFHVQCYKCEDCGLLLSSEAEGRGCYPLDDHVLCKSCNAK 65
>gnl|CDD|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein
3 (CRP3/MLP). The first LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP),
which is a striated muscle-specific factor that
enhances myogenic differentiation. CRP3/MLP interacts
with cytoskeletal protein beta-spectrin. CRP3/MLP also
interacts with the basic helix-loop-helix myogenic
transcriptio n factors MyoD, myogenin, and MRF4 thereby
increasing their affinity for specific DNA regulatory
elements. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 25.1 bits (54), Expect = 1.2
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C AC +++ +Q + +S+H C C C+ LD + + +YCK Y
Sbjct: 2 CGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDS-TTVAAHESEIYCKTCY 54
>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight cons erved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 25.4 bits (55), Expect = 1.2
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C AC + I + ++ K+WH + C CQ + + F +D YC++DY
Sbjct: 2 CGACKKPIAGQ-VVTAMGKTWHPEHFVCTHCQEEIGSR-NFFERDGQPYCEKDY 53
>gnl|CDD|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein
(CRP). The first LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function
not only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the
arrangement of the myofibrillar/cytoskeletal network.
It is evident that CRP1, CRP2, and CRP3/MLP are
involved in promoting protein assembly along the
actin-based cytoskeleton. Although members of the CRP
family share common binding partners, they are also
capable of recognizing different and specific targets.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 24.9 bits (54), Expect = 1.2
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C AC +++ +Q +S+H C C +C+ LD + ++ +YCK Y
Sbjct: 1 CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDS-TTVAAHEDEIYCKSCY 53
>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma
subfamily with unknown function. The third LIM domain
of an Enigma subfamily with unknown function: The
Enigma LIM domain family is comprised of three
characterized members: Enigma, ENH, and Cypher
(mouse)/ZASP (human). These subfamily members contain a
single PDZ domain at the N-terminus and three LIM
domains at the C-terminus. They serve as adaptor
proteins, where the PDZ domain tethers the protein to
the cytoskeleton and the LIM domains, recruit signaling
proteins to implement corresponding functions. The
members of the enigma family have been implicated in
regulating or organizing cytoskeletal structure, as
well as involving multiple signaling pathways. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 25.2 bits (55), Expect = 1.3
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 12 CVACGESIT--DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK 62
CV+CG I D+++ + + ++H+QC C C + L+ S + K +CK
Sbjct: 1 CVSCGFPIEAGDRWV-EALNNNYHSQCFNCTRCNVNLEGQ-SFYAKGGRPFCK 51
>gnl|CDD|188811 cd09427, LIM2_FHL3, The second LIM domain of Four and a half LIM
domains protein 3 (FHL3). The second LIM domain of
Four and a half LIM domains protein 3 (FHL3): FHL3 is
highly expressed in the skeleton and cardiac muscles
and possesses the transactivation and repression
activities. FHL3 interacts with many transcription
factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and
MZF_1. Moreover, FHL3 interacts with alpha- and
beta-subunits of the muscle alpha7beta1 integrin
receptor. FHL3 was also proved to possess the
auto-activation ability and was confirmed that the
second zinc finger motif in fourth LIM domain was
responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 58
Score = 25.2 bits (55), Expect = 1.4
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQ 43
CVACG+++ L+ ++WH C C C+
Sbjct: 4 CVACGKTVMPGSRKLEYEGQTWHEHCFICHGCE 36
>gnl|CDD|188816 cd09432, LIM6_LIMPETin, The sixth LIM domain of protein LIMPETin.
The sixth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 25.1 bits (55), Expect = 1.4
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 12 CVACGESITD---KYLLQVSDKSWHAQCLRCCICQLVL 46
C ACG+ IT + D+ WH C C C+ L
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSL 38
>gnl|CDD|188758 cd09372, LIM2_FBLP-1, The second LIM domain of the
filamin-binding LIM protein-1 (FBLP-1). The second LIM
domain of the filamin-binding LIM protein-1 (FBLP-1):
Fblp-1 contains a proline-rich domain near its N
terminus and two LIM domains at its C terminus. FBLP-1
mRNA was detected in a variety of tissues and cells
including platelets and endothelial cells. FBLP-1 binds
to Filamins. The association between filamin B and
FBLP-1 may play an unknown role in cytoskeletal
function, cell adhesion, and cell motility. As in other
LIM domains, this domain family is 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 24.7 bits (54), Expect = 1.5
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C IT+ ++++ K +H C C C + + VYC DY
Sbjct: 1 CAKCQGVITE-HIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein
(CRP) family. The LIM domains of Cysteine Rich Protein
(CRP) family: Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The known CRP
family members include CRP1, CRP2, and CRP3/MLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting
signal (K/R-K/R-Y-G-P-K), which supports the fact that
these proteins function not only in the cytoplasm but
also in the nucleus. CRPs control regulatory pathways
during cellular differentiation, and involve in complex
transcription control, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1, CRP2, and CRP3/MLP are involved in
promoting protein assembly along the actin-based
cytoskeleton. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 24.9 bits (55), Expect = 1.5
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG+S+ + + KSWH C C +C LD D +YCK Y
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLA-EHDGEIYCKSCY 53
>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin
like protein family. The third LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 25.0 bits (55), Expect = 1.5
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCIC 42
C C + I + Y+ + + WH +C C C
Sbjct: 1 CGGCNKPILENYISAL-NTQWHPECFVCREC 30
>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin. The
second LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 24.8 bits (54), Expect = 1.5
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFI-KDEAVYCKQDY 65
C C I +L D++WH + C C + F+ +D YC++D+
Sbjct: 1 CAYCAGPILQN-VLTAMDQTWHPEHFFCSHCGELFG--DEGFLERDGKPYCRRDF 52
>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin. The
second LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 24.9 bits (54), Expect = 1.6
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCF-IKDEAVYCKQDY 65
C C I DK + + D++WH + C C P F KD YC++DY
Sbjct: 1 CYYCNGPILDKVVTAL-DRTWHPEHFFCAQCGAFFG--PEGFHEKDGKAYCRKDY 52
>gnl|CDD|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma. The first
LIM domain of Enigma: Enigma was initially
characterized in humans as a protein containing three
LIM domains at the C-terminus and a PDZ domain at
N-terminus. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. Enigma is expressed in multiple
tissues, such as skeletal muscle, heart, bone and
brain. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 24.8 bits (54), Expect = 1.6
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C + I +YL+ + +S+H + C C+ VLD F + +++C + Y
Sbjct: 1 CAQCNKIIRGRYLVALG-RSYHPEEFTCSQCKKVLDEG-GFFEEKGSIFCPKCY 52
>gnl|CDD|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP. The LIM domain of
N-RAP: N-RAP is a muscle-specific protein concentrated
at myotendinous junctions in skeletal muscle and
intercalated disks in cardiac muscle. LIM domain is
found at the N-terminus of N-RAP and the C-terminal of
N-RAP contains a region with multiple of nebulin
repeats. N-RAP functions as a scaffolding protein that
organizes alpha-actinin and actin into symmetrical
I-Z-I structures in developing myofibrils. Nebulin
repeat is known as actin binding domain. The N-RAP is
hypothesized to form antiparallel dimerization via its
LIM domain. As in other LIM domains, this domain family
is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 24.9 bits (54), Expect = 1.7
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL 46
C CG + + D++WH C C +C+++L
Sbjct: 1 CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMML 35
>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin
like protein family. The first LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 24.6 bits (54), Expect = 1.8
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C AC + I + ++ K+WH + C C+ L + F +D YC++DY
Sbjct: 1 CAACKKPIVGQ-VVTALGKTWHPEHFVCAECKTELGTK-NFFERDGQPYCEKDY 52
>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin.
The first LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 24.7 bits (54), Expect = 1.8
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 32 WHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
WH C RC C+ +L C + D+ +YC++ Y
Sbjct: 26 WHPACFRCSTCEELLVDLTYC-VHDDQIYCERHY 58
>gnl|CDD|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM
domains protein 1 (FHL1). The fourth LIM domain of
Four and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth,
differentiation, and sarcomere assembly by acting as a
modulator of transcription factors. Defects in FHL1
gene are responsible for a number of Muscular
dystrophy-like muscle disorders. It has been detected
that FHL1 binds to Myosin-binding protein C, regulating
myosin filament formation and sarcomere assembly. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 64
Score = 24.7 bits (54), Expect = 1.8
Identities = 11/39 (28%), Positives = 14/39 (35%), Gaps = 1/39 (2%)
Query: 29 DKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
SWH C C C L L + + +YC K
Sbjct: 26 GSSWHDYCFNCKKCSLNL-ANKRFVFHNGQIYCSDCAKK 63
>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The second LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 24.6 bits (54), Expect = 2.0
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG ++ Y+ + + +H + C +C V + S + + +YC Y
Sbjct: 1 CFKCGGALRGSYITAL-GRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated
LIM protein) family. This family represents the LIM
domain of ALP (actinin-associated LIM protein) family.
Four proteins: ALP, CLP36, RIL, and Mystique have been
classified into the ALP subfamily of LIM domain
proteins. Each member of the subfamily contains an
N-terminal PDZ domain and a C-terminal LIM domain.
Functionally, these proteins bind to alpha-actinin
through their PDZ domains and bind or other signaling
molecules through their LIM domains. ALP proteins have
been implicated in cardiac and skeletal muscle
structure, function and disease, platelet, and
epithelial cell motility. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 24.6 bits (54), Expect = 2.0
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYC 61
C CG I +++ DK+ H +C C C L L FI+DE +YC
Sbjct: 1 CDKCGNGIVGV-VVKARDKNRHPECFVCADCGLNLKNKGYFFIEDE-LYC 48
>gnl|CDD|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein
(TLP). The second LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a
role in development of normal thymus and in controlling
the development and differentiation of thymic
epithelial cells. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 54
Score = 24.6 bits (53), Expect = 2.3
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL 46
C CG+ + + ++WH CLRC C+ L
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTL 35
>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9
family. The second LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Although Lhx2 and Lhx9 are highly homologous, they
seems to play regulatory roles in different organs. In
animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. Lhx9 is expressed in several
regions of the developing mouse brain, the spinal cord,
the pancreas, in limb mesenchyme, and in the urogenital
region. Lhx9 plays critical roles in gonad development.
Homozygous mice lacking functional Lhx9 alleles
exhibit numerous urogenital defects, such as gonadal
agenesis, infertility, and undetectable levels of
testosterone and estradiol coupled with high FSH
levels. Lhx9 null mice are phenotypically female, even
those that are genotypically male. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 59
Score = 24.2 bits (53), Expect = 2.5
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 10 RYCVACGESITDKYL-LQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
+ C C I+ L ++ D +H C C C L + ++D VYC+ Y
Sbjct: 3 KRCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A.
The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A
belong to the CRP LIM domain protein family. The Mlp84B
protein contains five copies of the LIM domains, each
followed by a Glycin Rich Region (GRR). However, only
the first LIM domain of Mlp84B is in this family.
Mlp60A exhibits only one LIM domain linked to a
glycin-rich region. Mlp84B and Mlp60A are muscle
specific proteins and have been implicated in muscle
differentiation. While Mlp84B transcripts are enriched
at the terminal ends of muscle fibers, Mlp60A
transcripts are found throughout the muscle fibers. All
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 24.0 bits (52), Expect = 2.9
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQ 63
C CG+S+ WH C +C +C +LD +C + +YCKQ
Sbjct: 2 CPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDS-TNCAEHEGELYCKQ 52
>gnl|CDD|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule
interacting with CasL) like family. The LIM domain of
Mical (molecule interacting with CasL) like family:
Known members of this family includes LIM domain
containing proteins; Mical (molecule interacting with
CasL), pollen specific protein SF3, Eplin, xin
actin-binding repeat-containing protein 2 (XIRP2) and
Ltd-1. The members of this family function mainly at
the cytoskeleton and focal adhesions. They interact
with transcription factors or other signaling molecules
to play roles in muscle development, neuronal
differentiation, cell growth and mobility. Eplin has
also found to be tumor suppressor. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs..
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 24.2 bits (53), Expect = 2.9
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIK-DEAVYCKQDY 65
C CG+++ L K +H C RC C L + + +YCK +
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTL--RLGNYASLEGKLYCKPHF 53
>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like
family. The third LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and
the second LIM domain interacts with the receptor
tyrosine kinase Ret and the adaptor protein APS. Thus
Enigma is implicated in signal transduction processes,
such as mitogenic activity, insulin related actin
organization, and glucose metabolism. The second
member, ENH protein, was first identified in rat brain.
It has been shown that ENH interacts with protein
kinase D1 (PKD1) via its LIM domains and forms a
complex with PKD1 and the alpha1C subunit of cardiac
L-type voltage-gated calcium channel in rat neonatal
cardiomyocytes. The N-terminal PDZ domain interacts
with alpha-actinin at the Z-line. ZASP/Cypher is
required for maintenance of Z-line structure during
muscle contraction, but not required for Z-line
assembly. In heart, Cypher/ZASP plays a structural role
through its interaction with cytoskeletal Z-line
proteins. In addition, there is increasing evidence
that Cypher/ZASP also performs signaling functions.
Studies reveal that Cypher/ZASP interacts with and
directs PKC to the Z-line, where PKC phosphorylates
downstream signaling targets. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 23.9 bits (52), Expect = 3.3
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 12 CVACGESIT--DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK 62
C C I D++L + +WH C C +C + L+ + K + CK
Sbjct: 1 CHGCDFPIEAGDRFL-EALGHTWHDTCFVCAVCHVNLEGQT-FYSKKDKPLCK 51
>gnl|CDD|188818 cd09434, LIM4_FHL3, The fourth LIM domain of Four and a half LIM
domains protein 3 (FHL3). The fourth LIM domain of
Four and a half LIM domains protein 3 (FHL3): FHL3 is
highly expressed in the skeleton and cardiac muscles
and possesses the transactivation and repression
activities. FHL3 interacts with many transcription
factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and
MZF_1. Moreover, FHL3 interacts with alpha- and
beta-subunits of the muscle alpha7beta1 integrin
receptor. FHL3 was also proved to possess the
auto-activation ability and was confirmed that the
second zinc finger motif in fourth LIM domain was
responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 56
Score = 24.0 bits (52), Expect = 3.4
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 12 CVACGESITD----KYLLQVSDKSWHAQCLRCCICQLVL 46
C AC + IT KY+ D+ WH C +C C + L
Sbjct: 1 CAACNKPITGFGGGKYV-SFEDRQWHQPCFKCSRCSVSL 38
>gnl|CDD|188804 cd09420, LIM3_Prickle, The third LIM domain of Prickle. The
third LIM domain of Prickle: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Two
forms of prickles have been identified; namely prickle
1 and prickle 2. Prickle 1 and prickle 2 are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle
2 is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 59
Score = 23.9 bits (52), Expect = 3.6
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 11 YCVACGESI-TDKYLLQVSDKSWHA--QCLRCCICQLVL 46
YC CGE I D+ + + WHA +C C C+ L
Sbjct: 2 YCDTCGEHIGVDQGQMTYDGQHWHATEKCFCCAQCKKSL 40
>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH. The
fourth LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated
protein-protein interactions. PINCH comprises an array
of five LIM domains that interact with integrin-linked
kinase (ILK), Nck2 (also called Nckbeta or Grb4) and
other interaction partners. These interactions are
essential for triggering the FA assembly and for
relaying diverse mechanical and biochemical signals
between Cell-extracellular matrix and the actin
cytoskeleton. The PINCH LIM4 domain recognizes the
third SH3 domain of another adaptor protein, Nck2. This
step is an important component of integrin signaling
event. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assem bly of multimeric
protein complexes.
Length = 54
Score = 23.9 bits (52), Expect = 4.1
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 11 YCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C AC I + + + K WH + C C+ H + K YC+ Y
Sbjct: 2 ICGACRRPIEGRVVTALG-KHWHVEHFVCAKCEKPFLGHRH-YEKKGLAYCETHY 54
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 24.7 bits (54), Expect = 4.1
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 7/58 (12%)
Query: 4 TIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCIC--QLVLDRHPSCFIKDEAV 59
T + + C C K D+ +HAQ + C C QL +D+A+
Sbjct: 113 TSMADFPLCPDC-----AKEYKDPLDRRFHAQPIACPRCGPQLNFVSRGGHAEQDDAL 165
>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The second LIM
domain of LMO1 and LMO3 (LIM domain only protein 1 and
3): LMO1 and LMO3 are highly homologous and belong to
the LMO protein family. LMO1 and LMO3 are nuclear
protein that plays important roles in transcriptional
regulation and development. As LIM domains lack
intrinsic DNA-binding activity, nuclear LMOs are
involved in transcriptional regulation by forming
complexes with other transcription factors or
cofactors. For example, LMO1 interacts with the the
bHLH domain of bHLH transcription factor, TAL1 (T-cell
acute leukemia1)/SCL (stem cell leukemia) . LMO1
inhibits the expression of TAL1/SCL target genes. LMO3
facilitates p53 binding to its response elements, which
suggests that LMO3 acts as a co-repressor of p53,
suppressing p53-dependent transcriptional regulation.
In addition, LMO3 interacts with neuronal transcription
factor, HEN2, and acts as an oncogene in neuroblastoma.
Another binding partner of LMO3 is calcium- and
integrin-binding protein CIB, which binds via the
second LIM domain (LIM2) of LMO3. One role of the
CIB/LMO3 complex is to inhibit cell proliferation.
Although LMO1 and LMO3 are highly homologous proteins,
they play different roles in the regulation of the
pituitary glycoprotein hormone alpha-subunit (alpha
GSU) gene. Alpha GSU promoter activity was markedly
repressed by LMO1 but activated by LMO3. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 23.8 bits (51), Expect = 4.3
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 12 CVACGESITD-KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C AC + I + +++ D +H C C +C F+K+ + C+ DY
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55
>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein
(TLP). The LIM domain of thymus LIM protein (TLP) like
proteins: This family includes the LIM domains of TLP
and CRIP (Cysteine-Rich Intestinal Protein). TLP is the
distant member of the CRP family of proteins. TLP has
two isomers (TLP-A and TLP-B) and sharing approximately
30% with each of the three other CRPs. Like CRP1, CRP2
and CRP3/MLP, TLP has two LIM domains, connected by a
flexible linker region. Unlike the CRPs, TLP lacks the
nuclear targeting signal (K/R-K/R-Y-G-P-K) and is
localized solely in the cytoplasm. TLP is specifically
expressed in the thymus in a subset of cortical
epithelial cells. TLP has a role in development of
normal thymus and in controlling the development and
differentiation of thymic epithelial cells. CRIP is a
short LIM protein with only one LIM domain. CRIP gene
is developmentally regulated and can be induced by
glucocorticoid hormones during the first three
postnatal weeks. The domain shows close sequence
homology to LIM domain of thymus LIM protein. However,
unlike the TLP proteins which have two LIM domains, the
members of this family have only one LIM domain. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 23.5 bits (51), Expect = 4.5
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 5/56 (8%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRC--CICQLVLDRHPSCFIKDEAVYCKQDY 65
C CG+ + + WH CLRC C L +H + YC + Y
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHS---EHEGKPYCNKCY 53
>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain
only protein 4). The second LIM domain of LMO4 (LIM
domain only protein 4): LMO4 is a nuclear protein that
plays important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact
with Smad proteins, and associate with the promoter of
the PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential
role for LMO4 as a negative regulator of BRCA1 in
sporadic breast cancer. LMO4 also forms complex to
both ERa (oestrogen receptor alpha), MTA1 (metastasis
tumor antigen 1), and HDACs (histone deacetylases),
implying that LMO4 is also a component of the MTA1
corepressor complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 23.6 bits (51), Expect = 4.7
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 12 CVACGESI-TDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64
C ACG+SI + +++ +H +C C C L + +++C+ D
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 54
>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The first LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 57
Score = 23.4 bits (51), Expect = 5.2
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQ 43
C CG+ IT +++ + +H C C C
Sbjct: 1 CAKCGKPITGQFV-RALGDVYHLDCFTCHDCG 31
>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2. The second
LIM domain of Lhx2: Lhx2 belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. The Lhx2 protein has been shown
to bind to the mouse M71 olfactory receptor promoter.
Similar to other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 59
Score = 23.5 bits (50), Expect = 5.3
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 9 LRYCVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK 62
++ C C I+ + +++ D +H C C C +L +KD VYC+
Sbjct: 2 VQRCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCR 56
>gnl|CDD|163542 TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/helix-turn-helix
protein, YgiT family. This model describes a family of
predicted regulatory proteins with a conserved zinc
finger/HTH architecture. The amino-terminal region
contains a novel domain, featuring two CXXC motifs and
occuring in a number of small bacterial proteins as
well as in the present family. The carboxyl-terminal
region consists of a helix-turn-helix domain, modeled
by pfam01381. The predicted function is DNA binding and
transcriptional regulation.
Length = 127
Score = 24.1 bits (53), Expect = 6.0
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 10 RYCVACGESITDKYLLQVSDK 30
YC ACGE + D + +
Sbjct: 32 WYCPACGEELLDPEESKRNSA 52
>gnl|CDD|188832 cd09448, LIM_CLP36, This family represents the LIM domain of
CLP36. This family represents the LIM domain of CLP36.
CLP36 has also been named as CLIM1, Elfin, or PDLIM1.
CLP36 contains a C-terminal LIM domain and an
N-terminal PDZ domain. CLP36 is highly expressed in
heart and is present in many other tissues including
lung, liver, spleen, and blood. CLP36 has been
implicated in many processes including hypoxia and
regulation of actin stress fibers. CLP36 co-localizes
with alpha-actinin-2 at the Z-lines in myocardium. In
addition, CLP36 binds to alpha-actinin-1 and
alpha-actinin-4, and associates with F-actin filaments
and stress fibers. CLP36 might be involved in not only
the function of sarcomeres in muscle cells, but also in
actin stress fiber-mediated cellular processes, such as
cell shape, migration, polarit, and cytokinesis in
non-muscle cells. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 23.0 bits (49), Expect = 7.2
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQ 63
C CG I ++ ++ DK H +C C C L + F++D+ +YC++
Sbjct: 1 CDKCGSGIVGVFV-KIRDKPRHPECYVCTDCGTNLKQKGHFFVEDQ-IYCEK 50
>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9. The second
LIM domain of Lhx9: Lhx9 belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx9 is highly homologous to Lhx2. It is expressed in
several regions of the developing mouse brain, the
spinal cord, the pancreas, in limb mesenchyme, and in
the urogenital region. Lhx9 plays critical roles in
gonad development. Homozygous mice lacking functional
Lhx9 alleles exhibit numerous urogenital defects, such
as gonadal agenesis, infertility, and undetectable
levels of testosterone and estradiol coupled with high
FSH levels. Lhx9 null mice have reduced levels of the
Sf1 nuclear receptor that is required for
gonadogenesis, and recent studies have shown that Lhx9
is able to activate the Sf1/FtzF1 gene. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 59
Score = 23.1 bits (49), Expect = 7.2
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 9 LRYCVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK 62
++ C C I+ + +++ + +H C C C L +KD VYC+
Sbjct: 2 VQRCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCR 56
>gnl|CDD|188799 cd09415, LIM1_Prickle, The first LIM domain of Prickle. The
first LIM domain of Prickle: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 23.0 bits (50), Expect = 7.5
Identities = 6/16 (37%), Positives = 8/16 (50%)
Query: 31 SWHAQCLRCCICQLVL 46
WH C C C+ +L
Sbjct: 25 CWHPACFVCSTCKELL 40
>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 59
Score = 23.1 bits (50), Expect = 7.9
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCIC 42
C C E D+ ++ + + +H QC C C
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQC 32
>gnl|CDD|188800 cd09416, LIM2_Testin, The second LIM domain of Testin. The
second LIM domain of Testin: Testin contains three
C-terminal LIM domains and a PET protein-protein
interaction domain at the N-terminal. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion
events. Knockout mice experiments reveal that tumor
repressor function of testin. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 22.9 bits (49), Expect = 8.2
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C E I Q +++WH + C C +L + D+ V CK Y
Sbjct: 3 CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPV-CKPCY 55
>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain
only protein 2). The second LIM domain of LMO2 (LIM
domain only protein 2): LMO2 is a nuclear protein that
plays important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex
that is capable of transcriptional activation. LMOs
have also been shown to be involved in oncogenesis.
LMO1 and LMO2 are activated in T-cell acute
lymphoblastic leukemia by distinct chromosomal
translocations. LMO2 was also shown to be involved in
erythropoiesis and is required for the hematopoiesis in
the adult animals. All LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 23.0 bits (49), Expect = 8.5
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 12 CVACGESITD-KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64
C +C + I + ++V DK +H +C +C CQ + + + C+QD
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQD 54
>gnl|CDD|188848 cd09464, LIM2_LIMK1, The second LIM domain of LIMK1 (LIM domain
Kinase 1). The second LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture
of the actin cytoskeleton by regulating the activity of
the cofilin family proteins cofilin1, cofilin2, and
destrin. The mechanism of the activation is to
phosphorylates cofilin on serine 3 and inactivates its
actin-severing activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. LIMK1 is expressed in all tissues and is
localized to focal adhesions in the cell. LIMK1 can
form homodimers upon binding of HSP90 and is activated
by Rho effector Rho kinase and MAPKAPK2. LIMK1 is
important for normal central nervous system
development, and its deletion has been implicated in
the development of the human genetic disorder Williams
syndrome. Moreover, LIMK1 up-regulates the promoter
activity of urokinase type plasminogen activator and
induces its mRNA and protein expression in breast
cancer cells. The LIM domains have been shown to play
an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 22.9 bits (49), Expect = 8.5
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDY 65
C C E+IT ++ ++ +H +C C C + D ++ +YC Y
Sbjct: 1 CHGCSETITTGLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYCGHCY 55
>gnl|CDD|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma. The third
LIM domain of Enigma: Enigma was initially
characterized in humans as a protein containing three
LIM domains at the C-terminus and a PDZ domain at
N-terminus. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. Enigma is expressed in multiple
tissues, such as skeletal muscle, heart, bone, and
brain. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 23.1 bits (49), Expect = 9.1
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 31 SWHAQCLRCCICQLVLD 47
SWH C C ICQ+ L+
Sbjct: 21 SWHDTCFVCAICQINLE 37
>gnl|CDD|214532 smart00136, LamNT, Laminin N-terminal domain (domain VI).
N-terminal domain of laminins and laminin-related
protein such as Unc-6/ netrins.
Length = 238
Score = 23.9 bits (52), Expect = 9.1
Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 5/45 (11%)
Query: 15 CGESITDKYLLQVSDKSWHAQCLRCCIC--QLVLDRHPSCFIKDE 57
CGE ++Y V + C C + HP+ + D
Sbjct: 26 CGEPGPERYCKLVGHTEQGKK---CDYCDARNPRRSHPAENLTDG 67
>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like
family. The third LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion
events. Prickles have been implicated in roles of
regulating tissue polarity or planar cell polarity
(PCP). Dyxin involves in lung and heart development by
interaction with GATA6 and blocking GATA6 activated
target genes. LIMPETin might be the recombinant product
of genes coding testin and four and half LIM proteins
and its function is not well understood. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 57
Score = 22.7 bits (49), Expect = 9.2
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 12 CVACGESI-TDKYLLQVSDKSWHA--QCLRCCICQLVLDRHP 50
C ACGE I D + + + WHA +C C C+ L P
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLLGQP 42
>gnl|CDD|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins
of unknown function: This domain belongs to the LIM
domain family which are found on Mical (molecule
interacting with CasL) like proteins. Known members of
the Mical-like family includes single LIM domain
containing proteins, Mical (molecule interacting with
CasL), pollen specific protein SF3, Eplin, xin
actin-binding repeat-containing protein 2 (XIRP2), and
Ltd-1. The members of this family function mainly at
the cytoskeleton and focal adhesions. They interact
with transcription factors or other signaling molecules
to play roles in muscle development, neuronal
differentiation, cell growth, and mobility. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 22.8 bits (49), Expect = 9.3
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 12 CVACGESITDKYLLQ---VSDKSWHAQCLRCCICQLVL 46
C ACG+ + +L+Q V K +H C RC C L
Sbjct: 1 CAACGQHV---HLVQRHLVDGKLYHRNCFRCKECSSTL 35
>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin.
The third LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 22.9 bits (49), Expect = 9.4
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 12 CVACGESI-TDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
C C + I D L DK WH C C C++ L P K + +YC Y
Sbjct: 5 CEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFG-SKADRIYCGNCY 58
>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM
domains protein (FHL). The fourth LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in
tandem and an N-terminal single zinc finger domain with
a consensus sequence equivalent to the C-terminal half
of a LIM domain. LIMPETin is an exception, containing
six LIM domains. FHL1, 2 and 3 are predominantly
expressed in muscle tissues, and FHL5 is highly
expressed in male germ cells. FHL proteins exert their
roles as transcription co-activators or co-repressors
through a wide array of interaction partners. For
example, FHL1 binds to Myosin-binding protein C,
regulating myosin filament formation and sarcomere
assembly. FHL2 has shown to interact with more than 50
different proteins, including receptors, structural
proteins, transcription factors and cofactors, signal
transducers, splicing factors, DNA replication and
repair enzymes, and metabolic enzymes. FHL3 interacts
with many transcription factors, such as CREB,
BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 22.7 bits (49), Expect = 9.5
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 12 CVACGESITD----KYLLQVSDKSWHAQCLRCCICQLVL 46
C AC + IT K++ ++ WH+ C C C + L
Sbjct: 1 CAACTKPITGLGGAKFI-SFEERQWHSDCFNCGKCSVSL 38
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
0.330 0.139 0.479
Gapped
Lambda K H
0.267 0.0598 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,058,194
Number of extensions: 196516
Number of successful extensions: 406
Number of sequences better than 10.0: 1
Number of HSP's gapped: 371
Number of HSP's successfully gapped: 152
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.5 bits)