RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4325
(306 letters)
>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 = 122 bits (309), Expect = 7e-36
Identities = 46/56 (82%), Positives = 48/56 (85%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CAGC+ GIPPTQVVRRAQD VYHL CFAC MC RQL TGDEFYLMED +LVCK DY
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
>gnl|CDD|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b. The second
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 = 57
Score = 104 bits (260), Expect = 9e-29
Identities = 45/57 (78%), Positives = 50/57 (87%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
KCA C+ GIPPTQVVRRAQD VYHL+CFAC++C RQL TGDEFYLMED +LVCK DY
Sbjct: 1 KCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57
>gnl|CDD|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4. The second 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 = 56
Score = 102 bits (256), Expect = 4e-28
Identities = 42/56 (75%), Positives = 49/56 (87%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C C+ GIPPTQVVR+AQD VYHL+CFAC++C+RQL TGDEFYLMED +LVCK DY
Sbjct: 1 CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56
>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 = 100 bits (252), Expect = 2e-27
Identities = 38/52 (73%), Positives = 47/52 (90%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
CGGC + ILDRFILKVL+RTWHA+CLKC++CGA L +KCFARNG ++CK+DF
Sbjct: 1 CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFARNGHVYCKDDF 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 = 90.2 bits (224), Expect = 3e-23
Identities = 34/56 (60%), Positives = 43/56 (76%)
Query: 70 IPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFF 125
IPKC GC I DRFILKV ++ WH++CLKC +C A L +KCF+R G ++CKEDFF
Sbjct: 1 IPKCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDKCFSRGGQVYCKEDFF 56
Score = 30.1 bits (68), Expect = 0.15
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
KCAGC+ I + + + QD +H C CV C QL D+ + ++ CK D+
Sbjct: 3 KCAGCDHPIF-DRFILKVQDKPWHSKCLKCVDCQAQLT--DKCF-SRGGQVYCKEDF 55
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 89.8 bits (224), Expect = 3e-23
Identities = 28/57 (49%), Positives = 38/57 (66%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R RTT T +QLE L+ + + P+ RE+L++ GL R V+VWFQNRRAK KR
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>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 = 89.7 bits (223), Expect = 4e-23
Identities = 31/56 (55%), Positives = 45/56 (80%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CAGC+ GI P +VRRA+D V+HLNCF C++C +QL+TG+E Y++++ K +CK DY
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
>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 = 82.7 bits (204), Expect = 2e-20
Identities = 33/55 (60%), Positives = 42/55 (76%)
Query: 70 IPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
IP C GC I+DRFILKVL+R WH++CLKC +C LAEKCF+R ++CK+DF
Sbjct: 1 IPLCAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCFSRGDSVYCKDDF 55
>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 = 81.7 bits (202), Expect = 3e-20
Identities = 29/52 (55%), Positives = 39/52 (75%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
C GC ILD+F+L VL+R WHA+C++C +C PL EKCF+R G L+C+ DF
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCFSREGKLYCRNDF 52
>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 = 80.8 bits (199), Expect = 9e-20
Identities = 32/52 (61%), Positives = 40/52 (76%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
C GC ILD+FILKVL+R WH+ CLKC +C LAE+CF+R G ++CKEDF
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFSRAGNVYCKEDF 52
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 80.4 bits (199), Expect = 1e-19
Identities = 28/59 (47%), Positives = 41/59 (69%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
+R RT T +QLE L+ + +P P+R RE+L+++ GL R V++WFQNRRAK KR +
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 79.6 bits (197), Expect = 2e-19
Identities = 28/57 (49%), Positives = 39/57 (68%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
+R RT+ T +QLE L+ + +P P+R RE+L++ GL R V+VWFQNRRAK K
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH). The
second 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 = 55
Score = 73.6 bits (181), Expect = 4e-17
Identities = 32/56 (57%), Positives = 39/56 (69%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C I + VRRA+D VYHL CFAC C RQL+TG+EF L+EDR ++CK Y
Sbjct: 1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDR-VLCKAHY 55
>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 = 73.5 bits (181), Expect = 4e-17
Identities = 29/54 (53%), Positives = 37/54 (68%), Gaps = 2/54 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE--KCFARNGLLFCKEDF 124
C GCG+ I DRF L ++R WHA CLKC EC PL CF+R+G ++CKED+
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
Score = 26.9 bits (60), Expect = 2.0
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CAGC I + A D +H +C C C L++ + D + CK DY
Sbjct: 1 CAGCGEKIQ-DRFYLLAVDRQWHASCLKCCECRLPLDSELSCFS-RDGNIYCKEDY 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 = 70.9 bits (174), Expect = 4e-16
Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
C GC I DR++L+V ER+WH CL+C C PL C+ R+ L+CK+D+
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCYFRDRKLYCKQDY 52
Score = 33.1 bits (76), Expect = 0.013
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
CAGC+ I + + R + +H C C +C +Q T ++ DRKL CK DY+
Sbjct: 1 CAGCQRPIS-DRYLLRVNERSWHEECLQCSVC-QQPLTTSCYF--RDRKLYCKQDYQ 53
>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 = 70.9 bits (174), Expect = 4e-16
Identities = 26/55 (47%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDF 124
C GCG I+DRF+L L+R WH CLKC C A L E C+ + G++ CK D+
Sbjct: 1 CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
>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 = 68.6 bits (168), Expect = 3e-15
Identities = 30/56 (53%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C+GC I P+++V RA + VYHL CF C +C RQL GDEF L E + L+CK DY
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQ-LLCKSDY 55
Score = 34.3 bits (79), Expect = 0.005
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 73 CGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPL--AEKCFARNGLLFCKEDF 124
C GC + I +++ LE +H RC C C L ++ + G L CK D+
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
>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 = 66.6 bits (163), Expect = 1e-14
Identities = 30/57 (52%), Positives = 36/57 (63%), Gaps = 7/57 (12%)
Query: 73 CGGCGDLILDRFILKV---LERTWHARCLKCHECGAPLAEK--CFARNGLLFCKEDF 124
C GCG I D++IL+V LE WHA CLKC ECG L E CF R+G +CK D+
Sbjct: 1 CVGCGGKIHDQYILRVAPDLE--WHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
Score = 33.5 bits (77), Expect = 0.010
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C GC I ++R A DL +H C C C + L+ + D K CK DY
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDE-TCTCFVRDGKTYCKRDY 55
>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 = 66.1 bits (162), Expect = 2e-14
Identities = 26/57 (45%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+CA C +GI +++V RA+DLV+HLNCF C C + L GD F M D + C+ Y
Sbjct: 4 RCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFG-MRDGLVYCRLHY 59
>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 = 65.8 bits (161), Expect = 3e-14
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLA-EKCFARNGLLFCKEDF 124
C GCG I R +L+ L + WH C KC CG PL + + ++G +C++ +
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 52.3 bits (126), Expect = 2e-09
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CAGC I + + RA +H CF C +C + L G + + +D K C+ Y
Sbjct: 1 CAGCGKPIEG-RELLRALGKKWHPECFKCSVCGKPL--GGDSFYEKDGKPYCEKCY 53
>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 = 64.7 bits (158), Expect = 8e-14
Identities = 26/54 (48%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEK--CFARNGLLFCKEDF 124
C GCG+ I DRF+LKV R+WH CL+C C PL + CF R+ ++CK D+
Sbjct: 1 CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
Score = 26.6 bits (59), Expect = 2.7
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C GC I + + + +H++C C +C L + DR++ CK DY
Sbjct: 1 CTGCGEPIT-DRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFT-RDRQIYCKADY 54
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 64.7 bits (158), Expect = 9e-14
Identities = 25/58 (43%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 73 CGGCGDLILDRFILK-VLERTWHARCLKCHECGAPLAEK-CFARNGLLFCKEDFFKRF 128
C GCG I DR +++ L + WH C +C CG PL F ++G L+CK D+FK F
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 63.9 bits (156), Expect = 1e-13
Identities = 25/60 (41%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAK 191
CAGC I ++VRRA V+H CF C +C + L GD F+ + KL CK DY
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDG-KLYCKHDYFKLF 58
>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 = 62.9 bits (153), Expect = 3e-13
Identities = 26/52 (50%), Positives = 34/52 (65%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
C GC +I DRF+L+V + WH RCL+C C PL CF R+ L+CKED+
Sbjct: 1 CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLETTCFYRDKKLYCKEDY 52
Score = 29.7 bits (67), Expect = 0.24
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C GC I + + R D ++H C C C L T FY D+KL CK DY
Sbjct: 1 CEGCNRVIQ-DRFLLRVNDSLWHERCLQCASCKEPLET-TCFY--RDKKLYCKEDY 52
>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 = 60.5 bits (146), Expect = 3e-12
Identities = 27/54 (50%), Positives = 37/54 (68%), Gaps = 1/54 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
+CA C +GI +++V RA+DLVYHLNCF C C + L TGD F M+D + C+
Sbjct: 4 RCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFG-MKDNLVYCR 56
>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 = 59.8 bits (145), Expect = 4e-12
Identities = 25/56 (44%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C+ V RA+ +YH+ CF C C+RQL GDEF L +D L CK D+
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDD-GLFCKADH 55
Score = 27.4 bits (61), Expect = 1.6
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPL--AEKCFARNGLLFCKED 123
KC + F+++ + +H C +C C L ++ R+ LFCK D
Sbjct: 2 AKCQQS--FSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKAD 54
>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 = 59.4 bits (144), Expect = 5e-12
Identities = 24/55 (43%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPD 186
C+ C IP +++V RAQ VYHL CF C C QL GD F+ + L C+ D
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGS-LFCEHD 54
Score = 31.7 bits (72), Expect = 0.044
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 73 CGGCGDLI-LDRFILKVLERTWHARCLKCHECGAPL--AEKCFARNGLLFCKEDF 124
C CG I +++ +H +C C C L ++ NG LFC+ D
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHDR 55
>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 = 58.7 bits (142), Expect = 1e-11
Identities = 18/53 (33%), Positives = 30/53 (56%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFF 125
C GC ILD ++ L + WH C +C C L+ F ++G L+C++D++
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYFEKDGKLYCRKDYW 53
Score = 37.9 bits (88), Expect = 2e-04
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CAGC I +Q V+ +H +CF C +C+ L+ +Y +D KL C+ DY
Sbjct: 1 CAGCRGKILDSQYVQALNQ-DWHCDCFRCSVCSDSLSN---WYFEKDGKLYCRKDY 52
>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 = 58.5 bits (141), Expect = 1e-11
Identities = 26/54 (48%), Positives = 36/54 (66%), Gaps = 2/54 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEK--CFARNGLLFCKEDF 124
C GCG I DR+ L +++ WH RCLKC EC L + CFA++G ++CKED+
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2. The second LIM
domain of Isl2: Isl is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. 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 proteins are found in the nucleus and act as
transcription factors or cofactors. Isl1 and Isl2 are
the two conserved members of this family. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Isl2 may 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 = 58.0 bits (140), Expect = 2e-11
Identities = 27/56 (48%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C +G + +V RA+D VYH+ CF C +C+RQL GDEF L E +L+C+ D+
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLRE-HELLCRADH 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 = 58.1 bits (140), Expect = 3e-11
Identities = 25/54 (46%), Positives = 36/54 (66%), Gaps = 2/54 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEK--CFARNGLLFCKEDF 124
C GCG I DR+ L +++ WH RCLKC EC L + CF+++G ++CKED+
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 60.5 bits (147), Expect = 3e-11
Identities = 26/74 (35%), Positives = 38/74 (51%)
Query: 199 DGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
DG P K R T +QL L+ + +P P+ R +LS + + VQ+WFQN+RAK
Sbjct: 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK 105
Query: 259 EKRLKKDAGRTRWS 272
EK+ + R
Sbjct: 106 EKKKRSGKVEQRPG 119
>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx). The
second LIM domain of dLMO (Beaderx): dLMO is a nuclear
protein that plays important roles in transcriptional
regulation and development. In Drosophila dLMO modulates
the activity of LIM-homeodomain protein Apterous (Ap),
which regulates the formation of the dorsal-ventral axis
of the Drosophila wing. Biochemical analysis shows that
dLMO protein influences the activity of Apterous by
binding of its cofactor Chip. Further studies shown that
dLMO proteins might function in an evolutionarily
conserved mechanism involved in patterning the
appendages. 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 = 56.4 bits (136), Expect = 6e-11
Identities = 27/56 (48%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C IP ++V RA+ VYHL CFAC C + GD FYL E+ K++C+ DY
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCEN-KILCEYDY 55
>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 = 56.6 bits (137), Expect = 7e-11
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPD 186
KCAGC I T+ V RA V+H CF C C + L+ + + +D KL CK
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLS--GDTFFEKDGKLYCKDC 54
Score = 52.8 bits (127), Expect = 1e-09
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 72 KCGGCGDLILDR-FILKVLERTWHARCLKCHECGAPLAEK-CFARNGLLFCKED 123
KC GCG I +L+ L + WH C KC CG PL+ F ++G L+CK+
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
>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 = 57.2 bits (138), Expect = 7e-11
Identities = 24/57 (42%), Positives = 34/57 (59%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFF 125
+P C CG I D L+ L WHA C +C ECGA L+ + ++G LFCK+D++
Sbjct: 18 VLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYYEKDGRLFCKKDYW 74
Score = 32.9 bits (75), Expect = 0.024
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C I Q ++ A + +H +CF C C L+ +Y +D +L CK DY
Sbjct: 22 CASCGQSIYDGQYLQ-ALNSDWHADCFRCCECGASLS---HWYYEKDGRLFCKKDY 73
>gnl|CDD|188769 cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of Lhx7 and Lhx8.
The second 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 = 55
Score = 56.2 bits (135), Expect = 9e-11
Identities = 29/56 (51%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C+ C I T VRRA+ VYHL CFAC C RQL+TG+EF L+E++ L C+ Y
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVL-CRVHY 55
>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 = 55.9 bits (134), Expect = 1e-10
Identities = 24/54 (44%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
+CA C +GI +++V RA++ VYHL+CF C C + L TGD F M+D + C+
Sbjct: 4 RCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFG-MKDNLVYCR 56
>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 = 55.4 bits (133), Expect = 2e-10
Identities = 25/56 (44%), Positives = 39/56 (69%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C IP ++V RA+D VYHL+CFAC +C ++ GD+F+L ++ ++C+ DY
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFL-KNNMILCQMDY 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 = 55.0 bits (133), Expect = 2e-10
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
C GCG I + L L++ WH C KC ECG L + ++G +C+ D+
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGEYMGKDGKPYCERDY 52
Score = 33.1 bits (76), Expect = 0.012
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CAGC I Q + A D +H+ CF C C + L G+ Y+ +D K C+ DY
Sbjct: 1 CAGCGQEIKNGQALL-ALDKQWHVWCFKCKECGKVLT-GE--YMGKDGKPYCERDY 52
>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 = 54.5 bits (131), Expect = 4e-10
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
C GCG I D F +V++ WH C +C C L + ++G L+C + +
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYEKDGKLYCHKHY 52
Score = 37.2 bits (86), Expect = 5e-04
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C GC I + R Q+ +H +CF C +C L +Y +D KL C Y
Sbjct: 1 CTGCGGRIQDSFHYRVVQE-AWHNSCFQCSVCQDLLTN---WYYEKDGKLYCHKHY 52
>gnl|CDD|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6. The second 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
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 = 55
Score = 53.6 bits (128), Expect = 9e-10
Identities = 28/56 (50%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C I + VRRA+ YHL CFAC C RQL+TG+EF L+E+ K++C+ Y
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEE-KVLCRIHY 55
>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 = 52.3 bits (125), Expect = 2e-09
Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE--KCFARNGLLFCKEDF 124
C CG ILDR++LKV WH RCL+C C L + C+ +N +FCK D+
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
Score = 32.3 bits (73), Expect = 0.031
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C+ C + I +++ +L++H+ C C +C L + Y+ +++++ CK DY
Sbjct: 1 CSSCGLEILDRYLLK-VNNLIWHVRCLECSVCRTSLRQHNSCYI-KNKEIFCKMDY 54
>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 = 51.8 bits (124), Expect = 4e-09
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDF 124
C GC I DR++LK L++ WH CLKC C L E + + L+ C+ D+
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
>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 = 50.4 bits (120), Expect = 1e-08
Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE--KCFARNGLLFCKEDFF 125
C CG I+D+++LKV + WH RCL C C L C+ ++ +FCK D+F
Sbjct: 2 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDYF 56
Score = 31.9 bits (72), Expect = 0.037
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C+ C + I +++ DL +H+ C +C +C L Y+ +D+ + CK DY
Sbjct: 2 CSSCGLEIVDKYLLK-VNDLCWHVRCLSCSVCRTSLGRHTSCYI-KDKDIFCKLDY 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 = 46.5 bits (110), Expect = 2e-07
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPD 186
CA C+ I ++ R +D VYHL CF C C + GD YL+ + +VC+ D
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDR-YLLINSDIVCEQD 54
>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 = 45.2 bits (107), Expect = 7e-07
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFF 125
CGGC I DR+ LK +++ WH CL C CG L E + + + G C+ D+
Sbjct: 1 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 56
Score = 27.9 bits (62), Expect = 1.1
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQL-NTGDEFYLMEDRKLVCKPDY 187
C GC+ I + +A D +H +C +C +C +L G Y RKL C+ DY
Sbjct: 1 CGGCQQNIG-DRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKL-CRRDY 55
>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 = 44.2 bits (105), Expect = 1e-06
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNG 116
CG CG+ ++ R I K + WH C +C C LA+ F +N
Sbjct: 1 CGKCGEFVIGRVI-KAMNNNWHPDCFRCEICNKELADIGFVKNA 43
>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 = 42.4 bits (100), Expect = 7e-06
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARN--GLLFCKEDF 124
C C +I + I++ L + +H C C CG + ++ FA + ++C +D+
Sbjct: 1 CAKCQGVITEH-IIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
Score = 37.4 bits (87), Expect = 4e-04
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDE-FYLMEDRKLVCKPDY 187
CA C+ I T+ + RA YH CF CV C R++ GDE F + E ++ C DY
Sbjct: 1 CAKCQGVI--TEHIIRALGKGYHPPCFTCVTCGRRI--GDESFAVDEQNEVYCLDDY 53
>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 = 42.3 bits (100), Expect = 7e-06
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF 112
C CG I +F ++ L +H C CH+CG P+A K F
Sbjct: 1 CAKCGKPITGQF-VRALGDVYHLDCFTCHDCGKPVASKFF 39
Score = 34.2 bits (79), Expect = 0.006
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRK-----LVCKPD 186
CA C I V RA VYHL+CF C C + + + +F+ ++D +C+ D
Sbjct: 1 CAKCGKPITGQFV--RALGDVYHLDCFTCHDCGKPVAS--KFFPVDDPDTSEQVPLCETD 56
Query: 187 Y 187
Y
Sbjct: 57 Y 57
>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin
like protein family. The second 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 = 52
Score = 41.6 bits (98), Expect = 1e-05
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
C C ILD+ + L++TWH C +CG P ++ F ++G +C+ED+
Sbjct: 1 CAYCNGPILDK-CVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 26.6 bits (59), Expect = 2.5
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C I V A D +H F C C + GDE + +D K C+ DY
Sbjct: 1 CAYCNGPILDKCVT--ALDKTWHPEHFFCAQCGKPF--GDEGFHEKDGKPYCREDY 52
>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 = 41.2 bits (97), Expect = 2e-05
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCK 121
CGGC IL+ +I L WH C C EC P F GL +C+
Sbjct: 1 CGGCNKPILENYI-SALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCE 49
Score = 25.4 bits (56), Expect = 7.1
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C GC P + A + +H CF C C + G F+ E C+ Y
Sbjct: 1 CGGC--NKPILENYISALNTQWHPECFVCRECHKPFING-SFFEHEGLPY-CETHY 52
>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 = 40.4 bits (95), Expect = 3e-05
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFF 125
C C I+ + ++ L +TWH C EC L K F R+G +C++D+
Sbjct: 1 CAACKKPIVGQ-VVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53
>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin. The first 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 cell substratum
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 or
scaffolds to support the assembly of multimeric protein.
Length = 87
Score = 40.6 bits (95), Expect = 6e-05
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLME 177
C C + TQ RA ++H+ CF C C +QL G +FY +E
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQ-GQQFYSLE 78
Score = 29.8 bits (67), Expect = 0.37
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 14/54 (25%)
Query: 73 CGGCGD-LILDRFILKVLERTWHARCLKCHEC-------------GAPLAEKCF 112
CG CG L + ++ L +H C CH+C G P E+C+
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
>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 = 39.2 bits (92), Expect = 1e-04
Identities = 17/45 (37%), Positives = 21/45 (46%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGL 117
C GC I L L WH C +CH C P+AE F+ +G
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGN 45
Score = 27.2 bits (61), Expect = 1.6
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYL 175
CAGC+ I + + A V+H CF C C + + EF +
Sbjct: 1 CAGCKSEIGHGRFLS-ALGAVWHPECFRCHACRKPI-AEHEFSV 42
>gnl|CDD|188849 cd09465, LIM2_LIMK2, The second LIM domain of LIMK2 (LIM domain
Kinase 2). The second 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 depolymerisation.
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 = 59
Score = 38.8 bits (90), Expect = 1e-04
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 127 RFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
+FG C GC + + T A + YH CFAC+ C + GD + L++ L C
Sbjct: 1 KFGELCHGCSLLM--TGPAMVAGEYKYHPECFACMSCKVIIEDGDTYALVQHTTLYC 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 = 38.5 bits (90), Expect = 2e-04
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCK 121
C CG + L R WH CL+C +C L + G +C
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCN 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 = 37.9 bits (88), Expect = 2e-04
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFAR-NGLLFCKEDF 124
C GCG + + + L WH C C +C P + F +G C+ +
Sbjct: 1 CSGCGRPVKENY-LSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52
Score = 28.6 bits (64), Expect = 0.47
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYL 175
C+GC G P + A + V+H CF C C + G F L
Sbjct: 1 CSGC--GRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFEL 42
>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin. The
third 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 = 53
Score = 37.9 bits (88), Expect = 3e-04
Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF 112
CGGC IL+ +I L WH C C EC P F
Sbjct: 1 CGGCARAILENYI-SALNTLWHPECFVCRECFTPFVNGSF 39
>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 = 37.5 bits (87), Expect = 4e-04
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKC-FARNGLLFCKEDF 124
C C I + + L +TWH C +CG L + F RNG +C+ED+
Sbjct: 3 CASCQKPIAGQVVT-ALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 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 = 37.2 bits (86), Expect = 5e-04
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
C GC I T +V A + YH CF+C+ C + GD + L+E KL C
Sbjct: 1 CHGCSETIT-TGLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYC 51
Score = 26.8 bits (59), Expect = 2.4
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGA 105
C GC + I ++ E+ +H C C CGA
Sbjct: 1 CHGCSETITTGLVMVAGEQKYHPECFSCLRCGA 33
>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 = 37.3 bits (87), Expect = 5e-04
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAK 191
C C G P + + + +YH CF C C + G FY E RK C+ D++
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDG-LFYEFEGRKY-CEHDFQVLF 58
Query: 192 A 192
A
Sbjct: 59 A 59
Score = 27.7 bits (62), Expect = 1.2
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 92 TWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
+H +C C +C P + F G +C+ DF
Sbjct: 21 LYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDF 54
>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 = 36.9 bits (86), Expect = 5e-04
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAP-LAEKCFARNGLLFCKEDF 124
P CG C I R ++ L + WH C +C P L + + + GL +C+ +
Sbjct: 1 PICGACRRPIEGR-VVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
>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 = 36.9 bits (86), Expect = 6e-04
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 145 VRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
V R QD +H+ CF C +C L G + +++ + C DY
Sbjct: 12 VLRVQDKYFHIKCFTCKVCGCDLAQGG--FFVKEGEYYCTDDY 52
Score = 33.4 bits (77), Expect = 0.012
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 85 ILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
+L+V ++ +H +C C CG LA+ F + G +C +D+
Sbjct: 12 VLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 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 = 36.1 bits (83), Expect = 0.001
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
C C ILD+ ++ L+RTWH C +CGA + F ++G +C++D+
Sbjct: 1 CYYCNGPILDK-VVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
>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 = 35.9 bits (83), Expect = 0.001
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C C G+ +A +YH NCF C C R L G FY + K+ C+ DY
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLR-GKAFYNVNG-KVYCEEDY 54
Score = 30.5 bits (69), Expect = 0.11
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 93 WHARCLKCHECGAPLAEKCFAR-NGLLFCKEDF 124
+H C C CG L K F NG ++C+ED+
Sbjct: 22 YHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
>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 = 35.9 bits (83), Expect = 0.001
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 90 ERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKE 122
+R WH C KC +C L +K FA ++ L C E
Sbjct: 23 DRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTE 56
>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner
(LPP). The first 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 = 54
Score = 35.5 bits (82), Expect = 0.002
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 148 AQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
A D VYH++CF C C L G FY ++ K C+ DY
Sbjct: 17 AMDQVYHISCFTCHQCQINLQ-GKPFYALDG-KPYCEEDY 54
Score = 29.3 bits (66), Expect = 0.30
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 89 LERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
+++ +H C CH+C L K F A +G +C+ED+
Sbjct: 18 MDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
>gnl|CDD|188743 cd09357, LIM3_Zyxin_like, The third LIM domain of Zyxin-like
family. The third LIM domain of Zyxin like family: This
family includes Ajuba, Limd1, WTIP, Zyxin, LPP, and
Trip6 LIM proteins. Members of Zyxin family contain
three tandem C-terminal LIM domains, and a proline-rich
N-terminal region. Zyxin proteins are detected
primarily in focal adhesion plaques. They function as
scaffolds, participating in the assembly of multiple
interactions and signal transduction networks, which
regulate cell adhesion, spreading, and motility. They
can also shuffle into nucleus. In nucleus, zyxin
proteins affect gene transcription by interaction with a
variety of nuclear proteins, including several
transcription factors, playing regulating roles in cell
proliferation, differentiation and apoptosis. 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 = 63
Score = 35.5 bits (82), Expect = 0.002
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 11/60 (18%)
Query: 73 CGGCGDLILDR------FILKVLERTWHARCLKCHECGAPLAEK-----CFARNGLLFCK 121
C CG+ I+ + L+R++H C KC +CG L+ + C+ +G L CK
Sbjct: 1 CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPLDGHLLCK 60
Score = 28.9 bits (65), Expect = 0.55
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 132 CAGCEMGIPPTQ----VVR-RAQDLVYHLNCFACVMCARQLNTGDE 172
C+ C I P VR A D +H+NC+ C C L++ DE
Sbjct: 1 CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLLSSEDE 46
>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The first 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 = 54
Score = 35.5 bits (82), Expect = 0.002
Identities = 17/40 (42%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 148 AQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
A D V+H++CF C+ C +L G FY +E +K C+P Y
Sbjct: 17 AMDQVFHVDCFTCMTCNGKLR-GQPFYAVE-KKAYCEPCY 54
>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog
(ENH) family. The second LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM domains
at the C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also 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. ENH
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 = 35.4 bits (81), Expect = 0.002
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
CG C IL ++ L++TWH C C C P+ F +G +C+ D+
Sbjct: 1 CGRCQRKILGE-VINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 28.5 bits (63), Expect = 0.73
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C C+ I V A +H++CF CV C + + + +ED + C+ DY
Sbjct: 1 CGRCQRKI--LGEVINALKQTWHVSCFVCVACHNPIR--NNVFHLEDGEPYCETDY 52
>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 = 35.0 bits (81), Expect = 0.003
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
C GC+ I D +H++CF C C ++L+ F ++ D L+C
Sbjct: 1 CVGCKESITEGHAYELGGDR-WHIHCFKCYKCDKKLSCDSNFLVLGDGSLIC 51
Score = 33.9 bits (78), Expect = 0.007
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPL 107
C GC + I + ++ WH C KC++C L
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKL 35
>gnl|CDD|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like
family. The second 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 = 56
Score = 34.9 bits (81), Expect = 0.004
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLA-EKCFARNGLLFC 120
P+C C +LI + + WH + C +C PL ++ R G +C
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51
Score = 29.1 bits (66), Expect = 0.33
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
+CA C+ I + + A+ +HL F C C L G + Y++ + K C YE
Sbjct: 2 RCAACDELIFSGEYTQ-AEGKNWHLKHFCCFQCDEPL--GGQRYVLREGKPYCLDCYE 56
>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 = 34.3 bits (79), Expect = 0.005
Identities = 14/32 (43%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 152 VYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
VYH CF C C QL G FY E C
Sbjct: 24 VYHRTCFKCARCGVQLTPG-SFYETEYGSYCC 54
Score = 28.9 bits (65), Expect = 0.52
Identities = 11/37 (29%), Positives = 15/37 (40%)
Query: 72 KCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLA 108
C CG + L + + +H C KC CG L
Sbjct: 4 PCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLT 40
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 33.6 bits (78), Expect = 0.006
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 227 PKPARHVREQLSQDTGLDMRVVQVWFQNRR 256
P P+ + +L++ TGL + + WF N R
Sbjct: 9 PYPSEEEKSELARQTGLSRKQIDNWFINAR 38
>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 = 34.1 bits (78), Expect = 0.006
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+CAGC+ I + + A++ +HL F C C L E Y+M + K VCKP Y
Sbjct: 2 RCAGCDELIFSNEYTQ-AENQNWHLKHFCCFDCDNIL--AGEIYVMVNDKPVCKPCY 55
Score = 28.7 bits (64), Expect = 0.59
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF 112
P+C GC +LI + + WH + C +C LA + +
Sbjct: 1 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIY 42
>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 = 34.0 bits (78), Expect = 0.006
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
C C IL +L +++TWH C CG ++ F R+G +C+ DF
Sbjct: 1 CAYCAGPILQN-VLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
>gnl|CDD|188819 cd09435, LIM3_Zyxin, The third LIM domain of Zyxin. The third 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 or
scaffolds to support the assembly of multimeric protein.
Length = 67
Score = 34.5 bits (79), Expect = 0.007
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 89 LERTWHARCLKCHECGAPL-----AEKCFARNGLLFCKE 122
LE+ +H +C KC +CG PL CF +G + C +
Sbjct: 23 LEKNFHMKCYKCEDCGRPLSIEADDNGCFPLDGHVLCMK 61
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second 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 = 52
Score = 33.6 bits (77), Expect = 0.009
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C I V A +H++CF C C + + G+ + MED + C+ DY
Sbjct: 1 CARCHKKI--LGEVMHALKQTWHVSCFVCAACKQPI--GNSLFHMEDGEPYCEKDY 52
Score = 32.4 bits (74), Expect = 0.025
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
C C IL ++ L++TWH C C C P+ F +G +C++D+
Sbjct: 1 CARCHKKILGE-VMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher
family. The first LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. 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 = 52
Score = 33.4 bits (76), Expect = 0.011
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF 112
CG C ++I F++ L R+WH CH C LA+ F
Sbjct: 1 CGHCNNIIRGPFLV-ALGRSWHPEEFTCHYCHTSLADVSF 39
>gnl|CDD|188751 cd09365, LIM2_LIMK, The second LIM domain of LIMK (LIM domain
Kinase ). The second 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 depolymerization. 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 = 54
Score = 33.1 bits (76), Expect = 0.013
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C GC I T V A D +H CF+C C + GD + L+E KL C Y
Sbjct: 1 CHGCSQII--TGPVMVAGDHKFHPECFSCSSCKAFIGDGDSYALVERSKLYCGVCY 54
>gnl|CDD|188829 cd09445, LIM_Mical_like_2, 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 = 53
Score = 32.8 bits (75), Expect = 0.016
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 148 AQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKP 185
A+ +YH NCF C C +QL + Y + L CK
Sbjct: 16 AEKHIYHKNCFRCKDCNKQLKV--DNYQSHEGNLYCKV 51
Score = 27.4 bits (61), Expect = 1.2
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 93 WHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
+H C +C +C L + + G L+CK F
Sbjct: 21 YHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 53
>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 = 0.016
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C+ I T + +A YH CF CV+C L G+ F + + + C DY
Sbjct: 1 CAVCDQKI--TDRMLKATGKSYHPQCFTCVVCKCPLE-GESFIVDQANQPHCVNDY 53
Score = 31.8 bits (72), Expect = 0.046
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA--RNGLLFCKEDFFKRFGT 130
C C I DR +LK +++H +C C C PL + F + C D+ +R+
Sbjct: 1 CAVCDQKITDR-MLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAP 59
Query: 131 K 131
+
Sbjct: 60 R 60
>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 = 32.9 bits (75), Expect = 0.019
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGL--LFCKEDFFKRFGT 130
C C ILDR IL+ + +H +C C CG L F + + C EDF K+F
Sbjct: 1 CSVCSKPILDR-ILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAP 59
Query: 131 K 131
+
Sbjct: 60 R 60
Score = 29.8 bits (67), Expect = 0.28
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLN 168
C+ C P + RA YH CF CV+C + L+
Sbjct: 1 CSVCSK--PILDRILRATGKPYHPQCFTCVVCGKSLD 35
>gnl|CDD|188714 cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM
(abLIM) proteins. The second 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 = 32.7 bits (75), Expect = 0.019
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 72 KCGGCGDLILDRFILKVLERTWHARCLKCHECGAP 106
KC C D + + L +T+H +C C C P
Sbjct: 3 KCDSCQDFVEGEVVS-ALGKTYHPKCFVCSVCRQP 36
Score = 31.2 bits (71), Expect = 0.069
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 129 GTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGD 171
GTKC C+ + V A YH CF C +C + GD
Sbjct: 1 GTKCDSCQDFV--EGEVVSALGKTYHPKCFVCSVCRQPFPPGD 41
>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 = 32.4 bits (74), Expect = 0.020
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGL-LFC 120
C CG I D IL + + + C +C C + + +A+ LFC
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDITDLKYAKTKRGLFC 49
Score = 26.7 bits (59), Expect = 2.7
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQL 167
C C I T ++ + D Y +CF C C+R +
Sbjct: 1 CKNCGKKIDDTAILL-SSDEAYCSDCFRCRRCSRDI 35
>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 = 32.3 bits (74), Expect = 0.023
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA--RNGLLFCKEDF 124
C CG LI++ IL+ L +++H C +C C L F ++C +D+
Sbjct: 1 CAVCGHLIMEM-ILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
Score = 28.5 bits (64), Expect = 0.64
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 153 YHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
YH CF C +C L+ G F + + + C DY
Sbjct: 20 YHPGCFRCCVCNECLD-GVPFTVDVENNIYCVKDY 53
>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 = 32.6 bits (75), Expect = 0.023
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 90 ERTWHARCLKCHECGAPLAEKC-FARNGLLFC 120
+ WH C C C L + F +G ++C
Sbjct: 23 DACWHPGCFVCETCNELLVDLIYFYHDGKIYC 54
Score = 28.7 bits (65), Expect = 0.62
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 4/40 (10%)
Query: 132 CAGCEMGIPPTQVV----RRAQDLVYHLNCFACVMCARQL 167
C C+ I P +V R +D +H CF C C L
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELL 40
>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 = 32.2 bits (74), Expect = 0.025
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 152 VYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
++H +CF C C + L G+ Y + KL CKP +
Sbjct: 20 LFHKSCFRCSHCNKTLRLGN--YASLEGKLYCKPHF 53
Score = 31.9 bits (73), Expect = 0.034
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 86 LKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCK 121
L + +H C +C C L +A G L+CK
Sbjct: 14 LVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCK 50
>gnl|CDD|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like
family. The first 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 = 52
Score = 31.6 bits (72), Expect = 0.043
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFC 120
C C +I F++ L R+WH C C LAE F G L+C
Sbjct: 1 CAHCNQVIRGPFLV-ALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYC 48
>gnl|CDD|188820 cd09436, LIM3_TRIP6, The third LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The third 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 = 66
Score = 31.9 bits (72), Expect = 0.054
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 4/37 (10%)
Query: 89 LERTWHARCLKCHECGAPLAE----KCFARNGLLFCK 121
L+R +H +C +C +CG+ L+E C+ +G + CK
Sbjct: 23 LDRDFHVQCYRCEDCGSLLSEGDNQGCYPLDGHILCK 59
>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 = 31.6 bits (72), Expect = 0.054
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 3/56 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C C + + + A YH+ F C +C D +Y E K+ C Y
Sbjct: 1 CFKCGGALRGSYIT--ALGRKYHVEHFTCSVCPTVFGPNDSYYEHEG-KIYCHYHY 53
>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 = 31.2 bits (70), Expect = 0.082
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
C GC+ I A +H CF C +C L G FY +D+ L CK
Sbjct: 1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLE-GKTFYSKKDKPL-CK 51
>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 = 30.8 bits (70), Expect = 0.085
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 4/52 (7%)
Query: 73 CGGCGDLI-LDRFILKVLERTWHA--RCLKCHECGAPLAEKCF-ARNGLLFC 120
C CG+ I D + + WHA C C C L + F +NG +FC
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFC 52
>gnl|CDD|188802 cd09418, LIM2_Prickle, The second LIM domain of Prickle. The
second 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 = 56
Score = 30.9 bits (70), Expect = 0.094
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPL 107
P+C C ++I + R WH + C EC L
Sbjct: 1 PRCSACDEIIFADECTEAEGRHWHMKHFCCFECECQL 37
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth 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 = 54
Score = 30.9 bits (70), Expect = 0.096
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 73 CGGCGDLILDRFILKVLE---RTWHARCLKCHECGAPLAEKCF-ARNGLLFC 120
C GCG++ R +K +E + WH +C C EC P+ K F ++ ++C
Sbjct: 1 CDGCGEIF--RAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50
>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 = 30.7 bits (69), Expect = 0.10
Identities = 20/53 (37%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
C C GI T V +A+D +YH CF C C LN Y D +L C+
Sbjct: 1 CTRCGNGIVGTIV--KARDKLYHPECFMCDDCG--LNLKQRGYFFIDEQLYCE 49
Score = 26.4 bits (58), Expect = 3.9
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFF 125
C CG+ I+ I+K ++ +H C C +CG L ++ G F E +
Sbjct: 1 CTRCGNGIVGT-IVKARDKLYHPECFMCDDCGLNLKQR-----GYFFIDEQLY 47
>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 = 30.3 bits (69), Expect = 0.12
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 73 CGGCGDLIL--DRFILKVLERTWHARCLKCHECGAPLAEKCF 112
C CG I+ + ++ + WH +C C EC P+ K F
Sbjct: 1 CKACGKAIMPGSK-KMEYKGKFWHEKCFTCSECKKPIGTKSF 41
>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 = 30.4 bits (68), Expect = 0.12
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFAR-NGLLFC 120
C GCG + + L R WH CL+C C L A +G +C
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH)
family. The third LIM domain of the Enigma Homolog
(ENH) family: ENH was initially identified in rat brain.
Same as enigma, it contains three LIM domains at the
C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also 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. ENH
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 = 30.3 bits (68), Expect = 0.12
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
C GCE I A +H CF C +C L G F+ +D K +CK
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLE-GQTFFSKKD-KPLCK 51
>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 = 30.2 bits (68), Expect = 0.14
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLN 168
C+ C P + + RA YH +CF CV+C R L+
Sbjct: 1 CSVCSK--PIMERILRATGKAYHPHCFTCVVCHRSLD 35
Score = 28.3 bits (63), Expect = 0.70
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARN--GLLFCKEDF 124
C C I++R IL+ + +H C C C L F + G + C EDF
Sbjct: 1 CSVCSKPIMER-ILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53
>gnl|CDD|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting
with CasL). The LIM domain of Mical (molecule
interacting with CasL): MICAL is a large, multidomain,
cytosolic protein with a single LIM domain, a calponin
homology (CH) domain and a flavoprotein monooxygenase
domain. In Drosophila, MICAL is expressed in axons,
interacts with the neuronal A (PlexA) receptor and is
required for Semapho-rin 1a (Sema-1a)-PlexA-mediated
repulsive axon guidance. The LIM domain and calporin
homology domain are known for interactions with the
cytoskeleton, cytoskeletal adaptor proteins, and other
signaling proteins. The flavoprotein monooxygenase (MO)
is required for semaphorin-plexin repulsive axon
guidance during axonal pathfinding in the Drosophila
neuromuscular system. In addition, MICAL was
characterized to interact with Rab13 and Rab8 to
coordinate the assembly of tight junctions and adherens
junctions in epithelial cells. Thus, MICAL was also
named junctional Rab13-binding protein (JRAB). 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 = 30.0 bits (68), Expect = 0.16
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 148 AQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
A+ L +H +CF C C L G + +D K CKP +
Sbjct: 16 AEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 55
Score = 25.7 bits (57), Expect = 5.8
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 91 RTWHARCLKCHECGAPLAEKCFA---RNGLLFCKEDF 124
+H C KC CG L +A +G +CK F
Sbjct: 19 LFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 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 = 30.0 bits (67), Expect = 0.19
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C+ I T + A + +H++CF C C + + + ME+ C+ DY
Sbjct: 1 CAKCKKKI--TGEIMHALKMTWHVHCFTCAAC--KTPIRNRAFYMEEGAPYCERDY 52
>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of
proteins with unknown function. This model represents a
LIM domain subfamily of Eplin-like family. This family
shows highest homology to the LIM domains on Eplin and
XIRP2 protein families. Epithelial Protein Lost in
Neoplasm is a cytoskeleton-associated tumor suppressor
whose expression inversely correlates with cell growth,
motility, invasion and cancer mortality. Xirp2 is
expressed in muscles and is an important effector of the
Ang II signaling pathway in the heart. 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 = 29.5 bits (66), Expect = 0.23
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C+ C+ + P + + A LV+H +CF C C +L+ G Y + CKP +
Sbjct: 1 CSSCQKTVYPMERLV-ADKLVFHNSCFCCKHCNAKLSLGS--YAALHGEFYCKPHF 53
>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 = 29.7 bits (67), Expect = 0.23
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCK 121
C CG + L L++ WH C KC CG L K + N +C
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCN 50
Score = 25.8 bits (57), Expect = 5.8
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLN 168
CA C + PT+ + D ++H CF C +C LN
Sbjct: 1 CARCGKTVYPTEKLN-CLDKIWHKGCFKCEVCGMTLN 36
>gnl|CDD|188822 cd09438, LIM3_Ajuba_like, The third LIM domain of Ajuba-like
proteins. The third 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 = 62
Score = 29.7 bits (67), Expect = 0.25
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 9/44 (20%)
Query: 132 CAGCEMGIPPTQ-------VVRRAQDLVYHLNCFACVMCARQLN 168
CA C I P + VV +D YH+ C+ C C QLN
Sbjct: 1 CAACGQPILPAEGSEETIRVVSMDKD--YHVECYHCEDCGLQLN 42
Score = 28.5 bits (64), Expect = 0.61
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 73 CGGCGDLIL-----DRFILKV-LERTWHARCLKCHECGAPLAEK----CFARNGLLFCK 121
C CG IL + I V +++ +H C C +CG L ++ C+ +G L C
Sbjct: 1 CAACGQPILPAEGSEETIRVVSMDKDYHVECYHCEDCGLQLNDEEGHRCYPLDGHLLCH 59
>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 = 29.4 bits (66), Expect = 0.25
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 73 CGGCGDLIL--DRFILKVLERTWHARCLKCHECGAPL-AEKCFARNGLLFCK 121
C CG I DR++ + L +H++C C C L + +A+ G FCK
Sbjct: 1 CVSCGFPIEAGDRWV-EALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51
Score = 25.6 bits (56), Expect = 6.7
Identities = 14/43 (32%), Positives = 15/43 (34%), Gaps = 1/43 (2%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFY 174
C C I A + YH CF C C L G FY
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLE-GQSFY 42
>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 = 29.4 bits (66), Expect = 0.29
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE-KCFARNGLLFC 120
C C +I R+++ L R++H C +C L E F G +FC
Sbjct: 1 CAQCNKIIRGRYLV-ALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFC 48
>gnl|CDD|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein
Lost in Neoplasm (Eplin). The Lim domain of Epithelial
Protein Lost in Neoplasm (Eplin): Epithelial Protein
Lost in Neoplasm is a cytoskeleton-associated tumor
suppressor whose expression inversely correlates with
cell growth, motility, invasion and cancer mortality.
Eplin interacts and stabilizes F-actin filaments and
stress fibers, which correlates with its ability to
suppress anchorage independent growth. In epithelial
cells, Eplin is required for formation of the F-actin
adhesion belt by binding to the E-cadherin-catenin
complex through alpha-catenin. Eplin is expressed in two
isoforms, a longer Eplin-beta and a shorter Eplin-alpha.
Eplin-alpha mRNA is detected in various tissues and cell
lines, but is absent or down regulated in cancer 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 = 29.1 bits (65), Expect = 0.33
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C C+ + P + + A +YH +CF C C +L+ G Y + CKP +
Sbjct: 1 CVSCQKTVYPLERLV-ANQQIYHNSCFRCSYCNTKLSLGT--YASLHGNIYCKPHF 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 = 28.9 bits (65), Expect = 0.37
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
C GC+ I A +H CF C +C L G FY +D+ L CK
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLE-GQTFYSKKDKPL-CK 51
>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM
domains protein 1 (FHL1). The third 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 = 53
Score = 29.0 bits (65), Expect = 0.38
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDR 179
C C I V QD +H CF C C+++L G F +ED+
Sbjct: 1 CVKCNKPITSGGVTY--QDQPWHSECFVCSSCSKKL-AGQRFTAVEDQ 45
>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 = 29.3 bits (66), Expect = 0.40
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 72 KCGGCGDLILD----RFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKED 123
KC GC + I ++ +WH C C +C LA K F NG ++C +
Sbjct: 4 KCSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60
>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 = 0.40
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCK 121
C CGD + + + WH C +C +CG L + G ++CK
Sbjct: 1 CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50
>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 = 28.8 bits (65), Expect = 0.42
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 90 ERTWHARCLKCHECGAPLAEKCF 112
ER WH+ C C +C L + F
Sbjct: 21 ERQWHSDCFNCGKCSVSLVGQGF 43
>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein
SF3. The first 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 = 63
Score = 29.0 bits (65), Expect = 0.43
Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 4/60 (6%)
Query: 72 KCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFAR-NGLLFCK---EDFFKR 127
KC C + L +H C +C C L ++ G+L+CK E FK
Sbjct: 4 KCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE 63
Score = 29.0 bits (65), Expect = 0.51
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
KC C+ + + A +VYH +CF C C L + Y + L CKP +E
Sbjct: 4 KCKACDKTVYLVDQLS-ADGVVYHKSCFRCSHCKGTLKLSN--YSSMEGVLYCKPHFE 58
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first 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 = 59
Score = 29.1 bits (65), Expect = 0.45
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
F C C+ I +D YH +CF C C R L DE + +D +L+C Y
Sbjct: 1 FANTCDECKELIGHDSRELYYEDRHYHEHCFRCFRCDRSL--ADEPFTCQDEELLCNDCY 58
>gnl|CDD|224562 COG1648, CysG, Siroheme synthase (precorrin-2
oxidase/ferrochelatase domain) [Coenzyme metabolism].
Length = 210
Score = 31.1 bits (71), Expect = 0.46
Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 7/51 (13%)
Query: 225 TSPKPARHVREQ----LSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRTRW 271
SP AR +RE+ L G + + R + L K R R+
Sbjct: 131 KSPVLARLLREKIEALLPPSLGEVAELAA---RLRERVKGSLPKGKERRRF 178
>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 = 28.9 bits (65), Expect = 0.54
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 132 CAGCEMGIPPTQVV----RRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C GC + ++ + + L++H CF C C L D Y + D ++ C+ Y
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLV--DLTYCVHDDQIYCERHY 58
Score = 26.2 bits (58), Expect = 4.3
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 11/39 (28%)
Query: 73 CGGCGD--------LILDRFILKVLERTWHARCLKCHEC 103
CGGC + + +F +L WH C +C C
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLL---WHPACFRCSTC 36
>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 = 28.4 bits (64), Expect = 0.62
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 153 YHLNCFACVMCARQLNTGDEFYLMEDR 179
+H CF C C Y+++D+
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDK 50
Score = 25.3 bits (56), Expect = 8.6
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 93 WHARCLKCHECGAPLAEK--CFARNGLLFCK 121
WH C C CG P C+ + +C+
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQ 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 = 28.3 bits (63), Expect = 0.65
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 91 RTWHARCLKCHECGAPLAEKCFA-RNGLLFCK 121
+ WH C +C +CG L A ++G ++CK
Sbjct: 19 KPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50
>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 = 28.3 bits (64), Expect = 0.65
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 91 RTWHARCLKCHECGAPL-AEKCFARNGLLFCK 121
++WH C C C L + +G ++CK
Sbjct: 19 KSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50
>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 = 28.3 bits (63), Expect = 0.72
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 72 KCGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPLAEKCF 112
KC CG ++ L+ +TWH C CH C P+ + F
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSF 44
Score = 27.5 bits (61), Expect = 1.5
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 130 TKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
+KC C + P + +H +CF C C + + G ++ + + C P YE
Sbjct: 2 SKCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPI--GSRSFIPDKDEHYCVPCYE 58
>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 = 28.1 bits (63), Expect = 0.72
Identities = 17/49 (34%), Positives = 19/49 (38%), Gaps = 8/49 (16%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQL------NTGDEFY 174
C C GI VV +A+D H CF C C L DE Y
Sbjct: 1 CDKCGNGI--VGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELY 47
Score = 27.7 bits (62), Expect = 1.2
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEK 110
C CG+ I+ + K ++ H C C +CG L K
Sbjct: 1 CDKCGNGIVGVVV-KARDKNRHPECFVCADCGLNLKNK 37
>gnl|CDD|188719 cd09333, LIM3_PINCH, The third LIM domain of protein PINCH. The
third LIM domain of protein PINCH: PINCH plays pivotal
roles 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 = 51
Score = 28.1 bits (63), Expect = 0.72
Identities = 8/28 (28%), Positives = 10/28 (35%)
Query: 93 WHARCLKCHECGAPLAEKCFARNGLLFC 120
+H C CG L G L+C
Sbjct: 20 YHPYHFNCANCGKELTADARELKGELYC 47
>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 = 28.0 bits (62), Expect = 0.98
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
CA C + PT+ V D +H CF C +C LN + Y +K C Y
Sbjct: 1 CARCGKIVYPTEKVN-CLDKTWHKACFHCEVCKMTLNMNN--YKGYQKKPYCNAHY 53
Score = 26.1 bits (57), Expect = 4.0
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF 112
C CG ++ + L++TWH C C C L +
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNY 40
>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost
in Neoplasm (Eplin) like proteins. The Lim domain of
Epithelial Protein Lost in Neoplasm (Eplin) like
proteins: This family contains Epithelial Protein Lost
in Neoplasm in Neoplasm (Eplin), xin actin-binding
repeat-containing protein 2 (XIRP2) and a group of
protein with unknown function. The members of this
family all contain a single LIM domain. Epithelial
Protein Lost in Neoplasm is a cytoskeleton-associated
tumor suppressor whose expression inversely correlates
with cell growth, motility, invasion and cancer
mortality. Eplin interacts and stabilizes F-actin
filaments and stress fibers, which correlates with its
ability to suppress anchorage independent growth. In
epithelial cells, Eplin is required for formation of the
F-actin adhesion belt by binding to the
E-cadherin-catenin complex through alpha-catenin. Eplin
is expressed in two isoforms, a longer Eplin-beta and a
shorter Eplin-alpha. Eplin-alpha mRNA is detected in
various tissues and cell lines, but is absent or down
regulated in cancer cells. Xirp2 contains a LIM domain
and Xin re peats for binding to and stabilising F-actin.
Xirp2 is expressed in muscles and is significantly
induced in the heart in response to systemic
administration of angiotensin II. Xirp2 is an important
effector of the Ang II signaling pathway in the heart.
The expression of Xirp2 is activated by myocyte enhancer
factor (MEF)2A, whose transcriptional activity is
stimulated by angiotersin II. Thus, Xirp2 plays
important pathological roles in the angiotensin II
induced hypertension. 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 = 27.8 bits (62), Expect = 1.0
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C C+ + P + + A +H +CF C C +L+ G+ Y ++ CKP +
Sbjct: 1 CTVCQKRVYPMERLI-ADKQNFHKSCFRCEHCNSKLSLGN--YASLHGRIYCKPHF 53
>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 = 27.7 bits (62), Expect = 1.0
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYL 175
C C+ I T V A YH C C C + G+E YL
Sbjct: 1 CEACDKFI--TGKVLEAGGKHYHPTCARCSRCGQMFGEGEEMYL 42
>gnl|CDD|145054 pfam01700, Orbi_VP3, Orbivirus VP3 (T2) protein. The orbivirus VP3
protein is part of the virus core and makes a 'subcore'
shell made up of 120 copies of the 100K protein. VP3
particles can also bind RNA and are fundamental in the
early stages of viral core formation. Also found in the
family is structural core protein VP2 from broadhaven
virus which is similar to VP3 in bluetongue virus.
Orbivirus are part of the larger reoviridae which have a
dsRNA genome of 10-12 linear segments; orbivirus found
in this family include bluetongue virus and epizootic
hemorrhagic disease virus.
Length = 890
Score = 30.5 bits (69), Expect = 1.4
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 207 PRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266
P +TA+ + K SP+P R + + + ++MR + W ++ + L
Sbjct: 614 PDVFVTARPSDFWKAVLKESPEPVRAIMDLSGSHSFINMRDIMRWVRS-PLLQDSLLLVL 672
Query: 267 GRTRW 271
R W
Sbjct: 673 EREAW 677
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung at
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. 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.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. 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 = 62
Score = 27.6 bits (61), Expect = 1.7
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 90 ERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKE 122
+R WH C C +C L +K FA + L C E
Sbjct: 23 DRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTE 56
>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher
family. The third LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. 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 = 55
Score = 27.3 bits (60), Expect = 1.7
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
C GC+ + A +H CF C +C L G FY +D+ L CK
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDKPL-CK 51
>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 = 27.4 bits (61), Expect = 1.7
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 89 LERTWHARCLKCHECGAPLAEK-----CFARNGLLFCKEDFFKR 127
L+R++H +C KC +CG L+ + C+ + + CK KR
Sbjct: 23 LDRSFHVQCYKCEDCGLLLSSEAEGRGCYPLDDHVLCKSCNAKR 66
>gnl|CDD|188730 cd09344, LIM1_FHL1, The first LIM domain of Four and a half LIM
domains protein 1. The first 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 = 54
Score = 27.0 bits (60), Expect = 1.9
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 90 ERTWHARCLKCHECGAPLAEKCF 112
R WH C +C +C PLA + F
Sbjct: 19 NRYWHETCFRCAKCYKPLANEPF 41
>gnl|CDD|188808 cd09424, LIM2_FHL1, The second LIM domain of Four and a half LIM
domains protein 1 (FHL1). The second 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 = 58
Score = 27.4 bits (61), Expect = 1.9
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEA 189
C GC I + V+H +CF C C + + T + + C P +E
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKS--FFPKGEDFYCVPCHEK 56
>gnl|CDD|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM
domains protein 2 (FHL2). The second LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. 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.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. 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 s upport the assembly of multimeric protein
complexes.
Length = 57
Score = 27.3 bits (60), Expect = 1.9
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 92 TWHARCLKCHECGAPLAEKCF 112
+WH C C C P+ K F
Sbjct: 21 SWHETCFICQRCQQPIGTKSF 41
>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 = 27.1 bits (60), Expect = 1.9
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 73 CGGCGDLI-LDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFC 120
C C +I +D L ++ WH C C +C L +K F ++ ++C
Sbjct: 5 CEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYC 54
>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 = 27.0 bits (60), Expect = 2.1
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 90 ERTWHARCLKCHECGAPLAEKCF 112
+R WH C KC C L F
Sbjct: 21 DRQWHQPCFKCSRCSVSLVGAGF 43
>gnl|CDD|188721 cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH. The
fifth LIM domain of protein PINCH: PINCH plays pivotal
roles 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 = 54
Score = 26.9 bits (60), Expect = 2.3
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 156 NCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
+ F+C C +L +FY D K VCK Y+
Sbjct: 23 DHFSCSFCDTKLTLKSKFYEF-DMKPVCKKCYD 54
>gnl|CDD|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2. The
first LIM domain of Prickle 2: 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 = 26.8 bits (59), Expect = 2.7
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 146 RRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
R + +H CF C +C L D Y +D K+ C
Sbjct: 19 RAGHGVCWHPQCFVCSVCNELLV--DLIYFYQDGKIYC 54
>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 = 26.3 bits (58), Expect = 3.4
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 90 ERTWHARCLKCHECGAPLAEKCFARNG 116
+R WH C C C L K F +G
Sbjct: 21 DRHWHNDCFNCAGCRTSLVGKGFITDG 47
>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 = 3.6
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 92 TWHARCLKCHECGAPLAEK--CFARNGL-LFCKED 123
+H C KC ECG L+ K F + ++C
Sbjct: 20 FYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54
>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin. The
fourth 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 = 26.2 bits (58), Expect = 3.7
Identities = 15/43 (34%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARN 115
CG CG I R I L R +H C C PL + F
Sbjct: 1 CGSCGLPITGRCI-SALGRKFHPEHFVCAFCLRPLTQGSFKEQ 42
Score = 25.5 bits (56), Expect = 8.2
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTG 170
C C G+P T A +H F C C R L G
Sbjct: 1 CGSC--GLPITGRCISALGRKFHPEHFVCAFCLRPLTQG 37
>gnl|CDD|202300 pfam02591, DUF164, Putative zinc ribbon domain. Structural
modelling suggests this domain may bind nucleic acids.
Length = 56
Score = 26.4 bits (59), Expect = 3.8
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 132 CAGCEMGIPPT--QVVRRAQDLVYHLNC 157
C GC M +PP +R+ ++V +C
Sbjct: 25 CGGCRMELPPQTLNELRKGDEIVRCPHC 52
>gnl|CDD|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal
Protein (CRIP). The LIM domain of Cysteine-Rich
Intestinal Protein (CRIP): CRIP is a short 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 = 54
Score = 26.0 bits (57), Expect = 4.8
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 89 LERTWHARCLKCHECGAPL 107
L + WH CLKC +CG L
Sbjct: 17 LGKDWHRPCLKCEKCGKTL 35
>gnl|CDD|188817 cd09433, LIM4_FHL2, The fourth LIM domain of Four and a half LIM
domains protein 2 (FHL2). The fourth LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. 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.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. 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 s upport the assembly of multimeric protein
complexes.
Length = 58
Score = 26.1 bits (57), Expect = 4.9
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 90 ERTWHARCLKCHECGAPLAEKCF 112
ER WH C C +C L + F
Sbjct: 21 ERQWHNDCFNCKKCSLSLVGRGF 43
>gnl|CDD|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein
(TLP). The first 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 = 25.7 bits (56), Expect = 5.6
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 89 LERTWHARCLKCHECGAPLAEKCFAR-NGLLFC 120
L + WH CLKC C L+ A +G +C
Sbjct: 17 LGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49
>gnl|CDD|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP,
actinin-associated LIM protein. This family represents
the LIM domain of ALP, actinin-associated LIM protein.
ALP contains an N-terminal PDZ domain, a C-terminal LIM
domain and an ALP-subfamily-specific 34-amino-acid motif
termed ALP-like motif (AM), which contains a putative
consensus protein kinase C (PKC) phosphorylation site
and two alpha-helices. ALP proteins are found in heart
and in skeletal muscle. ALP may act as a signaling
molecule which is regulated by PKC-dependent signaling.
ALP plays an essential role in the development of RV
(right ventricle) chamber. 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 = 5.8
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
C C GI T V +A+D H CF C C LN + Y + +L C+
Sbjct: 1 CDKCGSGIVGTVV--KARDKYRHPECFVCSDC--NLNLKQKGYFFVEGQLYCE 49
Score = 25.6 bits (56), Expect = 6.2
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEK-CFARNGLLFCK 121
C CG I+ ++K ++ H C C +C L +K F G L+C+
Sbjct: 1 CDKCGSGIVGT-VVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49
>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 = 25.7 bits (57), Expect = 6.5
Identities = 15/56 (26%), Positives = 19/56 (33%), Gaps = 6/56 (10%)
Query: 132 CAGCEMGIPPTQVV----RRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
C C I + R +H CF C C L D Y +D K+ C
Sbjct: 1 CEQCGEQISGGDIAVFASRAGPGACWHPACFVCSTCKELLV--DLIYFYQDGKVYC 54
>gnl|CDD|236693 PRK10433, PRK10433, putative RNA methyltransferase; Provisional.
Length = 228
Score = 27.6 bits (62), Expect = 6.7
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 8/36 (22%)
Query: 3 DVKAKSFLYQRIGLAVQRGNGLTVGICASKLHDLLH 38
D K +L QR+GL QR + LH LLH
Sbjct: 193 DEKLVDWLQQRLGLLEQRDTAM--------LHRLLH 220
>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 = 6.8
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 90 ERTWHARCLKCHECGAPLAEKC-FARNGLLFC 120
++ WH C C CG L + F +NG L+C
Sbjct: 23 DKLWHPACFVCSTCGELLVDMIYFWKNGKLYC 54
>gnl|CDD|227474 COG5145, RAD14, DNA excision repair protein [DNA replication,
recombination, and repair].
Length = 292
Score = 27.7 bits (61), Expect = 8.3
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 62 PVYMPIASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCK 121
P+ +PIA PKC C + LD LE T+ C C + +K + CK
Sbjct: 108 PILLPIALAPKCKECLQIELD----DELEDTFGISV--CRSCRHSMPDK-YKLLTKTECK 160
Query: 122 EDFF 125
D+
Sbjct: 161 SDYL 164
>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 = 25.4 bits (55), Expect = 8.6
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 91 RTWHARCLKCHECGAPLAEKCFA-RNGLLFCK 121
+ WH C +C CG L ++G L+CK
Sbjct: 19 KPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50
>gnl|CDD|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin. The
fourth 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 = 25.3 bits (55), Expect = 9.6
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTG 170
C+GC+ P T A +H F C C +QLN G
Sbjct: 1 CSGCQK--PITGRCITAMGKKFHPEHFVCAFCLKQLNKG 37
>gnl|CDD|216792 pfam01927, DUF82, Protein of unknown function DUF82. This
prokaryotic protein family has no known function. The
protein contains four conserved cysteines that may be
involved in metal binding or disulphide bridges.
Length = 146
Score = 26.8 bits (60), Expect = 9.9
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 80 ILDRFILKVLERTWHARCLKCHECGAPLA--EKCFARNGLLFCKEDFFKRFGTKCAGC 135
+++RF LK+ + +RCLKC+ PL K + + + F +C C
Sbjct: 76 VIERFGLKLSLKPEFSRCLKCN---GPLEPVSKEEVAGRVPPYVYERYDEF-WRCPKC 129
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
0.322 0.136 0.428
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,263,074
Number of extensions: 1400764
Number of successful extensions: 1381
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1345
Number of HSP's successfully gapped: 247
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.6 bits)