RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7479
(170 letters)
>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 = 104 bits (261), Expect = 2e-30
Identities = 49/55 (89%), Positives = 53/55 (96%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CAAC+K IPAFEMVMRA+ NVYHLECFACQ+CNHRFCVGDRFYLC+NKILCEYDY
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55
Score = 28.3 bits (63), Expect = 0.42
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 20 CASCGKRITE-RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA+C K I +++A +H +C C C+ R VG Y N ILC+ DY
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFC-VGDRFYLCENKILCEYDY 55
>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 = 95.3 bits (237), Expect = 1e-26
Identities = 43/55 (78%), Positives = 49/55 (89%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDY
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
Score = 27.9 bits (62), Expect = 0.54
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC-VGDRFYLCDNKILCEYDY 138
CA C + I +++A + +H +C C C+ R VG Y N ILC DY
Sbjct: 1 CAGCNRKIKD-RYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
>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 = 86.6 bits (214), Expect = 3e-23
Identities = 42/55 (76%), Positives = 50/55 (90%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CAAC+K+IPAFEMVMRAK+NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ DY
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55
Score = 35.4 bits (81), Expect = 0.001
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 20 CASCGKRITE-RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA+C K I +++A D +H DC C C+ R VG + K N+ILC+ DY
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFC-VGDKFFLKNNMILCQMDY 55
>gnl|CDD|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only
protein 4). The first LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact
with Smad proteins, and associate with the promoter of
the PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential
role for LMO4 as a negative regulator of BRCA1 in
sporadic breast cancer. LMO4 also forms complex to
both ERa (oestrogen receptor alpha), MTA1 (metastasis
tumor antigen 1), and HDACs (histone deacetylases),
implying that LMO4 is also a component of the MTA1
corepressor complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 74.8 bits (184), Expect = 1e-18
Identities = 33/55 (60%), Positives = 40/55 (72%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA CG +I +RFLL ALD +WH CLKC CC +LGE+GS+ Y K +ILCK DY
Sbjct: 1 CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
>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 = 70.6 bits (173), Expect = 5e-17
Identities = 27/54 (50%), Positives = 39/54 (72%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
C+AC + IPA E+VMRA+ NVYHL+CF C C+++ GDRF+ + + CE+D
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 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 = 66.8 bits (163), Expect = 1e-15
Identities = 32/56 (57%), Positives = 38/56 (67%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYL 75
C C + I +R+ LKA+D +WHEDCL C C CRLGEVG LY K LC+RDYL
Sbjct: 1 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 56
>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 = 64.7 bits (157), Expect = 8e-15
Identities = 31/54 (57%), Positives = 38/54 (70%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
CA+C K I A+EM MR K+ VYHLECF C C FCVGDR+ L ++ I+CE D
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQD 54
Score = 25.7 bits (56), Expect = 3.3
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 20 CASCGKRITE-RFLLKALDLFWHEDCLKCGCC 50
CASC KRI ++ D +H +C KC C
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAAC 32
>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 = 62.4 bits (152), Expect = 7e-14
Identities = 28/56 (50%), Positives = 39/56 (69%), Gaps = 1/56 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDY 138
CA C + IP ++V RA++NVYHLECFAC C + GD FYL D++++C+ DY
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
>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 = 57.7 bits (140), Expect = 4e-12
Identities = 24/55 (43%), Positives = 30/55 (54%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C I A E+VMRA++ V+HL CF C CN GD F + D + C Y
Sbjct: 5 CARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
>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 = 56.7 bits (137), Expect = 9e-12
Identities = 25/55 (45%), Positives = 33/55 (60%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C+ C + I E+VMRA NVYHL CF C C + GD F L + ++LC+ DY
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
Score = 28.2 bits (63), Expect = 0.46
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 20 CASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C+ C ++I +++AL+ +H C C C+ +L + G K +LCK DY
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQL-QKGDEFVLKEGQLLCKSDY 55
>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 = 55.5 bits (134), Expect = 3e-11
Identities = 23/55 (41%), Positives = 36/55 (65%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C++ I A + V RA+++VYHL CFAC C + G+ F L ++++LC+ Y
Sbjct: 1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55
>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 = 55.4 bits (134), Expect = 3e-11
Identities = 24/55 (43%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA CGK I R LL+AL WH +C KC C LG G + Y+K C++ Y
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLG--GDSFYEKDGKPYCEKCY 53
Score = 51.9 bits (125), Expect = 6e-10
Identities = 22/55 (40%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C K I ++RA +H ECF C C GD FY D K CE Y
Sbjct: 1 CAGCGKPIEG-RELLRALGKKWHPECFKCSVCGKPLG-GDSFYEKDGKPYCEKCY 53
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 53.9 bits (130), Expect = 1e-10
Identities = 24/58 (41%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
CA C K I E+V RA V+H ECF C C GD F+ D K+ C++DY +
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDGKLYCKHDYFKL 57
Score = 50.0 bits (120), Expect = 4e-09
Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 20 CASCGKRITERFLLK-ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
CA CGK I +R L++ AL WH +C +C C LG ++K + CK DY +LF
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGP--GDFFEKDGKLYCKHDYFKLF 58
>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 = 53.5 bits (129), Expect = 1e-10
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
CA C K I E V+RA V+H ECF C C GD F+ D K+ C+
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPL-SGDTFFEKDGKLYCKDC 54
Score = 42.8 bits (101), Expect = 2e-06
Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
CA CGK I +L+AL WH +C KC C L G T ++K + CK
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPL--SGDTFFEKDGKLYCKDC 54
>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 = 53.9 bits (129), Expect = 1e-10
Identities = 25/56 (44%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDY 138
C AC + IP ++V +A++ VYHL CFAC C+ + GD FYL D +++C+ DY
Sbjct: 1 CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 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 = 52.4 bits (125), Expect = 5e-10
Identities = 27/56 (48%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDY 138
CAAC + IP ++V RA++ VYHL CFAC C + GD FYL D++++C+ DY
Sbjct: 2 CAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57
>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 = 52.4 bits (125), Expect = 6e-10
Identities = 26/55 (47%), Positives = 31/55 (56%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C I A EMVMRA+ +VYHL CF C CN GD F + DN + C +
Sbjct: 5 CARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHF 59
Score = 25.0 bits (54), Expect = 7.0
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 17 LKECASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
++ CA C I+ +++A + +H C C C+ L G K NL+ C+
Sbjct: 2 VQRCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTL-TTGDHFGMKDNLVYCR 56
>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 = 51.2 bits (123), Expect = 1e-09
Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCD-NKILCEYDY 138
CA C + I ++V RA++ V+HL CF C C + G+ Y+ D NK +C+ DY
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 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 = 50.5 bits (121), Expect = 2e-09
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C + + VMRA+ +YH+ECF C C+ + GD F L D+ + C+ D+
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKADH 55
>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 = 49.9 bits (119), Expect = 4e-09
Identities = 22/55 (40%), Positives = 36/55 (65%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C + ++VMRA+++VYH+ECF C C+ + GD F L ++++LC D+
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCRADH 55
>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 = 48.9 bits (116), Expect = 9e-09
Identities = 24/55 (43%), Positives = 32/55 (58%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C+ C + I + + V RAK NVYHL CFAC C + G+ F L + K+LC Y
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55
>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 = 48.9 bits (116), Expect = 1e-08
Identities = 26/55 (47%), Positives = 31/55 (56%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C I A EMVMRA++ VYHL CF C CN GD F + DN + C +
Sbjct: 5 CARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCRLHF 59
Score = 25.4 bits (55), Expect = 4.1
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 17 LKECASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
++ CA C I+ +++A DL +H +C C C+ ++ G K NL+ C+
Sbjct: 2 VQRCARCHLGISASEMVMRARDLVYHLNCFTCTTCN-KMLTTGDHFGMKDNLVYCR 56
>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 = 47.4 bits (112), Expect = 4e-08
Identities = 24/55 (43%), Positives = 31/55 (56%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C + I A + V RA+ N YHL CFAC C + G+ F L + K+LC Y
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55
>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 = 46.7 bits (111), Expect = 6e-08
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C I +RF+LK D WH CLKC C +L + + + + CK D+
Sbjct: 4 CAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTD---KCFSRGGQVYCKEDF 55
>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b. The first
LIM domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 45.7 bits (108), Expect = 2e-07
Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C + I +RF+LK LD WH CLKC C +L E + + + + CK D+
Sbjct: 4 CAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAE---KCFSRGDSVYCKDDF 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 = 43.9 bits (104), Expect = 6e-07
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA CG++I +RF L A+D WH CLKC C L + + + + I CK DY
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPL-DSELSCFSRDGNIYCKEDY 54
>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 = 43.9 bits (104), Expect = 7e-07
Identities = 23/55 (41%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C CG+ IT+RFLLK WH CL+C C L S + + I CK DY
Sbjct: 1 CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSC-FTRDRQIYCKADY 54
>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 = 43.5 bits (102), Expect = 9e-07
Identities = 24/55 (43%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C+SCG I +R+LLK +L WH CL+C C L + ++ Y K I CK DY
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQ-HNSCYIKNKEIFCKMDY 54
Score = 24.6 bits (53), Expect = 7.9
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C++C I +++ N ++H+ C C C + Y+ + +I C+ DY
Sbjct: 1 CSSCGLEILD-RYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8.
The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as
the pituitary gland and the pancreas. Studies using
mutant mice have revealed roles for Lhx7 and Lhx8 in
the development of cholinergic neurons in the
telencephalon and in basal forebrain development. Mice
lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8
display dramatically reduced number of forebrain
cholinergic neurons. In addition, Lhx7 mutation affects
male and female mice differently, with females
appearing more affected than males. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 56
Score = 43.4 bits (102), Expect = 1e-06
Identities = 25/56 (44%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYL 75
C+SCG I +++LLK DL WH CL C C LG ++ Y K I CK DY
Sbjct: 2 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGR-HTSCYIKDKDIFCKLDYF 56
>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 = 44.1 bits (104), Expect = 1e-06
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
L CASCG+ I + L+AL+ WH DC +C C L Y+K + CK+D
Sbjct: 16 GNVLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSH---WYYEKDGRLFCKKD 72
Query: 74 Y 74
Y
Sbjct: 73 Y 73
Score = 25.6 bits (56), Expect = 4.8
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA+C + I ++A N+ +H +CF C +C + +Y D ++ C+ DY
Sbjct: 22 CASCGQSIYD-GQYLQALNSDWHADCFRCCECGAS--LSHWYYEKDGRLFCKKDY 73
>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 = 43.5 bits (102), Expect = 1e-06
Identities = 26/56 (46%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG-EVGSTLYQKANLILCKRDY 74
CA CG +I++R+ L A+D WH CLK CC+C+L E T + K I CK DY
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLK--CCECKLNLESELTCFSKDGSIYCKEDY 64
>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 = 42.4 bits (100), Expect = 2e-06
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C + I++R+LL+ + WHE+CL+C C L + Y + + CK+DY
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTT---SCYFRDRKLYCKQDY 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 = 41.5 bits (97), Expect = 6e-06
Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C + I ++F+LK LD WH CLKC C +L E + +A + CK D+
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAE---RCFSRAGNVYCKEDF 52
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx1 is required
for regulating the vertebrate head organizer, the
nervous system, and female reproductive tract
development. During embryogenesis in the mouse, Lhx1 is
expressed early in mesodermal tissue, then later during
urogenital, kidney, liver, and nervous system
development. In the adult, expression is restricted to
the kidney and brain. A mouse embryos with Lhx1 gene
knockout cannot grow normal anterior head structures,
kidneys, and gonads, but with normally developed trunk
and tail morphology. In the developing nervous system,
Lhx1 is required to direct the trajectories of motor
axons in the limb. Lhx1 null female mice lack the
oviducts and uterus. Lhx5 protein may play
complementary or overlapping roles with Lhx1. The
expression of Lhx5 in the anterior portion of the mouse
neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 41.3 bits (97), Expect = 7e-06
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C + I ++FLL LD WH C++C C C L E + + + C+ D+
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTE---KCFSREGKLYCRNDF 52
>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 = 41.2 bits (97), Expect = 7e-06
Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 20 CASCGKRITERFLLK-ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C CG +I ++++L+ A DL WH CLKC C L E T + + CKRDY
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDE-TCTCFVRDGKTYCKRDY 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 = 40.9 bits (96), Expect = 9e-06
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C +I + ++AL+ WH DC +C C L + ++K + C++DY
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL---SNWYFEKDGKLYCRKDY 52
Score = 29.4 bits (66), Expect = 0.16
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C I + V A N +H +CF C C+ + + ++ D K+ C DY
Sbjct: 1 CAGCRGKILDSQYVQ-ALNQDWHCDCFRCSVCSDS--LSNWYFEKDGKLYCRKDY 52
>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 = 40.5 bits (95), Expect = 1e-05
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C C + I +RFLL+ D WHE CL+C C L +T + + + CK DY
Sbjct: 1 CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPL---ETTCFYRDKKLYCKEDY 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 = 40.4 bits (94), Expect = 1e-05
Identities = 26/56 (46%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG-EVGSTLYQKANLILCKRDY 74
CA CG +I++R+ L A+D WH CLK CC+C+L E T + K I CK DY
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLK--CCECKLALESELTCFAKDGSIYCKEDY 54
>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 = 40.0 bits (94), Expect = 2e-05
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 100 AKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
A YH+E F C C F D +Y + KI C Y Y
Sbjct: 15 ALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
>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 = 38.6 bits (90), Expect = 6e-05
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C C + I +RF+LK LD WH CLKC C +L + + + + CK D+
Sbjct: 1 CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTD---KCFARNGHVYCKDDF 52
>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 = 38.3 bits (89), Expect = 2e-04
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 80 TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
T C C + + + +RA +++H+ CF C QC + G +FY + K CE Y
Sbjct: 30 TNELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQL-QGQQFYSLEGKPYCEECY 87
>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 = 37.2 bits (86), Expect = 2e-04
Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
CA C ++IT+R +LKA +H C C C C L E S + +AN C DY R +
Sbjct: 1 CAVCDQKITDR-MLKATGKSYHPQCFTCVVCKCPL-EGESFIVDQANQPHCVNDYHRRY 57
Score = 27.2 bits (60), Expect = 1.0
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQC 115
CA C + I + +++A YH +CF C C
Sbjct: 1 CAVCDQKIT--DRMLKATGKSYHPQCFTCVVC 30
>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 = 36.1 bits (84), Expect = 6e-04
Identities = 22/60 (36%), Positives = 27/60 (45%), Gaps = 8/60 (13%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNK-----ILCEYDY 138
CA C K I +RA +VYHL+CF C C + F + D LCE DY
Sbjct: 1 CAKCGKPITG--QFVRALGDVYHLDCFTCHDC-GKPVASKFFPVDDPDTSEQVPLCETDY 57
Score = 33.0 bits (76), Expect = 0.007
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCC 50
CA CGK IT +F+ +AL +H DC C C
Sbjct: 1 CAKCGKPITGQFV-RALGDVYHLDCFTCHDC 30
>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 = 35.1 bits (81), Expect = 0.001
Identities = 20/55 (36%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C + + A + VYH+ CF C QC G FY D K CE DY
Sbjct: 1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINL-QGKPFYALDGKPYCEEDY 54
>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 = 34.6 bits (80), Expect = 0.002
Identities = 23/56 (41%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRL-GEVGSTLYQKANLILCKRDY 74
CA CG+ I L ALD WH C KC C L GE K C+RDY
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGEYMG----KDGKPYCERDY 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 = 34.2 bits (79), Expect = 0.002
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C C K I E ++ AL+ WH +C C +C + + ++ L C+ Y
Sbjct: 1 CGGCNKPILENYI-SALNTQWHPECFVCR--ECHKPFINGSFFEHEGLPYCETHY 52
Score = 32.3 bits (74), Expect = 0.011
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C K P E + A N +H ECF C++C+ F G F+ + CE Y
Sbjct: 1 CGGCNK--PILENYISALNTQWHPECFVCRECHKPFINGS-FFEHEGLPYCETHY 52
>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 = 34.0 bits (78), Expect = 0.003
Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE 135
CA C K I A + KN +H CF C +C + F DNKILC
Sbjct: 1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPL-ANEPFVAKDNKILCG 51
>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 = 32.9 bits (75), Expect = 0.007
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C CG RI + F + + WH C +C C L + Y+K + C + Y
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL---TNWYYEKDGKLYCHKHY 52
>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 = 33.2 bits (76), Expect = 0.008
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 80 TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCN 116
TT C AC K + + + A VYH CF C C
Sbjct: 1 TTQKCKACDKTVYLVDQ-LSADGVVYHKSCFRCSHCK 36
>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 = 33.1 bits (76), Expect = 0.008
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C + E ++ + +YH +CF C QC F FY + + CE+D+
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPF-PDGLFYEFEGRKYCEHDF 54
>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 = 32.8 bits (75), Expect = 0.009
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C K + +A N+YH CF C C G FY + K+ CE DY
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL-RGKAFYNVNGKVYCEEDY 54
>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 = 32.4 bits (74), Expect = 0.012
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQC 115
C C K I A + + K NV+H +CF C C
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNC 32
>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 = 32.3 bits (74), Expect = 0.014
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVG 58
C CG+ + R ++KA++ WH DC +C C+ L ++G
Sbjct: 1 CGKCGEFVIGR-VIKAMNNNWHPDCFRCEICNKELADIG 38
Score = 26.5 bits (59), Expect = 1.5
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 97 VMRAKNNVYHLECFACQQCN 116
V++A NN +H +CF C+ CN
Sbjct: 12 VIKAMNNNWHPDCFRCEICN 31
>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 = 32.2 bits (74), Expect = 0.015
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C K V+R ++ +H++CF C+ C G F++ + + C DY
Sbjct: 1 CYKCGK--KCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGG-FFVKEGEYYCTDDY 52
Score = 29.5 bits (67), Expect = 0.11
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C CGK+ +L+ D ++H C C C C L + G + K C DY
Sbjct: 1 CYKCGKKCKGE-VLRVQDKYFHIKCFTCKVCGCDLAQGG--FFVKEGEYYCTDDY 52
>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 = 32.0 bits (73), Expect = 0.018
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCD--NKILCEYDY 138
CA C VI E ++RA YH CF C C +GD + D N++ C DY
Sbjct: 1 CAKCQGVIT--EHIIRALGKGYHPPCFTCVTC--GRRIGDESFAVDEQNEVYCLDDY 53
Score = 25.8 bits (57), Expect = 2.7
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C ITE +++AL +H C C C R+G+ S + N + C DY
Sbjct: 1 CAKCQGVITEH-IIRALGKGYHPPCFTCVTCGRRIGD-ESFAVDEQNEVYCLDDY 53
>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 = 31.7 bits (72), Expect = 0.021
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C + E + A N ++H ECF C++C F V F+ D + CE Y
Sbjct: 1 CGGCAR--AILENYISALNTLWHPECFVCRECFTPF-VNGSFFEHDGQPYCEAHY 52
Score = 24.8 bits (54), Expect = 7.3
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDC 52
C C + I E ++ AL+ WH +C C C
Sbjct: 1 CGGCARAILENYI-SALNTLWHPECFVCRECFT 32
>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 = 31.6 bits (72), Expect = 0.022
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C AC + I V+ A +H+E F C +C F +G R Y CE Y
Sbjct: 2 ICGACRRPI--EGRVVTALGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHY 54
Score = 26.2 bits (58), Expect = 2.5
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C +C + I R ++ AL WH + C C+ +G Y+K L C+ Y
Sbjct: 3 CGACRRPIEGR-VVTALGKHWHVEHFVCAKCEKPF--LGHRHYEKKGLAYCETHY 54
>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight cons erved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 31.1 bits (70), Expect = 0.041
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDR-FYLCDNKILCEYDY 138
C AC K P V+ A +H E F C C +G R F+ D + CE DY
Sbjct: 2 CGACKK--PIAGQVVTAMGKTWHPEHFVCTHCQEE--IGSRNFFERDGQPYCEKDY 53
>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 = 30.8 bits (70), Expect = 0.048
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVG 58
CA C + I FL+ AL WH + C C C L E+G
Sbjct: 1 CAHCNQVIRGPFLV-ALGRSWHPEEFTCSHCHCSLAEIG 38
>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 = 30.7 bits (70), Expect = 0.050
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 105 YHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
+H ECF C C F Y+ D+K C+ Y
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>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 = 30.8 bits (70), Expect = 0.050
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C + + A + V+H++CF C CN + G FY + K CE Y
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKL-RGQPFYAVEKKAYCEPCY 54
>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 = 30.4 bits (69), Expect = 0.062
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CAAC K I V+ A +H E F C +C F+ D + CE DY
Sbjct: 1 CAACKKPIVG--QVVTALGKTWHPEHFVCAECKTEL-GTKNFFERDGQPYCEKDY 52
Score = 30.0 bits (68), Expect = 0.080
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA+C K I + ++ AL WH + C C LG +++ C++DY
Sbjct: 1 CAACKKPIVGQ-VVTALGKTWHPEHFVCAECKTELGT--KNFFERDGQPYCEKDY 52
>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 = 30.2 bits (68), Expect = 0.072
Identities = 22/55 (40%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C+ C + P E + A N V+H ECF C C F G F L D + LCE Y
Sbjct: 1 CSGCGR--PVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFEL-DGRPLCELHY 52
Score = 29.8 bits (67), Expect = 0.11
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCC 50
C+ CG+ + E +L A + WH +C C C
Sbjct: 1 CSGCGRPVKENYL-SAANGVWHPECFVCSDC 30
>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 = 30.1 bits (68), Expect = 0.074
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
CA C K I VM A +H+ CF C C F++ D + CE DY
Sbjct: 1 CARCHKKILG--EVMHALKQTWHVSCFVCAACKQPI-GNSLFHMEDGEPYCEKDY 52
>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 = 30.0 bits (68), Expect = 0.077
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 139
C C +VI V+ A N + ++ F+C C+ + + +FY D K +C+ Y+
Sbjct: 1 CYHCNQVIEG--DVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVCKKCYD 54
Score = 25.8 bits (57), Expect = 3.0
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRL 54
C C + I ++ AL+ W D C CD +L
Sbjct: 1 CYHCNQVIEGD-VVSALNKTWCVDHFSCSFCDTKL 34
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a
Rho-type GTPase activating protein (RhoGap) domain. Rga
activates GTPases during polarized morphogenesis. In
yeast, a known regulating target of Rga is CDC42p, a
small GTPase. The LIM domain is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 55
Score = 30.0 bits (68), Expect = 0.084
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 55
C C + ITE + WH C KC CD +L
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLS 36
>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 = 30.1 bits (68), Expect = 0.086
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE 135
CA+C + E ++ VYH CF C +C + G + CE
Sbjct: 5 CASCGLPVFLAERLLIEGK-VYHRTCFKCARCGVQLTPGSFYETEYGSYCCE 55
>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 = 29.8 bits (67), Expect = 0.11
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFY 126
C +C I A + + A NN YH +CF C +CN G FY
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNL-EGQSFY 42
>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 = 29.5 bits (66), Expect = 0.12
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCN 116
C+ C+K P E ++RA YH CF C C+
Sbjct: 1 CSVCSK--PIMERILRATGKAYHPHCFTCVVCH 31
Score = 26.4 bits (58), Expect = 2.1
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C+ C K I ER +L+A +H C C C L + T+ I C D+
Sbjct: 1 CSVCSKPIMER-ILRATGKAYHPHCFTCVVCHRSLDGIPFTV-DATGQIHCIEDF 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 = 29.6 bits (67), Expect = 0.15
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKI 132
C AC K I V+ A YH C C +C F G+ YL ++I
Sbjct: 1 CEACDKFITG--KVLEAGGKHYHPTCARCSRCGQMFGEGEEMYLQGSEI 47
Score = 25.4 bits (56), Expect = 4.5
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGE 56
C +C K IT + +L+A +H C +C C GE
Sbjct: 1 CEACDKFITGK-VLEAGGKHYHPTCARCSRCGQMFGE 36
>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 = 29.6 bits (66), Expect = 0.15
Identities = 21/54 (38%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 20 CASCGKRIT--ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
C C +I +RFL +AL WH+ C C C L G T Y K + LCK
Sbjct: 1 CHGCDFKIDAGDRFL-EALGFSWHDTCFVCAICQINLE--GKTFYSKKDKPLCK 51
>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 = 29.2 bits (65), Expect = 0.15
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDR-FYLCDNKILCEYDY 138
CA C K I +M A +H+ CF C C + + +R FY+ + CE DY
Sbjct: 1 CAKCKKKITG--EIMHALKMTWHVHCFTCAAC--KTPIRNRAFYMEEGAPYCERDY 52
>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 = 29.2 bits (66), Expect = 0.17
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCN 116
C AC K I M K +H +CF C +C
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECK 33
>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 = 29.2 bits (66), Expect = 0.19
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 105 YHLECFACQQCNHRFCVGDRFYLCDNKILCEY 136
YH +CF C C F GDR + LC+
Sbjct: 23 YHPKCFVCSVCRQPFPPGDRVTFNGKECLCQK 54
>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin. The
first LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 29.1 bits (65), Expect = 0.21
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CASC K I + ++ AL WH + C C LG +++ C+ DY
Sbjct: 3 CASCQKPIAGQ-VVTALGQTWHPEHFVCCQCGKELGS--RPFFERNGQAYCEEDY 54
Score = 28.3 bits (63), Expect = 0.39
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDR-FYLCDNKILCEYDY 138
G CA+C K P V+ A +H E F C QC +G R F+ + + CE DY
Sbjct: 1 GDCASCQK--PIAGQVVTALGQTWHPEHFVCCQCGKE--LGSRPFFERNGQAYCEEDY 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 = 29.0 bits (65), Expect = 0.22
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 20 CASCGKRIT---ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
CA+C K IT + D WH+ C KC C L VG+ + + ILC+
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSL--VGAGFFPDGDQILCRD 54
Score = 24.3 bits (53), Expect = 9.3
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 84 CAACTKVIPAF--EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
CAAC K I F + ++ +H CF C +C+ VG F+ ++ILC
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSL-VGAGFFPDGDQILC 52
>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The third LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 28.8 bits (65), Expect = 0.23
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC----VGDRFYLCDNKILC 134
CA+C K I + ++ ++ +HL+CF C +C HR F D +ILC
Sbjct: 1 CASCGKSIE--DECIKFEDKRWHLKCFTCSRC-HREISSELSDAAFNNKDQRILC 52
Score = 28.1 bits (63), Expect = 0.49
Identities = 19/55 (34%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG--EVGSTLYQKANLILCKR 72
CASCGK I E +K D WH C C C + + K ILC
Sbjct: 1 CASCGKSI-EDECIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSN 54
>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 = 28.9 bits (64), Expect = 0.25
Identities = 17/51 (33%), Positives = 20/51 (39%), Gaps = 13/51 (25%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQC-------------NHRFCV 121
C+ C K I M K N +H CF CQ+C N FCV
Sbjct: 1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCV 51
>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin.
The fifth 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 = 52
Score = 28.6 bits (64), Expect = 0.26
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
C+ C K+I + + KN +H ECF C C+ G RF D K C
Sbjct: 1 CSKCNKIINSGGVTY--KNEPWHRECFTCTNCSKSL-AGQRFTSRDEKPYC 48
>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 = 28.8 bits (64), Expect = 0.30
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVG 122
C++C K + E ++ A V+H CF C+ CN + +G
Sbjct: 1 CSSCQKTVYPMERLV-ADKLVFHNSCFCCKHCNAKLSLG 38
>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 = 28.7 bits (64), Expect = 0.30
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVG 122
C +C K + E ++ A +YH CF C CN + +G
Sbjct: 1 CVSCQKTVYPLERLV-ANQQIYHNSCFRCSYCNTKLSLG 38
>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 = 28.5 bits (64), Expect = 0.31
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 55
C CGK + +L WH+ CL+C C L
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLT 36
>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 = 28.4 bits (64), Expect = 0.35
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 20 CASCGKRI--TERFLLKALDLFWHEDCLKCGCCDCRL 54
CA CGK + ER L A +H+ C +C C+ L
Sbjct: 1 CAVCGKTVYPMER--LVADGKLFHKSCFRCSHCNKTL 35
Score = 27.2 bits (61), Expect = 0.77
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCN 116
CA C K + E + A ++H CF C CN
Sbjct: 1 CAVCGKTVYPMERL-VADGKLFHKSCFRCSHCN 32
>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 = 28.7 bits (64), Expect = 0.37
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQC 115
C+ C+K P + ++RA YH +CF C C
Sbjct: 1 CSVCSK--PILDRILRATGKPYHPQCFTCVVC 30
Score = 25.6 bits (56), Expect = 3.6
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
C+ C K I +R +L+A +H C C C L + T+ N I C D+ + F
Sbjct: 1 CSVCSKPILDR-ILRATGKPYHPQCFTCVVCGKSLDGIPFTV-DATNQIHCIEDFHKKF 57
>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 = 28.2 bits (63), Expect = 0.41
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCN 116
C +C K + E ++ K+ +YH CF C+ CN
Sbjct: 1 CRSCGKPVYKMEEIIAEKH-IYHKNCFRCKDCN 32
Score = 25.9 bits (57), Expect = 2.5
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCC 50
C SCGK + + + A +H++C +C C
Sbjct: 1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDC 31
>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 = 0.42
Identities = 16/45 (35%), Positives = 19/45 (42%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQK 64
CA CGK + + LD WH+ C C C L YQK
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQK 45
>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 = 28.1 bits (63), Expect = 0.43
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYL-CDNKILC 134
C C+++I VM A ++ +H ECF+C C GD + L +K+ C
Sbjct: 1 CHGCSQIITG--PVMVAGDHKFHPECFSCSSCKAFIGDGDSYALVERSKLYC 50
>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1. The Lim domain of DA1:
DA1 contains one copy of LIM domain and a domain of
unknown function. DA1 is predicted as an ubiquitin
receptor, which sets final seed and organ size by
restricting the period of cell proliferation. The LIM
domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 28.0 bits (63), Expect = 0.54
Identities = 12/32 (37%), Positives = 14/32 (43%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCD 51
CA C I L AL WH +C +C C
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACR 32
Score = 26.1 bits (58), Expect = 2.6
Identities = 14/48 (29%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNK 131
CA C I + A V+H ECF C C F + N
Sbjct: 1 CAGCKSEI-GHGRFLSALGAVWHPECFRCHACRKP-IAEHEFSVSGND 46
>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 = 27.7 bits (61), Expect = 0.56
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C + I V+ A +H+ CF C C H + F+L D + CE DY
Sbjct: 1 CGRCQRKI--LGEVINALKQTWHVSCFVCVAC-HNPIRNNVFHLEDGEPYCETDY 52
>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 = 27.7 bits (62), Expect = 0.59
Identities = 14/31 (45%), Positives = 16/31 (51%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCC 50
CA CGK + L LD WH+ C KC C
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVC 31
>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 = 27.7 bits (62), Expect = 0.59
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 84 CAACTKVIPAFEMVMRA----KNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
C C++ + E+ + A ++ ++H CF C C V + + D++I CE Y
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCE-ELLVDLTYCVHDDQIYCERHY 58
>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM
domains protein (FHL). The fourth LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 interacts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 56
Score = 27.7 bits (62), Expect = 0.59
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 84 CAACTKVIPAFE--MVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
CAACTK I + + +H +CF C +C+ VG F ++ILC
Sbjct: 1 CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSL-VGQGFLTQRDEILC 52
Score = 25.4 bits (56), Expect = 4.6
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 20 CASCGKRITERFLLKAL---DLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILC 70
CA+C K IT K + + WH DC CG C L VG + + ILC
Sbjct: 1 CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSL--VGQGFLTQRDEILC 52
>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 = 27.7 bits (62), Expect = 0.63
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYL-CDNKILCEYDY 138
CA C +I EM+++A YH CF C CN C+ G F + +N I C DY
Sbjct: 1 CAVCGHLI--MEMILQALGKSYHPGCFRCCVCNE--CLDGVPFTVDVENNIYCVKDY 53
Score = 27.3 bits (61), Expect = 0.90
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA CG I E +L+AL +H C +C C+ L V T+ N I C +DY
Sbjct: 1 CAVCGHLIMEM-ILQALGKSYHPGCFRCCVCNECLDGVPFTV-DVENNIYCVKDY 53
>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 = 27.2 bits (61), Expect = 1.0
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
CAAC ++I + E +A+ +HL+ F C QC+ G R+ L + K C
Sbjct: 3 CAACDELIFSGEYT-QAEGKNWHLKHFCCFQCDEPL-GGQRYVLREGKPYC 51
>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 = 26.9 bits (59), Expect = 1.3
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 32 LLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
L+AL WH+ C C C L G T + K + LCK+
Sbjct: 14 FLEALGHTWHDTCFVCSVCCESLE--GQTFFSKKDKPLCKK 52
Score = 25.7 bits (56), Expect = 3.2
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE 135
C C I A + + A + +H CF C C G F+ +K LC+
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESL-EGQTFFSKKDKPLCK 51
>gnl|CDD|185729 cd08988, GH43_ABN, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes mostly enzymes with
alpha-L-arabinofuranosidase (AFN; EC 3.2.1.55) and
endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities.
These are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. The GH43
ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside
linkages while the ABF enzymes cleave arabinose side
chains so that the combined actions of these two enzymes
reduce arabinan to L-arabinose and/or
arabinooligosaccharides. These arabinan-degrading
enzymes are important in the food industry for efficient
production of L-arabinose from agricultural waste;
L-arabinose is often used as a bioactive sweetener. A
common structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 279
Score = 28.6 bits (64), Expect = 1.4
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 68 ILCKRDYLRLFGTTGYCAACTKVIPAFEM-VMRAKN 102
IL + DY LF + G C C +++ V R+KN
Sbjct: 179 ILYRGDYYYLFVSFGLC--CRGGDSTYKIAVGRSKN 212
>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 = 26.7 bits (59), Expect = 1.4
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCC 50
C +CGK+I + +L + D + DC +C C
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRC 31
>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 = 26.5 bits (59), Expect = 1.7
Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 20 CASCGKR--ITERFLLKALDLFWHEDCLKCGCCDCRL 54
C C KR + ER L A LF+H C KC C L
Sbjct: 1 CYFCKKRVYVMER--LSAEGLFFHRSCFKCSYCGTTL 35
>gnl|CDD|188275 TIGR03055, photo_alph_chp2, putative photosynthetic complex
assembly protein 2. This uncharacterized protein family
was identified, by the method of partial phylogenetic
profiling, as having a matching phylogenetic
distribution to that of the photosynthetic reaction
center of the alpha-proteobacterial type. It is nearly
always encoded near other photosynthesis-related genes,
including puhA [Energy metabolism, Photosynthesis].
Length = 245
Score = 28.2 bits (63), Expect = 1.8
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 9 LAGGASGGLKECASCGKRITERFLLKALDLFWHEDCL 45
L+G +G + G R ERFL + WHE CL
Sbjct: 78 LSGWVTGPRADPCPPGARGFERFLRALGTILWHEICL 114
>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 = 26.2 bits (58), Expect = 2.0
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
CA C I ++ + ALD WH + C C G+ G ++K C+ DY
Sbjct: 1 CAYCNGPILDK-CVTALDKTWHPEHFFCAQCGKPFGDEG--FHEKDGKPYCREDY 52
>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 = 26.2 bits (57), Expect = 2.0
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 32 LLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
++AL WH+ C C C L G Y K + LCK+
Sbjct: 14 FIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDKPLCKK 52
Score = 25.4 bits (55), Expect = 4.5
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE 135
C C + A + + A + +H CF C C H G FY +K LC+
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVC-HVNLEGQPFYSKKDKPLCK 51
>gnl|CDD|239199 cd02800, tRNA_bind_EcMetRS_like, tRNA-binding-domain-containing
Escherichia coli methionyl-tRNA synthetase
(EcMetRS)-like proteins. This family includes EcMetRS
and Aquifex aeolicus Trbp111 (AaTrbp111). This domain
has general tRNA binding properties. MetRS
aminoacylates methionine transfer RNAs (tRNAmet).
AaTrbp111 is structure-specific molecular chaperone
recognizing the L-shape of the tRNA fold. AaTrbp111
plays a role in nuclear trafficking of tRNAs. The
functional unit of EcMetRs and AaTrbp111 is a homodimer,
this domain acts as the dimerization domain.
Length = 105
Score = 27.1 bits (61), Expect = 2.1
Identities = 9/18 (50%), Positives = 11/18 (61%), Gaps = 2/18 (11%)
Query: 139 EERQVFANIA--YNPSSL 154
EERQ+ + IA Y P L
Sbjct: 38 EERQIVSGIAKFYPPEEL 55
>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 = 26.3 bits (58), Expect = 2.3
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVG 122
C C K + E ++ K N +H CF C+ CN + +G
Sbjct: 1 CTVCQKRVYPMERLIADKQN-FHKSCFRCEHCNSKLSLG 38
>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 = 2.3
Identities = 21/55 (38%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 20 CASCGKRIT----ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILC 70
CA+CGK IT +F+ D WH DC C C L VG ILC
Sbjct: 1 CAACGKPITGIGGTKFI-SFEDRHWHNDCFNCAGCRTSL--VGKGFITDGGRILC 52
>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 = 26.0 bits (57), Expect = 2.3
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 97 VMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE 135
+++A++ +YH ECF C C F++ D ++ CE
Sbjct: 12 IVKARDKLYHPECFMCDDCGLNLKQRGYFFI-DEQLYCE 49
>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 = 25.9 bits (57), Expect = 2.5
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
YCA P + V+ A + +H E F C C F + F D K C D+
Sbjct: 2 AYCAG-----PILQNVLTAMDQTWHPEHFFCSHCGELFGD-EGFLERDGKPYCRRDF 52
>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 = 25.6 bits (56), Expect = 3.1
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCD-NKILCEYDY 138
C C++ I +VM A YH ECF+C +C GD + L + +K+ C + Y
Sbjct: 1 CHGCSETITT-GLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYCGHCY 55
>gnl|CDD|188812 cd09428, LIM2_FHL5, The second LIM domain of Four and a half LIM
domains protein 5 (FHL5). The second LIM domain of Four
and a half LIM domains protein 5 (FHL5): FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors , which are highly expressed in
male germ cells and is required for post-meiotic gene
expression. FHL5 associates with CREM and confers a
powerful transcriptional activation function. Activation
by CREB has known to occur upon phosphorylation at an
essential regulatory site and the subsequent interaction
with the ubiquitous coactivator CREB-binding protein
(CBP). However, the activation by FHL5 is independent of
phosphorylation and CBP association. It represents a new
route for transcriptional activation by CREM and CREB.
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 = 25.6 bits (56), Expect = 3.5
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQC 115
C C K I + + N +H CF CQ C
Sbjct: 1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSC 32
>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 = 25.5 bits (56), Expect = 4.2
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 20 CASCGKRIT------ERFLLKALDLFWHEDCLKCGCCDCRLGE--VGSTLYQKANLILCK 71
C+ CG+ I E + ALD +H +C KC C L G Y +LCK
Sbjct: 1 CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPLDGHLLCK 60
>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 = 25.1 bits (55), Expect = 4.6
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
C C I A + + A + +H CF C C H G FY +K LC
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVC-HVNLEGQTFYSKKDKPLC 50
Score = 25.1 bits (55), Expect = 5.9
Identities = 21/54 (38%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 20 CASCGKRIT--ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
C C I +RFL +AL WH+ C C C L G T Y K + LCK
Sbjct: 1 CHGCDFPIEAGDRFL-EALGHTWHDTCFVCAVCHVNLE--GQTFYSKKDKPLCK 51
>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 = 25.5 bits (56), Expect = 4.6
Identities = 16/54 (29%), Positives = 20/54 (37%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
C CGK + F+H+ C KC C RL T Q + C R
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54
>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM
domains protein (FHL). The third 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 = 52
Score = 25.0 bits (55), Expect = 5.0
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
CA C K I + + R + +H ECF C C + G RF D C
Sbjct: 1 CAKCKKAITSGGVTYR--DQPWHKECFVCTGCKKQLA-GQRFTSRDEYPYC 48
>gnl|CDD|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog
(ENH) family. The first 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 = 25.0 bits (54), Expect = 5.8
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVG 58
CA+C + I FL+ AL WH + C C + +G
Sbjct: 1 CATCNQVIRGPFLV-ALGKSWHPEEFNCAHCKSSMAYIG 38
>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 = 25.1 bits (55), Expect = 5.9
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
C+AC ++I A E A+ +H++ F C +C + G R+ + + + C
Sbjct: 3 CSACDEIIFADECT-EAEGRHWHMKHFCCFECECQLG-GQRYIMREGRPYC 51
>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin. The
second LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 24.9 bits (54), Expect = 6.2
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
C C I ++ ++ ALD WH + C C G G ++K C++DY
Sbjct: 1 CYYCNGPILDK-VVTALDRTWHPEHFFCAQCGAFFGPEG--FHEKDGKAYCRKDY 52
Score = 24.9 bits (54), Expect = 7.0
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 92 PAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
P + V+ A + +H E F C QC F + F+ D K C DY
Sbjct: 7 PILDKVVTALDRTWHPEHFFCAQCG-AFFGPEGFHEKDGKAYCRKDY 52
>gnl|CDD|185759 cd09220, GH64-GluB-like, glycoside hydrolase family 64:
beta-1,3-glucanase B (GluB)-like. This subfamily is
represented by GluB, beta-1,3-glucanase B , from
Lysobacter enzymogenes Strain N4-7 and related bacterial
and ascomycete proteins. GluB is a member of the
glycoside hydrolase family 64 (GH64) involved in the
cleavage of long-chain polysaccharide beta-1,3-glucans,
into specific pentasaccharide oligomers. Among bacteria,
many beta-1,3-glucanases are implicated in fungal cell
wall degradation. GluB possesses the conserved Glu and
Asp residues required to cleave substrate
beta-1,3-glucans. Recombinant GluB demonstrated higher
relative activity toward the branched-chain beta-1,3
glucan substrate zymosan A than toward linear beta-1,3
glucan substrates. Based on the structure of
laminaripentaose-producing, beta-1,3-glucanase (LPHase)
of Streptomyces matensis, which belongs to the same
family as GluB but to a different subfamily, this cd is
a two-domain model. Sometimes these two domains are
found associated with other domains such as in the
Catenulispora acidiphila DSM 44928 carbohydrate binding
family 6 protein in which they are positioned N-terminal
of a carbohydrate binding module, family 6 (CBM_6)
domain.
Length = 369
Score = 26.5 bits (59), Expect = 7.1
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 134 CEYDYEERQVFANIAY 149
CE+ Y Q++ANI+Y
Sbjct: 117 CEFTYNSGQLYANISY 132
>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 = 24.7 bits (54), Expect = 8.9
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 84 CAACTKVIPAFEMVMR-----AKNNVYHLECFACQQCNHRFC--VGDRFYLCDNKILC 134
CAAC + I E + + YH+EC+ C+ C + G R Y D +LC
Sbjct: 1 CAACGQPILPAEGSEETIRVVSMDKDYHVECYHCEDCGLQLNDEEGHRCYPLDGHLLC 58
>gnl|CDD|218613 pfam05502, Dynactin_p62, Dynactin p62 family. Dynactin is a
multi-subunit complex and a required cofactor for most,
or all, of the cellular processes powered by the
microtubule-based motor cytoplasmic dynein. p62 binds
directly to the Arp1 subunit of dynactin.
Length = 456
Score = 26.4 bits (58), Expect = 9.5
Identities = 19/81 (23%), Positives = 27/81 (33%), Gaps = 24/81 (29%)
Query: 37 DLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEM 96
L + EDC + C C E+ YC C +P+ E
Sbjct: 4 QLLFCEDCHQIRCPRCVTEEIVCY----------------------YCPNCLFEVPSSE- 40
Query: 97 VMRAKNNVYHLECFACQQCNH 117
+R++ N CF C C H
Sbjct: 41 -VRSEKNRCARNCFDCPICTH 60
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.329 0.140 0.469
Gapped
Lambda K H
0.267 0.0819 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,303,493
Number of extensions: 701192
Number of successful extensions: 1202
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1147
Number of HSP's successfully gapped: 268
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 55 (24.8 bits)