RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11756
(233 letters)
>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 = 68.5 bits (168), Expect = 9e-16
Identities = 27/52 (51%), Positives = 34/52 (65%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C+ PI VVTAL +TWHP+HFVC C T+L K F+ER+G +C Y
Sbjct: 1 CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52
Score = 67.0 bits (164), Expect = 4e-15
Identities = 26/52 (50%), Positives = 32/52 (61%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CAAC+ I +V AL KTWHPEHF C C+ + T+ F G PYC +DY
Sbjct: 1 CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52
Score = 32.3 bits (74), Expect = 0.019
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 6/51 (11%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTF------RVCEAD 204
C C KPI + + WH F C C+ + F CE D
Sbjct: 1 CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKD 51
>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 = 62.4 bits (152), Expect = 2e-13
Identities = 24/52 (46%), Positives = 32/52 (61%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C PI D VTAL++TWHP+HF C CG +GF+E++G +C Y
Sbjct: 1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 62.0 bits (151), Expect = 3e-13
Identities = 29/52 (55%), Positives = 31/52 (59%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C G I + V ALDKTWHPEHF C C P + FH G PYC EDY
Sbjct: 1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 25.4 bits (56), Expect = 5.0
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPI 193
C C PI + + D+ WH F C +C +P
Sbjct: 1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPF 34
>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 = 58.1 bits (141), Expect = 8e-12
Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 42 CAACQGLIQ-NIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C I+ +++AL K WHPE F+C+ C P+ F+ G PYC + Y
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 55.8 bits (135), Expect = 7e-11
Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 101 CQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC PI+ ++ AL + WHP+ F C CG L FYE++G +C CY
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 50.0 bits (120), Expect = 7e-09
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 160 CFGCGKPITETAI-KVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C GCGKPI + + +KWH CF+C C +P+ G +F + C +C
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKC 52
>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 = 58.3 bits (141), Expect = 8e-12
Identities = 28/52 (53%), Positives = 34/52 (65%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C+ PI VVTAL QTWHP+HFVC CG +L + F+ER G A+C Y
Sbjct: 3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
Score = 57.2 bits (138), Expect = 2e-11
Identities = 24/52 (46%), Positives = 30/52 (57%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA+CQ I +V AL +TWHPEHF C C + ++ F G YC EDY
Sbjct: 3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
Score = 27.1 bits (60), Expect = 1.5
Identities = 11/39 (28%), Positives = 16/39 (41%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C C KPI + + WH F C +C + + F
Sbjct: 3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPF 41
>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 = 56.9 bits (137), Expect = 2e-11
Identities = 26/52 (50%), Positives = 34/52 (65%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C PI D VVTAL++TWHP+HF C CG +GF+E++G A+C Y
Sbjct: 1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
Score = 52.7 bits (126), Expect = 1e-09
Identities = 24/52 (46%), Positives = 29/52 (55%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C G I + +V ALD+TWHPEHF C C + FH G YC +DY
Sbjct: 1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
Score = 29.2 bits (65), Expect = 0.27
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRC 189
C+ C PI + + DR WH F C +C
Sbjct: 1 CYYCNGPILDKVVTALDRTWHPEHFFCAQC 30
>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin. The
second LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 55.6 bits (134), Expect = 8e-11
Identities = 23/52 (44%), Positives = 30/52 (57%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C G I ++ A+D+TWHPEHF C+HC + F G PYC D+
Sbjct: 1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
Score = 53.7 bits (129), Expect = 3e-10
Identities = 23/48 (47%), Positives = 30/48 (62%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C C PI V+TA++QTWHP+HF C CG +GF ER+G +C
Sbjct: 1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYC 48
Score = 26.3 bits (58), Expect = 3.1
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRC 189
C C PI + + D+ WH F C C
Sbjct: 1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHC 30
>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 = 55.4 bits (133), Expect = 8e-11
Identities = 26/52 (50%), Positives = 33/52 (63%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C AC+ I +V A+ KTWHPEHF CTHC+ I ++ F G PYC +DY
Sbjct: 2 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
Score = 52.3 bits (125), Expect = 1e-09
Identities = 23/52 (44%), Positives = 33/52 (63%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C+ PI VVTA+ +TWHP+HFVC C ++ + F+ER+G +C Y
Sbjct: 2 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
Score = 26.5 bits (58), Expect = 2.6
Identities = 12/39 (30%), Positives = 15/39 (38%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C C KPI + + WH F C C+ I F
Sbjct: 2 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNF 40
>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH. The
fourth LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated
protein-protein interactions. PINCH comprises an array
of five LIM domains that interact with integrin-linked
kinase (ILK), Nck2 (also called Nckbeta or Grb4) and
other interaction partners. These interactions are
essential for triggering the FA assembly and for
relaying diverse mechanical and biochemical signals
between Cell-extracellular matrix and the actin
cytoskeleton. The PINCH LIM4 domain recognizes the
third SH3 domain of another adaptor protein, Nck2. This
step is an important component of integrin signaling
event. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assem bly of multimeric
protein complexes.
Length = 54
Score = 54.7 bits (132), Expect = 2e-10
Identities = 21/54 (38%), Positives = 26/54 (48%)
Query: 40 PKCAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
P C AC+ I+ +V AL K WH EHF C C P + + G YC Y
Sbjct: 1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
Score = 53.9 bits (130), Expect = 3e-10
Identities = 23/48 (47%), Positives = 29/48 (60%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C CR PI+ VVTAL + WH +HFVC C L YE++G A+C
Sbjct: 3 CGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYC 50
Score = 36.6 bits (85), Expect = 5e-04
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 158 PKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISG 195
P C C +PI + + WH F C +C +P G
Sbjct: 1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLG 38
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 54.3 bits (131), Expect = 2e-10
Identities = 24/58 (41%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 42 CAACQGLIQN--IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLF 97
CA C I + ++ +AL K WHPE FRC C P+ F G YC DY LF
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 49.6 bits (119), Expect = 1e-08
Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 101 CQGCRLPIKD--VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKF 156
C GC PI D +V AL + WHP+ F C CG L F+E++G +C Y F
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 39.6 bits (93), Expect = 5e-05
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 160 CFGCGKPI--TETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECSEK 213
C GCGKPI E + + WH CFRC C +P+ F + + C K
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFK 56
>gnl|CDD|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma
subfamily with unknown function. The first 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 = 53.6 bits (129), Expect = 5e-10
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCI--SCGTKLLYKGFYEREGNAFCTACY 152
C+ C I+ +TAL + W PDHF+C SC L GF E +G +C C+
Sbjct: 1 CESCNQQIRGPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCEYCF 54
Score = 34.4 bits (79), Expect = 0.004
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTH--CRIPIATQKFHVHAGSPYC 89
C +C I+ + AL K W P+HF C + CR P+ F G YC
Sbjct: 1 CESCNQQIRGPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYC 50
>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 = 52.7 bits (127), Expect = 7e-10
Identities = 21/52 (40%), Positives = 28/52 (53%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC PI + ++ALN WHP+ FVC C + F+E EG +C Y
Sbjct: 1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52
Score = 45.8 bits (109), Expect = 3e-07
Identities = 19/48 (39%), Positives = 21/48 (43%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C C I + AL+ WHPE F C C P F H G PYC
Sbjct: 1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYC 48
Score = 40.4 bits (95), Expect = 3e-05
Identities = 16/39 (41%), Positives = 20/39 (51%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C GC KPI E I + +WH CF C C +P +F
Sbjct: 1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSF 39
>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 = 52.4 bits (126), Expect = 1e-09
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 41 KCAACQGLIQ--NIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVED 92
KCA C I +++AL K WHPE F+C C P++ F G YC +
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 50.5 bits (121), Expect = 6e-09
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 100 KCQGCRLPI--KDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTAC 151
KC GC PI + V+ AL + WHP+ F C +CG L F+E++G +C C
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 45.8 bits (109), Expect = 2e-07
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 159 KCFGCGKPITETA--IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
KC GCGKPI T ++ + WH CF+C C +P+SG TF + + C +C
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
>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 = 51.7 bits (124), Expect = 2e-09
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHV-HAGSPYCVEDY 93
CA CQG+I I++AL K +HP F C C I + F V YC++DY
Sbjct: 1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
Score = 35.5 bits (82), Expect = 0.002
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCE-ADVVCVE 209
C C ITE I+ + +H CF C C R I +F V E +V C++
Sbjct: 1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLD 51
Score = 32.4 bits (74), Expect = 0.016
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYERE-GNAFCTACY 152
C C+ I + ++ AL + +HP F C++CG ++ + F E +C Y
Sbjct: 1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 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 = 50.4 bits (121), Expect = 5e-09
Identities = 19/52 (36%), Positives = 27/52 (51%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C I+ + AL ++WHP+ F C C L GF E +G+ +C CY
Sbjct: 1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
Score = 43.5 bits (103), Expect = 2e-06
Identities = 21/52 (40%), Positives = 28/52 (53%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C +I+ + AL ++WHPE F C+HC +A F GS YC Y
Sbjct: 1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
>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 = 50.3 bits (121), Expect = 7e-09
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 40 PKCAACQGLI-QNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
P+CAAC LI QA K WH +HF C C P+ Q++ + G PYC++ Y
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCY 55
Score = 37.2 bits (87), Expect = 4e-04
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 115 ALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYE 153
A + WH HF C C L + + REG +C CYE
Sbjct: 18 AEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56
Score = 26.4 bits (59), Expect = 2.6
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 158 PKCFGCGKPI-TETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECSE 212
P+C C + I + + + WH F C +C P+ G + + E C++C E
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56
>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 = 49.2 bits (117), Expect = 1e-08
Identities = 22/52 (42%), Positives = 29/52 (55%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C+ I I+ AL TWH F C C+ PI + F++ G+PYC DY
Sbjct: 1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 35.0 bits (80), Expect = 0.002
Identities = 18/52 (34%), Positives = 25/52 (48%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C+ I ++ AL TWH F C +C T + + FY EG +C Y
Sbjct: 1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 29.2 bits (65), Expect = 0.24
Identities = 16/48 (33%), Positives = 19/48 (39%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVC 207
C C K IT + WH CF C C+ PI F + E C
Sbjct: 1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYC 48
>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 = 48.7 bits (116), Expect = 3e-08
Identities = 21/52 (40%), Positives = 29/52 (55%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC I + ++ALN WHP+ FVC C T + F+E +G +C A Y
Sbjct: 1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
Score = 41.8 bits (98), Expect = 7e-06
Identities = 20/52 (38%), Positives = 22/52 (42%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C I + AL+ WHPE F C C P F H G PYC Y
Sbjct: 1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
Score = 34.0 bits (78), Expect = 0.005
Identities = 15/48 (31%), Positives = 19/48 (39%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVC 207
C GC + I E I + WH CF C C P +F + C
Sbjct: 1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYC 48
>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 = 48.2 bits (115), Expect = 3e-08
Identities = 22/52 (42%), Positives = 28/52 (53%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C I ++ AL +TWH F C C+ PI FH+ G PYC +DY
Sbjct: 1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
Score = 37.8 bits (88), Expect = 2e-04
Identities = 18/52 (34%), Positives = 24/52 (46%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C I V+ AL QTWH FVC +C + F+ +G +C Y
Sbjct: 1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
Score = 32.4 bits (74), Expect = 0.016
Identities = 14/48 (29%), Positives = 22/48 (45%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVC 207
C C K I + + WH +CF C C++PI F + + + C
Sbjct: 1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYC 48
>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM
domains protein 1 (FHL1). The third LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 48.3 bits (115), Expect = 4e-08
Identities = 19/51 (37%), Positives = 25/51 (49%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C C KPIT + D+ WH CF C C + ++G F E CV+C
Sbjct: 1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDC 51
Score = 41.0 bits (96), Expect = 2e-05
Identities = 21/53 (39%), Positives = 26/53 (49%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYE 153
C C PI VT +Q WH + FVC SC KL + F E +C CY+
Sbjct: 1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53
Score = 35.9 bits (83), Expect = 0.001
Identities = 18/52 (34%), Positives = 24/52 (46%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C I + V D+ WH E F C+ C +A Q+F YCV+ Y
Sbjct: 1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52
>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 = 46.9 bits (111), Expect = 1e-07
Identities = 22/52 (42%), Positives = 26/52 (50%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C CQ I ++ AL +TWH F C C PI FH+ G PYC DY
Sbjct: 1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 38.9 bits (90), Expect = 1e-04
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C+ I V+ AL QTWH FVC++C + F+ +G +C Y
Sbjct: 1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 30.8 bits (69), Expect = 0.075
Identities = 14/48 (29%), Positives = 20/48 (41%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVC 207
C C + I I + WH +CF C C PI F + + + C
Sbjct: 1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYC 48
>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 = 46.4 bits (110), Expect = 2e-07
Identities = 19/52 (36%), Positives = 26/52 (50%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC P+K+ ++A N WHP+ FVC C F+E +G C Y
Sbjct: 1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52
Score = 37.1 bits (86), Expect = 4e-04
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C GCG+P+ E + + WH CF C C +P + +F
Sbjct: 1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSF 39
Score = 34.8 bits (80), Expect = 0.002
Identities = 15/48 (31%), Positives = 21/48 (43%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C+ C ++ + A + WHPE F C+ C P F G P C
Sbjct: 1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48
>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin. The
fourth LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners PYK2,
FAK, PEP and p95PKL. When expressed in human leukocytic
cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 45.9 bits (109), Expect = 2e-07
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C LPI ++AL + +HP+HFVC C L F E+ G +C+ C+
Sbjct: 1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
Score = 43.2 bits (102), Expect = 3e-06
Identities = 18/48 (37%), Positives = 24/48 (50%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C +C I + AL + +HPEHF C C P+ F +G PYC
Sbjct: 1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48
Score = 34.7 bits (80), Expect = 0.003
Identities = 18/51 (35%), Positives = 23/51 (45%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C CG PIT I RK+H F C C RP++ +F+ C C
Sbjct: 1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTC 51
>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 = 45.7 bits (109), Expect = 3e-07
Identities = 21/48 (43%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 42 CAACQG-LIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPY 88
CA C+ + + AL WHPE FRC CR PIA +F V PY
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48
Score = 39.5 bits (93), Expect = 6e-05
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 101 CQGCRLPIKDV-VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC+ I ++AL WHP+ F C +C + F + + +CY
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53
Score = 38.8 bits (91), Expect = 1e-04
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRCRRPISGPTFRV 200
C GC I + WH CFRC CR+PI+ F V
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSV 42
>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 = 45.8 bits (109), Expect = 3e-07
Identities = 22/56 (39%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISG----PTFRVCEADVVCVECS 211
C CGK I + IK D++WH CF C RC R IS F + ++C CS
Sbjct: 1 CASCGKSIEDECIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNCS 56
Score = 28.1 bits (63), Expect = 0.63
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHC 71
CA+C I++ ++ DK WH + F C+ C
Sbjct: 1 CASCGKSIEDECIKFEDKRWHLKCFTCSRC 30
>gnl|CDD|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma. The first
LIM domain of Enigma: Enigma was initially characterized
in humans as a protein containing three LIM domains at
the C-terminus and a PDZ domain at N-terminus. The
third LIM domain specifically interacts with the insulin
receptor and the second LIM domain interacts with the
receptor tyrosine kinase Ret and the adaptor protein
APS. Thus Enigma is implicated in signal transduction
processes such as mitogenic activity, insulin related
actin organization, and glucose metabolism. Enigma is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 45.2 bits (107), Expect = 5e-07
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C I+ + AL +++HP+ F C C L GF+E +G+ FC CY
Sbjct: 1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
Score = 36.3 bits (84), Expect = 8e-04
Identities = 17/52 (32%), Positives = 28/52 (53%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C +I+ + AL +++HPE F C+ C+ + F GS +C + Y
Sbjct: 1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
>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 = 45.0 bits (106), Expect = 6e-07
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C I+ + AL ++WHP+ F C C + + Y GF E +G +C CY
Sbjct: 1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52
Score = 43.5 bits (102), Expect = 2e-06
Identities = 20/48 (41%), Positives = 27/48 (56%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
CA C +I+ + AL K+WHPE F C HC+ +A F G+ YC
Sbjct: 1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYC 48
>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the
Paxillin-like protein family. The fourth 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 = 44.6 bits (106), Expect = 7e-07
Identities = 19/52 (36%), Positives = 29/52 (55%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC PI +TA+ + +HP+HFVC C +L F E++ +C C+
Sbjct: 1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
Score = 38.1 bits (89), Expect = 1e-04
Identities = 16/52 (30%), Positives = 23/52 (44%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C I + A+ + +HPEHF C C ++ F PYC +
Sbjct: 1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
Score = 34.2 bits (79), Expect = 0.003
Identities = 20/51 (39%), Positives = 25/51 (49%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C GCGKPIT I RK+H F C C + +S TF+ + C C
Sbjct: 1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPC 51
>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 = 43.1 bits (102), Expect = 3e-06
Identities = 25/54 (46%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKG-FYEREGNAFCTACYE 153
C C I+ VV+ALN+TW DHF C C TKL K FYE + C CY+
Sbjct: 1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVCKKCYD 54
Score = 32.3 bits (74), Expect = 0.018
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQ-KFHVHAGSPYC 89
C C +I+ +V AL+KTW +HF C+ C + + KF+ P C
Sbjct: 1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVC 49
Score = 30.0 bits (68), Expect = 0.13
Identities = 7/35 (20%), Positives = 14/35 (40%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPIS 194
C+ C + I + ++ W F C C ++
Sbjct: 1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLT 35
>gnl|CDD|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin. The
fourth LIM domain of Paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 42.6 bits (100), Expect = 4e-06
Identities = 19/52 (36%), Positives = 29/52 (55%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC+ PI +TA+ + +HP+HFVC C +L F E+ +C C+
Sbjct: 1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52
Score = 34.9 bits (80), Expect = 0.002
Identities = 17/48 (35%), Positives = 22/48 (45%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C+ CQ I + A+ K +HPEHF C C + F PYC
Sbjct: 1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYC 48
Score = 31.1 bits (70), Expect = 0.047
Identities = 17/51 (33%), Positives = 23/51 (45%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C GC KPIT I +K+H F C C + ++ TF+ C C
Sbjct: 1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNC 51
>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 = 42.8 bits (101), Expect = 4e-06
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 160 CFGCGKPITETA----IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECS 211
C CGKPIT I DR WH CF C CR + G F ++C +C+
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDCA 56
Score = 37.1 bits (86), Expect = 4e-04
Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 101 CQGCRLPIKDVVVTAL----NQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTAC 151
C C PI + T ++ WH D F C C T L+ KGF G C C
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55
>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM
domains protein 2 (FHL2). The third 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 = 42.3 bits (99), Expect = 6e-06
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C C KPIT + D+ WH+ CF C C++ +SG F + C+ C
Sbjct: 1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNC 51
Score = 35.7 bits (82), Expect = 0.001
Identities = 19/52 (36%), Positives = 27/52 (51%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C+ PI VT +Q WH + FVC C +L + F R+ A+C C+
Sbjct: 1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCF 52
Score = 34.6 bits (79), Expect = 0.003
Identities = 17/56 (30%), Positives = 27/56 (48%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLF 97
C C+ I V D+ WH E F CT C+ ++ Q+F YC+ + +L+
Sbjct: 1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLY 56
>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 = 42.3 bits (100), Expect = 6e-06
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C C K IT + D+ WH+ CF C C++ ++G F + CV+C
Sbjct: 1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDC 51
Score = 40.0 bits (94), Expect = 3e-05
Identities = 20/52 (38%), Positives = 28/52 (53%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C+ I + V D+ WH E F CT C+ +A Q+F PYCV+ +
Sbjct: 1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
Score = 36.2 bits (84), Expect = 7e-04
Identities = 17/52 (32%), Positives = 25/52 (48%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C+ I VT +Q WH + FVC C +L + F R+ +C C+
Sbjct: 1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
>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 = 42.0 bits (99), Expect = 8e-06
Identities = 17/40 (42%), Positives = 24/40 (60%)
Query: 113 VTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
TA++Q +H D F C++C KL + FY E A+C CY
Sbjct: 15 CTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
Score = 26.6 bits (59), Expect = 2.3
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 56 ALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
A+D+ +H + F C C + Q F+ YC Y
Sbjct: 17 AMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
Score = 26.2 bits (58), Expect = 3.5
Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 160 CFGCGKPIT--ETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C CG+ + T D+ +H CF C C + G F E C C
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPC 53
>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 = 40.9 bits (96), Expect = 2e-05
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 160 CFGCGKPITETAIKVHDRK--WHEACFRCGRCRRPISGPTFRVCEADVVCVECSEK 213
C GC K I V + WH+ CF C C++PI +F D CV C EK
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEK 56
Score = 36.3 bits (84), Expect = 9e-04
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 101 CQGCRLPIK--DVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKF 156
C+GC I D V WH D F C +C + K F+ + + +C C+E KF
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
Score = 31.3 bits (71), Expect = 0.056
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 45 CQGLIQNII-----VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLF 97
C+G ++I+ V+ WH + F C++C+ PI T+ F YCV + F
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 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 = 40.8 bits (96), Expect = 2e-05
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 160 CFGCGKPITETA----IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C C KPIT I +R+WH CF CG+C + G F +++C EC
Sbjct: 1 CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55
Score = 29.2 bits (66), Expect = 0.23
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 101 CQGCRLPIKDV----VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTAC 151
C C PI + ++ + WH D F C C L+ +GF + C C
Sbjct: 1 CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung at
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 62
Score = 40.3 bits (94), Expect = 3e-05
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 160 CFGCGKPITETA--IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C C KPI + DR WHE+CF C +C+ + F E ++C EC
Sbjct: 5 CEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTEC 57
Score = 32.6 bits (74), Expect = 0.018
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 97 FLNKCQGCRLPI----KDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
+ N C+ C+ PI KD+ + ++ WH F C C L+ K F +E + CT CY
Sbjct: 1 YSNTCEECKKPIGCDCKDL--SYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECY 58
Query: 153 EGKF 156
++
Sbjct: 59 SNEY 62
>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 = 40.0 bits (94), Expect = 4e-05
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 41 KCAACQGLIQNIIVQALDKTWHPEHFRCTHCRIP 74
KC +CQ ++ +V AL KT+HP+ F C+ CR P
Sbjct: 3 KCDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQP 36
Score = 37.7 bits (88), Expect = 3e-04
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 159 KCFGCGKPITETAIKVHDRKWHEACFRCGRCRRP 192
KC C + + + +H CF C CR+P
Sbjct: 3 KCDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQP 36
Score = 35.0 bits (81), Expect = 0.002
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 100 KCQGCRLPIKDVVVTALNQTWHPDHFVCISCG 131
KC C+ ++ VV+AL +T+HP FVC C
Sbjct: 3 KCDSCQDFVEGEVVSALGKTYHPKCFVCSVCR 34
>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 = 39.7 bits (93), Expect = 4e-05
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 160 CFGCGKPITETAIKVH--DRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECS 211
C C KPI + ++H +R WHE CFRC +C +P++ F + ++C +C+
Sbjct: 1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKCT 54
Score = 25.5 bits (56), Expect = 6.1
Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 101 CQGCRLPI--KDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTAC 151
C CR PI + N+ WH F C C L + F ++ C C
Sbjct: 1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53
>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 = 39.6 bits (93), Expect = 4e-05
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 160 CFGCGKPITETAIKVH--DRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C CGK I + K+ + WHE CF C C++PI +F + + CV C
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPC 53
Score = 32.3 bits (74), Expect = 0.020
Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 2/54 (3%)
Query: 101 CQGCRLPIK--DVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C+ C I + + WH F C C + K F ++ +C CY
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
Score = 31.9 bits (73), Expect = 0.024
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 59 KTWHPEHFRCTHCRIPIATQKFHVHAGSPYCV 90
K WH + F C+ C+ PI T+ F YCV
Sbjct: 20 KFWHEKCFTCSECKKPIGTKSFIPKDDKIYCV 51
>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 = 39.6 bits (93), Expect = 5e-05
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQK-FHVHAGSPYCVEDY 93
C C G ++ + AL + +H EHF C+ C ++ H G YC Y
Sbjct: 1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
Score = 38.1 bits (89), Expect = 2e-04
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKL-LYKGFYEREGNAFC 148
C C ++ +TAL + +H +HF C C T +YE EG +C
Sbjct: 1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYC 49
Score = 26.9 bits (60), Expect = 1.8
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPI-SGPTFRVCEADVVC 207
CF CG + + I RK+H F C C ++ E + C
Sbjct: 1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYC 49
>gnl|CDD|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like
proteins. The second LIM domain of Ajuba-like
proteins: Ajuba like LIM protein family includes three
highly homologous proteins Ajuba, Limd1, and WTIP.
Members of the family contain three tandem C-terminal
LIM domains and a proline-rich N-terminal region. This
family of proteins functions as scaffolds,
participating in the assembly of numerous protein
complexes. In the cytoplasm, Ajuba binds Grb2 to
modulate serum-stimulated ERK activation. Ajuba also
recruits the TNF receptor-associated factor 6 (TRAF6)
to p62 and activates PKCKappa activity. Ajuba interacts
with alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 39.6 bits (93), Expect = 5e-05
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHV-HAGSPYCVEDY 93
CA C LI +I+QAL K++HP FRC C + F V + YCV+DY
Sbjct: 1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
Score = 27.7 bits (62), Expect = 0.92
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRV-CEADVVCVE 209
C CG I E ++ + +H CFRC C + G F V E ++ CV+
Sbjct: 1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVK 51
>gnl|CDD|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM
domains protein 1 (FHL1). The fourth LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 64
Score = 39.7 bits (93), Expect = 5e-05
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 159 KCFGCGKPIT-----ETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECSEK 213
KC GC PIT + WH+ CF C +C ++ F + C +C++K
Sbjct: 4 KCSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDCAKK 63
Score = 35.5 bits (82), Expect = 0.002
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 41 KCAACQGLIQNI-----IVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYAS 95
KC+ CQ I +V +WH F C C + +A ++F H G YC +
Sbjct: 4 KCSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDCAKK 63
Query: 96 L 96
L
Sbjct: 64 L 64
Score = 31.7 bits (72), Expect = 0.045
Identities = 19/57 (33%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 100 KCQGCRLPIKDV-----VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTAC 151
KC GC+ PI VV +WH F C C L K F G +C+ C
Sbjct: 4 KCSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60
>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 = 39.4 bits (92), Expect = 6e-05
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 160 CFGCGKPITETA----IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECS 211
C C KPIT + DR+WH+ CF+C RC + G F ++C +C+
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDCN 56
Score = 26.3 bits (58), Expect = 2.8
Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 4/55 (7%)
Query: 101 CQGCRLPIKDV----VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTAC 151
C C PI V+ ++ WH F C C L+ GF+ C C
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55
>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher
family. The first LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 38.8 bits (90), Expect = 1e-04
Identities = 19/52 (36%), Positives = 26/52 (50%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C I+ + AL ++WHP+ F C C T L F E + N +C CY
Sbjct: 1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
Score = 36.1 bits (83), Expect = 8e-04
Identities = 17/52 (32%), Positives = 25/52 (48%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C +I+ + AL ++WHPE F C +C +A F + YC Y
Sbjct: 1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b. The first
LIM domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 38.8 bits (90), Expect = 1e-04
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 40 PKCAAC-QGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
P CA C Q ++ I++ LD+ WH + +C+ C+ +A + F S YC +D+
Sbjct: 2 PLCAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCFS-RGDSVYCKDDF 55
Score = 34.1 bits (78), Expect = 0.005
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 158 PKCFGCGKPITETAI-KVHDRKWHEACFRCGRCRRPISGPTF 198
P C GC + I + I KV DR WH C +C C+ ++ F
Sbjct: 2 PLCAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCF 43
>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 = 38.5 bits (90), Expect = 1e-04
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C I+N + ALDK WH F+C C + T ++ G PYC DY
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVL-TGEYMGKDGKPYCERDY 52
Score = 34.2 bits (79), Expect = 0.004
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 160 CFGCGKPITE-TAIKVHDRKWHEACFRCGRCRRPISG 195
C GCG+ I A+ D++WH CF+C C + ++G
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTG 37
Score = 32.7 bits (75), Expect = 0.012
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 101 CQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC IK+ + AL++ WH F C CG K+L + ++G +C Y
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECG-KVLTGEYMGKDGKPYCERDY 52
>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 = 38.5 bits (90), Expect = 1e-04
Identities = 19/51 (37%), Positives = 24/51 (47%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTAC 151
C C + V+ A+N WHPD F C C +L GF + G A C C
Sbjct: 1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51
Score = 33.8 bits (78), Expect = 0.005
Identities = 15/48 (31%), Positives = 24/48 (50%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C C + +++A++ WHP+ FRC C +A F +AG C
Sbjct: 1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALC 48
Score = 31.9 bits (73), Expect = 0.028
Identities = 15/51 (29%), Positives = 22/51 (43%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C CG+ + IK + WH CFRC C + ++ F +C C
Sbjct: 1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51
>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 = 38.1 bits (89), Expect = 2e-04
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 160 CFGCGKPITE-TAIKVHDRKWHEACFRCGRCRRPISG 195
C GCG+ I + + DR+WH +C +C CR P+
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDS 37
Score = 35.4 bits (82), Expect = 0.002
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQ-KFHVHAGSPYCVEDY 93
CA C IQ+ + A+D+ WH +C CR+P+ ++ G+ YC EDY
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>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 = 38.0 bits (88), Expect = 2e-04
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 42 CAAC-QGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C Q ++ I++ LD+ WH +C C++ +A + F AG+ YC ED+
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFS-RAGNVYCKEDF 52
Score = 32.6 bits (74), Expect = 0.014
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 160 CFGCGKPITETAI-KVHDRKWHEACFRCGRCRRPISGPTF 198
C GC + I + I KV DR WH +C +C C+ ++ F
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCF 40
Score = 26.5 bits (58), Expect = 2.2
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 101 CQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C GC I D ++ L++ WH C C +L + F R GN +C
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFS-RAGNVYC 48
>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 = 38.2 bits (89), Expect = 2e-04
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 158 PKCFGCGKPITETAI-KVHDRKWHEACFRCGRCRRPISGPTF 198
PKC GC PI + I KV D+ WH C +C C+ ++ F
Sbjct: 2 PKCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDKCF 43
Score = 32.4 bits (74), Expect = 0.016
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 40 PKCAAC-QGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
PKCA C + I++ DK WH + +C C+ + T K G YC ED+
Sbjct: 2 PKCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQL-TDKCFSRGGQVYCKEDF 55
Score = 27.4 bits (61), Expect = 1.1
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 100 KCQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
KC GC PI D ++ ++ WH C+ C +L K + R G +C
Sbjct: 3 KCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDK-CFSRGGQVYC 51
>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 = 37.9 bits (88), Expect = 2e-04
Identities = 22/53 (41%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 101 CQGCRLPIKDV-VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GCR I D V ALNQ WH D F C C L ++E++G +C Y
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDS-LSNWYFEKDGKLYCRKDY 52
Score = 36.3 bits (84), Expect = 8e-04
Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C+G I + VQAL++ WH + FRC+ C ++ F G YC +DY
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYFE-KDGKLYCRKDY 52
Score = 28.2 bits (63), Expect = 0.56
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 160 CFGCGKPITETA-IKVHDRKWHEACFRCGRC 189
C GC I ++ ++ ++ WH CFRC C
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVC 31
>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 = 37.4 bits (87), Expect = 3e-04
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 101 CQGCRLPIK--DVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C GC PI+ D + AL TWH FVC C L + FY ++ C
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
Score = 29.7 bits (67), Expect = 0.15
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 54 VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
++AL TWH F C C + + Q F+ P C
Sbjct: 15 LEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
Score = 28.6 bits (64), Expect = 0.48
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 160 CFGCGKPIT--ETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C GC PI + ++ WH+ CF C C + G TF
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTF 41
>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 = 37.5 bits (87), Expect = 3e-04
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C+ C +I + V ++ WH E F CT+C +A Q+F PYC + +
Sbjct: 1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
Score = 32.4 bits (74), Expect = 0.015
Identities = 16/52 (30%), Positives = 23/52 (44%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C I VT N+ WH + F C +C L + F R+ +C C+
Sbjct: 1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
Score = 32.1 bits (73), Expect = 0.021
Identities = 14/51 (27%), Positives = 21/51 (41%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C C K I + + WH CF C C + ++G F + C +C
Sbjct: 1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADC 51
>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 = 37.3 bits (87), Expect = 3e-04
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 160 CFGCGKPITE-TAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEAD--VVCVECS 211
C GC + ITE A ++ +WH CF+C +C + +S + + D ++C +CS
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLSCDSNFLVLGDGSLICSDCS 55
Score = 25.8 bits (57), Expect = 3.7
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 101 CQGCRLPIKDVVVTALNQT-WHPDHFVCISCGTKL 134
C GC+ I + L WH F C C KL
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKL 35
>gnl|CDD|188817 cd09433, LIM4_FHL2, The fourth LIM domain of Four and a half LIM
domains protein 2 (FHL2). The fourth LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to s upport the assembly of multimeric protein
complexes.
Length = 58
Score = 37.3 bits (86), Expect = 3e-04
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 160 CFGCGKPIT----ETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECSE 212
C GC PI+ I +R+WH CF C +C + G F D++C EC +
Sbjct: 1 CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPECGK 57
Score = 29.2 bits (65), Expect = 0.25
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 101 CQGCRLPIKDV----VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTAC 151
C GC PI + ++ + WH D F C C L+ +GF + C C
Sbjct: 1 CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55
>gnl|CDD|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM
domains protein (FHL). The first LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 36.6 bits (85), Expect = 6e-04
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 156 FCPKCFGCGKPITETA--IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
F C C K I + + DR WHE CF+C +C+R + F + D++C EC
Sbjct: 1 FANTCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTEC 57
Score = 28.9 bits (65), Expect = 0.35
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 97 FLNKCQGCRLPI----KDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
F N C+ C+ I KD+ ++ WH F C C L+ K F ++ + CT CY
Sbjct: 1 FANTCEECKKKIGCDSKDLSYK--DRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58
>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 = 36.4 bits (84), Expect = 7e-04
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHV-HAGSPYCVEDY 93
CA C I + +++A K++HP+ F C C+ P+ + F V A P+CV DY
Sbjct: 1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDY 53
Score = 35.3 bits (81), Expect = 0.002
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEAD 204
C C + IT+ +K + +H CF C C+ P+ G +F V +A+
Sbjct: 1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQAN 45
Score = 29.1 bits (65), Expect = 0.32
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGN-AFCTACYEGKFCPK 159
C C I D ++ A +++HP F C+ C L + F + N C Y ++ P+
Sbjct: 1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAPR 60
>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 = 36.6 bits (85), Expect = 7e-04
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 160 CFGCGKPITETAI-KVHDRKWHEACFRCGRCRRPISG-PTFRVCEADVVC 207
C GCG+PIT+ + KV R WH +C RC C+ P+ P+ + + C
Sbjct: 1 CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYC 50
Score = 26.2 bits (58), Expect = 2.7
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKF-HVHAGSPYCVEDY 93
C C I + +++ ++WH RC C+ P+ Q YC DY
Sbjct: 1 CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
>gnl|CDD|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP,
actinin-associated LIM protein. This family represents
the LIM domain of ALP, actinin-associated LIM protein.
ALP contains an N-terminal PDZ domain, a C-terminal LIM
domain and an ALP-subfamily-specific 34-amino-acid motif
termed ALP-like motif (AM), which contains a putative
consensus protein kinase C (PKC) phosphorylation site
and two alpha-helices. ALP proteins are found in heart
and in skeletal muscle. ALP may act as a signaling
molecule which is regulated by PKC-dependent signaling.
ALP plays an essential role in the development of RV
(right ventricle) chamber. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 36.4 bits (84), Expect = 7e-04
Identities = 19/50 (38%), Positives = 25/50 (50%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTA 150
C C I VV A ++ HP+ FVC C L KG++ EG +C A
Sbjct: 1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCEA 50
Score = 29.9 bits (67), Expect = 0.13
Identities = 16/48 (33%), Positives = 23/48 (47%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C C I +V+A DK HPE F C+ C + + + + G YC
Sbjct: 1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYC 48
Score = 28.3 bits (63), Expect = 0.60
Identities = 14/48 (29%), Positives = 19/48 (39%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVC 207
C CG I T +K D+ H CF C C + + E + C
Sbjct: 1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYC 48
>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated
LIM protein) family. This family represents the LIM
domain of ALP (actinin-associated LIM protein) family.
Four proteins: ALP, CLP36, RIL, and Mystique have been
classified into the ALP subfamily of LIM domain
proteins. Each member of the subfamily contains an
N-terminal PDZ domain and a C-terminal LIM domain.
Functionally, these proteins bind to alpha-actinin
through their PDZ domains and bind or other signaling
molecules through their LIM domains. ALP proteins have
been implicated in cardiac and skeletal muscle
structure, function and disease, platelet, and
epithelial cell motility. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 36.2 bits (84), Expect = 8e-04
Identities = 19/48 (39%), Positives = 25/48 (52%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C C I VVV A ++ HP+ FVC CG L KG++ E +C
Sbjct: 1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYC 48
Score = 30.4 bits (69), Expect = 0.090
Identities = 15/48 (31%), Positives = 22/48 (45%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C C I ++V+A DK HPE F C C + + + + YC
Sbjct: 1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYC 48
Score = 29.3 bits (66), Expect = 0.21
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRC 189
C CG I +K D+ H CF C C
Sbjct: 1 CDKCGNGIVGVVVKARDKNRHPECFVCADC 30
>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 = 37.1 bits (86), Expect = 9e-04
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 160 CFGCGKPI--TETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C CG+P+ T+ A++ +H CF C +C + + G F E C EC
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEEC 86
Score = 35.6 bits (82), Expect = 0.003
Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 30 PPPNAASTMYPKCAAC-QGLIQ-NIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSP 87
PP A+T C C Q L + V+AL +H F C C + Q+F+ G P
Sbjct: 23 PPAAEAATN-ELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKP 81
Query: 88 YCVEDY 93
YC E Y
Sbjct: 82 YCEECY 87
Score = 34.4 bits (79), Expect = 0.006
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 101 CQGCRLPI--KDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C P+ V AL +H F C C +L + FY EG +C CY
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
>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 = 35.8 bits (82), Expect = 0.001
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 160 CFGCGKPITETAIKVHDR--KWHEACFRCGRCRRPISGPTFRVCEADVVCVECSEK 213
C C K I K+ + WHE CF C RC++PI +F + CV C EK
Sbjct: 1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEK 56
Score = 29.6 bits (66), Expect = 0.18
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 119 TWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYE 153
+WH F+C C + K F ++ FC CYE
Sbjct: 21 SWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYE 55
Score = 25.8 bits (56), Expect = 4.3
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 60 TWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
+WH F C C+ PI T+ F +CV Y
Sbjct: 21 SWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCY 54
>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b. The first LIM
domain of Lmx1b: Lmx1b belongs to the LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. In mouse, Lmx1b
functions in the developing limbs and eyes, the kidneys,
the brain, and in cranial mesenchyme. The disruption of
Lmx1b gene results kidney and limb defects. In the
brain, Lmx1b is important for generation of
mesencephalic dopamine neurons and the differentiation
of serotonergic neurons. In the mouse eye, Lmx1b
regulates anterior segment (cornea, iris, ciliary body,
trabecular meshwork, and lens) development. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 35.4 bits (82), Expect = 0.002
Identities = 14/40 (35%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 160 CFGCGKPITETAI-KVHDRKWHEACFRCGRCRRPISGPTF 198
C GC +PI++ + +V++R WHE C +C C++P++ +
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCY 40
Score = 28.1 bits (63), Expect = 0.71
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA CQ I + +++ +++WH E +C+ C+ P+ T + YC +DY
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPL-TTSCYFRDRKLYCKQDY 52
Score = 26.6 bits (59), Expect = 2.4
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 101 CQGCRLPIKDVVVTALNQ-TWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYE 153
C GC+ PI D + +N+ +WH + C C L ++ R+ +C Y+
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCYF-RDRKLYCKQDYQ 53
>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 = 35.1 bits (81), Expect = 0.002
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 40 PKCAACQGLI-QNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
P+C+AC +I + +A + WH +HF C C + Q++ + G PYC
Sbjct: 1 PRCSACDEIIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51
Score = 35.1 bits (81), Expect = 0.002
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 100 KCQGC-RLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYE 153
+C C + D A + WH HF C C +L + + REG +C C+E
Sbjct: 2 RCSACDEIIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 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 = 35.6 bits (82), Expect = 0.002
Identities = 21/53 (39%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 101 CQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C I D + ALN WH D F C CG L + +YE++G FC Y
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKDY 73
Score = 34.5 bits (79), Expect = 0.005
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 36 STMYPKCAAC-QGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
+ P CA+C Q + +QAL+ WH + FRC C ++ ++ G +C +DY
Sbjct: 16 GNVLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKDY 73
Score = 29.5 bits (66), Expect = 0.28
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 153 EGKFCPKCFGCGKPI-TETAIKVHDRKWHEACFRCGRCRRPIS 194
EG P C CG+ I ++ + WH CFRC C +S
Sbjct: 15 EGNVLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLS 57
>gnl|CDD|188811 cd09427, LIM2_FHL3, The second LIM domain of Four and a half LIM
domains protein 3 (FHL3). The second LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 58
Score = 35.2 bits (81), Expect = 0.002
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 159 KCFGCGKPITETAIKVH--DRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECSE 212
KC CGK + + K+ + WHE CF C C +PI +F + + CV C E
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCYE 58
Score = 31.7 bits (72), Expect = 0.037
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 118 QTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYE 153
QTWH F+C C + + F + +C CYE
Sbjct: 23 QTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCYE 58
Score = 28.7 bits (64), Expect = 0.38
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 58 DKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
+TWH F C C PI ++ F YCV Y
Sbjct: 22 GQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCY 57
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 34.7 bits (80), Expect = 0.003
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 160 CFGCGKPITETAIKVH--DRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C GCG+ K+ ++WHE CF C C++PI +F + DV CV C
Sbjct: 1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPC 53
Score = 33.2 bits (76), Expect = 0.010
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 118 QTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
Q WH F C C + K F ++ + +C CY
Sbjct: 20 QQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54
Score = 30.1 bits (68), Expect = 0.11
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 59 KTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
+ WH + F C C+ PI T+ F YCV Y
Sbjct: 20 QQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54
>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 = 34.7 bits (80), Expect = 0.003
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 42 CAACQGLI-QNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C CQ I I++ LD+TWH + +C C + + F G YC +D+
Sbjct: 1 CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFA-RNGHVYCKDDF 52
Score = 31.2 bits (71), Expect = 0.052
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 160 CFGCGKPITETAI-KVHDRKWHEACFRCGRCRRPISGPTF 198
C GC + I + I KV DR WH C +C C ++ F
Sbjct: 1 CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCF 40
Score = 28.5 bits (64), Expect = 0.46
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 101 CQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C GC+ I D ++ L++TWH C CG +L K F R G+ +C
Sbjct: 1 CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFA-RNGHVYC 48
>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 = 34.7 bits (80), Expect = 0.003
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 56 ALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
A+D+ +H F C C+I + + F+ G PYC EDY
Sbjct: 17 AMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
Score = 27.0 bits (60), Expect = 1.5
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 114 TALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
TA++Q +H F C C L K FY +G +C Y
Sbjct: 16 TAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
>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 = 34.6 bits (79), Expect = 0.003
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 101 CQGCRLPIK--DVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C GC PI+ D + AL TWH FVC C L + F+ ++ C
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLC 50
Score = 26.1 bits (57), Expect = 3.5
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 160 CFGCGKPIT--ETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C GC PI + ++ WH+ CF C C + G TF
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTF 41
>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 = 34.4 bits (79), Expect = 0.004
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 101 CQGCRLPIK--DVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTA 150
C C PI+ D V ALN +H F C C L + FY + G FC
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKL 52
Score = 31.4 bits (71), Expect = 0.039
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 54 VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
V+AL+ +H + F CT C + + Q F+ G P+C
Sbjct: 15 VEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFC 50
Score = 27.9 bits (62), Expect = 0.74
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 160 CFGCGKPIT--ETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C CG PI + ++ + +H CF C RC + G +F
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSF 41
>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 = 34.2 bits (79), Expect = 0.004
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 42 CAACQGLIQ-NIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C C + +L + WH RC C+ + + H G PYC
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYC 49
Score = 31.5 bits (72), Expect = 0.039
Identities = 13/40 (32%), Positives = 16/40 (40%)
Query: 113 VTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
T+L + WH C C L E EG +C CY
Sbjct: 14 KTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
Score = 30.8 bits (70), Expect = 0.064
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 160 CFGCGKPITETAIKVH-DRKWHEACFRCGRCRRPIS 194
C CGKP+ K R WH+ C RC +C++ ++
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLT 36
>gnl|CDD|188801 cd09417, LIM2_LIMPETin_like, The second LIM domain of protein
LIMPETin and related proteins. The second 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 = 34.4 bits (79), Expect = 0.004
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 101 CQGCRLPIKDVVVT-ALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYE 153
C I T A+N+ WH HF C C L + + R+ + +C CYE
Sbjct: 3 SVQCDELIFSGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56
Score = 32.5 bits (74), Expect = 0.019
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 55 QALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
+A++K WH HF C C + Q++ + PYC++ Y
Sbjct: 17 KAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCY 55
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Lhx1 is required for regulating
the vertebrate head organizer, the nervous system, and
female reproductive tract development. During
embryogenesis in the mouse, Lhx1 is expressed early in
mesodermal tissue, then later during urogenital, kidney,
liver, and nervous system development. In the adult,
expression is restricted to the kidney and brain. A
mouse embryos with Lhx1 gene knockout cannot grow normal
anterior head structures, kidneys, and gonads, but with
normally developed trunk and tail morphology. In the
developing nervous system, Lhx1 is required to direct
the trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 33.9 bits (78), Expect = 0.004
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRCRRPISGPTF 198
C GC +PI + + V DR WH C +C C+ P++ F
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCF 40
Score = 30.9 bits (70), Expect = 0.065
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C I + ++ LD+ WH + +C C+ P+ T+K G YC D+
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPL-TEKCFSREGKLYCRNDF 52
Score = 30.1 bits (68), Expect = 0.14
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 101 CQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C GC PI D ++ L++ WH C C L K F REG +C
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYC 48
>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 = 34.2 bits (79), Expect = 0.005
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKF 80
CA C I V+AL +H + F C C P+A++ F
Sbjct: 1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFF 39
Score = 33.8 bits (78), Expect = 0.005
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADV 205
C CGKPIT ++ +H CF C C +P++ F V + D
Sbjct: 1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDT 46
Score = 30.3 bits (69), Expect = 0.089
Identities = 15/39 (38%), Positives = 17/39 (43%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGF 139
C C PI V AL +H D F C CG + K F
Sbjct: 1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFF 39
>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 = 33.8 bits (78), Expect = 0.005
Identities = 17/52 (32%), Positives = 24/52 (46%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C C K V+ ++ +H F C CG L GF+ +EG +CT Y
Sbjct: 1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52
Score = 32.2 bits (74), Expect = 0.018
Identities = 15/50 (30%), Positives = 24/50 (48%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVE 209
C+ CGK ++V D+ +H CF C C ++ F V E + C +
Sbjct: 1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTD 50
Score = 28.4 bits (64), Expect = 0.47
Identities = 16/52 (30%), Positives = 24/52 (46%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C + +++ DK +H + F C C +A F V G YC +DY
Sbjct: 1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 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 = 33.8 bits (77), Expect = 0.005
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C C I +V A ++ +HP+ F+C CG L +G++ + +C
Sbjct: 1 CTRCGNGIVGTIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYC 48
Score = 31.1 bits (70), Expect = 0.065
Identities = 16/48 (33%), Positives = 22/48 (45%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
C C I IV+A DK +HPE F C C + + + + YC
Sbjct: 1 CTRCGNGIVGTIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYC 48
Score = 28.4 bits (63), Expect = 0.59
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRC 189
C CG I T +K D+ +H CF C C
Sbjct: 1 CTRCGNGIVGTIVKARDKLYHPECFMCDDC 30
>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 = 33.7 bits (77), Expect = 0.006
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 160 CFGCGKPITETA--IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
CF C K I + ++ +WHE CF C C++PI E CV C
Sbjct: 1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPC 53
Score = 25.2 bits (55), Expect = 7.0
Identities = 11/32 (34%), Positives = 13/32 (40%)
Query: 59 KTWHPEHFRCTHCRIPIATQKFHVHAGSPYCV 90
WH F C C+ PI T+ YCV
Sbjct: 20 NEWHETCFVCQSCQQPIGTKPLITKENKNYCV 51
>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 = 33.9 bits (77), Expect = 0.006
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 101 CQGCRLPIK--DVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C GC P++ D + AL TWH F+C C L + FY ++ C
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 50
Score = 26.9 bits (59), Expect = 1.5
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 54 VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
++AL TWH F C C + + Q F+ P C
Sbjct: 15 IEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 50
Score = 26.2 bits (57), Expect = 3.8
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 160 CFGCGKPIT--ETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C GC P+ + I+ WH+ CF C C + G F
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPF 41
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 33.7 bits (77), Expect = 0.007
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 176 DRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
DR +HE CFRC RC R ++ F + +++C +C
Sbjct: 23 DRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDC 57
>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 = 33.3 bits (76), Expect = 0.010
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNA-FCTACYEGKFCPK 159
C C PI D ++ A + +HP F C+ CG L F N C + KF P+
Sbjct: 1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAPR 60
Score = 30.2 bits (68), Expect = 0.12
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVV-CVECSEK 213
C C KPI + ++ + +H CF C C + + G F V + + C+E K
Sbjct: 1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHK 55
Score = 29.4 bits (66), Expect = 0.26
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSP-YCVEDYASLF 97
C+ C I + I++A K +HP+ F C C + F V A + +C+ED+ F
Sbjct: 1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKF 57
>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 = 33.0 bits (76), Expect = 0.011
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVC 207
C CGK + + + +H++CFRC C + + + E + C
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYC 49
Score = 27.2 bits (61), Expect = 1.4
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 54 VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
+ A K +H FRC+HC + + G YC
Sbjct: 14 LVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYC 49
>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 = 0.012
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C G IQ+ + + + WH F+C+ C+ + T ++ G YC + Y
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL-TNWYYEKDGKLYCHKHY 52
Score = 31.8 bits (72), Expect = 0.033
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 101 CQGCRLPIKDVV-VTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
C GC I+D + + WH F C C LL +YE++G +C Y
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVC-QDLLTNWYYEKDGKLYCHKHY 52
Score = 29.1 bits (65), Expect = 0.28
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 160 CFGCGKPITETA-IKVHDRKWHEACFRCGRCRRPIS 194
C GCG I ++ +V WH +CF+C C+ ++
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLT 36
>gnl|CDD|188719 cd09333, LIM3_PINCH, The third LIM domain of protein PINCH. The
third LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 51
Score = 32.7 bits (75), Expect = 0.013
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
CQ C I++ + +HP HF C +CG +L E +G +C C+
Sbjct: 1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTADA-RELKGELYCLRCH 51
Score = 27.0 bits (60), Expect = 1.4
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHC 71
C C +I+ ++ +HP HF C +C
Sbjct: 1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANC 30
>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like
family. The first LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 58
Score = 32.6 bits (75), Expect = 0.017
Identities = 12/39 (30%), Positives = 14/39 (35%), Gaps = 6/39 (15%)
Query: 160 CFGCGKPITETAIKV------HDRKWHEACFRCGRCRRP 192
C C +PI + V D WH CF C C
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNEL 39
Score = 31.4 bits (72), Expect = 0.051
Identities = 17/58 (29%), Positives = 21/58 (36%), Gaps = 6/58 (10%)
Query: 42 CAACQGLIQ--NIIVQAL----DKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C+ I + V A D WHP F C C + + H G YC Y
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58
Score = 29.1 bits (66), Expect = 0.31
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 101 CQGCRLPIK--DVVVTAL----NQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C+ C+ PI +V V A + WHP FVC +C L+ ++ +G +C
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYC 54
>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 = 32.3 bits (74), Expect = 0.019
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 42 CAACQGLIQNI-IVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
CA C + + LDK WH F+C C + + + + + PYC
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYC 49
Score = 25.0 bits (55), Expect = 6.8
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 116 LNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
L++ WH F C CG L K + +C A Y
Sbjct: 17 LDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53
>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 = 32.4 bits (74), Expect = 0.020
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 160 CFGCGKPITET--AIKVHDRKWHEACFRCGRCRRPIS-GPTFRVCEADVVC 207
C C + I+ + + D +H ACF C C+R +S G F + E V+C
Sbjct: 1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLC 51
>gnl|CDD|188800 cd09416, LIM2_Testin, The second LIM domain of Testin. The
second LIM domain of Testin: Testin contains three
C-terminal LIM domains and a PET protein-protein
interaction domain at the N-terminal. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion
events. Knockout mice experiments reveal that tumor
repressor function of testin. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 32.1 bits (73), Expect = 0.022
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 40 PKCAACQGLI-QNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
P+CA C LI N QA ++ WH +HF C C +A + + + P C
Sbjct: 1 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVC 51
Score = 30.2 bits (68), Expect = 0.10
Identities = 17/54 (31%), Positives = 21/54 (38%), Gaps = 1/54 (1%)
Query: 100 KCQGC-RLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
+C GC L + A NQ WH HF C C L + + C CY
Sbjct: 2 RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCKPCY 55
>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 = 31.8 bits (73), Expect = 0.033
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 160 CFGCGKPITETAIKVHDR----KWHEACFRCGRCRRPIS 194
C CG I +I D +WH CF C C P
Sbjct: 1 CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQ 39
Score = 30.3 bits (69), Expect = 0.11
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 61 WHPEHFRCTHCRIPIATQK-FHVHAGSPYCVEDY 93
WH E F CT C P +V PYC + Y
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
Score = 25.7 bits (57), Expect = 5.4
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 101 CQGCRLPIKDVVVT----ALNQTWHPDHFVCISCGTKLLYKG-FYEREGNAFCTACY 152
C+ C L I+ ++ L+ WH + FVC +CG + Y + +C Y
Sbjct: 1 CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>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 = 31.7 bits (72), Expect = 0.036
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRCRRPISGPTF 198
C GC + I + ++V+D WHE C +C C+ P+ F
Sbjct: 1 CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLETTCF 40
Score = 28.6 bits (64), Expect = 0.46
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C +IQ+ +++ D WH +C C+ P+ T F YC EDY
Sbjct: 1 CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLETTCF-YRDKKLYCKEDY 52
>gnl|CDD|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3 (LIM
domain only protein 1 and 3). The first LIM domain of
LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1
and LMO3 are highly homologous and belong to the LMO
protein family. LMO1 and LMO3 are nuclear protein that
plays important roles in transcriptional regulation and
development. As LIM domains lack intrinsic DNA-binding
activity, nuclear LMOs are involved in transcriptional
regulation by forming complexes with other transcription
factors or cofactors. For example, LMO1 interacts with
the the bHLH domain of bHLH transcription factor, TAL1
(T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1
inhibits the expression of TAL1/SCL target genes. LMO3
facilitates p53 binding to its response elements, which
suggests that LMO3 acts as a co-repressor of p53,
suppressing p53-dependent transcriptional regulation. In
addition, LMO3 interacts with neuronal transcription
factor, HEN2, and acts as an oncogene in neuroblastoma.
Another binding partner of LMO3 is calcium- and
integrin-binding protein CIB, which binds via the second
LIM domain (LIM2) of LMO3. One role of the CIB/LMO3
complex is to inhibit cell proliferation. Although LMO1
and LMO3 are highly homologous proteins, they play
different roles in the regulation of the pituitary
glycoprotein hormone alpha-subunit (alpha GSU) gene.
Alpha GSU promoter activity was markedly repressed by
LMO1 but activated by LMO3. All LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 31.8 bits (72), Expect = 0.036
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRC 189
C GC + I + +K D+ WHE C +C C
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACC 31
Score = 27.9 bits (62), Expect = 0.88
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCT--HCRIPIATQKFHVHAGSPYCVEDY 93
CA C I++ +++ALD+ WH + +C CR+ + A C DY
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
Score = 26.7 bits (59), Expect = 2.2
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 101 CQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKL 134
C GC IKD ++ AL+Q WH D C C +L
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRL 35
>gnl|CDD|188797 cd09413, LIM1_Testin, The first LIM domain of Testin. The first
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction domain
at the N-terminal. Testin is a cytoskeleton associated
focal adhesion protein that localizes along actin stress
fibers, at cell-cell-contact areas, and at focal
adhesion plaques. Testin interacts with a variety of
cytoskeletal proteins, including zyxin, mena, VASP,
talin, and actin and it is involved in cell motility and
adhesion events. Knockout mice experiments reveal that
tumor repressor function of Testin. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 31.7 bits (72), Expect = 0.037
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 101 CQGCRLPIK--DVVVTA----LNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C C+ P+K D V A ++ WHP FVC +CG L+ ++ + G +C
Sbjct: 1 CYCCKQPMKEGDPAVYAERAGYDKLWHPACFVCSTCGELLVDMIYFWKNGKLYC 54
Score = 26.7 bits (59), Expect = 2.0
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 6/36 (16%)
Query: 160 CFGCGKPITETAIKV------HDRKWHEACFRCGRC 189
C+ C +P+ E V +D+ WH ACF C C
Sbjct: 1 CYCCKQPMKEGDPAVYAERAGYDKLWHPACFVCSTC 36
>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 = 31.9 bits (72), Expect = 0.041
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 32 PNAASTMYPKCAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQ-KFHVHAGSPYC 89
P+ +S CA C G I + + A+DK WH +C C++ + ++ GS YC
Sbjct: 1 PSISSDRAALCAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYC 60
Query: 90 VEDY 93
EDY
Sbjct: 61 KEDY 64
Score = 26.1 bits (57), Expect = 4.2
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 160 CFGCGKPITETA-IKVHDRKWHEACFRCGRCR 190
C GCG I++ + D++WH C +C C+
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECK 42
>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 = 31.3 bits (71), Expect = 0.042
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 160 CFGCGKPITETAI-KVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C CGK I +TAI D + CFRC RC R I+ + + + C+ C
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDITDLKYAKTKRGLFCMSC 52
>gnl|CDD|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3
(CRP3/MLP). The first LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. CRP3/MLP interacts with
cytoskeletal protein beta-spectrin. CRP3/MLP also
interacts with the basic helix-loop-helix myogenic
transcriptio n factors MyoD, myogenin, and MRF4 thereby
increasing their affinity for specific DNA regulatory
elements. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 31.3 bits (70), Expect = 0.047
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 159 KCFGCGKPITETA-IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
KC C K + I+ + R +H+ CF C CR+ + T E+++ C C
Sbjct: 1 KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTC 53
>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 = 31.2 bits (70), Expect = 0.049
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQ-KFHVHAGSPYCVEDY 93
CA C G I + + A+DK WH +C C++ + ++ GS YC EDY
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
Score = 25.0 bits (54), Expect = 7.8
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 160 CFGCGKPITETA-IKVHDRKWHEACFRCGRCR 190
C GCG I++ + D++WH C +C C+
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECK 32
>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin.
The third LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 31.4 bits (71), Expect = 0.053
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 156 FCPKCFGCGKPI--TETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
F +C C K I + D+ WHEACF C +C+ + F + C C
Sbjct: 1 FANQCEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNC 57
Score = 31.0 bits (70), Expect = 0.061
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 97 FLNKCQGCRLPI----KDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
F N+C+ C I KD+ + ++ WH F+C C L+ K F + +C CY
Sbjct: 1 FANQCEECSKIIGIDSKDL--SYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 58
Query: 153 E 153
+
Sbjct: 59 D 59
Score = 26.8 bits (59), Expect = 2.3
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 58 DKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
DK WH F C+ C+I + + F A YC Y
Sbjct: 23 DKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 58
>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 = 31.0 bits (70), Expect = 0.056
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSP-YCVEDY 93
C+ C I I++A K +HP F C C + F V A +C+ED+
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53
Score = 30.6 bits (69), Expect = 0.070
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRV-CEADVVCVE 209
C C KPI E ++ + +H CF C C R + G F V + C+E
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIE 51
Score = 26.8 bits (59), Expect = 1.7
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISC 130
C C PI + ++ A + +HP F C+ C
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVC 30
>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 = 31.1 bits (70), Expect = 0.062
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 42 CAAC-QGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
CA C + + V LDKTWH F C C++ + + + PYC Y
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53
Score = 26.8 bits (59), Expect = 1.7
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVC 207
C CGK + T + D+ WH+ACF C C+ ++ ++ + C
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYC 49
>gnl|CDD|152822 pfam12387, Peptidase_C74, Pestivirus NS2 peptidase. The pestivirus
NS2 peptidase is responsible for single cleavage between
NS2 and NS3 of the bovine viral diarrhea virus
polyprotein, a cleavage that is correlated with
cytopathogenicity. The peptidase is activated by its
interaction with 'J-domain protein interacting with
viral protein' - Jiv.
Length = 200
Score = 33.2 bits (76), Expect = 0.062
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 4/25 (16%)
Query: 148 CTAC----YEGKFCPKCFGCGKPIT 168
CT C ++G CPKC G PIT
Sbjct: 165 CTVCENRDWKGGNCPKCGRQGPPIT 189
Score = 27.4 bits (61), Expect = 5.5
Identities = 8/20 (40%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 176 DRKWH-EACFRCGRCRRPIS 194
+R W C +CGR PI+
Sbjct: 170 NRDWKGGNCPKCGRQGPPIT 189
>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 = 30.8 bits (69), Expect = 0.070
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 101 CQGCRLPIK--DVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTA 150
C GC I D + AL +WH FVC C L K FY ++ C +
Sbjct: 1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCKS 52
Score = 25.0 bits (54), Expect = 7.9
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 179 WHEACFRCGRCRRPISGPTF 198
WH+ CF C C+ + G TF
Sbjct: 22 WHDTCFVCAICQINLEGKTF 41
>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 = 30.9 bits (70), Expect = 0.073
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 115 ALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
A+ +H + F C SCG L K FY G +C
Sbjct: 17 AMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYC 50
Score = 28.2 bits (63), Expect = 0.63
Identities = 16/52 (30%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 160 CFGCGKPITET--AIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVE 209
C CGK + A + +H CF C C R + G F V C E
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEE 52
Score = 26.2 bits (58), Expect = 3.2
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 55 QALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
QA+ +H F C C + + F+ G YC EDY
Sbjct: 16 QAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
>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 = 30.8 bits (69), Expect = 0.077
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 160 CFGCGKPIT--ETAIKVHDRKWHEACFRCGRCRRPIS-GPTFRVCEADVVC 207
C C K I E ++V D+ +H CF+C C++ G + + +D+VC
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVC 51
>gnl|CDD|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein
2 (CRP2). The second LIM domain of Cysteine Rich
Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 30.8 bits (69), Expect = 0.079
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 113 VTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
+ + WH + F C CG L E+EG +C CY
Sbjct: 14 IMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
Score = 29.3 bits (65), Expect = 0.23
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 177 RKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
+ WH+ CFRC +C + + T E ++ C C
Sbjct: 19 KPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGC 52
>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 = 30.1 bits (68), Expect = 0.12
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 42 CAACQGLI--QNIIVQALDKTWHPEHFRCTHCRIPIAT-QKFHVHAGSPYCVED 92
C+AC I ++++A +H + F C+ C + +FH GS +C D
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 54
Score = 29.0 bits (65), Expect = 0.36
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 3/51 (5%)
Query: 160 CFGCGK--PITETAIKVHDRKWHEACFRCGRCR-RPISGPTFRVCEADVVC 207
C CG+ P +E ++ +H CF C C + + G F + C
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFC 51
Score = 28.6 bits (64), Expect = 0.45
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 101 CQGC--RLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKG-FYEREGNAFC 148
C C +P ++V+ A +H F C +C +L+ F+ G+ FC
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFC 51
>gnl|CDD|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein
(TLP). The second LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a role
in development of normal thymus and in controlling the
development and differentiation of thymic epithelial
cells. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 30.0 bits (67), Expect = 0.13
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 160 CFGCGKPIT-ETAIKVHDRKWHEACFRCGRCRRPIS 194
C GCGKP+ + R WH C RC RC++ ++
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLT 36
Score = 27.3 bits (60), Expect = 1.2
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 54 VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
V +L + WH RC C+ + H GSPYC
Sbjct: 14 VMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
>gnl|CDD|188832 cd09448, LIM_CLP36, This family represents the LIM domain of CLP36.
This family represents the LIM domain of CLP36. CLP36
has also been named as CLIM1, Elfin, or PDLIM1. CLP36
contains a C-terminal LIM domain and an N-terminal PDZ
domain. CLP36 is highly expressed in heart and is
present in many other tissues including lung, liver,
spleen, and blood. CLP36 has been implicated in many
processes including hypoxia and regulation of actin
stress fibers. CLP36 co-localizes with alpha-actinin-2
at the Z-lines in myocardium. In addition, CLP36 binds
to alpha-actinin-1 and alpha-actinin-4, and associates
with F-actin filaments and stress fibers. CLP36 might be
involved in not only the function of sarcomeres in
muscle cells, but also in actin stress fiber-mediated
cellular processes, such as cell shape, migration,
polarit, and cytokinesis in non-muscle cells. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 29.9 bits (67), Expect = 0.15
Identities = 17/48 (35%), Positives = 23/48 (47%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C C I V V ++ HP+ +VC CGT L KG + E +C
Sbjct: 1 CDKCGSGIVGVFVKIRDKPRHPECYVCTDCGTNLKQKGHFFVEDQIYC 48
Score = 24.9 bits (54), Expect = 9.6
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHC 71
C C I + V+ DK HPE + CT C
Sbjct: 1 CDKCGSGIVGVFVKIRDKPRHPECYVCTDC 30
>gnl|CDD|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein
(CRP). The second LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function not
only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the arrangement
of the myofibrillar/cytoskeletal network. It is evident
that CRP1, CRP2, and CRP3/MLP are involved in promoting
protein assembly along the actin-based cytoskeleton.
Although members of the CRP family share common binding
partners, they are also capable of recognizing different
and specific targets. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residu es,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 29.9 bits (67), Expect = 0.16
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 118 QTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
+ WH + F C CG L +++G +C CY
Sbjct: 19 KPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
Score = 28.3 bits (63), Expect = 0.61
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 179 WHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
WH+ CFRC +C + + T + ++ C C
Sbjct: 21 WHKNCFRCAKCGKSLESTTLADKDGEIYCKGC 52
>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 = 30.0 bits (68), Expect = 0.17
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 42 CAACQGLIQNI--IVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLF 97
C C+ + IV + + +H + F C C P F+ G YC D+ LF
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLF 58
Score = 29.6 bits (67), Expect = 0.22
Identities = 12/41 (29%), Positives = 18/41 (43%)
Query: 112 VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
+V + + +H FVC C FYE EG +C +
Sbjct: 14 IVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDF 54
Score = 26.9 bits (60), Expect = 1.7
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 160 CFGCGKPIT--ETAIKVHDRKWHEACFRCGRCRRPISGPTF------RVCEADV 205
C C + E + + +HE CF C +C +P F + CE D
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDF 54
>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein
SF3. The second Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 61
Score = 29.7 bits (67), Expect = 0.17
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 42 CAACQGLIQNIIVQALDKT-WHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNK 100
C AC + I ++ T +H F+C+H I+ + H G YC ++ LF K
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60
>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 = 29.5 bits (66), Expect = 0.19
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 101 CQGCRLPI-KDVVVTALNQTWHPDHFVCISCG 131
C GC I +V+ A Q +HP+ F C+ CG
Sbjct: 1 CHGCSETITTGLVMVAGEQKYHPECFSCLRCG 32
Score = 28.3 bits (63), Expect = 0.53
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 160 CFGCGKPITETAIKVH-DRKWHEACFRCGRCR 190
C GC + IT + V ++K+H CF C RC
Sbjct: 1 CHGCSETITTGLVMVAGEQKYHPECFSCLRCG 32
>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 = 29.4 bits (66), Expect = 0.25
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 13/55 (23%)
Query: 160 CFGCGKP-------ITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVC 207
C CGKP I E I +H+ CFRC C + + ++ E ++ C
Sbjct: 1 CRSCGKPVYKMEEIIAEKHI------YHKNCFRCKDCNKQLKVDNYQSHEGNLYC 49
Score = 26.3 bits (58), Expect = 2.5
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 61 WHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
+H FRC C + + H G+ YC
Sbjct: 21 YHKNCFRCKDCNKQLKVDNYQSHEGNLYC 49
>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like
family. The third LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 57
Score = 29.3 bits (66), Expect = 0.25
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 101 CQGCRLPIKDVV--VTALNQTWH--PDHFVCISCGTKLLYKGFYEREGNAFCT 149
C C PI V V Q WH + F C +C LL + F + G FC+
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFCS 53
Score = 28.1 bits (63), Expect = 0.68
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 160 CFGCGKPITETAIKVHDRK--WH--EACFRCGRCRRPISGPTFRVCEADVVC-VECS 211
C CG+PI +V WH E CF C C++ + G F + C +C
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFCSPKCK 57
Score = 25.0 bits (55), Expect = 8.5
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 61 WH--PEHFRCTHCRIPIATQKFHVHAGSPYC 89
WH E F C++C+ + Q F G +C
Sbjct: 22 WHATEECFCCSNCKKSLLGQPFLPKNGQIFC 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 = 29.2 bits (66), Expect = 0.28
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 160 CFGCGKPITETAI-KVH-DRKWHEACFRCGRCRRPI 193
C GCG I + I +V D +WH AC +C C + +
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYL 36
Score = 27.3 bits (61), Expect = 1.4
Identities = 18/55 (32%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 42 CAACQGLIQN--IIVQALDKTWHPEHFRCTHCRIPI-ATQKFHVHAGSPYCVEDY 93
C C G I + I+ A D WH +C C + T V G YC DY
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
Score = 25.4 bits (56), Expect = 6.0
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 101 CQGCRLPIKD--VVVTALNQTWHPDHFVCISCGTKLLYK-GFYEREGNAFCTACY 152
C GC I D ++ A + WH C CG L + R+G +C Y
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>gnl|CDD|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP. The LIM domain of
N-RAP: N-RAP is a muscle-specific protein concentrated
at myotendinous junctions in skeletal muscle and
intercalated disks in cardiac muscle. LIM domain is
found at the N-terminus of N-RAP and the C-terminal of
N-RAP contains a region with multiple of nebulin
repeats. N-RAP functions as a scaffolding protein that
organizes alpha-actinin and actin into symmetrical
I-Z-I structures in developing myofibrils. Nebulin
repeat is known as actin binding domain. The N-RAP is
hypothesized to form antiparallel dimerization via its
LIM domain. As in other LIM domains, this domain family
is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 29.1 bits (65), Expect = 0.32
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 54 VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
+ +D+TWH F C C++ + F H PYC
Sbjct: 14 INCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYC 49
Score = 26.8 bits (59), Expect = 2.0
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 157 CPKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTF 198
C +C P + I D+ WH+ACF C C+ ++ F
Sbjct: 1 CARCGYGVYPAEK--INCIDQTWHKACFHCEVCKMMLTVNNF 40
>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific
protein SF3. The first Lim domain of pollen specific
protein SF3: SF3 is a Lim protein that is found
exclusively in mature plant pollen grains. It contains
two LIM domains. The exact function of SF3 is unknown.
It may be a transcription factor required for the
expression of late pollen genes. It is possible that
SF3 protein is involved in controlling pollen-specific
processes such as male gamete maturation, pollen tube
formation, or even fertilization. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 63
Score = 29.0 bits (65), Expect = 0.35
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 41 KCAACQGLIQNIIVQALD-KTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLF 97
KC AC + + + D +H FRC+HC+ + + G YC + LF
Sbjct: 4 KCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 61
>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 = 28.9 bits (65), Expect = 0.36
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHC 71
C AC I +++A K +HP RC+ C
Sbjct: 1 CEACDKFITGKVLEAGGKHYHPTCARCSRC 30
Score = 28.1 bits (63), Expect = 0.58
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRC 189
C C K IT ++ + +H C RC RC
Sbjct: 1 CEACDKFITGKVLEAGGKHYHPTCARCSRC 30
>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 = 28.7 bits (64), Expect = 0.42
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 157 CPKCFGCGKPITETAIKVHDRKWHEACFRCGRC-RRPISGPTFRVCEADVVC 207
C +C G ++ ++ D +H CFRC C R+ + G F + E +++C
Sbjct: 1 CAQC-RLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLC 51
>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2
(CRP2). The first LIM domain of Cysteine Rich Protein 2
(CRP2): The CRP family members include CRP1, CRP2,
CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved
nuclear targeting signal (K/R-K/R-Y-G-P-K), which
supports the fact that these proteins function not only
in the cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation, and
involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network. CRP2 specifically
binds to protein inhibitor of activated STAT-1 (PIAS1)
and a novel human protein designed CRP2BP (for CRP2
binding partner). PIAS1 specifically inhibits the STAT-1
pathway and CRP2BP is homologous to members of the
histone acetyltransferase family raising the possibility
that CRP2 is a modulator of cytokine-controlled pathways
or is functionally active in the transcriptional
regulatory network. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 28.8 bits (64), Expect = 0.43
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 159 KCFGCGKPITETA-IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
KC CG+ + ++ R +H+ CF C CR+ + T + + ++ C C
Sbjct: 1 KCGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSC 53
>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein
3 (CRP3/MLP). The second LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 28.4 bits (63), Expect = 0.44
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 118 QTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
+ WH F C CG L +++G +C CY
Sbjct: 19 KPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53
Score = 26.5 bits (58), Expect = 2.6
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 177 RKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
+ WH+ CFRC C + + T + ++ C C
Sbjct: 19 KPWHKTCFRCAICGKSLESTTVTDKDGELYCKVC 52
>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A.
The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A
belong to the CRP LIM domain protein family. The Mlp84B
protein contains five copies of the LIM domains, each
followed by a Glycin Rich Region (GRR). However, only
the first LIM domain of Mlp84B is in this family. Mlp60A
exhibits only one LIM domain linked to a glycin-rich
region. Mlp84B and Mlp60A are muscle specific proteins
and have been implicated in muscle differentiation.
While Mlp84B transcripts are enriched at the terminal
ends of muscle fibers, Mlp60A transcripts are found
throughout the muscle fibers. All LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 28.6 bits (64), Expect = 0.47
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 159 KCFGCGKPITETAIKVH-DRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
KC CGK + ++ KWH+ CF+CG C + + E ++ C +C
Sbjct: 1 KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQC 53
>gnl|CDD|188849 cd09465, LIM2_LIMK2, The second LIM domain of LIMK2 (LIM domain
Kinase 2). The second LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, altering the rate of actin depolymerisation.
LIMK activity is activated by phosphorylation of a
threonine residue within the activation loop of the
kinase by p21-activated kinases 1 and 4 and by Rho
kinase. LIMKs can function in both cytoplasm and
nucleus. Both LIMK1 and LIMK2 can act in the nucleus to
suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2
is expressed in all tissues. While LIMK1 localizes
mainly at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 28.7 bits (64), Expect = 0.48
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 7/65 (10%)
Query: 97 FLNKCQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKF 156
F C GC L + + A +HP+ F C+SC + +G+ + + +
Sbjct: 2 FGELCHGCSLLMTGPAMVAGEYKYHPECFACMSCKVII-------EDGDTYALVQHTTLY 54
Query: 157 CPKCF 161
C KC
Sbjct: 55 CGKCH 59
Score = 28.0 bits (62), Expect = 0.74
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKC 101
C C L+ + A + +HPE F C C++ I G Y + + +L+ KC
Sbjct: 6 CHGCSLLMTGPAMVAGEYKYHPECFACMSCKVII-------EDGDTYALVQHTTLYCGKC 58
Score = 27.6 bits (61), Expect = 1.1
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 155 KFCPKCFGCGKPITETAIKVHDRKWHEACFRCGRCR 190
KF C GC +T A+ + K+H CF C C+
Sbjct: 1 KFGELCHGCSLLMTGPAMVAGEYKYHPECFACMSCK 36
>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 = 28.3 bits (63), Expect = 0.59
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 101 CQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKL 134
C GC+ I D + A++Q WH D C CG +L
Sbjct: 1 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRL 35
Score = 25.2 bits (55), Expect = 7.5
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 160 CFGCGKPITETA-IKVHDRKWHEACFRCGRC 189
C GC + I + +K D+ WHE C C C
Sbjct: 1 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLC 31
>gnl|CDD|188804 cd09420, LIM3_Prickle, The third LIM domain of Prickle. The third
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Two
forms of prickles have been identified; namely prickle 1
and prickle 2. Prickle 1 and prickle 2 are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 28.2 bits (63), Expect = 0.59
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 160 CFGCGKPI-TETAIKVHD-RKWH--EACFRCGRCRRPISGPTF 198
C CG+ I + +D + WH E CF C +C++ + G F
Sbjct: 3 CDTCGEHIGVDQGQMTYDGQHWHATEKCFCCAQCKKSLLGRPF 45
>gnl|CDD|188799 cd09415, LIM1_Prickle, The first LIM domain of Prickle. The first
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4. The
best characterized is prickle 1 and prickle 2 which are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. Mutations in
prickle 1 have been linked to progressive myoclonus
epilepsy. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 28.4 bits (64), Expect = 0.60
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 101 CQGCRLPIK--DVVVTA----LNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C+ C I D+ V A WHP FVC +C L+ ++ ++G +C
Sbjct: 1 CEQCGEQISGGDIAVFASRAGPGACWHPACFVCSTCKELLVDLIYFYQDGKVYC 54
Score = 28.0 bits (63), Expect = 0.69
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 6/37 (16%)
Query: 160 CFGCGKPITETAIKVHDRK------WHEACFRCGRCR 190
C CG+ I+ I V + WH ACF C C+
Sbjct: 1 CEQCGEQISGGDIAVFASRAGPGACWHPACFVCSTCK 37
>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 = 28.2 bits (63), Expect = 0.61
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 100 KCQGCRLPIKDV-VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
C C LP+ + + +H F C CG +L FYE E ++C
Sbjct: 4 PCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53
>gnl|CDD|188803 cd09419, LIM3_Testin, The third LIM domain of Testin. The third
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction domain
at the N-terminal. Testin is a cytoskeleton associated
focal adhesion protein that localizes along actin stress
fibers at cell-cell-contact areas and at focal adhesion
plaques. Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Knockout mice experiments reveal that tumor repressor
function of Testin. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 28.3 bits (63), Expect = 0.65
Identities = 20/59 (33%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 160 CFGCGKPITETAIKV--HDRKWH--EACFRCGRCRRPISGPTFRVCEADVVC-VECSEK 213
C GC I +V ++ WH CF C C + + G F E V C VEC +K
Sbjct: 1 CQGCHNAIDPEVQRVSYNNFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKK 59
Score = 26.8 bits (59), Expect = 2.2
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 101 CQGCRLPIKDVV--VTALNQTWH--PDHFVCISCGTKLLYKGFYEREGNAFCT 149
CQGC I V V+ N WH P+ F+C C L+ + F EG FC+
Sbjct: 1 CQGCHNAIDPEVQRVSYNNFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFCS 53
>gnl|CDD|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein
(CRP). The first LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function not
only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the arrangement
of the myofibrillar/cytoskeletal network. It is evident
that CRP1, CRP2, and CRP3/MLP are involved in promoting
protein assembly along the actin-based cytoskeleton.
Although members of the CRP family share common binding
partners, they are also capable of recognizing different
and specific targets. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 28.0 bits (62), Expect = 0.65
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 160 CFGCGKPITETA-IKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
C C K + ++ R +H++CF C CR+ + T E ++ C C
Sbjct: 1 CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCKSC 52
>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 = 27.7 bits (62), Expect = 0.74
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 160 CFGCGKPITETAIKVHDRKWHEACFRCGRCRRPIS 194
C GC + IT + D K+H CF C C+ I
Sbjct: 1 CHGCSQIITGPVMVAGDHKFHPECFSCSSCKAFIG 35
Score = 27.3 bits (61), Expect = 1.0
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 42 CAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIA 76
C C +I ++ A D +HPE F C+ C+ I
Sbjct: 1 CHGCSQIITGPVMVAGDHKFHPECFSCSSCKAFIG 35
Score = 25.4 bits (56), Expect = 6.0
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCG 131
C GC I V+ A + +HP+ F C SC
Sbjct: 1 CHGCSQIITGPVMVAGDHKFHPECFSCSSCK 31
>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 = 27.8 bits (62), Expect = 0.79
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 157 CPKCFGCGKPITETAIKVHDRKWHEACFRCGRC-RRPISGPTFRVCEADVVC 207
C KC + ++ + +H CFRC C R+ I G F + + + C
Sbjct: 1 CAKC-QQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFC 51
Score = 26.2 bits (58), Expect = 2.8
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 99 NKCQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLY-KGFYEREGNAFCTA 150
KCQ D V+ A + +H + F C +C +L+ F R+ FC A
Sbjct: 2 AKCQQS-FSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKA 53
>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 = 27.7 bits (61), Expect = 0.83
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 160 CFGCGKPI--TETAIKVHDRKWHEACFRCGRCRRPIS-GPTFRVCEADVVC 207
C CG+ I ++ + +H ACF C C+R +S G F + E V+C
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLC 51
>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein
(CRP) family. The LIM domains of Cysteine Rich Protein
(CRP) family: Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The known CRP
family members include CRP1, CRP2, and CRP3/MLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription control, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1, CRP2, and CRP3/MLP are involved in
promoting protein assembly along the actin-based
cytoskeleton. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 27.6 bits (62), Expect = 0.90
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 113 VTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACY 152
V A ++WH F C C +L E +G +C +CY
Sbjct: 14 VIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKSCY 53
Score = 26.4 bits (59), Expect = 2.6
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 177 RKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
+ WH++CF C C + + T + ++ C C
Sbjct: 19 KSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKSC 52
>gnl|CDD|224299 COG1381, RecO, Recombinational DNA repair protein (RecF pathway)
[DNA replication, recombination, and repair].
Length = 251
Score = 30.0 bits (68), Expect = 0.93
Identities = 18/126 (14%), Positives = 31/126 (24%), Gaps = 31/126 (24%)
Query: 43 AACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQ 102
+ + + + ++ +PE F + + E F K
Sbjct: 93 YSASYVAELLDRLLPEEDPNPELFE-------LYLETLEYLLSDGNDPELLLRRFELKL- 144
Query: 103 GCRLPIKDVVVTALNQT-WHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCF 161
L + P+ C CGT + F + G G C KC
Sbjct: 145 -------------LGELGIGPNLTSCARCGTPVDPVYFSPKSG---------GFLCSKCA 182
Query: 162 GCGKPI 167
Sbjct: 183 RAAPKP 188
>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 = 27.3 bits (60), Expect = 1.3
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 160 CFGCGKPI--TETAIKVHDRKWHEACFRCGRCRRPIS-GPTFRVCEADVVC 207
C CG+ I T+ + +H ACF C C+R +S G F + E V+C
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLC 51
>gnl|CDD|220551 pfam10071, DUF2310, Zn-ribbon-containing, possibly
nucleic-acid-binding protein (DUF2310). Members of this
family of proteobacterial zinc ribbon proteins are
thought to bind to nucleic acids, however their exact
function has not as yet been defined.
Length = 259
Score = 29.5 bits (67), Expect = 1.4
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 7/42 (16%)
Query: 33 NAASTMYPKCAACQGLIQNIIVQALDKTWHPE-HFRCTHCRI 73
+ AS KC +C G + L + H F+C CR+
Sbjct: 215 SLASEQARKCPSCGGDWR------LAEPLHDIFDFKCDKCRL 250
>gnl|CDD|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2. The
first LIM domain of Prickle 2: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts with
Dishevelled, thereby modulating Frizzled/Dishevelled
activity and PCP signaling. Four forms of prickles have
been identified: prickle 1-4. The best characterized is
prickle 1 and prickle 2 which are differentially
expressed. While prickle 1 is expressed in fetal heart
and hematological malignancies, prickle 2 is found in
fetal brain, adult cartilage, pancreatic islet, and some
types of timorous cells. Mutations in prickle 1 have
been linked to progressive myoclonus epilepsy. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 26.8 bits (59), Expect = 1.8
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 120 WHPDHFVCISCGTKLLYKGFYEREGNAFC 148
WHP FVC C L+ ++ ++G +C
Sbjct: 26 WHPQCFVCSVCNELLVDLIYFYQDGKIYC 54
>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 = 26.7 bits (59), Expect = 2.0
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 160 CFGCGK--PITETAIKVHDRKWHEACFRCGRC-RRPISGPTFRVCEADVVCV 208
C C K P E ++ +H CF C RC R G F +CE ++C
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCE 52
>gnl|CDD|216500 pfam01432, Peptidase_M3, Peptidase family M3. This is the Thimet
oligopeptidase family, large family of mammalian and
bacterial oligopeptidases that cleave medium sized
peptides. The group also contains mitochondrial
intermediate peptidase which is encoded by nuclear DNA
but functions within the mitochondria to remove the
leader sequence.
Length = 450
Score = 28.9 bits (65), Expect = 2.2
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 9/56 (16%)
Query: 115 ALNQTWHPD--HFVCISCGTKLLYKGFY----EREG---NAFCTACYEGKFCPKCF 161
L + WH D + + L FY R+G A+ G+ P +
Sbjct: 160 PLGEVWHEDVRFYSVFDELSGGLIGEFYLDLYPRKGKRGGAYSFGLVPGRKDPVPY 215
>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 = 26.6 bits (59), Expect = 2.3
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRC 189
C GCG I + + DR WH C +C C
Sbjct: 1 CAGCGGKIVDRFLLHALDRYWHNGCLKCSCC 31
>gnl|CDD|151220 pfam10739, DUF2550, Protein of unknown function (DUF2550). This
family is conserved in Corynebacterineae. The function
is not known though most members are annotated as either
secreted, or membrane, proteins.
Length = 129
Score = 28.0 bits (63), Expect = 2.4
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 190 RRPISGPTFRVCEADVVCVECSEKGRE 216
RRP G +D V VE +GR
Sbjct: 79 RRPPEGDEAVALPSDAVIVELRYRGRV 105
>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also
known as Lim1) and Lhx5. The second LIM domain of Lhx1
(also known as Lim1) and Lhx5. Lhx1 and Lhx5 are
closely related members of LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx1 is required for regulating the vertebrate head
organizer, the nervous system, and female reproductive
tract development. During embryogenesis in the mouse,
Lhx1 is expressed early in mesodermal tissue, then
later during urogenital, kidney, liver, and nervous
system development. In the adult, expression is
restricted to the kidney and brain. A mouse embryos
with Lhx1 gene knockout cannot grow normal anterior
head structures, kidneys, and gonads, but with normally
developed trunk and tail morphology. In the developing
nervous system, Lhx1 is required to direct the
trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 56
Score = 26.6 bits (59), Expect = 2.7
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 42 CAAC-QGLIQNIIV-QALDKTWHPEHFRCTHCRIPIAT--QKFHVHAGSPYCVEDY 93
CA C QG+ N +V +A DK +H F C CR ++T + + + C EDY
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
Score = 25.4 bits (56), Expect = 7.0
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 160 CFGCGKPI--TETAIKVHDRKWHEACFRCGRCRRPIS 194
C GC + I + + D+ +H CF C CR+ +S
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLS 37
>gnl|CDD|201817 pfam01475, FUR, Ferric uptake regulator family. This family
includes metal ion uptake regulator proteins, that bind
to the operator DNA and controls transcription of metal
ion-responsive genes. This family is also known as the
FUR family.
Length = 120
Score = 27.6 bits (62), Expect = 2.8
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 116 LNQTWHPDHFVCISCGT 132
LNQ H DH +C CG
Sbjct: 72 LNQGHHHDHLICEKCGK 88
>gnl|CDD|220087 pfam08996, zf-DNA_Pol, DNA Polymerase alpha zinc finger. The DNA
Polymerase alpha zinc finger domain adopts an
alpha-helix-like structure, followed by three turns, all
of which involve proline. The resulting motif is a
helix-turn-helix motif, in contrast to other zinc finger
domains, which show anti-parallel sheet and helix
conformation. Zinc binding occurs due to the presence of
four cysteine residues positioned to bind the metal
centre in a tetrahedral coordination geometry. Function
of this domain is uncertain: it has been proposed that
the zinc finger motif may be an essential part of the
DNA binding domain.
Length = 187
Score = 28.0 bits (63), Expect = 3.1
Identities = 18/70 (25%), Positives = 26/70 (37%), Gaps = 14/70 (20%)
Query: 125 FVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPIT--------ETAIKVHD 176
C SCGT+ ++G + G G C K C I E AI+ H
Sbjct: 19 LKCPSCGTEFPFEGIFASSGERV---TPSGLQCSK---CNALIPLLQIVNQLELAIRAHI 72
Query: 177 RKWHEACFRC 186
+ ++E C
Sbjct: 73 KLYYEGWLVC 82
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 28.2 bits (64), Expect = 3.8
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 7/29 (24%)
Query: 118 QTWHPDHFVCISCGTKLL---YKGFYERE 143
QT+HP+H V I LL Y F E+E
Sbjct: 545 QTYHPEHPV-IQA---LLAQDYDAFAEQE 569
>gnl|CDD|190989 pfam04435, SPK, Domain of unknown function (DUF545). Family of
uncharacterized C. elegans proteins. The region
represented by this family can is found to be repeated
up to four time in some proteins.
Length = 109
Score = 27.2 bits (61), Expect = 3.9
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 133 KLLYKGFYEREGNAFCTACYEGKFCPK 159
K +++ F E EG+ + Y +F K
Sbjct: 22 KSVFEEFSELEGSGLSESTYRKRFHRK 48
>gnl|CDD|223425 COG0348, NapH, Polyferredoxin [Energy production and conversion].
Length = 386
Score = 28.2 bits (63), Expect = 4.0
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 8/57 (14%)
Query: 133 KLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITETAIKVHDRKWHEACFRCGRC 189
K+ Y ++ G C C K CP+ + I + D C CGRC
Sbjct: 205 KVNYD---DKRGCPRCKRCK--KVCPEPIPLWVQVCPAGIDIRDG---LECIGCGRC 253
>gnl|CDD|202278 pfam02545, Maf, Maf-like protein. Maf is a putative inhibitor of
septum formation in eukaryotes, bacteria, and archaea.
Length = 193
Score = 27.6 bits (62), Expect = 4.2
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 84 AGSPYCVEDYASLFLNKCQGCR-----LPIKDVV--VTALNQTWHP 122
AG+ Y ++ + LF+ K +G LP+ + + L P
Sbjct: 148 AGA-YGIQGFGGLFIKKIEGDYYNVVGLPLPKLRSLLRRLGILKDP 192
>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 = 25.8 bits (57), Expect = 4.2
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 160 CFGCGKPITETAIKVHDRK------WHEACFRCGRC 189
C GC +P+ + V K WH ACFRC C
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTC 36
Score = 25.8 bits (57), Expect = 4.6
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 42 CAACQGLIQN--IIVQA----LDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDY 93
C C ++ + V A WHP FRC+ C + + VH YC Y
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58
>gnl|CDD|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase
domains protein (Ltd-1). The LIM domain of LIM and
transglutaminase domains protein (Ltd-1): This family
includes mouse Ky protein and Caenorhabditis elegans
Ltd-1 protein. The members of this family consists a
N-terminal Lim domain and a C-terminal transglutaminase
domain. The mouse Ky protein has putative function in
muscle development. The mouse with ky mutant exhibits
combined posterior and lateral curvature of the spine.
The Ltd-1 gene in C. elegans is expressed in developing
hypodermal cells from the twofold stage embryo through
adulthood. These data define the ltd-1 gene as a novel
marker for C. elegans epithelial cell development. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 25.8 bits (57), Expect = 4.5
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRC--RRPISGPTFRVCEADVVC 207
C CGK ++ +H+ CF+C C R + TF + +V C
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYC 51
>gnl|CDD|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1
(CRP1). The first LIM domain of Cysteine Rich Protein 1
(CRP1): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and
CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1 can associate with the actin cytoskeleton
and are capable of interacting with alpha-actinin and
zyxin. CRP1 was shown to regulate actin filament
bundling by interaction with alpha-actinin and direct
binding to actin filaments. 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 = 25.7 bits (56), Expect = 4.5
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 159 KCFGCGKPIT-ETAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVEC 210
KC C K + ++ R +H++CF C C++ + T V ++ C C
Sbjct: 2 KCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSC 54
>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 = 25.8 bits (57), Expect = 4.6
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 160 CFGCGKPI-----TETAIKV--HDRKWHEACFRCGRCRRPISGPTFRVC 201
C CG+PI +E I+V D+ +H C+ C C ++ C
Sbjct: 1 CAACGQPILPAEGSEETIRVVSMDKDYHVECYHCEDCGLQLNDEEGHRC 49
>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 = 25.8 bits (57), Expect = 4.9
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 160 CFGCGKPI--TETAIKVHDRKWHEACFRCGRCRR 191
C GC + I T+ + D +H CF C C+R
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKR 34
>gnl|CDD|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3. The
first LIM domain of Prickle 3/LIM domain only 6 (LM06):
Prickle contains three C-terminal LIM domains and a
N-terminal PET domain. Prickles have been implicated in
roles of regulating tissue polarity or planar cell
polarity (PCP). PCP establishment requires the
conserved Frizzled/Dishevelled PCP pathway. Prickle
interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4. The
best characterized is prickle 1 and prickle 2 which are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. Mutations in
prickle 1 have been linked to progressive myoclonus
epilepsy. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 25.6 bits (56), Expect = 5.7
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 120 WHPDHFVCISCGTKLLYKGFYEREGNAFC 148
WHP F C SC L+ ++ ++G +C
Sbjct: 26 WHPQCFQCASCQELLVDLIYFYQDGKIYC 54
Score = 24.8 bits (54), Expect = 9.3
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 61 WHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYA 94
WHP+ F+C C+ + + G YC +A
Sbjct: 26 WHPQCFQCASCQELLVDLIYFYQDGKIYCGRHHA 59
>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 = 25.2 bits (55), Expect = 5.9
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 101 CQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFC 148
CQ P++ +V A Q +H F C C TKL + GN +C
Sbjct: 4 CQKTVYPLERLV--ANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYC 49
Score = 25.2 bits (55), Expect = 7.5
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 160 CFGCGKPITETAIKVHDRK-WHEACFRCGRCRRPISGPTFRVCEADVVC 207
C C K + V +++ +H +CFRC C +S T+ ++ C
Sbjct: 1 CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYC 49
>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 = 25.4 bits (55), Expect = 6.2
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRCR 190
C CG I + +KV++ WH C C CR
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCR 32
>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 = 25.3 bits (55), Expect = 6.3
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 160 CFGCGKPITET-AIKVHDRKWHEACFRCGRCRRPISGPT 197
C CG I + +KV+D WH C C CR + T
Sbjct: 2 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHT 40
>gnl|CDD|236527 PRK09462, fur, ferric uptake regulator; Provisional.
Length = 148
Score = 27.0 bits (60), Expect = 6.4
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 113 VTALNQTWHPDHFVCISCG 131
V L Q H DH +C+ CG
Sbjct: 79 VFELTQQHHHDHLICLDCG 97
>gnl|CDD|188867 cd09483, LIM1_Prickle_1, The first LIM domain of Prickle 1. The
first LIM domain of Prickle 1. Prickle contains three
C-terminal LIM domains and a N-terminal PET domain
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts with
Dishevelled, thereby modulating Frizzled/Dishevelled
activity and PCP signaling. Four forms of prickles have
been identified: prickle 1-4. The best characterized is
prickle 1 and prickle 2 which are differentially
expressed. While prickle 1 is expressed in fetal heart
and hematological malignancies, prickle 2 is found in
mainly expressed in fetal brain, adult cartilage,
pancreatic islet, and some types of timorous cells. In
addition, Prickle 1 regulates cell movements during
gastrulation and neuronal migration through interaction
with the noncanonical Wnt11/Wnt5 pathway in zebrafish.
Mutations in prickle 1 have been linked to progressive
myoclonus epilepsy. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 25.3 bits (55), Expect = 7.2
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 120 WHPDHFVCISCGTKLLYKGFYEREGNAFC 148
WHP FVC +C L+ ++ ++G C
Sbjct: 26 WHPSCFVCFTCNELLVDLIYFYQDGKIHC 54
>gnl|CDD|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal
Protein (CRIP). The LIM domain of Cysteine-Rich
Intestinal Protein (CRIP): CRIP is a short protein with
only one LIM domain. CRIP gene is developmentally
regulated and can be induced by glucocorticoid hormones
during the first three postnatal weeks. The domain
shows close sequence homology to LIM domain of thymus
LIM protein. However, unlike the TLP proteins which
have two LIM domains, the members of this family have
only one LIM domain. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 25.2 bits (55), Expect = 7.3
Identities = 12/36 (33%), Positives = 15/36 (41%)
Query: 54 VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYC 89
V +L K WH +C C + H G PYC
Sbjct: 14 VTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49
>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 = 25.0 bits (54), Expect = 8.0
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 159 KCFGC--GKPITETAIKVHDRKWHEACFRCGRCRRPIS 194
KC C G P T+ + D +H CF C C+R ++
Sbjct: 1 KCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLA 38
>gnl|CDD|236379 PRK09104, PRK09104, hypothetical protein; Validated.
Length = 464
Score = 27.2 bits (61), Expect = 9.3
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 12/50 (24%)
Query: 72 RIPI-ATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDVVVTALNQTW 120
R+P + +FH H GSP Y S L + AL+ W
Sbjct: 358 RLPADCSVEFHDHGGSPAIALPYDSPALAAAKA-----------ALSDEW 396
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
0.323 0.138 0.470
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,472,122
Number of extensions: 997570
Number of successful extensions: 1628
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1561
Number of HSP's successfully gapped: 461
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.8 bits)