RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3653
(202 letters)
>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 = 98.5 bits (245), Expect = 1e-27
Identities = 46/52 (88%), Positives = 49/52 (94%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C+GC KPITGRCITAM +KFHPEHFVCAFCL+QLNKGTFKEQNDKPYCH CF
Sbjct: 1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52
Score = 39.9 bits (93), Expect = 3e-05
Identities = 19/38 (50%), Positives = 26/38 (68%)
Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
+C+TA+ K +H EHF CA C KQ + F E++ KPYC
Sbjct: 11 RCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYC 48
Score = 29.1 bits (65), Expect = 0.19
Identities = 16/52 (30%), Positives = 24/52 (46%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C GC + I ++A+ ++H FVC C K + +F KP C F
Sbjct: 1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52
>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 = 92.4 bits (230), Expect = 3e-25
Identities = 46/52 (88%), Positives = 49/52 (94%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CAGC KPITGRCITAM RKFHPEHFVCAFCL+QL+KGTFKEQ+DKPYCH CF
Sbjct: 1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
Score = 41.2 bits (97), Expect = 9e-06
Identities = 19/42 (45%), Positives = 27/42 (64%)
Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+C+TA+ + +H EHF CA C KQ + F E+D KPYC +
Sbjct: 11 RCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
Score = 28.5 bits (64), Expect = 0.39
Identities = 16/52 (30%), Positives = 26/52 (50%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C GC + I ++A+ ++H FVC C K ++ +F + KP C F
Sbjct: 1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin
like protein family. The third LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton. Paxillin
serves as a platform for the recruitment of numerous
regulatory and structural proteins that together control
the dynamic changes in cell adhesion, cytoskeletal
reorganization and gene expression that are necessary
for cell migration and survival. Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. It associates with
focal adhesion kinases PYK2 and pp125FAK and identified
to be a component of the osteoclast pososomal signaling
complex. Hic-5 controls cell proliferation, migration
and senescence by functioning as coactivator for steroid
receptors such as androgen receptor, glucocorticoid
receptor and progesterone receptor. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 87.4 bits (217), Expect = 3e-23
Identities = 41/71 (57%), Positives = 47/71 (66%), Gaps = 18/71 (25%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
CGGCN+ I+ENY+SALNTQWH CFVCR +C +PF GSFF+H
Sbjct: 1 CGGCNKPILENYISALNTQWHPECFVCR------------------ECHKPFINGSFFEH 42
Query: 129 EGLPYCETHYH 139
EGLPYCETHYH
Sbjct: 43 EGLPYCETHYH 53
Score = 44.2 bits (105), Expect = 8e-07
Identities = 21/48 (43%), Positives = 28/48 (58%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C GC+KPI I+A+ ++HPE FVC C + G+F E PYC
Sbjct: 1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYC 48
Score = 36.5 bits (85), Expect = 4e-04
Identities = 17/40 (42%), Positives = 21/40 (52%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
++AL WH E F C +C K F F E +G PYC Y
Sbjct: 13 ISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52
>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 = 84.4 bits (209), Expect = 5e-22
Identities = 37/52 (71%), Positives = 42/52 (80%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C C PITGRCI+A+ RKFHPEHFVCAFCLR L +G+FKEQ+ KPYC CF
Sbjct: 1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
Score = 40.5 bits (95), Expect = 2e-05
Identities = 17/38 (44%), Positives = 25/38 (65%)
Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
+C++AL + +H EHF CA C + + F E+ GKPYC
Sbjct: 11 RCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48
Score = 37.4 bits (87), Expect = 3e-04
Identities = 21/52 (40%), Positives = 26/52 (50%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
CG C I +SAL ++H FVC C +P+T SF GKP C F
Sbjct: 1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
>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 = 81.7 bits (202), Expect = 5e-21
Identities = 36/43 (83%), Positives = 40/43 (93%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
KCVTAL+KTWH EHFFCAQCGK FG++GFHEKDGKPYCR+DY
Sbjct: 10 DKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 53.9 bits (130), Expect = 2e-10
Identities = 22/48 (45%), Positives = 31/48 (64%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
CA C+ PI +C+TA+ + +HPEHF CA C + F E++ KPYC
Sbjct: 1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYC 48
Score = 42.4 bits (100), Expect = 3e-06
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C CN I++ V+AL+ WH F C C KP + F+ +GKP CR+ +
Sbjct: 1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
>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 = 73.7 bits (181), Expect = 5e-18
Identities = 38/71 (53%), Positives = 43/71 (60%), Gaps = 18/71 (25%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
CGGC RAI+ENY+SALNT WH CFVCR +C PF GSFF+H
Sbjct: 1 CGGCARAILENYISALNTLWHPECFVCR------------------ECFTPFVNGSFFEH 42
Query: 129 EGLPYCETHYH 139
+G PYCE HYH
Sbjct: 43 DGQPYCEAHYH 53
Score = 39.8 bits (93), Expect = 3e-05
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C GC + I I+A+ +HPE FVC C G+F E + +PYC
Sbjct: 1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYC 48
Score = 34.0 bits (78), Expect = 0.004
Identities = 17/40 (42%), Positives = 21/40 (52%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
++AL WH E F C +C F F E DG+PYC Y
Sbjct: 13 ISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin. The
second LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 65.7 bits (160), Expect = 6e-15
Identities = 32/42 (76%), Positives = 35/42 (83%)
Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
K VTAL++TWH EHFFCAQCG FG +GFHEKDGK YCR DY
Sbjct: 11 KVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
Score = 38.4 bits (89), Expect = 9e-05
Identities = 20/48 (41%), Positives = 27/48 (56%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C C+ PI + +TA+ R +HPEHF CA C F E++ K YC
Sbjct: 1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYC 48
Score = 32.6 bits (74), Expect = 0.015
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C CN I++ V+AL+ WH F C C + F+ +GK CR+ +
Sbjct: 1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
>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 = 64.8 bits (158), Expect = 1e-14
Identities = 26/43 (60%), Positives = 36/43 (83%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
Q +TA+++TWH EHFFC+ CG+ FG++GF E+DGKPYCR D+
Sbjct: 10 QNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
Score = 46.7 bits (111), Expect = 9e-08
Identities = 22/52 (42%), Positives = 28/52 (53%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CA C PI +TAM + +HPEHF C+ C F E++ KPYC F
Sbjct: 1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
Score = 35.6 bits (82), Expect = 0.001
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C C I++N ++A++ WH F C C + + F +GKP CR+ F
Sbjct: 1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin
like protein family. The first LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 62.7 bits (153), Expect = 8e-14
Identities = 24/43 (55%), Positives = 29/43 (67%)
Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62
+ VTAL KTWH EHF CA+C + G F E+DG+PYC DY
Sbjct: 11 QVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53
Score = 59.3 bits (144), Expect = 2e-12
Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CA C KPI G+ +TA+ + +HPEHFVCA C +L F E++ +PYC +
Sbjct: 1 CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52
Score = 46.2 bits (110), Expect = 1e-07
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
C C + I+ V+AL WH FVC +CK + K+F+ +G+P C
Sbjct: 1 CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYC 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 = 61.8 bits (150), Expect = 2e-13
Identities = 32/71 (45%), Positives = 36/71 (50%), Gaps = 18/71 (25%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
C GC R + ENY+SA N WH CFVC DC K PF GSFF+
Sbjct: 1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLK------------------PFTDGSFFEL 42
Query: 129 EGLPYCETHYH 139
+G P CE HYH
Sbjct: 43 DGRPLCELHYH 53
Score = 42.1 bits (99), Expect = 4e-06
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C+GC +P+ ++A +HPE FVC+ CL+ G+F E + +P C
Sbjct: 1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48
Score = 35.2 bits (81), Expect = 0.001
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
++A WH E F C+ C K F + F E DG+P C
Sbjct: 13 LSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 55.8 bits (135), Expect = 4e-11
Identities = 26/58 (44%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 146 CAGCHKPITGRCIT--AMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
CAGC KPI R + A+ + +HPE F CA C + L G F E++ K YC + KLF
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 54.3 bits (131), Expect = 2e-10
Identities = 26/47 (55%), Positives = 28/47 (59%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
+ AL K WH E F CA CGK G F EKDGK YC+ DYF LF
Sbjct: 12 ELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 44.3 bits (105), Expect = 7e-07
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 69 CGGCNRAIMENYVS--ALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
C GC + I + + AL WH CF C C KP+ F+ +GK C+ +
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYF 55
>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain,
containing two zinc fingers. LIM domains are identified
in a diverse group of proteins with wide variety of
biological functions, including gene expression
regulation, cell fate determination, cytoskeleton
organization, tumor formation and development. LIM
domains function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. They perform
their functions through interactions with other protein
partners. LIM domains are 50-60 amino acids in size and
share two characteristic highly conserved zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. The consensus
sequence of LIM domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 53
Score = 54.6 bits (132), Expect = 1e-10
Identities = 25/53 (47%), Positives = 35/53 (66%), Gaps = 1/53 (1%)
Query: 146 CAGCHKPITGRCI-TAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CAGC KPI GR + A+ +K+HPE F C+ C + L +F E++ KPYC C+
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 50.8 bits (122), Expect = 3e-09
Identities = 23/40 (57%), Positives = 26/40 (65%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+ AL K WH E F C+ CGK G D F+EKDGKPYC Y
Sbjct: 14 LRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 45.4 bits (108), Expect = 3e-07
Identities = 22/51 (43%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 69 CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
C GC + I + AL +WH CF C C KP+ G SFY +GKP C +
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEK 51
>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 = 52.0 bits (125), Expect = 1e-09
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 144 SLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
+C C +PI GR +TA+ + +H EHFVCA C + E+ YC
Sbjct: 1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYC 50
Score = 50.0 bits (120), Expect = 5e-09
Identities = 21/44 (47%), Positives = 24/44 (54%)
Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+ VTAL K WH EHF CA+C K F +EK G YC Y
Sbjct: 11 EGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
Score = 45.0 bits (107), Expect = 3e-07
Identities = 27/72 (37%), Positives = 32/72 (44%), Gaps = 18/72 (25%)
Query: 67 PKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFF 126
P CG C R I V+AL WH FVC C+K PF G +
Sbjct: 1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEK------------------PFLGHRHY 42
Query: 127 DHEGLPYCETHY 138
+ +GL YCETHY
Sbjct: 43 EKKGLAYCETHY 54
>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin. The
first LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 51.8 bits (124), Expect = 1e-09
Identities = 23/42 (54%), Positives = 30/42 (71%)
Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+ VTAL +TWH EHF C QCGK+ G F E++G+ YC +DY
Sbjct: 13 QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
Score = 50.3 bits (120), Expect = 5e-09
Identities = 23/48 (47%), Positives = 32/48 (66%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
CA C KPI G+ +TA+ + +HPEHFVC C ++L F E+N + YC
Sbjct: 3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYC 50
Score = 33.7 bits (77), Expect = 0.006
Identities = 16/52 (30%), Positives = 24/52 (46%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C C + I V+AL WH FVC C K + + F+ G+ C + +
Sbjct: 3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight cons erved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 48.5 bits (115), Expect = 2e-08
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 145 LCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
+C C KPI G+ +TAM + +HPEHFVC C ++ F E++ +PYC
Sbjct: 1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYC 49
Score = 47.3 bits (112), Expect = 7e-08
Identities = 22/42 (52%), Positives = 28/42 (66%)
Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+ VTA+ KTWH EHF C C ++ G F E+DG+PYC DY
Sbjct: 12 QVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
Score = 37.7 bits (87), Expect = 2e-04
Identities = 16/53 (30%), Positives = 29/53 (54%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
CG C + I V+A+ WH FVC C++ + ++F+ +G+P C + +
Sbjct: 2 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54
>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 = 46.3 bits (110), Expect = 1e-07
Identities = 19/38 (50%), Positives = 24/38 (63%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
AL++TWH F CA C + G FH +DG+PYC DY
Sbjct: 15 ALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
Score = 44.8 bits (106), Expect = 5e-07
Identities = 18/52 (34%), Positives = 30/52 (57%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C C++ I+ + AL WH +CFVC CK+P+ F+ +G+P C + +
Sbjct: 1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
Score = 37.1 bits (86), Expect = 3e-04
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
CA CHK I G + A+ + +H FVCA C + + F ++ +PYC
Sbjct: 1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYC 48
>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 = 45.8 bits (109), Expect = 2e-07
Identities = 22/42 (52%), Positives = 26/42 (61%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDD 60
++ + AL K WH E F CA CGK D F EKDGK YC+D
Sbjct: 13 ERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 44.3 bits (105), Expect = 7e-07
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 68 KCGGCNRAIMEN--YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
KC GC + I + AL WH CF C C KP++G +F+ +GK C+
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCK 52
Score = 43.5 bits (103), Expect = 1e-06
Identities = 25/53 (47%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 146 CAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
CAGC KPI G R + A+ + +HPE F CA C + L+ TF E++ K YC C
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog
(ENH) family. The second LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM domains
at the C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also been shown that ENH
interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line. ENH
is expressed in multiple tissues, such as skeletal
muscle, heart, bone, and brain. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 45.0 bits (106), Expect = 4e-07
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
CG C R I+ ++AL WH +CFVC C P+ F+ +G+P C +
Sbjct: 1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 42.3 bits (99), Expect = 4e-06
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+ AL++TWH F C C + FH +DG+PYC DY
Sbjct: 13 INALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 33.8 bits (77), Expect = 0.005
Identities = 15/48 (31%), Positives = 23/48 (47%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C C + I G I A+ + +H FVC C + F ++ +PYC
Sbjct: 1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYC 48
>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 = 44.0 bits (104), Expect = 9e-07
Identities = 21/52 (40%), Positives = 32/52 (61%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CA C+K I GR + A+ R +HPE F C+ C + L++G F E+ +C C+
Sbjct: 1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
Score = 35.2 bits (81), Expect = 0.001
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
+ AL +++H E F C+QC K E GF E+ G +C
Sbjct: 13 LVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFC 48
Score = 30.9 bits (70), Expect = 0.049
Identities = 16/48 (33%), Positives = 22/48 (45%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
C CN+ I Y+ AL +H F C CKK + F+ +G C
Sbjct: 1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFC 48
>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 = 43.9 bits (104), Expect = 1e-06
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CA C++ I G + A+ R +HPE F C+ C L + F E+ YC C+
Sbjct: 1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
Score = 34.6 bits (80), Expect = 0.002
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
+ AL ++WH E F C+ C E GF E+ G YC
Sbjct: 13 LVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYC 48
Score = 29.3 bits (66), Expect = 0.20
Identities = 17/70 (24%), Positives = 23/70 (32%), Gaps = 18/70 (25%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
C CN+ I ++ AL WH F C C + F +
Sbjct: 1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSL------------------AEIGFVEE 42
Query: 129 EGLPYCETHY 138
+G YCE Y
Sbjct: 43 KGSLYCELCY 52
>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin. The first LIM
domain of Zyxin: Zyxin exhibits three copies of the LIM
domain, an extensive proline-rich domain and a nuclear
export signal. Localized at sites of cell substratum
adhesion in fibroblasts, Zyxin interacts with
alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 87
Score = 44.8 bits (106), Expect = 1e-06
Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
CG C + + + V AL +H TCF C C++ + G+ FY++EGKP C +
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEE 85
Score = 38.7 bits (90), Expect = 2e-04
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 145 LCAGCHKPI--TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
LC C +P+ T + A+ FH F C C +QL F KPYC C+
Sbjct: 33 LCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
Score = 38.7 bits (90), Expect = 2e-04
Identities = 17/43 (39%), Positives = 22/43 (51%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
Q V AL +H F C QC +Q F+ +GKPYC + Y
Sbjct: 45 QPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
>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 = 43.6 bits (103), Expect = 1e-06
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
C CN+ I V+ + WHS CFVC C K + G+ F A+E + C
Sbjct: 1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48
Score = 36.3 bits (84), Expect = 6e-04
Identities = 19/53 (35%), Positives = 29/53 (54%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFE 198
C C+KPIT +T + +H E FVC+ C ++L F D+ YC C++
Sbjct: 1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53
Score = 28.6 bits (64), Expect = 0.31
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
VT ++ WH+E F C+ C K+ F + + YC D Y
Sbjct: 13 VTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52
>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 = 43.6 bits (103), Expect = 2e-06
Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
C GC+ I + ++ AL WH TCFVC C + G++FY+ + KP C+
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCK 51
Score = 31.6 bits (72), Expect = 0.031
Identities = 20/50 (40%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 146 CAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C GC PI R + A+ +H FVCA C L TF + DKP C
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
Score = 30.5 bits (69), Expect = 0.068
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCR 58
+ AL TWH F CA C F+ K KP C+
Sbjct: 15 LEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCK 51
>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 = 42.8 bits (101), Expect = 3e-06
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCA--FCLRQLNKGTFKEQNDKPYCHGCF 197
C C++ I G ITA+ + + P+HF+CA C R L F E+ + YC CF
Sbjct: 1 CESCNQQIRGPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCEYCF 54
Score = 35.5 bits (82), Expect = 0.001
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 22 VTALEKTWHTEHFFCA--QCGKQFGEDGFHEKDGKPYC 57
+TAL K W +HF CA C + + GF E+ G+ YC
Sbjct: 13 ITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYC 50
Score = 28.6 bits (64), Expect = 0.33
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 16/67 (23%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
C CN+ I +++AL W F+C + CR+P Q F +
Sbjct: 1 CESCNQQIRGPFITALGKIWCPDHFICAN----------------ASCRRPLQDIGFVEE 44
Query: 129 EGLPYCE 135
+G YCE
Sbjct: 45 KGQLYCE 51
>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma. The second
LIM domain of Enigma: Enigma was initially characterized
in humans as a protein containing three LIM domains at
the C-terminus and a PDZ domain at N-terminus. The
third LIM domain specifically interacts with the insulin
receptor and the second LIM domain interacts with the
receptor tyrosine kinase Ret and the adaptor protein
APS. Thus Enigma is implicated in signal transduction
processes, such as mitogenic activity, insulin related
actin organization, and glucose metabolism. Enigma is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 42.7 bits (100), Expect = 3e-06
Identities = 19/52 (36%), Positives = 26/52 (50%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C C + I + AL WH CF C CK P+ ++FY EG P C + +
Sbjct: 1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 36.1 bits (83), Expect = 7e-04
Identities = 16/38 (42%), Positives = 20/38 (52%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
AL+ TWH F CA C F+ ++G PYC DY
Sbjct: 15 ALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 32.3 bits (73), Expect = 0.017
Identities = 17/48 (35%), Positives = 22/48 (45%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
CA C K ITG + A+ +H F CA C + F + PYC
Sbjct: 1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYC 48
>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 = 42.7 bits (101), Expect = 3e-06
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 21 CVTALEKTWHTEHFFCAQCGKQFG-EDGFHEKDGKPYCRDDY 61
+TAL + +H EHF C+ C FG D ++E +GK YC Y
Sbjct: 12 YITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
Score = 38.1 bits (89), Expect = 1e-04
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKG-TFKEQNDKPYCH 194
C C + G ITA+ RK+H EHF C+ C ++ E K YCH
Sbjct: 1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCH 50
Score = 32.3 bits (74), Expect = 0.018
Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 17/70 (24%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
C C A+ +Y++AL ++H F C C S+++H
Sbjct: 1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFG-----------------PNDSYYEH 43
Query: 129 EGLPYCETHY 138
EG YC HY
Sbjct: 44 EGKIYCHYHY 53
>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 = 42.2 bits (100), Expect = 5e-06
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 69 CGGCNRAIME-NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP 114
C GC I ++SAL WH CF C C+KP+ F P
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDP 47
Score = 39.9 bits (94), Expect = 3e-05
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 146 CAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CAGC I GR ++A+ +HPE F C C + + + F + PY C+
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53
Score = 33.0 bits (76), Expect = 0.008
Identities = 14/41 (34%), Positives = 17/41 (41%)
Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
++AL WH E F C C K E F PY + Y
Sbjct: 13 FLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53
>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The first LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 57
Score = 41.9 bits (99), Expect = 6e-06
Identities = 17/39 (43%), Positives = 20/39 (51%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
C C + I +V AL +H CF C DC KPV K F
Sbjct: 1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFF 39
Score = 30.3 bits (69), Expect = 0.089
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFC 175
CA C KPITG+ + A+ +H + F C C
Sbjct: 1 CAKCGKPITGQFVRALGDVYHLDCFTCHDC 30
Score = 25.3 bits (56), Expect = 4.8
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 5/48 (10%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQ-----FGEDGFHEKDGKPYCRDDY 61
+ V AL +H + F C CGK F D + P C DY
Sbjct: 10 GQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDTSEQVPLCETDY 57
>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 = 41.8 bits (98), Expect = 8e-06
Identities = 18/40 (45%), Positives = 25/40 (62%)
Query: 78 ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
+ +V ALN +HS CF C C + G+SFYA G+P C+
Sbjct: 12 DRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51
Score = 31.4 bits (71), Expect = 0.037
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 146 CAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C C PI R + A+ +H + F C C L +F + +P+C
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFC 50
Score = 30.6 bits (69), Expect = 0.073
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 12 HFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCR 58
F + + V AL +H++ F C +C F+ K G+P+C+
Sbjct: 5 GFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51
>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin.
The fifth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 41.3 bits (97), Expect = 1e-05
Identities = 19/52 (36%), Positives = 26/52 (50%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C CN+ I V+ N WH CF C +C K + G+ F + + KP C F
Sbjct: 1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
Score = 35.1 bits (81), Expect = 0.002
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C+ C+K I +T +H E F C C + L F +++KPYC CF
Sbjct: 1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
Score = 31.7 bits (72), Expect = 0.024
Identities = 16/40 (40%), Positives = 19/40 (47%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
VT + WH E F C C K F +D KPYC D +
Sbjct: 13 VTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher
family. The first LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 40.3 bits (94), Expect = 2e-05
Identities = 18/52 (34%), Positives = 27/52 (51%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C C+ I G + A+ R +HPE F C +C L +F E+ + YC C+
Sbjct: 1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
Score = 28.0 bits (62), Expect = 0.59
Identities = 14/39 (35%), Positives = 17/39 (43%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
CG CN I ++ AL WH F C C + SF
Sbjct: 1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSF 39
Score = 27.6 bits (61), Expect = 0.69
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+ AL ++WH E F C C + F E+ YC + Y
Sbjct: 13 LVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 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 = 39.9 bits (94), Expect = 3e-05
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 146 CAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFE 198
CA C + I +G A + +H +HF C C L + + KPYC C+E
Sbjct: 3 CAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56
Score = 36.8 bits (86), Expect = 5e-04
Identities = 17/41 (41%), Positives = 22/41 (53%)
Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
A K WH +HF C QC + G + ++GKPYC D Y
Sbjct: 15 YTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCY 55
Score = 35.7 bits (83), Expect = 0.001
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 67 PKCGGCNRAI-MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
P+C C+ I Y A WH F C C +P+ G+ + EGKP C
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCL 52
>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 = 39.7 bits (93), Expect = 4e-05
Identities = 15/39 (38%), Positives = 26/39 (66%)
Query: 82 SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
+A++ +H +CF C C+ + GK FYA++GKP C + +
Sbjct: 16 TAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
Score = 34.7 bits (80), Expect = 0.002
Identities = 16/39 (41%), Positives = 22/39 (56%)
Query: 23 TALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
TA+++ +H F C QC F+ DGKPYC +DY
Sbjct: 16 TAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM
domains protein (FHL). The third LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 39.2 bits (92), Expect = 6e-05
Identities = 21/52 (40%), Positives = 28/52 (53%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CA C K IT +T + +H E FVC C +QL F +++ PYC CF
Sbjct: 1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
Score = 38.8 bits (91), Expect = 7e-05
Identities = 19/52 (36%), Positives = 26/52 (50%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C C +AI V+ + WH CFVC CKK + G+ F + + P C F
Sbjct: 1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
Score = 35.0 bits (81), Expect = 0.002
Identities = 16/40 (40%), Positives = 20/40 (50%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
VT ++ WH E F C C KQ F +D PYC D +
Sbjct: 13 VTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 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 = 38.9 bits (91), Expect = 7e-05
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
CG C ++ +A++ +H CF C C + G+ FYA+E K C
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYC 50
Score = 29.7 bits (67), Expect = 0.14
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 146 CAGCHKPITGR--CITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C C + + G TAM + FH + F C C +L F K YC C+
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
Score = 28.1 bits (63), Expect = 0.47
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
TA+++ +H + F C C + F+ + K YC Y
Sbjct: 15 CTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
>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 = 38.9 bits (90), Expect = 9e-05
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 69 CGGCNRAI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
C GC+ I + ++ AL WH TCFVC C+ + GK+FY+ + KP C+
Sbjct: 1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCK 51
Score = 27.3 bits (60), Expect = 1.2
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 146 CAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C GC I R + A+ +H FVCA C L TF + DKP C
Sbjct: 1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLC 50
Score = 25.4 bits (55), Expect = 5.5
Identities = 15/50 (30%), Positives = 21/50 (42%)
Query: 13 FSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62
F + + + AL +WH F CA C F+ K KP C+ F
Sbjct: 6 FKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCKSHAF 55
>gnl|CDD|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM
(abLIM) proteins. The third LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to
function as a tumor suppressor. AbLIM-2 and -3, mainly
expressed in muscle and neuronal tissue, bind to
F-actin strongly. They may serve as a scaffold for
signaling modules of the actin cytoskeleton and thereby
modulate transcription. It has shown that LIM domains
of abLIMs interact with STARS (striated muscle
activator of Rho signaling), which directly binds actin
and stimulates serum-response factor (SRF)-dependent
transcription. All LIM domains are 50-60 amino acids in
size and share two characteristic highly conserved zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 38.5 bits (90), Expect = 9e-05
Identities = 19/38 (50%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
AL+K WH F C +CGK + + KDGKPYC DY
Sbjct: 16 ALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52
Score = 36.9 bits (86), Expect = 4e-04
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 69 CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C GC + I AL+ QWH CF C++C K +TG+ + +GKP C + +
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52
Score = 29.6 bits (67), Expect = 0.17
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 146 CAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CAGC + I G+ + A+ +++H F C C + L G + ++ KPYC +
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLT-GEYMGKDGKPYCERDY 52
>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 = 38.4 bits (89), Expect = 1e-04
Identities = 22/57 (38%), Positives = 30/57 (52%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
C C KPIT +T + +H E FVC C +QL+ F ++D YC CF L+
Sbjct: 1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57
Score = 35.7 bits (82), Expect = 0.001
Identities = 17/52 (32%), Positives = 25/52 (48%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C C + I V+ + WH CFVC CKK ++G+ F + + C F
Sbjct: 1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCF 52
Score = 32.3 bits (73), Expect = 0.017
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA 66
VT ++ WH E F C C KQ F +D YC + + +L+A
Sbjct: 13 VTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57
>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 = 38.5 bits (90), Expect = 1e-04
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA 66
+K V + + +H + F CAQC + F + F+E +G+ YC D+ LFA
Sbjct: 12 EKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59
Score = 35.0 bits (81), Expect = 0.002
Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 18/62 (29%)
Query: 78 ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETH 137
E V++ +H CFVC C QPF G F++ EG YCE
Sbjct: 12 EKIVNSNGELYHEQCFVC------------------AQCFQPFPDGLFYEFEGRKYCEHD 53
Query: 138 YH 139
+
Sbjct: 54 FQ 55
Score = 33.1 bits (76), Expect = 0.010
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 165 FHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
+H + FVCA C + G F E + YC F+ LF
Sbjct: 22 YHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLF 58
>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 = 38.2 bits (89), Expect = 1e-04
Identities = 23/53 (43%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 69 CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C GC+R I++ ++ + L+ WH+ C C DCK P+T K F + EGK CR F
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYCRNDF 52
Score = 28.5 bits (64), Expect = 0.41
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 25 LEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
L++ WH + C C E F ++GK YCR+D+
Sbjct: 17 LDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYCRNDF 52
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription. Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 52
Score = 37.8 bits (88), Expect = 2e-04
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 69 CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFY 108
CGGC I++ ++ L+ WH+ C C DC +T K F
Sbjct: 1 CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFA 41
Score = 28.5 bits (64), Expect = 0.38
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
L++TWH + C CG Q + F ++G YC+DD+
Sbjct: 16 VLDRTWHAKCLKCNDCGAQLTDKCFA-RNGHVYCKDDF 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 = 37.6 bits (87), Expect = 2e-04
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 67 PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSF 107
P C GCN+ I++ ++ L+ WHS C C DC+ + K F
Sbjct: 2 PLCAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCF 43
Score = 27.2 bits (60), Expect = 1.3
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
L++ WH++ C+ C Q E F D YC+DD+
Sbjct: 19 VLDRHWHSKCLKCSDCQTQLAEKCFSRGDSV-YCKDDF 55
>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 = 37.3 bits (86), Expect = 3e-04
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
C GC+ + + ++ AL WH TCF+C C + G+ FY+ + KP C++
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 52
Score = 28.1 bits (62), Expect = 0.66
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 146 CAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C GC P+ + I A+ +H F+CA C L F + DKP C
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 50
Score = 27.7 bits (61), Expect = 0.81
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCR 58
K + AL TWH F CA C F+ K KP C+
Sbjct: 13 KFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 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 = 36.3 bits (84), Expect = 5e-04
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62
V AL + WH + F C+ C + + EKDGK YCR DY+
Sbjct: 14 VQALNQDWHCDCFRCSVC-SDSLSNWYFEKDGKLYCRKDYW 53
Score = 33.2 bits (76), Expect = 0.007
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 69 CGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
C GC I+++ YV ALN WH CF C C ++ ++ +GK CR+
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNW-YFEKDGKLYCRK 50
>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 = 36.2 bits (84), Expect = 6e-04
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 143 GSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPY-CHGC 196
G+ C C + G ++A+ + +HP+ FVC+ C + G N K C C
Sbjct: 1 GTKCDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKECLCQKC 55
Score = 31.5 bits (72), Expect = 0.031
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 68 KCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKP 101
KC C + VSAL +H CFVC C++P
Sbjct: 3 KCDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQP 36
Score = 27.3 bits (61), Expect = 1.2
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 22 VTALEKTWHTEHFFCAQCGKQF 43
V+AL KT+H + F C+ C + F
Sbjct: 16 VSALGKTYHPKCFVCSVCRQPF 37
>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 = 36.1 bits (83), Expect = 7e-04
Identities = 18/52 (34%), Positives = 27/52 (51%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CA C++ I G + A+ + +HPE F CA C + F E+ YC C+
Sbjct: 1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52
Score = 33.8 bits (77), Expect = 0.005
Identities = 16/36 (44%), Positives = 19/36 (52%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
+ AL K+WH E F CA C GF E+ G YC
Sbjct: 13 LVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYC 48
Score = 28.1 bits (62), Expect = 0.58
Identities = 15/48 (31%), Positives = 20/48 (41%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
C CN+ I ++ AL WH F C CK + F +G C
Sbjct: 1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYC 48
>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 = 36.1 bits (83), Expect = 7e-04
Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
C GC I + ++ AL WH TCFVC C + + G++F++ + KP C++
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKK 52
Score = 28.8 bits (64), Expect = 0.34
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 146 CAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C GC PI R + A+ +H FVC+ C L TF + DKP C
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLC 50
Score = 25.7 bits (56), Expect = 4.2
Identities = 14/46 (30%), Positives = 20/46 (43%)
Query: 13 FSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCR 58
F + + + AL TWH F C+ C + F K KP C+
Sbjct: 6 FPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCK 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 = 36.0 bits (83), Expect = 8e-04
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 67 PKCGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
P+C GC+ I N Y A N WH F C DC + G+ + + KP C+
Sbjct: 1 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCK 52
Score = 25.2 bits (55), Expect = 5.4
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 146 CAGCHKPITGRCIT-AMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
CAGC + I T A + +H +HF C C L + NDKP C C+
Sbjct: 3 CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCKPCY 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 = 36.1 bits (84), Expect = 8e-04
Identities = 20/75 (26%), Positives = 25/75 (33%), Gaps = 21/75 (28%)
Query: 69 CGGCNRAIMENYVS----ALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGS 124
C C I +S L+ QWH CFVC C P
Sbjct: 1 CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSV-----------------P 43
Query: 125 FFDHEGLPYCETHYH 139
+ + PYC+ HYH
Sbjct: 44 CYVLDDKPYCQQHYH 58
Score = 28.8 bits (65), Expect = 0.32
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 146 CAGCHKPITGRCIT----AMFRKFHPEHFVCAFCLRQLNK-GTFKEQNDKPYCHGCF 197
C C I G+ I+ + ++H E FVC C +DKPYC +
Sbjct: 1 CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
Score = 24.9 bits (55), Expect = 8.6
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 29 WHTEHFFCAQCGKQF-GEDGFHEKDGKPYCRDDY 61
WH E F C CG F + D KPYC+ Y
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>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 = 35.3 bits (81), Expect = 0.001
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTF-KEQNDKPYC 193
CA C + IT R + A + +HP+ F C C L +F +Q ++P+C
Sbjct: 1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHC 49
Score = 31.8 bits (72), Expect = 0.029
Identities = 19/73 (26%), Positives = 28/73 (38%), Gaps = 17/73 (23%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
C C++ I + + A +H CF C CK P+ G+SF D
Sbjct: 1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESF-----------------IVDQ 43
Query: 129 EGLPYCETHYHAK 141
P+C YH +
Sbjct: 44 ANQPHCVNDYHRR 56
>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 = 35.0 bits (81), Expect = 0.002
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 146 CAGCHKPITGR-CITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C C KP+ T++ R +H C C + L G E KPYC+ C+
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
Score = 34.6 bits (80), Expect = 0.003
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
T+L + WH C +C K E +GKPYC Y
Sbjct: 14 KTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
Score = 33.5 bits (77), Expect = 0.006
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 69 CGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
C C + + ++L WH C C CKK +T EGKP C +
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51
>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 = 34.6 bits (79), Expect = 0.003
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 69 CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFY 108
C GCN+ I++ ++ L+ WHS+C C DC+ + + F
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFS 41
Score = 24.5 bits (53), Expect = 9.8
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 25 LEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
L++ WH+ CA C Q E F + G YC++D+
Sbjct: 17 LDRHWHSSCLKCADCQMQLAERCFS-RAGNVYCKEDF 52
>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 = 34.9 bits (80), Expect = 0.003
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 67 PKCGGCNRAIM-ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
P C C ++I Y+ ALN+ WH+ CF C +C ++ +Y +G+ C++ +
Sbjct: 20 PVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLS-HWYYEKDGRLFCKKDY 73
Score = 32.9 bits (75), Expect = 0.015
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62
AL WH + F C +CG ++EKDG+ +C+ DY+
Sbjct: 37 ALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKDYW 74
>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 = 34.3 bits (79), Expect = 0.003
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
C A + WH +HF C +C Q G + ++G+PYC
Sbjct: 15 CTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51
Score = 32.0 bits (73), Expect = 0.025
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 146 CAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFE 198
C+ C + I C A R +H +HF C C QL + + +PYC CFE
Sbjct: 3 CSACDEIIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56
Score = 29.3 bits (66), Expect = 0.22
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 67 PKCGGCNRAIM-ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
P+C C+ I + A WH F C +C+ + G+ + EG+P C F+
Sbjct: 1 PRCSACDEIIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56
>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 = 34.2 bits (79), Expect = 0.004
Identities = 15/49 (30%), Positives = 21/49 (42%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
CG C ++ + A+N WH CF C C K + F G+ C
Sbjct: 1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCH 49
Score = 32.7 bits (75), Expect = 0.011
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
C C + + GR I AM +HP+ F C C ++L F + + CH C
Sbjct: 1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51
Score = 25.8 bits (57), Expect = 3.1
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRD 59
A+ WH + F C C K+ + GF + G+ C
Sbjct: 15 AMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50
>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 = 33.9 bits (78), Expect = 0.004
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 69 CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGK-SFYAMEGKPDCRQ 118
C GC I + + A++ QWH++C C +C+ P+ + S ++ +G C++
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKE 52
Score = 28.1 bits (63), Expect = 0.49
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 24 ALEKTWHTEHFFCAQCGKQF-GEDGFHEKDGKPYCRDDY 61
A+++ WH C +C E +DG YC++DY
Sbjct: 16 AVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>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 = 33.8 bits (78), Expect = 0.005
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
C C +AIM + WH CF C +CKKP+ KSF + K C
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYC 50
Score = 28.4 bits (64), Expect = 0.37
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 26 EKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
K WH + F C++C K G F KD K YC
Sbjct: 19 GKFWHEKCFTCSECKKPIGTKSFIPKDDKIYC 50
>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 = 33.2 bits (76), Expect = 0.008
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 146 CAGCHKPITGRCITAMFRK--FHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
C GC+K I ++ +H + F C+ C + + +F + + YC C EK F
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
Score = 32.0 bits (73), Expect = 0.022
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFY 108
C GC + I+ + V WH CF C +CK+P+ KSF+
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFF 42
Score = 24.7 bits (54), Expect = 9.0
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 27 KTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
WH + F C+ C + G F K YC
Sbjct: 20 NVWHKDCFTCSNCKQPIGTKSFFPKGEDFYC 50
>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 = 33.2 bits (76), Expect = 0.008
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 69 CGGCNRAIM----ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
C CN+ I YVS + QWH CF C C + G F+ + CR
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCR 53
Score = 27.4 bits (61), Expect = 0.93
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 146 CAGCHKPITG----RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
CA C+KPITG + ++ R++H F C+ C L F D+ C C
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55
>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 = 33.1 bits (76), Expect = 0.009
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFG-EDGFHEKDGKPYCRDDY 61
V+AL KTW +HF C+ C + + F+E D KP C+ Y
Sbjct: 13 VSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVCKKCY 53
Score = 32.7 bits (75), Expect = 0.011
Identities = 21/50 (42%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKS-FYAMEGKPDCR 117
C CN+ I + VSALN W F C C +T KS FY + KP C+
Sbjct: 1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVCK 50
Score = 30.8 bits (70), Expect = 0.064
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLN-KGTFKEQNDKPYCHGCFE 198
C C++ I G ++A+ + + +HF C+FC +L K F E + KP C C++
Sbjct: 1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVCKKCYD 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 = 33.3 bits (76), Expect = 0.009
Identities = 18/40 (45%), Positives = 21/40 (52%)
Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
F + VT+L K WH C +CGK E DGKPYC
Sbjct: 10 FAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49
Score = 31.4 bits (71), Expect = 0.034
Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 67 PKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQP 119
PKC V++L WH C C C K +T S +GKP C P
Sbjct: 2 PKCD--KEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCNHP 52
>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 = 32.9 bits (75), Expect = 0.009
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLN 180
C+ C KPI R + A + +HP F C C R L+
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLD 35
Score = 27.1 bits (60), Expect = 1.1
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
C C++ IME + A +H CF C C + + G F
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPF 39
>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 = 0.009
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK-EQNDKPYCHGCFEKLF 201
C+ C KPI R + A + +HP+ F C C + L+ F + ++ +C F K F
Sbjct: 1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKF 57
Score = 26.0 bits (57), Expect = 3.5
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
C C++ I++ + A +H CF C C K + G F
Sbjct: 1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPF 39
>gnl|CDD|188758 cd09372, LIM2_FBLP-1, The second LIM domain of the filamin-binding
LIM protein-1 (FBLP-1). The second LIM domain of the
filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains
a proline-rich domain near its N terminus and two LIM
domains at its C terminus. FBLP-1 mRNA was detected in a
variety of tissues and cells including platelets and
endothelial cells. FBLP-1 binds to Filamins. The
association between filamin B and FBLP-1 may play an
unknown role in cytoskeletal function, cell adhesion,
and cell motility. As in other LIM domains, this domain
family is 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 53
Score = 32.8 bits (75), Expect = 0.010
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK--EQNDKPYC 193
CA C IT I A+ + +HP F C C R++ +F EQN+ YC
Sbjct: 1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEV-YC 49
Score = 32.0 bits (73), Expect = 0.022
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
C C I E+ + AL +H CF C C + + +SF
Sbjct: 1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESF 39
Score = 31.2 bits (71), Expect = 0.037
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFH-EKDGKPYCRDDY 61
+ + AL K +H F C CG++ G++ F ++ + YC DDY
Sbjct: 10 EHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
>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 = 32.8 bits (75), Expect = 0.011
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 67 PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSF 107
PKC GC+ I + ++ + WHS C C DC+ +T K F
Sbjct: 2 PKCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDKCF 43
Score = 27.4 bits (61), Expect = 0.94
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 25 LEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62
+K WH++ C C Q + F + G+ YC++D+F
Sbjct: 20 QDKPWHSKCLKCVDCQAQLTDKCF-SRGGQVYCKEDFF 56
>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 = 32.3 bits (74), Expect = 0.015
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C CH I + + +HP HF CA C ++L +E + YC C
Sbjct: 1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELT-ADARELKGELYCLRCH 51
Score = 26.6 bits (59), Expect = 2.1
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 29 WHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
+H HF CA CGK+ D E G+ YC
Sbjct: 20 YHPYHFNCANCGKELTADA-RELKGELYC 47
>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 = 31.8 bits (73), Expect = 0.020
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 16 RCFQKC----VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+C +KC + +K +H + F C CG + GF K+G+ YC DDY
Sbjct: 3 KCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52
>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 = 32.0 bits (72), Expect = 0.021
Identities = 15/35 (42%), Positives = 19/35 (54%)
Query: 27 KTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
K WH F CA+CGK EK+G+ YC+ Y
Sbjct: 19 KPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
Score = 25.8 bits (56), Expect = 4.2
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 163 RKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
+ +H F CA C + L T E+ + YC GC+
Sbjct: 19 KPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
>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 = 31.9 bits (73), Expect = 0.024
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 69 CGGCNRAIME----NYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
C C + I ++S QWHS CF C C + G+ F
Sbjct: 1 CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSLVGQGF 43
Score = 29.2 bits (66), Expect = 0.19
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 146 CAGCHKPITG----RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
CA C KPITG + I+ R++H + F C C L F Q D+ C C
Sbjct: 1 CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55
>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 = 31.7 bits (72), Expect = 0.027
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 69 CGGCNRAIM----ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGK---PDC 116
C C + I ++S + WH+ CF C C+ + GK F G+ PDC
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55
Score = 26.3 bits (58), Expect = 3.0
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 146 CAGCHKPITG----RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
CA C KPITG + I+ R +H + F CA C L F + C C
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a Rho-type
GTPase activating protein (RhoGap) domain. Rga activates
GTPases during polarized morphogenesis. In yeast, a
known regulating target of Rga is CDC42p, a small
GTPase. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 55
Score = 31.6 bits (72), Expect = 0.031
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 69 CGGCNRAIMENYVSALNT-QWHSTCFVCRDCKKPVTGKS 106
C GC +I E + L +WH CF C C K ++ S
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLSCDS 39
>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 = 31.6 bits (72), Expect = 0.031
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 69 CGGCNRAI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C C + + A+ +H+ CF C C + + GK+FY + GK C + +
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
Score = 28.2 bits (63), Expect = 0.47
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
A+ +HT F C CG+ F+ +GK YC +DY
Sbjct: 17 AMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
Score = 25.5 bits (56), Expect = 4.1
Identities = 17/50 (34%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 146 CAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C C K + G + AM +H F C C R L F N K YC
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYC 50
>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 = 31.5 bits (71), Expect = 0.035
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 69 CGGCNRAI-MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQP 119
C GC + + V +L WH C C+ CKK +T +G P C P
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYCHVP 52
Score = 28.8 bits (64), Expect = 0.30
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
F + V +L + WH C +C K G E DG PYC
Sbjct: 10 FAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
Score = 27.7 bits (61), Expect = 0.78
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 146 CAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCH 194
C GC KP+ + ++ R +H C C + L G E + PYCH
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYCH 50
>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 = 31.4 bits (71), Expect = 0.039
Identities = 15/35 (42%), Positives = 19/35 (54%)
Query: 27 KTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
K WH F CA+CGK +KDG+ YC+ Y
Sbjct: 19 KPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
>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 = 31.2 bits (70), Expect = 0.045
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
C C + IM + WH TCF+C+ C++P+ KSF
Sbjct: 1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSF 41
>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 = 31.1 bits (70), Expect = 0.049
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 69 CGGCNRAIM----ENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
C GC I Y+S QWH+ CF C+ C + G+ F
Sbjct: 1 CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGF 43
Score = 25.3 bits (55), Expect = 6.1
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 146 CAGCHKPITG----RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
CAGC PI+G + I+ R++H + F C C L F + D C C
Sbjct: 1 CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 30.9 bits (70), Expect = 0.054
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
CG RA M+ QWH CF C +CK+P+ KSF + C
Sbjct: 4 CGEIFRAGMKKM-EYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50
Score = 26.6 bits (59), Expect = 1.9
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 27 KTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
+ WH + F C +C + G F KD YC
Sbjct: 20 QQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50
>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 = 30.6 bits (69), Expect = 0.072
Identities = 16/48 (33%), Positives = 23/48 (47%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
C C I+ V A + H CFVC DC + K ++ +EG+ C
Sbjct: 1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYC 48
Score = 25.3 bits (55), Expect = 5.8
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
V A +K H E F C+ C + G+ +G+ YC
Sbjct: 13 VKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYC 48
>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 = 30.2 bits (68), Expect = 0.082
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+++ WH F C+ C + ++EKDGK YC Y
Sbjct: 14 YRVVQEAWHNSCFQCSVCQDLL-TNWYYEKDGKLYCHKHY 52
Score = 29.1 bits (65), Expect = 0.21
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 69 CGGCNRAIMENY-VSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C GC I +++ + WH++CF C C+ +T +Y +GK C + +
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLT-NWYYEKDGKLYCHKHY 52
>gnl|CDD|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a. The first LIM
domain of Lmx1a: Lmx1a belongs to the LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Mouse Lmx1a is
expressed in multiple tissues, including the roof plate
of the neural tube, the developing brain, the otic
vesicles, the notochord, and the pancreas. Human Lmx1a
can be found in pancreas, skeletal muscle, adipose
tissue, developing brain, mammary glands, and pituitary.
The functions of Lmx1a in the developing nervous system
were revealed by studies of mutant mouse. In mouse,
mutations in Lmx1a result in failure of the roof plate
to develop. Lmx1a may act upstream of other roof plate
markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further
characterization of these mice reveals numerous defects
including disorganized cerebellum, hippocampus, and
cortex; altered pigmentation; female sterility; skeletal
defects; and behavioral abnormalities. Within pancreatic
cells, the Lmx1a protein interacts synergistically with
the bHLH transcription factor E47 to activate the
insulin gene enhancer/promoter. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 52
Score = 30.5 bits (69), Expect = 0.083
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 69 CGGCNRAIMENYVSALNTQ-WHSTCFVCRDCKKPVTGKSFY 108
C GCNR I + ++ +N WH C C CK+P+ FY
Sbjct: 1 CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLETTCFY 41
>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 = 30.2 bits (68), Expect = 0.092
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 69 CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
C C + IM + +WH TCFVC+ C++P+ K E K C
Sbjct: 1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50
>gnl|CDD|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein
(TLP). The first LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a
role in development of normal thymus and in controlling
the development and differentiation of thymic
epithelial cells. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 54
Score = 29.9 bits (67), Expect = 0.12
Identities = 17/40 (42%), Positives = 21/40 (52%)
Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
F + V++L K WH C +C K G E DGKPYC
Sbjct: 10 FAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49
Score = 27.6 bits (61), Expect = 0.72
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 81 VSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQP 119
VS+L WH C C C K ++ +GKP C +P
Sbjct: 14 VSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHKP 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 = 29.8 bits (67), Expect = 0.13
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 69 CGGCNRAIMENY-VSALNTQWHSTCFVCR--DCKKPVTGKSFYAMEGKPDCRQPF 120
C GCNR I + Y + AL+ WH C C DC+ G + Y CR+ +
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
>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 = 29.8 bits (67), Expect = 0.14
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 68 KCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
KC C + +M + WH CF+C C++P+ +SF
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSF 44
>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 = 29.8 bits (67), Expect = 0.15
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
A+ K WH+ HF C QC + + +D PYC
Sbjct: 18 AMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYC 51
Score = 29.0 bits (65), Expect = 0.26
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 146 CAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFE 198
C + I +G AM + +H HF C C L + +++ PYC C+E
Sbjct: 3 SVQCDELIFSGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56
Score = 28.3 bits (63), Expect = 0.45
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 67 PKCGGCNRAIME-NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
+ C+ I Y A+N WHS F C C + +TG+ + + P C
Sbjct: 1 DRSVQCDELIFSGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYC 51
>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 = 29.6 bits (66), Expect = 0.16
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 27 KTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCR 58
K WH F CA CGK +KDG+ YC+
Sbjct: 19 KPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50
>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 = 29.5 bits (66), Expect = 0.19
Identities = 16/35 (45%), Positives = 19/35 (54%)
Query: 141 KRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFC 175
K G LC GC +TG + A K+HPE F C C
Sbjct: 1 KFGELCHGCSLLMTGPAMVAGEYKYHPECFACMSC 35
Score = 26.1 bits (57), Expect = 3.7
Identities = 13/46 (28%), Positives = 20/46 (43%)
Query: 65 FAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAM 110
F C GC+ + + A ++H CF C CK + YA+
Sbjct: 2 FGELCHGCSLLMTGPAMVAGEYKYHPECFACMSCKVIIEDGDTYAL 47
>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 = 29.5 bits (66), Expect = 0.20
Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 69 CGGCNRAI--MENYVSALNTQWHST--CFVCRDCKKPVTGKSFYAMEGKPDC 116
C GC+ AI VS N WH+ CF+C C K + G+ F +EG C
Sbjct: 1 CQGCHNAIDPEVQRVSYNNFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFC 52
>gnl|CDD|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM
domains protein 1 (FHL1). The fourth LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 64
Score = 29.3 bits (66), Expect = 0.21
Identities = 19/59 (32%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 66 APKCGGCNRAIM-----ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGK---PDC 116
A KC GC I N V+ + WH CF C+ C + K F G+ DC
Sbjct: 2 AKKCSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60
Score = 25.5 bits (56), Expect = 5.3
Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 5/60 (8%)
Query: 146 CAGCHKPITG-----RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKL 200
C+GC PITG + +H F C C L F N + YC C +KL
Sbjct: 5 CSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDCAKKL 64
>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 = 29.3 bits (66), Expect = 0.24
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 24 ALEKTWHTEHFFCAQCGKQF--GEDGFHEKDGKPYCRDDY 61
A +K +H F C C KQ GE+ + + K C++DY
Sbjct: 17 ARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
Score = 26.6 bits (59), Expect = 2.1
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 69 CGGCNRAIMENYV--SALNTQWHSTCFVCRDCKKPV-TGKSFYAM-EGKPDCRQPF 120
C GC++ I N + A + +H CF C C+K + TG+ Y + E K C++ +
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
>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 = 28.7 bits (64), Expect = 0.31
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 81 VSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
++ ++ WH CF C CK +T +F + + KP C+
Sbjct: 14 INCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQ 50
>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 = 28.5 bits (64), Expect = 0.34
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 69 CGGCNRAIMENYVSALN-TQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
C GC R I + Y+ +N WH C C C++P+T S Y + K C+Q +Q
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTT-SCYFRDRKLYCKQDYQ 53
>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 = 28.6 bits (64), Expect = 0.38
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 68 KCGGCNRAI-MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
KC C++ + + + +SA +H +CF C CK + ++ +MEG C+ F+
Sbjct: 4 KCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFE 58
>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 = 28.1 bits (63), Expect = 0.52
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 29 WHTEHFFCAQCGKQFGED-GFHEKDGKPYCRDDY 61
WH CA+CG+ E +DGK YC+ DY
Sbjct: 22 WHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>gnl|CDD|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein
(LASP)-like proteins. The LIM domain of LIM and SH3
Protein (LASP) like proteins: This family contains two
types of LIM containing proteins; LASP and N-RAP. LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their LIM,
nebulin-like, and SH3 domains, but differ significantly
at their linker regions. Both proteins are ubiquitously
expressed and involved in cytoskeletal architecture,
especially in the organization of focal adhesions.
LASP-1 and LASP-2, are important during early embryo-
and fetogenesis and are highly expressed in the central
nervous system of the adult. However, only LASP-1 seems
to participate significantly in neuronal differentiation
and plays an important functional role in migration and
proliferation of certain cancer cells while the role of
LASP-2 is more structural. The expression of LASP-1 in
breast tumors is increased significantly. N-RAP is a
muscle-specific protein concentrated at myotendinous
junctions in skeletal muscle and intercalated disks in
cardiac muscle. LIM domain is found at the N-terminus of
N-RAP and the C-terminal of N-RAP contains a region with
multiple of nebulin repeats. N-RAP functions as a
scaffolding protein that organizes alpha-actinin and
actin into symmetrical I-Z-I structures in developing
myofibrils. Nebulin repeat is known as actin binding
domain. The N-RAP is hypothesized to form antiparallel
dimerization via its LIM domain. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 28.0 bits (62), Expect = 0.56
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 81 VSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
V+ L+ WH CF C CK + ++ + KP C
Sbjct: 14 VNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYC 49
Score = 27.2 bits (60), Expect = 1.3
Identities = 14/40 (35%), Positives = 17/40 (42%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
V L+KTWH F C C + + KPYC Y
Sbjct: 14 VNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53
>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 = 28.1 bits (63), Expect = 0.66
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 69 CGGCNRAIMENYV--SALNTQWHSTCFVCRDCKKPV-TGKSFYAME 111
C GC+ I V A + +H CF C CK+ + TG FY ME
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLME 46
Score = 25.4 bits (56), Expect = 5.3
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 24 ALEKTWHTEHFFCAQCGKQF--GEDGFHEKDGKPYCRDDY 61
A + +H E F C C +Q G++ + +D + C+ DY
Sbjct: 17 AQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
Score = 25.0 bits (55), Expect = 6.5
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 8/42 (19%)
Query: 146 CAGCHKPITGRCITAMFRK-----FHPEHFVCAFCLRQLNKG 182
CAGC + I T + R+ +H E F C C RQL G
Sbjct: 1 CAGCDEGI---PPTQVVRRAQDNVYHLECFACFMCKRQLETG 39
>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 = 27.9 bits (62), Expect = 0.69
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 69 CGGCNRAIMENY-VSALNTQWHSTCFVCR--DCKKPVTGKSFYAMEGKPDCRQPF 120
CGGC + I + Y + A++ WH C C C+ G+ Y G+ CR+ +
Sbjct: 1 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 55
Score = 27.5 bits (61), Expect = 0.95
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFH--EKDGKPYCRDDYF 62
A+++ WH + C CG + GE G K G+ CR DY
Sbjct: 16 AIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 56
>gnl|CDD|188716 cd09330, LIM4_abLIM, The fourth LIM domain of actin binding LIM
(abLIM) proteins. The fourth LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to function
as a tumor suppressor. AbLIM-2 and -3, mainly expressed
in muscle and neuronal tissue, bind to F-actin strongly.
They may serve as a scaffold for signaling modules of
the actin cytoskeleton and thereby modulate
transcription. It has shown that LIM domains of abLIMs
interact with STARS (striated muscle activator of Rho
signaling), which directly binds actin and stimulates
serum-response factor (SRF)-dependent transcription. All
LIM domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 56
Score = 27.3 bits (61), Expect = 0.93
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLR 177
C C K ITG+ + A + +HP CA C R
Sbjct: 1 CEACDKFITGKVLEAGGKHYHPT---CARCSR 29
>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 = 27.4 bits (61), Expect = 1.0
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 29 WHTEHFFCAQCGKQFGEDGFHEKDGKPYCR 58
+H F C C KQ D + +G YC+
Sbjct: 21 YHKNCFRCKDCNKQLKVDNYQSHEGNLYCK 50
Score = 25.5 bits (56), Expect = 4.2
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 88 WHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
+H CF C+DC K + ++ + EG C+ F
Sbjct: 21 YHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 53
>gnl|CDD|188730 cd09344, LIM1_FHL1, The first LIM domain of Four and a half LIM
domains protein 1. The first LIM domain of Four and a
half LIM domains protein 1 (FHL1): FHL1 is heavily
expressed in skeletal and cardiac muscles. It plays
important roles in muscle growth, differentiation, and
sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. .
Length = 54
Score = 27.4 bits (61), Expect = 1.0
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 85 NTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
N WH TCF C C KP+ + F A + K C
Sbjct: 19 NRYWHETCFRCAKCYKPLANEPFVAKDNKILC 50
Score = 26.6 bits (59), Expect = 2.1
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 146 CAGCHKPITGRCITAMF--RKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
CA C KPI R +H F CA C + L F +++K C C
Sbjct: 1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53
>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 = 27.7 bits (61), Expect = 1.0
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 69 CGGCNRAIMENY-VSALNTQWHSTCFVCRDCK 99
C GC I + Y + A++ QWH C C +CK
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECK 42
Score = 26.1 bits (57), Expect = 3.4
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 24 ALEKTWHTEHFFCAQCGKQF-GEDGFHEKDGKPYCRDDY 61
A++K WH C +C E KDG YC++DY
Sbjct: 26 AVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
>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 = 26.9 bits (60), Expect = 1.2
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFC 175
C GC + ITG + A KFHPE F C+ C
Sbjct: 1 CHGCSQIITGPVMVAGDHKFHPECFSCSSC 30
>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 = 27.2 bits (61), Expect = 1.2
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 81 VSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
+ A +H +CF C C K + ++ ++EGK C+ F
Sbjct: 14 LVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53
Score = 26.8 bits (60), Expect = 1.3
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 165 FHPEHFVCAFCLRQLNKGTFKEQNDKPYCH 194
FH F C+ C + L G + K YC
Sbjct: 21 FHKSCFRCSHCNKTLRLGNYASLEGKLYCK 50
>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin.
The third LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 27.1 bits (60), Expect = 1.3
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 65 FAPKCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
FA +C C++ I +S + WH CF+C CK + K F + + C
Sbjct: 1 FANQCEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYC 54
Score = 24.8 bits (54), Expect = 8.6
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 26 EKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
+K WH F C++C + F K + YC + Y
Sbjct: 23 DKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 58
>gnl|CDD|238517 cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase
family. This family consists of a group of secreted
bacterial lyase enzymes capable of acting on
glycosaminoglycans, such as hyaluronan and chondroitin,
in the extracellular matrix of host tissues,
contributing to the invasive capacity of the pathogen.
These are broad-specificity glycosaminoglycan lyases
which recognize uronyl residues in polysaccharides and
cleave their glycosidic bonds via a beta-elimination
reaction to form a double bond between C-4 and C-5 of
the non-reducing terminal uronyl residues of released
products. Substrates include chondroitin, chondroitin
4-sulfate, chondroitin 6-sulfate, and hyaluronic acid.
Family members include chondroitin AC lyase, chondroitin
abc lyase, xanthan lyase, and hyalurate lyase.
Length = 693
Score = 29.3 bits (66), Expect = 1.4
Identities = 15/61 (24%), Positives = 20/61 (32%), Gaps = 17/61 (27%)
Query: 74 RAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEG-KPDCRQPFQGGSFFDHEGLP 132
R ++E L V + VT +G D GSF H G+P
Sbjct: 184 RGLLEKDAVKLKQASDGLSSVL----QYVTEG-----DGFYAD-------GSFIQHGGVP 227
Query: 133 Y 133
Y
Sbjct: 228 Y 228
>gnl|CDD|236854 PRK11125, nrfA, cytochrome c nitrite reductase subunit c552;
Provisional.
Length = 480
Score = 29.2 bits (66), Expect = 1.5
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 6/58 (10%)
Query: 95 CRDCKKPVTGKSFYAMEGKPDCR--QPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCH 150
C DC S +GKP R +P+ + G P+ + +R +CA CH
Sbjct: 161 CADCHDT---ASMEFAKGKPALRLSRPY-AERAMEAIGKPFEKASRQDQRSMVCAQCH 214
>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9
family. The second LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Although Lhx2 and
Lhx9 are highly homologous, they seems to play
regulatory roles in different organs. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. Lhx9 is expressed in several regions of the
developing mouse brain, the spinal cord, the pancreas,
in limb mesenchyme, and in the urogenital region. Lhx9
plays critical roles in gonad development. Homozygous
mice lacking functional Lhx9 alleles exhibit numerous
urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 59
Score = 26.9 bits (60), Expect = 1.6
Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 19/73 (26%)
Query: 68 KCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
+C C+ I E + A + +H CF C C KP+T + M
Sbjct: 4 RCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGM--------------- 48
Query: 126 FDHEGLPYCETHY 138
+GL YC HY
Sbjct: 49 --RDGLVYCRLHY 59
>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 = 26.9 bits (59), Expect = 1.6
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 69 CGGCNRAIMENY-VSALNTQWHSTCFVCRDCKKPVTGK-SFYAMEGKPDCRQPF 120
C GC I + Y + A++ QWH C C +CK + + + +A +G C++ +
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
>gnl|CDD|188781 cd09395, LIM2_Rga, The second LIM domain of Rga GTPase-Activating
Proteins. The second LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a Rho-type
GTPase activating protein (RhoGap) domain. Rga activates
GTPases during polarized morphogenesis. In yeast, a
known regulating target of Rga is CDC42p, a small
GTPase. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 26.7 bits (59), Expect = 1.6
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 69 CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVT 103
C C + I + + + + + S CF CR C + +T
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDIT 36
>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and
Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a
and Lmx1b belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. In mouse, mutations in Lmx1a result in
failure of the roof plate to develop. Lmx1a may act
upstream of other roof plate markers such as MafB,
Gdf7, Bmp6, and Bmp7. Further characterization of these
mice reveals numerous defects including disorganized
cerebellum, hippocampus, and cortex; altered
pigmentation; female sterility, skeletal defects, and
behavioral abnormalities. In the mouse, Lmx1b
functions in the developing limbs and eyes, the
kidneys, the brain, and in cranial mesenchyme. The
disruption of Lmx1b gene results kidney and limb
defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 26.6 bits (59), Expect = 1.7
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGE-DGFHEKDGKPYCRDDY 61
ALE +H F C C +Q + D F K+G+ C+ DY
Sbjct: 17 ALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
>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 = 26.5 bits (59), Expect = 2.3
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLN 180
CA C K I CI +++H + F C+ C R+++
Sbjct: 1 CASCGKSIEDECIKFEDKRWHLKCFTCSRCHREIS 35
Score = 25.7 bits (57), Expect = 3.6
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKK 100
C C ++I + + + +WH CF C C +
Sbjct: 1 CASCGKSIEDECIKFEDKRWHLKCFTCSRCHR 32
>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).
The LIM domain of LIM and SH3 Protein (LASP): LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their LIM,
nebulin-like, and SH3 domains ,but differ significantly
at their linker regions. Both proteins are ubiquitously
expressed and involved in cytoskeletal architecture,
especially in the organization of focal adhesions.
LASP-1 and LASP-2, are important during early embryo-
and fetogenesis and are highly expressed in the central
nervous system of the adult. However, only LASP-1 seems
to participate significantly in neuronal differentiation
and plays an important functional role in migration and
proliferation of certain cancer cells while the role of
LASP-2 is more structural. The expression of LASP-1 in
breast tumors is increased significantly. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 26.2 bits (58), Expect = 2.7
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 81 VSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
++ L+ WH CF C C + K++ KP C
Sbjct: 14 LNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYC 49
Score = 25.4 bits (56), Expect = 5.5
Identities = 13/37 (35%), Positives = 16/37 (43%)
Query: 25 LEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
L+K WH F C CG + + KPYC Y
Sbjct: 17 LDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53
>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 = 26.2 bits (58), Expect = 2.8
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 6/37 (16%)
Query: 69 CGGCNRAIMENYV------SALNTQWHSTCFVCRDCK 99
CGGC+ + + + WH CF C C+
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCE 37
>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 = 26.2 bits (58), Expect = 3.0
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
C C IME + AL +H CF C C + + G F
Sbjct: 1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPF 39
>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 = 26.0 bits (57), Expect = 3.0
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 146 CAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKE--QNDKPYCHGCF 197
C GC + IT G + A +K+HPE F C C + G ++ K YC C+
Sbjct: 1 CHGCSETITTGLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYCGHCY 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 = 26.4 bits (58), Expect = 3.1
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 65 FAPKCGGCNRAIMENY--VSALNTQWHSTCFVCRDCKKPVTGKSFYAME 111
++ C C + I + +S + WH +CF C CK + K F A E
Sbjct: 1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKE 49
>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL. The LIM domain of RIL:
RIL contains an N-terminal PDZ domain, a LIM domain, and
a short consensus C-terminal region. It is the smallest
molecule in the ALP LIM domain containing protein
family. RIL was identified in rat fibroblasts and in
human lymphocytes. The LIM domain interacts with the
AMPA glutamate receptor in dendritic spines. The
consensus C-terminus interacts with PTP-BL, a
submembranous protein tyrosine phosphatase and the PDZ
domain is responsible to interact with alpha-actinin
molecules. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 26.0 bits (57), Expect = 3.2
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
C C I+ V A + +H CF+C DC + + ++ ++ + C
Sbjct: 1 CTRCGNGIVGTIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYC 48
Score = 25.7 bits (56), Expect = 4.6
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
C C I G + A + +HPE F+C C L + + +++ YC
Sbjct: 1 CTRCGNGIVGTIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYC 48
Score = 25.3 bits (55), Expect = 6.1
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
V A +K +H E F C CG + G+ D + YC
Sbjct: 13 VKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYC 48
>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 = 25.9 bits (57), Expect = 3.3
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 26 EKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
++ WH F C +C + + F KD C + Y
Sbjct: 23 DRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58
>gnl|CDD|239325 cd03027, GRX_DEP, Glutaredoxin (GRX) family, Dishevelled, Egl-10,
and Pleckstrin (DEP) subfamily; composed of
uncharacterized proteins containing a GRX domain and
additional domains DEP and DUF547, both of which have
unknown functions. GRX is a glutathione (GSH) dependent
reductase containing a redox active CXXC motif in a TRX
fold. It has preference for mixed GSH disulfide
substrates, in which it uses a monothiol mechanism where
only the N-terminal cysteine is required. By altering
the redox state of target proteins, GRX is involved in
many cellular functions.
Length = 73
Score = 26.2 bits (58), Expect = 3.4
Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 106 SFYAMEGKPDCRQPFQGGSFFDHEGLPYCE 135
+ Y+ G DC F +GLPY E
Sbjct: 4 TIYSRLGCEDCTA---VRLFLREKGLPYVE 30
>gnl|CDD|188743 cd09357, LIM3_Zyxin_like, The third LIM domain of Zyxin-like
family. The third LIM domain of Zyxin like family: This
family includes Ajuba, Limd1, WTIP, Zyxin, LPP, and
Trip6 LIM proteins. Members of Zyxin family contain
three tandem C-terminal LIM domains, and a proline-rich
N-terminal region. Zyxin proteins are detected
primarily in focal adhesion plaques. They function as
scaffolds, participating in the assembly of multiple
interactions and signal transduction networks, which
regulate cell adhesion, spreading, and motility. They
can also shuffle into nucleus. In nucleus, zyxin
proteins affect gene transcription by interaction with a
variety of nuclear proteins, including several
transcription factors, playing regulating roles in cell
proliferation, differentiation and apoptosis. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 63
Score = 26.2 bits (58), Expect = 3.4
Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 15/59 (25%)
Query: 146 CAGCHKPITGRC-------ITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C+ C +PI I A+ R FH + C C L + + GC+
Sbjct: 1 CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLL--------SSEDEGQGCY 51
>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like
family. The third LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 57
Score = 25.8 bits (57), Expect = 3.5
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 85 NTQWHST--CFVCRDCKKPVTGKSFYAMEGKPDC 116
WH+T CF C +CKK + G+ F G+ C
Sbjct: 19 GQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFC 52
>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of
proteins with unknown function. This model represents a
LIM domain subfamily of Eplin-like family. This family
shows highest homology to the LIM domains on Eplin and
XIRP2 protein families. Epithelial Protein Lost in
Neoplasm is a cytoskeleton-associated tumor suppressor
whose expression inversely correlates with cell growth,
motility, invasion and cancer mortality. Xirp2 is
expressed in muscles and is an important effector of the
Ang II signaling pathway in the heart. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 25.7 bits (56), Expect = 3.6
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 69 CGGCNRAI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
C C + + ME V A +H++CF C+ C ++ S+ A+ G+ C+ F
Sbjct: 1 CSSCQKTVYPMERLV-ADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53
>gnl|CDD|181283 PRK08197, PRK08197, threonine synthase; Validated.
Length = 394
Score = 28.0 bits (63), Expect = 3.8
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 124 SFFDHEGLPYCETHYHAKR-GSLCAGCHKPITGRC-ITAMFRKFHPE 168
S+ H C Y A + +LC C KP+ R + A+ + E
Sbjct: 3 SYVSHLECSKCGETYDADQVHNLCK-CGKPLLVRYDLEAVKQAVTRE 48
>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 = 25.8 bits (56), Expect = 3.9
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 68 KCGGCNRAIMENYV--SALNTQWHSTCFVCRDCKKPV-TGKSFYAME 111
KC C + I V A + +H CF C CK+ + TG FY ME
Sbjct: 1 KCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLME 47
>gnl|CDD|234699 PRK00241, nudC, NADH pyrophosphatase; Reviewed.
Length = 256
Score = 27.5 bits (62), Expect = 4.0
Identities = 5/13 (38%), Positives = 7/13 (53%)
Query: 28 TWHTEHFFCAQCG 40
++ H FC CG
Sbjct: 94 EFYRSHRFCGYCG 106
>gnl|CDD|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3
(CRP3/MLP). The first LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. CRP3/MLP interacts with
cytoskeletal protein beta-spectrin. CRP3/MLP also
interacts with the basic helix-loop-helix myogenic
transcriptio n factors MyoD, myogenin, and MRF4 thereby
increasing their affinity for specific DNA regulatory
elements. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 25.9 bits (56), Expect = 4.1
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 68 KCGGCNRAIMENYVSALNTQ-WHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
KCG C + + N + +H TCF+C C+K + + A E + C+
Sbjct: 1 KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCK 51
Score = 24.7 bits (53), Expect = 8.2
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 146 CAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
C C K + I R FH F+C C + L+ T + YC C+
Sbjct: 2 CGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54
>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 = 25.2 bits (56), Expect = 4.9
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 69 CGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPV 102
C C +++ V A WH +CF C C K +
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRL 35
Score = 24.9 bits (55), Expect = 6.9
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCR 58
V A K+WH F CA C K+ E DG+ YC+
Sbjct: 14 VIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50
>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 = 25.4 bits (55), Expect = 5.1
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 69 CGGCNRAIMEN--YVSALNTQWHSTCFVCRDCKKPV-TGKSFYAMEGKPDCR 117
C C R I + A +H CF C CK+ + TG+ F +E K CR
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCR 52
>gnl|CDD|188832 cd09448, LIM_CLP36, This family represents the LIM domain of CLP36.
This family represents the LIM domain of CLP36. CLP36
has also been named as CLIM1, Elfin, or PDLIM1. CLP36
contains a C-terminal LIM domain and an N-terminal PDZ
domain. CLP36 is highly expressed in heart and is
present in many other tissues including lung, liver,
spleen, and blood. CLP36 has been implicated in many
processes including hypoxia and regulation of actin
stress fibers. CLP36 co-localizes with alpha-actinin-2
at the Z-lines in myocardium. In addition, CLP36 binds
to alpha-actinin-1 and alpha-actinin-4, and associates
with F-actin filaments and stress fibers. CLP36 might be
involved in not only the function of sarcomeres in
muscle cells, but also in actin stress fiber-mediated
cellular processes, such as cell shape, migration,
polarit, and cytokinesis in non-muscle cells. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 25.3 bits (55), Expect = 5.2
Identities = 13/50 (26%), Positives = 22/50 (44%)
Query: 69 CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
C C I+ +V + H C+VC DC + K + +E + C +
Sbjct: 1 CDKCGSGIVGVFVKIRDKPRHPECYVCTDCGTNLKQKGHFFVEDQIYCEK 50
>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 = 25.5 bits (56), Expect = 5.3
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 24 ALEKTWHTEHFFCAQCGKQFGEDG--FHEKDGKPYCRDDY 61
AL++ WH C+ C Q GE G + K G C++DY
Sbjct: 16 ALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
Score = 25.1 bits (55), Expect = 7.8
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 69 CGGCNRAIMENY-VSALNTQWHSTCFVCRDC 98
C GC I++ + + AL+ WH+ C C C
Sbjct: 1 CAGCGGKIVDRFLLHALDRYWHNGCLKCSCC 31
>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 = 25.4 bits (56), Expect = 6.7
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 10/59 (16%)
Query: 69 CGGCNRAIMEN-------YVSALNTQWHSTCFVCRDCKKPVT---GKSFYAMEGKPDCR 117
C C + I+ V +++ +H C+ C DC + G Y ++G C
Sbjct: 1 CAACGQPILPAEGSEETIRVVSMDKDYHVECYHCEDCGLQLNDEEGHRCYPLDGHLLCH 59
>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 = 25.0 bits (54), Expect = 7.7
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 69 CGGCNRAIMEN--YVSALNTQWHSTCFVCRDCKKPV-TGKSFYAMEGKPDCRQPF 120
C C R I A +H CF C CK+ + TG+ F +E K CR +
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55
>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 = 24.9 bits (54), Expect = 7.9
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 88 WHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
WH +CFVC C + + ++ +GK C
Sbjct: 26 WHPSCFVCFTCNELLVDLIYFYQDGKIHC 54
>gnl|CDD|172627 PRK14138, PRK14138, NAD-dependent deacetylase; Provisional.
Length = 244
Score = 26.7 bits (59), Expect = 8.5
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 32 EHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYV 81
E ++C +CGK++ + EK K D P+C C+ I N V
Sbjct: 118 EEYYCVRCGKRYTVEDVIEKLEK----SD-----VPRCDDCSGLIRPNIV 158
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.330 0.144 0.521
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,098,224
Number of extensions: 867543
Number of successful extensions: 1585
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1475
Number of HSP's successfully gapped: 438
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 56 (25.4 bits)