RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16551
(281 letters)
>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 = 87.3 bits (217), Expect = 2e-22
Identities = 30/54 (55%), Positives = 37/54 (68%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
CPRCG V+AAE+V+A G WH+ CF C CNK LDS + D +IYCK+CY
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAE-HDGEIYCKSCY 53
Score = 81.1 bits (201), Expect = 3e-20
Identities = 30/54 (55%), Positives = 38/54 (70%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
CPRCG +V+AAE+ +A G WHK CF+C VC + LDS + D EIYCK+CY
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAE-HDGEIYCKSCY 53
>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A.
The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A
belong to the CRP LIM domain protein family. The Mlp84B
protein contains five copies of the LIM domains, each
followed by a Glycin Rich Region (GRR). However, only
the first LIM domain of Mlp84B is in this family. Mlp60A
exhibits only one LIM domain linked to a glycin-rich
region. Mlp84B and Mlp60A are muscle specific proteins
and have been implicated in muscle differentiation.
While Mlp84B transcripts are enriched at the terminal
ends of muscle fibers, Mlp60A transcripts are found
throughout the muscle fibers. All LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 69.8 bits (171), Expect = 6e-16
Identities = 28/54 (51%), Positives = 38/54 (70%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
CP+CG V+AAE+ LA G +WH+ CFKC CNK LDS N + + ++YCK C+
Sbjct: 2 CPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEH-EGELYCKQCH 54
Score = 64.0 bits (156), Expect = 8e-14
Identities = 26/54 (48%), Positives = 37/54 (68%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
CP+CG +V+AAE++LA G WHK CF C +C + LDS + + E+YCK C+
Sbjct: 2 CPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEH-EGELYCKQCH 54
>gnl|CDD|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein
(CRP). The second LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function not
only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the arrangement
of the myofibrillar/cytoskeletal network. It is evident
that CRP1, CRP2, and CRP3/MLP are involved in promoting
protein assembly along the actin-based cytoskeleton.
Although members of the CRP family share common binding
partners, they are also capable of recognizing different
and specific targets. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residu es,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 63.7 bits (155), Expect = 1e-13
Identities = 27/54 (50%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
CPRCG V+AAE+++ G WH+ CF+C C K+L+S D D +IYCK CY
Sbjct: 1 CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLAD-KDGEIYCKGCY 53
Score = 60.7 bits (147), Expect = 2e-12
Identities = 28/54 (51%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
CPRCG +V+AAE+ + G WHK CF C C + L+S D D EIYCK CY
Sbjct: 1 CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLAD-KDGEIYCKGCY 53
>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein
3 (CRP3/MLP). The second LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 62.7 bits (152), Expect = 3e-13
Identities = 27/54 (50%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
CPRCG V+AAE+V+ G WH+ CF+C C K+L+S D D ++YCK CY
Sbjct: 1 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTD-KDGELYCKVCY 53
Score = 60.4 bits (146), Expect = 2e-12
Identities = 27/54 (50%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
CPRCG +V+AAE+ + G WHK CF C +C + L+S D D E+YCK CY
Sbjct: 1 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTD-KDGELYCKVCY 53
>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 = 58.6 bits (141), Expect = 1e-11
Identities = 24/55 (43%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYG 152
C RCG V+AAE+++ G WH+ CF+C C K+L+S + + +IYCK CY
Sbjct: 1 CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTE-KEGEIYCKGCYA 54
Score = 56.7 bits (136), Expect = 5e-11
Identities = 25/55 (45%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYG 255
C RCG +V+AAE+ + G WHK CF C C + L+S + + EIYCK CY
Sbjct: 1 CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTE-KEGEIYCKGCYA 54
>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 = 57.4 bits (139), Expect = 2e-11
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
CP+CG V+ AE+ + G +WH+ C +C C KTL + K YC CY
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGK-PYCNKCY 53
Score = 53.5 bits (129), Expect = 6e-10
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
CP+CG V+ AE++ + G WHK C C CK+ L + + + YC CY
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSE-HEGKPYCNKCY 53
>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 = 51.9 bits (125), Expect = 2e-09
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
C CG V+ E+++A G +H+ CF+C CNKTL N K +YCK
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGK-LYCK 50
Score = 45.7 bits (109), Expect = 4e-07
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL--DSVLACDGPDKEIYCK 251
C CG V+ E+ +A G ++HK CF C+ C + L + + +G ++YCK
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEG---KLYCK 50
>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 = 51.3 bits (123), Expect = 4e-09
Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 5/53 (9%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL--DSINACDGPDKDIYCK 148
C CG V+ E+++A+ +H+ CF+C+DCNK L D+ + +G ++YCK
Sbjct: 1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEG---NLYCK 50
Score = 41.7 bits (98), Expect = 1e-05
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL--DSVLACDGPDKEIYCK 251
C CG V+ E+ +A+ ++HK CF C C + L D+ + +G +YCK
Sbjct: 1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEG---NLYCK 50
>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2
(CRP2). The first LIM domain of Cysteine Rich Protein 2
(CRP2): The CRP family members include CRP1, CRP2,
CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved
nuclear targeting signal (K/R-K/R-Y-G-P-K), which
supports the fact that these proteins function not only
in the cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation, and
involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network. CRP2 specifically
binds to protein inhibitor of activated STAT-1 (PIAS1)
and a novel human protein designed CRP2BP (for CRP2
binding partner). PIAS1 specifically inhibits the STAT-1
pathway and CRP2BP is homologous to members of the
histone acetyltransferase family raising the possibility
that CRP2 is a modulator of cytokine-controlled pathways
or is functionally active in the transcriptional
regulatory network. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 50.4 bits (120), Expect = 9e-09
Identities = 26/55 (47%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYG 255
C CG V+ AE+ G +HK CF C VC++ LDS D+EIYCK+CYG
Sbjct: 2 CGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIH-DQEIYCKSCYG 55
Score = 50.0 bits (119), Expect = 1e-08
Identities = 25/55 (45%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYG 152
C CG V+ AE+V G +H+ CF C C K LDS D++IYCK+CYG
Sbjct: 2 CGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIH-DQEIYCKSCYG 55
>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1,
Mec-3. Zinc-binding domain family. Some LIM domains
bind protein partners via tyrosine-containing motifs.
LIM domains are found in many key regulators of
developmental pathways.
Length = 54
Score = 50.1 bits (120), Expect = 1e-08
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTC 150
C CG ++ E+VL A G WH +CFKC C K L D +YCK C
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDT-FFEKDGKLYCKDC 54
Score = 48.9 bits (117), Expect = 3e-08
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKAC 253
C CG ++ E+ L A G +WH +CF C C +PL D ++YCK C
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDT-FFEKDGKLYCKDC 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 = 49.9 bits (119), Expect = 1e-08
Identities = 21/54 (38%), Positives = 28/54 (51%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
CP+C V+ AE+V + G +WHR C KC C KTL + + K CY
Sbjct: 1 CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCNHPCY 54
Score = 36.4 bits (84), Expect = 9e-04
Identities = 16/54 (29%), Positives = 23/54 (42%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
CP+C V+ AE+ + G WH+ C C C + L + K CY
Sbjct: 1 CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCNHPCY 54
>gnl|CDD|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein
(CRP). The first LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function not
only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the arrangement
of the myofibrillar/cytoskeletal network. It is evident
that CRP1, CRP2, and CRP3/MLP are involved in promoting
protein assembly along the actin-based cytoskeleton.
Although members of the CRP family share common binding
partners, they are also capable of recognizing different
and specific targets. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 49.2 bits (117), Expect = 3e-08
Identities = 23/54 (42%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C C V+ AE+ +G +HK CF C VC++ LDS + EIYCK+CY
Sbjct: 1 CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVA-AHEDEIYCKSCY 53
Score = 48.4 bits (115), Expect = 4e-08
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C C V+ AE+V +G +H+ CF C C K LDS + +IYCK+CY
Sbjct: 1 CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVA-AHEDEIYCKSCY 53
>gnl|CDD|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1
(CRP1). The first LIM domain of Cysteine Rich Protein 1
(CRP1): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and
CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1 can associate with the actin cytoskeleton
and are capable of interacting with alpha-actinin and
zyxin. CRP1 was shown to regulate actin filament
bundling by interaction with alpha-actinin and direct
binding to actin filaments. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 48.9 bits (116), Expect = 3e-08
Identities = 25/55 (45%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYG 255
C C V+ AE+ +G +HK CF C VCK+ LDS + EIYCK+CYG
Sbjct: 3 CGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGE-EIYCKSCYG 56
Score = 48.5 bits (115), Expect = 4e-08
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 96 KGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYG 152
K C C V+ AE+V +G +H+ CF C C K LDS + +IYCK+CYG
Sbjct: 1 KKCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGE-EIYCKSCYG 56
>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 = 48.5 bits (116), Expect = 4e-08
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C CG + E + A G +WH +CFKC C K L + + D YC+ CY
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEK-DGKPYCEKCY 53
Score = 46.2 bits (110), Expect = 3e-07
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C CG + E A G WH +CF C+VC +PL + D + YC+ CY
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEK-DGKPYCEKCY 53
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 47.7 bits (114), Expect = 9e-08
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKK 154
C CG ++ E V A G WH +CF+C C K L + D +YCK Y K
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDGKLYCKHDYFKL 57
Score = 47.7 bits (114), Expect = 1e-07
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 201 CPRCGGAVFAAEQ-QLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYGKNF 258
C CG ++ E + A G +WH +CF C VC +PL D ++YCK Y K F
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDGKLYCKHDYFKLF 58
>gnl|CDD|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function.
LIM domain in proteins of unknown function: LIM domains
are identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation, and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. The LIM
domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. The consensus sequence of LIM domain
has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 61
Score = 47.8 bits (114), Expect = 1e-07
Identities = 20/54 (37%), Positives = 27/54 (50%)
Query: 97 GCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTC 150
C CG VF AE++L +G +HR CFKC C L + + C+TC
Sbjct: 4 PCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYCCETC 57
Score = 34.7 bits (80), Expect = 0.004
Identities = 18/55 (32%), Positives = 25/55 (45%)
Query: 199 EGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKAC 253
E C CG VF AE+ L +G ++H+ CF C C L + C+ C
Sbjct: 3 EPCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYCCETC 57
>gnl|CDD|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase
domains protein (Ltd-1). The LIM domain of LIM and
transglutaminase domains protein (Ltd-1): This family
includes mouse Ky protein and Caenorhabditis elegans
Ltd-1 protein. The members of this family consists a
N-terminal Lim domain and a C-terminal transglutaminase
domain. The mouse Ky protein has putative function in
muscle development. The mouse with ky mutant exhibits
combined posterior and lateral curvature of the spine.
The Ltd-1 gene in C. elegans is expressed in developing
hypodermal cells from the twofold stage embryo through
adulthood. These data define the ltd-1 gene as a novel
marker for C. elegans epithelial cell development. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 47.0 bits (112), Expect = 1e-07
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINAC-DGPDKDIYCKT 149
CPRCG + AE V G+ +H+ CFKCR+C L D ++YC
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCAR 53
Score = 41.3 bits (97), Expect = 1e-05
Identities = 20/52 (38%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLAC-DGPDKEIYCK 251
CPRCG + AE GT +HK CF C C L D E+YC
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCA 52
>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 = 46.5 bits (110), Expect = 2e-07
Identities = 18/35 (51%), Positives = 24/35 (68%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
CP CG V+ AE+V++ G WHR C +C+ C KTL
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTL 35
Score = 38.1 bits (88), Expect = 2e-04
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL 235
CP CG V+ AE+ ++ G WH+ C C CK+ L
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTL 35
>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 = 46.7 bits (110), Expect = 2e-07
Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C C V+ AE++ G +H+ CF C C K LDS + +IYCKTCY
Sbjct: 2 CGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVA-AHESEIYCKTCY 54
Score = 46.7 bits (110), Expect = 2e-07
Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C C V+ AE+ G +HK CF C C++ LDS + EIYCK CY
Sbjct: 2 CGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVA-AHESEIYCKTCY 54
>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 = 45.0 bits (106), Expect = 8e-07
Identities = 22/54 (40%), Positives = 27/54 (50%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
CPRC V+ AE+V + G WHR C KC C+K L + K K CY
Sbjct: 1 CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHKPCY 54
Score = 34.6 bits (79), Expect = 0.004
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL 235
CPRC V+ AE+ + G WH+ C C C + L
Sbjct: 1 CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKIL 35
>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 = 44.3 bits (104), Expect = 1e-06
Identities = 21/54 (38%), Positives = 27/54 (50%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C CGG + +LA +WH +C KC +C L+S C D IYCK Y
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
Score = 42.0 bits (98), Expect = 8e-06
Identities = 22/54 (40%), Positives = 25/54 (46%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C CGG + LA WH +C C CK L+S L C D IYCK Y
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
>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 = 43.8 bits (103), Expect = 2e-06
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C RCG V+ E+ WHK CF C VCK L ++ G K+ YC A Y
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTL-NMNNYKGYQKKPYCNAHY 53
Score = 43.4 bits (102), Expect = 3e-06
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C RCG +V+ E+V WH+ CF C C TL ++N G K YC Y
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTL-NMNNYKGYQKKPYCNAHY 53
>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).
The LIM domain of LIM and SH3 Protein (LASP): LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their LIM,
nebulin-like, and SH3 domains ,but differ significantly
at their linker regions. Both proteins are ubiquitously
expressed and involved in cytoskeletal architecture,
especially in the organization of focal adhesions.
LASP-1 and LASP-2, are important during early embryo-
and fetogenesis and are highly expressed in the central
nervous system of the adult. However, only LASP-1 seems
to participate significantly in neuronal differentiation
and plays an important functional role in migration and
proliferation of certain cancer cells while the role of
LASP-2 is more structural. The expression of LASP-1 in
breast tumors is increased significantly. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 43.5 bits (103), Expect = 2e-06
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C RCG V+ E++ WH+ CFKC C TL ++ G +K YC Y
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTL-NMKNYKGYNKKPYCNAHY 53
Score = 39.7 bits (93), Expect = 6e-05
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C RCG V+ E+ +WHK CF C VC L ++ G +K+ YC A Y
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTL-NMKNYKGYNKKPYCNAHY 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 = 43.1 bits (101), Expect = 5e-06
Identities = 21/54 (38%), Positives = 27/54 (50%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C CGG + +LA +WH +C KC +C L+S C D IYCK Y
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
Score = 42.3 bits (99), Expect = 9e-06
Identities = 22/54 (40%), Positives = 25/54 (46%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C CGG + LA WH +C C CK L+S L C D IYCK Y
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
>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 = 42.3 bits (100), Expect = 7e-06
Identities = 22/54 (40%), Positives = 25/54 (46%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C CG + LA WH C C C+ PLDS L+C D IYCK Y
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
Score = 41.6 bits (98), Expect = 1e-05
Identities = 21/54 (38%), Positives = 27/54 (50%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C CG + +LA +WH C KC +C LDS +C D +IYCK Y
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>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 = 40.1 bits (94), Expect = 4e-05
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL--DSINACDGPDKDIYCKTCY 151
C C V+ +Q+ A G +H+ CF+C C TL + ++ +G +YCK +
Sbjct: 5 CKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGV---LYCKPHF 57
Score = 35.1 bits (81), Expect = 0.003
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL--------DSVLAC 241
C C V+ +Q A G ++HK CF C+ CK L + VL C
Sbjct: 5 CKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYC 53
>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8.
The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs such as the pituitary
gland and the pancreas. Studies using mutant mice have
revealed roles for Lhx7 and Lhx8 in the development of
cholinergic neurons in the telencephalon and in basal
forebrain development. Mice lacking alleles of the
LIM-homeobox gene Lhx7 or Lhx8 display dramatically
reduced number of forebrain cholinergic neurons. In
addition, Lhx7 mutation affects male and female mice
differently, with females appearing more affected than
males. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 39.2 bits (91), Expect = 8e-05
Identities = 18/54 (33%), Positives = 25/54 (46%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C CG + WH +C SC+VC+ L +C DK+I+CK Y
Sbjct: 2 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 55
Score = 34.2 bits (78), Expect = 0.005
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
WH +C C C +L +C DKDI+CK Y
Sbjct: 22 WHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 55
>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 = 39.4 bits (92), Expect = 8e-05
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 201 CPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCKRPL--DSVLACDGPDKEIYCKACYGKN 257
C C + A +Q + KG +WHK CF+C+ CK+P+ S ++ YC C+ K
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFP---KGEDFYCVPCHEKK 57
Query: 258 F 258
F
Sbjct: 58 F 58
Score = 37.8 bits (88), Expect = 3e-04
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 98 CPRCGGVVFAAEQ-VLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKW 155
C C + A +Q V KG+ WH+ CF C +C + + + + +D YC C+ KK+
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFP-KGEDFYCVPCHEKKF 58
>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 = 39.1 bits (91), Expect = 8e-05
Identities = 16/32 (50%), Positives = 18/32 (56%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCK 232
C RCG V+ AE+ WHK CF C VCK
Sbjct: 1 CARCGYGVYPAEKINCIDQTWHKACFHCEVCK 32
Score = 38.0 bits (88), Expect = 3e-04
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
C RCG V+ AE++ WH+ CF C C L ++N K YC+
Sbjct: 1 CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMML-TVNNFVSHQKKPYCQ 50
>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9. The second LIM
domain of Lhx9: Lhx9 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx9 is highly
homologous to Lhx2. It is expressed in several regions
of the developing mouse brain, the spinal cord, the
pancreas, in limb mesenchyme, and in the urogenital
region. Lhx9 plays critical roles in gonad development.
Homozygous mice lacking functional Lhx9 alleles exhibit
numerous urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
have reduced levels of the Sf1 nuclear receptor that is
required for gonadogenesis, and recent studies have
shown that Lhx9 is able to activate the Sf1/FtzF1 gene.
Lhx9 null mice are phenotypically female, even those
that are genotypically male. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 59
Score = 38.5 bits (89), Expect = 1e-04
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 96 KGCPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
+ C RC + A+E V+ A+ S +H CF C CNKTL + + D +YC+
Sbjct: 3 QRCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCR 56
Score = 32.0 bits (72), Expect = 0.041
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCK 251
C RC + A+E + A+ +++H CF+C C + L + D +YC+
Sbjct: 5 CARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCR 56
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 6/57 (10%)
Query: 201 CPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCKRPL--DSVLACDGPDKEIYCKACY 254
C CG A+ +++ KG WH++CF+C+ CK+P+ S + D +IYC CY
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDD---KIYCVPCY 54
Score = 35.7 bits (83), Expect = 0.001
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 98 CPRCGGVVFAAEQVLA-KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C CG + + + KG WH KCF C +C K + + + D IYC CY
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGT-KSFIPKDDKIYCVPCY 54
>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase
). The first LIM domain of LIMK (LIM domain Kinase ):
LIMK protein family is comprised of two members LIMK1
and LIMK2. LIMK contains two LIM domains, a PDZ domain
and a kinase domain. LIMK is involved in the regulation
of actin polymerization and microtubule disassembly.
LIMK influences architecture of the actin cytoskeleton
by regulating the activity of the cofilin family
proteins cofilin1, cofilin2, and destrin. The mechanism
of the activation is to phosphorylates cofilin on serine
3 and inactivates its actin-severing activity, and
altering the rate of actin depolymerisation. LIMKs can
function in both cytoplasm and nucleus and are expressed
in all tissues. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. However, LIMK1 and LIMk2 have different
cellular locations. While LIMK1 localizes mainly at
focal adhesions, LIMK2 is found in cytoplasmic punctae,
suggesting that they may have different cellular
functions. The LIM domains of LIMK have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 53
Score = 38.2 bits (89), Expect = 2e-04
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C C G + ++ V A +WH CF+C C+ +L N D +YC+ Y
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLS--NWYFEKDGKLYCRKDY 52
Score = 34.8 bits (80), Expect = 0.003
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C C G + ++ A WH CF C+VC L + D ++YC+ Y
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYF--EKDGKLYCRKDY 52
>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 = 37.9 bits (88), Expect = 3e-04
Identities = 16/46 (34%), Positives = 24/46 (52%)
Query: 216 AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYGKNFGPK 261
A G +H QCF+C VC + LD + +I+C + K F P+
Sbjct: 15 ATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAPR 60
Score = 36.0 bits (83), Expect = 0.002
Identities = 16/45 (35%), Positives = 22/45 (48%)
Query: 113 AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGP 157
A G +H +CF C C K+LD I I+C + KK+ P
Sbjct: 15 ATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAP 59
>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 = 37.7 bits (88), Expect = 3e-04
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 221 WHKQCFSCNVCKRPLDSVL---ACDGPDKEIYCKAC 253
WH +CF+C+ C R + S L A + D+ I C C
Sbjct: 20 WHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
Score = 31.1 bits (71), Expect = 0.072
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 118 WHRKCFKCRDCNKTLDSIN---ACDGPDKDIYCKTC 150
WH KCF C C++ + S A + D+ I C C
Sbjct: 20 WHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
>gnl|CDD|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH). The
first LIM domain of Arrowhead (AWH): Arrowhead belongs
to the LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Members of LHX family are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 37.4 bits (87), Expect = 3e-04
Identities = 17/37 (45%), Positives = 22/37 (59%)
Query: 218 GTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
G WH C C VC+ PL+ +C D++IYCKA Y
Sbjct: 18 GRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
Score = 35.0 bits (81), Expect = 0.002
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 115 GSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
G WH C +C C L+ +C D+ IYCK Y
Sbjct: 18 GRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
>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 = 37.5 bits (87), Expect = 4e-04
Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 200 GCPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCKRPLDSVLACDGPDK-EIYCKACY 254
C CG V ++L +G WH+ CF C+ C++P+ S PDK E YC CY
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFI--PDKDEHYCVPCY 57
Score = 33.3 bits (76), Expect = 0.014
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 97 GCPRCGGVVFAAEQVLA-KGSEWHRKCFKCRDCNKTLDSINACDGPDKD-IYCKTCY 151
C CG V + L +G WH CF C C + + S + PDKD YC CY
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFI--PDKDEHYCVPCY 57
>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 = 36.6 bits (85), Expect = 9e-04
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 117 EWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
EWH C KC +C + LD C D YCK Y
Sbjct: 21 EWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
Score = 32.7 bits (75), Expect = 0.017
Identities = 13/34 (38%), Positives = 15/34 (44%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
WH C C C + LD C D + YCK Y
Sbjct: 22 WHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>gnl|CDD|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins of
unknown function: This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. Known members of the
Mical-like family includes single LIM domain containing
proteins, Mical (molecule interacting with CasL), pollen
specific protein SF3, Eplin, xin actin-binding
repeat-containing protein 2 (XIRP2), and Ltd-1. The
members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth, and mobility. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 55
Score = 36.2 bits (84), Expect = 0.001
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDS 134
C CG V ++ L G +HR CF+C++C+ TL
Sbjct: 1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLP 37
Score = 31.6 bits (72), Expect = 0.039
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDS 237
C CG V ++ L G ++H+ CF C C L
Sbjct: 1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLP 37
>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 = 35.9 bits (83), Expect = 0.001
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C +C ++ + V K WHR+CF C +C+K+L +K YC C+
Sbjct: 1 CSKCNKIINSG-GVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKP-YCADCF 52
Score = 31.7 bits (72), Expect = 0.034
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 217 KGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
K WH++CF+C C + L + D++ YC C+
Sbjct: 16 KNEPWHRECFTCTNCSKSL-AGQRFTSRDEKPYCADCF 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 = 35.5 bits (82), Expect = 0.001
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 220 MWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
+WH++C C CK PL++ C DK++YCK Y
Sbjct: 20 LWHERCLQCASCKEPLET--TCFYRDKKLYCKEDY 52
Score = 29.4 bits (66), Expect = 0.28
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 116 SEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
S WH +C +C C + L++ C DK +YCK Y
Sbjct: 19 SLWHERCLQCASCKEPLET--TCFYRDKKLYCKEDY 52
>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 = 35.6 bits (82), Expect = 0.002
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 99 PRCGG---VVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
PRC G ++F+ E A+ WH K F C DC+ L DK + CK CY
Sbjct: 1 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPV-CKPCY 55
Score = 30.2 bits (68), Expect = 0.13
Identities = 22/64 (34%), Positives = 28/64 (43%), Gaps = 20/64 (31%)
Query: 202 PRCGGA---VFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIY--------C 250
PRC G +F+ E A+ WH + F C C D++LA EIY C
Sbjct: 1 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDC----DNILA-----GEIYVMVNDKPVC 51
Query: 251 KACY 254
K CY
Sbjct: 52 KPCY 55
>gnl|CDD|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6. The first LIM
domain of Lhx6. Lhx6 is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as the
pituitary gland and the pancreas. Lhx6 functions in the
brain and nervous system. It is expressed at high
levels in several regions of the embryonic mouse CNS,
including the telencephalon and hypothalamus, and the
first branchial arch. Lhx6 is proposed to have a role in
patterning of the mandible and maxilla, and in signaling
during odontogenesis. In brain sections, knockdown of
Lhx6 gene blocks the normal migration of neurons to the
cortex. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 35.4 bits (81), Expect = 0.002
Identities = 17/54 (31%), Positives = 25/54 (46%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C CG + +WH +C C+VC+ L +C +KEI+CK Y
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
Score = 33.8 bits (77), Expect = 0.007
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C CG + + WH +C +C C +L N+C +K+I+CK Y
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
>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 = 35.1 bits (80), Expect = 0.002
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 201 CPRCGGAVFAAEQ-QLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C RCG ++A++ + A+G +H CF+C CKR L + ++++ C+ Y
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55
Score = 33.5 bits (76), Expect = 0.008
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C RCG ++A++ V A+G+ +H CF C C + L + ++ + C+ Y
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55
>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 = 35.0 bits (81), Expect = 0.003
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNK 130
C +CG + + V A G +H CF C DC K
Sbjct: 1 CAKCGKPI-TGQFVRALGDVYHLDCFTCHDCGK 32
Score = 28.0 bits (63), Expect = 0.95
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLDS 237
C +CG + Q + A G ++H CF+C+ C +P+ S
Sbjct: 1 CAKCGKPI--TGQFVRALGDVYHLDCFTCHDCGKPVAS 36
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 34.7 bits (80), Expect = 0.003
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 201 CPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCKRPL--DSVLACDGPDKEIYCKACY 254
C CG A +++ KG WH++CF C CK+P+ S + D ++YC CY
Sbjct: 1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDD---DVYCVPCY 54
Score = 34.7 bits (80), Expect = 0.004
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 98 CPRCGGVVFAAEQVLA-KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C CG + A + + KG +WH KCF C +C + + + + D D+YC CY
Sbjct: 1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGT-KSFIPKDDDVYCVPCY 54
>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b. The first LIM
domain of Lmx1b: Lmx1b belongs to the LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. In mouse, Lmx1b
functions in the developing limbs and eyes, the kidneys,
the brain, and in cranial mesenchyme. The disruption of
Lmx1b gene results kidney and limb defects. In the
brain, Lmx1b is important for generation of
mesencephalic dopamine neurons and the differentiation
of serotonergic neurons. In the mouse eye, Lmx1b
regulates anterior segment (cornea, iris, ciliary body,
trabecular meshwork, and lens) development. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 34.7 bits (80), Expect = 0.003
Identities = 14/34 (41%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
WH++C C+VC++PL +C D+++YCK Y
Sbjct: 21 WHEECLQCSVCQQPL--TTSCYFRDRKLYCKQDY 52
Score = 25.8 bits (57), Expect = 4.7
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 115 GSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
WH +C +C C + L +C D+ +YCK Y
Sbjct: 18 ERSWHEECLQCSVCQQPLT--TSCYFRDRKLYCKQDY 52
>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like
family. The first LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 58
Score = 34.9 bits (81), Expect = 0.003
Identities = 13/42 (30%), Positives = 15/42 (35%), Gaps = 9/42 (21%)
Query: 201 CPRCGG-------AVFAAEQQLAKGTMWHKQCFSCNVCKRPL 235
C +C AVFA + WH CF C C L
Sbjct: 1 CEKCKEPINPGEVAVFAER--AGEDACWHPGCFVCETCNELL 40
Score = 33.3 bits (77), Expect = 0.012
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 9/42 (21%)
Query: 98 CPRCGG-------VVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
C +C VFA + + WH CF C CN+ L
Sbjct: 1 CEKCKEPINPGEVAVFAER--AGEDACWHPGCFVCETCNELL 40
>gnl|CDD|188799 cd09415, LIM1_Prickle, The first LIM domain of Prickle. The first
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4. The
best characterized is prickle 1 and prickle 2 which are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. Mutations in
prickle 1 have been linked to progressive myoclonus
epilepsy. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 34.5 bits (80), Expect = 0.004
Identities = 15/35 (42%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 200 GCPRCGG--AVFAAEQQLAKGTMWHKQCFSCNVCK 232
G GG AVFA + G WH CF C+ CK
Sbjct: 5 GEQISGGDIAVFA--SRAGPGACWHPACFVCSTCK 37
Score = 25.7 bits (57), Expect = 5.9
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 97 GCPRCGG--VVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
G GG VFA+ G+ WH CF C C + L
Sbjct: 5 GEQISGGDIAVFASR--AGPGACWHPACFVCSTCKELL 40
>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2. The second LIM
domain of Lhx2: Lhx2 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. The Lhx2 protein has been shown to bind to
the mouse M71 olfactory receptor promoter. Similar to
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 59
Score = 34.7 bits (79), Expect = 0.004
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
C RC + A+E V+ A+ +H CF C CNK L + + D +YC+
Sbjct: 5 CARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCR 56
Score = 31.6 bits (71), Expect = 0.050
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCK 251
C RC + A+E + A+ ++H CF+C C + L + D +YC+
Sbjct: 5 CARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCR 56
>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 = 34.2 bits (79), Expect = 0.004
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 198 GEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKAC 253
G C C V E A G +H +CF C+VC++P KE C+ C
Sbjct: 1 GTKCDSCQDFV-EGEVVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKECLCQKC 55
Score = 32.3 bits (74), Expect = 0.022
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 1/56 (1%)
Query: 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTC 150
G C C V E V A G +H KCF C C + + K+ C+ C
Sbjct: 1 GTKCDSCQDFV-EGEVVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKECLCQKC 55
>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 = 34.2 bits (79), Expect = 0.005
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL-DSINACDGPDKDIYCKTCY 151
C C + + A G+ WH +CF+C C K + + + G D Y K+CY
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDP--YHKSCY 53
Score = 32.6 bits (75), Expect = 0.019
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL 235
C C + A G +WH +CF C+ C++P+
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPI 35
>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain
Kinase 2). The first LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, altering the rate of actin depolymerization.
LIMK activity is activated by phosphorylation of a
threonine residue within the activation loop of the
kinase by p21-activated kinases 1 and 4 and by Rho
kinase. LIMKs can function in both cytoplasm and
nucleus. Both LIMK1 and LIMK2 can act in the nucleus to
suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2
is expressed in all tissues. While LIMK1 localizes
mainly at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 34.1 bits (78), Expect = 0.005
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL 235
C CGG + + WH CF C+VC+ L
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL 35
Score = 32.9 bits (75), Expect = 0.015
Identities = 11/35 (31%), Positives = 14/35 (40%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
C CGG + + WH CF+C C L
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL 35
>gnl|CDD|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein
Lost in Neoplasm (Eplin). The Lim domain of Epithelial
Protein Lost in Neoplasm (Eplin): Epithelial Protein
Lost in Neoplasm is a cytoskeleton-associated tumor
suppressor whose expression inversely correlates with
cell growth, motility, invasion and cancer mortality.
Eplin interacts and stabilizes F-actin filaments and
stress fibers, which correlates with its ability to
suppress anchorage independent growth. In epithelial
cells, Eplin is required for formation of the F-actin
adhesion belt by binding to the E-cadherin-catenin
complex through alpha-catenin. Eplin is expressed in two
isoforms, a longer Eplin-beta and a shorter Eplin-alpha.
Eplin-alpha mRNA is detected in various tissues and cell
lines, but is absent or down regulated in cancer cells.
As in other LIM domains, this domain family is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 33.7 bits (77), Expect = 0.007
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
C C V+ E+++A +H CF+C CN L S+ +IYCK
Sbjct: 1 CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKL-SLGTYASLHGNIYCK 50
Score = 31.8 bits (72), Expect = 0.042
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCK 251
C C V+ E+ +A ++H CF C+ C L S+ IYCK
Sbjct: 1 CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKL-SLGTYASLHGNIYCK 50
>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 = 33.8 bits (78), Expect = 0.007
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 201 CPRC-----GGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C +C G ++ + + +L G WH++CF C C P + C D + YC+ Y
Sbjct: 1 CRKCGLEIEGKSISSKDGEL-SG-QWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
Score = 33.8 bits (78), Expect = 0.007
Identities = 12/34 (35%), Positives = 14/34 (41%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
WHR+CF C C C D YC+ Y
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>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 = 33.4 bits (77), Expect = 0.009
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPL 235
C RC + A+E + A+ ++H CF+C C +PL
Sbjct: 5 CARCHLGISASELVMRARDLVFHLNCFTCATCNKPL 40
Score = 32.6 bits (75), Expect = 0.018
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 96 KGCPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTL 132
K C RC + A+E V+ A+ +H CF C CNK L
Sbjct: 3 KRCARCHLGISASELVMRARDLVFHLNCFTCATCNKPL 40
>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 = 33.6 bits (77), Expect = 0.010
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 114 KGSEWHRKCFKCRDCNKTL-DSINACDGPDKDIYCKTCY 151
K WH CFKC C ++L D A D+D+ C CY
Sbjct: 22 KDRHWHEGCFKCFKCQRSLVDKPFAAK--DEDLLCTECY 58
Score = 33.6 bits (77), Expect = 0.011
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 221 WHKQCFSCNVCKRPL-DSVLACDGPDKEIYCKACY 254
WH+ CF C C+R L D A D+++ C CY
Sbjct: 26 WHEGCFKCFKCQRSLVDKPFAAK--DEDLLCTECY 58
>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 = 33.5 bits (77), Expect = 0.011
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 98 CPRCGGVVFAAEQVLAK-----GSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C C + E + WH CF+C C + L + C D+ IYC+ Y
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVHDDQ-IYCERHY 58
Score = 32.0 bits (73), Expect = 0.036
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 201 CPRCGG-------AVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKAC 253
C C AV A + + +WH CF C+ C+ L + C D+ IYC+
Sbjct: 1 CGGCSEPLKYGELAVTAP--KFGESLLWHPACFRCSTCEELLVDLTYCVHDDQ-IYCERH 57
Query: 254 Y 254
Y
Sbjct: 58 Y 58
>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 = 33.5 bits (76), Expect = 0.012
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 201 CPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYGK 256
C C + +++ KG WH+ CF C C++P+ + + D + +C CY K
Sbjct: 1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTK-SFIPKDNQNFCVPCYEK 56
Score = 29.2 bits (65), Expect = 0.30
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 114 KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKK 154
KG+ WH CF C+ C + + + + D +C CY K+
Sbjct: 18 KGNSWHETCFICQRCQQPIGT-KSFIPKDNQNFCVPCYEKQ 57
>gnl|CDD|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like
proteins. The second LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 32.7 bits (75), Expect = 0.015
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C CG ++ E +L A G +H CF+C CN+ LD + + +IYC Y
Sbjct: 1 CAVCGHLIM--EMILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
Score = 29.6 bits (67), Expect = 0.18
Identities = 15/39 (38%), Positives = 17/39 (43%)
Query: 216 AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
A G +H CF C VC LD V + IYC Y
Sbjct: 15 ALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
>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 = 33.1 bits (75), Expect = 0.016
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 201 CPRCGGAVFAAEQ-QLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C RCG + + + + AKG ++H CF+C CKR L + ++++ C+ Y
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55
Score = 30.4 bits (68), Expect = 0.12
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C RCG + + + V AKG+ +H CF C C + L + ++ + C+ Y
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55
>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein
SF3. The second Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 61
Score = 32.8 bits (75), Expect = 0.016
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKC 125
C CG V+ E+V +G+ +H+ CFKC
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKC 28
Score = 31.7 bits (72), Expect = 0.055
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCN--VCKRPLDSVLACDGPDKEIYCKACYGKNF 258
C CG V+ E+ +GT +HK CF C+ C + A +G +YCK + + F
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEG---RLYCKHHHSQLF 57
Query: 259 GPKG 262
KG
Sbjct: 58 KEKG 61
>gnl|CDD|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2. The
first LIM domain of Prickle 2: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts with
Dishevelled, thereby modulating Frizzled/Dishevelled
activity and PCP signaling. Four forms of prickles have
been identified: prickle 1-4. The best characterized is
prickle 1 and prickle 2 which are differentially
expressed. While prickle 1 is expressed in fetal heart
and hematological malignancies, prickle 2 is found in
fetal brain, adult cartilage, pancreatic islet, and some
types of timorous cells. Mutations in prickle 1 have
been linked to progressive myoclonus epilepsy. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 33.0 bits (75), Expect = 0.017
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 10/57 (17%)
Query: 201 CPRCGG-------AVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYC 250
C +CGG AVFA+ + G WH QCF C+VC L ++ D +IYC
Sbjct: 1 CEQCGGQINGGDIAVFAS--RAGHGVCWHPQCFVCSVCNELLVDLIYF-YQDGKIYC 54
Score = 27.2 bits (60), Expect = 1.7
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 98 CPRCGG-------VVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
C +CGG VFA+ G WH +CF C CN+ L
Sbjct: 1 CEQCGGQINGGDIAVFASRA--GHGVCWHPQCFVCSVCNELL 40
>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 = 32.8 bits (75), Expect = 0.018
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 201 CPRCGGAVFAAEQQLA-KGTMWH--KQCFSCNVCKRPL 235
C CG + Q++A G WH ++CF C+ CK+ L
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSL 38
Score = 26.2 bits (58), Expect = 3.8
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 98 CPRCGGVVFAAEQVLA-KGSEWH--RKCFKCRDCNKTL 132
C CG + Q +A G WH +CF C +C K+L
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSL 38
>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like
proteins. The first LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 32.4 bits (74), Expect = 0.021
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPL 235
C +CG V+ A Q A G ++H CF+C C R L
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL 36
Score = 28.9 bits (65), Expect = 0.37
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTL 132
C +CG V+ A Q A G+ +H CF C C +TL
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL 36
>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 = 32.9 bits (75), Expect = 0.023
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
C CG ++ + + A S+WH CF+C +C +L
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASL 56
Score = 26.4 bits (58), Expect = 4.8
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C CG +++ + A + WH CF C C L D ++CK Y
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYY--EKDGRLFCKKDY 73
>gnl|CDD|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting
with CasL). The LIM domain of Mical (molecule
interacting with CasL): MICAL is a large, multidomain,
cytosolic protein with a single LIM domain, a calponin
homology (CH) domain and a flavoprotein monooxygenase
domain. In Drosophila, MICAL is expressed in axons,
interacts with the neuronal A (PlexA) receptor and is
required for Semapho-rin 1a (Sema-1a)-PlexA-mediated
repulsive axon guidance. The LIM domain and calporin
homology domain are known for interactions with the
cytoskeleton, cytoskeletal adaptor proteins, and other
signaling proteins. The flavoprotein monooxygenase (MO)
is required for semaphorin-plexin repulsive axon
guidance during axonal pathfinding in the Drosophila
neuromuscular system. In addition, MICAL was
characterized to interact with Rab13 and Rab8 to
coordinate the assembly of tight junctions and adherens
junctions in epithelial cells. Thus, MICAL was also
named junctional Rab13-binding protein (JRAB). As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 32.3 bits (74), Expect = 0.023
Identities = 21/52 (40%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSIN-ACDGPDKDIYCK 148
C C V+ E++ A+G +HR CFKC C TL A D D YCK
Sbjct: 1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCK 52
Score = 26.5 bits (59), Expect = 3.4
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVC 231
C C V+ E+ A+G +H+ CF C+ C
Sbjct: 1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYC 31
>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 = 32.3 bits (74), Expect = 0.027
Identities = 12/37 (32%), Positives = 14/37 (37%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDS 134
C C + G WH CFKC C+K L
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLSC 37
Score = 31.6 bits (72), Expect = 0.040
Identities = 10/37 (27%), Positives = 13/37 (35%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDS 237
C C ++ G WH CF C C + L
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLSC 37
>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 = 31.9 bits (73), Expect = 0.033
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
C CG + + +LA +WH CFKC++C K L
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVL 35
Score = 29.2 bits (66), Expect = 0.27
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 205 GGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
G A+ A ++Q WH CF C C + L G D + YC+ Y
Sbjct: 11 GQALLALDKQ------WHVWCFKCKECGKVLTGEYM--GKDGKPYCERDY 52
>gnl|CDD|188821 cd09437, LIM3_LPP, The third LIM domain of lipoma preferred partner
(LPP). The third LIM domain of lipoma preferred partner
(LPP): LPP is a member of the zyxin LIM protein family
and contains three LIM zinc-binding domains at the
C-terminal and proline-rich region at the N-terminal.
LPP initially identified as the most frequent
translocation partner of HMGA2 (High Mobility Group A2)
in a subgroup of benign tumors of adipose tissue
(lipomas). It was also shown to be rearranged in a
number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP), Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 68
Score = 32.4 bits (74), Expect = 0.034
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 110 QVLAKGSEWHRKCFKCRDCNKTLDSI---NACDGPDKDIYCKTCYGKK 154
+V+A +H +C+KC DC L S C D + CK+C K+
Sbjct: 19 RVVALDRSFHVQCYKCEDCGLLLSSEAEGRGCYPLDDHVLCKSCNAKR 66
>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 = 31.8 bits (73), Expect = 0.034
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 99 PRCGG---VVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
PRC ++F+ E A+G WH K F C C++ L
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPL 37
Score = 27.2 bits (61), Expect = 1.4
Identities = 21/59 (35%), Positives = 25/59 (42%), Gaps = 10/59 (16%)
Query: 202 PRCGGA---VFAAEQQLAKGTMWHKQCFSCNVCKRPLDS---VLACDGPDKEIYCKACY 254
PRC +F+ E A+G WH + F C C PL VL P YC CY
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKP----YCLDCY 55
>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 = 32.0 bits (73), Expect = 0.035
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 110 QVLAKGSEWHRKCFKCRDCNKTLDSINACDG--P-DKDIYCKTC 150
+++A +H C+KC DC L S + G P D + CK+C
Sbjct: 19 RIVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPLDGHLLCKSC 62
>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 = 31.2 bits (71), Expect = 0.053
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 99 PRCGG---VVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
PRC ++FA E A+G WH K F C +C L
Sbjct: 1 PRCSACDEIIFADECTEAEGRHWHMKHFCCFECECQL 37
Score = 29.3 bits (66), Expect = 0.29
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 202 PRCGGA---VFAAEQQLAKGTMWHKQCFSCNVCKRPL 235
PRC +FA E A+G WH + F C C+ L
Sbjct: 1 PRCSACDEIIFADECTEAEGRHWHMKHFCCFECECQL 37
>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 = 31.3 bits (71), Expect = 0.062
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
WH KC KC DC L + C +YCK
Sbjct: 24 WHSKCLKCVDCQAQLT--DKCFSRGGQVYCK 52
Score = 28.2 bits (63), Expect = 0.64
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDKEIYCKA 252
WH +C C C+ L C ++YCK
Sbjct: 24 WHSKCLKCVDCQAQLTD--KCFSRGGQVYCKE 53
>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 = 31.1 bits (71), Expect = 0.072
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 201 CPRCGGAVFAAEQQ-LAKGTMWHKQCFSCNVCKRPL 235
C RC E+ + G ++H+QCF C C +P
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPF 36
Score = 31.1 bits (71), Expect = 0.078
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 98 CPRCGGVVFAAEQ-VLAKGSEWHRKCFKCRDC 128
C RC E+ V + G +H +CF C C
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQC 32
>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 = 30.9 bits (70), Expect = 0.075
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKD-IYCKTCY 151
C CG + +L+ + CF+CR C++ + + K ++C +C+
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDITDLK--YAKTKRGLFCMSCH 53
Score = 25.9 bits (57), Expect = 4.7
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKE-IYCKACY 254
C CG + L+ + CF C C R + + K ++C +C+
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDITDLK--YAKTKRGLFCMSCH 53
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription. Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 52
Score = 30.9 bits (70), Expect = 0.081
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
WH KC KC DC L + C + +YCK
Sbjct: 21 WHAKCLKCNDCGAQLT--DKCFARNGHVYCK 49
Score = 28.5 bits (64), Expect = 0.48
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDKEIYCK 251
WH +C CN C L C + +YCK
Sbjct: 21 WHAKCLKCNDCGAQLTD--KCFARNGHVYCK 49
>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 = 31.1 bits (70), Expect = 0.086
Identities = 15/46 (32%), Positives = 23/46 (50%)
Query: 216 AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYGKNFGPK 261
A G +H QCF+C VCK PL+ + +C Y + + P+
Sbjct: 15 ATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAPR 60
>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The second LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 30.6 bits (69), Expect = 0.096
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 216 AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYC 250
A G +H CF+C VC R LD + +I+C
Sbjct: 15 ATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHC 49
Score = 26.8 bits (59), Expect = 2.1
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 113 AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYC 147
A G +H CF C C+++LD I I+C
Sbjct: 15 ATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHC 49
>gnl|CDD|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like
family. The first LIM domain of Enigma-like family: The
Enigma LIM domain family is comprised of three members:
Enigma, ENH, and Cypher (mouse)/ZASP (human). These
subfamily members contain a single PDZ domain at the
N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and the
second LIM domain interacts with the receptor tyrosine
kinase Ret and the adaptor protein APS. Thus Enigma is
implicated in signal transduction processes, such as
mitogenic activity, insulin related actin organization,
and glucose metabolism. The second member, ENH protein,
was first identified in rat brain. It has been shown
that ENH interacts with protein kinase D1 (PKD1) via its
LIM domains and forms a complex with PKD1 and the
alpha1C subunit of cardiac L-type voltage-gated calcium
channel in rat neonatal cardiomyocytes. The N-terminal
PDZ domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 30.4 bits (69), Expect = 0.10
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 111 VLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
++A G WH + F C C+ +L I + +YC+ CY
Sbjct: 13 LVALGRSWHPEEFTCSHCHCSLAEIGFVE-EKGSLYCELCY 52
Score = 27.3 bits (61), Expect = 1.5
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 7/43 (16%)
Query: 215 LAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKE---IYCKACY 254
+A G WH + F+C+ C LA G +E +YC+ CY
Sbjct: 14 VALGRSWHPEEFTCSHCH----CSLAEIGFVEEKGSLYCELCY 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 = 30.4 bits (69), Expect = 0.10
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 216 AKGTMWHKQCFSCNVCKRP 234
A T WH +CF C C +P
Sbjct: 15 ALNTQWHPECFVCRECHKP 33
Score = 28.8 bits (65), Expect = 0.43
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 113 AKGSEWHRKCFKCRDCNK 130
A ++WH +CF CR+C+K
Sbjct: 15 ALNTQWHPECFVCRECHK 32
>gnl|CDD|188819 cd09435, LIM3_Zyxin, The third LIM domain of Zyxin. The third LIM
domain of Zyxin: Zyxin exhibits three copies of the LIM
domain, an extensive proline-rich domain and a nuclear
export signal. Localized at sites of cellsubstratum
adhesion in fibroblasts, Zyxin interacts with
alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 67
Score = 30.6 bits (69), Expect = 0.12
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 110 QVLAKGSEWHRKCFKCRDCNKTLDSI----NACDGPDKDIYCKTCY 151
+V+A +H KC+KC DC + L SI N C D + C C+
Sbjct: 19 RVVALEKNFHMKCYKCEDCGRPL-SIEADDNGCFPLDGHVLCMKCH 63
>gnl|CDD|188804 cd09420, LIM3_Prickle, The third LIM domain of Prickle. The third
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Two
forms of prickles have been identified; namely prickle 1
and prickle 2. Prickle 1 and prickle 2 are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 30.5 bits (69), Expect = 0.14
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 199 EGCPRCGGAVFAAEQQLA-KGTMWH--KQCFSCNVCKRPLDSVLACDGPDK--EIYC-KA 252
E C CG + + Q+ G WH ++CF C CK+ L L K +IYC +A
Sbjct: 1 EYCDTCGEHIGVDQGQMTYDGQHWHATEKCFCCAQCKKSL---LGRPFLPKQGQIYCSRA 57
Query: 253 C 253
C
Sbjct: 58 C 58
>gnl|CDD|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3. The
first LIM domain of Prickle 3/LIM domain only 6 (LM06):
Prickle contains three C-terminal LIM domains and a
N-terminal PET domain. Prickles have been implicated in
roles of regulating tissue polarity or planar cell
polarity (PCP). PCP establishment requires the
conserved Frizzled/Dishevelled PCP pathway. Prickle
interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4. The
best characterized is prickle 1 and prickle 2 which are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. Mutations in
prickle 1 have been linked to progressive myoclonus
epilepsy. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 30.2 bits (68), Expect = 0.17
Identities = 17/34 (50%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 204 CGG--AVFAAEQQLAKGTMWHKQCFSCNVCKRPL 235
CGG AVFA+ L G WH QCF C C+ L
Sbjct: 9 CGGDIAVFASRAGL--GACWHPQCFQCASCQELL 40
Score = 27.5 bits (61), Expect = 1.6
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 101 CGG--VVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
CGG VFA+ L G+ WH +CF+C C + L
Sbjct: 9 CGGDIAVFASRAGL--GACWHPQCFQCASCQELL 40
>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 = 30.0 bits (68), Expect = 0.17
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 221 WHKQCFSCNVCKRPL 235
WHK+CF C CK+ L
Sbjct: 20 WHKECFVCTGCKKQL 34
Score = 26.9 bits (60), Expect = 2.0
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
WH++CF C C K L + D+ YC C+
Sbjct: 20 WHKECFVCTGCKKQL-AGQRFTSRDEYPYCVDCF 52
>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost
in Neoplasm (Eplin) like proteins. The Lim domain of
Epithelial Protein Lost in Neoplasm (Eplin) like
proteins: This family contains Epithelial Protein Lost
in Neoplasm in Neoplasm (Eplin), xin actin-binding
repeat-containing protein 2 (XIRP2) and a group of
protein with unknown function. The members of this
family all contain a single LIM domain. Epithelial
Protein Lost in Neoplasm is a cytoskeleton-associated
tumor suppressor whose expression inversely correlates
with cell growth, motility, invasion and cancer
mortality. Eplin interacts and stabilizes F-actin
filaments and stress fibers, which correlates with its
ability to suppress anchorage independent growth. In
epithelial cells, Eplin is required for formation of the
F-actin adhesion belt by binding to the
E-cadherin-catenin complex through alpha-catenin. Eplin
is expressed in two isoforms, a longer Eplin-beta and a
shorter Eplin-alpha. Eplin-alpha mRNA is detected in
various tissues and cell lines, but is absent or down
regulated in cancer cells. Xirp2 contains a LIM domain
and Xin re peats for binding to and stabilising F-actin.
Xirp2 is expressed in muscles and is significantly
induced in the heart in response to systemic
administration of angiotensin II. Xirp2 is an important
effector of the Ang II signaling pathway in the heart.
The expression of Xirp2 is activated by myocyte enhancer
factor (MEF)2A, whose transcriptional activity is
stimulated by angiotersin II. Thus, Xirp2 plays
important pathological roles in the angiotensin II
induced hypertension. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 29.8 bits (67), Expect = 0.17
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C C V+ E+++A +H+ CF+C CN L S+ IYCK +
Sbjct: 1 CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKL-SLGNYASLHGRIYCKPHF 53
Score = 27.8 bits (62), Expect = 0.83
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVC--KRPLDSVLACDGPDKEIYCKACY 254
C C V+ E+ +A +HK CF C C K L + + G IYCK +
Sbjct: 1 CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHG---RIYCKPHF 53
>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 = 29.9 bits (67), Expect = 0.17
Identities = 13/31 (41%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
WH KC KC DC L C +YCK
Sbjct: 24 WHSKCLKCSDCQTQL--AEKCFSRGDSVYCK 52
Score = 26.4 bits (58), Expect = 3.6
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDKEIYCK 251
WH +C C+ C+ L C +YCK
Sbjct: 24 WHSKCLKCSDCQTQLAE--KCFSRGDSVYCK 52
>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain only
protein 4). The second LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact with
Smad proteins, and associate with the promoter of the
PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential role
for LMO4 as a negative regulator of BRCA1 in sporadic
breast cancer. LMO4 also forms complex to both ERa
(oestrogen receptor alpha), MTA1 (metastasis tumor
antigen 1), and HDACs (histone deacetylases), implying
that LMO4 is also a component of the MTA1 corepressor
complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 29.8 bits (67), Expect = 0.18
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTL 132
C CG + A+E V+ A+G+ +H KCF C C+ L
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQL 36
Score = 27.1 bits (60), Expect = 2.0
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPL 235
C CG ++ A+E + A+G ++H +CF+C+ C L
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQL 36
>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 = 29.7 bits (67), Expect = 0.18
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLD 236
C C + A ++ L A G WH CF C VC L+
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLE 37
>gnl|CDD|223344 COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA replication,
recombination, and repair].
Length = 273
Score = 32.6 bits (75), Expect = 0.18
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 11/56 (19%)
Query: 179 ISANRPFYNPNTTSIMA--------RKGEGCPRCGGAVFAAEQQLA-KGTMWHKQC 225
+ R F N + R GE C RCG + + +L + T + C
Sbjct: 218 GTTLRDFVNADGKPGYFQQELKVYGRAGEPCRRCGTPI--EKIKLGGRSTFYCPVC 271
Score = 28.4 bits (64), Expect = 4.3
Identities = 7/29 (24%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 95 GKGCPRCGGVVFAAEQVLA-KGSEWHRKC 122
G+ C RCG + + L + + + C
Sbjct: 245 GEPCRRCGTPI--EKIKLGGRSTFYCPVC 271
>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of
proteins with unknown function. This model represents a
LIM domain subfamily of Eplin-like family. This family
shows highest homology to the LIM domains on Eplin and
XIRP2 protein families. Epithelial Protein Lost in
Neoplasm is a cytoskeleton-associated tumor suppressor
whose expression inversely correlates with cell growth,
motility, invasion and cancer mortality. Xirp2 is
expressed in muscles and is an important effector of the
Ang II signaling pathway in the heart. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 29.5 bits (66), Expect = 0.20
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
C C V+ E+++A +H CF C+ CN L S+ + + YCK
Sbjct: 1 CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKL-SLGSYAALHGEFYCK 50
Score = 29.5 bits (66), Expect = 0.26
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVC--KRPLDSVLACDGPDKEIYCK 251
C C V+ E+ +A ++H CF C C K L S A G E YCK
Sbjct: 1 CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHG---EFYCK 50
>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 = 29.3 bits (66), Expect = 0.29
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 108 AEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTC 150
++++ K WH CF+C C K L + D I C C
Sbjct: 12 SKELHHKNRYWHETCFRCAKCYKPLANEPFV-AKDNKILCGKC 53
Score = 27.4 bits (61), Expect = 1.3
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 217 KGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKAC 253
K WH+ CF C C +PL + D +I C C
Sbjct: 18 KNRYWHETCFRCAKCYKPLANEPFV-AKDNKILCGKC 53
>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 = 29.5 bits (66), Expect = 0.29
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 201 CPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C C + + L+ K WH+ CF C+ CK L D+ IYC CY
Sbjct: 5 CEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADR-IYCGNCY 58
Score = 28.7 bits (64), Expect = 0.55
Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 114 KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
K WH CF C C +L D+ IYC CY
Sbjct: 22 KDKHWHEACFLCSKCKISLVDKPFGSKADR-IYCGNCY 58
>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 = 29.2 bits (65), Expect = 0.30
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
WHK+CF C CK+ L S D YC C+
Sbjct: 20 WHKECFVCTGCKKQL-SGQRFTSRDDFAYCLNCF 52
Score = 26.1 bits (57), Expect = 4.8
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
WH++CF C C K L S D YC C+
Sbjct: 20 WHKECFVCTGCKKQL-SGQRFTSRDDFAYCLNCF 52
>gnl|CDD|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH). The
second LIM domain of Arrowhead (AWH): Arrowhead belongs
to the LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Members of LHX family are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs such as the pituitary
gland and the pancreas. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 29.3 bits (66), Expect = 0.32
Identities = 12/36 (33%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 201 CPRCGGAVFAAEQ-QLAKGTMWHKQCFSCNVCKRPL 235
C +C + A++ + A+ ++H CF+C+ CKR L
Sbjct: 1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQL 36
>gnl|CDD|188719 cd09333, LIM3_PINCH, The third LIM domain of protein PINCH. The
third LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 51
Score = 28.9 bits (65), Expect = 0.32
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C +C ++ + + KG +H F C +C K L + ++YC C+
Sbjct: 1 CQKCHAII-EEQHLKFKGDPYHPYHFNCANCGKELTA--DARELKGELYCLRCH 51
>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM
domains protein 1 (FHL1). The third LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 29.0 bits (65), Expect = 0.35
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
WH +CF C+ C + L D+ YC CY
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQ-YYCVDCY 52
Score = 28.6 bits (64), Expect = 0.56
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
WH +CF C C+K L D+ YC CY
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQ-YYCVDCY 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 = 29.8 bits (67), Expect = 0.38
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 199 EGCPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
E C CG + + + A G ++H CF+C+ C++ L K YC+ CY
Sbjct: 32 ELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKP-YCEECY 87
Score = 29.1 bits (65), Expect = 0.68
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 2/62 (3%)
Query: 91 KAAPGKGCPRCG-GVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKT 149
+AA + C CG + V A G +H CF C C + L K YC+
Sbjct: 27 EAATNELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKP-YCEE 85
Query: 150 CY 151
CY
Sbjct: 86 CY 87
>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 = 29.1 bits (65), Expect = 0.41
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 201 CPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCKRPL-DSVLACDGPDKEIYCKACYGKNF 258
C C + + L+ K WH+ CF C CK L D A ++ + C CY +
Sbjct: 5 CEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFA--AKEEHLLCTECYSNEY 62
Score = 27.2 bits (60), Expect = 2.1
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 9/46 (19%)
Query: 114 KGSEWHRKCFKCRDCNKTLDSINACDGP----DKDIYCKTCYGKKW 155
K WH CF C C +L D P ++ + C CY ++
Sbjct: 22 KDRHWHESCFHCFQCKNSL-----VDKPFAAKEEHLLCTECYSNEY 62
>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM
domains protein (FHL). The fourth LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 interacts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 56
Score = 28.8 bits (65), Expect = 0.41
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 117 EWHRKCFKCRDCNKTLDSINACDGPD-KDIYCKTC 150
+WH CF C C+ +L + +I C C
Sbjct: 23 QWHSDCFNCGKCSVSL--VGQGFLTQRDEILCPEC 55
>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 = 28.9 bits (65), Expect = 0.43
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 201 CPRCGGAVFAAEQQL--AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
C +C G + + + A G +H CF+C C R + E+YC Y
Sbjct: 1 CAKCQGVI---TEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
Score = 27.0 bits (60), Expect = 1.8
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYC 147
C +C GV+ + A G +H CF C C + + + ++YC
Sbjct: 1 CAKCQGVI-TEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYC 49
>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 = 28.7 bits (64), Expect = 0.46
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 217 KGTMWHKQCFSCNVCKRPL 235
+G WH+ CF C C++P+
Sbjct: 18 EGNEWHETCFVCQSCQQPI 36
Score = 28.3 bits (63), Expect = 0.64
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 114 KGSEWHRKCFKCRDCNKTL 132
+G+EWH CF C+ C + +
Sbjct: 18 EGNEWHETCFVCQSCQQPI 36
>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX
protein family. The second LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved members
of this family. Proteins in this group are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Isl-1 is one of the LHX proteins
isolated originally by virtue of its ability to bind DNA
sequences from the 5'-flanking region of the rat insulin
gene in pancreatic insulin-producing cells. Mice
deficient in Isl-1 fail to form the dorsal exocrine
pancreas and islet cells fail to differentiate. On the
other hand, Isl-1 takes part in the pituitary
development by activating the gonadotropin-releasing
hormone receptor gene together with LHX3 and
steroidogenic factor 1. Mouse Isl2 is expressed in the
retinal ganglion cells and the developing spinal cord
where it plays a role in motor neuron development. Same
as Isl1, Isl2 may also be able to bind to the insulin
gene enhancer to promote gene activation. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 28.6 bits (64), Expect = 0.50
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPL 235
C +C + + + A+ ++H +CF C+ C R L
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQL 36
Score = 26.6 bits (59), Expect = 2.6
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
C +C + V+ A+ +H +CF+C C++ L + D ++CK
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCK 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 = 28.4 bits (63), Expect = 0.60
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 215 LAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
+A G WH + F+C+ C L V + +YC+ CY
Sbjct: 14 VALGRSWHPEEFTCHYCHTSLADVSFVE-EQNNVYCENCY 52
Score = 27.3 bits (60), Expect = 1.4
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 111 VLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
++A G WH + F C C+ +L ++ + ++YC+ CY
Sbjct: 13 LVALGRSWHPEEFTCHYCHTSLADVSFVE-EQNNVYCENCY 52
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Lhx1 is required for regulating
the vertebrate head organizer, the nervous system, and
female reproductive tract development. During
embryogenesis in the mouse, Lhx1 is expressed early in
mesodermal tissue, then later during urogenital, kidney,
liver, and nervous system development. In the adult,
expression is restricted to the kidney and brain. A
mouse embryos with Lhx1 gene knockout cannot grow normal
anterior head structures, kidneys, and gonads, but with
normally developed trunk and tail morphology. In the
developing nervous system, Lhx1 is required to direct
the trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 28.2 bits (63), Expect = 0.61
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKT 149
WH KC +C DC L C + +YC+
Sbjct: 21 WHAKCVQCCDCKCPLT--EKCFSREGKLYCRN 50
Score = 25.1 bits (55), Expect = 8.1
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDKEIYCK 251
WH +C C CK PL C + ++YC+
Sbjct: 21 WHAKCVQCCDCKCPLTE--KCFSREGKLYCR 49
>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family.
The second LIM domain of Lhx3-Lhx4 family: Lhx3 and
Lhx4 belong to the LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription.Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 56
Score = 28.1 bits (63), Expect = 0.78
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 216 AKGTMWHKQCFSCNVCKRPLDS 237
A+ ++H +CF+C +CKR L++
Sbjct: 17 AQDNVYHLECFACFMCKRQLET 38
>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx). The
second LIM domain of dLMO (Beaderx): dLMO is a nuclear
protein that plays important roles in transcriptional
regulation and development. In Drosophila dLMO modulates
the activity of LIM-homeodomain protein Apterous (Ap),
which regulates the formation of the dorsal-ventral axis
of the Drosophila wing. Biochemical analysis shows that
dLMO protein influences the activity of Apterous by
binding of its cofactor Chip. Further studies shown that
dLMO proteins might function in an evolutionarily
conserved mechanism involved in patterning the
appendages. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 28.3 bits (63), Expect = 0.78
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCN 129
C C + A E V+ A+ + +H +CF C+ CN
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCN 33
>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 = 28.1 bits (63), Expect = 0.82
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 216 AKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254
A G WH + F C CK L + + D + YC+ Y
Sbjct: 15 ALGKTWHPEHFVCAECKTELGTKNFFE-RDGQPYCEKDY 52
Score = 26.1 bits (58), Expect = 3.6
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C C + + V A G WH + F C +C L + N + D YC+ Y
Sbjct: 1 CAACKKPI-VGQVVTALGKTWHPEHFVCAECKTELGTKNFFE-RDGQPYCEKDY 52
>gnl|CDD|218214 pfam04695, Pex14_N, Peroxisomal membrane anchor protein (Pex14p)
conserved region. Family of peroxisomal membrane anchor
proteins which bind the PTS1 (peroxisomal targeting
signal) receptor and are required for the import of
PTS1-containing proteins into peroxisomes. Loss of
functional Pex14p results in defects in both the PTS1
and PTS2-dependent import pathways. Deletion analysis of
this conserved region implicates it in selective
peroxisome degradation. In the majority of members this
region is situated at the N-terminus of the protein.
Length = 79
Score = 28.8 bits (65), Expect = 0.82
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 168 FLQTDGLTEDEI 179
FL++ GLTE+EI
Sbjct: 29 FLESKGLTEEEI 40
>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 = 28.1 bits (62), Expect = 0.84
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL-DSVLACDGPDKEIYCKACY 254
C RC + K T WH CF C C P+ ++V + D E YC+ Y
Sbjct: 1 CGRCQRKILGEVINALKQT-WHVSCFVCVACHNPIRNNVFHLE--DGEPYCETDY 52
Score = 27.7 bits (61), Expect = 0.96
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C RC + E + A WH CF C C+ + + N D + YC+T Y
Sbjct: 1 CGRCQRKILG-EVINALKQTWHVSCFVCVACHNPIRN-NVFHLEDGEPYCETDY 52
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 28.0 bits (62), Expect = 0.89
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 221 WHKQCFSCNVCKRPL-DSVLACDGPDKEIYCKACY 254
+H+ CF C C R L D C D+E+ C CY
Sbjct: 26 YHEHCFRCFRCDRSLADEPFTCQ--DEELLCNDCY 58
>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 = 27.9 bits (62), Expect = 1.1
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 98 CPRCGGVVFAAEQ-VLAKGSEWHRKCFKCRDCNKTLD 133
C CG + A ++ V A + +H +CF C CN L+
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLE 37
Score = 26.0 bits (57), Expect = 4.7
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLD 236
C CG + A ++ + A +H QCF+C C L+
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLE 37
>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 = 27.8 bits (62), Expect = 1.1
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 114 KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGK 153
+GS WH CF C+ C+ L + + IYC C K
Sbjct: 25 EGSSWHDYCFNCKKCSLNL-ANKRFVFHNGQIYCSDCAKK 63
>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 = 27.7 bits (61), Expect = 1.1
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C C V+ ++A G WH + F C C ++ I + +YC+ CY
Sbjct: 1 CATCNQVI-RGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVE-EKGALYCEICY 52
Score = 25.0 bits (54), Expect = 8.9
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 7/43 (16%)
Query: 215 LAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKE---IYCKACY 254
+A G WH + F+C CK S +A G +E +YC+ CY
Sbjct: 14 VALGKSWHPEEFNCAHCK----SSMAYIGFVEEKGALYCEICY 52
>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 = 27.7 bits (61), Expect = 1.2
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL 235
C +C + K T WH CF+C CK P+
Sbjct: 1 CAKCKKKITGEIMHALKMT-WHVHCFTCAACKTPI 34
>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 = 27.6 bits (61), Expect = 1.2
Identities = 12/31 (38%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 118 WHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148
WH C KC DC L C ++YCK
Sbjct: 21 WHSSCLKCADCQMQL--AERCFSRAGNVYCK 49
>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2. The second LIM
domain of Isl2: Isl is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Isl proteins are found in the nucleus and act as
transcription factors or cofactors. Isl1 and Isl2 are
the two conserved members of this family. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Isl2 may be able to bind to the
insulin gene enhancer to promote gene activation. All
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 27.6 bits (61), Expect = 1.2
Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPL 235
C +C +++ + A+ +++H +CF C+VC R L
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQL 36
Score = 26.4 bits (58), Expect = 2.7
Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTL 132
C +C +++ V+ A+ S +H +CF+C C++ L
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQL 36
>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 = 27.4 bits (61), Expect = 1.2
Identities = 18/55 (32%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSI-NACDGPDKDIYCKTCY 151
C CGG + + A WH C KC C L I ++C I CK Y
Sbjct: 1 CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
>gnl|CDD|224909 COG1998, RPS31, Ribosomal protein S27AE [Translation, ribosomal
structure and biogenesis].
Length = 51
Score = 27.4 bits (61), Expect = 1.3
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 9/36 (25%)
Query: 196 RKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVC 231
RK CPRCG VF A+ HK ++C C
Sbjct: 17 RKNRFCPRCGPGVFMAD---------HKDRWACGKC 43
>gnl|CDD|188818 cd09434, LIM4_FHL3, The fourth LIM domain of Four and a half LIM
domains protein 3 (FHL3). The fourth LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 56
Score = 27.4 bits (61), Expect = 1.6
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 117 EWHRKCFKCRDCNKTLDSINACDGPDKD-IYCKTC 150
+WH+ CFKC C+ +L + A PD D I C+ C
Sbjct: 23 QWHQPCFKCSRCSVSL--VGAGFFPDGDQILCRDC 55
Score = 26.6 bits (59), Expect = 3.0
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 221 WHKQCFSCNVCKRPLDSVLACDGPDK-EIYCKAC 253
WH+ CF C+ C L V A PD +I C+ C
Sbjct: 24 WHQPCFKCSRCSVSL--VGAGFFPDGDQILCRDC 55
>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH. The
second LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 26.9 bits (60), Expect = 1.8
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 221 WHKQCFSCNVCKRPL 235
WH CF C +C + L
Sbjct: 20 WHPDCFRCEICNKEL 34
Score = 26.9 bits (60), Expect = 2.2
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 113 AKGSEWHRKCFKCRDCNKTL 132
A + WH CF+C CNK L
Sbjct: 15 AMNNNWHPDCFRCEICNKEL 34
>gnl|CDD|212160 cd11615, SAF_NeuB_like, C-terminal SAF domain of sialic acid
synthetase. Sialic acid synthetase
(N-acetylneuraminate synthase or
N-acetylneuraminate-9-phosphate synthase) catalyzes the
condensation of phosphoenolpyruvate with
N-acetylmannosamine (ManNAc, in bacteria) or
N-acetylmannosamine-6-phosphate (ManNAc-6P, in
mammals), to yield N-acetylneuramic acid (NeuNAc) or
N-acetylneuramic acid-9-phosphate (NeuNAc-9P),
respectively. The N-terminal NeuB domain, a
TIM-barrel-like structure, contains the catalytic site,
the function of the SAF domain is not as clear. It may
participate in domain-swapped dimerization and play a
role in binding the substrate, in either domain-swapped
dimers or by directly interacting with the N-terminal
domain. Also included in the family are PEP-sugar
pyruvyltransferases known as spore coat polysaccharide
biosynthesis proteins (SpsE).
Length = 58
Score = 26.9 bits (61), Expect = 1.9
Identities = 10/27 (37%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 38 RSVV--KDLRSGDRVSRVNIRKKRPPD 62
RS+V +D+++G+ ++ N+R KRP
Sbjct: 2 RSLVAARDIKAGEVLTEENLRVKRPGG 28
>gnl|CDD|188820 cd09436, LIM3_TRIP6, The third LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The third LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 66
Score = 27.3 bits (60), Expect = 1.9
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 110 QVLAKGSEWHRKCFKCRDCNKTLDSIN--ACDGPDKDIYCKTC 150
+++A ++H +C++C DC L + C D I CK C
Sbjct: 19 RIVALDRDFHVQCYRCEDCGSLLSEGDNQGCYPLDGHILCKAC 61
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes, such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. The second member, ENH protein, was
first identified in rat brain. It has been shown that
ENH interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 27.1 bits (60), Expect = 2.0
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL-DSVLACDGPDKEIYCKACY 254
C RC + K T WH CF C CK+P+ +S+ + D E YC+ Y
Sbjct: 1 CARCHKKILGEVMHALKQT-WHVSCFVCAACKQPIGNSLFHME--DGEPYCEKDY 52
>gnl|CDD|165005 PHA02610, uvsY.-2, hypothetical protein; Provisional.
Length = 53
Score = 27.1 bits (60), Expect = 2.1
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 228 CNVCKRPLDSVLACDGPDKEIYCKACY 254
C VCK+P++ L + ++ CY
Sbjct: 4 CVVCKQPIEKALVVETEKGPVHPGPCY 30
>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The second LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Lhx1 is required for regulating
the vertebrate head organizer, the nervous system, and
female reproductive tract development. During
embryogenesis in the mouse, Lhx1 is expressed early in
mesodermal tissue, then later during urogenital, kidney,
liver, and nervous system development. In the adult,
expression is restricted to the kidney and brain. A
mouse embryos with Lhx1 gene knockout cannot grow normal
anterior head structures, kidneys, and gonads, but with
normally developed trunk and tail morphology. In the
developing nervous system, Lhx1 is required to direct
the trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 56
Score = 26.6 bits (59), Expect = 2.5
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 216 AKGTMWHKQCFSCNVCKRPLDS 237
A+ ++H CF+C VC++ L +
Sbjct: 17 ARDKVFHLNCFTCMVCRKQLST 38
>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The second LIM
domain of LMO1 and LMO3 (LIM domain only protein 1 and
3): LMO1 and LMO3 are highly homologous and belong to
the LMO protein family. LMO1 and LMO3 are nuclear
protein that plays important roles in transcriptional
regulation and development. As LIM domains lack
intrinsic DNA-binding activity, nuclear LMOs are
involved in transcriptional regulation by forming
complexes with other transcription factors or cofactors.
For example, LMO1 interacts with the the bHLH domain of
bHLH transcription factor, TAL1 (T-cell acute
leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the
expression of TAL1/SCL target genes. LMO3 facilitates
p53 binding to its response elements, which suggests
that LMO3 acts as a co-repressor of p53, suppressing
p53-dependent transcriptional regulation. In addition,
LMO3 interacts with neuronal transcription factor, HEN2,
and acts as an oncogene in neuroblastoma. Another
binding partner of LMO3 is calcium- and integrin-binding
protein CIB, which binds via the second LIM domain
(LIM2) of LMO3. One role of the CIB/LMO3 complex is to
inhibit cell proliferation. Although LMO1 and LMO3 are
highly homologous proteins, they play different roles in
the regulation of the pituitary glycoprotein hormone
alpha-subunit (alpha GSU) gene. Alpha GSU promoter
activity was markedly repressed by LMO1 but activated by
LMO3. All LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 26.9 bits (59), Expect = 2.5
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNK 130
C C ++ A E V+ AK + +H CF C+ CN+
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQ 34
>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 = 26.6 bits (58), Expect = 2.6
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 216 AKGTMWHKQCFSCNVCKRPL---DSVLACDGPDKEIYCKACY 254
A+ ++H CF+C VCKR L D + D + CKA Y
Sbjct: 18 AQDFVYHLHCFACIVCKRQLATGDEFYLME--DSRLVCKADY 57
>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 = 26.3 bits (58), Expect = 3.2
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C +C ++ ++A G +H + F C C K LD + I+C CY
Sbjct: 1 CAQCNKII-RGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFE-EKGSIFCPKCY 52
Score = 25.9 bits (57), Expect = 4.9
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 7/43 (16%)
Query: 215 LAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKE---IYCKACY 254
+A G +H + F+C+ CK+ LD G +E I+C CY
Sbjct: 14 VALGRSYHPEEFTCSQCKKVLDE----GGFFEEKGSIFCPKCY 52
>gnl|CDD|179595 PRK03564, PRK03564, formate dehydrogenase accessory protein FdhE;
Provisional.
Length = 309
Score = 28.8 bits (65), Expect = 3.4
Identities = 25/82 (30%), Positives = 29/82 (35%), Gaps = 27/82 (32%)
Query: 98 CPRCG-----GVV-FAAEQVLAK------GSEWHRKCFKCRDCNKT-------LDSINA- 137
CP CG VV Q L SEWH KC +C ++ LDS A
Sbjct: 190 CPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAA 249
Query: 138 -----CDGPDKDIYCKTCYGKK 154
C D Y K Y +K
Sbjct: 250 VKAESCG--DCGTYLKILYQEK 269
>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH)
family. The third LIM domain of the Enigma Homolog
(ENH) family: ENH was initially identified in rat brain.
Same as enigma, it contains three LIM domains at the
C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also been shown that ENH
interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line. ENH
is expressed in multiple tissues, such as skeletal
muscle, heart, bone, and brain. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 26.5 bits (58), Expect = 3.6
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLD 236
C C + A ++ L A G WH CF C+VC L+
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLE 37
Score = 25.7 bits (56), Expect = 5.9
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 98 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLD 133
C C + A ++ L A G WH CF C C ++L+
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLE 37
>gnl|CDD|234899 PRK01103, PRK01103, formamidopyrimidine/5-formyluracil/
5-hydroxymethyluracil DNA glycosylase; Validated.
Length = 274
Score = 28.5 bits (65), Expect = 3.7
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 196 RKGEGCPRCGGAV 208
R+GE C RCG +
Sbjct: 243 REGEPCRRCGTPI 255
>gnl|CDD|146301 pfam03589, Antiterm, Antitermination protein.
Length = 95
Score = 27.3 bits (61), Expect = 3.7
Identities = 10/30 (33%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 79 APRTTVIDTAKIKAAPG----KGCPRCGGV 104
A + + KA G K C RCGG
Sbjct: 12 AGDGAALGMKQSKAQLGVPVFKTCERCGGR 41
>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 = 26.3 bits (58), Expect = 3.8
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
+C ++F+ E A +WH F C C+++L D+ YC CY
Sbjct: 3 SVQCDELIFSGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVL-RDEHPYCIKCY 55
Score = 26.0 bits (57), Expect = 5.0
Identities = 17/57 (29%), Positives = 21/57 (36%), Gaps = 7/57 (12%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDS---VLACDGPDKEIYCKACY 254
+C +F+ E A WH F C C L VL + P YC CY
Sbjct: 3 SVQCDELIFSGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHP----YCIKCY 55
>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 = 26.0 bits (57), Expect = 3.9
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132
C +CG + V A+ H +CF C DCN L
Sbjct: 1 CDKCGSGIVGT-VVKARDKYRHPECFVCSDCNLNL 34
>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 = 26.0 bits (57), Expect = 4.4
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 113 AKGSEWHRKCFKCRDC 128
A + WH +CF CR+C
Sbjct: 15 ALNTLWHPECFVCREC 30
Score = 25.2 bits (55), Expect = 7.6
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 216 AKGTMWHKQCFSCNVCKRPL 235
A T+WH +CF C C P
Sbjct: 15 ALNTLWHPECFVCRECFTPF 34
>gnl|CDD|214631 smart00350, MCM, minichromosome maintenance proteins.
Length = 509
Score = 28.4 bits (64), Expect = 4.9
Identities = 11/60 (18%), Positives = 19/60 (31%), Gaps = 7/60 (11%)
Query: 41 VKDLRSGDRVSRVNIRKKRPPDEGVISLI-------YIFFCRENNAPRTTVIDTAKIKAA 93
+D V ++ DE + YI + RE P+ + K+ A
Sbjct: 390 ERDRELAKHVVDLHRYSHPEEDEAFEPPLSQEKLRKYIAYAREKIKPKLSEEAADKLVKA 449
>gnl|CDD|224487 COG1571, COG1571, Predicted DNA-binding protein containing a
Zn-ribbon domain [General function prediction only].
Length = 421
Score = 28.5 bits (64), Expect = 5.0
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 10/39 (25%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSIN 136
CPRCGG ++ + G R F+C+ C
Sbjct: 353 CPRCGG------RMKSAG----RNGFRCKKCGTRARETL 381
>gnl|CDD|239498 cd03404, Band_7_HflK, Band_7_HflK: The band 7 domain of flotillin
(reggie) like proteins. This group includes proteins
similar to prokaryotic HlfK (High frequency of
lysogenization K). Although many members of the band 7
family are lipid raft associated, prokaryote plasma
membranes lack cholesterol and are unlikely to have
lipid raft domains. Individual proteins of this band 7
domain family may cluster to form membrane microdomains
which may in turn recruit multiprotein complexes.
Escherichia coli HflK is an integral membrane protein
which may localize to the plasma membrane. HflK
associates with another band 7 family member (HflC) to
form an HflKC complex. HflKC interacts with FtsH in a
large complex termed the FtsH holo-enzyme. FtsH is an
AAA ATP-dependent protease which exerts progressive
proteolysis against membrane-embedded and soluble
substrate proteins. HflKC can modulate the activity of
FtsH. HflKC plays a role in the decision between
lysogenic and lytic cycle growth during lambda phage
infection.
Length = 266
Score = 27.9 bits (63), Expect = 5.0
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 45 RSGDRVSRVNIRKKRPPDE 63
++G + VN++ PP+E
Sbjct: 159 KAGIEIVGVNLQDADPPEE 177
>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL. The LIM domain of RIL:
RIL contains an N-terminal PDZ domain, a LIM domain, and
a short consensus C-terminal region. It is the smallest
molecule in the ALP LIM domain containing protein
family. RIL was identified in rat fibroblasts and in
human lymphocytes. The LIM domain interacts with the
AMPA glutamate receptor in dendritic spines. The
consensus C-terminus interacts with PTP-BL, a
submembranous protein tyrosine phosphatase and the PDZ
domain is responsible to interact with alpha-actinin
molecules. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 25.7 bits (56), Expect = 5.4
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 98 CPRCG-GVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKT 149
C RCG G+V V A+ +H +CF C DC L D+ +YC+T
Sbjct: 1 CTRCGNGIV--GTIVKARDKLYHPECFMCDDCGLNLKQ-RGYFFIDEQLYCET 50
>gnl|CDD|226021 COG3490, COG3490, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 366
Score = 28.2 bits (63), Expect = 5.7
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 10/59 (16%)
Query: 1 MPEESTLSFNQYADRI---YSVRFILGLKPSGNVIYRNSPRSVVKDLRSGDRVSRVNIR 56
+PEE T +F Y I + P GN R+V+ D +G VS +
Sbjct: 270 LPEEQTAAFANYIGSIAANRRDGLVALTSPRGN-------RAVIWDAATGAVVSEAALP 321
>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 = 25.6 bits (56), Expect = 6.0
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 201 CPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDS 237
C C + A + A G WH + F C C + L S
Sbjct: 3 CASCQKPI-AGQVVTALGQTWHPEHFVCCQCGKELGS 38
>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 = 25.8 bits (57), Expect = 6.0
Identities = 15/54 (27%), Positives = 19/54 (35%), Gaps = 1/54 (1%)
Query: 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C C V+ + V A W F C C+ L + D CK CY
Sbjct: 1 CYHCNQVI-EGDVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVCKKCY 53
>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 = 25.4 bits (56), Expect = 6.8
Identities = 19/55 (34%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 98 CPRCG-GVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 151
C RCG VV A +H CF C CN L +K YC+ CY
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRG-QPFYAVEKKAYCEPCY 54
>gnl|CDD|188867 cd09483, LIM1_Prickle_1, The first LIM domain of Prickle 1. The
first LIM domain of Prickle 1. Prickle contains three
C-terminal LIM domains and a N-terminal PET domain
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts with
Dishevelled, thereby modulating Frizzled/Dishevelled
activity and PCP signaling. Four forms of prickles have
been identified: prickle 1-4. The best characterized is
prickle 1 and prickle 2 which are differentially
expressed. While prickle 1 is expressed in fetal heart
and hematological malignancies, prickle 2 is found in
mainly expressed in fetal brain, adult cartilage,
pancreatic islet, and some types of timorous cells. In
addition, Prickle 1 regulates cell movements during
gastrulation and neuronal migration through interaction
with the noncanonical Wnt11/Wnt5 pathway in zebrafish.
Mutations in prickle 1 have been linked to progressive
myoclonus epilepsy. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 25.7 bits (56), Expect = 7.5
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 5/40 (12%)
Query: 98 CPRCGGVVFAAEQVL-----AKGSEWHRKCFKCRDCNKTL 132
C +CG + E + G WH CF C CN+ L
Sbjct: 1 CEQCGIKINGGEVAVFASRAGPGVCWHPSCFVCFTCNELL 40
Score = 25.3 bits (55), Expect = 8.0
Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 5/40 (12%)
Query: 201 CPRCGGAVFAAE-----QQLAKGTMWHKQCFSCNVCKRPL 235
C +CG + E + G WH CF C C L
Sbjct: 1 CEQCGIKINGGEVAVFASRAGPGVCWHPSCFVCFTCNELL 40
>gnl|CDD|163337 TIGR03586, PseI, pseudaminic acid synthase. Members of this family
are included within the larger pfam03102 (NeuB) family.
NeuB itself (TIGR03569) is involved in the biosynthesis
of neuraminic acid by the condensation of
phosphoenolpyruvate (PEP) with N-Acetyl-D-Mannosamine.
In an analagous reaction, this enzyme, PseI , condenses
PEP with 6-deoxy-beta-L-AltNAc4NAc to generate
pseudaminic acid.
Length = 327
Score = 27.7 bits (62), Expect = 7.7
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 18 SVRFILGLKPSGNVIYRNSPRS--VVKDLRSGDRVSRVNIRKKRP 60
V + L K + +R RS VVKD++ G+ + N+R RP
Sbjct: 259 EVNYELSEKEKKSRQFR---RSLYVVKDIKKGETFTEENVRSVRP 300
>gnl|CDD|163543 TIGR03831, YgiT_finger, YgiT-type zinc finger domain. This domain
model describes a small domain with two copies of a
putative zinc-binding motif CXXC (usually CXXCG). Most
member proteins consist largely of this domain or else
carry an additional C-terminal helix-turn-helix domain,
resembling that of the phage protein Cro and modeled by
pfam01381.
Length = 46
Score = 25.0 bits (55), Expect = 8.8
Identities = 11/45 (24%), Positives = 15/45 (33%), Gaps = 7/45 (15%)
Query: 72 FFCRENNAPRTTVIDTAK-------IKAAPGKGCPRCGGVVFAAE 109
C T +T + I+ P CP+CG AE
Sbjct: 2 PICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEYLDAE 46
>gnl|CDD|225000 COG2089, SpsE, Sialic acid synthase [Cell envelope biogenesis,
outer membrane].
Length = 347
Score = 27.3 bits (61), Expect = 8.9
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 11/66 (16%)
Query: 2 PEESTLSFNQYADRIYSVRFILG-----LKPSGNVIYRNSPRSVV--KDLRSGDRVSRVN 54
P+E F + D I V LG + PS + RS+V KD++ G+ +S N
Sbjct: 253 PDE----FKEMVDAIRQVEKALGDGEKEILPSEEETRNFARRSLVATKDIKKGEILSEDN 308
Query: 55 IRKKRP 60
++ RP
Sbjct: 309 LKVLRP 314
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
0.320 0.138 0.446
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,971,077
Number of extensions: 1270228
Number of successful extensions: 1624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1583
Number of HSP's successfully gapped: 307
Length of query: 281
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 185
Effective length of database: 6,679,618
Effective search space: 1235729330
Effective search space used: 1235729330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.1 bits)