RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12252
(356 letters)
>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 = 98.7 bits (246), Expect = 3e-26
Identities = 45/54 (83%), Positives = 49/54 (90%)
Query: 23 KCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
KCP CGKSVYAAEER+AGGYK+HKMCFKC MC+K LDSTNC EHE ELYC+QCH
Sbjct: 1 KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQCH 54
Score = 61.3 bits (149), Expect = 2e-12
Identities = 28/54 (51%), Positives = 38/54 (70%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
CP+CG V+AAE+ LA G +WH+ CFKC CNK LDS N + + ++YCK C+
Sbjct: 2 CPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEH-EGELYCKQCH 54
Score = 54.8 bits (132), Expect = 4e-10
Identities = 23/54 (42%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
CP+CG VYAAE+ ++ WH+ CF C C++ LDSTN + + ++YC+ C+
Sbjct: 2 CPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEH-EGELYCKQCH 54
>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein
(CRP) family. The LIM domains of Cysteine Rich Protein
(CRP) family: Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The known CRP
family members include CRP1, CRP2, and CRP3/MLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting
signal (K/R-K/R-Y-G-P-K), which supports the fact that
these proteins function not only in the cytoplasm but
also in the nucleus. CRPs control regulatory pathways
during cellular differentiation, and involve in complex
transcription control, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1, CRP2, and CRP3/MLP are involved in
promoting protein assembly along the actin-based
cytoskeleton. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 85.3 bits (212), Expect = 3e-21
Identities = 31/53 (58%), Positives = 40/53 (75%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
CP CGKSVYAAEE +A G +HK CF C++C+K LDST EH+ E+YC+ C+
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKSCY 53
Score = 78.8 bits (195), Expect = 6e-19
Identities = 29/54 (53%), Positives = 40/54 (74%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
CPRCG VYAAE++I+ + WH+ CF+CA C++ LDST L + D +IYC+ CY
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAE-HDGEIYCKSCY 53
Score = 78.4 bits (194), Expect = 9e-19
Identities = 30/54 (55%), Positives = 37/54 (68%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
CPRCG V+AAE+V+A G WH+ CF C CNK LDS + D +IYCK+CY
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAE-HDGEIYCKSCY 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 = 62.3 bits (151), Expect = 7e-13
Identities = 29/53 (54%), Positives = 40/53 (75%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
CP CGKSVYAAE+ + GG +HK CF+C++C K L+ST T+ + ELYC+ C+
Sbjct: 1 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53
Score = 56.9 bits (137), Expect = 6e-11
Identities = 27/54 (50%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
CPRCG V+AAE+V+ G WH+ CF+C C K+L+S D D ++YCK CY
Sbjct: 1 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTD-KDGELYCKVCY 53
Score = 55.8 bits (134), Expect = 2e-10
Identities = 27/54 (50%), Positives = 38/54 (70%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
CPRCG VYAAE+++ + WH+ CF CA C +SL+ST + D D ++YC+ CY
Sbjct: 1 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTD-KDGELYCKVCY 53
>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 = 60.7 bits (147), Expect = 3e-12
Identities = 31/54 (57%), Positives = 39/54 (72%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
CPRCG VYAAE++I + WH+ CF CA C +SL+ST L D D +IYC+GCY
Sbjct: 1 CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLAD-KDGEIYCKGCY 53
Score = 59.9 bits (145), Expect = 5e-12
Identities = 26/53 (49%), Positives = 37/53 (69%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
CP CGKSVYAAE+ + G +HK CF+C+ C K L+ST + + E+YC+ C+
Sbjct: 1 CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
Score = 57.2 bits (138), Expect = 5e-11
Identities = 27/54 (50%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
CPRCG V+AAE+++ G WH+ CF+C C K+L+S D D +IYCK CY
Sbjct: 1 CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLAD-KDGEIYCKGCY 53
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 58.5 bits (142), Expect = 2e-11
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 24 CPACGKSVYAAEE-RVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCHGRKY 80
C CGK +Y E R A G +H CF+C++C K L + E + +LYC+ + + +
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 42.7 bits (101), Expect = 8e-06
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKH 230
C CG ++ E V A G WH +CF+C C K L + D +YCK Y K
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDGKLYCKHDYFKLF 58
Score = 41.9 bits (99), Expect = 1e-05
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 282 CPRCGFVVYAAEQ-MISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYGKNF 339
C CG +Y E + ++WH CF CA C + L + + D +YC+ Y K F
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFE-KDGKLYCKHDYFKLF 58
>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 = 58.1 bits (141), Expect = 2e-11
Identities = 23/53 (43%), Positives = 32/53 (60%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
CP CGK VY AE++ + G +HK C +C C K L +EHE + YC +C+
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
Score = 52.0 bits (125), Expect = 3e-09
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
CP+CG V+ AE+ + G +WH+ C +C C KTL + K YC CY
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGK-PYCNKCY 53
Score = 45.8 bits (109), Expect = 5e-07
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
CP+CG VY AE+ S R WH+ C C C ++L ++ + YC CY
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSE-HEGKPYCNKCY 53
>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 = 57.5 bits (138), Expect = 4e-11
Identities = 29/54 (53%), Positives = 33/54 (61%)
Query: 23 KCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
KC AC K+VY AEE G FHK CF C C K LDST HE E+YC+ C+
Sbjct: 1 KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54
Score = 41.3 bits (96), Expect = 2e-05
Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C C V+ AE++ G +H+ CF C C K LDS + +IYCKTCY
Sbjct: 2 CGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVA-AHESEIYCKTCY 54
Score = 40.5 bits (94), Expect = 4e-05
Identities = 21/54 (38%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C C VY AE++ R +H+ CF C C ++LDST + +++IYC+ CY
Sbjct: 2 CGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVA-AHESEIYCKTCY 54
>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 = 56.7 bits (136), Expect = 7e-11
Identities = 27/55 (49%), Positives = 38/55 (69%), Gaps = 1/55 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYG 336
C RCG VYAAE+++ + WH+ CF CA C +SL+ST L + + +IYC+GCY
Sbjct: 1 CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTE-KEGEIYCKGCYA 54
Score = 54.7 bits (131), Expect = 4e-10
Identities = 27/54 (50%), Positives = 36/54 (66%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCHG 77
C CG SVYAAE+ + G +HK CF+C+ C K L+ST TE E E+YC+ C+
Sbjct: 1 CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 54
Score = 52.4 bits (125), Expect = 2e-09
Identities = 24/55 (43%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYG 227
C RCG V+AAE+++ G WH+ CF+C C K+L+S + + +IYCK CY
Sbjct: 1 CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTE-KEGEIYCKGCYA 54
>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 = 55.8 bits (134), Expect = 2e-10
Identities = 29/55 (52%), Positives = 37/55 (67%)
Query: 23 KCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCHG 77
KC ACG++VY AEE G FHK CF C +C K LDST H++E+YC+ C+G
Sbjct: 1 KCGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSCYG 55
Score = 43.8 bits (103), Expect = 2e-06
Identities = 25/55 (45%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYG 227
C CG V+ AE+V G +H+ CF C C K LDS D++IYCK+CYG
Sbjct: 2 CGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIH-DQEIYCKSCYG 55
Score = 42.3 bits (99), Expect = 1e-05
Identities = 24/55 (43%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYG 336
C CG VY AE++ R +H+ CF C C ++LDST + D +IYC+ CYG
Sbjct: 2 CGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIH-DQEIYCKSCYG 55
>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 = 54.6 bits (132), Expect = 3e-10
Identities = 25/51 (49%), Positives = 30/51 (58%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQ 74
C CGK+VY E VA G FHK CF+CS C+K L N E +LYC+
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKP 51
Score = 46.9 bits (112), Expect = 2e-07
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
C CG V+ E+++A G +H+ CF+C CNKTL N K +YCK
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGK-LYCK 50
Score = 41.1 bits (97), Expect = 3e-05
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C CG VY E++++ +++H+ CF C+ C+++L N + +YC+
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYA-SLEGKLYCK 50
>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 = 54.6 bits (131), Expect = 4e-10
Identities = 28/53 (52%), Positives = 33/53 (62%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
C AC K+VY AEE G FHK CF C +C K LDST HE E+YC+ C+
Sbjct: 1 CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCKSCY 53
Score = 43.0 bits (101), Expect = 4e-06
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C C V+ AE+V +G +H+ CF C C K LDS + +IYCK+CY
Sbjct: 1 CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVA-AHEDEIYCKSCY 53
Score = 40.7 bits (95), Expect = 4e-05
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C C VY AE++ + R +H+ CF C C ++LDST + +++IYC+ 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 = 54.6 bits (131), Expect = 4e-10
Identities = 28/55 (50%), Positives = 34/55 (61%)
Query: 23 KCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCHG 77
KC C K+VY AEE G FHK CF C +C K LDST H +E+YC+ C+G
Sbjct: 2 KCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSCYG 56
Score = 43.5 bits (102), Expect = 4e-06
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 171 KGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYG 227
K C C V+ AE+V +G +H+ CF C C K LDS + +IYCK+CYG
Sbjct: 1 KKCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGE-EIYCKSCYG 56
Score = 39.6 bits (92), Expect = 8e-05
Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYG 336
C C VY AE++ + R +H+ CF C C ++LDST + +IYC+ CYG
Sbjct: 3 CGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVH-GEEIYCKSCYG 56
>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 = 49.3 bits (118), Expect = 3e-08
Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 23 KCPACGKSVYAAEE-RVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQC 75
KC CGK +Y E A G +H CFKC+ C K L E + +LYC+ C
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 43.5 bits (103), Expect = 3e-06
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTC 225
C CG ++ E+VL A G WH +CFKC C K L D +YCK C
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDT-FFEKDGKLYCKDC 54
Score = 40.1 bits (94), Expect = 5e-05
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 282 CPRCGFVVYAAEQMIS-KNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGC 334
C CG +Y E+++ ++WH CF CA C + L + D +YC+ C
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFE-KDGKLYCKDC 54
>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 = 6e-08
Identities = 21/53 (39%), Positives = 29/53 (54%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
C CGK + E A G K+H CFKCS+C K L + E + + YC +C+
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 42.7 bits (101), Expect = 6e-06
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C CG + E + A G +WH +CFKC C K L + + D YC+ CY
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEK-DGKPYCEKCY 53
Score = 41.1 bits (97), Expect = 2e-05
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C CG + E + + + WH CF C+ C + L + + D YC CY
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEK-DGKPYCEKCY 53
>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 = 47.8 bits (114), Expect = 9e-08
Identities = 23/50 (46%), Positives = 30/50 (60%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCR 73
C +CGK VY EE +A + +HK CF+C C+K L N HE LYC+
Sbjct: 1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCK 50
Score = 46.3 bits (110), Expect = 3e-07
Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 5/53 (9%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL--DSINACDGPDKDIYCK 223
C CG V+ E+++A+ +H+ CF+C+DCNK L D+ + +G ++YCK
Sbjct: 1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEG---NLYCK 50
Score = 42.1 bits (99), Expect = 1e-05
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 5/53 (9%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSL--DSTNLNDGPDNDIYCR 332
C CG VY E++I++ I+H+ CF C DC++ L D+ ++G ++YC+
Sbjct: 1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEG---NLYCK 50
>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 = 47.8 bits (114), Expect = 1e-07
Identities = 22/51 (43%), Positives = 30/51 (58%)
Query: 23 KCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCR 73
KC AC K+VY ++ A G +HK CF+CS C L +N + E LYC+
Sbjct: 4 KCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCK 54
Score = 36.7 bits (85), Expect = 0.001
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL--DSINACDGPDKDIYCKTCY 226
C C V+ +Q+ A G +H+ CF+C C TL + ++ +G +YCK +
Sbjct: 5 CKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGV---LYCKPHF 57
Score = 34.0 bits (78), Expect = 0.008
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 280 DGCPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYGKNF 339
C C VY +Q+ + ++H+ CF C+ C +L +N + + +YC+ + + F
Sbjct: 3 QKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSS-MEGVLYCKPHFEQLF 61
>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 = 45.6 bits (108), Expect = 6e-07
Identities = 21/54 (38%), Positives = 28/54 (51%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
CP+C V+ AE+V + G +WHR C KC C KTL + + K CY
Sbjct: 1 CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCNHPCY 54
Score = 40.6 bits (95), Expect = 3e-05
Identities = 20/51 (39%), Positives = 26/51 (50%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQ 74
CP C K VY AE + G +H+ C KC C K L + EH+ + YC
Sbjct: 1 CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCNH 51
Score = 34.5 bits (79), Expect = 0.005
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDS 318
CP+C VY AE++ S + WHR C C C ++L
Sbjct: 1 CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTP 37
>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 = 45.5 bits (108), Expect = 7e-07
Identities = 25/61 (40%), Positives = 33/61 (54%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCHGRKYGPK 83
C ACGK+VY E+ G +HK CFKCS + +N HE LYC+ H + + K
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60
Query: 84 G 84
G
Sbjct: 61 G 61
Score = 30.5 bits (69), Expect = 0.18
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKC 200
C CG V+ E+V +G+ +H+ CFKC
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKC 28
Score = 25.9 bits (57), Expect = 6.9
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCA 310
C CG VY E++ + +H+ CF C+
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKCS 29
>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 = 45.5 bits (108), Expect = 7e-07
Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFL--DSTNCTEHEKELYCR 73
CP CGK+ Y AE G +HK CFKC C L + + + E+YC
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCA 52
Score = 42.4 bits (100), Expect = 9e-06
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINAC-DGPDKDIYCKT 224
CPRCG + AE V G+ +H+ CFKCR+C L D ++YC
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCAR 53
Score = 37.0 bits (86), Expect = 7e-04
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADC--HRSLDSTNLNDGPDNDIYCRG 333
CPRCG Y AE + +H+ CF C +C SL + G D ++YC
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQG-DGEVYCAR 53
>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 = 44.7 bits (106), Expect = 1e-06
Identities = 20/54 (37%), Positives = 27/54 (50%)
Query: 172 GCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTC 225
C CG VF AE++L +G +HR CFKC C L + + C+TC
Sbjct: 4 PCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYCCETC 57
Score = 40.5 bits (95), Expect = 4e-05
Identities = 16/55 (29%), Positives = 27/55 (49%)
Query: 280 DGCPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGC 334
+ C CG V+ AE+++ + +++HR CF CA C L + + C C
Sbjct: 3 EPCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYCCETC 57
Score = 39.3 bits (92), Expect = 1e-04
Identities = 18/50 (36%), Positives = 25/50 (50%)
Query: 23 KCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYC 72
C +CG V+ AE + G +H+ CFKC+ C L + E E YC
Sbjct: 4 PCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53
>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 = 42.7 bits (100), Expect = 6e-06
Identities = 18/35 (51%), Positives = 24/35 (68%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 207
CP CG V+ AE+V++ G WHR C +C+ C KTL
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTL 35
Score = 40.8 bits (95), Expect = 3e-05
Identities = 20/49 (40%), Positives = 28/49 (57%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYC 72
CP CGK VY AE+ ++ G +H+ C +C C K L + EH+ YC
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
Score = 38.5 bits (89), Expect = 2e-04
Identities = 17/35 (48%), Positives = 22/35 (62%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSL 316
CP CG VY AE+++S R WHR C C C ++L
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTL 35
>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 = 41.1 bits (96), Expect = 2e-05
Identities = 22/54 (40%), Positives = 27/54 (50%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
CPRC V+ AE+V + G WHR C KC C+K L + K K CY
Sbjct: 1 CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHKPCY 54
Score = 40.7 bits (95), Expect = 3e-05
Identities = 21/51 (41%), Positives = 29/51 (56%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQ 74
CP C K+VY AE+ + G +H+ C KC CSK L EH+ + YC +
Sbjct: 1 CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHK 51
Score = 34.9 bits (80), Expect = 0.004
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSL 316
CPRC VY AE++ S + WHR 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 = 40.0 bits (93), Expect = 5e-05
Identities = 21/54 (38%), Positives = 27/54 (50%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C CGG + +LA +WH +C KC +C L+S C D IYCK Y
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
Score = 31.6 bits (71), Expect = 0.060
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C CG + +++ ++ WH RC C +C +L+S D IYC+ Y
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
>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 = 39.6 bits (92), Expect = 1e-04
Identities = 21/54 (38%), Positives = 27/54 (50%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C CGG + +LA +WH +C KC +C L+S C D IYCK Y
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
Score = 32.3 bits (73), Expect = 0.046
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C CG + +++ ++ WH RC C +C +L+S D IYC+ Y
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
>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 = 1e-04
Identities = 19/50 (38%), Positives = 25/50 (50%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCR 73
C CG VY AE+ +HK CF C +C L N H+K+ YC+
Sbjct: 1 CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQ 50
Score = 36.8 bits (85), Expect = 9e-04
Identities = 16/39 (41%), Positives = 22/39 (56%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTN 320
C RCG+ VY AE++ ++ WH+ CF C C L N
Sbjct: 1 CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNN 39
Score = 34.5 bits (79), Expect = 0.004
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
C RCG V+ AE++ WH+ CF C C L ++N K YC+
Sbjct: 1 CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMML-TVNNFVSHQKKPYCQ 50
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C RCG V+ E++ WH+ CFKC C TL ++ G +K YC Y
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTL-NMKNYKGYNKKPYCNAHY 53
Score = 38.5 bits (90), Expect = 2e-04
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C RCG VY E++ ++IWH+ CF C C +L+ N G + YC Y
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYK-GYNKKPYCNAHY 53
Score = 33.9 bits (78), Expect = 0.009
Identities = 19/49 (38%), Positives = 26/49 (53%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYC 72
C CGK+VY E+ +HK CFKC +C L+ N + K+ YC
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYC 49
>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 = 38.8 bits (90), Expect = 2e-04
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C RCG +V+ E+V WH+ CF C C TL ++N G K YC Y
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTL-NMNNYKGYQKKPYCNAHY 53
Score = 38.0 bits (88), Expect = 3e-04
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C RCG +VY E++ ++ WH+ CF C C +L+ N G YC Y
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYK-GYQKKPYCNAHY 53
Score = 37.6 bits (87), Expect = 4e-04
Identities = 18/49 (36%), Positives = 25/49 (51%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYC 72
C CGK VY E+ +HK CF C +C L+ N ++K+ YC
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYC 49
>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 = 39.1 bits (91), Expect = 3e-04
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 1/77 (1%)
Query: 1 MRVKQYKKKLDIIMPFVPAENPKCPACGKSVYAAEERV-AGGYKFHKMCFKCSMCSKFLD 59
M +Q + +D A N C CG+ + + V A G+ FH CF C C + L
Sbjct: 11 MLTQQLMQDMDHPPAAEAATNELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQ 70
Query: 60 STNCTEHEKELYCRQCH 76
E + YC +C+
Sbjct: 71 GQQFYSLEGKPYCEECY 87
Score = 29.4 bits (66), Expect = 0.73
Identities = 19/69 (27%), Positives = 25/69 (36%), Gaps = 13/69 (18%)
Query: 270 PTSGLKGRNGDGCPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDST---NLNDGPD 326
T+ L G G R V A + +H CF+C C + L +L P
Sbjct: 29 ATNELCGICGQPLSRTQPAVRALGHL------FHVTCFTCHQCEQQLQGQQFYSLEGKP- 81
Query: 327 NDIYCRGCY 335
YC CY
Sbjct: 82 ---YCEECY 87
Score = 27.1 bits (60), Expect = 4.4
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 2/62 (3%)
Query: 166 KAAPGKGCPRCG-GVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKT 224
+AA + C CG + V A G +H CF C C + L K YC+
Sbjct: 27 EAATNELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKP-YCEE 85
Query: 225 CY 226
CY
Sbjct: 86 CY 87
>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9
family. The first LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Although Lhx2 and
Lhx9 are highly homologous, they seems to play
regulatory roles in different organs. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. Lhx9 is expressed in several regions of the
developing mouse brain , the spinal cord, the pancreas,
in limb mesenchyme, and in the urogenital region. Lhx9
plays critical roles in gonad development. Homozygous
mice lacking functional Lhx9 alleles exhibit numerous
urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 54
Score = 38.1 bits (89), Expect = 3e-04
Identities = 21/54 (38%), Positives = 27/54 (50%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C CG + +LA +WH C KC +C LDS +C D +IYCK Y
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
Score = 28.5 bits (64), Expect = 0.81
Identities = 17/54 (31%), Positives = 25/54 (46%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C CG + +++ +R WH C C +C LDS D +IYC+ Y
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
Score = 27.7 bits (62), Expect = 1.2
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTN-CTEHEKELYCRQ 74
C CG+ + +A ++H C KC C LDS C + +YC++
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKE 52
>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 = 37.2 bits (86), Expect = 5e-04
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCR 73
C +C K+VY E VA +H CF+CS C+ L +YC+
Sbjct: 1 CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCK 50
Score = 32.2 bits (73), Expect = 0.030
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C C VY E++++ +I+H CF C+ C+ L +IYC+
Sbjct: 1 CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYAS-LHGNIYCK 50
Score = 31.4 bits (71), Expect = 0.072
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
C C V+ E+++A +H CF+C CN L S+ +IYCK
Sbjct: 1 CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKL-SLGTYASLHGNIYCK 50
>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 = 36.3 bits (84), Expect = 0.001
Identities = 18/50 (36%), Positives = 23/50 (46%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCR 73
C C K VY E +A FHK CF+C C+ L N +YC+
Sbjct: 1 CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCK 50
Score = 28.6 bits (64), Expect = 0.60
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSL 316
C C VY E++I+ + +H+ CF C C+ L
Sbjct: 1 CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKL 35
Score = 27.1 bits (60), Expect = 2.4
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C C V+ E+++A +H+ CF+C CN L S+ IYCK +
Sbjct: 1 CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKL-SLGNYASLHGRIYCKPHF 53
>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 = 36.2 bits (83), Expect = 0.002
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 282 CPRCGFVVYAAEQ-MISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C RC + A+E M ++ ++H CF+C C+++L + + DN +YCR
Sbjct: 5 CARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCR 56
Score = 35.8 bits (82), Expect = 0.002
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 171 KGCPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
+ C RC + A+E V+ A+ S +H CF C CNKTL + + D +YC+
Sbjct: 3 QRCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCR 56
>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 = 34.8 bits (80), Expect = 0.004
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C C G + ++ V A +WH CF+C C+ +L N D +YC+ Y
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLS--NWYFEKDGKLYCRKDY 52
Score = 33.6 bits (77), Expect = 0.010
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQ 74
C C + ++ A +H CF+CS+CS L S E + +LYCR+
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL-SNWYFEKDGKLYCRK 50
Score = 32.8 bits (75), Expect = 0.017
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C C + ++ + + N+ WH CF C+ C SL +N D +YCR Y
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL--SNWYFEKDGKLYCRKDY 52
>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The third LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 35.0 bits (81), Expect = 0.004
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTNLND---GPDNDIYCRGC 334
+++ WH +CF+C+ CHR + S + D I C C
Sbjct: 16 EDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
Score = 30.7 bits (70), Expect = 0.12
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 24 CPACGKSVYAAEERVA--GGYKFHKMCFKCSMCSKFLDSTNCTE----HEKELYCRQC 75
C +CGKS+ E+ ++H CF CS C + + S ++ + C C
Sbjct: 1 CASCGKSI---EDECIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
Score = 28.4 bits (64), Expect = 0.70
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 193 WHRKCFKCRDCNKTLDSIN---ACDGPDKDIYCKTC 225
WH KCF C C++ + S A + D+ I C C
Sbjct: 20 WHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
>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 = 34.6 bits (79), Expect = 0.005
Identities = 18/50 (36%), Positives = 23/50 (46%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCR 73
C +C K+VY E VA FH CF C C+ L + E YC+
Sbjct: 1 CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCK 50
Score = 30.3 bits (68), Expect = 0.14
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSL 316
C C VY E++++ ++H CF C C+ L
Sbjct: 1 CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKL 35
Score = 26.5 bits (58), Expect = 3.4
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
C C V+ E+++A +H CF C+ CN L S+ + + YCK
Sbjct: 1 CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKL-SLGSYAALHGEFYCK 50
>gnl|CDD|188808 cd09424, LIM2_FHL1, The second LIM domain of Four and a half LIM
domains protein 1 (FHL1). The second LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 34.4 bits (79), Expect = 0.006
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 184 EQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKK 229
+ V KG+ WH+ CF C +C + + + + +D YC C+ KK
Sbjct: 13 QNVEYKGNVWHKDCFTCSNCKQPIGTKSFFP-KGEDFYCVPCHEKK 57
Score = 32.0 bits (73), Expect = 0.043
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 24 CPACGKSVYAAEERVA-GGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCHGRKY 80
C C K + A ++ V G +HK CF CS C + + + + ++ YC CH +K+
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
Score = 32.0 bits (73), Expect = 0.050
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYGKNF 339
K +WH+ CF+C++C + + + + D YC C+ K F
Sbjct: 18 KGNVWHKDCFTCSNCKQPIGTKSFFP-KGEDFYCVPCHEKKF 58
>gnl|CDD|188751 cd09365, LIM2_LIMK, The second LIM domain of LIMK (LIM domain
Kinase ). The second LIM domain of LIMK (LIM domain
Kinase ): LIMK protein family is comprised of two
members LIMK1 and LIMK2. LIMK contains two LIM domains,
a PDZ domain and a kinase domain. LIMK is involved in
the regulation of actin polymerization and microtubule
disassembly. LIMK influences architecture of the actin
cytoskeleton by regulating the activity of the cofilin
family proteins cofilin1, cofilin2, and destrin. The
mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus and are expressed in all tissues. Both
LIMK1 and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. However,
LIMK1 and LIMk2 have different cellular locations.
While LIMK1 localizes mainly at focal adhesions, LIMK2
is found in cytoplasmic punctae, suggesting that they
may have different cellular functions. The LIM domains
of LIMK have been shown to play an important role in
regulating kinase activity and likely also contribute
to LIMK function by acting as sites of
protein-to-protein interactions. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 34.3 bits (79), Expect = 0.007
Identities = 20/42 (47%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 38 VAGGYKFHKMCFKCSMCSKFL---DSTNCTEHEKELYCRQCH 76
VAG +KFH CF CS C F+ DS E K LYC C+
Sbjct: 14 VAGDHKFHPECFSCSSCKAFIGDGDSYALVERSK-LYCGVCY 54
>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 = 34.2 bits (79), Expect = 0.008
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 282 CPRCGFVVYAAEQ-MISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C RC + A+E M +++ ++H CF+CA C++ L + D +YCR
Sbjct: 5 CARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCR 56
Score = 30.3 bits (69), Expect = 0.19
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 171 KGCPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTL 207
K C RC + A+E V+ A+ +H CF C CNK L
Sbjct: 3 KRCARCHLGISASELVMRARDLVFHLNCFTCATCNKPL 40
>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 = 34.0 bits (78), Expect = 0.009
Identities = 13/53 (24%), Positives = 24/53 (45%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
C CGK + ++ + CF+C CS+ + + ++ L+C CH
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDITDLKYAKTKRGLFCMSCH 53
Score = 27.1 bits (60), Expect = 2.4
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDND-IYCRGCY 335
C CG + ++S + + CF C C R D T+L ++C C+
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSR--DITDLKYAKTKRGLFCMSCH 53
Score = 26.7 bits (59), Expect = 3.2
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKD-IYCKTCY 226
C CG + +L+ + CF+CR C++ + + K ++C +C+
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDITDLK--YAKTKRGLFCMSCH 53
>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 = 33.9 bits (77), Expect = 0.010
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 282 CPRCGFVVYAAEQ-MISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C RC + A+E M +++ ++H CF+C C++ L + + DN +YCR
Sbjct: 5 CARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCR 56
Score = 32.0 bits (72), Expect = 0.053
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
C RC + A+E V+ A+ +H CF C CNK L + + D +YC+
Sbjct: 5 CARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCR 56
>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 = 33.5 bits (77), Expect = 0.011
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 192 EWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
EWH C KC +C + LD C D YCK Y
Sbjct: 21 EWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
Score = 32.3 bits (74), Expect = 0.030
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 37 RVAGGYKFHKMCFKCSMCSKFLD-STNCTEHEKELYCRQCH 76
RVA ++H C KC+ C ++LD + C + + YC++ +
Sbjct: 15 RVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
Score = 31.5 bits (72), Expect = 0.065
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 302 WHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
WH C CA+C + LD T D YC+ Y
Sbjct: 22 WHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>gnl|CDD|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM
domains protein (FHL). The first LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 33.2 bits (76), Expect = 0.016
Identities = 18/42 (42%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTNLNDGP----DNDIYCRGCY 335
K+R WH CF C C RS L D P D D+ C CY
Sbjct: 22 KDRHWHEGCFKCFKCQRS-----LVDKPFAAKDEDLLCTECY 58
Score = 29.7 bits (67), Expect = 0.26
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 189 KGSEWHRKCFKCRDCNKTL-DSINACDGPDKDIYCKTCY 226
K WH CFKC C ++L D A D+D+ C CY
Sbjct: 22 KDRHWHEGCFKCFKCQRSLVDKPFAAK--DEDLLCTECY 58
Score = 27.0 bits (60), Expect = 2.4
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 44 FHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
+H+ CFKC C + L +++L C +C+
Sbjct: 26 WHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58
>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 = 33.0 bits (76), Expect = 0.017
Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKE--LYCRQ 74
C C K VY E A G FH+ CFKCS C L + YC+
Sbjct: 1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKP 53
Score = 29.6 bits (67), Expect = 0.29
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 207
C C V+ E++ A+G +HR CFKC C TL
Sbjct: 1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTL 35
Score = 28.4 bits (64), Expect = 0.77
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSL 316
C C VY E++ ++ +HR CF C+ C +L
Sbjct: 1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTL 35
>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 = 32.8 bits (75), Expect = 0.019
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDS 209
C CG V ++ L G +HR CF+C++C+ TL
Sbjct: 1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLP 37
Score = 32.0 bits (73), Expect = 0.040
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDS 60
C ACG+ V+ + + G +H+ CF+C CS L
Sbjct: 1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLP 37
Score = 28.5 bits (64), Expect = 0.65
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPD 326
C CG V+ ++ + +++HR CF C +C +L + GP+
Sbjct: 1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPE 45
>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 = 32.4 bits (74), Expect = 0.025
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C +C ++ + V K WHR+CF C +C+K+L +K YC C+
Sbjct: 1 CSKCNKIINSG-GVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKP-YCADCF 52
Score = 29.0 bits (65), Expect = 0.40
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
KN WHR CF+C +C +SL D YC C+
Sbjct: 16 KNEPWHRECFTCTNCSKSLAGQRFTS-RDEKPYCADCF 52
Score = 27.4 bits (61), Expect = 1.6
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 41 GYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQC 75
+H+ CF C+ CSK L T +++ YC C
Sbjct: 17 NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADC 51
>gnl|CDD|188800 cd09416, LIM2_Testin, The second LIM domain of Testin. The second
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction domain
at the N-terminal. Testin is a cytoskeleton associated
focal adhesion protein that localizes along actin stress
fibers, at cell-cell-contact areas, and at focal
adhesion plaques. Testin interacts with a variety of
cytoskeletal proteins, including zyxin, mena, VASP,
talin, and actin and it is involved in cell motility and
adhesion events. Knockout mice experiments reveal that
tumor repressor function of testin. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 32.5 bits (74), Expect = 0.025
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C C ++F+ E A+ WH K F C DC+ L DK + CK CY
Sbjct: 3 CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPV-CKPCY 55
Score = 27.9 bits (62), Expect = 1.1
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDS---TNLNDGPDNDIYCRGCY 335
C C ++++ E ++N+ WH + F C DC L +ND P C+ CY
Sbjct: 3 CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKP----VCKPCY 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 = 32.3 bits (74), Expect = 0.026
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 190 GSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
G WH C +C C L+ +C D+ IYCK Y
Sbjct: 18 GRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
Score = 25.8 bits (57), Expect = 7.6
Identities = 12/36 (33%), Positives = 14/36 (38%)
Query: 300 RIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
R WH C C C L+ D IYC+ Y
Sbjct: 19 RSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
>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 = 32.6 bits (75), Expect = 0.026
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 28 GKSVYAAEERVAGGYKFHKMCFKCSMCS-KFLDSTNCTEHEKELYCRQC 75
GKS+ + + ++G ++H+ CF C+ C F S C + + YC+Q
Sbjct: 10 GKSISSKDGELSG--QWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQH 56
Score = 31.1 bits (71), Expect = 0.080
Identities = 12/34 (35%), Positives = 14/34 (41%)
Query: 193 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
WHR+CF C C C D YC+ Y
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
Score = 27.2 bits (61), Expect = 1.9
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 8/38 (21%)
Query: 302 WHRRCFSCADCHRSLDSTN----LNDGPDNDIYCRGCY 335
WHR CF C C + L+D P YC+ Y
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKP----YCQQHY 57
>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain
Kinase 2). The first LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, altering the rate of actin depolymerization.
LIMK activity is activated by phosphorylation of a
threonine residue within the activation loop of the
kinase by p21-activated kinases 1 and 4 and by Rho
kinase. LIMKs can function in both cytoplasm and
nucleus. Both LIMK1 and LIMK2 can act in the nucleus to
suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2
is expressed in all tissues. While LIMK1 localizes
mainly at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 32.5 bits (74), Expect = 0.027
Identities = 16/54 (29%), Positives = 20/54 (37%), Gaps = 2/54 (3%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C CG + + WH CF C+ C L TN D +YC Y
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL--TNWYYEKDGKLYCHKHY 52
Score = 30.2 bits (68), Expect = 0.15
Identities = 11/35 (31%), Positives = 14/35 (40%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 207
C CGG + + WH CF+C C L
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL 35
Score = 27.9 bits (62), Expect = 1.1
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCT-EHEKELYCRQ 74
C CG + + +H CF+CS+C L TN E + +LYC +
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL--TNWYYEKDGKLYCHK 50
>gnl|CDD|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred
partner (LPP). The second LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at the
N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 60
Score = 32.5 bits (74), Expect = 0.029
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 302 WHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYGKNFGPK 342
+H +CF+C C +SLD N I+C + K F P+
Sbjct: 20 YHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAPR 60
Score = 31.4 bits (71), Expect = 0.074
Identities = 15/42 (35%), Positives = 20/42 (47%)
Query: 188 AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKK 229
A G +H +CF C C K+LD I I+C + KK
Sbjct: 15 ATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKK 56
Score = 31.0 bits (70), Expect = 0.10
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 24 CPACGKSVYAAEERV--AGGYKFHKMCFKCSMCSKFLDSTNCT-EHEKELYCRQCHGRKY 80
C C K + +R+ A G +H CF C +C K LD T + +++C + +K+
Sbjct: 1 CSVCSKPIL---DRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKF 57
Query: 81 GPK 83
P+
Sbjct: 58 APR 60
>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 = 32.3 bits (74), Expect = 0.031
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNK 205
C +CG + + V A G +H CF C DC K
Sbjct: 1 CAKCGKPI-TGQFVRALGDVYHLDCFTCHDCGK 32
Score = 25.7 bits (57), Expect = 8.2
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 282 CPRCGFVVYAAEQMISK-NRIWHRRCFSCADCHR 314
C +CG + Q + ++H CF+C DC +
Sbjct: 1 CAKCGKPI--TGQFVRALGDVYHLDCFTCHDCGK 32
>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8.
The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs such as the pituitary
gland and the pancreas. Studies using mutant mice have
revealed roles for Lhx7 and Lhx8 in the development of
cholinergic neurons in the telencephalon and in basal
forebrain development. Mice lacking alleles of the
LIM-homeobox gene Lhx7 or Lhx8 display dramatically
reduced number of forebrain cholinergic neurons. In
addition, Lhx7 mutation affects male and female mice
differently, with females appearing more affected than
males. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 31.9 bits (72), Expect = 0.044
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 193 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
WH +C C C +L +C DKDI+CK Y
Sbjct: 22 WHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 55
Score = 31.5 bits (71), Expect = 0.072
Identities = 16/51 (31%), Positives = 22/51 (43%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C CG + + + WH RC SC+ C SL D DI+C+
Sbjct: 2 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCK 52
Score = 26.1 bits (57), Expect = 5.2
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDS-TNCTEHEKELYCR 73
C +CG + +H C CS+C L T+C +K+++C+
Sbjct: 2 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCK 52
>gnl|CDD|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM
domains protein (FHL). The second LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 31.9 bits (73), Expect = 0.045
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 173 CPRCGGVVFAAEQVLA-KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C CG + + + KG WH KCF C +C K + + + D IYC CY
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGT-KSFIPKDDKIYCVPCY 54
Score = 30.0 bits (68), Expect = 0.23
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 24 CPACGKSVYAAEERVA-GGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
C ACGK++ +++ G +H+ CF CS C K + + + + ++YC C+
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
>gnl|CDD|188848 cd09464, LIM2_LIMK1, The second LIM domain of LIMK1 (LIM domain
Kinase 1). The second LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture
of the actin cytoskeleton by regulating the activity of
the cofilin family proteins cofilin1, cofilin2, and
destrin. The mechanism of the activation is to
phosphorylates cofilin on serine 3 and inactivates its
actin-severing activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. LIMK1 is expressed in all tissues and is
localized to focal adhesions in the cell. LIMK1 can
form homodimers upon binding of HSP90 and is activated
by Rho effector Rho kinase and MAPKAPK2. LIMK1 is
important for normal central nervous system
development, and its deletion has been implicated in
the development of the human genetic disorder Williams
syndrome. Moreover, LIMK1 up-regulates the promoter
activity of urokinase type plasminogen activator and
induces its mRNA and protein expression in breast
cancer cells. The LIM domains have been shown to play
an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 31.8 bits (72), Expect = 0.046
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFL---DSTNCTEHEKELYCRQCH 76
C C +++ VAG K+H CF C C F+ D+ EH K LYC C+
Sbjct: 1 CHGCSETITTGLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSK-LYCGHCY 55
>gnl|CDD|188811 cd09427, LIM2_FHL3, The second LIM domain of Four and a half LIM
domains protein 3 (FHL3). The second LIM domain of
Four and a half LIM domains protein 3 (FHL3): FHL3 is
highly expressed in the skeleton and cardiac muscles
and possesses the transactivation and repression
activities. FHL3 interacts with many transcription
factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and
MZF_1. Moreover, FHL3 interacts with alpha- and
beta-subunits of the muscle alpha7beta1 integrin
receptor. FHL3 was also proved to possess the
auto-activation ability and was confirmed that the
second zinc finger motif in fourth LIM domain was
responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 58
Score = 31.7 bits (72), Expect = 0.051
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 23 KCPACGKSVYAAEERVA-GGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
KC ACGK+V ++ G +H+ CF C C + + S + + E YC C+
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCY 57
Score = 29.8 bits (67), Expect = 0.30
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 172 GCPRCGGVVFAAEQVLA-KGSEWHRKCFKCRDCNKTLDSINACDGPDKD-IYCKTCY 226
C CG V + L +G WH CF C C + + S + PDKD YC CY
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFI--PDKDEHYCVPCY 57
Score = 26.0 bits (57), Expect = 5.7
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 281 GCPRCGFVVYAAEQMISKN-RIWHRRCFSCADCHRSLDSTNLNDGPDND-IYCRGCY 335
C CG V + + + WH CF C C + + S + PD D YC CY
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFI--PDKDEHYCVPCY 57
>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 = 31.5 bits (71), Expect = 0.057
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C CG + + WH +C +C C +L N+C +K+I+CK Y
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
Score = 30.4 bits (68), Expect = 0.17
Identities = 17/54 (31%), Positives = 24/54 (44%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C CG + + N IWH RC C+ C SL N + +I+C+ Y
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
>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 = 31.3 bits (71), Expect = 0.060
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 44 FHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
+H CF CS CSK L T E + YC C+
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52
Score = 26.7 bits (59), Expect = 2.7
Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 302 WHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
WH CF C+ C + L D YC CY
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQ-YYCVDCY 52
Score = 26.3 bits (58), Expect = 4.9
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 193 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
WH +CF C C+K L D+ YC CY
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQ-YYCVDCY 52
>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain
Kinase 1). The first LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture
of the actin cytoskeleton by regulating the activity of
the cofilin family proteins cofilin1, cofilin2, and
destrin. The mechanism of the activation is to
phosphorylates cofilin on serine 3 and inactivates its
actin-severing activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. LIMK1 is expressed in all tissues and is
localized to focal adhesions in the cell. LIMK1 can
form homodimers upon binding of HSP90 and is activated
by Rho effector Rho kinase and MAPKAPK2. LIMK1 is
important for normal central nervous system
development, and its deletion has been implicated in
the development of the human genetic disorder Williams
syndrome. Moreover, LIMK1 up-regulates the promoter
activity of urokinase type plasminogen activator and
induces its mRNA and protein expression in breast
cancer cells. The LIM domains have been shown to play
an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 74
Score = 31.8 bits (72), Expect = 0.069
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 22 PKCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQ 74
P C +CG+S+Y + A +H CF+C C L S E + L+C++
Sbjct: 20 PVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASL-SHWYYEKDGRLFCKK 71
Score = 30.6 bits (69), Expect = 0.22
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 207
C CG ++ + + A S+WH CF+C +C +L
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASL 56
Score = 28.7 bits (64), Expect = 0.83
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSL 316
C CG +Y + + + N WH CF C +C SL
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASL 56
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a
Rho-type GTPase activating protein (RhoGap) domain. Rga
activates GTPases during polarized morphogenesis. In
yeast, a known regulating target of Rga is CDC42p, a
small GTPase. The LIM domain is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 55
Score = 31.2 bits (71), Expect = 0.075
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDS 60
C C +S+ GG ++H CFKC C K L
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLSC 37
Score = 29.6 bits (67), Expect = 0.27
Identities = 12/37 (32%), Positives = 14/37 (37%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDS 209
C C + G WH CFKC C+K L
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLSC 37
Score = 26.2 bits (58), Expect = 5.3
Identities = 9/37 (24%), Positives = 11/37 (29%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDS 318
C C + WH CF C C + L
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLSC 37
>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 = 0.095
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 282 CPRCGFVVYAAEQMISKN-RIWHRRCFSCADCHR 314
C RC E++++ N ++H +CF CA C +
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQ 34
Score = 28.8 bits (65), Expect = 0.64
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 173 CPRCGGVVFAAEQ-VLAKGSEWHRKCFKCRDC 203
C RC E+ V + G +H +CF C C
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQC 32
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 30.9 bits (70), Expect = 0.10
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 282 CPRCGFVVYAA-EQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
C CG + A ++M K + WH +CF C +C + + + + D+D+YC CY
Sbjct: 1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIP-KDDDVYCVPCY 54
Score = 30.5 bits (69), Expect = 0.12
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 173 CPRCGGVVFAAEQVLA-KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C CG + A + + KG +WH KCF C +C + + + + D D+YC CY
Sbjct: 1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGT-KSFIPKDDDVYCVPCY 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 = 30.8 bits (69), Expect = 0.10
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C RCG ++A++ V A+G+ +H CF C C + L + ++ + C+ Y
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55
Score = 28.5 bits (63), Expect = 0.88
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 282 CPRCGFVVYAAEQMI-SKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C RCG +YA++ + ++ +H CF+C C R L + + + CR
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCR 52
Score = 28.1 bits (62), Expect = 1.1
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 24 CPACGKSVYAAE-ERVAGGYKFHKMCFKCSMCSKFLDS 60
C CG+ +YA++ R A G +H CF C C + L +
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLST 38
>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 = 30.7 bits (70), Expect = 0.11
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNK 205
C C + + A G+ WH +CF+C C K
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRK 33
Score = 26.8 bits (60), Expect = 2.6
Identities = 12/53 (22%), Positives = 20/53 (37%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
C C + A G +H CF+C C K + + + Y + C+
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53
>gnl|CDD|188730 cd09344, LIM1_FHL1, The first LIM domain of Four and a half LIM
domains protein 1. The first LIM domain of Four and a
half LIM domains protein 1 (FHL1): FHL1 is heavily
expressed in skeletal and cardiac muscles. It plays
important roles in muscle growth, differentiation, and
sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. .
Length = 54
Score = 30.5 bits (69), Expect = 0.15
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGC 334
KNR WH CF CA C++ L + DN I C C
Sbjct: 18 KNRYWHETCFRCAKCYKPLANEPFV-AKDNKILCGKC 53
Score = 26.6 bits (59), Expect = 3.5
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 183 AEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTC 225
++++ K WH CF+C C K L + D I C C
Sbjct: 12 SKELHHKNRYWHETCFRCAKCYKPLANEPFV-AKDNKILCGKC 53
>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 = 30.0 bits (68), Expect = 0.16
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 44 FHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
+H F C+ C K L + E + ELYC +CH
Sbjct: 20 YHPYHFNCANCGKELTAD-ARELKGELYCLRCH 51
Score = 25.4 bits (56), Expect = 8.7
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C +C ++ + + KG +H F C +C K L + ++YC C+
Sbjct: 1 CQKCHAII-EEQHLKFKGDPYHPYHFNCANCGKELTA--DARELKGELYCLRCH 51
>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 = 30.3 bits (68), Expect = 0.18
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 295 MISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
+++ R WH F+C CH SL + + N++YC CY
Sbjct: 13 LVALGRSWHPEEFTCHYCHTSLADVSFVE-EQNNVYCENCY 52
Score = 25.3 bits (55), Expect = 9.7
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 186 VLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
++A G WH + F C C+ +L ++ + ++YC+ CY
Sbjct: 13 LVALGRSWHPEEFTCHYCHTSLADVSFVE-EQNNVYCENCY 52
>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 = 30.1 bits (68), Expect = 0.20
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 173 CPRCGGVVFAAEQVLAK-----GSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C C + E + WH CF+C C + L + C D+ IYC+ Y
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVHDDQ-IYCERHY 58
Score = 28.5 bits (64), Expect = 0.81
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 24 CPACGKSVYAAEERVA-----GGYKFHKMCFKCSMCSKFL-DSTNCTEHEKELYC 72
C C + + E V +H CF+CS C + L D T C H+ ++YC
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCV-HDDQIYC 54
>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 = 30.0 bits (68), Expect = 0.22
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C CG ++ E +L A G +H CF+C CN+ LD + + +IYC Y
Sbjct: 1 CAVCGHLIM--EMILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
Score = 27.3 bits (61), Expect = 1.6
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 300 RIWHRRCFSCADCHRSLDSTNLNDGPDNDIYC 331
+ +H CF C C+ LD +N+IYC
Sbjct: 18 KSYHPGCFRCCVCNECLDGVPFTVDVENNIYC 49
Score = 26.9 bits (60), Expect = 2.8
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 39 AGGYKFHKMCFKCSMCSKFLDSTNCT-EHEKELYC 72
A G +H CF+C +C++ LD T + E +YC
Sbjct: 15 ALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYC 49
>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The second LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 29.8 bits (67), Expect = 0.23
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 300 RIWHRRCFSCADCHRSLDSTNLNDGPDNDIYC 331
+ +H CF+C CHRSLD I+C
Sbjct: 18 KAYHPHCFTCVVCHRSLDGIPFTVDATGQIHC 49
Score = 25.6 bits (56), Expect = 9.0
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 188 AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYC 222
A G +H CF C C+++LD I I+C
Sbjct: 15 ATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHC 49
>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 = 30.1 bits (68), Expect = 0.25
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 185 QVLAKGSEWHRKCFKCRDCNKTLDSI---NACDGPDKDIYCKTCYGKK 229
+V+A +H +C+KC DC L S C D + CK+C K+
Sbjct: 19 RVVALDRSFHVQCYKCEDCGLLLSSEAEGRGCYPLDDHVLCKSCNAKR 66
Score = 25.9 bits (57), Expect = 7.9
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 294 QMISKNRIWHRRCFSCADCHRSLDSTNLNDGP---DNDIYCRGCYGK 337
++++ +R +H +C+ C DC L S G D+ + C+ C K
Sbjct: 19 RVVALDRSFHVQCYKCEDCGLLLSSEAEGRGCYPLDDHVLCKSCNAK 65
>gnl|CDD|188714 cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM
(abLIM) proteins. The second LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to function
as a tumor suppressor. AbLIM-2 and -3, mainly expressed
in muscle and neuronal tissue, bind to F-actin strongly.
They may serve as a scaffold for signaling modules of
the actin cytoskeleton and thereby modulate
transcription. It has shown that LIM domains of abLIMs
interact with STARS (striated muscle activator of Rho
signaling), which directly binds actin and stimulates
serum-response factor (SRF)-dependent transcription. All
LIM domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 56
Score = 29.6 bits (67), Expect = 0.25
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 1/56 (1%)
Query: 170 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTC 225
G C C V E V A G +H KCF C C + + K+ C+ C
Sbjct: 1 GTKCDSCQDFV-EGEVVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKECLCQKC 55
Score = 26.9 bits (60), Expect = 2.8
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 23 KCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSK-FLDSTNCTEHEKELYCRQC 75
KC +C V E A G +H CF CS+C + F T + KE C++C
Sbjct: 3 KCDSCQDFV-EGEVVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKECLCQKC 55
>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM
(abLIM) proteins. The first LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to
function as a tumor suppressor. AbLIM-2 and -3, mainly
expressed in muscle and neuronal tissue, bind to
F-actin strongly. They may serve as a scaffold for
signaling modules of the actin cytoskeleton and thereby
modulate transcription. It has shown that LIM domains
of abLIMs interact with STARS (striated muscle
activator of Rho signaling), which directly binds actin
and stimulates serum-response factor (SRF)-dependent
transcription. All LIM domains are 50-60 amino acids in
size and share two characteristic highly conserved zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 29.5 bits (67), Expect = 0.26
Identities = 18/49 (36%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYC 72
C CGK RV Y FH CF C +C L E E YC
Sbjct: 1 CYKCGKKCKGEVLRVQDKY-FHIKCFTCKVCGCDLAQGGFFVKEGEYYC 48
>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 = 29.9 bits (68), Expect = 0.28
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 9/42 (21%)
Query: 173 CPRCGG-------VVFAAEQVLAKGSEWHRKCFKCRDCNKTL 207
C +C VFA + + WH CF C CN+ L
Sbjct: 1 CEKCKEPINPGEVAVFAER--AGEDACWHPGCFVCETCNELL 40
Score = 27.2 bits (61), Expect = 2.0
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 9/39 (23%)
Query: 282 CPRCG-------FVVYAAEQMISKNRIWHRRCFSCADCH 313
C +C V+A ++ WH CF C C+
Sbjct: 1 CEKCKEPINPGEVAVFAE--RAGEDACWHPGCFVCETCN 37
>gnl|CDD|188849 cd09465, LIM2_LIMK2, The second LIM domain of LIMK2 (LIM domain
Kinase 2). The second LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein
family, which comprises LIMK1 and LIMK2. LIMK contains
two LIM domains, a PDZ domain, and a kinase domain.
LIMK is involved in the regulation of actin
polymerization and microtubule disassembly. LIMK
influences architecture of the actin cytoskeleton by
regulating the activity of the cofilin family proteins
cofilin1, cofilin2, and destrin. The mechanism of the
activation is to phosphorylates cofilin on serine 3 and
inactivates its actin-severing activity, altering the
rate of actin depolymerisation. LIMK activity is
activated by phosphorylation of a threonine residue
within the activation loop of the kinase by
p21-activated kinases 1 and 4 and by Rho kinase. LIMKs
can function in both cytoplasm and nucleus. Both LIMK1
and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is
expressed in all tissues. While LIMK1 localizes mainly
at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 59
Score = 29.5 bits (66), Expect = 0.33
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 38 VAGGYKFHKMCFKCSMCSKFL---DSTNCTEHEKELYCRQCH 76
VAG YK+H CF C C + D+ +H LYC +CH
Sbjct: 19 VAGEYKYHPECFACMSCKVIIEDGDTYALVQHTT-LYCGKCH 59
>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 = 0.35
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
K++ WH CF C+ C SL D IYC CY
Sbjct: 22 KDKHWHEACFLCSKCKISLVDKPFGSKADR-IYCGNCY 58
Score = 26.4 bits (58), Expect = 5.2
Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 189 KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
K WH CF C C +L D+ IYC CY
Sbjct: 22 KDKHWHEACFLCSKCKISLVDKPFGSKADR-IYCGNCY 58
>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the
Paxillin-like protein family. The fourth LIM domain of
the Paxillin like protein family: This family consists
of paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 29.2 bits (66), Expect = 0.35
Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
C CGK + A G KFH F C+ C K L E + + YC C
Sbjct: 1 CAGCGKPI-TGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 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 = 29.4 bits (66), Expect = 0.35
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 24 CPACGKSVYAAEERV-AGGYKFHKMCFKCSMC 54
C ACG+S+ A+E + A G +H CF CS C
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTC 32
Score = 28.6 bits (64), Expect = 0.71
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 282 CPRCGFVVYAAEQ-MISKNRIWHRRCFSCADCHRSL 316
C CG + A+E M ++ ++H +CF+C+ CH L
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQL 36
Score = 27.8 bits (62), Expect = 1.4
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTL 207
C CG + A+E V+ A+G+ +H KCF C C+ L
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQL 36
>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 = 29.3 bits (66), Expect = 0.41
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 185 QVLAKGSEWHRKCFKCRDCNKTLDSINACDGP---DKDIYCKTC 225
+++A +H C+KC DC L S + G D + CK+C
Sbjct: 19 RIVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPLDGHLLCKSC 62
>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 = 29.2 bits (66), Expect = 0.43
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 207
C CG + + +LA +WH CFKC++C K L
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVL 35
Score = 26.9 bits (60), Expect = 2.3
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFL 58
C CG+ + + +A ++H CFKC C K L
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVL 35
>gnl|CDD|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like
family. The second LIM domain of Testin-like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 56
Score = 29.1 bits (66), Expect = 0.44
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 174 PRCGG---VVFAAEQVLAKGSEWHRKCFKCRDCNKTL 207
PRC ++F+ E A+G WH K F C C++ L
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPL 37
Score = 25.3 bits (56), Expect = 9.5
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNL---NDGPDNDIYCRGCY 335
C C ++++ E ++ + WH + F C C L P YC CY
Sbjct: 3 CAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKP----YCLDCY 55
>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a. The first LIM
domain of Lhx3a: Lhx3a is a member of LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx3a is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 29.0 bits (65), Expect = 0.52
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 193 WHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
WH KC KC DC L + C +YCK
Sbjct: 24 WHSKCLKCVDCQAQLT--DKCFSRGGQVYCK 52
>gnl|CDD|218613 pfam05502, Dynactin_p62, Dynactin p62 family. Dynactin is a
multi-subunit complex and a required cofactor for most,
or all, of the cellular processes powered by the
microtubule-based motor cytoplasmic dynein. p62 binds
directly to the Arp1 subunit of dynactin.
Length = 456
Score = 31.4 bits (71), Expect = 0.65
Identities = 17/45 (37%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 282 CPRCGFVVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPD 326
CP C F V ++E KNR R CF C C L L D
Sbjct: 29 CPNCLFEVPSSEVRSEKNRC-ARNCFDCPICTHPLSVRALEPSSD 72
Score = 28.7 bits (64), Expect = 5.5
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKHKY 232
CP C V ++E V ++ + R CF C C L S+ A + ++ Y
Sbjct: 29 CPNCLFEVPSSE-VRSEKNRCARNCFDCPICTHPL-SVRALEPSSDLPPDPAASSQQGPY 86
Query: 233 CKAC 236
+C
Sbjct: 87 YLSC 90
>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like
family. The third LIM domain of Enigma-like family: The
Enigma LIM domain family is comprised of three members:
Enigma, ENH, and Cypher (mouse)/ZASP (human). These
subfamily members contain a single PDZ domain at the
N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and the
second LIM domain interacts with the receptor tyrosine
kinase Ret and the adaptor protein APS. Thus Enigma is
implicated in signal transduction processes, such as
mitogenic activity, insulin related actin organization,
and glucose metabolism. The second member, ENH protein,
was first identified in rat brain. It has been shown
that ENH interacts with protein kinase D1 (PKD1) via its
LIM domains and forms a complex with PKD1 and the
alpha1C subunit of cardiac L-type voltage-gated calcium
channel in rat neonatal cardiomyocytes. The N-terminal
PDZ domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 28.6 bits (64), Expect = 0.65
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 282 CPRCGFVVYAAEQMISK-NRIWHRRCFSCADCHRSLD 317
C C F + A ++ + WH CF CA CH +L+
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLE 37
>gnl|CDD|224487 COG1571, COG1571, Predicted DNA-binding protein containing a
Zn-ribbon domain [General function prediction only].
Length = 421
Score = 31.5 bits (72), Expect = 0.67
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 11/56 (19%)
Query: 15 PFVPAENPKCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKEL 70
+ NP CP CG + +A G F+C C T E ++L
Sbjct: 345 RYER-VNPVCPRCGGRMKSAG---RNG-------FRCKKCGTRARETLIKEVPRDL 389
Score = 28.5 bits (64), Expect = 6.8
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 10/39 (25%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSIN 211
CPRCGG ++ + G R F+C+ C
Sbjct: 353 CPRCGG------RMKSAG----RNGFRCKKCGTRARETL 381
>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 = 28.7 bits (64), Expect = 0.67
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 44 FHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
+H+ CF+C C + L T ++EL C C+
Sbjct: 26 YHEHCFRCFRCDRSLADEPFTCQDEELLCNDCY 58
>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 = 28.5 bits (64), Expect = 0.68
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 282 CPRCGFVVYAAEQMI-SKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYC 331
C +C V+ E +I + + +H CF+C C R + + N++YC
Sbjct: 1 CAKCQGVI--TEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYC 49
>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The second LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 28.5 bits (64), Expect = 0.73
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 39 AGGYKFHKMCFKCSMCSKFLDSTNC-TEHEKELYC 72
A G K+H F CS+C + EHE ++YC
Sbjct: 15 ALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYC 49
>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 = 28.7 bits (64), Expect = 0.77
Identities = 17/62 (27%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 19 AENPKCPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFL----DSTNCTEHEKELYCRQ 74
P P G+ VA FH C+KC C + L D C + + C +
Sbjct: 4 CSEPIMPEPGRD--ETVRVVALEKNFHMKCYKCEDCGRPLSIEADDNGCFPLDGHVLCMK 61
Query: 75 CH 76
CH
Sbjct: 62 CH 63
Score = 28.3 bits (63), Expect = 1.1
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 185 QVLAKGSEWHRKCFKCRDCNKTLD---SINACDGPDKDIYCKTCY 226
+V+A +H KC+KC DC + L N C D + C C+
Sbjct: 19 RVVALEKNFHMKCYKCEDCGRPLSIEADDNGCFPLDGHVLCMKCH 63
>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 = 28.5 bits (64), Expect = 0.78
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 207
C C ++FA E A+G WH K F C +C L
Sbjct: 3 CSACDEIIFADECTEAEGRHWHMKHFCCFECECQL 37
>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 = 28.2 bits (63), Expect = 0.83
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTNLNDGPDND-IYCRGC 334
++R WH+ CF C+ C SL PD D I CR C
Sbjct: 20 EDRQWHQPCFKCSRCSVSLVGAGFF--PDGDQILCRDC 55
>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 = 27.8 bits (62), Expect = 1.1
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 193 WHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
WH KC KC DC L + C + +YCK
Sbjct: 21 WHAKCLKCNDCGAQLT--DKCFARNGHVYCK 49
Score = 26.6 bits (59), Expect = 3.1
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 299 NRIWHRRCFSCADCHRSL 316
+R WH +C C DC L
Sbjct: 18 DRTWHAKCLKCNDCGAQL 35
>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 = 28.1 bits (62), Expect = 1.2
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C RCG + + + V AKG+ +H CF C C + L + ++ + C+ Y
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55
Score = 26.5 bits (58), Expect = 3.6
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 282 CPRCGFVVYAAEQMI-SKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C RCG +++ + + +K ++H CF+C C R L + + + CR
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCR 52
>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 = 27.7 bits (62), Expect = 1.4
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 186 VLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
++A G WH + F C C+ +L I + +YC+ CY
Sbjct: 13 LVALGRSWHPEEFTCSHCHCSLAEIGFVE-EKGSLYCELCY 52
Score = 26.2 bits (58), Expect = 4.2
Identities = 14/39 (35%), Positives = 17/39 (43%)
Query: 38 VAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
VA G +H F CS C L E + LYC C+
Sbjct: 14 VALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
Score = 25.8 bits (57), Expect = 5.5
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 300 RIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
R WH F+C+ CH SL + +YC CY
Sbjct: 18 RSWHPEEFTCSHCHCSLAEIGFVE-EKGSLYCELCY 52
>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b. The first LIM
domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx3b is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 27.6 bits (61), Expect = 1.4
Identities = 13/31 (41%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 193 WHRKCFKCRDCNKTLDSINACDGPDKDIYCK 223
WH KC KC DC L C +YCK
Sbjct: 24 WHSKCLKCSDCQTQL--AEKCFSRGDSVYCK 52
Score = 27.6 bits (61), Expect = 1.6
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 299 NRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
+R WH +C C+DC L + G + +YC+
Sbjct: 21 DRHWHSKCLKCSDCQTQLAEKCFSRG--DSVYCK 52
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung at
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 62
Score = 27.9 bits (62), Expect = 1.4
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 290 YAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYGKNF 339
+ + K+R WH CF C C SL + + C CY +
Sbjct: 14 CDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFA-AKEEHLLCTECYSNEY 62
Score = 27.6 bits (61), Expect = 2.0
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 24 CPACGKSV-YAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCHGRKY 80
C C K + ++ +H+ CF C C L E+ L C +C+ +Y
Sbjct: 5 CEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECYSNEY 62
>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin. The
fourth LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 27.4 bits (61), Expect = 1.5
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
C +CG + A G KFH F C+ C + L + E + YC C
Sbjct: 1 CGSCGLPI-TGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
>gnl|CDD|180167 PRK05620, PRK05620, long-chain-fatty-acid--CoA ligase; Validated.
Length = 576
Score = 30.1 bits (68), Expect = 1.7
Identities = 34/147 (23%), Positives = 45/147 (30%), Gaps = 21/147 (14%)
Query: 109 NCTEHEKELYCRQCHGRKYGPKGYGFGGGAGCLSMDAGEHLTENNAPRTTVIDT--AKIK 166
NC EH + L+ C G + P L D H+ + V D A+
Sbjct: 73 NCAEHLEVLFAVACMGAVFNPLNKQ-------LMNDQIVHIINHAEDEVIVADPRLAEQL 125
Query: 167 AAPGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINAC-DGPDKDIYCKTC 225
K CP VVF + + K LD + D P+ D
Sbjct: 126 GEILKECPCVRAVVFIGPSDADSAAAHMPEGIKVYSYEALLDGRSTVYDWPELD------ 179
Query: 226 YGKKHKYCKACY--GKNFGPKGFGYGH 250
+ CY G PKG Y H
Sbjct: 180 ---ETTAAAICYSTGTTGAPKGVVYSH 203
>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 = 27.1 bits (60), Expect = 2.0
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCRQCH 76
C C K + VA G +H F CS C K LD E + ++C +C+
Sbjct: 1 CAQCNK-IIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX
protein family. The second LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved members
of this family. Proteins in this group are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Isl-1 is one of the LHX proteins
isolated originally by virtue of its ability to bind DNA
sequences from the 5'-flanking region of the rat insulin
gene in pancreatic insulin-producing cells. Mice
deficient in Isl-1 fail to form the dorsal exocrine
pancreas and islet cells fail to differentiate. On the
other hand, Isl-1 takes part in the pituitary
development by activating the gonadotropin-releasing
hormone receptor gene together with LHX3 and
steroidogenic factor 1. Mouse Isl2 is expressed in the
retinal ganglion cells and the developing spinal cord
where it plays a role in motor neuron development. Same
as Isl1, Isl2 may also be able to bind to the insulin
gene enhancer to promote gene activation. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 27.4 bits (61), Expect = 2.0
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 282 CPRCGFVVYAAE-QMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C +C + M ++ +I+H CF C+ C R L + D+ ++C+
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCK 52
>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 = 27.1 bits (60), Expect = 2.1
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 24 CPACGKSVYAAEERV-AGGYKFHKMCFKCSMCSKFLDSTNCTEHEKELYCR 73
C +CG + A + V A +H CF C+ C+ L+ + +C+
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51
Score = 26.0 bits (57), Expect = 5.3
Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 282 CPRCGFVVYAAEQMISK-NRIWHRRCFSCADCHRSLD 317
C CGF + A ++ + N +H +CF+C C+ +L+
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLE 37
Score = 25.6 bits (56), Expect = 9.3
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 173 CPRCGGVVFAAEQ-VLAKGSEWHRKCFKCRDCNKTLD 208
C CG + A ++ V A + +H +CF C CN L+
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLE 37
>gnl|CDD|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM
domains protein 2 (FHL2). The second LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to s upport the assembly of multimeric protein
complexes.
Length = 57
Score = 27.3 bits (60), Expect = 2.1
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 189 KGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKK 229
KG+ WH CF C+ C + + + + D +C CY K+
Sbjct: 18 KGNSWHETCFICQRCQQPIGT-KSFIPKDNQNFCVPCYEKQ 57
Score = 26.9 bits (59), Expect = 3.0
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 288 VVYAAEQMISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYGK 337
++ +M K WH CF C C + + + + DN +C CY K
Sbjct: 8 IMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIP-KDNQNFCVPCYEK 56
>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 = 27.0 bits (60), Expect = 2.5
Identities = 10/36 (27%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 282 CPRCGFVVYAAEQM-ISKNRIWHRRCFSCADCHRSL 316
C +C + A++ + +++ ++H CF+C C R L
Sbjct: 1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQL 36
>gnl|CDD|223501 COG0424, Maf, Nucleotide-binding protein implicated in inhibition
of septum formation [Cell division and chromosome
partitioning].
Length = 193
Score = 29.0 bits (66), Expect = 2.5
Identities = 13/57 (22%), Positives = 20/57 (35%)
Query: 140 CLSMDAGEHLTENNAPRTTVIDTAKIKAAPGKGCPRCGGVVFAAEQVLAKGSEWHRK 196
+ D E L + PR V+ A+ KA +V A+ V+ K
Sbjct: 27 VIPSDIDEPLLKAEEPREYVLRLAEEKARAVAARLPPDALVIGADTVVVLDGRILGK 83
>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 = 26.9 bits (60), Expect = 2.6
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCY 335
+++ WH+ CF C C + L D YC C+
Sbjct: 16 RDQPWHKECFVCTGCKKQLAGQRFT-SRDEYPYCVDCF 52
Score = 25.8 bits (57), Expect = 6.5
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 44 FHKMCFKCSMCSKFLDSTNCTEHEKELYCRQC 75
+HK CF C+ C K L T ++ YC C
Sbjct: 20 WHKECFVCTGCKKQLAGQRFTSRDEYPYCVDC 51
>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 = 26.7 bits (59), Expect = 2.9
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 191 SEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
S WH +C +C C + L++ C DK +YCK Y
Sbjct: 19 SLWHERCLQCASCKEPLET--TCFYRDKKLYCKEDY 52
>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher
family. The third LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 26.9 bits (59), Expect = 3.2
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 282 CPRCGFVVYAAEQMISK-NRIWHRRCFSCADCHRSLD 317
C C F V A ++ I WH CF CA CH +L+
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE 37
>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 = 26.5 bits (59), Expect = 3.3
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 188 AKGSEWHRKCFKCRDCNK 205
A ++WH +CF CR+C+K
Sbjct: 15 ALNTQWHPECFVCRECHK 32
>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 = 26.8 bits (59), Expect = 3.5
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 24 CPACGKSVYAAEERVAGGYKFHKMCFKCSMCSKFLDSTN-CTEHEKELYCRQCHGRKYGP 82
C C + + + A G +H CF C +C L+ + + + +C + R+Y P
Sbjct: 1 CAVCDQKITDRMLK-ATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAP 59
Query: 83 K 83
+
Sbjct: 60 R 60
Score = 26.0 bits (57), Expect = 5.8
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 302 WHRRCFSCADCHRSLDSTNLNDGPDNDIYCRGCYGKNFGPK 342
+H +CF+C C L+ + N +C Y + + P+
Sbjct: 20 YHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAPR 60
>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 = 26.5 bits (59), Expect = 3.5
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 192 EWHRKCFKCRDCNKTL 207
+WH CF C C+ +L
Sbjct: 23 QWHSDCFNCGKCSVSL 38
Score = 25.8 bits (57), Expect = 6.6
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 299 NRIWHRRCFSCADCHRSL 316
R WH CF+C C SL
Sbjct: 21 ERQWHSDCFNCGKCSVSL 38
>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 = 26.7 bits (59), Expect = 3.6
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 189 KGSEWHRKCFKCRDCNKTL 207
+G+EWH CF C+ C + +
Sbjct: 18 EGNEWHETCFVCQSCQQPI 36
>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 = 26.4 bits (58), Expect = 3.7
Identities = 12/52 (23%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 282 CPRCGFVVYAAEQ-MISKNRIWHRRCFSCADCHRSLDSTNLNDGPDNDIYCR 332
C +C +++ M +++ ++H CF C+ C R L + ++++ CR
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCR 52
Score = 26.4 bits (58), Expect = 4.2
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 44 FHKMCFKCSMCSK-FLDSTNCTEHEKELYCRQCH 76
+H CF+CS+CS+ L E EL CR H
Sbjct: 22 YHIECFRCSVCSRQLLPGDEFCLREHELLCRADH 55
>gnl|CDD|179595 PRK03564, PRK03564, formate dehydrogenase accessory protein FdhE;
Provisional.
Length = 309
Score = 28.8 bits (65), Expect = 3.8
Identities = 26/88 (29%), Positives = 31/88 (35%), Gaps = 27/88 (30%)
Query: 173 CPRCG-----GVV-FAAEQVLAK------GSEWHRKCFKCRDCNKT-------LDSINA- 212
CP CG VV Q L SEWH KC +C ++ LDS A
Sbjct: 190 CPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAA 249
Query: 213 -----CDGPDKDIYCKTCYGKKHKYCKA 235
C D Y K Y +K +A
Sbjct: 250 VKAESCG--DCGTYLKILYQEKDPKVEA 275
>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 = 26.2 bits (58), Expect = 4.9
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 193 WHRKCFKCRDCNKTLDSINACDGPDKDIYCKT 224
WH KC +C DC L C + +YC+
Sbjct: 21 WHAKCVQCCDCKCPLT--EKCFSREGKLYCRN 50
>gnl|CDD|233031 TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fpg). All
proteins in the FPG family with known functions are
FAPY-DNA glycosylases that function in base excision
repair. Homologous to endonuclease VIII (nei). This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 272
Score = 28.4 bits (64), Expect = 5.3
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 7/37 (18%)
Query: 276 GRNGDGCPRCGFVVYAAEQMISKNRIWHRRCFSCADC 312
GR G+ C RCG I K ++ R C C
Sbjct: 242 GRKGEPCRRCG-------TPIEKIKVGGRGTHFCPQC 271
>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 = 25.8 bits (56), Expect = 6.1
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 173 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCY 226
C RC + E + A WH CF C C+ + + N D + YC+T Y
Sbjct: 1 CGRCQRKILG-EVINALKQTWHVSCFVCVACHNPIRN-NVFHLEDGEPYCETDY 52
>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 = 25.8 bits (57), Expect = 6.6
Identities = 12/30 (40%), Positives = 22/30 (73%), Gaps = 1/30 (3%)
Query: 45 HKMCFKCSMCSKFLDSTNCTEHEKELYCRQ 74
H+ C +CS+C + L +T+C +++LYC+Q
Sbjct: 22 HEECLQCSVCQQPL-TTSCYFRDRKLYCKQ 50
>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx). The
second LIM domain of dLMO (Beaderx): dLMO is a nuclear
protein that plays important roles in transcriptional
regulation and development. In Drosophila dLMO modulates
the activity of LIM-homeodomain protein Apterous (Ap),
which regulates the formation of the dorsal-ventral axis
of the Drosophila wing. Biochemical analysis shows that
dLMO protein influences the activity of Apterous by
binding of its cofactor Chip. Further studies shown that
dLMO proteins might function in an evolutionarily
conserved mechanism involved in patterning the
appendages. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 26.0 bits (57), Expect = 6.8
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCN 204
C C + A E V+ A+ + +H +CF C+ CN
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCN 33
>gnl|CDD|223344 COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA replication,
recombination, and repair].
Length = 273
Score = 28.0 bits (63), Expect = 6.9
Identities = 7/29 (24%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 170 GKGCPRCGGVVFAAEQVLA-KGSEWHRKC 197
G+ C RCG + + L + + + C
Sbjct: 245 GEPCRRCGTPI--EKIKLGGRSTFYCPVC 271
>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 = 25.9 bits (57), Expect = 7.1
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 173 CPRCGGVVFAAEQVL-AKGSEWHRKCFKCRDCNKTL 207
C +CG V+ A Q A G+ +H CF C C +TL
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL 36
Score = 25.5 bits (56), Expect = 9.3
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 24 CPACGKSVYAAEERV-AGGYKFHKMCFKCSMCSKFL 58
C CGK VY A + A G +H CF C C + L
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL 36
>gnl|CDD|188816 cd09432, LIM6_LIMPETin, The sixth LIM domain of protein LIMPETin.
The sixth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 25.9 bits (57), Expect = 7.2
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 298 KNRIWHRRCFSCADCHRSLDSTN-LNDGPDNDIYCRGC 334
++R WH CF+CA C SL + DG I C C
Sbjct: 20 EDRHWHNDCFNCAGCRTSLVGKGFITDGG--RILCPDC 55
>gnl|CDD|238218 cd00368, Molybdopterin-Binding, Molybdopterin-Binding (MopB) domain
of the MopB superfamily of proteins, a large, diverse,
heterogeneous superfamily of enzymes that, in general,
bind molybdopterin as a cofactor. The MopB domain is
found in a wide variety of molybdenum- and
tungsten-containing enzymes, including formate
dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of
nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide
reductase (DMSOR), thiosulfate reductase,
formylmethanofuran dehydrogenase, and arsenite oxidase.
Molybdenum is present in most of these enzymes in the
form of molybdopterin, a modified pterin ring with a
dithiolene side chain, which is responsible for ligating
the Mo. In many bacterial and archaeal species,
molybdopterin is in the form of a dinucleotide, with two
molybdopterin dinucleotide units per molybdenum. These
proteins can function as monomers, heterodimers, or
heterotrimers, depending on the protein and organism.
Also included in the MopB superfamily is the
eukaryotic/eubacterial protein domain family of the
75-kDa subunit/Nad11/NuoG (second domain) of respiratory
complex 1/NADH-quinone oxidoreductase which is
postulated to have lost an ancestral formate
dehydrogenase activity and only vestigial sequence
evidence remains of a molybdopterin binding site.
Length = 374
Score = 28.1 bits (63), Expect = 7.8
Identities = 18/68 (26%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 79 KYGPKGYGFGGGAGCLSMDAGMCSKFLDS--TNCTEHEKELYCRQCHGRKYGPKGYGFGG 136
KYGP F GG G + +A + K L + +N + + R CH GG
Sbjct: 90 KYGPDAIAFYGGGGASNEEAYLLQKLLRALGSNNVDS----HARLCHASAVAALKAFGGG 145
Query: 137 GAGCLSMD 144
D
Sbjct: 146 APTNTLAD 153
>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 = 25.3 bits (55), Expect = 8.8
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 299 NRIWHRRCFSCADCHRSL 316
+R WH C CADC L
Sbjct: 18 DRHWHSSCLKCADCQMQL 35
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.140 0.474
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,302,842
Number of extensions: 1533105
Number of successful extensions: 2230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2165
Number of HSP's successfully gapped: 447
Length of query: 356
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 258
Effective length of database: 6,590,910
Effective search space: 1700454780
Effective search space used: 1700454780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (26.9 bits)